Application of automation and information systems to forensic genetic specimen processing.

PubMed

Leclair, Benoît; Scholl, Tom

2005-03-01

During the last 10 years, the introduction of PCR-based DNA typing technologies in forensic applications has been highly successful. This technology has become pervasive throughout forensic laboratories and it continues to grow in prevalence. For many criminal cases, it provides the most probative evidence. Criminal genotype data banking and victim identification initiatives that follow mass-fatality incidents have benefited the most from the introduction of automation for sample processing and data analysis. Attributes of offender specimens including large numbers, high quality and identical collection and processing are ideal for the application of laboratory automation. The magnitude of kinship analysis required by mass-fatality incidents necessitates the application of computing solutions to automate the task. More recently, the development activities of many forensic laboratories are focused on leveraging experience from these two applications to casework sample processing. The trend toward increased prevalence of forensic genetic analysis will continue to drive additional innovations in high-throughput laboratory automation and information systems.

The RABiT: a rapid automated biodosimetry tool for radiological triage. II. Technological developments.

PubMed

Garty, Guy; Chen, Youhua; Turner, Helen C; Zhang, Jian; Lyulko, Oleksandra V; Bertucci, Antonella; Xu, Yanping; Wang, Hongliang; Simaan, Nabil; Randers-Pehrson, Gerhard; Lawrence Yao, Y; Brenner, David J

2011-08-01

Over the past five years the Center for Minimally Invasive Radiation Biodosimetry at Columbia University has developed the Rapid Automated Biodosimetry Tool (RABiT), a completely automated, ultra-high throughput biodosimetry workstation. This paper describes recent upgrades and reliability testing of the RABiT. The RABiT analyses fingerstick-derived blood samples to estimate past radiation exposure or to identify individuals exposed above or below a cut-off dose. Through automated robotics, lymphocytes are extracted from fingerstick blood samples into filter-bottomed multi-well plates. Depending on the time since exposure, the RABiT scores either micronuclei or phosphorylation of the histone H2AX, in an automated robotic system, using filter-bottomed multi-well plates. Following lymphocyte culturing, fixation and staining, the filter bottoms are removed from the multi-well plates and sealed prior to automated high-speed imaging. Image analysis is performed online using dedicated image processing hardware. Both the sealed filters and the images are archived. We have developed a new robotic system for lymphocyte processing, making use of an upgraded laser power and parallel processing of four capillaries at once. This system has allowed acceleration of lymphocyte isolation, the main bottleneck of the RABiT operation, from 12 to 2 sec/sample. Reliability tests have been performed on all robotic subsystems. Parallel handling of multiple samples through the use of dedicated, purpose-built, robotics and high speed imaging allows analysis of up to 30,000 samples per day.

The RABiT: A Rapid Automated Biodosimetry Tool For Radiological Triage. II. Technological Developments

PubMed Central

Garty, Guy; Chen, Youhua; Turner, Helen; Zhang, Jian; Lyulko, Oleksandra; Bertucci, Antonella; Xu, Yanping; Wang, Hongliang; Simaan, Nabil; Randers-Pehrson, Gerhard; Yao, Y. Lawrence; Brenner, David J.

2011-01-01

Purpose Over the past five years the Center for Minimally Invasive Radiation Biodosimetry at Columbia University has developed the Rapid Automated Biodosimetry Tool (RABiT), a completely automated, ultra-high throughput biodosimetry workstation. This paper describes recent upgrades and reliability testing of the RABiT. Materials and methods The RABiT analyzes fingerstick-derived blood samples to estimate past radiation exposure or to identify individuals exposed above or below a cutoff dose. Through automated robotics, lymphocytes are extracted from fingerstick blood samples into filter-bottomed multi-well plates. Depending on the time since exposure, the RABiT scores either micronuclei or phosphorylation of the histone H2AX, in an automated robotic system, using filter-bottomed multi-well plates. Following lymphocyte culturing, fixation and staining, the filter bottoms are removed from the multi-well plates and sealed prior to automated high-speed imaging. Image analysis is performed online using dedicated image processing hardware. Both the sealed filters and the images are archived. Results We have developed a new robotic system for lymphocyte processing, making use of an upgraded laser power and parallel processing of four capillaries at once. This system has allowed acceleration of lymphocyte isolation, the main bottleneck of the RABiT operation, from 12 to 2 sec/sample. Reliability tests have been performed on all robotic subsystems. Conclusions Parallel handling of multiple samples through the use of dedicated, purpose-built, robotics and high speed imaging allows analysis of up to 30,000 samples per day. PMID:21557703

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.

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. Published by Elsevier B.V.

The LabTube - a novel microfluidic platform for assay automation in laboratory centrifuges.

PubMed

Kloke, A; Fiebach, A R; Zhang, S; Drechsel, L; Niekrawietz, S; Hoehl, M M; Kneusel, R; Panthel, K; Steigert, J; von Stetten, F; Zengerle, R; Paust, N

2014-05-07

Assay automation is the key for successful transformation of modern biotechnology into routine workflows. Yet, it requires considerable investment in processing devices and auxiliary infrastructure, which is not cost-efficient for laboratories with low or medium sample throughput or point-of-care testing. To close this gap, we present the LabTube platform, which is based on assay specific disposable cartridges for processing in laboratory centrifuges. LabTube cartridges comprise interfaces for sample loading and downstream applications and fluidic unit operations for release of prestored reagents, mixing, and solid phase extraction. Process control is achieved by a centrifugally-actuated ballpen mechanism. To demonstrate the workflow and functionality of the LabTube platform, we show two LabTube automated sample preparation assays from laboratory routines: DNA extractions from whole blood and purification of His-tagged proteins. Equal DNA and protein yields were observed compared to manual reference runs, while LabTube automation could significantly reduce the hands-on-time to one minute per extraction.

Automatic sample changer control software for automation of neutron activation analysis process in Malaysian Nuclear Agency

NASA Astrophysics Data System (ADS)

Yussup, N.; Ibrahim, M. M.; Rahman, N. A. A.; Mokhtar, M.; Salim, N. A. A.; Soh@Shaari, S. C.; Azman, A.; Lombigit, L.; Azman, A.; Omar, S. A.

2018-01-01

Most of the procedures in neutron activation analysis (NAA) process that has been established in Malaysian Nuclear Agency (Nuclear Malaysia) since 1980s were performed manually. These manual procedures carried out by the NAA laboratory personnel are time consuming and inefficient especially for sample counting and measurement process. The sample needs to be changed and the measurement software needs to be setup for every one hour counting time. Both of these procedures are performed manually for every sample. Hence, an automatic sample changer system (ASC) that consists of hardware and software is developed to automate sample counting process for up to 30 samples consecutively. This paper describes the ASC control software for NAA process which is designed and developed to control the ASC hardware and call GammaVision software for sample measurement. The software is developed by using National Instrument LabVIEW development package.

AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsai, Yingssu; Stanford University, 333 Campus Drive, Mudd Building, Stanford, CA 94305-5080; McPhillips, Scott E.

New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples. AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data,more » performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully demonstrated. This workflow was run once on the same 96 samples that the group had examined manually and the workflow cycled successfully through all of the samples, collected data from the same samples that were selected manually and located the same peaks of unmodeled density in the resulting difference Fourier maps.« less

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

NASA Astrophysics Data System (ADS)

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

2016-03-01

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

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

ICECAP: an integrated, general-purpose, automation-assisted IC50/EC50 assay platform.

PubMed

Li, Ming; Chou, Judy; King, Kristopher W; Jing, Jing; Wei, Dong; Yang, Liyu

2015-02-01

IC50 and EC50 values are commonly used to evaluate drug potency. Mass spectrometry (MS)-centric bioanalytical and biomarker labs are now conducting IC50/EC50 assays, which, if done manually, are tedious and error-prone. Existing bioanalytical sample preparation automation systems cannot meet IC50/EC50 assay throughput demand. A general-purpose, automation-assisted IC50/EC50 assay platform was developed to automate the calculations of spiking solutions and the matrix solutions preparation scheme, the actual spiking and matrix solutions preparations, as well as the flexible sample extraction procedures after incubation. In addition, the platform also automates the data extraction, nonlinear regression curve fitting, computation of IC50/EC50 values, graphing, and reporting. The automation-assisted IC50/EC50 assay platform can process the whole class of assays of varying assay conditions. In each run, the system can handle up to 32 compounds and up to 10 concentration levels per compound, and it greatly improves IC50/EC50 assay experimental productivity and data processing efficiency. © 2014 Society for Laboratory Automation and Screening.

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.

Automation in clinical bacteriology: what system to choose?

PubMed

Greub, G; Prod'hom, G

2011-05-01

With increased activity and reduced financial and human resources, there is a need for automation in clinical bacteriology. Initial processing of clinical samples includes repetitive and fastidious steps. These tasks are suitable for automation, and several instruments are now available on the market, including the WASP (Copan), Previ-Isola (BioMerieux), Innova (Becton-Dickinson) and Inoqula (KIESTRA) systems. These new instruments allow efficient and accurate inoculation of samples, including four main steps: (i) selecting the appropriate Petri dish; (ii) inoculating the sample; (iii) spreading the inoculum on agar plates to obtain, upon incubation, well-separated bacterial colonies; and (iv) accurate labelling and sorting of each inoculated media. The challenge for clinical bacteriologists is to determine what is the ideal automated system for their own laboratory. Indeed, different solutions will be preferred, according to the number and variety of samples, and to the types of sample that will be processed with the automated system. The final choice is troublesome, because audits proposed by industrials risk being biased towards the solution proposed by their company, and because these automated systems may not be easily tested on site prior to the final decision, owing to the complexity of computer connections between the laboratory information system and the instrument. This article thus summarizes the main parameters that need to be taken into account for choosing the optimal system, and provides some clues to help clinical bacteriologists to make their choice. © 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.

Automated processing of whole blood samples for the determination of immunosuppressants by liquid chromatography tandem-mass spectrometry.

PubMed

Vogeser, Michael; Spöhrer, Ute

2006-01-01

Liquid chromatography tandem-mass spectrometry (LC-MS/MS) is an efficient technology for routine determination of immunosuppressants in whole blood; however, time-consuming manual sample preparation remains a significant limitation of this technique. Using a commercially available robotic pipetting system (Tecan Freedom EVO), we developed an automated sample-preparation protocol for quantification of tacrolimus in whole blood by LC-MS/MS. Barcode reading, sample resuspension, transfer of whole blood aliquots into a deep-well plate, addition of internal standard solution, mixing, and protein precipitation by addition of an organic solvent is performed by the robotic system. After centrifugation of the plate, the deproteinized supernatants are submitted to on-line solid phase extraction, using column switching prior to LC-MS/MS analysis. The only manual actions within the entire process are decapping of the tubes, and transfer of the deep-well plate from the robotic system to a centrifuge and finally to the HPLC autosampler. Whole blood pools were used to assess the reproducibility of the entire analytical system for measuring tacrolimus concentrations. A total coefficient of variation of 1.7% was found for the entire automated analytical process (n=40; mean tacrolimus concentration, 5.3 microg/L). Close agreement between tacrolimus results obtained after manual and automated sample preparation was observed. The analytical system described here, comprising automated protein precipitation, on-line solid phase extraction and LC-MS/MS analysis, is convenient and precise, and minimizes hands-on time and the risk of mistakes in the quantification of whole blood immunosuppressant concentrations compared to conventional methods.

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.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Egorov, Oleg; O'Hara, Matthew J.; Grate, Jay W.

An automated fluidic instrument is described that rapidly determines the total 99Tc content of aged nuclear waste samples, where the matrix is chemically and radiologically complex and the existing speciation of the 99Tc 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 99Tc. We developed amore » 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 99Tc 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.« less

Semi-automated 96-well liquid-liquid extraction for quantitation of drugs in biological fluids.

PubMed

Zhang, N; Hoffman, K L; Li, W; Rossi, D T

2000-02-01

A semi-automated liquid-liquid extraction (LLE) technique for biological fluid sample preparation was introduced for the quantitation of four drugs in rat plasma. All liquid transferring during the sample preparation was automated using a Tomtec Quadra 96 Model 320 liquid handling robot, which processed up to 96 samples in parallel. The samples were either in 96-deep-well plate or tube-rack format. One plate of samples can be prepared in approximately 1.5 h, and the 96-well plate is directly compatible with the autosampler of an LC/MS system. Selection of organic solvents and recoveries are discussed. Also, precision, relative error, linearity and quantitation of the semi automated LLE method are estimated for four example drugs using LC/MS/MS with a multiple reaction monitoring (MRM) approach. The applicability of this method and future directions are evaluated.

Cost assessment of the automated VERSANT 440 Molecular System versus the semi-automated System 340 bDNA Analyzer platforms.

PubMed

Elbeik, Tarek; Loftus, Richard A; Beringer, Scott

2007-11-01

Labor, supply and waste were evaluated for HIV-1 and HCV bDNA on the semi-automated System 340 bDNA Analyzer and the automated VERSANT 440 Molecular System (V440). HIV-1 sample processing was evaluated using a 24- and 48-position centrifuge rotor. Vigilance time (hands-on manipulations plus incubation time except initial target hybridization) and disposables were approximately 37 and 12% lower for HIV-1, and 64 and 31% lower for HCV bDNA, respectively, with V440. Biohazardous solid waste was approximately twofold lower for both assays and other waste types were the same for either assay on both platforms. HIV-1 sample processing vigilance time for the 48-position rotor was reduced by 2 h. V440 provides cost savings and improved workflow.

[Establishment of Automation System for Detection of Alcohol in Blood].

PubMed

Tian, L L; Shen, Lei; Xue, J F; Liu, M M; Liang, L J

2017-02-01

To establish an automation system for detection of alcohol content in blood. The determination was performed by automated workstation of extraction-headspace gas chromatography （HS-GC）. The blood collection with negative pressure, sealing time of headspace bottle and sample needle were checked and optimized in the abstraction of automation system. The automatic sampling was compared with the manual sampling. The quantitative data obtained by the automated workstation of extraction-HS-GC for alcohol was stable. The relative differences of two parallel samples were less than 5%. The automated extraction was superior to the manual extraction. A good linear relationship was obtained at the alcohol concentration range of 0.1-3.0 mg/mL （ r ≥0.999） with good repeatability. The method is simple and quick, with more standard experiment process and accurate experimental data. It eliminates the error from the experimenter and has good repeatability, which can be applied to the qualitative and quantitative detections of alcohol in blood. Copyright© by the Editorial Department of Journal of Forensic Medicine

Automated processing integrated with a microflow cytometer for pathogen detection in clinical matrices

PubMed Central

Golden, J.P.; Verbarg, J.; Howell, P.B.; Shriver-Lake, L.C.; Ligler, F.S.

2012-01-01

A spinning magnetic trap (MagTrap) for automated sample processing was integrated with a microflow cytometer capable of simultaneously detecting multiple targets to provide an automated sample-to-answer diagnosis in 40 min. After target capture on fluorescently coded magnetic microspheres, the magnetic trap automatically concentrated the fluorescently coded microspheres, separated the captured target from the sample matrix, and exposed the bound target sequentially to biotinylated tracer molecules and streptavidin-labeled phycoerythrin. The concentrated microspheres were then hydrodynamically focused in a microflow cytometer capable of 4-color analysis (two wavelengths for microsphere identification, one for light scatter to discriminate single microspheres and one for phycoerythrin bound to the target). A three-fold decrease in sample preparation time and an improved detection limit, independent of target preconcentration, was demonstrated for detection of Escherichia coli 0157:H7 using the MagTrap as compared to manual processing. Simultaneous analysis of positive and negative controls, along with the assay reagents specific for the target, was used to obtain dose–response curves, demonstrating the potential for quantification of pathogen load in buffer and serum. PMID:22960010

Automated processing integrated with a microflow cytometer for pathogen detection in clinical matrices.

PubMed

Golden, J P; Verbarg, J; Howell, P B; Shriver-Lake, L C; Ligler, F S

2013-02-15

A spinning magnetic trap (MagTrap) for automated sample processing was integrated with a microflow cytometer capable of simultaneously detecting multiple targets to provide an automated sample-to-answer diagnosis in 40 min. After target capture on fluorescently coded magnetic microspheres, the magnetic trap automatically concentrated the fluorescently coded microspheres, separated the captured target from the sample matrix, and exposed the bound target sequentially to biotinylated tracer molecules and streptavidin-labeled phycoerythrin. The concentrated microspheres were then hydrodynamically focused in a microflow cytometer capable of 4-color analysis (two wavelengths for microsphere identification, one for light scatter to discriminate single microspheres and one for phycoerythrin bound to the target). A three-fold decrease in sample preparation time and an improved detection limit, independent of target preconcentration, was demonstrated for detection of Escherichia coli 0157:H7 using the MagTrap as compared to manual processing. Simultaneous analysis of positive and negative controls, along with the assay reagents specific for the target, was used to obtain dose-response curves, demonstrating the potential for quantification of pathogen load in buffer and serum. Published by Elsevier B.V.

Automated process for solvent separation of organic/inorganic substance

DOEpatents

Schweighardt, F.K.

1986-07-29

There is described an automated process for the solvent separation of organic/inorganic substances that operates continuously and unattended and eliminates potential errors resulting from subjectivity and the aging of the sample during analysis. In the process, metered amounts of one or more solvents are passed sequentially through a filter containing the sample under the direction of a microprocessor control apparatus. The mixture in the filter is agitated by ultrasonic cavitation for a timed period and the filtrate is collected. The filtrate of each solvent extraction is collected individually and the residue on the filter element is collected to complete the extraction process. 4 figs.

Automated process for solvent separation of organic/inorganic substance

DOEpatents

Schweighardt, Frank K.

1986-01-01

There is described an automated process for the solvent separation of organic/inorganic substances that operates continuously and unattended and eliminates potential errors resulting from subjectivity and the aging of the sample during analysis. In the process, metered amounts of one or more solvents are passed sequentially through a filter containing the sample under the direction of a microprocessor control apparatus. The mixture in the filter is agitated by ultrasonic cavitation for a timed period and the filtrate is collected. The filtrate of each solvent extraction is collected individually and the residue on the filter element is collected to complete the extraction process.

Automated Sensitivity Analysis of Interplanetary Trajectories

NASA Technical Reports Server (NTRS)

Knittel, Jeremy; Hughes, Kyle; Englander, Jacob; Sarli, Bruno

2017-01-01

This work describes a suite of Python tools known as the Python EMTG Automated Trade Study Application (PEATSA). PEATSA was written to automate the operation of trajectory optimization software, simplify the process of performing sensitivity analysis, and was ultimately found to out-perform a human trajectory designer in unexpected ways. These benefits will be discussed and demonstrated on sample mission designs.

Robofurnace: A semi-automated laboratory chemical vapor deposition system for high-throughput nanomaterial synthesis and process discovery

PubMed Central

Oliver, C. Ryan; Westrick, William; Koehler, Jeremy; Brieland-Shoultz, Anna; Anagnostopoulos-Politis, Ilias; Cruz-Gonzalez, Tizoc; Hart, A. John

2013-01-01

Laboratory research and development on new materials, such as nanostructured thin films, often utilizes manual equipment such as tube furnaces due to its relatively low cost and ease of setup. However, these systems can be prone to inconsistent outcomes due to variations in standard operating procedures and limitations in performance such as heating and cooling rates restrict the parameter space that can be explored. Perhaps more importantly, maximization of research throughput and the successful and efficient translation of materials processing knowledge to production-scale systems, relies on the attainment of consistent outcomes. In response to this need, we present a semi-automated lab-scale chemical vapor deposition (CVD) furnace system, called “Robofurnace.” Robofurnace is an automated CVD system built around a standard tube furnace, which automates sample insertion and removal and uses motion of the furnace to achieve rapid heating and cooling. The system has a 10-sample magazine and motorized transfer arm, which isolates the samples from the lab atmosphere and enables highly repeatable placement of the sample within the tube. The system is designed to enable continuous operation of the CVD reactor, with asynchronous loading/unloading of samples. To demonstrate its performance, Robofurnace is used to develop a rapid CVD recipe for carbon nanotube (CNT) forest growth, achieving a 10-fold improvement in CNT forest mass density compared to a benchmark recipe using a manual tube furnace. In the long run, multiple systems like Robofurnace may be linked to share data among laboratories by methods such as Twitter. Our hope is Robofurnace and like automation will enable machine learning to optimize and discover relationships in complex material synthesis processes. PMID:24289435

Automated cell disruption is a reliable and effective method of isolating RNA from fresh snap-frozen normal and malignant oral mucosa samples.

PubMed

Van der Vorst, Sébastien; Dekairelle, Anne-France; Irenge, Léonid; Hamoir, Marc; Robert, Annie; Gala, Jean-Luc

2009-01-01

This study compared automated vs. manual tissue grinding in terms of RNA yield obtained from oral mucosa biopsies. A total of 20 patients undergoing uvulectomy for sleep-related disorders and 10 patients undergoing biopsy for head and neck squamous cell carcinoma were enrolled in the study. Samples were collected, snap-frozen in liquid nitrogen, and divided into two parts of similar weight. Sample grinding was performed on one sample from each pair, either manually or using an automated cell disruptor. The performance and efficacy of each homogenization approach was compared in terms of total RNA yield (spectrophotometry, fluorometry), mRNA quantity [densitometry of specific TP53 amplicons and TP53 quantitative reverse-transcribed real-time PCR (qRT-PCR)], and mRNA quality (functional analysis of separated alleles in yeast). Although spectrophotometry and fluorometry results were comparable for both homogenization methods, TP53 expression values obtained by amplicon densitometry and qRT-PCR were significantly and consistently better after automated homogenization (p<0.005) for both uvula and tumor samples. Functional analysis of separated alleles in yeast results was better with the automated technique for tumor samples. Automated tissue homogenization appears to be a versatile, quick, and reliable method of cell disruption and is especially useful in the case of small malignant samples, which show unreliable results when processed by manual homogenization.

Automation of laboratory testing for infectious diseases using the polymerase chain reaction-- our past, our present, our future.

PubMed

Jungkind, D

2001-01-01

While it is an extremely powerful and versatile assay method, polymerase chain reaction (PCR) can be a labor-intensive process. Since the advent of commercial test kits from Roche and the semi-automated microwell Amplicor system, PCR has become an increasingly useful and widespread clinical tool. However, more widespread acceptance of molecular testing will depend upon automation that allows molecular assays to enter the routine clinical laboratory. The forces driving the need for automated PCR are the requirements for diagnosis and treatment of chronic viral diseases, economic pressures to develop more automated and less expensive test procedures similar to those in the clinical chemistry laboratories, and a shortage in many areas of qualified laboratory personnel trained in the types of manual procedures used in past decades. The automated Roche COBAS AMPLICOR system has automated the amplification and detection process. Specimen preparation remains the most labor-intensive part of the PCR testing process, accounting for the majority of the hands-on-time in most of the assays. A new automated specimen preparation system, the COBAS AmpliPrep, was evaluated. The system automatically releases the target nucleic acid, captures the target with specific oligonucleotide probes, which become attached to magnetic beads via a biotin-streptavidin binding reaction. Once attached to the beads, the target is purified and concentrated automatically. Results of 298 qualitative and 57 quantitative samples representing a wide range of virus concentrations analyzed after the COBAS AmpliPrep and manual specimen preparation methods, showed that there was no significant difference in qualitative or quantitative hepatitis C virus (HCV) assay performance, respectively. The AmpliPrep instrument decreased the time required to prepare serum or plasma samples for HCV PCR to under 1 min per sample. This was a decrease of 76% compared to the manual specimen preparation method. Systems that can analyze more samples with higher throughput and that can answer more questions about the nature of the microbes that we can presently only detect and quantitate will be needed in the future.

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

Automated Sensitivity Analysis of Interplanetary Trajectories for Optimal Mission Design

NASA Technical Reports Server (NTRS)

Knittel, Jeremy; Hughes, Kyle; Englander, Jacob; Sarli, Bruno

2017-01-01

This work describes a suite of Python tools known as the Python EMTG Automated Trade Study Application (PEATSA). PEATSA was written to automate the operation of trajectory optimization software, simplify the process of performing sensitivity analysis, and was ultimately found to out-perform a human trajectory designer in unexpected ways. These benefits will be discussed and demonstrated on sample mission designs.

Economic and workflow analysis of a blood bank automated system.

PubMed

Shin, Kyung-Hwa; Kim, Hyung Hoi; Chang, Chulhun L; Lee, Eun Yup

2013-07-01

This study compared the estimated costs and times required for ABO/Rh(D) typing and unexpected antibody screening using an automated system and manual methods. The total cost included direct and labor costs. Labor costs were calculated on the basis of the average operator salaries and unit values (minutes), which was the hands-on time required to test one sample. To estimate unit values, workflows were recorded on video, and the time required for each process was analyzed separately. The unit values of ABO/Rh(D) typing using the manual method were 5.65 and 8.1 min during regular and unsocial working hours, respectively. The unit value was less than 3.5 min when several samples were tested simultaneously. The unit value for unexpected antibody screening was 2.6 min. The unit values using the automated method for ABO/Rh(D) typing, unexpected antibody screening, and both simultaneously were all 1.5 min. The total cost of ABO/Rh(D) typing of only one sample using the automated analyzer was lower than that of testing only one sample using the manual technique but higher than that of testing several samples simultaneously. The total cost of unexpected antibody screening using an automated analyzer was less than that using the manual method. ABO/Rh(D) typing using an automated analyzer incurs a lower unit value and cost than that using the manual technique when only one sample is tested at a time. Unexpected antibody screening using an automated analyzer always incurs a lower unit value and cost than that using the manual technique.

Robotics-assisted mass spectrometry assay platform enabled by open-source electronics.

PubMed

Chiu, Shih-Hao; Urban, Pawel L

2015-02-15

Mass spectrometry (MS) is an important analytical technique with numerous applications in clinical analysis, biochemistry, environmental analysis, geology and physics. Its success builds on the ability of MS to determine molecular weights of analytes, and elucidate their structures. However, sample handling prior to MS requires a lot of attention and labor. In this work we were aiming to automate processing samples for MS so that analyses could be conducted without much supervision of experienced analysts. The goal of this study was to develop a robotics and information technology-oriented platform that could control the whole analysis process including sample delivery, reaction-based assay, data acquisition, and interaction with the analyst. The proposed platform incorporates a robotic arm for handling sample vials delivered to the laboratory, and several auxiliary devices which facilitate and secure the analysis process. They include: multi-relay board, infrared sensors, photo-interrupters, gyroscopes, force sensors, fingerprint scanner, barcode scanner, touch screen panel, and internet interface. The control of all the building blocks is achieved through implementation of open-source electronics (Arduino), and enabled by custom-written programs in C language. The advantages of the proposed system include: low cost, simplicity, small size, as well as facile automation of sample delivery and processing without the intervention of the analyst. It is envisaged that this simple robotic system may be the forerunner of automated laboratories dedicated to mass spectrometric analysis of biological samples. Copyright © 2014 Elsevier B.V. All rights reserved.

A Liquid-Handling Robot for Automated Attachment of Biomolecules to Microbeads.

PubMed

Enten, Aaron; Yang, Yujia; Ye, Zihan; Chu, Ryan; Van, Tam; Rothschild, Ben; Gonzalez, Francisco; Sulchek, Todd

2016-08-01

Diagnostics, drug delivery, and other biomedical industries rely on cross-linking ligands to microbead surfaces. Microbead functionalization requires multiple steps of liquid exchange, incubation, and mixing, which are laborious and time intensive. Although automated systems exist, they are expensive and cumbersome, limiting their routine use in biomedical laboratories. We present a small, bench-top robotic system that automates microparticle functionalization and streamlines sample preparation. The robot uses a programmable microcontroller to regulate liquid exchange, incubation, and mixing functions. Filters with a pore diameter smaller than the minimum bead diameter are used to prevent bead loss during liquid exchange. The robot uses three liquid reagents and processes up to 10(7) microbeads per batch. The effectiveness of microbead functionalization was compared with a manual covalent coupling process and evaluated via flow cytometry and fluorescent imaging. The mean percentages of successfully functionalized beads were 91% and 92% for the robot and manual methods, respectively, with less than 5% bead loss. Although the two methods share similar qualities, the automated approach required approximately 10 min of active labor, compared with 3 h for the manual approach. These results suggest that a low-cost, automated microbead functionalization system can streamline sample preparation with minimal operator intervention. © 2015 Society for Laboratory Automation and Screening.

A high-throughput semi-automated preparation for filtered synaptoneurosomes.

PubMed

Murphy, Kathryn M; Balsor, Justin; Beshara, Simon; Siu, Caitlin; Pinto, Joshua G A

2014-09-30

Synaptoneurosomes have become an important tool for studying synaptic proteins. The filtered synaptoneurosomes preparation originally developed by Hollingsworth et al. (1985) is widely used and is an easy method to prepare synaptoneurosomes. The hand processing steps in that preparation, however, are labor intensive and have become a bottleneck for current proteomic studies using synaptoneurosomes. For this reason, we developed new steps for tissue homogenization and filtration that transform the preparation of synaptoneurosomes to a high-throughput, semi-automated process. We implemented a standardized protocol with easy to follow steps for homogenizing multiple samples simultaneously using a FastPrep tissue homogenizer (MP Biomedicals, LLC) and then filtering all of the samples in centrifugal filter units (EMD Millipore, Corp). The new steps dramatically reduce the time to prepare synaptoneurosomes from hours to minutes, increase sample recovery, and nearly double enrichment for synaptic proteins. These steps are also compatible with biosafety requirements for working with pathogen infected brain tissue. The new high-throughput semi-automated steps to prepare synaptoneurosomes are timely technical advances for studies of low abundance synaptic proteins in valuable tissue samples. Copyright © 2014 Elsevier B.V. All rights reserved.

Automated forensic DNA purification optimized for FTA card punches and identifiler STR-based PCR analysis.

PubMed

Tack, Lois C; Thomas, Michelle; Reich, Karl

2007-03-01

Forensic labs globally face the same problem-a growing need to process a greater number and wider variety of samples for DNA analysis. The same forensic lab can be tasked all at once with processing mixed casework samples from crime scenes, convicted offender samples for database entry, and tissue from tsunami victims for identification. Besides flexibility in the robotic system chosen for forensic automation, there is a need, for each sample type, to develop new methodology that is not only faster but also more reliable than past procedures. FTA is a chemical treatment of paper, unique to Whatman Bioscience, and is used for the stabilization and storage of biological samples. Here, the authors describe optimization of the Whatman FTA Purification Kit protocol for use with the AmpFlSTR Identifiler PCR Amplification Kit.

Establishment of a fully automated microtiter plate-based system for suspension cell culture and its application for enhanced process optimization.

PubMed

Markert, Sven; Joeris, Klaus

2017-01-01

We developed an automated microtiter plate (MTP)-based system for suspension cell culture to meet the increased demands for miniaturized high throughput applications in biopharmaceutical process development. The generic system is based on off-the-shelf commercial laboratory automation equipment and is able to utilize MTPs of different configurations (6-24 wells per plate) in orbital shaken mode. The shaking conditions were optimized by Computational Fluid Dynamics simulations. The fully automated system handles plate transport, seeding and feeding of cells, daily sampling, and preparation of analytical assays. The integration of all required analytical instrumentation into the system enables a hands-off operation which prevents bottlenecks in sample processing. The modular set-up makes the system flexible and adaptable for a continuous extension of analytical parameters and add-on components. The system proved suitable as screening tool for process development by verifying the comparability of results for the MTP-based system and bioreactors regarding profiles of viable cell density, lactate, and product concentration of CHO cell lines. These studies confirmed that 6 well MTPs as well as 24 deepwell MTPs were predictive for a scale up to a 1000 L stirred tank reactor (scale factor 1:200,000). Applying the established cell culture system for automated media blend screening in late stage development, a 22% increase in product yield was achieved in comparison to the reference process. The predicted product increase was subsequently confirmed in 2 L bioreactors. Thus, we demonstrated the feasibility of the automated MTP-based cell culture system for enhanced screening and optimization applications in process development and identified further application areas such as process robustness. The system offers a great potential to accelerate time-to-market for new biopharmaceuticals. Biotechnol. Bioeng. 2017;114: 113-121. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

RNA isolation from mammalian cells using porous polymer monoliths: an approach for high-throughput automation.

PubMed

Chatterjee, Anirban; Mirer, Paul L; Zaldivar Santamaria, Elvira; Klapperich, Catherine; Sharon, Andre; Sauer-Budge, Alexis F

2010-06-01

The life science and healthcare communities have been redefining the importance of ribonucleic acid (RNA) through the study of small molecule RNA (in RNAi/siRNA technologies), micro RNA (in cancer research and stem cell research), and mRNA (gene expression analysis for biologic drug targets). Research in this field increasingly requires efficient and high-throughput isolation techniques for RNA. Currently, several commercial kits are available for isolating RNA from cells. Although the quality and quantity of RNA yielded from these kits is sufficiently good for many purposes, limitations exist in terms of extraction efficiency from small cell populations and the ability to automate the extraction process. Traditionally, automating a process decreases the cost and personnel time while simultaneously increasing the throughput and reproducibility. As the RNA field matures, new methods for automating its extraction, especially from low cell numbers and in high throughput, are needed to achieve these improvements. The technology presented in this article is a step toward this goal. The method is based on a solid-phase extraction technology using a porous polymer monolith (PPM). A novel cell lysis approach and a larger binding surface throughout the PPM extraction column ensure a high yield from small starting samples, increasing sensitivity and reducing indirect costs in cell culture and sample storage. The method ensures a fast and simple procedure for RNA isolation from eukaryotic cells, with a high yield both in terms of quality and quantity. The technique is amenable to automation and streamlined workflow integration, with possible miniaturization of the sample handling process making it suitable for high-throughput applications.

Automated grain mapping using wide angle convergent beam electron diffraction in transmission electron microscope for nanomaterials.

PubMed

Kumar, Vineet

2011-12-01

The grain size statistics, commonly derived from the grain map of a material sample, are important microstructure characteristics that greatly influence its properties. The grain map for nanomaterials is usually obtained manually by visual inspection of the transmission electron microscope (TEM) micrographs because automated methods do not perform satisfactorily. While the visual inspection method provides reliable results, it is a labor intensive process and is often prone to human errors. In this article, an automated grain mapping method is developed using TEM diffraction patterns. The presented method uses wide angle convergent beam diffraction in the TEM. The automated technique was applied on a platinum thin film sample to obtain the grain map and subsequently derive grain size statistics from it. The grain size statistics obtained with the automated method were found in good agreement with the visual inspection method.

Flexible automation of cell culture and tissue engineering tasks.

PubMed

Knoll, Alois; Scherer, Torsten; Poggendorf, Iris; Lütkemeyer, Dirk; Lehmann, Jürgen

2004-01-01

Until now, the predominant use cases of industrial robots have been routine handling tasks in the automotive industry. In biotechnology and tissue engineering, in contrast, only very few tasks have been automated with robots. New developments in robot platform and robot sensor technology, however, make it possible to automate plants that largely depend on human interaction with the production process, e.g., for material and cell culture fluid handling, transportation, operation of equipment, and maintenance. In this paper we present a robot system that lends itself to automating routine tasks in biotechnology but also has the potential to automate other production facilities that are similar in process structure. After motivating the design goals, we describe the system and its operation, illustrate sample runs, and give an assessment of the advantages. We conclude this paper by giving an outlook on possible further developments.

Automation in high-content flow cytometry screening.

PubMed

Naumann, U; Wand, M P

2009-09-01

High-content flow cytometric screening (FC-HCS) is a 21st Century technology that combines robotic fluid handling, flow cytometric instrumentation, and bioinformatics software, so that relatively large numbers of flow cytometric samples can be processed and analysed in a short period of time. We revisit a recent application of FC-HCS to the problem of cellular signature definition for acute graft-versus-host-disease. Our focus is on automation of the data processing steps using recent advances in statistical methodology. We demonstrate that effective results, on par with those obtained via manual processing, can be achieved using our automatic techniques. Such automation of FC-HCS has the potential to drastically improve diagnosis and biomarker identification.

Automated indirect immunofluorescence evaluation of antinuclear autoantibodies on HEp-2 cells.

PubMed

Voigt, Jörn; Krause, Christopher; Rohwäder, Edda; Saschenbrecker, Sandra; Hahn, Melanie; Danckwardt, Maick; Feirer, Christian; Ens, Konstantin; Fechner, Kai; Barth, Erhardt; Martinetz, Thomas; Stöcker, Winfried

2012-01-01

Indirect immunofluorescence (IIF) on human epithelial (HEp-2) cells is considered as the gold standard screening method for the detection of antinuclear autoantibodies (ANA). However, in terms of automation and standardization, it has not been able to keep pace with most other analytical techniques used in diagnostic laboratories. Although there are already some automation solutions for IIF incubation in the market, the automation of result evaluation is still in its infancy. Therefore, the EUROPattern Suite has been developed as a comprehensive automated processing and interpretation system for standardized and efficient ANA detection by HEp-2 cell-based IIF. In this study, the automated pattern recognition was compared to conventional visual interpretation in a total of 351 sera. In the discrimination of positive from negative samples, concordant results between visual and automated evaluation were obtained for 349 sera (99.4%, kappa = 0.984). The system missed out none of the 272 antibody-positive samples and identified 77 out of 79 visually negative samples (analytical sensitivity/specificity: 100%/97.5%). Moreover, 94.0% of all main antibody patterns were recognized correctly by the software. Owing to its performance characteristics, EUROPattern enables fast, objective, and economic IIF ANA analysis and has the potential to reduce intra- and interlaboratory variability.

Automated Indirect Immunofluorescence Evaluation of Antinuclear Autoantibodies on HEp-2 Cells

PubMed Central

Voigt, Jörn; Krause, Christopher; Rohwäder, Edda; Saschenbrecker, Sandra; Hahn, Melanie; Danckwardt, Maick; Feirer, Christian; Ens, Konstantin; Fechner, Kai; Barth, Erhardt; Martinetz, Thomas; Stöcker, Winfried

2012-01-01

Indirect immunofluorescence (IIF) on human epithelial (HEp-2) cells is considered as the gold standard screening method for the detection of antinuclear autoantibodies (ANA). However, in terms of automation and standardization, it has not been able to keep pace with most other analytical techniques used in diagnostic laboratories. Although there are already some automation solutions for IIF incubation in the market, the automation of result evaluation is still in its infancy. Therefore, the EUROPattern Suite has been developed as a comprehensive automated processing and interpretation system for standardized and efficient ANA detection by HEp-2 cell-based IIF. In this study, the automated pattern recognition was compared to conventional visual interpretation in a total of 351 sera. In the discrimination of positive from negative samples, concordant results between visual and automated evaluation were obtained for 349 sera (99.4%, kappa = 0.984). The system missed out none of the 272 antibody-positive samples and identified 77 out of 79 visually negative samples (analytical sensitivity/specificity: 100%/97.5%). Moreover, 94.0% of all main antibody patterns were recognized correctly by the software. Owing to its performance characteristics, EUROPattern enables fast, objective, and economic IIF ANA analysis and has the potential to reduce intra- and interlaboratory variability. PMID:23251220

A LEAN approach toward automated analysis and data processing of polymers using proton NMR spectroscopy.

PubMed

de Brouwer, Hans; Stegeman, Gerrit

2011-02-01

To maximize utilization of expensive laboratory instruments and to make most effective use of skilled human resources, the entire chain of data processing, calculation, and reporting that is needed to transform raw NMR data into meaningful results was automated. The LEAN process improvement tools were used to identify non-value-added steps in the existing process. These steps were eliminated using an in-house developed software package, which allowed us to meet the key requirement of improving quality and reliability compared with the existing process while freeing up valuable human resources and increasing productivity. Reliability and quality were improved by the consistent data treatment as performed by the software and the uniform administration of results. Automating a single NMR spectrophotometer led to a reduction in operator time of 35%, doubling of the annual sample throughput from 1400 to 2800, and reducing the turn around time from 6 days to less than 2. Copyright © 2011 Society for Laboratory Automation and Screening. Published by Elsevier Inc. All rights reserved.

Contamination analyses of technology mirror assembly optical surfaces

NASA Technical Reports Server (NTRS)

Germani, Mark S.

1991-01-01

Automated electron microprobe analyses were performed on tape lift samples from the Technology Mirror Assembly (TMA) optical surfaces. Details of the analyses are given, and the contamination of the mirror surfaces is discussed. Based on the automated analyses of the tape lifts from the TMA surfaces and the control blank, we can conclude that the particles identified on the actual samples were not a result of contamination due to the handling or sampling process itself and that the particles reflect the actual contamination on the surface of the mirror.

Automated CD-SEM recipe creation technology for mass production using CAD data

NASA Astrophysics Data System (ADS)

Kawahara, Toshikazu; Yoshida, Masamichi; Tanaka, Masashi; Ido, Sanyu; Nakano, Hiroyuki; Adachi, Naokaka; Abe, Yuichi; Nagatomo, Wataru

2011-03-01

Critical Dimension Scanning Electron Microscope (CD-SEM) recipe creation needs sample preparation necessary for matching pattern registration, and recipe creation on CD-SEM using the sample, which hinders the reduction in test production cost and time in semiconductor manufacturing factories. From the perspective of cost reduction and improvement of the test production efficiency, automated CD-SEM recipe creation without the sample preparation and the manual operation has been important in the production lines. For the automated CD-SEM recipe creation, we have introduced RecipeDirector (RD) that enables the recipe creation by using Computer-Aided Design (CAD) data and text data that includes measurement information. We have developed a system that automatically creates the CAD data and the text data necessary for the recipe creation on RD; and, for the elimination of the manual operation, we have enhanced RD so that all measurement information can be specified in the text data. As a result, we have established an automated CD-SEM recipe creation system without the sample preparation and the manual operation. For the introduction of the CD-SEM recipe creation system using RD to the production lines, the accuracy of the pattern matching was an issue. The shape of design templates for the matching created from the CAD data was different from that of SEM images in vision. Thus, a development of robust pattern matching algorithm that considers the shape difference was needed. The addition of image processing of the templates for the matching and shape processing of the CAD patterns in the lower layer has enabled the robust pattern matching. This paper describes the automated CD-SEM recipe creation technology for the production lines without the sample preparation and the manual operation using RD applied in Sony Semiconductor Kyusyu Corporation Kumamoto Technology Center (SCK Corporation Kumamoto TEC).

Design and Practices for Use of Automated Drilling and Sample Handling in MARTE While Minimizing Terrestrial and Cross Contamination

NASA Astrophysics Data System (ADS)

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.

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.

Microfluidic Sample Preparation for Diagnostic Cytopathology

PubMed Central

Mach, Albert J.; Adeyiga, Oladunni B.; Di Carlo, Dino

2014-01-01

The cellular components of body fluids are routinely analyzed to identify disease and treatment approaches. While significant focus has been placed on developing cell analysis technologies, tools to automate the preparation of cellular specimens have been more limited, especially for body fluids beyond blood. Preparation steps include separating, concentrating, and exposing cells to reagents. Sample preparation continues to be routinely performed off-chip by technicians, preventing cell-based point-of-care diagnostics, increasing the cost of tests, and reducing the consistency of the final analysis following multiple manually-performed steps. Here, we review the assortment of biofluids for which suspended cells are analyzed, along with their characteristics and diagnostic value. We present an overview of the conventional sample preparation processes for cytological diagnosis. We finally discuss the challenges and opportunities in developing microfluidic devices for the purpose of automating or miniaturizing these processes, with particular emphases on preparing large or small volume samples, working with samples of high cellularity, automating multi-step processes, and obtaining high purity subpopulations of cells. We hope to convey the importance of and help identify new research directions addressing the vast biological and clinical applications in preparing and analyzing the array of available biological fluids. Successfully addressing the challenges described in this review can lead to inexpensive systems to improve diagnostic accuracy while simultaneously reducing overall systemic healthcare costs. PMID:23380972

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.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fong, Erika J.; Huang, Chao; Hamilton, Julie

Here, a major advantage of microfluidic devices is the ability to manipulate small sample volumes, thus reducing reagent waste and preserving precious sample. However, to achieve robust sample manipulation it is necessary to address device integration with the macroscale environment. To realize repeatable, sensitive particle separation with microfluidic devices, this protocol presents a complete automated and integrated microfluidic platform that enables precise processing of 0.15–1.5 ml samples using microfluidic devices. Important aspects of this system include modular device layout and robust fixtures resulting in reliable and flexible world to chip connections, and fully-automated fluid handling which accomplishes closed-loop sample collection,more » system cleaning and priming steps to ensure repeatable operation. Different microfluidic devices can be used interchangeably with this architecture. Here we incorporate an acoustofluidic device, detail its characterization, performance optimization, and demonstrate its use for size-separation of biological samples. By using real-time feedback during separation experiments, sample collection is optimized to conserve and concentrate sample. Although requiring the integration of multiple pieces of equipment, advantages of this architecture include the ability to process unknown samples with no additional system optimization, ease of device replacement, and precise, robust sample processing.« less

Smart management of sample dilution using an artificial neural network to achieve streamlined processes and saving resources: the automated nephelometric testing of serum free light chain as case study.

PubMed

Ialongo, Cristiano; Pieri, Massimo; Bernardini, Sergio

2017-02-01

Saving resources is a paramount issue for the modern laboratory, and new trainable as well as smart technologies can be used to allow the automated instrumentation to manage samples more efficiently in order to achieve streamlined processes. In this regard the serum free light chain (sFLC) testing represents an interesting challenge, as it usually causes using a number of assays before achieving an acceptable result within the analytical range. An artificial neural network based on the multi-layer perceptron (MLP-ANN) was used to infer the starting dilution status of sFLC samples based on the information available through the laboratory information system (LIS). After the learning phase, the MLP-ANN simulation was applied to the nephelometric testing routinely performed in our laboratory on a BN ProSpec® System analyzer (Siemens Helathcare) using the N Latex FLC kit. The MLP-ANN reduced the serum kappa free light chain (κ-FLC) and serum lambda free light chain (λ-FLC) wasted tests by 69.4% and 70.8% with respect to the naïve stepwise dilution scheme used by the automated analyzer, and by 64.9% and 66.9% compared to a "rational" dilution scheme based on a 4-step dilution. Although it was restricted to follow-up samples, the MLP-ANN showed good predictive performance, which alongside the possibility to implement it in any automated system, made it a suitable solution for achieving streamlined laboratory processes and saving resources.

Improving clinical laboratory efficiency: a time-motion evaluation of the Abbott m2000 RealTime and Roche COBAS AmpliPrep/COBAS TaqMan PCR systems for the simultaneous quantitation of HIV-1 RNA and HCV RNA.

PubMed

Amendola, Alessandra; Coen, Sabrina; Belladonna, Stefano; Pulvirenti, F Renato; Clemens, John M; Capobianchi, M Rosaria

2011-08-01

Diagnostic laboratories need automation that facilitates efficient processing and workflow management to meet today's challenges for expanding services and reducing cost, yet maintaining the highest levels of quality. Processing efficiency of two commercially available automated systems for quantifying HIV-1 and HCV RNA, Abbott m2000 system and Roche COBAS Ampliprep/COBAS TaqMan 96 (docked) systems (CAP/CTM), was evaluated in a mid/high throughput workflow laboratory using a representative daily workload of 24 HCV and 72 HIV samples. Three test scenarios were evaluated: A) one run with four batches on the CAP/CTM system, B) two runs on the Abbott m2000 and C) one run using the Abbott m2000 maxCycle feature (maxCycle) for co-processing these assays. Cycle times for processing, throughput and hands-on time were evaluated. Overall processing cycle time was 10.3, 9.1 and 7.6 h for Scenarios A), B) and C), respectively. Total hands-on time for each scenario was, in order, 100.0 (A), 90.3 (B) and 61.4 min (C). The interface of an automated analyzer to the laboratory workflow, notably system set up for samples and reagents and clean up functions, are as important as the automation capability of the analyzer for the overall impact to processing efficiency and operator hands-on time.

Topography-Assisted Electromagnetic Platform for Blood-to-PCR in a Droplet

PubMed Central

Chiou, Chi-Han; Shin, Dong Jin; Zhang, Yi; Wang, Tza-Huei

2013-01-01

This paper presents an electromagnetically actuated platform for automated sample preparation and detection of nucleic acids. The proposed platform integrates nucleic acid extraction using silica-coated magnetic particles with real-time polymerase chain reaction (PCR) on a single cartridge. Extraction of genomic material was automated by manipulating magnetic particles in droplets using a series of planar coil electromagnets assisted by topographical features, enabling efficient fluidic processing over a variety of buffers and reagents. The functionality of the platform was demonstrated by performing nucleic acid extraction from whole blood, followed by real-time PCR detection of KRAS oncogene. Automated sample processing from whole blood to PCR-ready droplet was performed in 15 minutes. We took a modular approach of decoupling the modules of magnetic manipulation and optical detection from the device itself, enabling a low-complexity cartridge that operates in tandem with simple external instruments. PMID:23835223

Robotic Surgery

ERIC Educational Resources Information Center

Childress, Vincent W.

2007-01-01

The medical field has many uses for automated and remote-controlled technology. For example, if a tissue sample is only handled in the laboratory by a robotic handling system, then it will never come into contact with a human. Such a system not only helps to automate the medical testing process, but it also helps to reduce the chances of…

An Automated Approach to Peanut dring with real-time monitoring of in-shell Kernel Moisture Content with a Microwave Sensor

USDA-ARS?s Scientific Manuscript database

Today’s peanut drying processes utilize decision support software based on modeling and require substantial human interaction for moisture sampling. These conditions increase the likelihood of peanuts being overdried or underdried. This research addresses the need for an automated controller with re...

Transformation From a Conventional Clinical Microbiology Laboratory to Full Automation.

PubMed

Moreno-Camacho, José L; Calva-Espinosa, Diana Y; Leal-Leyva, Yoseli Y; Elizalde-Olivas, Dolores C; Campos-Romero, Abraham; Alcántar-Fernández, Jonathan

2017-12-22

To validate the performance, reproducibility, and reliability of BD automated instruments in order to establish a fully automated clinical microbiology laboratory. We used control strains and clinical samples to assess the accuracy, reproducibility, and reliability of the BD Kiestra WCA, the BD Phoenix, and BD Bruker MALDI-Biotyper instruments and compared them to previously established conventional methods. The following processes were evaluated: sample inoculation and spreading, colony counts, sorting of cultures, antibiotic susceptibility test, and microbial identification. The BD Kiestra recovered single colonies in less time than conventional methods (e.g. E. coli, 7h vs 10h, respectively) and agreement between both methodologies was excellent for colony counts (κ=0.824) and sorting cultures (κ=0.821). Antibiotic susceptibility tests performed with BD Phoenix and disk diffusion demonstrated 96.3% agreement with both methods. Finally, we compared microbial identification in BD Phoenix and Bruker MALDI-Biotyper and observed perfect agreement (κ=1) and identification at a species level for control strains. Together these instruments allow us to process clinical urine samples in 36h (effective time). The BD automated technologies have improved performance compared with conventional methods, and are suitable for its implementation in very busy microbiology laboratories. © American Society for Clinical Pathology 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

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

Color features as an approach for the automated screening of Salmonella strain

NASA Astrophysics Data System (ADS)

Trujillo, Alejandra Serrano; González, Viridiana Contreras; Andrade Rincón, Saulo E.; Palafox, Luis E.

2016-11-01

We present the implementation of a feature extraction approach for the automated screening of Salmonella sp., a task visually carried out by a microbiologist, where the resulting color characteristics of the culture media plate indicate the presence of this strain. The screening of Salmonella sp. is based on the inoculation and incubation of a sample on an agar plate, allowing the isolation of this strain, if present. This process uses three media: Xylose lysine deoxycholate, Salmonella Shigella, and Brilliant Green agar plates, which exhibit specific color characteristics over the colonies and over the surrounding medium for a presumed positive interpretation. Under a controlled illumination environment, images of plates are captured and the characteristics found over each agar are processed separately. Each agar is analyzed using statistical descriptors for texture, to determine the presence of colonies, followed by the extraction of color features. A comparison among the color features seen over the three media, according to the FDA Bacteriological Analytical Manual, determines the presence of Salmonella sp. on a given sample. The implemented process proves that the task addressed can be accomplished under an image processing approach, leading to the future validation and automation of additional screening processes.

Integrated microfluidic systems for cell lysis, mixing/pumping and DNA amplification

NASA Astrophysics Data System (ADS)

Lee, Chia-Yen; Lee, Gwo-Bin; Lin, Jr-Lung; Huang, Fu-Chun; Liao, Chia-Sheng

2005-06-01

The present paper reports a fully automated microfluidic system for the DNA amplification process by integrating an electroosmotic pump, an active micromixer and an on-chip temperature control system. In this DNA amplification process, the cell lysis is initially performed in a micro cell lysis reactor. Extracted DNA samples, primers and reagents are then driven electroosmotically into a mixing region where they are mixed by the active micromixer. The homogeneous mixture is then thermally cycled in a micro-PCR (polymerase chain reaction) chamber to perform DNA amplification. Experimental results show that the proposed device can successfully automate the sample pretreatment operation for DNA amplification, thereby delivering significant time and effort savings. The new microfluidic system, which facilitates cell lysis, sample driving/mixing and DNA amplification, could provide a significant contribution to ongoing efforts to miniaturize bio-analysis systems by utilizing a simple fabrication process and cheap materials.

A microfluidic platform for precision small-volume sample processing and its use to size separate biological particles with an acoustic microdevice [Precision size separation of biological particles in small-volume samples by an acoustic microfluidic system

DOE PAGES

Fong, Erika J.; Huang, Chao; Hamilton, Julie; ...

2015-11-23

Here, a major advantage of microfluidic devices is the ability to manipulate small sample volumes, thus reducing reagent waste and preserving precious sample. However, to achieve robust sample manipulation it is necessary to address device integration with the macroscale environment. To realize repeatable, sensitive particle separation with microfluidic devices, this protocol presents a complete automated and integrated microfluidic platform that enables precise processing of 0.15–1.5 ml samples using microfluidic devices. Important aspects of this system include modular device layout and robust fixtures resulting in reliable and flexible world to chip connections, and fully-automated fluid handling which accomplishes closed-loop sample collection,more » system cleaning and priming steps to ensure repeatable operation. Different microfluidic devices can be used interchangeably with this architecture. Here we incorporate an acoustofluidic device, detail its characterization, performance optimization, and demonstrate its use for size-separation of biological samples. By using real-time feedback during separation experiments, sample collection is optimized to conserve and concentrate sample. Although requiring the integration of multiple pieces of equipment, advantages of this architecture include the ability to process unknown samples with no additional system optimization, ease of device replacement, and precise, robust sample processing.« less

Automating multistep flow synthesis: approach and challenges in integrating chemistry, machines and logic

PubMed Central

Shukla, Chinmay A

2017-01-01

The implementation of automation in the multistep flow synthesis is essential for transforming laboratory-scale chemistry into a reliable industrial process. In this review, we briefly introduce the role of automation based on its application in synthesis viz. auto sampling and inline monitoring, optimization and process control. Subsequently, we have critically reviewed a few multistep flow synthesis and suggested a possible control strategy to be implemented so that it helps to reliably transfer the laboratory-scale synthesis strategy to a pilot scale at its optimum conditions. Due to the vast literature in multistep synthesis, we have classified the literature and have identified the case studies based on few criteria viz. type of reaction, heating methods, processes involving in-line separation units, telescopic synthesis, processes involving in-line quenching and process with the smallest time scale of operation. This classification will cover the broader range in the multistep synthesis literature. PMID:28684977

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.

Detection of Respiratory Viruses in Sputum from Adults by Use of Automated Multiplex PCR

PubMed Central

Walsh, Edward E.; Formica, Maria A.; Falsey, Ann R.

2014-01-01

Respiratory tract infections (RTI) frequently cause hospital admissions among adults. Diagnostic viral reverse transcriptase PCR (RT-PCR) of nose and throat swabs (NTS) is useful for patient care by informing antiviral use and appropriate isolation. However, automated RT-PCR systems are not amenable to utilizing sputum due to its viscosity. We evaluated a simple method of processing sputum samples in a fully automated respiratory viral panel RT-PCR assay (FilmArray). Archived sputum and NTS samples collected in 2008-2012 from hospitalized adults with RTI were evaluated. A subset of sputum samples positive for 10 common viruses by a uniplex RT-PCR was selected. A sterile cotton-tip swab was dunked in sputum, swirled in 700 μL of sterile water (dunk and swirl method) and tested by the FilmArray assay. Quantitative RT-PCR was performed on “dunked” sputum and NTS samples for influenza A (Flu A), respiratory syncytial virus (RSV), coronavirus OC43 (OC43), and human metapneumovirus (HMPV). Viruses were identified in 31% of 965 illnesses using a uniplex RT-PCR. The sputum sample was the only sample positive for 105 subjects, including 35% (22/64) of influenza cases and significantly increased the diagnostic yield of NTS alone (302/965 [31%] versus 197/965 [20%]; P = 0.0001). Of 108 sputum samples evaluated by the FilmArray assay using the dunk and swirl method, 99 (92%) were positive. Quantitative RT-PCR revealed higher mean viral loads in dunked sputum samples compared to NTS samples for Flu A, RSV, and HMPV (P = 0.0001, P = 0.006, and P = 0.011, respectively). The dunk and swirl method is a simple and practical method for reliably processing sputum samples in a fully automated PCR system. The higher viral loads in sputa may increase detection over NTS testing alone. PMID:25056335

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.

Towards an integrated optofluidic system for highly sensitive detection of antibiotics in seawater incorporating bimodal waveguide photonic biosensors and complex, active microfluidics

NASA Astrophysics Data System (ADS)

Szydzik, C.; Gavela, A. F.; Roccisano, J.; Herranz de Andrés, S.; Mitchell, A.; Lechuga, L. M.

2016-12-01

We present recent results on the realisation and demonstration of an integrated optofluidic lab-on-a-chip measurement system. The system consists of an integrated on-chip automated microfluidic fluid handling subsystem, coupled with bimodal nano-interferometer waveguide technology, and is applied in the context of detection of antibiotics in seawater. The bimodal waveguide (BMWG) is a highly sensitive label-free biosensor. Integration of complex microfluidic systems with bimodal waveguide technology enables on-chip sample handling and fluid processing capabilities and allows for significant automation of experimental processes. The on-chip fluid-handling subsystem is realised through the integration of pneumatically actuated elastomer pumps and valves, enabling high temporal resolution sample and reagent delivery and facilitating multiplexed detection processes.

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

PubMed

Stangegaard, Michael; Hjort, Benjamin B; Hansen, Thomas N; Hoflund, Anders; Mogensen, Helle S; Hansen, Anders J; Morling, Niels

2013-05-01

The presence of PCR inhibitors in extracted DNA may interfere with the subsequent quantification and short tandem repeat (STR) reactions used in forensic genetic DNA typing. DNA extraction from fabric for forensic genetic purposes may be challenging due to the occasional presence of PCR inhibitors that may be co-extracted with the DNA. Using 120 forensic trace evidence samples consisting of various types of fabric, we compared three automated DNA extraction methods based on magnetic beads (PrepFiler Express Forensic DNA Extraction Kit on an AutoMate Express, QIAsyphony DNA Investigator kit either with the sample pre-treatment recommended by Qiagen or an in-house optimized sample pre-treatment on a QIAsymphony SP) and one manual method (Chelex) with the aim of reducing the amount of PCR inhibitors in the DNA extracts and increasing the proportion of reportable STR-profiles. A total of 480 samples were processed. The highest DNA recovery was obtained with the PrepFiler Express kit on an AutoMate Express while the lowest DNA recovery was obtained using a QIAsymphony SP with the sample pre-treatment recommended by Qiagen. Extraction using a QIAsymphony SP with the sample pre-treatment recommended by Qiagen resulted in the lowest percentage of PCR inhibition (0%) while extraction using manual Chelex resulted in the highest percentage of PCR inhibition (51%). The largest number of reportable STR-profiles was obtained with DNA from samples extracted with the PrepFiler Express kit (75%) while the lowest number was obtained with DNA from samples extracted using a QIAsymphony SP with the sample pre-treatment recommended by Qiagen (41%). Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

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.

Automated processing for proton spectroscopic imaging using water reference deconvolution.

PubMed

Maudsley, A A; Wu, Z; Meyerhoff, D J; Weiner, M W

1994-06-01

Automated formation of MR spectroscopic images (MRSI) is necessary before routine application of these methods is possible for in vivo studies; however, this task is complicated by the presence of spatially dependent instrumental distortions and the complex nature of the MR spectrum. A data processing method is presented for completely automated formation of in vivo proton spectroscopic images, and applied for analysis of human brain metabolites. This procedure uses the water reference deconvolution method (G. A. Morris, J. Magn. Reson. 80, 547(1988)) to correct for line shape distortions caused by instrumental and sample characteristics, followed by parametric spectral analysis. Results for automated image formation were found to compare favorably with operator dependent spectral integration methods. While the water reference deconvolution processing was found to provide good correction of spatially dependent resonance frequency shifts, it was found to be susceptible to errors for correction of line shape distortions. These occur due to differences between the water reference and the metabolite distributions.

Automated saliva processing for LC-MS/MS: Improving laboratory efficiency in cortisol and cortisone testing.

PubMed

Antonelli, Giorgia; Padoan, Andrea; Artusi, Carlo; Marinova, Mariela; Zaninotto, Martina; Plebani, Mario

2016-04-01

The aim of this study was to implement in our routine practice an automated saliva preparation protocol for quantification of cortisol (F) and cortisone (E) by LC-MS/MS using a liquid handling platform, maintaining the previously defined reference intervals with the manual preparation. Addition of internal standard solution to saliva samples and calibrators and SPE on μ-elution 96-well plate were performed by liquid handling platform. After extraction, the eluates were submitted to LC-MS/MS analysis. The manual steps within the entire process were to transfer saliva samples in suitable tubes, to put the cap mat and transfer of the collection plate to the LC auto sampler. Transference of the reference intervals from the manual to the automated procedure was established by Passing Bablok regression on 120 saliva samples analyzed simultaneously with the two procedures. Calibration curves were linear throughout the selected ranges. The imprecision ranged from 2 to 10%, with recoveries from 95 to 116%. Passing Bablok regression demonstrated no significant bias. The liquid handling platform translates the manual steps into automated operations allowing for saving hands-on time, while maintaining assay reproducibility and ensuring reliability of results, making it implementable in our routine with the previous established reference intervals. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Automated soil gas monitoring chamber

DOEpatents

Edwards, Nelson T.; Riggs, Jeffery S.

2003-07-29

A chamber for trapping soil gases as they evolve from the soil without disturbance to the soil and to the natural microclimate within the chamber has been invented. The chamber opens between measurements and therefore does not alter the metabolic processes that influence soil gas efflux rates. A multiple chamber system provides for repetitive multi-point sampling, undisturbed metabolic soil processes between sampling, and an essentially airtight sampling chamber operating at ambient pressure.

Automated Drug Identification for Urban Hospitals

NASA Technical Reports Server (NTRS)

Shirley, Donna L.

1971-01-01

Many urban hospitals are becoming overloaded with drug abuse cases requiring chemical analysis for identification of drugs. In this paper, the requirements for chemical analysis of body fluids for drugs are determined and a system model for automated drug analysis is selected. The system as modeled, would perform chemical preparation of samples, gas-liquid chromatographic separation of drugs in the chemically prepared samples, infrared spectrophotometric analysis of the drugs, and would utilize automatic data processing and control for drug identification. Requirements of cost, maintainability, reliability, flexibility, and operability are considered.

Interfacing of high temperature Z-meter setup using python

NASA Astrophysics Data System (ADS)

Patel, Ashutosh; Sisodia, Shashank; Pandey, Sudhir K.

2017-05-01

In this work, we interface high temperature Z-meter setup to automize the whole measurement process. A program is built on open source programming language `Python' which convert the manual measurement process into fully automated process without any cost addition. Using this program, simultaneous measurement of Seebeck coefficient (α), thermal conductivity (κ) and electrical resistivity (ρ), are performed and using all three, figure-of-merit (ZT) is calculated. Developed program is verified by performing measurement over p-type Bi0.36Sb1.45Te3 sample and the data obtained are found to be in good agreement with the reported data.

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. Copyright © 2011 Elsevier B.V. All rights reserved.

Automation of dimethylation after guanidination labeling chemistry and its compatibility with common buffers and surfactants for mass spectrometry-based shotgun quantitative proteome analysis.

PubMed

Lo, Andy; Tang, Yanan; Chen, Lu; Li, Liang

2013-07-25

Isotope labeling liquid chromatography-mass spectrometry (LC-MS) is a major analytical platform for quantitative proteome analysis. Incorporation of isotopes used to distinguish samples plays a critical role in the success of this strategy. In this work, we optimized and automated a chemical derivatization protocol (dimethylation after guanidination, 2MEGA) to increase the labeling reproducibility and reduce human intervention. We also evaluated the reagent compatibility of this protocol to handle biological samples in different types of buffers and surfactants. A commercially available liquid handler was used for reagent dispensation to minimize analyst intervention and at least twenty protein digest samples could be prepared in a single run. Different front-end sample preparation methods for protein solubilization (SDS, urea, Rapigest™, and ProteaseMAX™) and two commercially available cell lysis buffers were evaluated for compatibility with the automated protocol. It was found that better than 94% desired labeling could be obtained in all conditions studied except urea, where the rate was reduced to about 92% due to carbamylation on the peptide amines. This work illustrates the automated 2MEGA labeling process can be used to handle a wide range of protein samples containing various reagents that are often encountered in protein sample preparation for quantitative proteome analysis. Copyright © 2013 Elsevier B.V. All rights reserved.

Automation of diagnostic genetic testing: mutation detection by cyclic minisequencing.

PubMed

Alagrund, Katariina; Orpana, Arto K

2014-01-01

The rising role of nucleic acid testing in clinical decision making is creating a need for efficient and automated diagnostic nucleic acid test platforms. Clinical use of nucleic acid testing sets demands for shorter turnaround times (TATs), lower production costs and robust, reliable methods that can easily adopt new test panels and is able to run rare tests in random access principle. Here we present a novel home-brew laboratory automation platform for diagnostic mutation testing. This platform is based on the cyclic minisequecing (cMS) and two color near-infrared (NIR) detection. Pipetting is automated using Tecan Freedom EVO pipetting robots and all assays are performed in 384-well micro plate format. The automation platform includes a data processing system, controlling all procedures, and automated patient result reporting to the hospital information system. We have found automated cMS a reliable, inexpensive and robust method for nucleic acid testing for a wide variety of diagnostic tests. The platform is currently in clinical use for over 80 mutations or polymorphisms. Additionally to tests performed from blood samples, the system performs also epigenetic test for the methylation of the MGMT gene promoter, and companion diagnostic tests for analysis of KRAS and BRAF gene mutations from formalin fixed and paraffin embedded tumor samples. Automation of genetic test reporting is found reliable and efficient decreasing the work load of academic personnel.

Impact of collection container material and holding times on sample integrity for mercury and methylmercury in water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riscassi, Ami L; Miller, Carrie L; Brooks, Scott C

Mercury (Hg) and methylmercury (MeHg) concentrations in streamwater can vary on short timescales (hourly or less) during storm flow and on a diel cycle; the frequency and timing of sampling required to accurately characterize these dynamics may be difficult to accomplish manually. Automated sampling can assist in sample collection; however use has been limited for Hg and MeHg analysis due to stability concerns of trace concentrations during extended storage times. We examined the viability of using automated samplers with disposable low-density polyethylene (LDPE) sample bags to collect industrially contaminated streamwater for unfiltered and filtered Hg and MeHg analysis. Specifically wemore » investigated the effect of holding times ranging from hours to days on streamwater collected during baseflow and storm flow. Unfiltered and filtered Hg and MeHg concentrations decreased with increases in time prior to sample processing; holding times of 24 hours or less resulted in concentration changes (mean 11 7% different) similar to variability in duplicates collected manually during analogous field conditions (mean 7 10% different). Comparisons of samples collected with manual and automated techniques throughout a year for a wide range of stream conditions were also found to be similar to differences observed between duplicate grab samples. These results demonstrate automated sampling into LDPE bags with holding times of 24 hours or less can be effectively used to collect streamwater for Hg and MeHg analysis, and encourage the testing of these materials and methods for implementation in other aqueous systems where high-frequency sampling is warranted.« less

EPA Technology Available for Licensing: Portable Device to Concentrate Water Samples for Microorganism Analysis

EPA Pesticide Factsheets

Using a computer controlled system, this ultrafiltration device automates the process of concentrating a water sample and can be operated in the field. The system was also designed to reduce human exposure to potentially contaminated water.

Semiautomated Sample Preparation for Protein Stability and Formulation Screening via Buffer Exchange.

PubMed

Ying, William; Levons, Jaquan K; Carney, Andrea; Gandhi, Rajesh; Vydra, Vicky; Rubin, A Erik

2016-06-01

A novel semiautomated buffer exchange process workflow was developed to enable efficient early protein formulation screening. An antibody fragment protein, BMSdab, was used to demonstrate the workflow. The process afforded 60% to 80% cycle time and scientist time savings and significant material efficiencies. These efficiencies ultimately facilitated execution of this stability work earlier in the drug development process, allowing this tool to inform the developability of potential candidates for development from a formulation perspective. To overcome the key technical challenges, the protein solution was buffer-exchanged by centrifuge filtration into formulations for stability screening in a 96-well plate with an ultrafiltration membrane, leveraging automated liquid handling and acoustic volume measurements to allow several cycles of exchanges. The formulations were transferred into a vacuum manifold and sterile filtered into a rack holding 96 glass vials. The vials were sealed with a capmat of individual caps and placed in stability stations. Stability of the samples prepared by this process and by the standard process was demonstrated to be comparable. This process enabled screening a number of formulations of a protein at an early pharmaceutical development stage with a short sample preparation time. © 2015 Society for Laboratory Automation and Screening.

Semi-automated scoring of triple-probe FISH in human sperm using confocal microscopy.

PubMed

Branch, Francesca; Nguyen, GiaLinh; Porter, Nicholas; Young, Heather A; Martenies, Sheena E; McCray, Nathan; Deloid, Glen; Popratiloff, Anastas; Perry, Melissa J

2017-09-01

Structural and numerical sperm chromosomal aberrations result from abnormal meiosis and are directly linked to infertility. Any live births that arise from aneuploid conceptuses can result in syndromes such as Kleinfelter, Turners, XYY and Edwards. Multi-probe fluorescence in situ hybridization (FISH) is commonly used to study sperm aneuploidy, however manual FISH scoring in sperm samples is labor-intensive and introduces errors. Automated scoring methods are continuously evolving. One challenging aspect for optimizing automated sperm FISH scoring has been the overlap in excitation and emission of the fluorescent probes used to enumerate the chromosomes of interest. Our objective was to demonstrate the feasibility of combining confocal microscopy and spectral imaging with high-throughput methods for accurately measuring sperm aneuploidy. Our approach used confocal microscopy to analyze numerical chromosomal abnormalities in human sperm using enhanced slide preparation and rigorous semi-automated scoring methods. FISH for chromosomes X, Y, and 18 was conducted to determine sex chromosome disomy in sperm nuclei. Application of online spectral linear unmixing was used for effective separation of four fluorochromes while decreasing data acquisition time. Semi-automated image processing, segmentation, classification, and scoring were performed on 10 slides using custom image processing and analysis software and results were compared with manual methods. No significant differences in disomy frequencies were seen between the semi automated and manual methods. Samples treated with pepsin were observed to have reduced background autofluorescence and more uniform distribution of cells. These results demonstrate that semi-automated methods using spectral imaging on a confocal platform are a feasible approach for analyzing numerical chromosomal aberrations in sperm, and are comparable to manual methods. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

Decision Making In A High-Tech World: Automation Bias and Countermeasures

NASA Technical Reports Server (NTRS)

Mosier, Kathleen L.; Skitka, Linda J.; Burdick, Mark R.; Heers, Susan T.; Rosekind, Mark R. (Technical Monitor)

1996-01-01

Automated decision aids and decision support systems have become essential tools in many high-tech environments. In aviation, for example, flight management systems computers not only fly the aircraft, but also calculate fuel efficient paths, detect and diagnose system malfunctions and abnormalities, and recommend or carry out decisions. Air Traffic Controllers will soon be utilizing decision support tools to help them predict and detect potential conflicts and to generate clearances. Other fields as disparate as nuclear power plants and medical diagnostics are similarly becoming more and more automated. Ideally, the combination of human decision maker and automated decision aid should result in a high-performing team, maximizing the advantages of additional cognitive and observational power in the decision-making process. In reality, however, the presence of these aids often short-circuits the way that even very experienced decision makers have traditionally handled tasks and made decisions, and introduces opportunities for new decision heuristics and biases. Results of recent research investigating the use of automated aids have indicated the presence of automation bias, that is, errors made when decision makers rely on automated cues as a heuristic replacement for vigilant information seeking and processing. Automation commission errors, i.e., errors made when decision makers inappropriately follow an automated directive, or automation omission errors, i.e., errors made when humans fail to take action or notice a problem because an automated aid fails to inform them, can result from this tendency. Evidence of the tendency to make automation-related omission and commission errors has been found in pilot self reports, in studies using pilots in flight simulations, and in non-flight decision making contexts with student samples. Considerable research has found that increasing social accountability can successfully ameliorate a broad array of cognitive biases and resultant errors. To what extent these effects generalize to performance situations is not yet empirically established. The two studies to be presented represent concurrent efforts, with student and professional pilot samples, to determine the effects of accountability pressures on automation bias and on the verification of the accurate functioning of automated aids. Students (Experiment 1) and commercial pilots (Experiment 2) performed simulated flight tasks using automated aids. In both studies, participants who perceived themselves as accountable for their strategies of interaction with the automation were significantly more likely to verify its correctness, and committed significantly fewer automation-related errors than those who did not report this perception.

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.

A Simple Method for Automated Equilibration Detection in Molecular Simulations.

PubMed

Chodera, John D

2016-04-12

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

A simple method for automated equilibration detection in molecular simulations

PubMed Central

Chodera, John D.

2016-01-01

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

Using PATIMDB to Create Bacterial Transposon Insertion Mutant Libraries

PubMed Central

Urbach, Jonathan M.; Wei, Tao; Liberati, Nicole; Grenfell-Lee, Daniel; Villanueva, Jacinto; Wu, Gang; Ausubel, Frederick M.

2015-01-01

PATIMDB is a software package for facilitating the generation of transposon mutant insertion libraries. The software has two main functions: process tracking and automated sequence analysis. The process tracking function specifically includes recording the status and fates of multiwell plates and samples in various stages of library construction. Automated sequence analysis refers specifically to the pipeline of sequence analysis starting with ABI files from a sequencing facility and ending with insertion location identifications. The protocols in this unit describe installation and use of PATIMDB software. PMID:19343706

Sample registration software for process automation in the Neutron Activation Analysis (NAA) Facility in Malaysia nuclear agency

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rahman, Nur Aira Abd, E-mail: nur-aira@nuclearmalaysia.gov.my; Yussup, Nolida; Ibrahim, Maslina Bt. Mohd

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 ofmore » 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.« less

Digitally programmable microfluidic automaton for multiscale combinatorial mixing and sample processing†

PubMed Central

Jensen, Erik C.; Stockton, Amanda M.; Chiesl, Thomas N.; Kim, Jungkyu; Bera, Abhisek; Mathies, Richard A.

2013-01-01

A digitally programmable microfluidic Automaton consisting of a 2-dimensional array of pneumatically actuated microvalves is programmed to perform new multiscale mixing and sample processing operations. Large (µL-scale) volume processing operations are enabled by precise metering of multiple reagents within individual nL-scale valves followed by serial repetitive transfer to programmed locations in the array. A novel process exploiting new combining valve concepts is developed for continuous rapid and complete mixing of reagents in less than 800 ms. Mixing, transfer, storage, and rinsing operations are implemented combinatorially to achieve complex assay automation protocols. The practical utility of this technology is demonstrated by performing automated serial dilution for quantitative analysis as well as the first demonstration of on-chip fluorescent derivatization of biomarker targets (carboxylic acids) for microchip capillary electrophoresis on the Mars Organic Analyzer. A language is developed to describe how unit operations are combined to form a microfluidic program. Finally, this technology is used to develop a novel microfluidic 6-sample processor for combinatorial mixing of large sets (>26 unique combinations) of reagents. The digitally programmable microfluidic Automaton is a versatile programmable sample processor for a wide range of process volumes, for multiple samples, and for different types of analyses. PMID:23172232

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.

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...

The NOSAMS sample preparation laboratory in the next millenium: Progress after the WOCE program

NASA Astrophysics Data System (ADS)

Gagnon, Alan R.; McNichol, Ann P.; Donoghue, Joanne C.; Stuart, Dana R.; von Reden, Karl; Nosams

2000-10-01

Since 1991, the primary charge of the National Ocean Sciences AMS (NOSAMS) facility at the Woods Hole Oceanographic Institution has been to supply high throughput, high precision AMS 14C analyses for seawater samples collected as part of the World Ocean Circulation Experiment (WOCE). Approximately 13,000 samples taken as part of WOCE should be fully analyzed by the end of Y2K. Additional sample sources and techniques must be identified and incorporated if NOSAMS is to continue in its present operation mode. A trend in AMS today is the ability to routinely process and analyze radiocarbon samples that contain tiny amounts (<100 μg) of carbon. The capability to mass-produce small samples for 14C analysis has been recognized as a major facility goal. The installation of a new 134-position MC-SNICS ion source, which utilizes a smaller graphite target cartridge than presently used, is one step towards realizing this goal. New preparation systems constructed in the sample preparation laboratory (SPL) include an automated bank of 10 small-volume graphite reactors, an automated system to process organic carbon samples, and a multi-dimensional preparative capillary gas chromatograph (PCGC).

Significant increase in cultivation of Gardnerella vaginalis, Alloscardovia omnicolens, Actinotignum schaalii, and Actinomyces spp. in urine samples with total laboratory automation.

PubMed

Klein, Sabrina; Nurjadi, Dennis; Horner, Susanne; Heeg, Klaus; Zimmermann, Stefan; Burckhardt, Irene

2018-04-13

While total laboratory automation (TLA) is well established in laboratory medicine, only a few microbiological laboratories are using TLA systems. Especially in terms of speed and accuracy, working with TLA is expected to be superior to conventional microbiology. We compared in total 35,564 microbiological urine cultures with and without incubation and processing with BD Kiestra TLA for a 6-month period each retrospectively. Sixteen thousand three hundred thirty-eight urine samples were analyzed in the pre-TLA period and 19,226 with TLA. Sixty-two percent (n = 10,101/16338) of the cultures processed without TLA and 68% (n = 13,102/19226) of the cultures processed with TLA showed growth. There were significantly more samples with two or more species per sample and with low numbers of colony forming units (CFU) after incubation with TLA. Regarding the type of bacteria, there were comparable amounts of Enterobacteriaceae in the samples, slightly less non-fermenting Gram-negative bacteria, but significantly more Gram-positive cocci, and Gram-positive rods. Especially Alloscardivia omnicolens, Gardnerella vaginalis, Actinomyces spp., and Actinotignum schaalii were significantly more abundant in the samples incubated and processed with TLA. The time to report was significantly lower in the TLA processed samples by 1.5 h. We provide the first report in Europe of a large number of urine samples processed with TLA. TLA showed enhanced growth of non-classical and rarely cultured bacteria from urine samples. Our findings suggest that previously underestimated bacteria may be relevant pathogens for urinary tract infections. Further studies are needed to confirm our findings.

Automated tilt series alignment and tomographic reconstruction in IMOD.

PubMed

Mastronarde, David N; Held, Susannah R

2017-02-01

Automated tomographic reconstruction is now possible in the IMOD software package, including the merging of tomograms taken around two orthogonal axes. Several developments enable the production of high-quality tomograms. When using fiducial markers for alignment, the markers to be tracked through the series are chosen automatically; if there is an excess of markers available, a well-distributed subset is selected that is most likely to track well. Marker positions are refined by applying an edge-enhancing Sobel filter, which results in a 20% improvement in alignment error for plastic-embedded samples and 10% for frozen-hydrated samples. Robust fitting, in which outlying points are given less or no weight in computing the fitting error, is used to obtain an alignment solution, so that aberrant points from the automated tracking can have little effect on the alignment. When merging two dual-axis tomograms, the alignment between them is refined from correlations between local patches; a measure of structure was developed so that patches with insufficient structure to give accurate correlations can now be excluded automatically. We have also developed a script for running all steps in the reconstruction process with a flexible mechanism for setting parameters, and we have added a user interface for batch processing of tilt series to the Etomo program in IMOD. Batch processing is fully compatible with interactive processing and can increase efficiency even when the automation is not fully successful, because users can focus their effort on the steps that require manual intervention. Copyright © 2016 Elsevier Inc. All rights reserved.

Clinical Chemistry Laboratory Automation in the 21st Century - Amat Victoria curam (Victory loves careful preparation)

PubMed Central

Armbruster, David A; Overcash, David R; Reyes, Jaime

2014-01-01

The era of automation arrived with the introduction of the AutoAnalyzer using continuous flow analysis and the Robot Chemist that automated the traditional manual analytical steps. Successive generations of stand-alone analysers increased analytical speed, offered the ability to test high volumes of patient specimens, and provided large assay menus. A dichotomy developed, with a group of analysers devoted to performing routine clinical chemistry tests and another group dedicated to performing immunoassays using a variety of methodologies. Development of integrated systems greatly improved the analytical phase of clinical laboratory testing and further automation was developed for pre-analytical procedures, such as sample identification, sorting, and centrifugation, and post-analytical procedures, such as specimen storage and archiving. All phases of testing were ultimately combined in total laboratory automation (TLA) through which all modules involved are physically linked by some kind of track system, moving samples through the process from beginning-to-end. A newer and very powerful, analytical methodology is liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). LC-MS/MS has been automated but a future automation challenge will be to incorporate LC-MS/MS into TLA configurations. Another important facet of automation is informatics, including middleware, which interfaces the analyser software to a laboratory information systems (LIS) and/or hospital information systems (HIS). This software includes control of the overall operation of a TLA configuration and combines analytical results with patient demographic information to provide additional clinically useful information. This review describes automation relevant to clinical chemistry, but it must be recognised that automation applies to other specialties in the laboratory, e.g. haematology, urinalysis, microbiology. It is a given that automation will continue to evolve in the clinical laboratory, limited only by the imagination and ingenuity of laboratory scientists. PMID:25336760

Clinical Chemistry Laboratory Automation in the 21st Century - Amat Victoria curam (Victory loves careful preparation).

PubMed

Armbruster, David A; Overcash, David R; Reyes, Jaime

2014-08-01

The era of automation arrived with the introduction of the AutoAnalyzer using continuous flow analysis and the Robot Chemist that automated the traditional manual analytical steps. Successive generations of stand-alone analysers increased analytical speed, offered the ability to test high volumes of patient specimens, and provided large assay menus. A dichotomy developed, with a group of analysers devoted to performing routine clinical chemistry tests and another group dedicated to performing immunoassays using a variety of methodologies. Development of integrated systems greatly improved the analytical phase of clinical laboratory testing and further automation was developed for pre-analytical procedures, such as sample identification, sorting, and centrifugation, and post-analytical procedures, such as specimen storage and archiving. All phases of testing were ultimately combined in total laboratory automation (TLA) through which all modules involved are physically linked by some kind of track system, moving samples through the process from beginning-to-end. A newer and very powerful, analytical methodology is liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). LC-MS/MS has been automated but a future automation challenge will be to incorporate LC-MS/MS into TLA configurations. Another important facet of automation is informatics, including middleware, which interfaces the analyser software to a laboratory information systems (LIS) and/or hospital information systems (HIS). This software includes control of the overall operation of a TLA configuration and combines analytical results with patient demographic information to provide additional clinically useful information. This review describes automation relevant to clinical chemistry, but it must be recognised that automation applies to other specialties in the laboratory, e.g. haematology, urinalysis, microbiology. It is a given that automation will continue to evolve in the clinical laboratory, limited only by the imagination and ingenuity of laboratory scientists.

Effective application of multiple locus variable number of tandem repeats analysis to tracing Staphylococcus aureus in food-processing environment.

PubMed

Rešková, Z; Koreňová, J; Kuchta, T

2014-04-01

A total of 256 isolates of Staphylococcus aureus were isolated from 98 samples (34 swabs and 64 food samples) obtained from small or medium meat- and cheese-processing plants in Slovakia. The strains were genotypically characterized by multiple locus variable number of tandem repeats analysis (MLVA), involving multiplex polymerase chain reaction (PCR) with subsequent separation of the amplified DNA fragments by an automated flow-through gel electrophoresis. With the panel of isolates, MLVA produced 31 profile types, which was a sufficient discrimination to facilitate the description of spatial and temporal aspects of contamination. Further data on MLVA discrimination were obtained by typing a subpanel of strains by multiple locus sequence typing (MLST). MLVA coupled to automated electrophoresis proved to be an effective, comparatively fast and inexpensive method for tracing S. aureus contamination of food-processing factories. Subspecies genotyping of microbial contaminants in food-processing factories may facilitate identification of spatial and temporal aspects of the contamination. This may help to properly manage the process hygiene. With S. aureus, multiple locus variable number of tandem repeats analysis (MLVA) proved to be an effective method for the purpose, being sufficiently discriminative, yet comparatively fast and inexpensive. The application of automated flow-through gel electrophoresis to separation of DNA fragments produced by multiplex PCR helped to improve the accuracy and speed of the method. © 2013 The Society for Applied Microbiology.

A two-dimensionally coincident second difference cosmic ray spike removal method for the fully automated processing of Raman spectra.

PubMed

Schulze, H Georg; Turner, Robin F B

2014-01-01

Charge-coupled device detectors are vulnerable to cosmic rays that can contaminate Raman spectra with positive going spikes. Because spikes can adversely affect spectral processing and data analyses, they must be removed. Although both hardware-based and software-based spike removal methods exist, they typically require parameter and threshold specification dependent on well-considered user input. Here, we present a fully automated spike removal algorithm that proceeds without requiring user input. It is minimally dependent on sample attributes, and those that are required (e.g., standard deviation of spectral noise) can be determined with other fully automated procedures. At the core of the method is the identification and location of spikes with coincident second derivatives along both the spectral and spatiotemporal dimensions of two-dimensional datasets. The method can be applied to spectra that are relatively inhomogeneous because it provides fairly effective and selective targeting of spikes resulting in minimal distortion of spectra. Relatively effective spike removal obtained with full automation could provide substantial benefits to users where large numbers of spectra must be processed.

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 bulk shipment, an appropriate existing analytical method, i.e. a CEN method, can be used to measure the mycotoxins.The system, routinely in use for explosives detection, was able to screen bulk food and feed for mycotoxins, through non-destructive automated sampling of a whole batch/lot/sublot of commodities. The opportunity to sample a whole bulk would provide more effective tools for inspection at seaports, production facili-ties and distri-bution points. It will advance the current process of myco-toxins check because: (i) Checks will be automated and harmonized, (ii) Checks will be non-destructive, (iii) Checks will be faster and allow a greater amount of bulk commodities to be inspected and (iv) The ability to check, with automated equipment, larger portions of lots of a shipment will increase the probability to detect the heterogeneous mycotoxins contamination in bulk foods. The poster provides some results of feasibility experiments indicating the capability of this technology for inspection of commodities bulks for the detection of mycotoxins, at legal limits, in naturally contaminated food.

Automated interferometric synthetic aperture microscopy and computational adaptive optics for improved optical coherence tomography.

PubMed

Xu, Yang; Liu, Yuan-Zhi; Boppart, Stephen A; Carney, P Scott

2016-03-10

In this paper, we introduce an algorithm framework for the automation of interferometric synthetic aperture microscopy (ISAM). Under this framework, common processing steps such as dispersion correction, Fourier domain resampling, and computational adaptive optics aberration correction are carried out as metrics-assisted parameter search problems. We further present the results of this algorithm applied to phantom and biological tissue samples and compare with manually adjusted results. With the automated algorithm, near-optimal ISAM reconstruction can be achieved without manual adjustment. At the same time, the technical barrier for the nonexpert using ISAM imaging is also significantly lowered.

High-throughput, automated extraction of DNA and RNA from clinical samples using TruTip technology on common liquid handling robots.

PubMed

Holmberg, Rebecca C; Gindlesperger, Alissa; Stokes, Tinsley; Brady, Dane; Thakore, Nitu; Belgrader, Philip; Cooney, Christopher G; Chandler, Darrell P

2013-06-11

TruTip is a simple nucleic acid extraction technology whereby a porous, monolithic binding matrix is inserted into a pipette tip. The geometry of the monolith can be adapted for specific pipette tips ranging in volume from 1.0 to 5.0 ml. The large porosity of the monolith enables viscous or complex samples to readily pass through it with minimal fluidic backpressure. Bi-directional flow maximizes residence time between the monolith and sample, and enables large sample volumes to be processed within a single TruTip. The fundamental steps, irrespective of sample volume or TruTip geometry, include cell lysis, nucleic acid binding to the inner pores of the TruTip monolith, washing away unbound sample components and lysis buffers, and eluting purified and concentrated nucleic acids into an appropriate buffer. The attributes and adaptability of TruTip are demonstrated in three automated clinical sample processing protocols using an Eppendorf epMotion 5070, Hamilton STAR and STARplus liquid handling robots, including RNA isolation from nasopharyngeal aspirate, genomic DNA isolation from whole blood, and fetal DNA extraction and enrichment from large volumes of maternal plasma (respectively).

Model Identification of Integrated ARMA Processes

ERIC Educational Resources Information Center

Stadnytska, Tetiana; Braun, Simone; Werner, Joachim

2008-01-01

This article evaluates the Smallest Canonical Correlation Method (SCAN) and the Extended Sample Autocorrelation Function (ESACF), automated methods for the Autoregressive Integrated Moving-Average (ARIMA) model selection commonly available in current versions of SAS for Windows, as identification tools for integrated processes. SCAN and ESACF can…

A fully automated liquid–liquid extraction system utilizing interface detection

PubMed Central

Maslana, Eugene; Schmitt, Robert; Pan, Jeffrey

2000-01-01

The development of the Abbott Liquid-Liquid Extraction Station was a result of the need for an automated system to perform aqueous extraction on large sets of newly synthesized organic compounds used for drug discovery. The system utilizes a cylindrical laboratory robot to shuttle sample vials between two loading racks, two identical extraction stations, and a centrifuge. Extraction is performed by detecting the phase interface (by difference in refractive index) of the moving column of fluid drawn from the bottom of each vial containing a biphasic mixture. The integration of interface detection with fluid extraction maximizes sample throughput. Abbott-developed electronics process the detector signals. Sample mixing is performed by high-speed solvent injection. Centrifuging of the samples reduces interface emulsions. Operating software permits the user to program wash protocols with any one of six solvents per wash cycle with as many cycle repeats as necessary. Station capacity is eighty, 15 ml vials. This system has proven successful with a broad spectrum of both ethyl acetate and methylene chloride based chemistries. The development and characterization of this automated extraction system will be presented. PMID:18924693

Automated high-throughput flow-through real-time diagnostic system

DOEpatents

Regan, John Frederick

2012-10-30

An automated real-time flow-through system capable of processing multiple samples in an asynchronous, simultaneous, and parallel fashion for nucleic acid extraction and purification, followed by assay assembly, genetic amplification, multiplex detection, analysis, and decontamination. The system is able to hold and access an unlimited number of fluorescent reagents that may be used to screen samples for the presence of specific sequences. The apparatus works by associating extracted and purified sample with a series of reagent plugs that have been formed in a flow channel and delivered to a flow-through real-time amplification detector that has a multiplicity of optical windows, to which the sample-reagent plugs are placed in an operative position. The diagnostic apparatus includes sample multi-position valves, a master sample multi-position valve, a master reagent multi-position valve, reagent multi-position valves, and an optical amplification/detection system.

Predicting Stored Grain Insect Population Densities Using an Electronic Probe Trap

USDA-ARS?s Scientific Manuscript database

Manual sampling of insects in stored grain is a laborious and time consuming process. Automation of grain sampling should help to increase the adoption of stored-grain integrated pest management. A new commercial electronic grain probe trap (OPI Insector™) has recently been marketed. We field tested...

Technology Transfer Opportunities: Automated Ground-Water Monitoring, A Proven Technology

USGS Publications Warehouse

Smith, Kirk P.; Granato, Gregory E.

1998-01-01

Introduction The U.S. Geological Survey (USGS) has developed and tested an automated ground-water monitoring system that measures and records values of selected water-quality properties and constituents using protocols approved for manual sampling. Prototypes using the automated process have demonstrated the ability to increase the quantity and quality of data collected and have shown the potential for reducing labor and material costs for ground-water quality data collection. Automated ground-water monitoring systems can be used to monitor known or potential contaminant sites, such as near landfills, underground storage tanks, or other facilities where potential contaminants are stored, to serve as early warning systems monitoring ground-water quality near public water-supply wells, and for ground-water quality research.

Automated agar plate streaker: a linear plater on Society for Biomolecular Sciences standard plates.

PubMed

King, Gregory W; Kath, Gary S; Siciliano, Sal; Simpson, Neal; Masurekar, Prakash; Sigmund, Jan; Polishook, Jon; Skwish, Stephen; Bills, Gerald; Genilloud, Olga; Peláez, Fernando; Martín, Jesus; Dufresne, Claude

2006-09-01

Several protocols for bacterial isolation and techniques for aerobic plate counting rely on the use of a spiral plater to deposit concentration gradients of microbial suspensions onto a circular agar plate to isolate colony growth. The advantage of applying a gradient of concentrations across the agar surface is that the original microbiological sample can be applied at a single concentration rather than as multiple serial dilutions. The spiral plater gradually dilutes the sample across a compact area and therefore saves time preparing dilutions and multiple agar plates. Commercial spiral platers are not automated and require manual sample loading. Dispensing of the sample volume and rate of gradients are often very limited in range. Furthermore, the spiral sample application cannot be used with rectangular microplates. Another limitation of commercial spiral platers is that they are useful only for dilute, filtered suspensions and cannot plate suspensions of coarse organic particles therefore precluding the use of many kinds of microorganism-containing substrata. An automated agar plate spreader capable of processing 99 rectangular microplates in unattended mode is described. This novel instrument is capable of dispensing discrete volumes of sample in a linear pattern. It can be programmed to dispense a sample suspense at a uniform application rate or across a decreasing concentration gradient.

A 96-well screen filter plate for high-throughput biological sample preparation and LC-MS/MS analysis.

PubMed

Peng, Sean X; Cousineau, Martin; Juzwin, Stephen J; Ritchie, David M

2006-01-01

A novel 96-well screen filter plate (patent pending) has been invented to eliminate a time-consuming and labor-intensive step in preparation of in vivo study samples--to remove blood or plasma clots. These clots plug the pipet tips during a manual or automated sample-transfer step causing inaccurate pipetting or total pipetting failure. Traditionally, these blood and plasma clots are removed by picking them out manually one by one from each sample tube before any sample transfer can be made. This has significantly slowed the sample preparation process and has become a bottleneck for automated high-throughput sample preparation using robotic liquid handlers. Our novel screen filter plate was developed to solve this problem. The 96-well screen filter plate consists of 96 stainless steel wire-mesh screen tubes connected to the 96 openings of a top plate so that the screen filter plate can be readily inserted into a 96-well sample storage plate. Upon insertion, the blood and plasma clots are excluded from entering the screen tube while clear sample solutions flow freely into it. In this way, sample transfer can be easily completed by either manual or automated pipetting methods. In this report, three structurally diverse compounds were selected to evaluate and validate the use of the screen filter plate. The plasma samples of these compounds were transferred and processed in the presence and absence of the screen filter plate and then analyzed by LC-MS/MS methods. Our results showed a good agreement between the samples prepared with and without the screen filter plate, demonstrating the utility and efficiency of this novel device for preparation of blood and plasma samples. The device is simple, easy to use, and reusable. It can be employed for sample preparation of other biological fluids that contain floating particulates or aggregates.

Automated Protist Analysis of Complex Samples: Recent Investigations Using Motion and Thresholding

DTIC Science & Technology

2012-01-01

Report No: CG-D-15-13 Automated Protist Analysis of Complex Samples: Recent Investigations Using Motion and Thresholding...Distribution Statement A: Approved for public release; distribution is unlimited. January 2012 Automated Protist Analysis of Complex Samples...Chelsea Street New London, CT 06320 Automated Protist Analysis of Complex Samples iii UNCLAS//PUBLIC | CG-926 R&DC | B. Nelson, et al

A new highly automated sputter equipment for in situ investigation of deposition processes with synchrotron radiation.

PubMed

Döhrmann, Ralph; Botta, Stephan; Buffet, Adeline; Santoro, Gonzalo; Schlage, Kai; Schwartzkopf, Matthias; Bommel, Sebastian; Risch, Johannes F H; Mannweiler, Roman; Brunner, Simon; Metwalli, Ezzeldin; Müller-Buschbaum, Peter; Roth, Stephan V

2013-04-01

HASE (Highly Automated Sputter Equipment) is a new mobile setup developed to investigate deposition processes with synchrotron radiation. HASE is based on an ultra-high vacuum sputter deposition chamber equipped with an in-vacuum sample pick-and-place robot. This enables a fast and reliable sample change without breaking the vacuum conditions and helps to save valuable measurement time, which is required for experiments at synchrotron sources like PETRA III at DESY. An advantageous arrangement of several sputter guns, mounted on a rotative flange, gives the possibility to sputter under different deposition angles or to sputter different materials on the same substrate. The chamber is also equipped with a modular sample stage, which allows for the integration of different sample environments, such as a sample heating and cooling device. The design of HASE is unique in the flexibility. The combination of several different sputtering methods like standard deposition, glancing angle deposition, and high pressure sputter deposition combined with heating and cooling possibilities of the sample, the large exit windows, and the degree of automation facilitate many different grazing incidence X-ray scattering experiments, such as grazing incidence small and wide angle X-ray scattering, in one setup. In this paper we describe in detail the design and the performance of the new equipment and present the installation of the HASE apparatus at the Micro and Nano focus X-ray Scattering beamline (MiNaXS) at PETRA III. Furthermore, we describe the measurement options and present some selected results. The HASE setup has been successfully commissioned and is now available for users.

A new highly automated sputter equipment for in situ investigation of deposition processes with synchrotron radiation

NASA Astrophysics Data System (ADS)

Döhrmann, Ralph; Botta, Stephan; Buffet, Adeline; Santoro, Gonzalo; Schlage, Kai; Schwartzkopf, Matthias; Bommel, Sebastian; Risch, Johannes F. H.; Mannweiler, Roman; Brunner, Simon; Metwalli, Ezzeldin; Müller-Buschbaum, Peter; Roth, Stephan V.

2013-04-01

HASE (Highly Automated Sputter Equipment) is a new mobile setup developed to investigate deposition processes with synchrotron radiation. HASE is based on an ultra-high vacuum sputter deposition chamber equipped with an in-vacuum sample pick-and-place robot. This enables a fast and reliable sample change without breaking the vacuum conditions and helps to save valuable measurement time, which is required for experiments at synchrotron sources like PETRA III at DESY. An advantageous arrangement of several sputter guns, mounted on a rotative flange, gives the possibility to sputter under different deposition angles or to sputter different materials on the same substrate. The chamber is also equipped with a modular sample stage, which allows for the integration of different sample environments, such as a sample heating and cooling device. The design of HASE is unique in the flexibility. The combination of several different sputtering methods like standard deposition, glancing angle deposition, and high pressure sputter deposition combined with heating and cooling possibil-ities of the sample, the large exit windows, and the degree of automation facilitate many different grazing incidence X-ray scattering experiments, such as grazing incidence small and wide angle X-ray scattering, in one setup. In this paper we describe in detail the design and the performance of the new equipment and present the installation of the HASE apparatus at the Micro and Nano focus X-ray Scattering beamline (MiNaXS) at PETRA III. Furthermore, we describe the measurement options and present some selected results. The HASE setup has been successfully commissioned and is now available for users.

Mass spectrometry-based monitoring of millisecond protein–ligand binding dynamics using an automated microfluidic platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cong, Yongzheng; Katipamula, Shanta; Trader, Cameron D.

2016-01-01

Characterizing protein-ligand binding dynamics is crucial for understanding protein function and developing new therapeutic agents. We have developed a novel microfluidic platform that features rapid mixing of protein and ligand solutions, variable incubation times, and on-chip electrospray ionization to perform label-free, solution-based monitoring of protein-ligand binding dynamics. This platform offers many advantages including automated processing, rapid mixing, and low sample consumption.

Automated space processing payloads study. Volume 2, book 2: Technical report, appendices A through E. [instrument packages and space shuttles

NASA Technical Reports Server (NTRS)

1975-01-01

Experiment hardware and operational requirements for space shuttle experiments are discussed along with payload and system concepts. Appendixes are included in which experiment data sheets, chamber environmental control and monitoring, method for collection and storage of electrophoretically-separated samples, preliminary thermal evaluation of electromagnetic levitation facilities L1, L2, and L3, and applicable industrial automation equipment are discussed.

Note: Automated optical focusing on encapsulated devices for scanning light stimulation systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bitzer, L. A.; Benson, N., E-mail: niels.benson@uni-due.de; Schmechel, R.

Recently, a scanning light stimulation system with an automated, adaptive focus correction during the measurement was introduced. Here, its application on encapsulated devices is discussed. This includes the changes an encapsulating optical medium introduces to the focusing process as well as to the subsequent light stimulation measurement. Further, the focusing method is modified to compensate for the influence of refraction and to maintain a minimum beam diameter on the sample surface.

Device for modular input high-speed multi-channel digitizing of electrical data

DOEpatents

VanDeusen, Alan L.; Crist, Charles E.

1995-09-26

A multi-channel high-speed digitizer module converts a plurality of analog signals to digital signals (digitizing) and stores the signals in a memory device. The analog input channels are digitized simultaneously at high speed with a relatively large number of on-board memory data points per channel. The module provides an automated calibration based upon a single voltage reference source. Low signal noise at such a high density and sample rate is accomplished by ensuring the A/D converters are clocked at the same point in the noise cycle each time so that synchronous noise sampling occurs. This sampling process, in conjunction with an automated calibration, yields signal noise levels well below the noise level present on the analog reference voltages.

Automated apparatus for solvent separation of a coal liquefaction product stream

DOEpatents

Schweighardt, Frank K.

1985-01-01

An automated apparatus for the solvent separation of a coal liquefaction product stream that operates continuously and unattended and eliminates potential errors resulting from subjectivity and the aging of the sample during analysis. In use of the apparatus, metered amounts of one or more solvents are passed sequentially through a filter containing the sample under the direction of a microprocessor control means. The mixture in the filter is agitated by means of ultrasonic cavitation for a timed period and the filtrate is collected. The filtrate of each solvent extraction is collected individually and the residue on the filter element is collected to complete the extraction process.

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 CO 2 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. Copyright © 2016. Published by Elsevier Ltd.

Microfluidic-Based Robotic Sampling System for Radioactive Solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jack D. Law; Julia L. Tripp; Tara E. Smith

A novel microfluidic based robotic sampling system has been developed for sampling and analysis of liquid solutions in nuclear processes. This system couples the use of a microfluidic sample chip with a robotic system designed to allow remote, automated sampling of process solutions in-cell and facilitates direct coupling of the microfluidic sample chip with analytical instrumentation. This system provides the capability for near real time analysis, reduces analytical waste, and minimizes the potential for personnel exposure associated with traditional sampling methods. A prototype sampling system was designed, built and tested. System testing demonstrated operability of the microfluidic based sample systemmore » and identified system modifications to optimize performance.« less

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

Robotic solid phase extraction and high performance liquid chromatographic analysis of ranitidine in serum or plasma.

PubMed

Lloyd, T L; Perschy, T B; Gooding, A E; Tomlinson, J J

1992-01-01

A fully automated assay for the analysis of ranitidine in serum and plasma, with and without an internal standard, was validated. It utilizes robotic solid phase extraction with on-line high performance liquid chromatographic (HPLC) analysis. The ruggedness of the assay was demonstrated over a three-year period. A Zymark Py Technology II robotic system was used for serial processing from initial aspiration of samples from original collection containers, to final direct injection onto the on-line HPLC system. Automated serial processing with on-line analysis provided uniform sample history and increased productivity by freeing the chemist to analyse data and perform other tasks. The solid phase extraction efficiency was 94% throughout the assay range of 10-250 ng/mL. The coefficients of variation for within- and between-day quality control samples ranged from 1 to 6% and 1 to 5%, respectively. Mean accuracy for between-day standards and quality control results ranged from 97 to 102% of the respective theoretical concentrations.

Experiment Automation with a Robot Arm using the Liquids Reflectometer Instrument at the Spallation Neutron Source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zolnierczuk, Piotr A; Vacaliuc, Bogdan; Sundaram, Madhan

The Liquids Reflectometer instrument installed at the Spallation Neutron Source (SNS) enables observations of chemical kinetics, solid-state reactions and phase-transitions of thin film materials at both solid and liquid surfaces. Effective measurement of these behaviors requires each sample to be calibrated dynamically using the neutron beam and the data acquisition system in a feedback loop. Since the SNS is an intense neutron source, the time needed to perform the measurement can be the same as the alignment process, leading to a labor-intensive operation that is exhausting to users. An update to the instrument control system, completed in March 2013, implementedmore » the key features of automated sample alignment and robot-driven sample management, allowing for unattended operation over extended periods, lasting as long as 20 hours. We present a case study of the effort, detailing the mechanical, electrical and software modifications that were made as well as the lessons learned during the integration, verification and testing process.« less

Automated in situ observations of upper ocean biogeochemistry, bio-optics, and physics and their potential use for global studies

NASA Technical Reports Server (NTRS)

Dickey, Tommy D.; Granata, Timothy C.; Taupier-Letage, Isabelle

1992-01-01

The processes controlling the flux of carbon in the upper ocean have dynamic ranges in space and time of at least nine orders of magnitude. These processes depend on a broad suite of inter-related biogeochemical, bio-optical, and physical variables. These variables should be sampled on scales matching the relevant phenomena. Traditional ship-based sampling, while critical for detailed and more comprehensive observations, can span only limited portions of these ranges because of logistical and financial constraints. Further, remote observations from satellite platforms enable broad horizontal coverage which is restricted to the upper few meters of the ocean. For these main reasons, automated subsurface measurement systems are important for the fulfillment of research goals related to the regional and global estimation and modeling of time varying biogeochemical fluxes. Within the past few years, new sensors and systems capable of autonomously measuring several of the critical variables have been developed. The platforms for deploying these systems now include moorings and drifters and it is likely that autonomous underwater vehicles (AUV's) will become available for use in the future. Each of these platforms satisfies particular sampling needs and can be used to complement both shipboard and satellite observations. In the present review, (1) sampling considerations will be summarized, (2) examples of data obtained from some of the existing automated in situ sampling systems will be highlighted, (3) future sensors and systems will be discussed, (4) data management issues for present and future automated systems will be considered, and (5) the status of near real-time data telemetry will be outlined. Finally, we wish to make it clear at the outset that the perspectives presented here are those of the authors and are not intended to represent those of the United States JGOFS program, the International JGOFS program, NOAA's C&GC program, or other global ocean programs.

Technology Transfer Opportunities: Automated Ground-Water Monitoring

USGS Publications Warehouse

Smith, Kirk P.; Granato, Gregory E.

1997-01-01

Introduction A new automated ground-water monitoring system developed by the U.S. Geological Survey (USGS) measures and records values of selected water-quality properties and constituents using protocols approved for manual sampling. Prototypes using the automated process have demonstrated the ability to increase the quantity and quality of data collected and have shown the potential for reducing labor and material costs for ground-water quality data collection. Automation of water-quality monitoring systems in the field, in laboratories, and in industry have increased data density and utility while reducing operating costs. Uses for an automated ground-water monitoring system include, (but are not limited to) monitoring ground-water quality for research, monitoring known or potential contaminant sites, such as near landfills, underground storage tanks, or other facilities where potential contaminants are stored, and as an early warning system monitoring groundwater quality near public water-supply wells.

Automation in photogrammetry: Recent developments and applications (1972-1976)

USGS Publications Warehouse

Thompson, M.M.; Mikhail, E.M.

1976-01-01

An overview of recent developments in the automation of photogrammetry in various countries is presented. Conclusions regarding automated photogrammetry reached at the 1972 Congress in Ottawa are reviewed first as a background for examining the developments of 1972-1976. Applications are described for each country reporting significant developments. Among fifteen conclusions listed are statements concerning: the widespread practice of equipping existing stereoplotters with simple digitizers; the growing tendency to use minicomputers on-line with stereoplotters; the optimization of production of digital terrain models by progressive sampling in stereomodels; the potential of digitization of a photogrammetric model by density correlation on epipolar lines; the capabilities and economic aspects of advanced systems which permit simultaneous production of orthophotos, contours, and digital terrain models; the economy of off-line orthophoto systems; applications of digital image processing; automation by optical techniques; applications of sensors other than photographic imagery, and the role of photogrammetric phases in a completely automated cartographic system. ?? 1976.

Disposable and removable nucleic acid extraction and purification cartridges for automated flow-through systems

DOEpatents

Regan, John Frederick

2014-09-09

Removable cartridges are used on automated flow-through systems for the purpose of extracting and purifying genetic material from complex matrices. Different types of cartridges are paired with specific automated protocols to concentrate, extract, and purifying pathogenic or human genetic material. Their flow-through nature allows large quantities sample to be processed. Matrices may be filtered using size exclusion and/or affinity filters to concentrate the pathogen of interest. Lysed material is ultimately passed through a filter to remove the insoluble material before the soluble genetic material is delivered past a silica-like membrane that binds the genetic material, where it is washed, dried, and eluted. Cartridges are inserted into the housing areas of flow-through automated instruments, which are equipped with sensors to ensure proper placement and usage of the cartridges. Properly inserted cartridges create fluid- and air-tight seals with the flow lines of an automated instrument.

Self-Sealing Wet Chemistry Cell for Field Analysis

NASA Technical Reports Server (NTRS)

Beegle, Luther W.; Soto, Juancarlos; Lasnik, James; Roark, Shane

2012-01-01

In most analytical investigations, there is a need to process complex field samples for the unique detection of analytes, especially when detecting low concentration organic molecules that may identify extraterrestrial life. Wet chemistry based instruments are the techniques of choice for most laboratory- based analysis of organic molecules due to several factors including less fragmentation of fragile biomarkers, and ability to concentrate target species resulting in much lower limits of detection. Development of an automated wet chemistry preparation system that can operate autonomously on Earth and is also designed to operate under Martian ambient conditions will demonstrate the technical feasibility of including wet chemistry on future missions. An Automated Sample Processing System (ASPS) has recently been developed that receives fines, extracts organics through solvent extraction, processes the extract by removing non-organic soluble species, and delivers sample to multiple instruments for analysis (including for non-organic soluble species). The key to this system is a sample cell that can autonomously function under field conditions. As a result, a self-sealing sample cell was developed that can autonomously hermetically seal fines and powder into a container, regardless of orientation of the apparatus. The cap is designed with a beveled edge, which allows the cap to be self-righted as the capping motor engages. Each cap consists of a C-clip lock ring below a crucible O-ring that is placed into a groove cut into the sample cap.

Application of the BioMek 2000 Laboratory Automation Workstation and the DNA IQ System to the extraction of forensic casework samples.

PubMed

Greenspoon, Susan A; Ban, Jeffrey D; Sykes, Karen; Ballard, Elizabeth J; Edler, Shelley S; Baisden, Melissa; Covington, Brian L

2004-01-01

Robotic systems are commonly utilized for the extraction of database samples. However, the application of robotic extraction to forensic casework samples is a more daunting task. Such a system must be versatile enough to accommodate a wide range of samples that may contain greatly varying amounts of DNA, but it must also pose no more risk of contamination than the manual DNA extraction methods. This study demonstrates that the BioMek 2000 Laboratory Automation Workstation, used in combination with the DNA IQ System, is versatile enough to accommodate the wide range of samples typically encountered by a crime laboratory. The use of a silica coated paramagnetic resin, as with the DNA IQ System, facilitates the adaptation of an open well, hands off, robotic system to the extraction of casework samples since no filtration or centrifugation steps are needed. Moreover, the DNA remains tightly coupled to the silica coated paramagnetic resin for the entire process until the elution step. A short pre-extraction incubation step is necessary prior to loading samples onto the robot and it is at this step that most modifications are made to accommodate the different sample types and substrates commonly encountered with forensic evidentiary samples. Sexual assault (mixed stain) samples, cigarette butts, blood stains, buccal swabs, and various tissue samples were successfully extracted with the BioMek 2000 Laboratory Automation Workstation and the DNA IQ System, with no evidence of contamination throughout the extensive validation studies reported here.

Pre-analytical phase: The automated ProTube device supports quality assurance in the phlebotomy process.

PubMed

Piva, Elisa; Tosato, Francesca; Plebani, Mario

2015-12-07

Most errors in laboratory medicine occur in the pre-analytical phase of the total testing process. Phlebotomy, a crucial step in the pre-analytical phase influencing laboratory results and patient outcome, calls for quality assurance procedures and automation in order to prevent errors and ensure patient safety. We compared the performance of a new small, automated device, the ProTube Inpeco, designed for use in phlebotomy with a complete traceability of the process, with a centralized automated system, BC ROBO. ProTube was used for 15,010 patients undergoing phlebotomy with 48,776 tubes being labeled. The mean time and standard deviation (SD) for blood sampling was 3:03 (min:sec; SD ± 1:24) when using ProTube, against 5:40 (min:sec; SD ± 1:57) when using BC ROBO. The mean number of patients per hour managed at each phlebotomy point was 16 ± 3 with ProTube, and 10 ± 2 with BC ROBO. No tubes were labeled erroneously or incorrectly, even if process failure occurred in 2.8% of cases when ProTube was used. Thanks to its cutting edge technology, the ProTube has many advantages over BC ROBO, above all in verifying patient identity, and in allowing a reduction in both identification error and tube mislabeling.

A Hybrid DNA Extraction Method for the Qualitative and Quantitative Assessment of Bacterial Communities from Poultry Production Samples

PubMed Central

Rothrock, Michael J.; Hiett, Kelli L.; Gamble, John; Caudill, Andrew C.; Cicconi-Hogan, Kellie M.; Caporaso, J. Gregory

2014-01-01

The efficacy of DNA extraction protocols can be highly dependent upon both the type of sample being investigated and the types of downstream analyses performed. Considering that the use of new bacterial community analysis techniques (e.g., microbiomics, metagenomics) is becoming more prevalent in the agricultural and environmental sciences and many environmental samples within these disciplines can be physiochemically and microbiologically unique (e.g., fecal and litter/bedding samples from the poultry production spectrum), appropriate and effective DNA extraction methods need to be carefully chosen. Therefore, a novel semi-automated hybrid DNA extraction method was developed specifically for use with environmental poultry production samples. This method is a combination of the two major types of DNA extraction: mechanical and enzymatic. A two-step intense mechanical homogenization step (using bead-beating specifically formulated for environmental samples) was added to the beginning of the “gold standard” enzymatic DNA extraction method for fecal samples to enhance the removal of bacteria and DNA from the sample matrix and improve the recovery of Gram-positive bacterial community members. Once the enzymatic extraction portion of the hybrid method was initiated, the remaining purification process was automated using a robotic workstation to increase sample throughput and decrease sample processing error. In comparison to the strict mechanical and enzymatic DNA extraction methods, this novel hybrid method provided the best overall combined performance when considering quantitative (using 16S rRNA qPCR) and qualitative (using microbiomics) estimates of the total bacterial communities when processing poultry feces and litter samples. PMID:25548939

Introducing automation to the molecular diagnosis of Trypanosoma cruzi infection: A comparative study of sample treatments, DNA extraction methods and real-time PCR assays.

PubMed

Abras, Alba; Ballart, Cristina; Llovet, Teresa; Roig, Carme; Gutiérrez, Cristina; Tebar, Silvia; Berenguer, Pere; Pinazo, María-Jesús; Posada, Elizabeth; Gascón, Joaquim; Schijman, Alejandro G; Gállego, Montserrat; Muñoz, Carmen

2018-01-01

Polymerase chain reaction (PCR) has become a useful tool for the diagnosis of Trypanosoma cruzi infection. The development of automated DNA extraction methodologies and PCR systems is an important step toward the standardization of protocols in routine diagnosis. To date, there are only two commercially available Real-Time PCR assays for the routine laboratory detection of T. cruzi DNA in clinical samples: TCRUZIDNA.CE (Diagnostic Bioprobes Srl) and RealCycler CHAG (Progenie Molecular). Our aim was to evaluate the RealCycler CHAG assay taking into account the whole process. We assessed the usefulness of an automated DNA extraction system based on magnetic particles (EZ1 Virus Mini Kit v2.0, Qiagen) combined with a commercially available Real-Time PCR assay targeting satellite DNA (SatDNA) of T. cruzi (RealCycler CHAG), a methodology used for routine diagnosis in our hospital. It was compared with a well-known strategy combining a commercial DNA isolation kit based on silica columns (High Pure PCR Template Preparation Kit, Roche Diagnostics) with an in-house Real-Time PCR targeting SatDNA. The results of the two methodologies were in almost perfect agreement, indicating they can be used interchangeably. However, when variations in protocol factors were applied (sample treatment, extraction method and Real-Time PCR), the results were less convincing. A comprehensive fine-tuning of the whole procedure is the key to successful results. Guanidine EDTA-blood (GEB) samples are not suitable for DNA extraction based on magnetic particles due to inhibition, at least when samples are not processed immediately. This is the first study to evaluate the RealCycler CHAG assay taking into account the overall process, including three variables (sample treatment, extraction method and Real-Time PCR). Our findings may contribute to the harmonization of protocols between laboratories and to a wider application of Real-Time PCR in molecular diagnostic laboratories associated with health centers.

Rapid Multiplex PCR Assay To Identify Respiratory Viral Pathogens: Moving Forward Diagnosing The Common Cold

PubMed Central

Gordon, Sarah M; Elegino-Steffens, Diane U; Agee, Willie; Barnhill, Jason; Hsue, Gunther

2013-01-01

Upper respiratory tract infections (URIs) can be a serious burden to the healthcare system. The majority of URIs are viral in etiology, but definitive diagnosis can prove difficult due to frequently overlapping clinical presentations of viral and bacterial infections, and the variable sensitivity, and lengthy turn-around time of viral culture. We tested new automated nested multiplex PCR technology, the FilmArray® system, in the TAMC department of clinical investigations, to determine the feasibility of replacing the standard viral culture with a rapid turn-around system. We conducted a feasibility study using a single-blinded comparison study, comparing PCR results with archived viral culture results from a convenience sample of cryopreserved archived nasopharyngeal swabs from acutely ill ED patients who presented with complaints of URI symptoms. A total of 61 archived samples were processed. Viral culture had previously identified 31 positive specimens from these samples. The automated nested multiplex PCR detected 38 positive samples. In total, PCR was 94.5% concordant with the previously positive viral culture results. However, PCR was only 63.4% concordant with the negative viral culture results, owing to PCR detection of 11 additional viral pathogens not recovered on viral culture. The average time to process a sample was 75 minutes. We determined that an automated nested multiplex PCR is a feasible alternative to viral culture in an acute clinical setting. We were able to detect at least 94.5% as many viral pathogens as viral culture is able to identify, with a faster turn-around time. PMID:24052914

Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

PubMed

O'Farrell, Brian; Haase, Jana K; Velayudhan, Vimalkumar; Murphy, Ronan A; Achtman, Mark

2012-01-01

Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST) of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS) consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of < €25 per strain. Since developing this pipeline, >200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.

Transforming Microbial Genotyping: A Robotic Pipeline for Genotyping Bacterial Strains

PubMed Central

Velayudhan, Vimalkumar; Murphy, Ronan A.; Achtman, Mark

2012-01-01

Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST) of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS) consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of < €25 per strain. Since developing this pipeline, >200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost. PMID:23144721

[Optimization of blood gas analysis in intensive care units : Reduction of preanalytical errors and improvement of workflow].

PubMed

Kieninger, M; Zech, N; Mulzer, Y; Bele, S; Seemann, M; Künzig, H; Schneiker, A; Gruber, M

2015-05-01

Point of care testing with blood gas analysis (BGA) is an important factor for intensive care medicine. Continuous efforts to optimize workflow, improve safety for the staff and avoid preanalytical mistakes are important and should reflect quality management standards. In a prospective observational study it was investigated whether the implementation of a new system for BGA using labeled syringes and automated processing of the specimens leads to improvements compared to the previously used procedure. In a 4-week test period the time until receiving the final results of the BGA with the standard method used in the clinical routine (control group) was compared to the results in a second 4-week test period using the new labeled syringes and automated processing of the specimens (intervention group). In addition, preanalytical mistakes with both systems were checked during routine daily use. Finally, it was investigated whether a delay of 10 min between taking and analyzing the blood samples alters the results of the BGA. Preanalytical errors were frequently observed in the control group where non-deaerated samples were recorded in 87.3 % but in the intervention group almost all samples (98.9 %) were correctly deaerated. Insufficient homogenization due to omission of manual pivoting was seen in 83.2 % in the control group and in 89.9 % in the intervention group; however, in the intervention group the samples were homogenized automatically during the further analytical process. Although a survey among the staff revealed a high acceptance of the new system and a subjective improvement of workflow, a measurable gain in time after conversion to the new procedure could not be seen. The mean time needed for a complete analysis process until receiving the final results was 244 s in the intervention group and 201 s in the control group. A 10-min delay between taking and analyzing the blood samples led to a significant and clinically relevant elevation of the values for partial pressure of oxygen (pO2) in both groups compared to the results when analyzing the samples immediately (118.4 vs. 148.6 mmHg in the control group and 115.3 vs. 123.7 mmHg in the intervention group). When using standard syringes the partial pressure of carbon dioxide (pCO2) was significantly lower (40.5 vs. 38.3 mmHg) whereas no alterations were seen when using the labeled syringes. The implementation of a new BGA system with labeled syringes and automated processing of the specimens was possible without any difficulties under daily clinical routine conditions in this 10-bed intensive care unit (ICU). A gain of time could not be measured but a reduction in preanalytical errors using the labeled syringes with automated processing was found. Delayed analysis of blood samples can lead to significant changes in pO2 and pCO2 depending on the type of syringe used.

Device for modular input high-speed multi-channel digitizing of electrical data

DOEpatents

VanDeusen, A.L.; Crist, C.E.

1995-09-26

A multi-channel high-speed digitizer module converts a plurality of analog signals to digital signals (digitizing) and stores the signals in a memory device. The analog input channels are digitized simultaneously at high speed with a relatively large number of on-board memory data points per channel. The module provides an automated calibration based upon a single voltage reference source. Low signal noise at such a high density and sample rate is accomplished by ensuring the A/D converters are clocked at the same point in the noise cycle each time so that synchronous noise sampling occurs. This sampling process, in conjunction with an automated calibration, yields signal noise levels well below the noise level present on the analog reference voltages. 1 fig.

Automated methods for multiplexed pathogen detection.

PubMed

Straub, Timothy M; Dockendorff, Brian P; Quiñonez-Díaz, Maria D; Valdez, Catherine O; Shutthanandan, Janani I; Tarasevich, Barbara J; Grate, Jay W; Bruckner-Lea, Cynthia J

2005-09-01

Detection of pathogenic microorganisms in environmental samples is a difficult process. Concentration of the organisms of interest also co-concentrates inhibitors of many end-point detection methods, notably, nucleic acid methods. In addition, sensitive, highly multiplexed pathogen detection continues to be problematic. The primary function of the BEADS (Biodetection Enabling Analyte Delivery System) platform is the automated concentration and purification of target analytes from interfering substances, often present in these samples, via a renewable surface column. In one version of BEADS, automated immunomagnetic separation (IMS) is used to separate cells from their samples. Captured cells are transferred to a flow-through thermal cycler where PCR, using labeled primers, is performed. PCR products are then detected by hybridization to a DNA suspension array. In another version of BEADS, cell lysis is performed, and community RNA is purified and directly labeled. Multiplexed detection is accomplished by direct hybridization of the RNA to a planar microarray. The integrated IMS/PCR version of BEADS can successfully purify and amplify 10 E. coli O157:H7 cells from river water samples. Multiplexed PCR assays for the simultaneous detection of E. coli O157:H7, Salmonella, and Shigella on bead suspension arrays was demonstrated for the detection of as few as 100 cells for each organism. Results for the RNA version of BEADS are also showing promising results. Automation yields highly purified RNA, suitable for multiplexed detection on microarrays, with microarray detection specificity equivalent to PCR. Both versions of the BEADS platform show great promise for automated pathogen detection from environmental samples. Highly multiplexed pathogen detection using PCR continues to be problematic, but may be required for trace detection in large volume samples. The RNA approach solves the issues of highly multiplexed PCR and provides "live vs. dead" capabilities. However, sensitivity of the method will need to be improved for RNA analysis to replace PCR.

Automated Methods for Multiplexed Pathogen Detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Straub, Tim M.; Dockendorff, Brian P.; Quinonez-Diaz, Maria D.

2005-09-01

Detection of pathogenic microorganisms in environmental samples is a difficult process. Concentration of the organisms of interest also co-concentrates inhibitors of many end-point detection methods, notably, nucleic acid methods. In addition, sensitive, highly multiplexed pathogen detection continues to be problematic. The primary function of the BEADS (Biodetection Enabling Analyte Delivery System) platform is the automated concentration and purification of target analytes from interfering substances, often present in these samples, via a renewable surface column. In one version of BEADS, automated immunomagnetic separation (IMS) is used to separate cells from their samples. Captured cells are transferred to a flow-through thermal cyclermore » where PCR, using labeled primers, is performed. PCR products are then detected by hybridization to a DNA suspension array. In another version of BEADS, cell lysis is performed, and community RNA is purified and directly labeled. Multiplexed detection is accomplished by direct hybridization of the RNA to a planar microarray. The integrated IMS/PCR version of BEADS can successfully purify and amplify 10 E. coli O157:H7 cells from river water samples. Multiplexed PCR assays for the simultaneous detection of E. coli O157:H7, Salmonella, and Shigella on bead suspension arrays was demonstrated for the detection of as few as 100 cells for each organism. Results for the RNA version of BEADS are also showing promising results. Automation yields highly purified RNA, suitable for multiplexed detection on microarrays, with microarray detection specificity equivalent to PCR. Both versions of the BEADS platform show great promise for automated pathogen detection from environmental samples. Highly multiplexed pathogen detection using PCR continues to be problematic, but may be required for trace detection in large volume samples. The RNA approach solves the issues of highly multiplexed PCR and provides ''live vs. dead'' capabilities. However, sensitivity of the method will need to be improved for RNA analysis to replace PCR.« less

Automation of DNA and miRNA co-extraction for miRNA-based identification of human body fluids and tissues.

PubMed

Kulstein, Galina; Marienfeld, Ralf; Miltner, Erich; Wiegand, Peter

2016-10-01

In the last years, microRNA (miRNA) analysis came into focus in the field of forensic genetics. Yet, no standardized and recommendable protocols for co-isolation of miRNA and DNA from forensic relevant samples have been developed so far. Hence, this study evaluated the performance of an automated Maxwell® 16 System-based strategy (Promega) for co-extraction of DNA and miRNA from forensically relevant (blood and saliva) samples compared to (semi-)manual extraction methods. Three procedures were compared on the basis of recovered quantity of DNA and miRNA (as determined by real-time PCR and Bioanalyzer), miRNA profiling (shown by Cq values and extraction efficiency), STR profiles, duration, contamination risk and handling. All in all, the results highlight that the automated co-extraction procedure yielded the highest miRNA and DNA amounts from saliva and blood samples compared to both (semi-)manual protocols. Also, for aged and genuine samples of forensically relevant traces the miRNA and DNA yields were sufficient for subsequent downstream analysis. Furthermore, the strategy allows miRNA extraction only in cases where it is relevant to obtain additional information about the sample type. Besides, this system enables flexible sample throughput and labor-saving sample processing with reduced risk of cross-contamination. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Automated blood-sample handling in the clinical laboratory.

PubMed

Godolphin, W; Bodtker, K; Uyeno, D; Goh, L O

1990-09-01

The only significant advances in blood-taking in 25 years have been the disposable needle and evacuated blood-drawing tube. With the exception of a few isolated barcode experiments, most sample-tracking is performed through handwritten or computer-printed labels. Attempts to reduce the hazards of centrifugation have resulted in air-tight lids or chambers, the use of which is time-consuming and cumbersome. Most commonly used clinical analyzers require serum or plasma, distributed into specialized containers, unique to that analyzer. Aliquots for different tests are prepared by handpouring or pipetting. Moderate to large clinical laboratories perform so many different tests that even multi-analyzers performing multiple analyses on a single sample may account for only a portion of all tests ordered for a patient. Thus several aliquots of each specimen are usually required. We have developed a proprietary serial centrifuge and blood-collection tube suitable for incorporation into an automated or robotic sample-handling system. The system we propose is (a) safe--avoids or prevents biological danger to the many "handlers" of blood; (b) small--minimizes the amount of sample taken and space required to adapt to the needs of satellite and mobile testing, and direct interfacing with analyzers; (c) serial--permits each sample to be treated according to its own "merits," optimizes throughput, and facilitates flexible automation; and (d) smart--ensures quality results through monitoring and intelligent control of patient identification, sample characteristics, and separation process.

An automated synthesis-purification-sample-management platform for the accelerated generation of pharmaceutical candidates.

PubMed

Sutherland, J David; Tu, Noah P; Nemcek, Thomas A; Searle, Philip A; Hochlowski, Jill E; Djuric, Stevan W; Pan, Jeffrey Y

2014-04-01

A flexible and integrated flow-chemistry-synthesis-purification compound-generation and sample-management platform has been developed to accelerate the production of small-molecule organic-compound drug candidates in pharmaceutical research. Central to the integrated system is a Mitsubishi robot, which hands off samples throughout the process to the next station, including synthesis and purification, sample dispensing for purity and quantification analysis, dry-down, and aliquot generation.

The Israel DNA database--the establishment of a rapid, semi-automated analysis system.

PubMed

Zamir, Ashira; Dell'Ariccia-Carmon, Aviva; Zaken, Neomi; Oz, Carla

2012-03-01

The Israel Police DNA database, also known as IPDIS (Israel Police DNA Index System), has been operating since February 2007. During that time more than 135,000 reference samples have been uploaded and more than 2000 hits reported. We have developed an effective semi-automated system that includes two automated punchers, three liquid handler robots and four genetic analyzers. An inhouse LIMS program enables full tracking of every sample through the entire process of registration, pre-PCR handling, analysis of profiles, uploading to the database, hit reports and ultimately storage. The LIMS is also responsible for the future tracking of samples and their profiles to be expunged from the database according to the Israeli DNA legislation. The database is administered by an in-house developed software program, where reference and evidentiary profiles are uploaded, stored, searched and matched. The DNA database has proven to be an effective investigative tool which has gained the confidence of the Israeli public and on which the Israel National Police force has grown to rely. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Analysis of irradiated U-7wt%Mo dispersion fuel microstructures using automated image processing

DOE PAGES

Collette, R.; King, J.; Buesch, C.; ...

2016-04-01

The High Performance Research Reactor Fuel Development (HPPRFD) program is responsible for developing low enriched uranium (LEU) fuel substitutes for high performance reactors fueled with highly enriched uranium (HEU) that have not yet been converted to LEU. The uranium-molybdenum (U-Mo) fuel system was selected for this effort. In this study, fission gas pore segmentation was performed on U-7wt%Mo dispersion fuel samples at three separate fission densities using an automated image processing interface developed in MATLAB. Pore size distributions were attained that showed both expected and unexpected fission gas behavior. In general, it proved challenging to identify any dominant trends whenmore » comparing fission bubble data across samples from different fuel plates due to varying compositions and fabrication techniques. Here, the results exhibited fair agreement with the fission density vs. porosity correlation developed by the Russian reactor conversion program.« less

Analysis of irradiated U-7wt%Mo dispersion fuel microstructures using automated image processing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Collette, R.; King, J.; Buesch, C.

The High Performance Research Reactor Fuel Development (HPPRFD) program is responsible for developing low enriched uranium (LEU) fuel substitutes for high performance reactors fueled with highly enriched uranium (HEU) that have not yet been converted to LEU. The uranium-molybdenum (U-Mo) fuel system was selected for this effort. In this study, fission gas pore segmentation was performed on U-7wt%Mo dispersion fuel samples at three separate fission densities using an automated image processing interface developed in MATLAB. Pore size distributions were attained that showed both expected and unexpected fission gas behavior. In general, it proved challenging to identify any dominant trends whenmore » comparing fission bubble data across samples from different fuel plates due to varying compositions and fabrication techniques. Here, the results exhibited fair agreement with the fission density vs. porosity correlation developed by the Russian reactor conversion program.« less

[The segmentation of urinary cells--a first step in the automated processing in urine cytology (author's transl)].

PubMed

Liedtke, C E; Aeikens, B

1980-01-01

By segmentation of cell images we understand the automated decomposition of microscopic cell scenes into nucleus, plasma and background. A segmentation is achieved by using information from the microscope image and prior knowledge about the content of the scene. Different algorithms have been investigated and applied to samples of urothelial cells. A particular algorithm based on a histogram approach which can be easily implemented in hardware is discussed in more detail.

Automated solid-phase extraction workstations combined with quantitative bioanalytical LC/MS.

PubMed

Huang, N H; Kagel, J R; Rossi, D T

1999-03-01

An automated solid-phase extraction workstation was used to develop, characterize and validate an LC/MS/MS method for quantifying a novel lipid-regulating drug in dog plasma. Method development was facilitated by workstation functions that allowed wash solvents of varying organic composition to be mixed and tested automatically. Precision estimates for this approach were within 9.8% relative standard deviation (RSD) across the calibration range. Accuracy for replicate determinations of quality controls was between -7.2 and +6.2% relative error (RE) over 5-1,000 ng/ml(-1). Recoveries were evaluated for a wide variety of wash solvents, elution solvents and sorbents. Optimized recoveries were generally > 95%. A sample throughput benchmark for the method was approximately equal 8 min per sample. Because of parallel sample processing, 100 samples were extracted in less than 120 min. The approach has proven useful for use with LC/MS/MS, using a multiple reaction monitoring (MRM) approach.

Automated Phase Segmentation for Large-Scale X-ray Diffraction Data Using a Graph-Based Phase Segmentation (GPhase) Algorithm.

PubMed

Xiong, Zheng; He, Yinyan; Hattrick-Simpers, Jason R; Hu, Jianjun

2017-03-13

The creation of composition-processing-structure relationships currently represents a key bottleneck for data analysis for high-throughput experimental (HTE) material studies. Here we propose an automated phase diagram attribution algorithm for HTE data analysis that uses a graph-based segmentation algorithm and Delaunay tessellation to create a crystal phase diagram from high throughput libraries of X-ray diffraction (XRD) patterns. We also propose the sample-pair based objective evaluation measures for the phase diagram prediction problem. Our approach was validated using 278 diffraction patterns from a Fe-Ga-Pd composition spread sample with a prediction precision of 0.934 and a Matthews Correlation Coefficient score of 0.823. The algorithm was then applied to the open Ni-Mn-Al thin-film composition spread sample to obtain the first predicted phase diagram mapping for that sample.

Automated MRI segmentation for individualized modeling of current flow in the human head.

PubMed

Huang, Yu; Dmochowski, Jacek P; Su, Yuzhuo; Datta, Abhishek; Rorden, Christopher; Parra, Lucas C

2013-12-01

High-definition transcranial direct current stimulation (HD-tDCS) and high-density electroencephalography require accurate models of current flow for precise targeting and current source reconstruction. At a minimum, such modeling must capture the idiosyncratic anatomy of the brain, cerebrospinal fluid (CSF) and skull for each individual subject. Currently, the process to build such high-resolution individualized models from structural magnetic resonance images requires labor-intensive manual segmentation, even when utilizing available automated segmentation tools. Also, accurate placement of many high-density electrodes on an individual scalp is a tedious procedure. The goal was to develop fully automated techniques to reduce the manual effort in such a modeling process. A fully automated segmentation technique based on Statical Parametric Mapping 8, including an improved tissue probability map and an automated correction routine for segmentation errors, was developed, along with an automated electrode placement tool for high-density arrays. The performance of these automated routines was evaluated against results from manual segmentation on four healthy subjects and seven stroke patients. The criteria include segmentation accuracy, the difference of current flow distributions in resulting HD-tDCS models and the optimized current flow intensities on cortical targets. The segmentation tool can segment out not just the brain but also provide accurate results for CSF, skull and other soft tissues with a field of view extending to the neck. Compared to manual results, automated segmentation deviates by only 7% and 18% for normal and stroke subjects, respectively. The predicted electric fields in the brain deviate by 12% and 29% respectively, which is well within the variability observed for various modeling choices. Finally, optimized current flow intensities on cortical targets do not differ significantly. Fully automated individualized modeling may now be feasible for large-sample EEG research studies and tDCS clinical trials.

Automated sample-preparation technologies in genome sequencing projects.

PubMed

Hilbert, H; Lauber, J; Lubenow, H; Düsterhöft, A

2000-01-01

A robotic workstation system (BioRobot 96OO, QIAGEN) and a 96-well UV spectrophotometer (Spectramax 250, Molecular Devices) were integrated in to the process of high-throughput automated sequencing of double-stranded plasmid DNA templates. An automated 96-well miniprep kit protocol (QIAprep Turbo, QIAGEN) provided high-quality plasmid DNA from shotgun clones. The DNA prepared by this procedure was used to generate more than two mega bases of final sequence data for two genomic projects (Arabidopsis thaliana and Schizosaccharomyces pombe), three thousand expressed sequence tags (ESTs) plus half a mega base of human full-length cDNA clones, and approximately 53,000 single reads for a whole genome shotgun project (Pseudomonas putida).

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

PubMed

Ibrahim, Sarah A; Martini, Luigi

2014-08-01

Dissolution method transfer is a complicated yet common process in the pharmaceutical industry. With increased pharmaceutical product manufacturing and dissolution acceptance requirements, dissolution testing has become one of the most labor-intensive quality control testing methods. There is an increased trend for automation in dissolution testing, particularly for large pharmaceutical companies to reduce variability and increase personnel efficiency. There is no official guideline for dissolution testing method transfer from a manual, semi-automated, to automated dissolution tester. In this study, a manual multipoint dissolution testing procedure for an enteric-coated aspirin tablet was transferred effectively and reproducibly to a fully automated dissolution testing device, RoboDis II. Enteric-coated aspirin samples were used as a model formulation to assess the feasibility and accuracy of media pH change during continuous automated dissolution testing. Several RoboDis II parameters were evaluated to ensure the integrity and equivalency of dissolution method transfer from a manual dissolution tester. This current study provides a systematic outline for the transfer of the manual dissolution testing protocol to an automated dissolution tester. This study further supports that automated dissolution testers compliant with regulatory requirements and similar to manual dissolution testers facilitate method transfer. © 2014 Society for Laboratory Automation and Screening.

Oak ridge national laboratory automated clean chemistry for bulk analysis of environmental swipe samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bostick, Debra A.; Hexel, Cole R.; Ticknor, Brian W.

2016-11-01

To shorten the lengthy and costly manual chemical purification procedures, sample preparation methods for mass spectrometry are being automated using commercial-off-the-shelf (COTS) equipment. This addresses a serious need in the nuclear safeguards community to debottleneck the separation of U and Pu in environmental samples—currently performed by overburdened chemists—with a method that allows unattended, overnight operation. In collaboration with Elemental Scientific Inc., the prepFAST-MC2 was designed based on current COTS equipment that was modified for U/Pu separations utilizing Eichrom™ TEVA and UTEVA resins. Initial verification of individual columns yielded small elution volumes with consistent elution profiles and good recovery. Combined columnmore » calibration demonstrated ample separation without crosscontamination of the eluent. Automated packing and unpacking of the built-in columns initially showed >15% deviation in resin loading by weight, which can lead to inconsistent separations. Optimization of the packing and unpacking methods led to a reduction in the variability of the packed resin to less than 5% daily. The reproducibility of the automated system was tested with samples containing 30 ng U and 15 pg Pu, which were separated in a series with alternating reagent blanks. These experiments showed very good washout of both the resin and the sample from the columns as evidenced by low blank values. Analysis of the major and minor isotope ratios for U and Pu provided values well within data quality limits for the International Atomic Energy Agency. Additionally, system process blanks spiked with 233U and 244Pu tracers were separated using the automated system after it was moved outside of a clean room and yielded levels equivalent to clean room blanks, confirming that the system can produce high quality results without the need for expensive clean room infrastructure. Comparison of the amount of personnel time necessary for successful manual vs. automated chemical separations showed a significant decrease in hands-on time from 9.8 hours to 35 minutes for seven samples, respectively. This documented time savings and reduced labor translates to a significant cost savings per sample. Overall, the system will enable faster sample reporting times at reduced costs by limiting personnel hours dedicated to the chemical separation.« less

Advantages and challenges in automated apatite fission track counting

NASA Astrophysics Data System (ADS)

Enkelmann, E.; Ehlers, T. A.

2012-04-01

Fission track thermochronometer data are often a core element of modern tectonic and denudation studies. Soon after the development of the fission track methods interest emerged for the developed an automated counting procedure to replace the time consuming labor of counting fission tracks under the microscope. Automated track counting became feasible in recent years with increasing improvements in computer software and hardware. One such example used in this study is the commercial automated fission track counting procedure from Autoscan Systems Pty that has been highlighted through several venues. We conducted experiments that are designed to reliably and consistently test the ability of this fully automated counting system to recognize fission tracks in apatite and a muscovite external detector. Fission tracks were analyzed in samples with a step-wise increase in sample complexity. The first set of experiments used a large (mm-size) slice of Durango apatite cut parallel to the prism plane. Second, samples with 80-200 μm large apatite grains of Fish Canyon Tuff were analyzed. This second sample set is characterized by complexities often found in apatites in different rock types. In addition to the automated counting procedure, the same samples were also analyzed using conventional counting procedures. We found for all samples that the fully automated fission track counting procedure using the Autoscan System yields a larger scatter in the fission track densities measured compared to conventional (manual) track counting. This scatter typically resulted from the false identification of tracks due surface and mineralogical defects, regardless of the image filtering procedure used. Large differences between track densities analyzed with the automated counting persisted between different grains analyzed in one sample as well as between different samples. As a result of these differences a manual correction of the fully automated fission track counts is necessary for each individual surface area and grain counted. This manual correction procedure significantly increases (up to four times) the time required to analyze a sample with the automated counting procedure compared to the conventional approach.

Small Libraries Online: Automating Circulation and Public Access Catalogs. Participant Workbook.

ERIC Educational Resources Information Center

Garcia, C. Rebecca; Bridge, Frank R.

This workbook, meant to be used in a workshop, presents information on and guidelines for automating small libraries: (1) planning for automation; (2) automated system procurement and evaluation; (3) data conversion issues; (4) sample configuration worksheets; (5) sample configuration costs; (6) site preparation; (7) training; and (8) acceptance…

Statistical Methods in Assembly Quality Management of Multi-Element Products on Automatic Rotor Lines

NASA Astrophysics Data System (ADS)

Pries, V. V.; Proskuriakov, N. E.

2018-04-01

To control the assembly quality of multi-element mass-produced products on automatic rotor lines, control methods with operational feedback are required. However, due to possible failures in the operation of the devices and systems of automatic rotor line, there is always a real probability of getting defective (incomplete) products into the output process stream. Therefore, a continuous sampling control of the products completeness, based on the use of statistical methods, remains an important element in managing the quality of assembly of multi-element mass products on automatic rotor lines. The feature of continuous sampling control of the multi-element products completeness in the assembly process is its breaking sort, which excludes the possibility of returning component parts after sampling control to the process stream and leads to a decrease in the actual productivity of the assembly equipment. Therefore, the use of statistical procedures for continuous sampling control of the multi-element products completeness when assembled on automatic rotor lines requires the use of such sampling plans that ensure a minimum size of control samples. Comparison of the values of the limit of the average output defect level for the continuous sampling plan (CSP) and for the automated continuous sampling plan (ACSP) shows the possibility of providing lower limit values for the average output defects level using the ACSP-1. Also, the average sample size when using the ACSP-1 plan is less than when using the CSP-1 plan. Thus, the application of statistical methods in the assembly quality management of multi-element products on automatic rotor lines, involving the use of proposed plans and methods for continuous selective control, will allow to automating sampling control procedures and the required level of quality of assembled products while minimizing sample size.

Analysis of nitrosamines in water by automated SPE and isotope dilution GC/HRMS Occurrence in the different steps of a drinking water treatment plant, and in chlorinated samples from a reservoir and a sewage treatment plant effluent.

PubMed

Planas, Carles; Palacios, Oscar; Ventura, Francesc; Rivera, Josep; Caixach, Josep

2008-08-15

A method based on automated solid-phase extraction (SPE) and isotope dilution gas chromatography/high resolution mass spectrometry (GC/HRMS) has been developed for the analysis of nine nitrosamines in water samples. The combination of automated SPE and GC/HRMS for the analysis of nitrosamines has not been reported previously. The method shows as advantages the selectivity and sensitivity of GC/HRMS analysis and the high efficiency of automated SPE with coconut charcoal EPA 521 cartridges. Low method detection limits (MDLs) were achieved, along with a greater facility of the procedure and less dependence on the operator with regard to the methods based on manual SPE. Quality requirements for isotope dilution-based methods were accomplished for most analysed nitrosamines, regarding to trueness (80-120%), method precision (<15%) and MDLs (0.08-1.7 ng/L). Nineteen water samples (16 samples from a drinking water treatment plant {DWTP}, 2 chlorinated samples from a sewage treatment plant {STP} effluent, and 1 chlorinated sample from a reservoir) were analysed. Concentrations of nitrosamines in the STP effluent were 309.4 and 730.2 ng/L, being higher when higher doses of chlorine were applied. N-Nitrosodimethylamine (NDMA) and N-nitrosodiethylamine (NDEA) were the main compounds identified in the STP effluent, and NDEA was detected above 200 ng/L, regulatory level for NDMA in effluents stated in Ontario (Canada). Lower concentrations of nitrosamines were found in the reservoir (20.3 ng/L) and in the DWTP samples (n.d. -28.6 ng/L). NDMA and NDEA were respectively found in the reservoir and in treated and highly chlorinated DWTP samples at concentrations above 10 ng/L (guide value established in different countries). The highest concentrations of nitrosamines were found after chlorination and ozonation processes (ozonated, treated and highly chlorinated water) in DWTP samples.

Smart fast blood counting of trace volumes of body fluids from various mammalian species using a compact custom-built microscope cytometer (Conference Presentation)

NASA Astrophysics Data System (ADS)

Smith, Zachary J.; Gao, Tingjuan; Lin, Tzu-Yin; Carrade-Holt, Danielle; Lane, Stephen M.; Matthews, Dennis L.; Dwyre, Denis M.; Wachsmann-Hogiu, Sebastian

2016-03-01

Cell counting in human body fluids such as blood, urine, and CSF is a critical step in the diagnostic process for many diseases. Current automated methods for cell counting are based on flow cytometry systems. However, these automated methods are bulky, costly, require significant user expertise, and are not well suited to counting cells in fluids other than blood. Therefore, their use is limited to large central laboratories that process enough volume of blood to recoup the significant capital investment these instruments require. We present in this talk a combination of a (1) low-cost microscope system, (2) simple sample preparation method, and (3) fully automated analysis designed for providing cell counts in blood and body fluids. We show results on both humans and companion and farm animals, showing that accurate red cell, white cell, and platelet counts, as well as hemoglobin concentration, can be accurately obtained in blood, as well as a 3-part white cell differential in human samples. We can also accurately count red and white cells in body fluids with a limit of detection ~3 orders of magnitude smaller than current automated instruments. This method uses less than 1 microliter of blood, and less than 5 microliters of body fluids to make its measurements, making it highly compatible with finger-stick style collections, as well as appropriate for small animals such as laboratory mice where larger volume blood collections are dangerous to the animal's health.

An automation-assisted generic approach for biological sample preparation and LC-MS/MS method validation.

PubMed

Zhang, Jie; Wei, Shimin; Ayres, David W; Smith, Harold T; Tse, Francis L S

2011-09-01

Although it is well known that automation can provide significant improvement in the efficiency of biological sample preparation in quantitative LC-MS/MS analysis, it has not been widely implemented in bioanalytical laboratories throughout the industry. This can be attributed to the lack of a sound strategy and practical procedures in working with robotic liquid-handling systems. Several comprehensive automation assisted procedures for biological sample preparation and method validation were developed and qualified using two types of Hamilton Microlab liquid-handling robots. The procedures developed were generic, user-friendly and covered the majority of steps involved in routine sample preparation and method validation. Generic automation procedures were established as a practical approach to widely implement automation into the routine bioanalysis of samples in support of drug-development programs.

Precise turnaround time measurement of laboratory processes using radiofrequency identification technology.

PubMed

Mayer, Horst; Brümmer, Jens; Brinkmann, Thomas

2011-01-01

To implement Lean Six Sigma in our central laboratory we conducted a project to measure single pre-analytical steps influencing turnaround time (TAT) of emergency department (ED) serum samples. The traditional approach of extracting data from the Laboratory Information System (LIS) for a retrospective calculation of a mean TAT is not suitable. Therefore, we used radiofrequency identification (RFID) chips for real time tracking of individual samples at any pre-analytical step. 1,200 serum tubes were labelled with RFID chips and were provided to the emergency department. 3 RFID receivers were installed in the laboratory: at the outlet of the pneumatic tube system, at the centrifuge, and in the analyser area. In addition, time stamps of sample entry at the automated sample distributor and communication of results from the analyser were collected from LIS. 1,023 labelled serum tubes arrived at our laboratory. 899 RFID tags were used for TAT calculation. The following transfer times were determined (median 95th percentile in min:sec): pneumatic tube system --> centrifuge (01:25/04:48), centrifuge --> sample distributor (14:06/5:33), sample distributor --> analysis system zone (02:39/15:07), analysis system zone --> result communication (12:42/22:21). Total TAT was calculated at 33:19/57:40 min:sec. Manual processes around centrifugation were identified as a major part of TAT with 44%/60% (median/95th percentile). RFID is a robust, easy to use, and error-free technology and not susceptible to interferences in the laboratory environment. With this study design we were able to measure significant variations in a single manual sample transfer process. We showed that TAT is mainly influenced by manual steps around the centrifugation process and we concluded that centrifugation should be integrated in solutions for total laboratory automation.

Eye blink detection for different driver states in conditionally automated driving and manual driving using EOG and a driver camera.

PubMed

Schmidt, Jürgen; Laarousi, Rihab; Stolzmann, Wolfgang; Karrer-Gauß, Katja

2018-06-01

In this article, we examine the performance of different eye blink detection algorithms under various constraints. The goal of the present study was to evaluate the performance of an electrooculogram- and camera-based blink detection process in both manually and conditionally automated driving phases. A further comparison between alert and drowsy drivers was performed in order to evaluate the impact of drowsiness on the performance of blink detection algorithms in both driving modes. Data snippets from 14 monotonous manually driven sessions (mean 2 h 46 min) and 16 monotonous conditionally automated driven sessions (mean 2 h 45 min) were used. In addition to comparing two data-sampling frequencies for the electrooculogram measures (50 vs. 25 Hz) and four different signal-processing algorithms for the camera videos, we compared the blink detection performance of 24 reference groups. The analysis of the videos was based on very detailed definitions of eyelid closure events. The correct detection rates for the alert and manual driving phases (maximum 94%) decreased significantly in the drowsy (minus 2% or more) and conditionally automated (minus 9% or more) phases. Blinking behavior is therefore significantly impacted by drowsiness as well as by automated driving, resulting in less accurate blink detection.

Automated Desalting Apparatus

NASA Technical Reports Server (NTRS)

Spencer, Maegan K.; Liu, De-Ling; Kanik, Isik; Beegle, Luther

2010-01-01

Because salt and metals can mask the signature of a variety of organic molecules (like amino acids) in any given sample, an automated system to purify complex field samples has been created for the analytical techniques of electrospray ionization/ mass spectroscopy (ESI/MS), capillary electrophoresis (CE), and biological assays where unique identification requires at least some processing of complex samples. This development allows for automated sample preparation in the laboratory and analysis of complex samples in the field with multiple types of analytical instruments. Rather than using tedious, exacting protocols for desalting samples by hand, this innovation, called the Automated Sample Processing System (ASPS), takes analytes that have been extracted through high-temperature solvent extraction and introduces them into the desalting column. After 20 minutes, the eluent is produced. This clear liquid can then be directly analyzed by the techniques listed above. The current apparatus including the computer and power supplies is sturdy, has an approximate mass of 10 kg, and a volume of about 20 20 20 cm, and is undergoing further miniaturization. This system currently targets amino acids. For these molecules, a slurry of 1 g cation exchange resin in deionized water is packed into a column of the apparatus. Initial generation of the resin is done by flowing sequentially 2.3 bed volumes of 2N NaOH and 2N HCl (1 mL each) to rinse the resin, followed by .5 mL of deionized water. This makes the pH of the resin near neutral, and eliminates cross sample contamination. Afterward, 2.3 mL of extracted sample is then loaded into the column onto the top of the resin bed. Because the column is packed tightly, the sample can be applied without disturbing the resin bed. This is a vital step needed to ensure that the analytes adhere to the resin. After the sample is drained, oxalic acid (1 mL, pH 1.6-1.8, adjusted with NH4OH) is pumped into the column. Oxalic acid works as a chelating reagent to bring out metal ions, such as calcium and iron, which would otherwise interfere with amino acid analysis. After oxalic acid, 1 mL 0.01 N HCl and 1 mL deionized water is used to sequentially rinse the resin. Finally, the amino acids attached to the resin, and the analytes are eluted using 2.5 M NH4OH (1 mL), and the NH4OH eluent is collected in a vial for analysis.

Validation of a DNA IQ-based extraction method for TECAN robotic liquid handling workstations for processing casework.

PubMed

Frégeau, Chantal J; Lett, C Marc; Fourney, Ron M

2010-10-01

A semi-automated DNA extraction process for casework samples based on the Promega DNA IQ™ system was optimized and validated on TECAN Genesis 150/8 and Freedom EVO robotic liquid handling stations configured with fixed tips and a TECAN TE-Shake™ unit. The use of an orbital shaker during the extraction process promoted efficiency with respect to DNA capture, magnetic bead/DNA complex washes and DNA elution. Validation studies determined the reliability and limitations of this shaker-based process. Reproducibility with regards to DNA yields for the tested robotic workstations proved to be excellent and not significantly different than that offered by the manual phenol/chloroform extraction. DNA extraction of animal:human blood mixtures contaminated with soil demonstrated that a human profile was detectable even in the presence of abundant animal blood. For exhibits containing small amounts of biological material, concordance studies confirmed that DNA yields for this shaker-based extraction process are equivalent or greater to those observed with phenol/chloroform extraction as well as our original validated automated magnetic bead percolation-based extraction process. Our data further supports the increasing use of robotics for the processing of casework samples. Crown Copyright © 2009. Published by Elsevier Ireland Ltd. All rights reserved.

Integrating machine learning techniques into robust data enrichment approach and its application to gene expression data.

PubMed

Erdoğdu, Utku; Tan, Mehmet; Alhajj, Reda; Polat, Faruk; Rokne, Jon; Demetrick, Douglas

2013-01-01

The availability of enough samples for effective analysis and knowledge discovery has been a challenge in the research community, especially in the area of gene expression data analysis. Thus, the approaches being developed for data analysis have mostly suffered from the lack of enough data to train and test the constructed models. We argue that the process of sample generation could be successfully automated by employing some sophisticated machine learning techniques. An automated sample generation framework could successfully complement the actual sample generation from real cases. This argument is validated in this paper by describing a framework that integrates multiple models (perspectives) for sample generation. We illustrate its applicability for producing new gene expression data samples, a highly demanding area that has not received attention. The three perspectives employed in the process are based on models that are not closely related. The independence eliminates the bias of having the produced approach covering only certain characteristics of the domain and leading to samples skewed towards one direction. The first model is based on the Probabilistic Boolean Network (PBN) representation of the gene regulatory network underlying the given gene expression data. The second model integrates Hierarchical Markov Model (HIMM) and the third model employs a genetic algorithm in the process. Each model learns as much as possible characteristics of the domain being analysed and tries to incorporate the learned characteristics in generating new samples. In other words, the models base their analysis on domain knowledge implicitly present in the data itself. The developed framework has been extensively tested by checking how the new samples complement the original samples. The produced results are very promising in showing the effectiveness, usefulness and applicability of the proposed multi-model framework.

Process development for automated solar cell and module production. Task 4: Automated array assembly

NASA Technical Reports Server (NTRS)

1980-01-01

A process sequence which can be used in conjunction with automated equipment for the mass production of solar cell modules for terrestrial use was developed. The process sequence was then critically analyzed from a technical and economic standpoint to determine the technological readiness of certain process steps for implementation. The steps receiving analysis were: back contact metallization, automated cell array layup/interconnect, and module edge sealing. For automated layup/interconnect, both hard automation and programmable automation (using an industrial robot) were studied. The programmable automation system was then selected for actual hardware development.

Comparison Between Conventional and Automated Techniques for Blood Grouping and Crossmatching: Experience from a Tertiary Care Centre.

PubMed

Bhagwat, Swarupa Nikhil; Sharma, Jayashree H; Jose, Julie; Modi, Charusmita J

2015-01-01

The routine immunohematological tests can be performed by automated as well as manual techniques. These techniques have advantages and disadvantages inherent to them. The present study aims to compare the results of manual and automated techniques for blood grouping and crossmatching so as to validate the automated system effectively. A total of 1000 samples were subjected to blood grouping by the conventional tube technique (CTT) and the automated microplate LYRA system on Techno TwinStation. A total of 269 samples (multitransfused patients and multigravida females) were compared for 927 crossmatches by the CTT in indirect antiglobulin phase against the column agglutination technique (CAT) performed on Techno TwinStation. For blood grouping, the study showed a concordance in results for 942/1000 samples (94.2%), discordance for 4/1000 (0.4%) samples and uninterpretable result for 54/1000 samples (5.4%). On resolution, the uninterpretable results reduced to 49/1000 samples (4.9%) with 951/1000 samples (95.1%) showing concordant results. For crossmatching, the automated CAT showed concordant results in 887/927 (95.6%) and discordant results in 3/927 (0.32%) crossmatches as compared to the CTT. Total 37/927 (3.9%) crossmatches were not interpretable by the automated technique. The automated system shows a high concordance of results with CTT and hence can be brought into routine use. However, the high proportion of uninterpretable results emphasizes on the fact that proper training and standardization are needed prior to its use.

Automation--down to the nuts and bolts.

PubMed

Fix, R J; Rowe, J M; McConnell, B C

2000-01-01

Laboratories that once viewed automation as an expensive luxury are now looking to automation as a solution to increase sample throughput, to help ensure data integrity and to improve laboratory safety. The question is no longer, 'Should we automate?', but 'How should we approach automation?' A laboratory may choose from three approaches when deciding to automate: (1) contract with a third party vendor to produce a turnkey system, (2) develop and fabricate the system in-house or (3) some combination of approaches (1) and (2). The best approach for a given laboratory depends upon its available resources. The first lesson to be learned in automation is that no matter how straightforward an idea appears in the beginning, the solution will not be realized until many complex problems have been resolved. Issues dealing with sample vessel manipulation, liquid handling and system control must be addressed before a final design can be developed. This requires expertise in engineering, electronics, programming and chemistry. Therefore, the team concept of automation should be employed to help ensure success. This presentation discusses the advantages and disadvantages of the three approaches to automation. The development of an automated sample handling and control system for the STAR System focused microwave will be used to illustrate the complexities encountered in a seemingly simple project, and to highlight the importance of the team concept to automation no matter which approach is taken. The STAR System focused microwave from CEM Corporation is an open vessel digestion system with six microwave cells. This system is used to prepare samples for trace metal determination. The automated sample handling was developed around a XYZ motorized gantry system. Grippers were specially designed to perform several different functions and to provide feedback to the control software. Software was written in Visual Basic 5.0 to control the movement of the samples and the operation and monitoring of the STAR microwave. This software also provides a continuous update of the system's status to the computer screen. The system provides unattended preparation of up to 59 samples per run.

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 order to obtain cores and ice profiles at the drilling site. In the course of DAME drilling automation testing, the drilling-induced temperature gradients and their effects on encountered subsurface permafrost and ice layers were observed while drilling in frozen impact breccia at Haughton Crater. In repeated tests of robotic core removal processing and handling in the MARTE project, including field tests, cross-contamination issues arose between successive cores and samples, and procedures and metrics were developed for minimizing the cross-contamination. The MARTE core processing cross-contamination aspects were tested by analyzing a set of pristine samples (those stratigraphically known) vs. cuttings (loose clays) or artifacts from the robotic drilling (indurated clay layers). MARTE ground truth drilling, in parallel with the automated tests, provided control information on the discontinuity/continuity of the stratigraphic record (i.e., texture, color and structure of loose and consolidated materials).

Automated DBS microsampling, microscale automation and microflow LC-MS for therapeutic protein PK.

PubMed

Zhang, Qian; Tomazela, Daniela; Vasicek, Lisa A; Spellman, Daniel S; Beaumont, Maribel; Shyong, BaoJen; Kenny, Jacqueline; Fauty, Scott; Fillgrove, Kerry; Harrelson, Jane; Bateman, Kevin P

2016-04-01

Reduce animal usage for discovery-stage PK studies for biologics programs using microsampling-based approaches and microscale LC-MS. We report the development of an automated DBS-based serial microsampling approach for studying the PK of therapeutic proteins in mice. Automated sample preparation and microflow LC-MS were used to enable assay miniaturization and improve overall assay throughput. Serial sampling of mice was possible over the full 21-day study period with the first six time points over 24 h being collected using automated DBS sample collection. Overall, this approach demonstrated comparable data to a previous study using single mice per time point liquid samples while reducing animal and compound requirements by 14-fold. Reduction in animals and drug material is enabled by the use of automated serial DBS microsampling for mice studies in discovery-stage studies of protein therapeutics.

Automated Immunomagnetic Separation and Microarray Detection of E. coli O157:H7 from Poultry Carcass Rinse

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chandler, Darrell P.; Brown, Jeremy D.; Call, Douglas R.

2001-09-01

We describe the development and application of a novel electromagnetic flow cell and fluidics system for automated immunomagnetic separation of E. coli directly from unprocessed poultry carcass rinse, and the biochemical coupling of automated sample preparation with nucleic acid microarrays without cell growth. Highly porous nickel foam was used as a magnetic flux conductor. Up to 32% recovery efficiency of 'total' E. coli was achieved within the automated system with 6 sec contact times and 15 minute protocol (from sample injection through elution), statistically similar to cell recovery efficiencies in > 1 hour 'batch' captures. The electromagnet flow cell allowedmore » complete recovery of 2.8 mm particles directly from unprocessed poultry carcass rinse whereas the batch system did not. O157:H7 cells were reproducibly isolated directly from unprocessed poultry rinse with 39% recovery efficiency at 103 cells ml-1 inoculum. Direct plating of washed beads showed positive recovery of O 157:H7 directly from carcass rinse at an inoculum of 10 cells ml-1. Recovered beads were used for direct PCR amplification and microarray detection, with a process-level detection limit (automated cell concentration through microarray detection) of < 103 cells ml-1 carcass rinse. The fluidic system and analytical approach described here are generally applicable to most microbial detection problems and applications.« less

Can the black box be cracked? The augmentation of microbial ecology by high-resolution, automated sensing technologies.

PubMed

Shade, Ashley; Carey, Cayelan C; Kara, Emily; Bertilsson, Stefan; McMahon, Katherine D; Smith, Matthew C

2009-08-01

Automated sensing technologies, 'ASTs,' are tools that can monitor environmental or microbial-related variables at increasingly high temporal resolution. Microbial ecologists are poised to use AST data to couple microbial structure, function and associated environmental observations on temporal scales pertinent to microbial processes. In the context of aquatic microbiology, we discuss three applications of ASTs: windows on the microbial world, adaptive sampling and adaptive management. We challenge microbial ecologists to push AST potential in helping to reveal relationships between microbial structure and function.

Evaluation of four automated protocols for extraction of DNA from FTA cards.

PubMed

Stangegaard, Michael; Børsting, Claus; Ferrero-Miliani, Laura; Frank-Hansen, Rune; Poulsen, Lena; Hansen, Anders J; Morling, Niels

2013-10-01

Extraction of DNA using magnetic bead-based techniques on automated DNA extraction instruments provides a fast, reliable, and reproducible method for DNA extraction from various matrices. Here, we have compared the yield and quality of DNA extracted from FTA cards using four automated extraction protocols on three different instruments. The extraction processes were repeated up to six times with the same pieces of FTA cards. The sample material on the FTA cards was either blood or buccal cells. With the QIAamp DNA Investigator and QIAsymphony DNA Investigator kits, it was possible to extract DNA from the FTA cards in all six rounds of extractions in sufficient amount and quality to obtain complete short tandem repeat (STR) profiles on a QIAcube and a QIAsymphony SP. With the PrepFiler Express kit, almost all the extractable DNA was extracted in the first two rounds of extractions. Furthermore, we demonstrated that it was possible to successfully extract sufficient DNA for STR profiling from previously processed FTA card pieces that had been stored at 4 °C for up to 1 year. This showed that rare or precious FTA card samples may be saved for future analyses even though some DNA was already extracted from the FTA cards.

Performance Evaluation of the Sysmex CS-5100 Automated Coagulation Analyzer.

PubMed

Chen, Liming; Chen, Yu

2015-01-01

Coagulation testing is widely applied clinically, and laboratories increasingly demand automated coagulation analyzers with short turn-around times and high-throughput. The purpose of this study was to evaluate the performance of the Sysmex CS-5100 automated coagulation analyzer for routine use in a clinical laboratory. The prothrombin time (PT), international normalized ratio (INR), activated partial thromboplastin time (APTT), fibrinogen (Fbg), and D-dimer were compared between the Sysmex CS-5100 and Sysmex CA-7000 analyzers, and the imprecision, comparison, throughput, STAT function, and performance for abnormal samples were measured in each. The within-run and between-run coefficients of variation (CV) for the PT, APTT, INR, and D-dimer analyses showed excellent results both in the normal and pathologic ranges. The correlation coefficients between the Sysmex CS-5100 and Sysmex CA-7000 were highly correlated. The throughput of the Sysmex CS-5100 was faster than that of the Sysmex CA-7000. There was no interference at all by total bilirubin concentrations and triglyceride concentrations in the Sysmex CS-5100 analyzer. We demonstrated that the Sysmex CS-5100 performs with satisfactory imprecision and is well suited for coagulation analysis in laboratories processing large sample numbers and icteric and lipemic samples.

Generic and Automated Data Evaluation in Analytical Measurement.

PubMed

Adam, Martin; Fleischer, Heidi; Thurow, Kerstin

2017-04-01

In the past year, automation has become more and more important in the field of elemental and structural chemical analysis to reduce the high degree of manual operation and processing time as well as human errors. Thus, a high number of data points are generated, which requires fast and automated data evaluation. To handle the preprocessed export data from different analytical devices with software from various vendors offering a standardized solution without any programming knowledge should be preferred. In modern laboratories, multiple users will use this software on multiple personal computers with different operating systems (e.g., Windows, Macintosh, Linux). Also, mobile devices such as smartphones and tablets have gained growing importance. The developed software, Project Analytical Data Evaluation (ADE), is implemented as a web application. To transmit the preevaluated data from the device software to the Project ADE, the exported XML report files are detected and the included data are imported into the entities database using the Data Upload software. Different calculation types of a sample within one measurement series (e.g., method validation) are identified using information tags inside the sample name. The results are presented in tables and diagrams on different information levels (general, detailed for one analyte or sample).

Automated genomic DNA purification options in agricultural applications using MagneSil paramagnetic particles

NASA Astrophysics Data System (ADS)

Bitner, Rex M.; Koller, Susan C.

2002-06-01

The automated high throughput purification of genomic DNA form plant materials can be performed using MagneSil paramagnetic particles on the Beckman-Coulter FX, BioMek 2000, and the Tecan Genesis robot. Similar automated methods are available for DNA purifications from animal blood. These methods eliminate organic extractions, lengthy incubations and cumbersome filter plates. The DNA is suitable for applications such as PCR and RAPD analysis. Methods are described for processing traditionally difficult samples such as those containing large amounts of polyphenolics or oils, while still maintaining a high level of DNA purity. The robotic protocols have ben optimized for agricultural applications such as marker assisted breeding, seed-quality testing, and SNP discovery and scoring. In addition to high yield purification of DNA from plant samples or animal blood, the use of Promega's DNA-IQ purification system is also described. This method allows for the purification of a narrow range of DNA regardless of the amount of additional DNA that is present in the initial sample. This simultaneous Isolation and Quantification of DNA allows the DNA to be used directly in applications such as PCR, SNP analysis, and RAPD, without the need for separate quantitation of the DNA.

Automated Micro-Object Detection for Mobile Diagnostics Using Lens-Free Imaging Technology

PubMed Central

Roy, Mohendra; Seo, Dongmin; Oh, Sangwoo; Chae, Yeonghun; Nam, Myung-Hyun; Seo, Sungkyu

2016-01-01

Lens-free imaging technology has been extensively used recently for microparticle and biological cell analysis because of its high throughput, low cost, and simple and compact arrangement. However, this technology still lacks a dedicated and automated detection system. In this paper, we describe a custom-developed automated micro-object detection method for a lens-free imaging system. In our previous work (Roy et al.), we developed a lens-free imaging system using low-cost components. This system was used to generate and capture the diffraction patterns of micro-objects and a global threshold was used to locate the diffraction patterns. In this work we used the same setup to develop an improved automated detection and analysis algorithm based on adaptive threshold and clustering of signals. For this purpose images from the lens-free system were then used to understand the features and characteristics of the diffraction patterns of several types of samples. On the basis of this information, we custom-developed an automated algorithm for the lens-free imaging system. Next, all the lens-free images were processed using this custom-developed automated algorithm. The performance of this approach was evaluated by comparing the counting results with standard optical microscope results. We evaluated the counting results for polystyrene microbeads, red blood cells, HepG2, HeLa, and MCF7 cells lines. The comparison shows good agreement between the systems, with a correlation coefficient of 0.91 and linearity slope of 0.877. We also evaluated the automated size profiles of the microparticle samples. This Wi-Fi-enabled lens-free imaging system, along with the dedicated software, possesses great potential for telemedicine applications in resource-limited settings. PMID:27164146

Automated Comprehensive Evaluation of mTBI Visual Dysfunction

DTIC Science & Technology

2017-04-01

Discussion: The results show that all ANAM subcomponents, except for math processing, are reduced in the mTBI population compared to controls. In...0.002534553 Math  Processing  0.099382065 Match to Sample  0.004264635     Table 2. MACE  p‐value  Orientation ‐ Month  0.325052733 Orientation ‐ Date

Canadian macromolecular crystallography facility: a suite of fully automated beamlines.

PubMed

Grochulski, Pawel; Fodje, Michel; Labiuk, Shaunivan; Gorin, James; Janzen, Kathryn; Berg, Russ

2012-06-01

The Canadian light source is a 2.9 GeV national synchrotron radiation facility located on the University of Saskatchewan campus in Saskatoon. The small-gap in-vacuum undulator illuminated beamline, 08ID-1, together with the bending magnet beamline, 08B1-1, constitute the Canadian Macromolecular Crystallography Facility (CMCF). The CMCF provides service to more than 50 Principal Investigators in Canada and the United States. Up to 25% of the beam time is devoted to commercial users and the general user program is guaranteed up to 55% of the useful beam time through a peer-review process. CMCF staff provides "Mail-In" crystallography service to users with the highest scored proposals. Both beamlines are equipped with very robust end-stations including on-axis visualization systems, Rayonix 300 CCD series detectors and Stanford-type robotic sample auto-mounters. MxDC, an in-house developed beamline control system, is integrated with a data processing module, AutoProcess, allowing full automation of data collection and data processing with minimal human intervention. Sample management and remote monitoring of experiments is enabled through interaction with a Laboratory Information Management System developed at the facility.

Selecting automation for the clinical chemistry laboratory.

PubMed

Melanson, Stacy E F; Lindeman, Neal I; Jarolim, Petr

2007-07-01

Laboratory automation proposes to improve the quality and efficiency of laboratory operations, and may provide a solution to the quality demands and staff shortages faced by today's clinical laboratories. Several vendors offer automation systems in the United States, with both subtle and obvious differences. Arriving at a decision to automate, and the ensuing evaluation of available products, can be time-consuming and challenging. Although considerable discussion concerning the decision to automate has been published, relatively little attention has been paid to the process of evaluating and selecting automation systems. To outline a process for evaluating and selecting automation systems as a reference for laboratories contemplating laboratory automation. Our Clinical Chemistry Laboratory staff recently evaluated all major laboratory automation systems in the United States, with their respective chemistry and immunochemistry analyzers. Our experience is described and organized according to the selection process, the important considerations in clinical chemistry automation, decisions and implementation, and we give conclusions pertaining to this experience. Including the formation of a committee, workflow analysis, submitting a request for proposal, site visits, and making a final decision, the process of selecting chemistry automation took approximately 14 months. We outline important considerations in automation design, preanalytical processing, analyzer selection, postanalytical storage, and data management. Selecting clinical chemistry laboratory automation is a complex, time-consuming process. Laboratories considering laboratory automation may benefit from the concise overview and narrative and tabular suggestions provided.

Comparison Between Conventional and Automated Techniques for Blood Grouping and Crossmatching: Experience from a Tertiary Care Centre

PubMed Central

Bhagwat, Swarupa Nikhil; Sharma, Jayashree H; Jose, Julie; Modi, Charusmita J

2015-01-01

Context: The routine immunohematological tests can be performed by automated as well as manual techniques. These techniques have advantages and disadvantages inherent to them. Aims: The present study aims to compare the results of manual and automated techniques for blood grouping and crossmatching so as to validate the automated system effectively. Materials and Methods: A total of 1000 samples were subjected to blood grouping by the conventional tube technique (CTT) and the automated microplate LYRA system on Techno TwinStation. A total of 269 samples (multitransfused patients and multigravida females) were compared for 927 crossmatches by the CTT in indirect antiglobulin phase against the column agglutination technique (CAT) performed on Techno TwinStation. Results: For blood grouping, the study showed a concordance in results for 942/1000 samples (94.2%), discordance for 4/1000 (0.4%) samples and uninterpretable result for 54/1000 samples (5.4%). On resolution, the uninterpretable results reduced to 49/1000 samples (4.9%) with 951/1000 samples (95.1%) showing concordant results. For crossmatching, the automated CAT showed concordant results in 887/927 (95.6%) and discordant results in 3/927 (0.32%) crossmatches as compared to the CTT. Total 37/927 (3.9%) crossmatches were not interpretable by the automated technique. Conclusions: The automated system shows a high concordance of results with CTT and hence can be brought into routine use. However, the high proportion of uninterpretable results emphasizes on the fact that proper training and standardization are needed prior to its use. PMID:26417159

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.

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.

Automated identification of patients with pulmonary nodules in an integrated health system using administrative health plan data, radiology reports, and natural language processing.

PubMed

Danforth, Kim N; Early, Megan I; Ngan, Sharon; Kosco, Anne E; Zheng, Chengyi; Gould, Michael K

2012-08-01

Lung nodules are commonly encountered in clinical practice, yet little is known about their management in community settings. An automated method for identifying patients with lung nodules would greatly facilitate research in this area. Using members of a large, community-based health plan from 2006 to 2010, we developed a method to identify patients with lung nodules, by combining five diagnostic codes, four procedural codes, and a natural language processing algorithm that performed free text searches of radiology transcripts. An experienced pulmonologist reviewed a random sample of 116 radiology transcripts, providing a reference standard for the natural language processing algorithm. With the use of an automated method, we identified 7112 unique members as having one or more incident lung nodules. The mean age of the patients was 65 years (standard deviation 14 years). There were slightly more women (54%) than men, and Hispanics and non-whites comprised 45% of the lung nodule cohort. Thirty-six percent were never smokers whereas 11% were current smokers. Fourteen percent of the patients were subsequently diagnosed with lung cancer. The sensitivity and specificity of the natural language processing algorithm for identifying the presence of lung nodules were 96% and 86%, respectively, compared with clinician review. Among the true positive transcripts in the validation sample, only 35% were solitary and unaccompanied by one or more associated findings, and 56% measured 8 to 30 mm in diameter. A combination of diagnostic codes, procedural codes, and a natural language processing algorithm for free text searching of radiology reports can accurately and efficiently identify patients with incident lung nodules, many of whom are subsequently diagnosed with lung cancer.

Automated high-throughput protein purification using an ÄKTApurifier and a CETAC autosampler.

PubMed

Yoo, Daniel; Provchy, Justin; Park, Cynthia; Schulz, Craig; Walker, Kenneth

2014-05-30

As the pace of drug discovery accelerates there is an increased focus on screening larger numbers of protein therapeutic candidates to identify those that are functionally superior and to assess manufacturability earlier in the process. Although there have been advances toward high throughput (HT) cloning and expression, protein purification is still an area where improvements can be made to conventional techniques. Current methodologies for purification often involve a tradeoff between HT automation or capacity and quality. We present an ÄKTA combined with an autosampler, the ÄKTA-AS, which has the capability of purifying up to 240 samples in two chromatographic dimensions without the need for user intervention. The ÄKTA-AS has been shown to be reliable with sample volumes between 0.5 mL and 100 mL, and the innovative use of a uniquely configured loading valve ensures reliability by efficiently removing air from the system as well as preventing sample cross contamination. Incorporation of a sample pump flush minimizes sample loss and enables recoveries ranging from the low tens of micrograms to milligram quantities of protein. In addition, when used in an affinity capture-buffer exchange format the final samples are formulated in a buffer compatible with most assays without requirement of additional downstream processing. The system is designed to capture samples in 96-well microplate format allowing for seamless integration of downstream HT analytic processes such as microfluidic or HPLC analysis. Most notably, there is minimal operator intervention to operate this system, thereby increasing efficiency, sample consistency and reducing the risk of human error. Copyright © 2014 Elsevier B.V. All rights reserved.

Automation and control of off-planet oxygen production processes

NASA Technical Reports Server (NTRS)

Marner, W. J.; Suitor, J. W.; Schooley, L. S.; Cellier, F. E.

1990-01-01

This paper addresses several aspects of the automation and control of off-planet production processes. First, a general approach to process automation and control is discussed from the viewpoint of translating human process control procedures into automated procedures. Second, the control issues for the automation and control of off-planet oxygen processes are discussed. Sensors, instruments, and components are defined and discussed in the context of off-planet applications, and the need for 'smart' components is clearly established.

Mechanical properties of bovine cortical bone based on the automated ball indentation technique and graphics processing method.

PubMed

Zhang, Airong; Zhang, Song; Bian, Cuirong

2018-02-01

Cortical bone provides the main form of support in humans and other vertebrates against various forces. Thus, capturing its mechanical properties is important. In this study, the mechanical properties of cortical bone were investigated by using automated ball indentation and graphics processing at both the macroscopic and microstructural levels under dry conditions. First, all polished samples were photographed under a metallographic microscope, and the area ratio of the circumferential lamellae and osteons was calculated through the graphics processing method. Second, fully-computer-controlled automated ball indentation (ABI) tests were performed to explore the micro-mechanical properties of the cortical bone at room temperature and a constant indenter speed. The indentation defects were examined with a scanning electron microscope. Finally, the macroscopic mechanical properties of the cortical bone were estimated with the graphics processing method and mixture rule. Combining ABI and graphics processing proved to be an effective tool to obtaining the mechanical properties of the cortical bone, and the indenter size had a significant effect on the measurement. The methods presented in this paper provide an innovative approach to acquiring the macroscopic mechanical properties of cortical bone in a nondestructive manner. Copyright © 2017 Elsevier Ltd. All rights reserved.

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 in the Science Instruments.

Automated smear counting and data processing using a notebook computer in a biomedical research facility.

PubMed

Ogata, Y; Nishizawa, K

1995-10-01

An automated smear counting and data processing system for a life science laboratory was developed to facilitate routine surveys and eliminate human errors by using a notebook computer. This system was composed of a personal computer, a liquid scintillation counter and a well-type NaI(Tl) scintillation counter. The radioactivity of smear samples was automatically measured by these counters. The personal computer received raw signals from the counters through an interface of RS-232C. The software for the computer evaluated the surface density of each radioisotope and printed out that value along with other items as a report. The software was programmed in Pascal language. This system was successfully applied to routine surveys for contamination in our facility.

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…

Study and Analysis of The Robot-Operated Material Processing Systems (ROMPS)

NASA Technical Reports Server (NTRS)

Nguyen, Charles C.

1996-01-01

This is a report presenting the progress of a research grant funded by NASA for work performed during 1 Oct. 1994 - 31 Sep. 1995. The report deals with the development and investigation of potential use of software for data processing for the Robot Operated Material Processing System (ROMPS). It reports on the progress of data processing of calibration samples processed by ROMPS in space and on earth. First data were retrieved using the I/O software and manually processed using MicroSoft Excel. Then the data retrieval and processing process was automated using a program written in C which is able to read the telemetry data and produce plots of time responses of sample temperatures and other desired variables. LabView was also employed to automatically retrieve and process the telemetry data.

Automated MRI Segmentation for Individualized Modeling of Current Flow in the Human Head

PubMed Central

Huang, Yu; Dmochowski, Jacek P.; Su, Yuzhuo; Datta, Abhishek; Rorden, Christopher; Parra, Lucas C.

2013-01-01

Objective High-definition transcranial direct current stimulation (HD-tDCS) and high-density electroencephalography (HD-EEG) require accurate models of current flow for precise targeting and current source reconstruction. At a minimum, such modeling must capture the idiosyncratic anatomy of brain, cerebrospinal fluid (CSF) and skull for each individual subject. Currently, the process to build such high-resolution individualized models from structural magnetic resonance images (MRI) requires labor-intensive manual segmentation, even when leveraging available automated segmentation tools. Also, accurate placement of many high-density electrodes on individual scalp is a tedious procedure. The goal was to develop fully automated techniques to reduce the manual effort in such a modeling process. Approach A fully automated segmentation technique based on Statical Parametric Mapping 8 (SPM8), including an improved tissue probability map (TPM) and an automated correction routine for segmentation errors, was developed, along with an automated electrode placement tool for high-density arrays. The performance of these automated routines was evaluated against results from manual segmentation on 4 healthy subjects and 7 stroke patients. The criteria include segmentation accuracy, the difference of current flow distributions in resulting HD-tDCS models and the optimized current flow intensities on cortical targets. Main results The segmentation tool can segment out not just the brain but also provide accurate results for CSF, skull and other soft tissues with a field of view (FOV) extending to the neck. Compared to manual results, automated segmentation deviates by only 7% and 18% for normal and stroke subjects, respectively. The predicted electric fields in the brain deviate by 12% and 29% respectively, which is well within the variability observed for various modeling choices. Finally, optimized current flow intensities on cortical targets do not differ significantly. Significance Fully automated individualized modeling may now be feasible for large-sample EEG research studies and tDCS clinical trials. PMID:24099977

Automated MRI segmentation for individualized modeling of current flow in the human head

NASA Astrophysics Data System (ADS)

Huang, Yu; Dmochowski, Jacek P.; Su, Yuzhuo; Datta, Abhishek; Rorden, Christopher; Parra, Lucas C.

2013-12-01

Objective. High-definition transcranial direct current stimulation (HD-tDCS) and high-density electroencephalography require accurate models of current flow for precise targeting and current source reconstruction. At a minimum, such modeling must capture the idiosyncratic anatomy of the brain, cerebrospinal fluid (CSF) and skull for each individual subject. Currently, the process to build such high-resolution individualized models from structural magnetic resonance images requires labor-intensive manual segmentation, even when utilizing available automated segmentation tools. Also, accurate placement of many high-density electrodes on an individual scalp is a tedious procedure. The goal was to develop fully automated techniques to reduce the manual effort in such a modeling process. Approach. A fully automated segmentation technique based on Statical Parametric Mapping 8, including an improved tissue probability map and an automated correction routine for segmentation errors, was developed, along with an automated electrode placement tool for high-density arrays. The performance of these automated routines was evaluated against results from manual segmentation on four healthy subjects and seven stroke patients. The criteria include segmentation accuracy, the difference of current flow distributions in resulting HD-tDCS models and the optimized current flow intensities on cortical targets.Main results. The segmentation tool can segment out not just the brain but also provide accurate results for CSF, skull and other soft tissues with a field of view extending to the neck. Compared to manual results, automated segmentation deviates by only 7% and 18% for normal and stroke subjects, respectively. The predicted electric fields in the brain deviate by 12% and 29% respectively, which is well within the variability observed for various modeling choices. Finally, optimized current flow intensities on cortical targets do not differ significantly.Significance. Fully automated individualized modeling may now be feasible for large-sample EEG research studies and tDCS clinical trials.

Development and validation of an automated, microscopy-based method for enumeration of groups of intestinal bacteria.

PubMed

Jansen, G J; Wildeboer-Veloo, A C; Tonk, R H; Franks, A H; Welling, G W

1999-09-01

An automated microscopy-based method using fluorescently labelled 16S rRNA-targeted oligonucleotide probes directed against the predominant groups of intestinal bacteria was developed and validated. The method makes use of the Leica 600HR image analysis system, a Kodak MegaPlus camera model 1.4 and a servo-controlled Leica DM/RXA ultra-violet microscope. Software for automated image acquisition and analysis was developed and tested. The performance of the method was validated using a set of four fluorescent oligonucleotide probes: a universal probe for the detection of all bacterial species, one probe specific for Bifidobacterium spp., a digenus-probe specific for Bacteroides spp. and Prevotella spp. and a trigenus-probe specific for Ruminococcus spp., Clostridium spp. and Eubacterium spp. A nucleic acid stain, 4',6-diamidino-2-phenylindole (DAPI), was also included in the validation. In order to quantify the assay-error, one faecal sample was measured 20 times using each separate probe. Thereafter faecal samples of 20 different volunteers were measured following the same procedure in order to quantify the error due to individual-related differences in gut flora composition. It was concluded that the combination of automated microscopy and fluorescent whole-cell hybridisation enables distinction in gut flora-composition between volunteers at a significant level. With this method it is possible to process 48 faecal samples overnight, with coefficients of variation ranging from 0.07 to 0.30.

Expertise Development With Different Types of Automation: A Function of Different Cognitive Abilities.

PubMed

Jipp, Meike

2016-02-01

I explored whether different cognitive abilities (information-processing ability, working-memory capacity) are needed for expertise development when different types of automation (information vs. decision automation) are employed. It is well documented that expertise development and the employment of automation lead to improved performance. Here, it is argued that a learner's ability to reason about an activity may be hindered by the employment of information automation. Additional feedback needs to be processed, thus increasing the load on working memory and decelerating expertise development. By contrast, the employment of decision automation may stimulate reasoning, increase the initial load on information-processing ability, and accelerate expertise development. Authors of past research have not investigated the interrelations between automation assistance, individual differences, and expertise development. Sixty-one naive learners controlled simulated air traffic with two types of automation: information automation and decision automation. Their performance was captured across 16 trials. Well-established tests were used to assess information-processing ability and working-memory capacity. As expected, learners' performance benefited from expertise development and decision automation. Furthermore, individual differences moderated the effect of the type of automation on expertise development: The employment of only information automation increased the load on working memory during later expertise development. The employment of decision automation initially increased the need to process information. These findings highlight the importance of considering individual differences and expertise development when investigating human-automation interaction. The results are relevant for selecting automation configurations for expertise development. © 2015, Human Factors and Ergonomics Society.

An automated optofluidic biosensor platform combining interferometric sensors and injection moulded microfluidics.

PubMed

Szydzik, C; Gavela, A F; Herranz, S; Roccisano, J; Knoerzer, M; Thurgood, P; Khoshmanesh, K; Mitchell, A; Lechuga, L M

2017-08-08

A primary limitation preventing practical implementation of photonic biosensors within point-of-care platforms is their integration with fluidic automation subsystems. For most diagnostic applications, photonic biosensors require complex fluid handling protocols; this is especially prominent in the case of competitive immunoassays, commonly used for detection of low-concentration, low-molecular weight biomarkers. For this reason, complex automated microfluidic systems are needed to realise the full point-of-care potential of photonic biosensors. To fulfil this requirement, we propose an on-chip valve-based microfluidic automation module, capable of automating such complex fluid handling. This module is realised through application of a PDMS injection moulding fabrication technique, recently described in our previous work, which enables practical fabrication of normally closed pneumatically actuated elastomeric valves. In this work, these valves are configured to achieve multiplexed reagent addressing for an on-chip diaphragm pump, providing the sample and reagent processing capabilities required for automation of cyclic competitive immunoassays. Application of this technique simplifies fabrication and introduces the potential for mass production, bringing point-of-care integration of complex automated microfluidics into the realm of practicality. This module is integrated with a highly sensitive, label-free bimodal waveguide photonic biosensor, and is demonstrated in the context of a proof-of-concept biosensing assay, detecting the low-molecular weight antibiotic tetracycline.

Improvement in the stability of serum samples stored in an automated refrigerated module.

PubMed

Parra-Robert, Marina; Rico-Santana, Naira; Alcaraz-Quiles, José; Sandalinas, Silvia; Fernández, Esther; Falcón, Isabel; Pérez-Riedweg, Margarita; Bedini, Josep Lluís

2016-12-01

In clinical laboratories it is necessary to know for how long the analytes are stable in the samples with specific storage conditions. Our laboratory has implemented the new Aptio Automation System (AAS) (Siemens Healthcare Diagnostics) where the analyzed samples are stored in a refrigerated storage module (RSM) after being sealed. The aim of the study was to evaluate the stability of serum samples with the AAS and comparing the results with a previous study using a conventional refrigerated system. Serum samples from a total of 50 patients were collected and for each of them 27 biochemical analytes were analyzed. The samples were divided in 5 sets of 10 samples. Each set was re-analyzed at one of the following times: 24, 48, 72, 96 and 120h. Stability was evaluated according to the Total Limit of Change (TLC) criteria, which combine both analytical and biologic variation. A total of 26 out of 27 analytes were stable at the end of the study according to TLC criteria. Lactate dehydrogenase was not stable at 48h observing a decrease in its concentration until the end of the study. In the previous study (conventional storage system) 9 biochemical analytes were not stable with an increase of their levels due to the evaporation process. The RSM connected to the AAS improves the stability of serum samples. This system avoids the evaporation process due to the sealing of samples and allows better control of the samples during their storage. Copyright © 2016 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Automating data analysis for two-dimensional gas chromatography/time-of-flight mass spectrometry non-targeted analysis of comparative samples.

PubMed

Titaley, Ivan A; Ogba, O Maduka; Chibwe, Leah; Hoh, Eunha; Cheong, Paul H-Y; Simonich, Staci L Massey

2018-03-16

Non-targeted analysis of environmental samples, using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC × GC/ToF-MS), poses significant data analysis challenges due to the large number of possible analytes. Non-targeted data analysis of complex mixtures is prone to human bias and is laborious, particularly for comparative environmental samples such as contaminated soil pre- and post-bioremediation. To address this research bottleneck, we developed OCTpy, a Python™ script that acts as a data reduction filter to automate GC × GC/ToF-MS data analysis from LECO ® ChromaTOF ® software and facilitates selection of analytes of interest based on peak area comparison between comparative samples. We used data from polycyclic aromatic hydrocarbon (PAH) contaminated soil, pre- and post-bioremediation, to assess the effectiveness of OCTpy in facilitating the selection of analytes that have formed or degraded following treatment. Using datasets from the soil extracts pre- and post-bioremediation, OCTpy selected, on average, 18% of the initial suggested analytes generated by the LECO ® ChromaTOF ® software Statistical Compare feature. Based on this list, 63-100% of the candidate analytes identified by a highly trained individual were also selected by OCTpy. This process was accomplished in several minutes per sample, whereas manual data analysis took several hours per sample. OCTpy automates the analysis of complex mixtures of comparative samples, reduces the potential for human error during heavy data handling and decreases data analysis time by at least tenfold. Copyright © 2018 Elsevier B.V. All rights reserved.

The Harvard Automated Processing Pipeline for Electroencephalography (HAPPE): Standardized Processing Software for Developmental and High-Artifact Data.

PubMed

Gabard-Durnam, Laurel J; Mendez Leal, Adriana S; Wilkinson, Carol L; Levin, April R

2018-01-01

Electroenchephalography (EEG) recordings collected with developmental populations present particular challenges from a data processing perspective. These EEGs have a high degree of artifact contamination and often short recording lengths. As both sample sizes and EEG channel densities increase, traditional processing approaches like manual data rejection are becoming unsustainable. Moreover, such subjective approaches preclude standardized metrics of data quality, despite the heightened importance of such measures for EEGs with high rates of initial artifact contamination. There is presently a paucity of automated resources for processing these EEG data and no consistent reporting of data quality measures. To address these challenges, we propose the Harvard Automated Processing Pipeline for EEG (HAPPE) as a standardized, automated pipeline compatible with EEG recordings of variable lengths and artifact contamination levels, including high-artifact and short EEG recordings from young children or those with neurodevelopmental disorders. HAPPE processes event-related and resting-state EEG data from raw files through a series of filtering, artifact rejection, and re-referencing steps to processed EEG suitable for time-frequency-domain analyses. HAPPE also includes a post-processing report of data quality metrics to facilitate the evaluation and reporting of data quality in a standardized manner. Here, we describe each processing step in HAPPE, perform an example analysis with EEG files we have made freely available, and show that HAPPE outperforms seven alternative, widely-used processing approaches. HAPPE removes more artifact than all alternative approaches while simultaneously preserving greater or equivalent amounts of EEG signal in almost all instances. We also provide distributions of HAPPE's data quality metrics in an 867 file dataset as a reference distribution and in support of HAPPE's performance across EEG data with variable artifact contamination and recording lengths. HAPPE software is freely available under the terms of the GNU General Public License at https://github.com/lcnhappe/happe.

The Harvard Automated Processing Pipeline for Electroencephalography (HAPPE): Standardized Processing Software for Developmental and High-Artifact Data

PubMed Central

Gabard-Durnam, Laurel J.; Mendez Leal, Adriana S.; Wilkinson, Carol L.; Levin, April R.

2018-01-01

Electroenchephalography (EEG) recordings collected with developmental populations present particular challenges from a data processing perspective. These EEGs have a high degree of artifact contamination and often short recording lengths. As both sample sizes and EEG channel densities increase, traditional processing approaches like manual data rejection are becoming unsustainable. Moreover, such subjective approaches preclude standardized metrics of data quality, despite the heightened importance of such measures for EEGs with high rates of initial artifact contamination. There is presently a paucity of automated resources for processing these EEG data and no consistent reporting of data quality measures. To address these challenges, we propose the Harvard Automated Processing Pipeline for EEG (HAPPE) as a standardized, automated pipeline compatible with EEG recordings of variable lengths and artifact contamination levels, including high-artifact and short EEG recordings from young children or those with neurodevelopmental disorders. HAPPE processes event-related and resting-state EEG data from raw files through a series of filtering, artifact rejection, and re-referencing steps to processed EEG suitable for time-frequency-domain analyses. HAPPE also includes a post-processing report of data quality metrics to facilitate the evaluation and reporting of data quality in a standardized manner. Here, we describe each processing step in HAPPE, perform an example analysis with EEG files we have made freely available, and show that HAPPE outperforms seven alternative, widely-used processing approaches. HAPPE removes more artifact than all alternative approaches while simultaneously preserving greater or equivalent amounts of EEG signal in almost all instances. We also provide distributions of HAPPE's data quality metrics in an 867 file dataset as a reference distribution and in support of HAPPE's performance across EEG data with variable artifact contamination and recording lengths. HAPPE software is freely available under the terms of the GNU General Public License at https://github.com/lcnhappe/happe. PMID:29535597

Creation of a virtual cutaneous tissue bank

NASA Astrophysics Data System (ADS)

LaFramboise, William A.; Shah, Sujal; Hoy, R. W.; Letbetter, D.; Petrosko, P.; Vennare, R.; Johnson, Peter C.

2000-04-01

Cellular and non-cellular constituents of skin contain fundamental morphometric features and structural patterns that correlate with tissue function. High resolution digital image acquisitions performed using an automated system and proprietary software to assemble adjacent images and create a contiguous, lossless, digital representation of individual microscope slide specimens. Serial extraction, evaluation and statistical analysis of cutaneous feature is performed utilizing an automated analysis system, to derive normal cutaneous parameters comprising essential structural skin components. Automated digital cutaneous analysis allows for fast extraction of microanatomic dat with accuracy approximating manual measurement. The process provides rapid assessment of feature both within individual specimens and across sample populations. The images, component data, and statistical analysis comprise a bioinformatics database to serve as an architectural blueprint for skin tissue engineering and as a diagnostic standard of comparison for pathologic specimens.

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.

Anti-nuclear antibody screening using HEp-2 cells.

PubMed

Buchner, Carol; Bryant, Cassandra; Eslami, Anna; Lakos, Gabriella

2014-06-23

The American College of Rheumatology position statement on ANA testing stipulates the use of IIF as the gold standard method for ANA screening(1). Although IIF is an excellent screening test in expert hands, the technical difficulties of processing and reading IIF slides--such as the labor intensive slide processing, manual reading, the need for experienced, trained technologists and the use of dark room--make the IIF method difficult to fit in the workflow of modern, automated laboratories. The first and crucial step towards high quality ANA screening is careful slide processing. This procedure is labor intensive, and requires full understanding of the process, as well as attention to details and experience. Slide reading is performed by fluorescent microscopy in dark rooms, and is done by trained technologists who are familiar with the various patterns, in the context of cell cycle and the morphology of interphase and dividing cells. Provided that IIF is the first line screening tool for SARD, understanding the steps to correctly perform this technique is critical. Recently, digital imaging systems have been developed for the automated reading of IIF slides. These systems, such as the NOVA View Automated Fluorescent Microscope, are designed to streamline the routine IIF workflow. NOVA View acquires and stores high resolution digital images of the wells, thereby separating image acquisition from interpretation; images are viewed an interpreted on high resolution computer monitors. It stores images for future reference and supports the operator's interpretation by providing fluorescent light intensity data on the images. It also preliminarily categorizes results as positive or negative, and provides pattern recognition for positive samples. In summary, it eliminates the need for darkroom, and automates and streamlines the IIF reading/interpretation workflow. Most importantly, it increases consistency between readers and readings. Moreover, with the use of barcoded slides, transcription errors are eliminated by providing sample traceability and positive patient identification. This results in increased patient data integrity and safety. The overall goal of this video is to demonstrate the IIF procedure, including slide processing, identification of common IIF patterns, and the introduction of new advancements to simplify and harmonize this technique.

Multi-spectral brain tissue segmentation using automatically trained k-Nearest-Neighbor classification.

PubMed

Vrooman, Henri A; Cocosco, Chris A; van der Lijn, Fedde; Stokking, Rik; Ikram, M Arfan; Vernooij, Meike W; Breteler, Monique M B; Niessen, Wiro J

2007-08-01

Conventional k-Nearest-Neighbor (kNN) classification, which has been successfully applied to classify brain tissue in MR data, requires training on manually labeled subjects. This manual labeling is a laborious and time-consuming procedure. In this work, a new fully automated brain tissue classification procedure is presented, in which kNN training is automated. This is achieved by non-rigidly registering the MR data with a tissue probability atlas to automatically select training samples, followed by a post-processing step to keep the most reliable samples. The accuracy of the new method was compared to rigid registration-based training and to conventional kNN-based segmentation using training on manually labeled subjects for segmenting gray matter (GM), white matter (WM) and cerebrospinal fluid (CSF) in 12 data sets. Furthermore, for all classification methods, the performance was assessed when varying the free parameters. Finally, the robustness of the fully automated procedure was evaluated on 59 subjects. The automated training method using non-rigid registration with a tissue probability atlas was significantly more accurate than rigid registration. For both automated training using non-rigid registration and for the manually trained kNN classifier, the difference with the manual labeling by observers was not significantly larger than inter-observer variability for all tissue types. From the robustness study, it was clear that, given an appropriate brain atlas and optimal parameters, our new fully automated, non-rigid registration-based method gives accurate and robust segmentation results. A similarity index was used for comparison with manually trained kNN. The similarity indices were 0.93, 0.92 and 0.92, for CSF, GM and WM, respectively. It can be concluded that our fully automated method using non-rigid registration may replace manual segmentation, and thus that automated brain tissue segmentation without laborious manual training is feasible.

Espina: A Tool for the Automated Segmentation and Counting of Synapses in Large Stacks of Electron Microscopy Images

PubMed Central

Morales, Juan; Alonso-Nanclares, Lidia; Rodríguez, José-Rodrigo; DeFelipe, Javier; Rodríguez, Ángel; Merchán-Pérez, Ángel

2011-01-01

The synapses in the cerebral cortex can be classified into two main types, Gray's type I and type II, which correspond to asymmetric (mostly glutamatergic excitatory) and symmetric (inhibitory GABAergic) synapses, respectively. Hence, the quantification and identification of their different types and the proportions in which they are found, is extraordinarily important in terms of brain function. The ideal approach to calculate the number of synapses per unit volume is to analyze 3D samples reconstructed from serial sections. However, obtaining serial sections by transmission electron microscopy is an extremely time consuming and technically demanding task. Using focused ion beam/scanning electron microscope microscopy, we recently showed that virtually all synapses can be accurately identified as asymmetric or symmetric synapses when they are visualized, reconstructed, and quantified from large 3D tissue samples obtained in an automated manner. Nevertheless, the analysis, segmentation, and quantification of synapses is still a labor intensive procedure. Thus, novel solutions are currently necessary to deal with the large volume of data that is being generated by automated 3D electron microscopy. Accordingly, we have developed ESPINA, a software tool that performs the automated segmentation and counting of synapses in a reconstructed 3D volume of the cerebral cortex, and that greatly facilitates and accelerates these processes. PMID:21633491

Automated sample preparation using membrane microtiter extraction for bioanalytical mass spectrometry.

PubMed

Janiszewski, J; Schneider, P; Hoffmaster, K; Swyden, M; Wells, D; Fouda, H

1997-01-01

The development and application of membrane solid phase extraction (SPE) in 96-well microtiter plate format is described for the automated analysis of drugs in biological fluids. The small bed volume of the membrane allows elution of the analyte in a very small solvent volume, permitting direct HPLC injection and negating the need for the time consuming solvent evaporation step. A programmable liquid handling station (Quadra 96) was modified to automate all SPE steps. To avoid drying of the SPE bed and to enhance the analytical precision a novel protocol for performing the condition, load and wash steps in rapid succession was utilized. A block of 96 samples can now be extracted in 10 min., about 30 times faster than manual solvent extraction or single cartridge SPE methods. This processing speed complements the high-throughput speed of contemporary high performance liquid chromatography mass spectrometry (HPLC/MS) analysis. The quantitative analysis of a test analyte (Ziprasidone) in plasma demonstrates the utility and throughput of membrane SPE in combination with HPLC/MS. The results obtained with the current automated procedure compare favorably with those obtained using solvent and traditional solid phase extraction methods. The method has been used for the analysis of numerous drug prototypes in biological fluids to support drug discovery efforts.

Experimental studies on the effect of automation on pilot situational awareness in the datalink ATC environment

NASA Technical Reports Server (NTRS)

Hahn, Edward C.; Hansman, R. J., Jr.

1992-01-01

An experiment to study how automation, when used in conjunction with datalink for the delivery of ATC clearance amendments, affects the situational awareness of aircrews was conducted. The study was focused on the relationship of situational awareness to automated Flight Management System (FMS) programming of datalinked clearances and the readback of ATC clearances. Situational awareness was tested by issuing nominally unacceptable ATC clearances and measuring whether the error was detected by the subject pilots. The experiment also varied the mode of clearance delivery: Verbal, Textual, and Graphical. The error detection performance and pilot preference results indicate that the automated programming of the FMS may be superior to manual programming. It is believed that automated FMS programming may relieve some of the cognitive load, allowing pilots to concentrate on the strategic implications of a clearance amendment. Also, readback appears to have value, but the small sample size precludes a definite conclusion. Furthermore, because textual and graphical modes of delivery offer different but complementary advantages for cognitive processing, a combination of these modes of delivery may be advantageous in a datalink presentation.

An Experimental Study of the Effects of Automation on Pilot Situational Awareness in the Datalink ATC Environment

NASA Technical Reports Server (NTRS)

Hahn, Edward C.; Hansman, R. John, Jr.

1992-01-01

An experiment to study how automation, when used in conjunction with datalink for the delivery of air traffic control (ATC) clearance amendments, affects the situational awareness of aircrews was conducted. The study was focused on the relationship of situational awareness to automated Flight Management System (FMS) programming and the readback of ATC clearances. Situational awareness was tested by issuing nominally unacceptable ATC clearances and measuring whether the error was detected by the subject pilots. The experiment also varied the mode of clearance delivery: Verbal, Textual, and Graphical. The error detection performance and pilot preference results indicate that the automated programming of the FMS may be superior to manual programming. It is believed that automated FMS programming may relieve some of the cognitive load, allowing pilots to concentrate on the strategic implications of a clearance amendment. Also, readback appears to have value, but the small sample size precludes a definite conclusion. Furthermore, because textual and graphical modes of delivery offer different but complementary advantages for cognitive processing, a combination of these modes of delivery may be advantageous in a datalink presentation.

Evaluation of canine red blood cell quality after processing with an automated cell salvage device.

PubMed

Hofbauer, Nina; Windberger, Ursula; Schwendenwein, Ilse; Tichy, Alexander; Eberspächer, Eva

2016-05-01

To evaluate the properties of RBC concentrate harvested after processing fresh whole blood units from healthy dogs with an automated cell salvage device. Prospective, in vitro, experimental study. University teaching hospital. Sixteen healthy, privately owned dogs of various breeds. Fresh canine whole blood collected in bags with citrate phosphate dextrose adenine solution was processed with an automated cell salvage device and analyzed in vitro. Laboratory values determined before (baseline, from a catheter sample) and after processing RBCs (procRBCs) included a complete blood count, selected blood chemistry analytes, erythrocyte osmotic resistance, whole blood viscosity, RBC aggregation, and RBC deformability. Total recovery of RBCs was 80% ± 12%. Hematocrit of the procRBCs yielded by the device was 77% ± 3.7% (mean ± standard deviation). Gross morphology of the RBCs remained unchanged. The mean corpuscular volume, erythrocyte osmotic resistance, RBC deformability, RBC aggregation, and the activity of lactate dehydrogenase showed minor but statistically significant changes from baseline. No differences in the concentrations of free hemoglobin were observed. Whole blood viscosity was less in the procRBCs. Seventy-seven percent (mean) of the platelets were washed out, while a mean of 57% of the leukocytes remained in the procRBCs. Although processing canine blood with this automated cell salvage device leads to slight changes in some properties of RBCs, most of these changes are comparable to changes seen in human blood after processing. Present data indicate that the use of this cell salvage device does not induce changes in canine RBC concentrate that would preclude its use for transfusion. © Veterinary Emergency and Critical Care Society 2016.

Collection, transport and general processing of clinical specimens in Microbiology laboratory.

PubMed

Sánchez-Romero, M Isabel; García-Lechuz Moya, Juan Manuel; González López, Juan José; Orta Mira, Nieves

2018-02-06

The interpretation and the accuracy of the microbiological results still depend to a great extent on the quality of the samples and their processing within the Microbiology laboratory. The type of specimen, the appropriate time to obtain the sample, the way of sampling, the storage and transport are critical points in the diagnostic process. The availability of new laboratory techniques for unusual pathogens, makes necessary the review and update of all the steps involved in the processing of the samples. Nowadays, the laboratory automation and the availability of rapid techniques allow the precision and turn-around time necessary to help the clinicians in the decision making. In order to be efficient, it is very important to obtain clinical information to use the best diagnostic tools. Copyright © 2018 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

The Automation of Reserve Processing.

ERIC Educational Resources Information Center

Self, James

1985-01-01

Describes an automated reserve processing system developed locally at Clemons Library, University of Virginia. Discussion covers developments in the reserve operation at Clemons Library, automation of the processing and circulation functions of reserve collections, and changes in reserve operation performance and staffing needs due to automation.…

Automated total and radioactive strontium separation and preconcentration in samples of environmental interest exploiting a lab-on-valve system.

PubMed

Rodríguez, Rogelio; Avivar, Jessica; Ferrer, Laura; Leal, Luz O; Cerdà, Victor

2012-07-15

A novel lab-on-valve system has been developed for strontium determination in environmental samples. Miniaturized lab-on-valve system potentially offers facilities to allow any kind of chemical and physical processes, including fluidic and microcarrier bead control, homogenous reaction and liquid-solid interaction. A rapid, inexpensive and fully automated method for the separation and preconcentration of total and radioactive strontium, using a solid phase extraction material (Sr-Resin), has been developed. Total strontium concentrations are determined by ICP-OES and (90)Sr activities by a low background proportional counter. The method has been successfully applied to different water samples of environmental interest. The proposed system offers minimization of sample handling, drastic reduction of reagent volume, improvement of the reproducibility and sample throughput and attains a significant decrease of both time and cost per analysis. The LLD of the total Sr reached is 1.8ng and the minimum detectable activity for (90)Sr is 0.008Bq. The repeatability of the separation procedure is 1.2% (n=10). Copyright © 2011 Elsevier B.V. All rights reserved.

Three-level sampler having automated thresholds

NASA Technical Reports Server (NTRS)

Jurgens, R. F.

1976-01-01

A three-level sampler is described that has its thresholds controlled automatically so as to track changes in the statistics of the random process being sampled. In particular, the mean value is removed and the ratio of the standard deviation of the random process to the threshold is maintained constant. The system is configured in such a manner that slow drifts in the level comparators and digital-to-analog converters are also removed. The ratio of the standard deviation to threshold level may be chosen within the constraints of the ratios of two integers N and M. These may be chosen to minimize the quantizing noise of the sampled process.

Using continuous in-situ measurements to adaptively trigger urban storm water samples

NASA Astrophysics Data System (ADS)

Wong, B. P.; Kerkez, B.

2015-12-01

Until cost-effective in-situ sensors are available for biological parameters, nutrients and metals, automated samplers will continue to be the primary source of reliable water quality measurements. Given limited samples bottles, however, autosamplers often obscure insights on nutrient sources and biogeochemical processes which would otherwise be captured using a continuous sampling approach. To that end, we evaluate the efficacy a novel method to measure first-flush nutrient dynamics in flashy, urban watersheds. Our approach reduces the number of samples required to capture water quality dynamics by leveraging an internet-connected sensor node, which is equipped with a suite of continuous in-situ sensors and an automated sampler. To capture both the initial baseflow as well as storm concentrations, a cloud-hosted adaptive algorithm analyzes the high-resolution sensor data along with local weather forecasts to optimize a sampling schedule. The method was tested in a highly developed urban catchment in Ann Arbor, Michigan and collected samples of nitrate, phosphorus, and suspended solids throughout several storm events. Results indicate that the watershed does not exhibit first flush dynamics, a behavior that would have been obscured when using a non-adaptive sampling approach.

Migration monitoring with automated technology

Treesearch

Rhonda L. Millikin

2005-01-01

Automated technology can supplement ground-based methods of migration monitoring by providing: (1) unbiased and automated sampling; (2) independent validation of current methods; (3) a larger sample area for landscape-level analysis of habitat selection for stopover, and (4) an opportunity to study flight behavior. In particular, radar-acoustic sensor fusion can...

AUTOMATED SOLID PHASE EXTRACTION GC/MS FOR ANALYSIS OF SEMIVOLATILES IN WATER AND SEDIMENTS

EPA Science Inventory

Data is presented on the development of a new automated system combining solid phase extraction (SPE) with GC/MS spectrometry for the single-run analysis of water samples containing a broad range of organic compounds. The system uses commercially available automated in-line sampl...

FaSTR DNA: a new expert system for forensic DNA analysis.

PubMed

Power, Timothy; McCabe, Brendan; Harbison, Sally Ann

2008-06-01

The automation of DNA profile analysis of reference and crime samples continues to gain pace driven in part by a realisation by the criminal justice system of the positive impact DNA technology can have in aiding in the solution of crime and the apprehension of suspects. Expert systems to automate the profile analysis component of the process are beginning to be developed. In this paper, we report the validation of a new expert system FaSTR DNA, an expert system suitable for the analysis of DNA profiles from single source reference samples and from crime samples. We compare the performance of FaSTR DNA with that of other equivalent systems, GeneMapper ID v3.2 (Applied Biosystems, Foster City, CA) and FSS-i(3) v4 (The Forensic Science Service((R)) DNA expert System Suite FSS-i(3), Forensic Science Service, Birmingham, UK) with GeneScan Analysis v3.7/Genotyper v3.7 software (Applied Biosystems, Foster City, CA, USA) with manual review. We have shown that FaSTR DNA provides an alternative solution to automating DNA profile analysis and is appropriate for implementation into forensic laboratories. The FaSTR DNA system was demonstrated to be comparable in performance to that of GeneMapper ID v3.2 and superior to that of FSS-i(3) v4 for the analysis of DNA profiles from crime samples.

An Automated Platform for High-Resolution Tissue Imaging Using Nanospray Desorption Electrospray Ionization Mass Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lanekoff, Ingela T.; Heath, Brandi S.; Liyu, Andrey V.

2012-10-02

An automated platform has been developed for acquisition and visualization of mass spectrometry imaging (MSI) data using nanospray desorption electrospray ionization (nano-DESI). The new system enables robust operation of the nano-DESI imaging source over many hours. This is achieved by controlling the distance between the sample and the probe by mounting the sample holder onto an automated XYZ stage and defining the tilt of the sample plane. This approach is useful for imaging of relatively flat samples such as thin tissue sections. Custom software called MSI QuickView was developed for visualization of large data sets generated in imaging experiments. MSImore » QuickView enables fast visualization of the imaging data during data acquisition and detailed processing after the entire image is acquired. The performance of the system is demonstrated by imaging rat brain tissue sections. High resolution mass analysis combined with MS/MS experiments enabled identification of lipids and metabolites in the tissue section. In addition, high dynamic range and sensitivity of the technique allowed us to generate ion images of low-abundance isobaric lipids. High-spatial resolution image acquired over a small region of the tissue section revealed the spatial distribution of an abundant brain metabolite, creatine, in the white and gray matter that is consistent with the literature data obtained using magnetic resonance spectroscopy.« less

Fully automated methods for the determination of hydrochlorothiazide in human plasma and urine.

PubMed

Hsieh, J Y; Lin, C; Matuszewski, B K; Dobrinska, M R

1994-12-01

LC assays utilizing fully automated sample preparation procedures on Zymark PyTechnology Robot and BenchMate Workstation for the quantification of hydrochlorothiazide (HCTZ) in human plasma and urine have been developed. After aliquoting plasma and urine samples, and adding internal standard (IS) manually, the robot executed buffer and organic solvent addition, liquid-liquid extraction, solvent evaporation and on-line LC injection steps for plasma samples, whereas, BenchMate performed buffer and organic solvent addition, liquid-liquid and solid-phase extractions, and on-line LC injection steps for urine samples. Chromatographic separations were carried out on Beckman Octyl Ultrasphere column using the mobile phase composed of 12% (v/v) acetonitrile and 88% of either an ion-pairing reagent (plasma) or 0.1% trifluoroacetic acid (urine). The eluent from the column was monitored with UV detector (271 nm). Peak heights for HCTZ and IS were automatically processed using a PE-Nelson ACCESS*CHROM laboratory automation system. The assays have been validated in the concentration range of 2-100 ng ml-1 in plasma and 0.1-20 micrograms ml-1 in urine. Both plasma and urine assays have the sensitivity and specificity necessary to determine plasma and urine concentrations of HCTZ from low dose (6.25/12.5 mg) administration of HCTZ to human subjects in the presence or absence of losartan.

Fully Automated Centrifugal Microfluidic Device for Ultrasensitive Protein Detection from Whole Blood.

PubMed

Park, Yang-Seok; Sunkara, Vijaya; Kim, Yubin; Lee, Won Seok; Han, Ja-Ryoung; Cho, Yoon-Kyoung

2016-04-16

Enzyme-linked immunosorbent assay (ELISA) is a promising method to detect small amount of proteins in biological samples. The devices providing a platform for reduced sample volume and assay time as well as full automation are required for potential use in point-of-care-diagnostics. Recently, we have demonstrated ultrasensitive detection of serum proteins, C-reactive protein (CRP) and cardiac troponin I (cTnI), utilizing a lab-on-a-disc composed of TiO2 nanofibrous (NF) mats. It showed a large dynamic range with femto molar (fM) detection sensitivity, from a small volume of whole blood in 30 min. The device consists of several components for blood separation, metering, mixing, and washing that are automated for improved sensitivity from low sample volumes. Here, in the video demonstration, we show the experimental protocols and know-how for the fabrication of NFs as well as the disc, their integration and the operation in the following order: processes for preparing TiO2 NF mat; transfer-printing of TiO2 NF mat onto the disc; surface modification for immune-reactions, disc assembly and operation; on-disc detection and representative results for immunoassay. Use of this device enables multiplexed analysis with minimal consumption of samples and reagents. Given the advantages, the device should find use in a wide variety of applications, and prove beneficial in facilitating the analysis of low abundant proteins.

Quantification of Parvovirus B19 DNA Using COBAS AmpliPrep Automated Sample Preparation and LightCycler Real-Time PCR

PubMed Central

Schorling, Stefan; Schalasta, Gunnar; Enders, Gisela; Zauke, Michael

2004-01-01

The COBAS AmpliPrep instrument (Roche Diagnostics GmbH, D-68305 Mannheim, Germany) automates the entire sample preparation process of nucleic acid isolation from serum or plasma for polymerase chain reaction analysis. We report the analytical performance of the LightCycler Parvovirus B19 Quantification Kit (Roche Diagnostics) using nucleic acids isolated with the COBAS AmpliPrep instrument. Nucleic acids were extracted using the Total Nucleic Acid Isolation Kit (Roche Diagnostics) and amplified with the LightCycler Parvovirus B19 Quantification Kit. The kit combination processes 72 samples per 8-hour shift. The lower detection limit is 234 IU/ml at a 95% hit-rate, linear range approximately 104-1010 IU/ml, and overall precision 16 to 40%. Relative sensitivity and specificity in routine samples from pregnant women are 100% and 93%, respectively. Identification of a persistent parvovirus B19-infected individual by the polymerase chain reaction among 51 anti-parvovirus B19 IgM-negative samples underlines the importance of additional nucleic acid testing in pregnancy and its superiority to serology in identifying the risk of parvovirus B19 transmission via blood or blood products. Combination of the Total Nucleic Acid Isolation Kit on the COBAS AmpliPrep instrument with the LightCycler Parvovirus B19 Quantification Kit provides a reliable and time-saving tool for sensitive and accurate detection of parvovirus B19 DNA. PMID:14736825

Electronic Data Interchange in Procurement

DTIC Science & Technology

1990-04-01

contract management and order processing systems. This conversion of automated information to paper and back to automated form is not only slow and...automated purchasing computer and the contractor’s order processing computer through telephone lines, as illustrated in Figure 1-1. Computer-to-computer...into the contractor’s order processing or contract management system. This approach - converting automated information to paper and back to automated

An automated system for whole microscopic image acquisition and analysis.

PubMed

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

2014-09-01

The field of anatomic pathology has experienced major changes over the last decade. Virtual microscopy (VM) systems have allowed experts in pathology and other biomedical areas to work in a safer and more collaborative way. VMs are automated systems capable of digitizing microscopic samples that were traditionally examined one by one. The possibility of having digital copies reduces the risk of damaging original samples, and also makes it easier to distribute copies among other pathologists. This article describes the development of an automated high-resolution whole slide imaging (WSI) system tailored to the needs and problems encountered in digital imaging for pathology, from hardware control to the full digitization of samples. The system has been built with an additional digital monochromatic camera together with the color camera by default and LED transmitted illumination (RGB). Monochrome cameras are the preferred method of acquisition for fluorescence microscopy. The system is able to digitize correctly and form large high resolution microscope images for both brightfield and fluorescence. The quality of the digital images has been quantified using three metrics based on sharpness, contrast and focus. It has been proved on 150 tissue samples of brain autopsies, prostate biopsies and lung cytologies, at five magnifications: 2.5×, 10×, 20×, 40×, and 63×. The article is focused on the hardware set-up and the acquisition software, although results of the implemented image processing techniques included in the software and applied to the different tissue samples are also presented. © 2014 Wiley Periodicals, Inc.

New procedure to reduce the time and cost of broncho-pulmonary specimen management using the Previ Isola® automated inoculation system.

PubMed

Nebbad-Lechani, Biba; Emirian, Aurélie; Maillebuau, Fabienne; Mahjoub, Nadia; Fihman, Vincent; Legrand, Patrick; Decousser, Jean-Winoc

2013-12-01

The microbiological diagnosis of respiratory tract infections requires serial manual dilutions of the clinical specimen before agar plate inoculation, disrupting the workflow in bacteriology clinical laboratories. Automated plating instrument systems have been designed to increase the speed, reproducibility and safety of this inoculating step; nevertheless, data concerning respiratory specimens are lacking. We tested a specific procedure that uses the Previ Isola® (bioMérieux, Craponne, France) to inoculate with broncho-pulmonary specimens (BPS). A total of 350 BPS from a university-affiliated hospital were managed in parallel using the manual reference and the automated methods (expectoration: 75; broncho-alveolar lavage: 68; tracheal aspiration: 17; protected distal sample: 190). A specific enumeration reading grid, a pre-liquefaction step and a fluidity test, performed before the inoculation, were designed for the automated method. The qualitative (i.e., the number of specimens yielding a bacterial count greater than the clinical threshold) and quantitative (i.e., the discrepancy within a 0.5 log value) concordances were 100% and 98.2%, respectively. The slimmest subgroup of expectorations could not be managed by the automated method (8%, 6/75). The technical time and cost savings (i.e., number of consumed plates) reached 50%. Additional studies are required for specific populations, such as cystic fibrosis specimens and associated bacterial variants. An automated decapper should be implemented to increase the biosafety of the process. The PREVI Isola® adapted procedure is a time- and cost-saving method for broncho-pulmonary specimen processing. © 2013.

Evaluation of an automated microplate technique in the Galileo system for ABO and Rh(D) blood grouping.

PubMed

Xu, Weiyi; Wan, Feng; Lou, Yufeng; Jin, Jiali; Mao, Weilin

2014-01-01

A number of automated devices for pretransfusion testing have recently become available. This study evaluated the Immucor Galileo System, a fully automated device based on the microplate hemagglutination technique for ABO/Rh (D) determinations. Routine ABO/Rh typing tests were performed on 13,045 samples using the Immucor automated instruments. Manual tube method was used to resolve ABO forward and reverse grouping discrepancies. D-negative test results were investigated and confirmed manually by the indirect antiglobulin test (IAT). The system rejected 70 tests for sample inadequacy. 87 samples were read as "No-type-determined" due to forward and reverse grouping discrepancies. 25 tests gave these results because of sample hemolysis. After further tests, we found 34 tests were caused by weakened RBC antibodies, 5 tests were attributable to weak A and/or B antigens, 4 tests were due to mixed-field reactions, and 8 tests had high titer cold agglutinin with blood qualifications which react only at temperatures below 34 degrees C. In the remaining 11 cases, irregular RBC antibodies were identified in 9 samples (seven anti-M and two anti-P) and two subgroups were identified in 2 samples (one A1 and one A2) by a reference laboratory. As for D typing, 2 weak D+ samples missed by automated systems gave negative results, but weak-positive reactions were observed in the IAT. The Immucor Galileo System is reliable and suited for ABO and D blood groups, some reasons may cause a discrepancy in ABO/D typing using a fully automated system. It is suggested that standardization of sample collection may improve the performance of the fully automated system.

Potential of Laboratory Execution Systems (LESs) to Simplify the Application of Business Process Management Systems (BPMSs) in Laboratory Automation.

PubMed

Neubert, Sebastian; Göde, Bernd; Gu, Xiangyu; Stoll, Norbert; Thurow, Kerstin

2017-04-01

Modern business process management (BPM) is increasingly interesting for laboratory automation. End-to-end workflow automation and improved top-level systems integration for information technology (IT) and automation systems are especially prominent objectives. With the ISO Standard Business Process Model and Notation (BPMN) 2.X, a system-independent and interdisciplinary accepted graphical process control notation is provided, allowing process analysis, while also being executable. The transfer of BPM solutions to structured laboratory automation places novel demands, for example, concerning the real-time-critical process and systems integration. The article discusses the potential of laboratory execution systems (LESs) for an easier implementation of the business process management system (BPMS) in hierarchical laboratory automation. In particular, complex application scenarios, including long process chains based on, for example, several distributed automation islands and mobile laboratory robots for a material transport, are difficult to handle in BPMSs. The presented approach deals with the displacement of workflow control tasks into life science specialized LESs, the reduction of numerous different interfaces between BPMSs and subsystems, and the simplification of complex process modelings. Thus, the integration effort for complex laboratory workflows can be significantly reduced for strictly structured automation solutions. An example application, consisting of a mixture of manual and automated subprocesses, is demonstrated by the presented BPMS-LES approach.

Advanced automation for in-space vehicle processing

NASA Technical Reports Server (NTRS)

Sklar, Michael; Wegerif, D.

1990-01-01

The primary objective of this 3-year planned study is to assure that the fully evolved Space Station Freedom (SSF) can support automated processing of exploratory mission vehicles. Current study assessments show that required extravehicular activity (EVA) and to some extent intravehicular activity (IVA) manpower requirements for required processing tasks far exceeds the available manpower. Furthermore, many processing tasks are either hazardous operations or they exceed EVA capability. Thus, automation is essential for SSF transportation node functionality. Here, advanced automation represents the replacement of human performed tasks beyond the planned baseline automated tasks. Both physical tasks such as manipulation, assembly and actuation, and cognitive tasks such as visual inspection, monitoring and diagnosis, and task planning are considered. During this first year of activity both the Phobos/Gateway Mars Expedition and Lunar Evolution missions proposed by the Office of Exploration have been evaluated. A methodology for choosing optimal tasks to be automated has been developed. Processing tasks for both missions have been ranked on the basis of automation potential. The underlying concept in evaluating and describing processing tasks has been the use of a common set of 'Primitive' task descriptions. Primitive or standard tasks have been developed both for manual or crew processing and automated machine processing.

HTAPP: High-Throughput Autonomous Proteomic Pipeline

PubMed Central

Yu, Kebing; Salomon, Arthur R.

2011-01-01

Recent advances in the speed and sensitivity of mass spectrometers and in analytical methods, the exponential acceleration of computer processing speeds, and the availability of genomic databases from an array of species and protein information databases have led to a deluge of proteomic data. The development of a lab-based automated proteomic software platform for the automated collection, processing, storage, and visualization of expansive proteomic datasets is critically important. The high-throughput autonomous proteomic pipeline (HTAPP) described here is designed from the ground up to provide critically important flexibility for diverse proteomic workflows and to streamline the total analysis of a complex proteomic sample. This tool is comprised of software that controls the acquisition of mass spectral data along with automation of post-acquisition tasks such as peptide quantification, clustered MS/MS spectral database searching, statistical validation, and data exploration within a user-configurable lab-based relational database. The software design of HTAPP focuses on accommodating diverse workflows and providing missing software functionality to a wide range of proteomic researchers to accelerate the extraction of biological meaning from immense proteomic data sets. Although individual software modules in our integrated technology platform may have some similarities to existing tools, the true novelty of the approach described here is in the synergistic and flexible combination of these tools to provide an integrated and efficient analysis of proteomic samples. PMID:20336676

An automated, high-throughput plant phenotyping system using machine learning-based plant segmentation and image analysis.

PubMed

Lee, Unseok; Chang, Sungyul; Putra, Gian Anantrio; Kim, Hyoungseok; Kim, Dong Hwan

2018-01-01

A high-throughput plant phenotyping system automatically observes and grows many plant samples. Many plant sample images are acquired by the system to determine the characteristics of the plants (populations). Stable image acquisition and processing is very important to accurately determine the characteristics. However, hardware for acquiring plant images rapidly and stably, while minimizing plant stress, is lacking. Moreover, most software cannot adequately handle large-scale plant imaging. To address these problems, we developed a new, automated, high-throughput plant phenotyping system using simple and robust hardware, and an automated plant-imaging-analysis pipeline consisting of machine-learning-based plant segmentation. Our hardware acquires images reliably and quickly and minimizes plant stress. Furthermore, the images are processed automatically. In particular, large-scale plant-image datasets can be segmented precisely using a classifier developed using a superpixel-based machine-learning algorithm (Random Forest), and variations in plant parameters (such as area) over time can be assessed using the segmented images. We performed comparative evaluations to identify an appropriate learning algorithm for our proposed system, and tested three robust learning algorithms. We developed not only an automatic analysis pipeline but also a convenient means of plant-growth analysis that provides a learning data interface and visualization of plant growth trends. Thus, our system allows end-users such as plant biologists to analyze plant growth via large-scale plant image data easily.

Standardization of pitch-range settings in voice acoustic analysis.

PubMed

Vogel, Adam P; Maruff, Paul; Snyder, Peter J; Mundt, James C

2009-05-01

Voice acoustic analysis is typically a labor-intensive, time-consuming process that requires the application of idiosyncratic parameters tailored to individual aspects of the speech signal. Such processes limit the efficiency and utility of voice analysis in clinical practice as well as in applied research and development. In the present study, we analyzed 1,120 voice files, using standard techniques (case-by-case hand analysis), taking roughly 10 work weeks of personnel time to complete. The results were compared with the analytic output of several automated analysis scripts that made use of preset pitch-range parameters. After pitch windows were selected to appropriately account for sex differences, the automated analysis scripts reduced processing time of the 1,120 speech samples to less than 2.5 h and produced results comparable to those obtained with hand analysis. However, caution should be exercised when applying the suggested preset values to pathological voice populations.

21 CFR 864.5200 - Automated cell counter.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Automated cell counter. 864.5200 Section 864.5200....5200 Automated cell counter. (a) Identification. An automated cell counter is a fully-automated or semi-automated device used to count red blood cells, white blood cells, or blood platelets using a sample of the...

21 CFR 864.5240 - Automated blood cell diluting apparatus.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Automated blood cell diluting apparatus. 864.5240... § 864.5240 Automated blood cell diluting apparatus. (a) Identification. An automated blood cell diluting apparatus is a fully automated or semi-automated device used to make appropriate dilutions of a blood sample...

21 CFR 864.5240 - Automated blood cell diluting apparatus.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Automated blood cell diluting apparatus. 864.5240... § 864.5240 Automated blood cell diluting apparatus. (a) Identification. An automated blood cell diluting apparatus is a fully automated or semi-automated device used to make appropriate dilutions of a blood sample...

Flexible software architecture for user-interface and machine control in laboratory automation.

PubMed

Arutunian, E B; Meldrum, D R; Friedman, N A; Moody, S E

1998-10-01

We describe a modular, layered software architecture for automated laboratory instruments. The design consists of a sophisticated user interface, a machine controller and multiple individual hardware subsystems, each interacting through a client-server architecture built entirely on top of open Internet standards. In our implementation, the user-interface components are built as Java applets that are downloaded from a server integrated into the machine controller. The user-interface client can thereby provide laboratory personnel with a familiar environment for experiment design through a standard World Wide Web browser. Data management and security are seamlessly integrated at the machine-controller layer using QNX, a real-time operating system. This layer also controls hardware subsystems through a second client-server interface. This architecture has proven flexible and relatively easy to implement and allows users to operate laboratory automation instruments remotely through an Internet connection. The software architecture was implemented and demonstrated on the Acapella, an automated fluid-sample-processing system that is under development at the University of Washington.

Automated solid-phase extraction and liquid chromatography for assay of cyclosporine in whole blood.

PubMed

Kabra, P M; Wall, J H; Dimson, P

1987-12-01

In this rapid, precise, accurate, cost-effective, automated liquid-chromatographic procedure for determining cyclosporine in whole blood, the cyclosporine is extracted from 0.5 mL of whole blood together with 300 micrograms of cyclosporin D per liter, added as internal standard, by using an Advanced Automated Sample Processing unit. The on-line solid-phase extraction is performed on an octasilane sorbent cartridge, which is interfaced with a RP-8 guard column and an octyl analytical column, packed with 5-microns packing material. Both columns are eluted with a mobile phase containing acetonitrile/methanol/water (53/20/27 by vol) at a flow rate of 1.5 mL/min and column temperature of 70 degrees C. Absolute recovery of cyclosporine exceeded 85% and the standard curve was linear to 5000 micrograms/L. Within-run and day-to-day CVs were less than 8%. Correlation between automated and manual Bond-Elut extraction methods was excellent (r = 0.987). None of 18 drugs and four steroids tested interfered.

Improving single molecule force spectroscopy through automated real-time data collection and quantification of experimental conditions

PubMed Central

Scholl, Zackary N.; Marszalek, Piotr E.

2013-01-01

The benefits of single molecule force spectroscopy (SMFS) clearly outweigh the challenges which include small sample sizes, tedious data collection and introduction of human bias during the subjective data selection. These difficulties can be partially eliminated through automation of the experimental data collection process for atomic force microscopy (AFM). Automation can be accomplished using an algorithm that triages usable force-extension recordings quickly with positive and negative selection. We implemented an algorithm based on the windowed fast Fourier transform of force-extension traces that identifies peaks using force-extension regimes to correctly identify usable recordings from proteins composed of repeated domains. This algorithm excels as a real-time diagnostic because it involves <30 ms computational time, has high sensitivity and specificity, and efficiently detects weak unfolding events. We used the statistics provided by the automated procedure to clearly demonstrate the properties of molecular adhesion and how these properties change with differences in the cantilever tip and protein functional groups and protein age. PMID:24001740

Implementing a laboratory automation system: experience of a large clinical laboratory.

PubMed

Lam, Choong Weng; Jacob, Edward

2012-02-01

Laboratories today face increasing pressure to automate their operations as they are challenged by a continuing increase in workload, need to reduce expenditure, and difficulties in recruitment of experienced technical staff. Was the implementation of a laboratory automation system (LAS) in the Clinical Biochemistry Laboratory at Singapore General Hospital successful? There is no simple answer, so the following topics comparing and contrasting pre- and post-LAS have been explored: turnaround time (TAT), laboratory errors, and staff satisfaction. The benefits and limitations of LAS from the laboratory experience were also reviewed. The mean TAT for both stat and routine samples decreased post-LAS (30% and 13.4%, respectively). In the 90th percentile TAT chart, a 29% reduction was seen in the processing of stat samples on the LAS. However, no significant difference in the 90th percentile TAT was observed with routine samples. It was surprising to note that laboratory errors increased post-LAS. Considerable effort was needed to overcome the initial difficulties associated with adjusting to a new system, new software, and new working procedures. Although some of the known advantages and limitations of LAS have been validated, the claimed benefits such as improvements in TAT, laboratory errors, and staff morale were not evident in the initial months.

NASA Tech Briefs, August 2007

NASA Technical Reports Server (NTRS)

2007-01-01

Topics include: Program Merges SAR Data on Terrain and Vegetation Heights; Using G(exp 4)FETs as a Data Router for In-Plane Crossing of Signal Paths; Two Algorithms for Processing Electronic Nose Data; Radiation-Tolerant Dual Data Bus; General-Purpose Front End for Real-Time Data Processing; Nanocomposite Photoelectrochemical Cells; Ultracapacitor-Powered Cordless Drill, Cumulative Timers for Microprocessors; Photocatalytic/Magnetic Composite Particles; Separation and Sealing of a Sample Container Using Brazing; Automated Aerial Refueling Hitches a Ride on AFF; Cobra Probes Containing Replaceable Thermocouples; High-Speed Noninvasive Eye-Tracking System; Detergent-Specific Membrane Protein Crystallization Screens; Evaporation-Cooled Protective Suits for Firefighters; Plasmonic Antenna Coupling for QWIPs; Electronic Tongue Containing Redox and Conductivity Sensors; Improved Heat-Stress Algorithm; A Method of Partly Automated Testing of Software; Rover Wheel-Actuated Tool Interface; and Second-Generation Electronic Nose.

A new and standardized method to sample and analyse vitreous samples by the Cellient automated cell block system.

PubMed

Van Ginderdeuren, Rita; Van Calster, Joachim; Stalmans, Peter; Van den Oord, Joost

2014-08-01

In this prospective study, a universal protocol for sampling and analysing vitreous material was investigated. Vitreous biopsies are difficult to handle because of the paucity of cells and the gelatinous structure of the vitreous. Histopathological analysis of the vitreous is useful in difficult uveitis cases to differentiate uveitis from lymphoma or infection and to define the type of cellular reaction. Hundred consecutive vitreous samples were analysed with the Cellient tissue processor (Hologic). This machine is a fully automated processor starting from a specified container with PreservCyt (fixative fluid) with cells to paraffin. Cytology was compared with fixatives Cytolyt (contains a mucolyticum) and PreservCyt. Routine histochemical and immunostainings were evaluated. In 92% of the cases, sufficient material was found for diagnosis. In 14%, a Cytolyt wash was necessary to prevent clotting of the tubes in the Cellient due to the viscosity of the sample. In 23%, the diagnosis was an acute inflammation (presence of granulocytes); in 33%, chronic active inflammation (presence of T lymphocytes); in 33%, low-grade inflammation (presence of CD68 cells, without T lymphocytes); and in 3%, a malignant process. A standardized protocol for sampling and handling vitreous biopsies, fixing in PreservCyt and processing by the Cellient gives a satisfactory result in morphology, number of cells and possibility of immuno-histochemical stainings. The diagnosis can be established or confirmed in more than 90% of cases. © 2014 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

Fe, Zn, and Cd stable isotopes from the eastern tropical South Pacific from GEOTRACES cruise GP16 - Methods and data

NASA Astrophysics Data System (ADS)

Helgoe, J. M.; Townsend, E.; John, S.

2014-12-01

A new method has been developed for the rapid analysis of metal concentrations and stable isotope ratios using a prepFAST automated sample processing robot. Although concentrations and isotopes are processed separately, similar methods are used for both. Initially all seawater is acidified to pH 2. Then Nobias resin with EDTA/IDA functional groups is added to either 10mL of sample for concentrations or ~1L samples for isotopes. Fe binds to the resin at low pH, and the pH is subsequently raised to allow Zn and Cd to bind. For concentration analyses, all subsequent chemistry is automated on the prepFAST including removal of seawater, rinsing of resin, and elution of resin into acid. For isotope samples these extraction techniques are performed manually, but the subsequent purification of Fe, Zn, and Cd by anion exchange chromatography is automated using the prepFAST. With these new methods, samples from the US GEOTRACES cruise GP16, in the eastern tropical South Pacific, are being analyzed. High concentrations of dissolved Fe are observed near the continental shelf and near submarine hydrothermal vents. Interestingly, isotope data show that dissolved Fe near the continental shelf generally has a δ56Fe close to 0 ‰. This δ56 Fe signature is suggestive of a non-reductive dissolution source for Fe, as Fe(II) released by reductive dissolution is typically closer to -2 ‰. Preliminary data show nutrient-type profiles for Zn and Cd, with Zn matching Si and Cd having a similar distribution to P. An increase in dissolved Zn near hydrothermal vents suggests a possible hydrothermal zinc source to the deep ocean. Continuing analysis of isotope data will reveal more about the source and biogeochemical cycling of these three chemically and biologically important trace metals throughout the eastern tropical Pacific Ocean.

Adaptive Algorithms for Automated Processing of Document Images

DTIC Science & Technology

2011-01-01

ABSTRACT Title of dissertation: ADAPTIVE ALGORITHMS FOR AUTOMATED PROCESSING OF DOCUMENT IMAGES Mudit Agrawal, Doctor of Philosophy, 2011...2011 4. TITLE AND SUBTITLE Adaptive Algorithms for Automated Processing of Document Images 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM...ALGORITHMS FOR AUTOMATED PROCESSING OF DOCUMENT IMAGES by Mudit Agrawal Dissertation submitted to the Faculty of the Graduate School of the University

Automated processing of endoscopic surgical instruments.

PubMed

Roth, K; Sieber, J P; Schrimm, H; Heeg, P; Buess, G

1994-10-01

This paper deals with the requirements for automated processing of endoscopic surgical instruments. After a brief analysis of the current problems, solutions are discussed. Test-procedures have been developed to validate the automated processing, so that the cleaning results are guaranteed and reproducable. Also a device for testing and cleaning was designed together with Netzsch Newamatic and PCI, called TC-MIC, to automate processing and reduce manual work.

Proof-of-concept automation of propellant processing

NASA Technical Reports Server (NTRS)

Ramohalli, Kumar; Schallhorn, P. A.

1989-01-01

For space-based propellant production, automation of the process is needed. Currently, all phases of terrestrial production have some form of human interaction. A mixer was acquired to help perform the tasks of automation. A heating system to be used with the mixer was designed, built, and installed. Tests performed on the heating system verify design criteria. An IBM PS/2 personal computer was acquired for the future automation work. It is hoped that some the mixing process itself will be automated. This is a concept demonstration task; proving that propellant production can be automated reliably.

Automated Long-Term Monitoring of Parallel Microfluidic Operations Applying a Machine Vision-Assisted Positioning Method

PubMed Central

Yip, Hon Ming; Li, John C. S.; Cui, Xin; Gao, Qiannan; Leung, Chi Chiu

2014-01-01

As microfluidics has been applied extensively in many cell and biochemical applications, monitoring the related processes is an important requirement. In this work, we design and fabricate a high-throughput microfluidic device which contains 32 microchambers to perform automated parallel microfluidic operations and monitoring on an automated stage of a microscope. Images are captured at multiple spots on the device during the operations for monitoring samples in microchambers in parallel; yet the device positions may vary at different time points throughout operations as the device moves back and forth on a motorized microscopic stage. Here, we report an image-based positioning strategy to realign the chamber position before every recording of microscopic image. We fabricate alignment marks at defined locations next to the chambers in the microfluidic device as reference positions. We also develop image processing algorithms to recognize the chamber positions in real-time, followed by realigning the chambers to their preset positions in the captured images. We perform experiments to validate and characterize the device functionality and the automated realignment operation. Together, this microfluidic realignment strategy can be a platform technology to achieve precise positioning of multiple chambers for general microfluidic applications requiring long-term parallel monitoring of cell and biochemical activities. PMID:25133248

An Automated Scheme for the Large-Scale Survey of Herbig-Haro Objects

NASA Astrophysics Data System (ADS)

Deng, Licai; Yang, Ji; Zheng, Zhongyuan; Jiang, Zhaoji

2001-04-01

Owing to their spectral properties, Herbig-Haro (HH) objects can be discovered using photometric methods through a combination of filters, sampling the characteristic spectral lines and the nearby continuum. The data are commonly processed through direct visual inspection of the images. To make data reduction more efficient and the results more uniform and complete, an automated searching scheme for HH objects is developed to manipulate the images using IRAF. This approach helps to extract images with only intrinsic HH emissions. By using this scheme, the pointlike stellar sources and extended nebulous sources with continuum emission can be eliminated from the original images. The objects with only characteristic HH emission become prominent and can be easily picked up. In this paper our scheme is illustrated by a sample field and has been applied to our surveys for HH objects.

Global sensing of gaseous and aerosol trace species using automated instrumentation on 747 airliners

NASA Technical Reports Server (NTRS)

Perkins, P. J.; Papathakos, L. C.

1977-01-01

The Global Atmospheric Sampling Program (GASP) by NASA is collecting and analyzing data on gaseous and aerosol trace species in the upper troposphere and lower stratosphere. Measurements are obtained from automated systems installed on four 747 airliners flying global air routes. Advances were made in airborne sampling instrumentation. Improved instruments and analysis techniques are providing an expanding data base for trace species including ozone, carbon monoxide, water vapor, condensation nuclei and mass concentrations of sulfates and nitrates. Simultaneous measurements of several trace species obtained frequently can be used to uniquely identify the source of the air mass as being typically tropospheric or stratospheric. A quantitative understanding of the tropospheric-stratospheric exchange processes leads to better knowledge of the atmospheric impact of pollution through the development of improved simulation models of the atmosphere.

Microgravity

NASA Image and Video Library

1991-09-01

The Advanced Automated Directional Solidification Furnace (AADSF) flew during the USMP-2 mission. During USMP-2, the AADSF was used to study the growth of mercury cadmium telluride crystals in microgravity by directional solidification, a process commonly used on earth to process metals and grow crystals. The furnace is tubular and has three independently controlled temperature zones. The sample travels from the hot zone of the furnace (1600 degrees F) where the material solidifies as it cools. The solidification region, known as the solid/liquid interface, moves from one end of the sample to the other at a controlled rate, thus the term directional solidification.

Automated Microflow NMR: Routine Analysis of Five-Microliter Samples

PubMed Central

Jansma, Ariane; Chuan, Tiffany; Geierstanger, Bernhard H.; Albrecht, Robert W.; Olson, Dean L.; Peck, Timothy L.

2006-01-01

A microflow CapNMR probe double-tuned for 1H and 13C was installed on a 400-MHz NMR spectrometer and interfaced to an automated liquid handler. Individual samples dissolved in DMSO-d6 are submitted for NMR analysis in vials containing as little as 10 μL of sample. Sets of samples are submitted in a low-volume 384-well plate. Of the 10 μL of sample per well, as with vials, 5 μL is injected into the microflow NMR probe for analysis. For quality control of chemical libraries, 1D NMR spectra are acquired under full automation from 384-well plates on as many as 130 compounds within 24 h using 128 scans per spectrum and a sample-to-sample cycle time of ∼11 min. Because of the low volume requirements and high mass sensitivity of the microflow NMR system, 30 nmol of a typical small molecule is sufficient to obtain high-quality, well-resolved, 1D proton or 2D COSY NMR spectra in ∼6 or 20 min of data acquisition time per experiment, respectively. Implementation of pulse programs with automated solvent peak identification and suppression allow for reliable data collection, even for samples submitted in fully protonated DMSO. The automated microflow NMR system is controlled and monitored using web-based software. PMID:16194121

Automated working distance adjustment for a handheld OCT-Laryngoscope

NASA Astrophysics Data System (ADS)

Donner, Sabine; Bleeker, Sebastian; Ripken, Tammo; Krueger, Alexander

2014-03-01

Optical coherence tomography (OCT) is an imaging technique which enables diagnosis of vocal cord tissue structure by non-contact optical biopsies rather than invasive tissue biopsies. For diagnosis on awake patients OCT was adapted to a rigid indirect laryngoscope. The working distance must match the probe-sample distance, which varies from patient to patient. Therefore the endoscopic OCT sample arm has a variable working distance of 40 mm to 80 mm. The current axial position is identified by automated working distance adjustments based on image processing. The OCT reference plane and the focal plane of the sample arm are moved according to position errors. Repeated position adjustment during the whole diagnostic procedure keeps the tissue sample at the optimal axial position. The auto focus identifies and adjusts the working distance within the range of 50 mm within a maximum time of 2.7 s. Continuous image stabilisation reduces axial sample movement within the sampling depth for handheld OCT scanning. Rapid autofocus reduces the duration of the diagnostic procedure and axial position stabilisation eases the use of the OCT laryngoscope. Therefore this work is an important step towards the integration of OCT into indirect laryngoscopes.

Automated identification of wound information in clinical notes of patients with heart diseases: Developing and validating a natural language processing application.

PubMed

Topaz, Maxim; Lai, Kenneth; Dowding, Dawn; Lei, Victor J; Zisberg, Anna; Bowles, Kathryn H; Zhou, Li

2016-12-01

Electronic health records are being increasingly used by nurses with up to 80% of the health data recorded as free text. However, only a few studies have developed nursing-relevant tools that help busy clinicians to identify information they need at the point of care. This study developed and validated one of the first automated natural language processing applications to extract wound information (wound type, pressure ulcer stage, wound size, anatomic location, and wound treatment) from free text clinical notes. First, two human annotators manually reviewed a purposeful training sample (n=360) and random test sample (n=1100) of clinical notes (including 50% discharge summaries and 50% outpatient notes), identified wound cases, and created a gold standard dataset. We then trained and tested our natural language processing system (known as MTERMS) to process the wound information. Finally, we assessed our automated approach by comparing system-generated findings against the gold standard. We also compared the prevalence of wound cases identified from free-text data with coded diagnoses in the structured data. The testing dataset included 101 notes (9.2%) with wound information. The overall system performance was good (F-measure is a compiled measure of system's accuracy=92.7%), with best results for wound treatment (F-measure=95.7%) and poorest results for wound size (F-measure=81.9%). Only 46.5% of wound notes had a structured code for a wound diagnosis. The natural language processing system achieved good performance on a subset of randomly selected discharge summaries and outpatient notes. In more than half of the wound notes, there were no coded wound diagnoses, which highlight the significance of using natural language processing to enrich clinical decision making. Our future steps will include expansion of the application's information coverage to other relevant wound factors and validation of the model with external data. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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.

Toward reliable and repeatable automated STEM-EDS metrology with high throughput

NASA Astrophysics Data System (ADS)

Zhong, Zhenxin; Donald, Jason; Dutrow, Gavin; Roller, Justin; Ugurlu, Ozan; Verheijen, Martin; Bidiuk, Oleksii

2018-03-01

New materials and designs in complex 3D architectures in logic and memory devices have raised complexity in S/TEM metrology. In this paper, we report about a newly developed, automated, scanning transmission electron microscopy (STEM) based, energy dispersive X-ray spectroscopy (STEM-EDS) metrology method that addresses these challenges. Different methodologies toward repeatable and efficient, automated STEM-EDS metrology with high throughput are presented: we introduce the best known auto-EDS acquisition and quantification methods for robust and reliable metrology and present how electron exposure dose impacts the EDS metrology reproducibility, either due to poor signalto-noise ratio (SNR) at low dose or due to sample modifications at high dose conditions. Finally, we discuss the limitations of the STEM-EDS metrology technique and propose strategies to optimize the process both in terms of throughput and metrology reliability.

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.

Adapting the γ-H2AX assay for automated processing in human lymphocytes. 1. Technological aspects.

PubMed

Turner, Helen C; Brenner, David J; Chen, Youhua; Bertucci, Antonella; Zhang, Jian; Wang, Hongliang; Lyulko, Oleksandra V; Xu, Yanping; Shuryak, Igor; Schaefer, Julia; Simaan, Nabil; Randers-Pehrson, Gerhard; Yao, Y Lawrence; Amundson, Sally A; Garty, Guy

2011-03-01

The immunofluorescence-based detection of γ-H2AX is a reliable and sensitive method for quantitatively measuring DNA double-strand breaks (DSBs) in irradiated samples. Since H2AX phosphorylation is highly linear with radiation dose, this well-established biomarker is in current use in radiation biodosimetry. At the Center for High-Throughput Minimally Invasive Radiation Biodosimetry, we have developed a fully automated high-throughput system, the RABIT (Rapid Automated Biodosimetry Tool), that can be used to measure γ-H2AX yields from fingerstick-derived samples of blood. The RABIT workstation has been designed to fully automate the γ-H2AX immunocytochemical protocol, from the isolation of human blood lymphocytes in heparin-coated PVC capillaries to the immunolabeling of γ-H2AX protein and image acquisition to determine fluorescence yield. High throughput is achieved through the use of purpose-built robotics, lymphocyte handling in 96-well filter-bottomed plates, and high-speed imaging. The goal of the present study was to optimize and validate the performance of the RABIT system for the reproducible and quantitative detection of γ-H2AX total fluorescence in lymphocytes in a multiwell format. Validation of our biodosimetry platform was achieved by the linear detection of a dose-dependent increase in γ-H2AX fluorescence in peripheral blood samples irradiated ex vivo with γ rays over the range 0 to 8 Gy. This study demonstrates for the first time the optimization and use of our robotically based biodosimetry workstation to successfully quantify γ-H2AX total fluorescence in irradiated peripheral lymphocytes.

Comparison of modelling accuracy with and without exploiting automated optical monitoring information in predicting the treated wastewater quality.

PubMed

Tomperi, Jani; Leiviskä, Kauko

2018-06-01

Traditionally the modelling in an activated sludge process has been based on solely the process measurements, but as the interest to optically monitor wastewater samples to characterize the floc morphology has increased, in the recent years the results of image analyses have been more frequently utilized to predict the characteristics of wastewater. This study shows that the traditional process measurements or the automated optical monitoring variables by themselves are not capable of developing the best predictive models for the treated wastewater quality in a full-scale wastewater treatment plant, but utilizing these variables together the optimal models, which show the level and changes in the treated wastewater quality, are achieved. By this early warning, process operation can be optimized to avoid environmental damages and economic losses. The study also shows that specific optical monitoring variables are important in modelling a certain quality parameter, regardless of the other input variables available.

Automated Chromium Plating Line for Gun Barrels

DTIC Science & Technology

1979-09-01

consistent pretreatments and bath dwell times. Some of the advantages of automated processing include increased productivity (average of 20^) due to...when automated processing procedures’ are used. The current method of applying chromium electrodeposits to gun tubes is a manual, batch operation...currently practiced with rotary swaged gun tubes would substantially reduce the difficulties in automated processing . RECOMMENDATIONS

Colometer: a real-time quality feedback system for screening colonoscopy.

PubMed

Filip, Dobromir; Gao, Xuexin; Angulo-Rodríguez, Leticia; Mintchev, Martin P; Devlin, Shane M; Rostom, Alaa; Rosen, Wayne; Andrews, Christopher N

2012-08-28

To investigate the performance of a new software-based colonoscopy quality assessment system. The software-based system employs a novel image processing algorithm which detects the levels of image clarity, withdrawal velocity, and level of the bowel preparation in a real-time fashion from live video signal. Threshold levels of image blurriness and the withdrawal velocity below which the visualization could be considered adequate have initially been determined arbitrarily by review of sample colonoscopy videos by two experienced endoscopists. Subsequently, an overall colonoscopy quality rating was computed based on the percentage of the withdrawal time with adequate visualization (scored 1-5; 1, when the percentage was 1%-20%; 2, when the percentage was 21%-40%, etc.). In order to test the proposed velocity and blurriness thresholds, screening colonoscopy withdrawal videos from a specialized ambulatory colon cancer screening center were collected, automatically processed and rated. Quality ratings on the withdrawal were compared to the insertion in the same patients. Then, 3 experienced endoscopists reviewed the collected videos in a blinded fashion and rated the overall quality of each withdrawal (scored 1-5; 1, poor; 3, average; 5, excellent) based on 3 major aspects: image quality, colon preparation, and withdrawal velocity. The automated quality ratings were compared to the averaged endoscopist quality ratings using Spearman correlation coefficient. Fourteen screening colonoscopies were assessed. Adenomatous polyps were detected in 4/14 (29%) of the collected colonoscopy video samples. As a proof of concept, the Colometer software rated colonoscope withdrawal as having better visualization than the insertion in the 10 videos which did not have any polyps (average percent time with adequate visualization: 79% ± 5% for withdrawal and 50% ± 14% for insertion, P < 0.01). Withdrawal times during which no polyps were removed ranged from 4-12 min. The median quality rating from the automated system and the reviewers was 3.45 [interquartile range (IQR), 3.1-3.68] and 3.00 (IQR, 2.33-3.67) respectively for all colonoscopy video samples. The automated rating revealed a strong correlation with the reviewer's rating (ρ coefficient= 0.65, P = 0.01). There was good correlation of the automated overall quality rating and the mean endoscopist withdrawal speed rating (Spearman r coefficient= 0.59, P = 0.03). There was no correlation of automated overall quality rating with mean endoscopists image quality rating (Spearman r coefficient= 0.41, P = 0.15). The results from a novel automated real-time colonoscopy quality feedback system strongly agreed with the endoscopists' quality assessments. Further study is required to validate this approach.

21 CFR 864.5200 - Automated cell counter.

Code of Federal Regulations, 2014 CFR

2014-04-01

....5200 Automated cell counter. (a) Identification. An automated cell counter is a fully-automated or semi-automated device used to count red blood cells, white blood cells, or blood platelets using a sample of the patient's peripheral blood (blood circulating in one of the body's extremities, such as the arm). These...

21 CFR 864.5200 - Automated cell counter.

Code of Federal Regulations, 2011 CFR

2011-04-01

....5200 Automated cell counter. (a) Identification. An automated cell counter is a fully-automated or semi-automated device used to count red blood cells, white blood cells, or blood platelets using a sample of the patient's peripheral blood (blood circulating in one of the body's extremities, such as the arm). These...

21 CFR 864.5200 - Automated cell counter.

Code of Federal Regulations, 2012 CFR

2012-04-01

....5200 Automated cell counter. (a) Identification. An automated cell counter is a fully-automated or semi-automated device used to count red blood cells, white blood cells, or blood platelets using a sample of the patient's peripheral blood (blood circulating in one of the body's extremities, such as the arm). These...

21 CFR 864.5200 - Automated cell counter.

Code of Federal Regulations, 2013 CFR

2013-04-01

....5200 Automated cell counter. (a) Identification. An automated cell counter is a fully-automated or semi-automated device used to count red blood cells, white blood cells, or blood platelets using a sample of the patient's peripheral blood (blood circulating in one of the body's extremities, such as the arm). These...

A Unique Automation Platform for Measuring Low Level Radioactivity in Metabolite Identification Studies

PubMed Central

Krauser, Joel; Walles, Markus; Wolf, Thierry; Graf, Daniel; Swart, Piet

2012-01-01

Generation and interpretation of biotransformation data on drugs, i.e. identification of physiologically relevant metabolites, defining metabolic pathways and elucidation of metabolite structures, have become increasingly important to the drug development process. Profiling using 14C or 3H radiolabel is defined as the chromatographic separation and quantification of drug-related material in a given biological sample derived from an in vitro, preclinical in vivo or clinical study. Metabolite profiling is a very time intensive activity, particularly for preclinical in vivo or clinical studies which have defined limitations on radiation burden and exposure levels. A clear gap exists for certain studies which do not require specialized high volume automation technologies, yet these studies would still clearly benefit from automation. Use of radiolabeled compounds in preclinical and clinical ADME studies, specifically for metabolite profiling and identification are a very good example. The current lack of automation for measuring low level radioactivity in metabolite profiling requires substantial capacity, personal attention and resources from laboratory scientists. To help address these challenges and improve efficiency, we have innovated, developed and implemented a novel and flexible automation platform that integrates a robotic plate handling platform, HPLC or UPLC system, mass spectrometer and an automated fraction collector. PMID:22723932

A simple automated instrument for DNA extraction in forensic casework.

PubMed

Montpetit, Shawn A; Fitch, Ian T; O'Donnell, Patrick T

2005-05-01

The Qiagen BioRobot EZ1 is a small, rapid, and reliable automated DNA extraction instrument capable of extracting DNA from up to six samples in as few as 20 min using magnetic bead technology. The San Diego Police Department Crime Laboratory has validated the BioRobot EZ1 for the DNA extraction of evidence and reference samples in forensic casework. The BioRobot EZ1 was evaluated for use on a variety of different evidence sample types including blood, saliva, and semen evidence. The performance of the BioRobot EZ1 with regard to DNA recovery and potential cross-contamination was also assessed. DNA yields obtained with the BioRobot EZ1 were comparable to those from organic extraction. The BioRobot EZ1 was effective at removing PCR inhibitors, which often co-purify with DNA in organic extractions. The incorporation of the BioRobot EZ1 into forensic casework has streamlined the DNA analysis process by reducing the need for labor-intensive phenol-chloroform extractions.

Nuclear Magnetic Resonance Spectroscopy-Based Identification of Yeast.

PubMed

Himmelreich, Uwe; Sorrell, Tania C; Daniel, Heide-Marie

2017-01-01

Rapid and robust high-throughput identification of environmental, industrial, or clinical yeast isolates is important whenever relatively large numbers of samples need to be processed in a cost-efficient way. Nuclear magnetic resonance (NMR) spectroscopy generates complex data based on metabolite profiles, chemical composition and possibly on medium consumption, which can not only be used for the assessment of metabolic pathways but also for accurate identification of yeast down to the subspecies level. Initial results on NMR based yeast identification where comparable with conventional and DNA-based identification. Potential advantages of NMR spectroscopy in mycological laboratories include not only accurate identification but also the potential of automated sample delivery, automated analysis using computer-based methods, rapid turnaround time, high throughput, and low running costs.We describe here the sample preparation, data acquisition and analysis for NMR-based yeast identification. In addition, a roadmap for the development of classification strategies is given that will result in the acquisition of a database and analysis algorithms for yeast identification in different environments.

Automated mass spectrometer analysis system

NASA Technical Reports Server (NTRS)

Giffin, Charles E. (Inventor); Kuppermann, Aron (Inventor); Dreyer, William J. (Inventor); Boettger, Heinz G. (Inventor)

1982-01-01

An automated mass spectrometer analysis system is disclosed, in which samples are automatically processed in a sample processor and converted into volatilizable samples, or their characteristic volatilizable derivatives. Each volatilizable sample is sequentially volatilized and analyzed in a double focusing mass spectrometer, whose output is in the form of separate ion beams all of which are simultaneously focused in a focal plane. Each ion beam is indicative of a different sample component or different fragments of one or more sample components and the beam intensity is related to the relative abundance of the sample component. The system includes an electro-optical ion detector which automatically and simultaneously converts the ion beams, first into electron beams which in turn produce a related image which is transferred to the target of a vilicon unit. The latter converts the images into electrical signals which are supplied to a data processor, whose output is a list of the components of the analyzed sample and their abundances. The system is under the control of a master control unit, which in addition to monitoring and controlling various power sources, controls the automatic operation of the system under expected and some unexpected conditions and further protects various critical parts of the system from damage due to particularly abnormal conditions.

Automated mass spectrometer analysis system

NASA Technical Reports Server (NTRS)

Boettger, Heinz G. (Inventor); Giffin, Charles E. (Inventor); Dreyer, William J. (Inventor); Kuppermann, Aron (Inventor)

1978-01-01

An automated mass spectrometer analysis system is disclosed, in which samples are automatically processed in a sample processor and converted into volatilizable samples, or their characteristic volatilizable derivatives. Each volatizable sample is sequentially volatilized and analyzed in a double focusing mass spectrometer, whose output is in the form of separate ion beams all of which are simultaneously focused in a focal plane. Each ion beam is indicative of a different sample component or different fragments of one or more sample components and the beam intensity is related to the relative abundance of the sample component. The system includes an electro-optical ion detector which automatically and simultaneously converts the ion beams, first into electron beams which in turn produce a related image which is transferred to the target of a vidicon unit. The latter converts the images into electrical signals which are supplied to a data processor, whose output is a list of the components of the analyzed sample and their abundances. The system is under the control of a master control unit, which in addition to monitoring and controlling various power sources, controls the automatic operation of the system under expected and some unexpected conditions and further protects various critical parts of the system from damage due to particularly abnormal conditions.

A novel experimental approach to investigate radiolysis processes in liquid samples using collimated radiation sources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polin, Chris, E-mail: cpolin01@qub.ac.uk; Wardlow, Nathan; McQuaid, Harold

2015-03-15

Here is detailed a novel and low-cost experimental method for high-throughput automated fluid sample irradiation. The sample is delivered via syringe pump to a nozzle, where it is expressed in the form of a hanging droplet into the path of a beam of ionising radiation. The dose delivery is controlled by an upstream lead shutter, which allows the beam to reach the droplet for a user defined period of time. The droplet is then further expressed after irradiation until it falls into one well of a standard microplate. The entire system is automated and can be operated remotely using softwaremore » designed in-house, allowing for use in environments deemed unsafe for the user (synchrotron beamlines, for example). Depending on the number of wells in the microplate, several droplets can be irradiated before any human interaction is necessary, and the user may choose up to 10 samples per microplate using an array of identical syringe pumps, the design of which is described here. The nozzles consistently produce droplets of 25.1 ± 0.5 μl.« less

National survey on the pre-analytical variability in a representative cohort of Italian laboratories.

PubMed

Lippi, Giuseppe; Montagnana, Martina; Giavarina, Davide

2006-01-01

Owing to remarkable advances in automation, laboratory technology and informatics, the pre-analytical phase has become the major source of variability in laboratory testing. The present survey investigated the development of several pre-analytical processes within a representative cohort of Italian clinical laboratories. A seven-point questionnaire was designed to investigate the following issues: 1a) the mean outpatient waiting time before check-in and 1b) the mean time from check-in to sample collection; 2) the mean time from sample collection to analysis; 3) the type of specimen collected for clinical chemistry testing; 4) the degree of pre-analytical automation; 5a) the number of samples shipped to other laboratories and 5b) the availability of standardised protocols for transportation; 6) the conditions for specimen storage; and 7) the availability and type of guidelines for management of unsuitable specimens. The questionnaire was administered to 150 laboratory specialists attending the SIMEL (Italian Society of Laboratory Medicine) National Meeting in June 2006. 107 questionnaires (71.3%) were returned. Data analysis revealed a high degree of variability among laboratories for the time required for check-in, outpatient sampling, sample transportation to the referral laboratory and analysis upon the arrival. Only 31% of laboratories have automated some pre-analytical steps. Of the 87% of laboratories that ship specimens to other facilities without sample preparation, 19% have no standardised protocol for transportation. For conventional clinical chemistry testing, 74% of the laboratories use serum evacuated tubes (59% with and 15% without serum separator), whereas the remaining 26% use lithium-heparin evacuated tubes (11% with and 15% without plasma separator). The storage period and conditions for rerun/retest vary widely. Only 63% of laboratories have a codified procedure for the management of unsuitable specimens, which are recognised by visual inspection (69%) or automatic detection (29%). Only 56% of the laboratories have standardised procedures for the management of unsuitable specimens, which vary widely on a local basis. The survey highlights broad heterogeneity in several pre-analytical processes among Italian laboratories. The lack of reliable guidelines encompassing evidence-based practice is a major problem for the standardisation of this crucial part of the testing process and represents a major challenge for laboratory medicine in the 2000s.

Rapid-viability PCR method for detection of live, virulent Bacillus anthracis in environmental samples.

PubMed

Létant, Sonia E; Murphy, Gloria A; Alfaro, Teneile M; Avila, Julie R; Kane, Staci R; Raber, Ellen; Bunt, Thomas M; Shah, Sanjiv R

2011-09-01

In the event of a biothreat agent release, hundreds of samples would need to be rapidly processed to characterize the extent of contamination and determine the efficacy of remediation activities. Current biological agent identification and viability determination methods are both labor- and time-intensive such that turnaround time for confirmed results is typically several days. In order to alleviate this issue, automated, high-throughput sample processing methods were developed in which real-time PCR analysis is conducted on samples before and after incubation. The method, referred to as rapid-viability (RV)-PCR, uses the change in cycle threshold after incubation to detect the presence of live organisms. In this article, we report a novel RV-PCR method for detection of live, virulent Bacillus anthracis, in which the incubation time was reduced from 14 h to 9 h, bringing the total turnaround time for results below 15 h. The method incorporates a magnetic bead-based DNA extraction and purification step prior to PCR analysis, as well as specific real-time PCR assays for the B. anthracis chromosome and pXO1 and pXO2 plasmids. A single laboratory verification of the optimized method applied to the detection of virulent B. anthracis in environmental samples was conducted and showed a detection level of 10 to 99 CFU/sample with both manual and automated RV-PCR methods in the presence of various challenges. Experiments exploring the relationship between the incubation time and the limit of detection suggest that the method could be further shortened by an additional 2 to 3 h for relatively clean samples.

Automation in School Library Media Centers.

ERIC Educational Resources Information Center

Driver, Russell W.; Driver, Mary Anne

1982-01-01

Surveys the historical development of automated technical processing in schools and notes the impact of this automation in a number of cases. Speculations about the future involvement of school libraries in automated processing and networking are included. Thirty references are listed. (BBM)

Integrated multiplexed capillary electrophoresis system

DOEpatents

Yeung, Edward S.; Tan, Hongdong

2002-05-14

The present invention provides an integrated multiplexed capillary electrophoresis system for the analysis of sample analytes. The system integrates and automates multiple components, such as chromatographic columns and separation capillaries, and further provides a detector for the detection of analytes eluting from the separation capillaries. The system employs multiplexed freeze/thaw valves to manage fluid flow and sample movement. The system is computer controlled and is capable of processing samples through reaction, purification, denaturation, pre-concentration, injection, separation and detection in parallel fashion. Methods employing the system of the invention are also provided.

Automated quantitative cytological analysis using portable microfluidic microscopy.

PubMed

Jagannadh, Veerendra Kalyan; Murthy, Rashmi Sreeramachandra; Srinivasan, Rajesh; Gorthi, Sai Siva

2016-06-01

In this article, a portable microfluidic microscopy based approach for automated cytological investigations is presented. Inexpensive optical and electronic components have been used to construct a simple microfluidic microscopy system. In contrast to the conventional slide-based methods, the presented method employs microfluidics to enable automated sample handling and image acquisition. The approach involves the use of simple in-suspension staining and automated image acquisition to enable quantitative cytological analysis of samples. The applicability of the presented approach to research in cellular biology is shown by performing an automated cell viability assessment on a given population of yeast cells. Further, the relevance of the presented approach to clinical diagnosis and prognosis has been demonstrated by performing detection and differential assessment of malaria infection in a given sample. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bacterial and fungal DNA extraction from blood samples: automated protocols.

PubMed

Lorenz, Michael G; Disqué, Claudia; Mühl, Helge

2015-01-01

Automation in DNA isolation is a necessity for routine practice employing molecular diagnosis of infectious agents. To this end, the development of automated systems for the molecular diagnosis of microorganisms directly in blood samples is at its beginning. Important characteristics of systems demanded for routine use include high recovery of microbial DNA, DNA-free containment for the reduction of DNA contamination from exogenous sources, DNA-free reagents and consumables, ideally a walkaway system, and economical pricing of the equipment and consumables. Such full automation of DNA extraction evaluated and in use for sepsis diagnostics is yet not available. Here, we present protocols for the semiautomated isolation of microbial DNA from blood culture and low- and high-volume blood samples. The protocols include a manual pretreatment step followed by automated extraction and purification of microbial DNA.

Automated multimodal spectral histopathology for quantitative diagnosis of residual tumour during basal cell carcinoma surgery.

PubMed

Boitor, Radu; Kong, Kenny; Shipp, Dustin; Varma, Sandeep; Koloydenko, Alexey; Kulkarni, Kusum; Elsheikh, Somaia; Schut, Tom Bakker; Caspers, Peter; Puppels, Gerwin; van der Wolf, Martin; Sokolova, Elena; Nijsten, T E C; Salence, Brogan; Williams, Hywel; Notingher, Ioan

2017-12-01

Multimodal spectral histopathology (MSH), an optical technique combining tissue auto-fluorescence (AF) imaging and Raman micro-spectroscopy (RMS), was previously proposed for detection of residual basal cell carcinoma (BCC) at the surface of surgically-resected skin tissue. Here we report the development of a fully-automated prototype instrument based on MSH designed to be used in the clinic and operated by a non-specialist spectroscopy user. The algorithms for the AF image processing and Raman spectroscopy classification had been first optimised on a manually-operated laboratory instrument and then validated on the automated prototype using skin samples from independent patients. We present results on a range of skin samples excised during Mohs micrographic surgery, and demonstrate consistent diagnosis obtained in repeat test measurement, in agreement with the reference histopathology diagnosis. We also show that the prototype instrument can be operated by clinical users (a skin surgeon and a core medical trainee, after only 1-8 hours of training) to obtain consistent results in agreement with histopathology. The development of the new automated prototype and demonstration of inter-instrument transferability of the diagnosis models are important steps on the clinical translation path: it allows the testing of the MSH technology in a relevant clinical environment in order to evaluate its performance on a sufficiently large number of patients.

Demonstration of the feasibility of automated silicon solar cell fabrication

NASA Technical Reports Server (NTRS)

Taylor, W. E.; Schwartz, F. M.

1975-01-01

A study effort was undertaken to determine the process, steps and design requirements of an automated silicon solar cell production facility. Identification of the key process steps was made and a laboratory model was conceptually designed to demonstrate the feasibility of automating the silicon solar cell fabrication process. A detailed laboratory model was designed to demonstrate those functions most critical to the question of solar cell fabrication process automating feasibility. The study and conceptual design have established the technical feasibility of automating the solar cell manufacturing process to produce low cost solar cells with improved performance. Estimates predict an automated process throughput of 21,973 kilograms of silicon a year on a three shift 49-week basis, producing 4,747,000 hexagonal cells (38mm/side), a total of 3,373 kilowatts at an estimated manufacturing cost of $0.866 per cell or $1.22 per watt.

Method and apparatus for automated processing and aliquoting of whole blood samples for analysis in a centrifugal fast analyzer

DOEpatents

Burtis, C.A.; Johnson, W.F.; Walker, W.A.

1985-08-05

A rotor and disc assembly for use in a centrifugal fast analyzer. The assembly is designed to process multiple samples of whole blood followed by aliquoting of the resultant serum into precisely measured samples for subsequent chemical analysis. The assembly requires minimal operator involvement with no mechanical pipetting. The system comprises: (1) a whole blood sample disc; (2) a serum sample disc; (3) a sample preparation rotor; and (4) an analytical rotor. The blood sample disc and serum sample disc are designed with a plurality of precision bore capillary tubes arranged in a spoked array. Samples of blood are loaded into the blood sample disc by capillary action and centrifugally discharged into cavities of the sample preparation rotor where separation of serum and solids is accomplished. The serum is loaded into the capillaries of the serum sample disc by capillary action and subsequently centrifugally expelled into cuvettes of the analyticaly rotor for conventional methods. 5 figs.

Method and apparatus for automated processing and aliquoting of whole blood samples for analysis in a centrifugal fast analyzer

DOEpatents

Burtis, Carl A.; Johnson, Wayne F.; Walker, William A.

1988-01-01

A rotor and disc assembly for use in a centrifugal fast analyzer. The assembly is designed to process multiple samples of whole blood followed by aliquoting of the resultant serum into precisely measured samples for subsequent chemical analysis. The assembly requires minimal operator involvement with no mechanical pipetting. The system comprises (1) a whole blood sample disc, (2) a serum sample disc, (3) a sample preparation rotor, and (4) an analytical rotor. The blood sample disc and serum sample disc are designed with a plurality of precision bore capillary tubes arranged in a spoked array. Samples of blood are loaded into the blood sample disc in capillary tubes filled by capillary action and centrifugally discharged into cavities of the sample preparation rotor where separation of serum and solids is accomplished. The serum is loaded into the capillaries of the serum sample disc by capillary action and subsequently centrifugally expelled into cuvettes of the analytical rotor for analysis by conventional methods.

Microfluidic-Based sample chips for radioactive solutions

DOE PAGES

Tripp, J. L.; Law, J. D.; Smith, T. E.; ...

2015-01-01

Historical nuclear fuel cycle process sampling techniques required sample volumes ranging in the tens of milliliters. The radiation levels experienced by analytical personnel and equipment, in addition to the waste volumes generated from analysis of these samples, have been significant. These sample volumes also impacted accountability inventories of required analytes during process operations. To mitigate radiation dose and other issues associated with the historically larger sample volumes, a microcapillary sample chip was chosen for further investigation. The ability to obtain microliter volume samples coupled with a remote automated means of sample loading, tracking, and transporting to the analytical instrument wouldmore » greatly improve analytical efficiency while reducing both personnel exposure and radioactive waste volumes. Sample chip testing was completed to determine the accuracy, repeatability, and issues associated with the use of microfluidic sample chips used to supply µL sample volumes of lanthanide analytes dissolved in nitric acid for introduction to an analytical instrument for elemental analysis.« less

Automated Space Processing Payloads Study. Volume 1: Executive Summary

NASA Technical Reports Server (NTRS)

1975-01-01

An investigation is described which examined the extent to which the experiment hardware and operational requirements can be met by automatic control and material handling devices; payload and system concepts are defined which make extensive use of automation technology. Topics covered include experiment requirements and hardware data, capabilities and characteristics of industrial automation equipment and controls, payload grouping, automated payload conceptual design, space processing payload preliminary design, automated space processing payloads for early shuttle missions, and cost and scheduling.

Automated Analysis Workstation

NASA Technical Reports Server (NTRS)

1997-01-01

Information from NASA Tech Briefs of work done at Langley Research Center and the Jet Propulsion Laboratory assisted DiaSys Corporation in manufacturing their first product, the R/S 2000. Since then, the R/S 2000 and R/S 2003 have followed. Recently, DiaSys released their fourth workstation, the FE-2, which automates the process of making and manipulating wet-mount preparation of fecal concentrates. The time needed to read the sample is decreased, permitting technologists to rapidly spot parasites, ova and cysts, sometimes carried in the lower intestinal tract of humans and animals. Employing the FE-2 is non-invasive, can be performed on an out-patient basis, and quickly provides confirmatory results.

Kepler Planet Detection Metrics: Automatic Detection of Background Objects Using the Centroid Robovetter

NASA Technical Reports Server (NTRS)

Mullally, Fergal

2017-01-01

We present an automated method of identifying background eclipsing binaries masquerading as planet candidates in the Kepler planet candidate catalogs. We codify the manual vetting process for Kepler Objects of Interest (KOIs) described in Bryson et al. (2013) with a series of measurements and tests that can be performed algorithmically. We compare our automated results with a sample of manually vetted KOIs from the catalog of Burke et al. (2014) and find excellent agreement. We test the performance on a set of simulated transits and find our algorithm correctly identifies simulated false positives approximately 50 of the time, and correctly identifies 99 of simulated planet candidates.

Sampling and sample processing in pesticide residue analysis.

PubMed

Lehotay, Steven J; Cook, Jo Marie

2015-05-13

Proper sampling and sample processing in pesticide residue analysis of food and soil have always been essential to obtain accurate results, but the subject is becoming a greater concern as approximately 100 mg test portions are being analyzed with automated high-throughput analytical methods by agrochemical industry and contract laboratories. As global food trade and the importance of monitoring increase, the food industry and regulatory laboratories are also considering miniaturized high-throughput methods. In conjunction with a summary of the symposium "Residues in Food and Feed - Going from Macro to Micro: The Future of Sample Processing in Residue Analytical Methods" held at the 13th IUPAC International Congress of Pesticide Chemistry, this is an opportune time to review sampling theory and sample processing for pesticide residue analysis. If collected samples and test portions do not adequately represent the actual lot from which they came and provide meaningful results, then all costs, time, and efforts involved in implementing programs using sophisticated analytical instruments and techniques are wasted and can actually yield misleading results. This paper is designed to briefly review the often-neglected but crucial topic of sample collection and processing and put the issue into perspective for the future of pesticide residue analysis. It also emphasizes that analysts should demonstrate the validity of their sample processing approaches for the analytes/matrices of interest and encourages further studies on sampling and sample mass reduction to produce a test portion.

Computer-Assisted Automated Scoring of Polysomnograms Using the Somnolyzer System.

PubMed

Punjabi, Naresh M; Shifa, Naima; Dorffner, Georg; Patil, Susheel; Pien, Grace; Aurora, Rashmi N

2015-10-01

Manual scoring of polysomnograms is a time-consuming and tedious process. To expedite the scoring of polysomnograms, several computerized algorithms for automated scoring have been developed. The overarching goal of this study was to determine the validity of the Somnolyzer system, an automated system for scoring polysomnograms. The analysis sample comprised of 97 sleep studies. Each polysomnogram was manually scored by certified technologists from four sleep laboratories and concurrently subjected to automated scoring by the Somnolyzer system. Agreement between manual and automated scoring was examined. Sleep staging and scoring of disordered breathing events was conducted using the 2007 American Academy of Sleep Medicine criteria. Clinical sleep laboratories. A high degree of agreement was noted between manual and automated scoring of the apnea-hypopnea index (AHI). The average correlation between the manually scored AHI across the four clinical sites was 0.92 (95% confidence interval: 0.90-0.93). Similarly, the average correlation between the manual and Somnolyzer-scored AHI values was 0.93 (95% confidence interval: 0.91-0.96). Thus, interscorer correlation between the manually scored results was no different than that derived from manual and automated scoring. Substantial concordance in the arousal index, total sleep time, and sleep efficiency between manual and automated scoring was also observed. In contrast, differences were noted between manually and automated scored percentages of sleep stages N1, N2, and N3. Automated analysis of polysomnograms using the Somnolyzer system provides results that are comparable to manual scoring for commonly used metrics in sleep medicine. Although differences exist between manual versus automated scoring for specific sleep stages, the level of agreement between manual and automated scoring is not significantly different than that between any two human scorers. In light of the burden associated with manual scoring, automated scoring platforms provide a viable complement of tools in the diagnostic armamentarium of sleep medicine. © 2015 Associated Professional Sleep Societies, LLC.

Streamlining plant sample preparation: the use of high-throughput robotics to process echinacea samples for biomarker profiling by MALDI-TOF mass spectrometry.

PubMed

Greene, Leasa A; Isaac, Issa; Gray, Dean E; Schwartz, Sarah A

2007-09-01

Several species in the genus Echinacea are beneficial herbs popularly used for many ailments. The most popular Echinacea species for cultivation, wild collection, and herbal products include E. purpurea (L.) Moench, E. pallida (Nutt.) Nutt., and E. angustifolia (DC). Product adulteration is a key concern for the natural products industry, where botanical misidentification and introduction of other botanical and nonbotanical contaminants exist throughout the formulation and production process. Therefore, rapid and cost-effective methods that can be used to monitor these materials for complex product purity and consistency are of benefit to consumers and producers. The objective of this continuing research was to develop automated, high-throughput processing methods that, teamed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis, differentiate Echinacea species by their mass profiles. Small molecules, peptide, and proteins from aerial parts (leaf/stem/flowers), seeds, and roots from E. purpurea and E. angustifolia; seeds and roots from E. pallida; and off-the-shelf Echinacea supplements were extracted and analyzed by MS using methods developed on the ProPrep liquid handling system (Genomic Solutions). Analysis of these samples highlighted key MS signal patterns from both small molecules and proteins that characterized the individual Echinacea materials analyzed. Based on analysis of pure Echinacea samples, off-the-shelf products containing Echinacea could then be evaluated in a streamlined process. Corresponding analysis of dietary supplements was used to monitor for product composition, including Echinacea species and plant materials used. These results highlight the potential for streamlined, automated approaches for agricultural species differentiation and botanical product evaluation.

Understanding human management of automation errors

PubMed Central

McBride, Sara E.; Rogers, Wendy A.; Fisk, Arthur D.

2013-01-01

Automation has the potential to aid humans with a diverse set of tasks and support overall system performance. Automated systems are not always reliable, and when automation errs, humans must engage in error management, which is the process of detecting, understanding, and correcting errors. However, this process of error management in the context of human-automation interaction is not well understood. Therefore, we conducted a systematic review of the variables that contribute to error management. We examined relevant research in human-automation interaction and human error to identify critical automation, person, task, and emergent variables. We propose a framework for management of automation errors to incorporate and build upon previous models. Further, our analysis highlights variables that may be addressed through design and training to positively influence error management. Additional efforts to understand the error management process will contribute to automation designed and implemented to support safe and effective system performance. PMID:25383042

Understanding human management of automation errors.

PubMed

McBride, Sara E; Rogers, Wendy A; Fisk, Arthur D

2014-01-01

Automation has the potential to aid humans with a diverse set of tasks and support overall system performance. Automated systems are not always reliable, and when automation errs, humans must engage in error management, which is the process of detecting, understanding, and correcting errors. However, this process of error management in the context of human-automation interaction is not well understood. Therefore, we conducted a systematic review of the variables that contribute to error management. We examined relevant research in human-automation interaction and human error to identify critical automation, person, task, and emergent variables. We propose a framework for management of automation errors to incorporate and build upon previous models. Further, our analysis highlights variables that may be addressed through design and training to positively influence error management. Additional efforts to understand the error management process will contribute to automation designed and implemented to support safe and effective system performance.

Specimen coordinate automated measuring machine/fiducial automated measuring machine

DOEpatents

Hedglen, Robert E.; Jacket, Howard S.; Schwartz, Allan I.

1991-01-01

The Specimen coordinate Automated Measuring Machine (SCAMM) and the Fiducial Automated Measuring Machine (FAMM) is a computer controlled metrology system capable of measuring length, width, and thickness, and of locating fiducial marks. SCAMM and FAMM have many similarities in their designs, and they can be converted from one to the other without taking them out of the hot cell. Both have means for: supporting a plurality of samples and a standard; controlling the movement of the samples in the +/- X and Y directions; determining the coordinates of the sample; compensating for temperature effects; and verifying the accuracy of the measurements and repeating as necessary. SCAMM and FAMM are designed to be used in hot cells.

Drone inflight mixing of biochemical samples.

PubMed

Katariya, Mayur; Chung, Dwayne Chung Kim; Minife, Tristan; Gupta, Harshit; Zahidi, Alifa Afiah Ahmad; Liew, Oi Wah; Ng, Tuck Wah

2018-03-15

Autonomous systems for sample transport to the laboratory for analysis can be improved in terms of timeliness, cost and error mitigation in the pre-analytical testing phase. Drones have been reported for outdoor sample transport but incorporating devices on them to attain homogenous mixing of reagents during flight to enhance sample processing timeliness is limited by payload issues. It is shown here that flipping maneuvers conducted with quadcopters are able to facilitate complete and gentle mixing. This capability incorporated during automated sample transport serves to address an important factor contributing to pre-analytical variability which ultimately impacts on test result reliability. Copyright © 2018 Elsevier Inc. All rights reserved.

Automated SEM and TEM sample preparation applied to copper/low k materials

NASA Astrophysics Data System (ADS)

Reyes, R.; Shaapur, F.; Griffiths, D.; Diebold, A. C.; Foran, B.; Raz, E.

2001-01-01

We describe the use of automated microcleaving for preparation of both SEM and TEM samples as done by SELA's new MC500 and TEMstation tools. The MC500 is an automated microcleaving tool that is capable of producing cleaves with 0.25 μm accuracy resulting in SEM-ready samples. The TEMstation is capable of taking a sample output from the MC500 (or from SELA's earlier MC200 tool) and producing a FIB ready slice of 25±5 μm, mounted on a TEM-washer and ready for FIB thinning to electron transparency for TEM analysis. The materials selected for the tool set evaluation mainly included the Cu/TaN/HOSP low-k system. The paper is divided into three sections, experimental approach, SEM preparation and analysis of HOSP low-k, and TEM preparation and analysis of Cu/TaN/HOSP low-k samples. For the samples discussed, data is presented to show the quality of preparation provided by these new automated tools.

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

Automated paleomagnetic and rock magnetic data acquisition with an in-line horizontal "2G" system

NASA Astrophysics Data System (ADS)

Mullender, Tom A. T.; Frederichs, Thomas; Hilgenfeldt, Christian; de Groot, Lennart V.; Fabian, Karl; Dekkers, Mark J.

2016-09-01

Today's paleomagnetic and magnetic proxy studies involve processing of large sample collections while simultaneously demanding high quality data and high reproducibility. Here we describe a fully automated interface based on a commercial horizontal pass-through "2G" DC-SQUID magnetometer. This system is operational at the universities of Bremen (Germany) and Utrecht (Netherlands) since 1998 and 2006, respectively, while a system is currently being built at NGU Trondheim (Norway). The magnetometers are equipped with "in-line" alternating field (AF) demagnetization, a direct-current bias field coil along the coaxial AF demagnetization coil for the acquisition of anhysteretic remanent magnetization (ARM) and a long pulse-field coil for the acquisition of isothermal remanent magnetization (IRM). Samples are contained in dedicated low magnetization perspex holders that are manipulated by a pneumatic pick-and-place-unit. Upon desire samples can be measured in several positions considerably enhancing data quality in particular for magnetically weak samples. In the Bremen system, the peak of the IRM pulse fields is actively measured which reduces the discrepancy between the set field and the field that is actually applied. Techniques for quantifying and removing gyroremanent overprints and for measuring the viscosity of IRM further extend the range of applications of the system. Typically c. 300 paleomagnetic samples can be AF demagnetized per week (15 levels) in the three-position protocol. The versatility of the system is illustrated by several examples of paleomagnetic and rock magnetic data processing.

Development of critical dimension measurement scanning electron microscope for ULSI (S-8000 series)

NASA Astrophysics Data System (ADS)

Ezumi, Makoto; Otaka, Tadashi; Mori, Hiroyoshi; Todokoro, Hideo; Ose, Yoichi

1996-05-01

The semiconductor industry is moving from half-micron to quarter-micron design rules. To support this evolution, Hitachi has developed a new critical dimension measurement scanning electron microscope (CD-SEM), the model S-8800 series, for quality control of quarter- micron process lines. The new CD-SEM provides detailed examination of process conditions with 5 nm resolution and 5 nm repeatability (3 sigma) at accelerating voltage 800 V using secondary electron imaging. In addition, a newly developed load-lock system has a capability of achieving a high sample throughput of 20 wafers/hour (5 point measurements per wafer) under continuous operation. To support user friendliness, the system incorporates a graphical user interface (GUI), an automated pattern recognition system which helps locating measurement points, both manual and semi-automated operation, and user-programmable operating parameters.

Automated processing of first-pass radioisotope ventriculography data to determine essential central circulation parameters

NASA Astrophysics Data System (ADS)

Krotov, Aleksei; Pankin, Victor

2017-09-01

The assessment of central circulation (including heart function) parameters is vital in the preventive diagnostics of inherent and acquired heart failures and during polychemotherapy. The protocols currently applied in Russia do not fully utilize the first-pass assessment (FPRNA) and that results in poor data formalization, while the FPRNA is the one of the fastest, affordable and compact methods among other radioisotope diagnostics protocols. A non-imaging algorithm basing on existing protocols has been designed to use the readings of an additional detector above vena subclavia to determine the total blood volume (TBV), not requiring blood sampling in contrast to current protocols. An automated processing of precordial detector readings is presented, in order to determine the heart strike volume (SV). Two techniques to estimate the ejection fraction (EF) of the heart are discussed.

Methods for the preparation and analysis of solids and suspended solids for total mercury

USGS Publications Warehouse

Olund, Shane D.; DeWild, John F.; Olson, Mark L.; Tate, Michael T.

2004-01-01

The methods documented in this report are utilized by the Wisconsin District Mercury Lab for analysis of total mercury in solids (soils and sediments) and suspended solids (isolated on filters). Separate procedures are required for the different sample types. For solids, samples are prepared by room-temperature acid digestion and oxidation with aqua regia. The samples are brought up to volume with a 5 percent bromine monochloride solution to ensure complete oxidation and heated at 50?C in an oven overnight. Samples are then analyzed with an automated flow injection system incorporating a cold vapor atomic fluorescence spectrometer. A method detection limit of 0.3 ng of mercury per digestion bomb was established using multiple analyses of an environmental sample. Based on the range of masses processed, the minimum sample reporting limit varies from 0.6 ng/g to 6 ng/g. Suspended solids samples are oxidized with a 5 percent bromine monochloride solution and held at 50?C in an oven for 5 days. The samples are then analyzed with an automated flow injection system incorporating a cold vapor atomic fluorescence spectrometer. Using a certified reference material as a surrogate for an environmental sample, a method detection limit of 0.059 ng of mercury per filter was established. The minimum sample reporting limit varies from 0.059 ng/L to 1.18 ng/L, depending on the volume of water filtered.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 performedmore » 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%.« less

Automated high-throughput purification of genomic DNA from plant leaf or seed using MagneSil paramagnetic particles

NASA Astrophysics Data System (ADS)

Bitner, Rex M.; Koller, Susan C.

2004-06-01

Three different methods of automated high throughput purification of genomic DNA from plant materials processed in 96 well plates are described. One method uses MagneSil paramagnetic particles to purify DNA present in single leaf punch samples or small seed samples, using 320ul capacity 96 well plates which minimizes reagent and plate costs. A second method uses 2.2 ml and 1.2 ml capacity plates and allows the purification of larger amounts of DNA from 5-6 punches of materials or larger amounts of seeds. The third method uses the MagneSil ONE purification system to purify a fixed amount of DNA, thus simplifying the processing of downstream applications by normalizing the amounts of DNA so they do not require quantitation. Protocols for the purification of a fixed yield of DNA, e.g. 1 ug, from plant leaf or seed samples using MagneSil paramagnetic particles and a Beckman-Coulter BioMek FX robot are described. DNA from all three methods is suitable for applications such as PCR, RAPD, STR, READIT SNP analysis, and multiplexed PCR systems. The MagneSil ONE system is also suitable for use with SNP detection systems such as Third Wave Technology"s Invader methods.

Identification of Giardia lamblia and the human infectious-species of Cryptosporidium in drinking water resources in Western Saudi Arabia by nested-PCR assays.

PubMed

Hawash, Y; Ghonaim, M; Hussein, Y; Alhazmi, A; Alturkistani, A

2015-06-01

The presence of Cryptosporidium and/or Giardia in drinking water represents a major public health problem. This study was the first report concerned with the occurrence of these protozoa in drinking water in Saudi Arabia. The study was undertaken in Al-Taif, a high altitude region, Western Saudi Arabia. Eight underground wells water, six desalinated water and five domestic brands of bottled water samples, 10 liter each, were monthly collected between May 2013 and April 2014. All samples (n = 228), were processed using an automated wash/elution station (IDEXX Laboratories, Inc.). Genomic DNA was directly isolated and purified from samples concentrates with QIAamp® Stool Mini Kit (Qiagen). The target protozoan DNA sequences were amplified using two previously published nested-PCR protocols. Of all the analyzed water, 31 samples (≈14%) were found contaminated with the target protozoa. Giardia lamblia was detected in ≈10% (7/72) of desalinated water and in ≈9% (9/96) of wells water. On the other hand, Cryptosporidium was identified in ≈8% (8/72) of desalinated water and in ≈7% (7/96) of wells water. All bottled water samples (n = 60) were (oo)cysts-free. Protozoan (oo)cysts were more frequently identified in water samples collected in the spring than in other seasons. The methodology established in our study proved sensitive, cost-effective and is amenable for future automation or semi-automation. For better understanding of the current situation that represent an important health threat to the local inhabitants, further studies concerned with (oo)cyst viability, infectivity, concentration and genotype identification are recommended.

Sample to answer visualization pipeline for low-cost point-of-care blood cell counting

NASA Astrophysics Data System (ADS)

Smith, Suzanne; Naidoo, Thegaran; Davies, Emlyn; Fourie, Louis; Nxumalo, Zandile; Swart, Hein; Marais, Philip; Land, Kevin; Roux, Pieter

2015-03-01

We present a visualization pipeline from sample to answer for point-of-care blood cell counting applications. Effective and low-cost point-of-care medical diagnostic tests provide developing countries and rural communities with accessible healthcare solutions [1], and can be particularly beneficial for blood cell count tests, which are often the starting point in the process of diagnosing a patient [2]. The initial focus of this work is on total white and red blood cell counts, using a microfluidic cartridge [3] for sample processing. Analysis of the processed samples has been implemented by means of two main optical visualization systems developed in-house: 1) a fluidic operation analysis system using high speed video data to determine volumes, mixing efficiency and flow rates, and 2) a microscopy analysis system to investigate homogeneity and concentration of blood cells. Fluidic parameters were derived from the optical flow [4] as well as color-based segmentation of the different fluids using a hue-saturation-value (HSV) color space. Cell count estimates were obtained using automated microscopy analysis and were compared to a widely accepted manual method for cell counting using a hemocytometer [5]. The results using the first iteration microfluidic device [3] showed that the most simple - and thus low-cost - approach for microfluidic component implementation was not adequate as compared to techniques based on manual cell counting principles. An improved microfluidic design has been developed to incorporate enhanced mixing and metering components, which together with this work provides the foundation on which to successfully implement automated, rapid and low-cost blood cell counting tests.

Flow through electrode with automated calibration

DOEpatents

Szecsody, James E [Richland, WA; Williams, Mark D [Richland, WA; Vermeul, Vince R [Richland, WA

2002-08-20

The present invention is an improved automated flow through electrode liquid monitoring system. The automated system has a sample inlet to a sample pump, a sample outlet from the sample pump to at least one flow through electrode with a waste port. At least one computer controls the sample pump and records data from the at least one flow through electrode for a liquid sample. The improvement relies upon (a) at least one source of a calibration sample connected to (b) an injection valve connected to said sample outlet and connected to said source, said injection valve further connected to said at least one flow through electrode, wherein said injection valve is controlled by said computer to select between said liquid sample or said calibration sample. Advantages include improved accuracy because of more frequent calibrations, no additional labor for calibration, no need to remove the flow through electrode(s), and minimal interruption of sampling.

Isolation of Mitochondrial DNA from Single, Short Hairs without Roots Using Pressure Cycling Technology.

PubMed

Harper, Kathryn A; Meiklejohn, Kelly A; Merritt, Richard T; Walker, Jessica; Fisher, Constance L; Robertson, James M

2018-02-01

Hairs are commonly submitted as evidence to forensic laboratories, but standard nuclear DNA analysis is not always possible. Mitochondria (mt) provide another source of genetic material; however, manual isolation is laborious. In a proof-of-concept study, we assessed pressure cycling technology (PCT; an automated approach that subjects samples to varying cycles of high and low pressure) for extracting mtDNA from single, short hairs without roots. Using three microscopically similar donors, we determined the ideal PCT conditions and compared those yields to those obtained using the traditional manual micro-tissue grinder method. Higher yields were recovered from grinder extracts, but yields from PCT extracts exceeded the requirements for forensic analysis, with the DNA quality confirmed through sequencing. Automated extraction of mtDNA from hairs without roots using PCT could be useful for forensic laboratories processing numerous samples.

Automated centrifugal-microfluidic platform for DNA purification using laser burst valve and coriolis effect.

PubMed

Choi, Min-Seong; Yoo, Jae-Chern

2015-04-01

We report a fully automated DNA purification platform with a micropored membrane in the channel utilizing centrifugal microfluidics on a lab-on-a-disc (LOD). The microfluidic flow in the LOD, into which the reagents are injected for DNA purification, is controlled by a single motor and laser burst valve. The sample and reagents pass successively through the micropored membrane in the channel when each laser burst valve is opened. The Coriolis effect is used by rotating the LOD bi-directionally to increase the purity of the DNA, thereby preventing the mixing of the waste and elution solutions. The total process from the lysed sample injection into the LOD to obtaining the purified DNA was finished within 7 min with only one manual step. The experimental result for Salmonella shows that the proposed microfluidic platform is comparable to the existing devices in terms of the purity and yield of DNA.

Automated fiber tracking and tissue characterization of the anterior cruciate ligament with optical coherence tomography

NASA Astrophysics Data System (ADS)

Balasubramanian, Priya S.; Guo, Jiaqi; Yao, Xinwen; Qu, Dovina; Lu, Helen H.; Hendon, Christine P.

2017-02-01

The directionality of collagen fibers across the anterior cruciate ligament (ACL) as well as the insertion of this key ligament into bone are important for understanding the mechanical integrity and functionality of this complex tissue. Quantitative analysis of three-dimensional fiber directionality is of particular interest due to the physiological, mechanical, and biological heterogeneity inherent across the ACL-to-bone junction, the behavior of the ligament under mechanical stress, and the usefulness of this information in designing tissue engineered grafts. We have developed an algorithm to characterize Optical Coherence Tomography (OCT) image volumes of the ACL. We present an automated algorithm for measuring ligamentous fiber angles, and extracting attenuation and backscattering coefficients of ligament, interface, and bone regions within mature and immature bovine ACL insertion samples. Future directions include translating this algorithm for real time processing to allow three-dimensional volumetric analysis within dynamically moving samples.

Microfluidic Exosome Analysis toward Liquid Biopsy for Cancer.

PubMed

He, Mei; Zeng, Yong

2016-08-01

Assessment of a tumor's molecular makeup using biofluid samples, known as liquid biopsy, is a prominent research topic in precision medicine for cancer, due to its noninvasive property allowing repeat sampling for monitoring molecular changes of tumors over time. Circulating exosomes recently have been recognized as promising tumor surrogates because they deliver enriched biomarkers, such as proteins, RNAs, and DNA. However, purification and characterization of these exosomes are technically challenging. Microfluidic lab-on-a-chip technology effectively addresses these challenges owing to its inherent advantages in integration and automation of multiple functional modules, enhancing sensing performance, and expediting analysis processes. In this article, we review the state-of-the-art development of microfluidic technologies for exosome isolation and molecular characterization with emphasis on their applications toward liquid biopsy-based analysis of cancer. Finally, we share our perspectives on current challenges and future directions of microfluidic exosome analysis. © 2016 Society for Laboratory Automation and Screening.

Benefits of an automated GLP final report preparation software solution.

PubMed

Elvebak, Larry E

2011-07-01

The final product of analytical laboratories performing US FDA-regulated (or GLP) method validation and bioanalysis studies is the final report. Although there are commercial-off-the-shelf (COTS) software/instrument systems available to laboratory managers to automate and manage almost every aspect of the instrumental and sample-handling processes of GLP studies, there are few software systems available to fully manage the GLP final report preparation process. This lack of appropriate COTS tools results in the implementation of rather Byzantine and manual processes to cobble together all the information needed to generate a GLP final report. The manual nature of these processes results in the need for several iterative quality control and quality assurance events to ensure data accuracy and report formatting. The industry is in need of a COTS solution that gives laboratory managers and study directors the ability to manage as many portions as possible of the GLP final report writing process and the ability to generate a GLP final report with the click of a button. This article describes the COTS software features needed to give laboratory managers and study directors such a solution.

A combination of HPLC and automated data analysis for monitoring the efficiency of high-pressure homogenization.

PubMed

Eggenreich, Britta; Rajamanickam, Vignesh; Wurm, David Johannes; Fricke, Jens; Herwig, Christoph; Spadiut, Oliver

2017-08-01

Cell disruption is a key unit operation to make valuable, intracellular target products accessible for further downstream unit operations. Independent of the applied cell disruption method, each cell disruption process must be evaluated with respect to disruption efficiency and potential product loss. Current state-of-the-art methods, like measuring the total amount of released protein and plating-out assays, are usually time-delayed and involve manual intervention making them error-prone. An automated method to monitor cell disruption efficiency at-line is not available to date. In the current study we implemented a methodology, which we had originally developed to monitor E. coli cell integrity during bioreactor cultivations, to automatically monitor and evaluate cell disruption of a recombinant E. coli strain by high-pressure homogenization. We compared our tool with a library of state-of-the-art methods, analyzed the effect of freezing the biomass before high-pressure homogenization and finally investigated this unit operation in more detail by a multivariate approach. A combination of HPLC and automated data analysis describes a valuable, novel tool to monitor and evaluate cell disruption processes. Our methodology, which can be used both in upstream (USP) and downstream processing (DSP), describes a valuable tool to evaluate cell disruption processes as it can be implemented at-line, gives results within minutes after sampling and does not need manual intervention.

Microfluidic cartridges for DNA purification and genotyping processed in standard laboratory instruments

NASA Astrophysics Data System (ADS)

Focke, Maximilian; Mark, Daniel; Stumpf, Fabian; Müller, Martina; Roth, Günter; Zengerle, Roland; von Stetten, Felix

2011-06-01

Two microfluidic cartridges intended for upgrading standard laboratory instruments with automated liquid handling capability by use of centrifugal forces are presented. The first microfluidic cartridge enables purification of DNA from human whole blood and is operated in a standard laboratory centrifuge. The second microfluidic catridge enables genotyping of pathogens by geometrically multiplexed real-time PCR. It is operated in a slightly modified off-the-shelf thermal cycler. Both solutions aim at smart and cost-efficient ways to automate work flows in laboratories. The DNA purification cartridge automates all liquid handling steps starting from a lysed blood sample to PCR ready DNA. The cartridge contains two manually crushable glass ampoules with liquid reagents. The DNA yield extracted from a 32 μl blood sample is 192 +/- 30 ng which corresponds to 53 +/- 8% of a reference extraction. The genotyping cartridge is applied to analyse isolates of the multi-resistant Staphyloccus aureus (MRSA) by real-time PCR. The wells contain pre-stored dry reagents such as primers and probes. Evaluation of the system with 44 genotyping assays showed a 100% specificity and agreement with the reference assays in standard tubes. The lower limit of detection was well below 10 copies of DNA per reaction.

Automated quantification of pancreatic β-cell mass

PubMed Central

Golson, Maria L.; Bush, William S.

2014-01-01

β-Cell mass is a parameter commonly measured in studies of islet biology and diabetes. However, the rigorous quantification of pancreatic β-cell mass using conventional histological methods is a time-consuming process. Rapidly evolving virtual slide technology with high-resolution slide scanners and newly developed image analysis tools has the potential to transform β-cell mass measurement. To test the effectiveness and accuracy of this new approach, we assessed pancreata from normal C57Bl/6J mice and from mouse models of β-cell ablation (streptozotocin-treated mice) and β-cell hyperplasia (leptin-deficient mice), using a standardized systematic sampling of pancreatic specimens. Our data indicate that automated analysis of virtual pancreatic slides is highly reliable and yields results consistent with those obtained by conventional morphometric analysis. This new methodology will allow investigators to dramatically reduce the time required for β-cell mass measurement by automating high-resolution image capture and analysis of entire pancreatic sections. PMID:24760991

Automated oil spill detection with multispectral imagery

NASA Astrophysics Data System (ADS)

Bradford, Brian N.; Sanchez-Reyes, Pedro J.

2011-06-01

In this publication we present an automated detection method for ocean surface oil, like that which existed in the Gulf of Mexico as a result of the April 20, 2010 Deepwater Horizon drilling rig explosion. Regions of surface oil in airborne imagery are isolated using red, green, and blue bands from multispectral data sets. The oil shape isolation procedure involves a series of image processing functions to draw out the visual phenomenological features of the surface oil. These functions include selective color band combinations, contrast enhancement and histogram warping. An image segmentation process then separates out contiguous regions of oil to provide a raster mask to an analyst. We automate the detection algorithm to allow large volumes of data to be processed in a short time period, which can provide timely oil coverage statistics to response crews. Geo-referenced and mosaicked data sets enable the largest identified oil regions to be mapped to exact geographic coordinates. In our simulation, multispectral imagery came from multiple sources including first-hand data collected from the Gulf. Results of the simulation show the oil spill coverage area as a raster mask, along with histogram statistics of the oil pixels. A rough square footage estimate of the coverage is reported if the image ground sample distance is available.

Automation of Space Processing Applications Shuttle payloads

NASA Technical Reports Server (NTRS)

Crosmer, W. E.; Neau, O. T.; Poe, J.

1975-01-01

The Space Processing Applications Program is examining the effect of weightlessness on key industrial materials processes, such as crystal growth, fine-grain casting of metals, and production of unique and ultra-pure glasses. Because of safety and in order to obtain optimum performance, some of these processes lend themselves to automation. Automation can increase the number of potential Space Shuttle flight opportunities and increase the overall productivity of the program. Five automated facility design concepts and overall payload combinations incorporating these facilities are presented.

AUTOMATED ANALYSIS OF AQUEOUS SAMPLES CONTAINING PESTICIDES, ACIDIC/BASIC/NEUTRAL SEMIVOLATILES AND VOLATILE ORGANIC COMPOUNDS BY SOLID PHASE EXTRACTION COUPLED IN-LINE TO LARGE VOLUME INJECTION GC/MS

EPA Science Inventory

Data is presented on the development of a new automated system combining solid phase extraction (SPE) with GC/MS spectrometry for the single-run analysis of water samples containing a broad range of organic compounds. The system uses commercially available automated in-line 10-m...

Comparison study of membrane filtration direct count and an automated coliform and Escherichia coli detection system for on-site water quality testing.

PubMed

Habash, Marc; Johns, Robert

2009-10-01

This study compared an automated Escherichia coli and coliform detection system with the membrane filtration direct count technique for water testing. The automated instrument performed equal to or better than the membrane filtration test in analyzing E. coli-spiked samples and blind samples with interference from Proteus vulgaris or Aeromonas hydrophila.

Development of a plan for automating integrated circuit processing

NASA Technical Reports Server (NTRS)

1971-01-01

The operations analysis and equipment evaluations pertinent to the design of an automated production facility capable of manufacturing beam-lead CMOS integrated circuits are reported. The overall plan shows approximate cost of major equipment, production rate and performance capability, flexibility, and special maintenance requirements. Direct computer control is compared with supervisory-mode operations. The plan is limited to wafer processing operations from the starting wafer to the finished beam-lead die after separation etching. The work already accomplished in implementing various automation schemes, and the type of equipment which can be found for instant automation are described. The plan is general, so that small shops or large production units can perhaps benefit. Examples of major types of automated processing machines are shown to illustrate the general concepts of automated wafer processing.

The Hyperspectral Imager for the Coastal Ocean (HICO): Sensor and Data Processing Overview

DTIC Science & Technology

2010-01-20

backscattering coefficients, and others. Several of these software modules will be developed within the Automated Processing System (APS), a data... Automated Processing System (APS) NRL developed APS, which processes satellite data into ocean color data products. APS is a collection of methods...used for ocean color processing which provide the tools for the automated processing of satellite imagery [1]. These tools are in the process of

10 CFR 1017.28 - Processing on Automated Information Systems (AIS).

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 4 2010-01-01 2010-01-01 false Processing on Automated Information Systems (AIS). 1017.28... UNCLASSIFIED CONTROLLED NUCLEAR INFORMATION Physical Protection Requirements § 1017.28 Processing on Automated Information Systems (AIS). UCNI may be processed or produced on any AIS that complies with the guidance in OMB...

The Upgrade Programme for the Structural Biology beamlines at the European Synchrotron Radiation Facility - High throughput sample evaluation and automation

NASA Astrophysics Data System (ADS)

Theveneau, P.; Baker, R.; Barrett, R.; Beteva, A.; Bowler, M. W.; Carpentier, P.; Caserotto, H.; de Sanctis, D.; Dobias, F.; Flot, D.; Guijarro, M.; Giraud, T.; Lentini, M.; Leonard, G. A.; Mattenet, M.; McCarthy, A. A.; McSweeney, S. M.; Morawe, C.; Nanao, M.; Nurizzo, D.; Ohlsson, S.; Pernot, P.; Popov, A. N.; Round, A.; Royant, A.; Schmid, W.; Snigirev, A.; Surr, J.; Mueller-Dieckmann, C.

2013-03-01

Automation and advances in technology are the key elements in addressing the steadily increasing complexity of Macromolecular Crystallography (MX) experiments. Much of this complexity is due to the inter-and intra-crystal heterogeneity in diffraction quality often observed for crystals of multi-component macromolecular assemblies or membrane proteins. Such heterogeneity makes high-throughput sample evaluation an important and necessary tool for increasing the chances of a successful structure determination. The introduction at the ESRF of automatic sample changers in 2005 dramatically increased the number of samples that were tested for diffraction quality. This "first generation" of automation, coupled with advances in software aimed at optimising data collection strategies in MX, resulted in a three-fold increase in the number of crystal structures elucidated per year using data collected at the ESRF. In addition, sample evaluation can be further complemented using small angle scattering experiments on the newly constructed bioSAXS facility on BM29 and the micro-spectroscopy facility (ID29S). The construction of a second generation of automated facilities on the MASSIF (Massively Automated Sample Screening Integrated Facility) beam lines will build on these advances and should provide a paradigm shift in how MX experiments are carried out which will benefit the entire Structural Biology community.

Automatic instrument for chemical processing to detect microorganism in biological samples by measuring light reactions

NASA Technical Reports Server (NTRS)

Kelbaugh, B. N.; Picciolo, G. L.; Chappelle, E. W.; Colburn, M. E. (Inventor)

1973-01-01

An automated apparatus is reported for sequentially assaying urine samples for the presence of bacterial adenosine triphosphate (ATP) that comprises a rotary table which carries a plurality of sample containing vials and automatically dispenses fluid reagents into the vials preparatory to injecting a light producing luciferase-luciferin mixture into the samples. The device automatically measures the light produced in each urine sample by a bioluminescence reaction of the free bacterial adenosine triphosphate with the luciferase-luciferin mixture. The light measured is proportional to the concentration of bacterial adenosine triphosphate which, in turn, is proportional to the number of bacteria present in the respective urine sample.

Fission gas bubble identification using MATLAB's image processing toolbox

DOE Office of Scientific and Technical Information (OSTI.GOV)

Collette, R.

Automated image processing routines have the potential to aid in the fuel performance evaluation process by eliminating bias in human judgment that may vary from person-to-person or sample-to-sample. This study presents several MATLAB based image analysis routines designed for fission gas void identification in post-irradiation examination of uranium molybdenum (U–Mo) monolithic-type plate fuels. Frequency domain filtration, enlisted as a pre-processing technique, can eliminate artifacts from the image without compromising the critical features of interest. This process is coupled with a bilateral filter, an edge-preserving noise removal technique aimed at preparing the image for optimal segmentation. Adaptive thresholding proved to bemore » the most consistent gray-level feature segmentation technique for U–Mo fuel microstructures. The Sauvola adaptive threshold technique segments the image based on histogram weighting factors in stable contrast regions and local statistics in variable contrast regions. Once all processing is complete, the algorithm outputs the total fission gas void count, the mean void size, and the average porosity. The final results demonstrate an ability to extract fission gas void morphological data faster, more consistently, and at least as accurately as manual segmentation methods. - Highlights: •Automated image processing can aid in the fuel qualification process. •Routines are developed to characterize fission gas bubbles in irradiated U–Mo fuel. •Frequency domain filtration effectively eliminates FIB curtaining artifacts. •Adaptive thresholding proved to be the most accurate segmentation method. •The techniques established are ready to be applied to large scale data extraction testing.« less

An Automated Energy Detection Algorithm Based on Morphological Filter Processing with a Modified Watershed Transform

DTIC Science & Technology

2018-01-01

ARL-TR-8270 ● JAN 2018 US Army Research Laboratory An Automated Energy Detection Algorithm Based on Morphological Filter...Automated Energy Detection Algorithm Based on Morphological Filter Processing with a Modified Watershed Transform by Kwok F Tom Sensors and Electron...1 October 2016–30 September 2017 4. TITLE AND SUBTITLE An Automated Energy Detection Algorithm Based on Morphological Filter Processing with a

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.

Turbidity-controlled sampling for suspended sediment load estimation

Treesearch

Jack Lewis

2003-01-01

Abstract - Automated data collection is essential to effectively measure suspended sediment loads in storm events, particularly in small basins. Continuous turbidity measurements can be used, along with discharge, in an automated system that makes real-time sampling decisions to facilitate sediment load estimation. The Turbidity Threshold Sampling method distributes...

Microgravity

NASA Image and Video Library

1992-03-12

The Advanced Automated Directional Solidification Furnace (AADSF) with the Experimental Apparatus Container (EAC) removed flew during the USMP-2 mission. During USMP-2, the AADSF was used to study the growth of mercury cadmium telluride crystals in microgravity by directional solidification, a process commonly used on earth to process metals and grow crystals. The furnace is tubular and has three independently controlled temperature zones . The sample travels from the hot zone of the furnace (1600 degrees F) where the material solidifies as it cools. The solidification region, known as the solid/liquid interface, moves from one end of the sample to the other at a controlled rate, thus the term directional solidification.

[DNA Extraction from Old Bones by AutoMate Express™ System].

PubMed

Li, B; Lü, Z

2017-08-01

To establish a method for extracting DNA from old bones by AutoMate Express™ system. Bones were grinded into powder by freeze-mill. After extraction by AutoMate Express™, DNA were amplified and genotyped by Identifiler®Plus and MinFiler™ kits. DNA were extracted from 10 old bone samples, which kept in different environments with the postmortem interval from 10 to 20 years, in 3 hours by AutoMate Express™ system. Complete STR typing results were obtained from 8 samples. AutoMate Express™ system can quickly and efficiently extract DNA from old bones, which can be applied in forensic practice. Copyright© by the Editorial Department of Journal of Forensic Medicine

New possibilities of complex "Thermodyn" application for contactless remote diagnostics in medical practice

NASA Astrophysics Data System (ADS)

Belov, M. Ye.; Shayko-Shaykovskiy, O. G.; Makhrova, Ye. G.; Kramar, V. M.; Oleksuik, I. S.

2018-01-01

We represent here the theoretical justifications, block scheme and experimental sample of a new automated complex "Thermodyn" for remote contactless diagnostics of inflammatory processes of the surfaces and in subcutaneous areas of human body. Also we described here the methods and results of diagnostic measurements, and results of practical applications of this complex.

Automated wavelet denoising of photoacoustic signals for circulating melanoma cell detection and burn image reconstruction.

PubMed

Holan, Scott H; Viator, John A

2008-06-21

Photoacoustic image reconstruction may involve hundreds of point measurements, each of which contributes unique information about the subsurface absorbing structures under study. For backprojection imaging, two or more point measurements of photoacoustic waves induced by irradiating a biological sample with laser light are used to produce an image of the acoustic source. Each of these measurements must undergo some signal processing, such as denoising or system deconvolution. In order to process the numerous signals, we have developed an automated wavelet algorithm for denoising signals. We appeal to the discrete wavelet transform for denoising photoacoustic signals generated in a dilute melanoma cell suspension and in thermally coagulated blood. We used 5, 9, 45 and 270 melanoma cells in the laser beam path as test concentrations. For the burn phantom, we used coagulated blood in 1.6 mm silicon tube submerged in Intralipid. Although these two targets were chosen as typical applications for photoacoustic detection and imaging, they are of independent interest. The denoising employs level-independent universal thresholding. In order to accommodate nonradix-2 signals, we considered a maximal overlap discrete wavelet transform (MODWT). For the lower melanoma cell concentrations, as the signal-to-noise ratio approached 1, denoising allowed better peak finding. For coagulated blood, the signals were denoised to yield a clean photoacoustic resulting in an improvement of 22% in the reconstructed image. The entire signal processing technique was automated so that minimal user intervention was needed to reconstruct the images. Such an algorithm may be used for image reconstruction and signal extraction for applications such as burn depth imaging, depth profiling of vascular lesions in skin and the detection of single cancer cells in blood samples.

Performance of a Novel Algorithm Using Automated Digital Microscopy for Diagnosing Tuberculosis.

PubMed

Ismail, Nazir A; Omar, Shaheed V; Lewis, James J; Dowdy, David W; Dreyer, Andries W; van der Meulen, Hermina; Nconjana, George; Clark, David A; Churchyard, Gavin J

2015-06-15

TBDx automated microscopy is a novel technology that processes digital microscopic images to identify acid-fast bacilli (AFB). Use of TBDx as part of a diagnostic algorithm could improve the diagnosis of tuberculosis (TB), but its performance characteristics have not yet been formally tested. To evaluate the performance of the TBDx automated microscopy system in algorithms for diagnosis of TB. Prospective samples from patients with presumed TB were processed in parallel with conventional smear microscopy, TBDx microscopy, and liquid culture. All TBDx-positive specimens were also tested with the Xpert MTB/RIF (GXP) assay. We evaluated the sensitivity and specificity of two algorithms-(1) TBDx-GXP (TBDx with positive specimens tested by Xpert MTB/RIF) and (2) TBDx alone-against the gold standard liquid media culture. Of 1,210 samples, 1,009 were eligible for evaluation, of which 109 were culture positive for Mycobacterium tuberculosis. The TBDx system identified 70 specimens (68 culture positive) as having 10 or more putative AFB (high positive) and 207 (19 culture positive) as having 1-9 putative AFB (low positive). An algorithm in which "low-positive" results on TBDx were confirmed by GXP had 78% sensitivity (85 of 109) and 99.8% specificity (889 of 900), requiring 21% (207 of 1,009) specimens to be processed by GXP. As a stand-alone test, a "high-positive" result on TBDx had 62% sensitivity and 99.7% specificity. TBDx used in diagnostic algorithms with GXP provided reasonable sensitivity and high specificity for active TB while dramatically reducing the number GXP tests performed. As a stand-alone microscopy system, its performance was equivalent to that of a highly experienced TB microscopist.

Fully automated determination of nicotine and its major metabolites in whole blood by means of a DBS online-SPE LC-HR-MS/MS approach for sports drug testing.

PubMed

Tretzel, Laura; Thomas, Andreas; Piper, Thomas; Hedeland, Mikael; Geyer, Hans; Schänzer, Wilhelm; Thevis, Mario

2016-05-10

Dried blood spots (DBS) represent a sample matrix collected under minimal-invasive, straightforward and robust conditions. DBS specimens have been shown to provide appropriate test material for different analytical disciplines, e.g., preclinical drug development, therapeutic drug monitoring, forensic toxicology and diagnostic analysis of metabolic disorders in newborns. However, the sample preparation has occasionally been reported as laborious and time consuming. In order to minimize the manual workload and to substantiate the suitability of DBS for high sample-throughput, the automation of sample preparation processes is of paramount interest. In the current study, the development and validation of a fully automated DBS extraction method coupled to online solid-phase extraction using the example of nicotine, its major metabolites nornicotine, cotinine and trans-3'-hydroxycotinine and the tobacco alkaloids anabasine and anatabine is presented, based on the rationale that the use of nicotine-containing products for performance-enhancing purposes has been monitored by the World Anti-Doping Agency (WADA) for several years. Automation-derived DBS sample extracts were directed online to liquid chromatography high resolution/high mass accuracy tandem mass spectrometry, and target analytes were determined with support of four deuterated internal standards. Validation of the method yielded precise (CV <7.5% for intraday and <12.3% for interday measurements) and linear (r(2)>0.998) results. The limit of detection was established at 5 ng mL(-1) for all studied compounds, the extraction recovery ranged from 25 to 44%, and no matrix effects were observed. To exemplify the applicability of the DBS online-SPE LC-MS/MS approach for sports drug testing purposes, the method was applied to authentic DBS samples obtained from smokers, snus users, and e-cigarette users. Statistical evaluation of the obtained results indicated differences in metabolic behavior depending on the route of administration (inhalative versus buccal absorption) in terms of the ratio of nicotine and nornicotine. Copyright © 2016 Elsevier B.V. All rights reserved.

Semi-Automated Processing of Trajectory Simulator Output Files for Model Evaluation

DTIC Science & Technology

2018-01-01

ARL-TR-8284 ● JAN 2018 US Army Research Laboratory Semi-Automated Processing of Trajectory Simulator Output Files for Model......Do not return it to the originator. ARL-TR-8284 ● JAN 2018 US Army Research Laboratory Semi-Automated Processing of Trajectory

metAlignID: a high-throughput software tool set for automated detection of trace level contaminants in comprehensive LECO two-dimensional gas chromatography time-of-flight mass spectrometry data.

PubMed

Lommen, Arjen; van der Kamp, Henk J; Kools, Harrie J; van der Lee, Martijn K; van der Weg, Guido; Mol, Hans G J

2012-11-09

A new alternative data processing tool set, metAlignID, is developed for automated pre-processing and library-based identification and concentration estimation of target compounds after analysis by comprehensive two-dimensional gas chromatography with mass spectrometric detection. The tool set has been developed for and tested on LECO data. The software is developed to run multi-threaded (one thread per processor core) on a standard PC (personal computer) under different operating systems and is as such capable of processing multiple data sets simultaneously. Raw data files are converted into netCDF (network Common Data Form) format using a fast conversion tool. They are then preprocessed using previously developed algorithms originating from metAlign software. Next, the resulting reduced data files are searched against a user-composed library (derived from user or commercial NIST-compatible libraries) (NIST=National Institute of Standards and Technology) and the identified compounds, including an indicative concentration, are reported in Excel format. Data can be processed batch wise. The overall time needed for conversion together with processing and searching of 30 raw data sets for 560 compounds is routinely within an hour. The screening performance is evaluated for detection of pesticides and contaminants in raw data obtained after analysis of soil and plant samples. Results are compared to the existing data-handling routine based on proprietary software (LECO, ChromaTOF). The developed software tool set, which is freely downloadable at www.metalign.nl, greatly accelerates data-analysis and offers more options for fine-tuning automated identification toward specific application needs. The quality of the results obtained is slightly better than the standard processing and also adds a quantitative estimate. The software tool set in combination with two-dimensional gas chromatography coupled to time-of-flight mass spectrometry shows great potential as a highly-automated and fast multi-residue instrumental screening method. Copyright © 2012 Elsevier B.V. All rights reserved.

Martian oxidation processes and selection of ancient sedimentary samples for bio-organic analysis

NASA Technical Reports Server (NTRS)

Oro, J.

1988-01-01

The results obtained by the Viking Missions concerning organic and biological analysis are summarized and it is indicated that these results do not preclude the existence in buried or protected regions of the planet, organic molecules or fossil life. The use of automated instruments is suggested for the analyses of samples obtained from certain regions of the planet, as a preliminary step before they are selected, retrieved, and returned to Earth for more complete analysis.

Automation in biological crystallization.

PubMed

Stewart, Patrick Shaw; Mueller-Dieckmann, Jochen

2014-06-01

Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given.

Automation in biological crystallization

PubMed Central

Shaw Stewart, Patrick; Mueller-Dieckmann, Jochen

2014-01-01

Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given. PMID:24915074

Reproducibility of myelin content-based human habenula segmentation at 3 Tesla.

PubMed

Kim, Joo-Won; Naidich, Thomas P; Joseph, Joshmi; Nair, Divya; Glasser, Matthew F; O'halloran, Rafael; Doucet, Gaelle E; Lee, Won Hee; Krinsky, Hannah; Paulino, Alejandro; Glahn, David C; Anticevic, Alan; Frangou, Sophia; Xu, Junqian

2018-03-26

In vivo morphological study of the human habenula, a pair of small epithalamic nuclei adjacent to the dorsomedial thalamus, has recently gained significant interest for its role in reward and aversion processing. However, segmenting the habenula from in vivo magnetic resonance imaging (MRI) is challenging due to the habenula's small size and low anatomical contrast. Although manual and semi-automated habenula segmentation methods have been reported, the test-retest reproducibility of the segmented habenula volume and the consistency of the boundaries of habenula segmentation have not been investigated. In this study, we evaluated the intra- and inter-site reproducibility of in vivo human habenula segmentation from 3T MRI (0.7-0.8 mm isotropic resolution) using our previously proposed semi-automated myelin contrast-based method and its fully-automated version, as well as a previously published manual geometry-based method. The habenula segmentation using our semi-automated method showed consistent boundary definition (high Dice coefficient, low mean distance, and moderate Hausdorff distance) and reproducible volume measurement (low coefficient of variation). Furthermore, the habenula boundary in our semi-automated segmentation from 3T MRI agreed well with that in the manual segmentation from 7T MRI (0.5 mm isotropic resolution) of the same subjects. Overall, our proposed semi-automated habenula segmentation showed reliable and reproducible habenula localization, while its fully-automated version offers an efficient way for large sample analysis. © 2018 Wiley Periodicals, Inc.

Novel Automated Blood Separations Validate Whole Cell Biomarkers

PubMed Central

Burger, Douglas E.; Wang, Limei; Ban, Liqin; Okubo, Yoshiaki; Kühtreiber, Willem M.; Leichliter, Ashley K.; Faustman, Denise L.

2011-01-01

Background Progress in clinical trials in infectious disease, autoimmunity, and cancer is stymied by a dearth of successful whole cell biomarkers for peripheral blood lymphocytes (PBLs). Successful biomarkers could help to track drug effects at early time points in clinical trials to prevent costly trial failures late in development. One major obstacle is the inaccuracy of Ficoll density centrifugation, the decades-old method of separating PBLs from the abundant red blood cells (RBCs) of fresh blood samples. Methods and Findings To replace the Ficoll method, we developed and studied a novel blood-based magnetic separation method. The magnetic method strikingly surpassed Ficoll in viability, purity and yield of PBLs. To reduce labor, we developed an automated platform and compared two magnet configurations for cell separations. These more accurate and labor-saving magnet configurations allowed the lymphocytes to be tested in bioassays for rare antigen-specific T cells. The automated method succeeded at identifying 79% of patients with the rare PBLs of interest as compared with Ficoll's uniform failure. We validated improved upfront blood processing and show accurate detection of rare antigen-specific lymphocytes. Conclusions Improving, automating and standardizing lymphocyte detections from whole blood may facilitate development of new cell-based biomarkers for human diseases. Improved upfront blood processes may lead to broad improvements in monitoring early trial outcome measurements in human clinical trials. PMID:21799852

Materials for Heated Head Automated Thermoplastic Tape Placement

NASA Technical Reports Server (NTRS)

Jensen, Brian J.; Kinney, Megan C.; Cano, Roberto J.; Grimsley, Brian W.

2012-01-01

NASA Langley Research Center (LaRC) is currently pursuing multiple paths to develop out of autoclave (OOA) polymeric composite materials and processes. Polymeric composite materials development includes the synthesis of new and/or modified thermosetting and thermoplastic matrix resins designed for specific OOA processes. OOA processes currently under investigation include vacuum bag only (VBO) prepreg/composite fabrication, resin transfer molding (RTM), vacuum assisted resin transfer molding (VARTM) and heated head automated thermoplastic tape placement (HHATP). This paper will discuss the NASA Langley HHATP facility and capabilities and recent work on characterizing thermoplastic tape quality and requirements for quality part production. Samples of three distinct versions of APC-2 (AS4/PEEK) thermoplastic dry tape were obtained from two materials vendors, TENCATE, Inc. and CYTEC Engineered Materials** (standard grade and an experimental batch). Random specimens were taken from each of these samples and subjected to photo-microscopy and surface profilometry. The CYTEC standard grade of APC-2 tape had the most voids and splits and the highest surface roughness and/or waviness. Since the APC-2 tape is composed of a thermoplastic matrix, it offers the flexibility of reprocessing to improve quality, and thereby improve final quality of HHATP laminates. Discussions will also include potential research areas and future work that is required to advance the state of the art in the HHATP process for composite fabrication.

Short-Term Storage of Platelet-Rich Plasma at Room Temperature Does Not Affect Growth Factor or Catabolic Cytokine Concentration.

PubMed

Wilson, Brooke H; Cole, Brian J; Goodale, Margaret B; Fortier, Lisa A

2018-04-01

The aim of this study was to provide clinical recommendations about the use of platelet-rich plasma (PRP) that was subjected to short-term storage at room temperature. We determined bioactive growth factor and cytokine concentrations as indicators of platelet and white blood cell degranulation in blood and PRP. Additionally, this study sought to validate the use of manual, direct smear analysis as an alternative to automated methods for platelet quantification in PRP. Blood was used to generate low-leukocyte PRP (Llo PRP) or high-leukocyte PRP (Lhi PRP). Blood was either processed immediately or kept at room temperature for 2 or 4 hours prior to generation of PRP, which was then held at room temperature for 0, 1, 2, or 4 hours. Subsequently, bioactive transforming growth factor beta-1 and matrix metalloproteinase-9 were measured by ELISA (enzyme-linked immunosorbent assay). Manual and automated platelet counts were performed on all blood and PRP samples. There were no differences in growth factor or cytokine concentration when blood or Llo PRP or Lhi PRP was retained at room temperature for up to 4 hours. Manual, direct smear analysis for platelet quantification was not different from the use of automated machine counting for PRP samples, but in the starting blood samples, manual platelet counts were significantly higher than those generated using automated technology. When there is a delay of up to 4 hours in the generation of PRP from blood or in the application of PRP to the patient, bioactive growth factor and cytokine concentrations remain stable in both blood and PRP. A manual direct counting method is a simple, cost-effective, and valid method to measure the contents of the PRP product being delivered to the patient.

An Intelligent Automation Platform for Rapid Bioprocess Design.

PubMed

Wu, Tianyi; Zhou, Yuhong

2014-08-01

Bioprocess development is very labor intensive, requiring many experiments to characterize each unit operation in the process sequence to achieve product safety and process efficiency. Recent advances in microscale biochemical engineering have led to automated experimentation. A process design workflow is implemented sequentially in which (1) a liquid-handling system performs high-throughput wet lab experiments, (2) standalone analysis devices detect the data, and (3) specific software is used for data analysis and experiment design given the user's inputs. We report an intelligent automation platform that integrates these three activities to enhance the efficiency of such a workflow. A multiagent intelligent architecture has been developed incorporating agent communication to perform the tasks automatically. The key contribution of this work is the automation of data analysis and experiment design and also the ability to generate scripts to run the experiments automatically, allowing the elimination of human involvement. A first-generation prototype has been established and demonstrated through lysozyme precipitation process design. All procedures in the case study have been fully automated through an intelligent automation platform. The realization of automated data analysis and experiment design, and automated script programming for experimental procedures has the potential to increase lab productivity. © 2013 Society for Laboratory Automation and Screening.

Automated Student Aid Processing: The Challenge and Opportunity.

ERIC Educational Resources Information Center

St. John, Edward P.

1985-01-01

To utilize automated technology for student aid processing, it is necessary to work with multi-institutional offices (student aid, admissions, registration, and business) and to develop automated interfaces with external processing systems at state and federal agencies and perhaps at need-analysis organizations and lenders. (MLW)

Acoustic Sample Deposition MALDI-MS (ASD-MALDI-MS): A Novel Process Flow for Quality Control Screening of Compound Libraries.

PubMed

Chin, Jefferson; Wood, Elizabeth; Peters, Grace S; Drexler, Dieter M

2016-02-01

In the early stages of drug discovery, high-throughput screening (HTS) of compound libraries against pharmaceutical targets is a common method to identify potential lead molecules. For these HTS campaigns to be efficient and successful, continuous quality control of the compound collection is necessary and crucial. However, the large number of compound samples and the limited sample amount pose unique challenges. Presented here is a proof-of-concept study for a novel process flow for the quality control screening of small-molecule compound libraries that consumes only minimal amounts of samples and affords compound-specific molecular data. This process employs an acoustic sample deposition (ASD) technique for the offline sample preparation by depositing nanoliter volumes in an array format onto microscope glass slides followed by matrix-assisted laser desorption/ionization mass spectrometric (MALDI-MS) analysis. An initial study of a 384-compound array employing the ASD-MALDI-MS workflow resulted in a 75% first-pass positive identification rate with an analysis time of <1 s per sample. © 2015 Society for Laboratory Automation and Screening.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hiraki, Masahiko; Watanabe, Shokei; Yamada, Yusuke

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 ofmore » 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.« less

QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization.

PubMed

Zhao, Shanrong; Xi, Li; Quan, Jie; Xi, Hualin; Zhang, Ying; von Schack, David; Vincent, Michael; Zhang, Baohong

2016-01-08

RNA sequencing (RNA-seq), a next-generation sequencing technique for transcriptome profiling, is being increasingly used, in part driven by the decreasing cost of sequencing. Nevertheless, the analysis of the massive amounts of data generated by large-scale RNA-seq remains a challenge. Multiple algorithms pertinent to basic analyses have been developed, and there is an increasing need to automate the use of these tools so as to obtain results in an efficient and user friendly manner. Increased automation and improved visualization of the results will help make the results and findings of the analyses readily available to experimental scientists. By combing the best open source tools developed for RNA-seq data analyses and the most advanced web 2.0 technologies, we have implemented QuickRNASeq, a pipeline for large-scale RNA-seq data analyses and visualization. The QuickRNASeq workflow consists of three main steps. In Step #1, each individual sample is processed, including mapping RNA-seq reads to a reference genome, counting the numbers of mapped reads, quality control of the aligned reads, and SNP (single nucleotide polymorphism) calling. Step #1 is computationally intensive, and can be processed in parallel. In Step #2, the results from individual samples are merged, and an integrated and interactive project report is generated. All analyses results in the report are accessible via a single HTML entry webpage. Step #3 is the data interpretation and presentation step. The rich visualization features implemented here allow end users to interactively explore the results of RNA-seq data analyses, and to gain more insights into RNA-seq datasets. In addition, we used a real world dataset to demonstrate the simplicity and efficiency of QuickRNASeq in RNA-seq data analyses and interactive visualizations. The seamless integration of automated capabilites with interactive visualizations in QuickRNASeq is not available in other published RNA-seq pipelines. The high degree of automation and interactivity in QuickRNASeq leads to a substantial reduction in the time and effort required prior to further downstream analyses and interpretation of the analyses findings. QuickRNASeq advances primary RNA-seq data analyses to the next level of automation, and is mature for public release and adoption.

Coniferous forest classification and inventory using Landsat and digital terrain data

NASA Technical Reports Server (NTRS)

Franklin, J.; Logan, T. L.; Woodcock, C. E.; Strahler, A. H.

1986-01-01

Machine-processing techniques were used in a Forest Classification and Inventory System (FOCIS) procedure to extract and process tonal, textural, and terrain information from registered Landsat multispectral and digital terrain data. Using FOCIS as a basis for stratified sampling, the softwood timber volumes of the Klamath National Forest and Eldorado National Forest were estimated within standard errors of 4.8 and 4.0 percent, respectively. The accuracy of these large-area inventories is comparable to the accuracy yielded by use of conventional timber inventory methods, but, because of automation, the FOCIS inventories are more rapid (9-12 months compared to 2-3 years for conventional manual photointerpretation, map compilation and drafting, field sampling, and data processing) and are less costly.

Atmosphere Processing Module Automation and Catalyst Durability Analysis for Mars ISRU Pathfinder

NASA Technical Reports Server (NTRS)

Petersen, Elspeth M.

2016-01-01

The Mars In-Situ Resource Utilization Pathfinder was designed to create fuel using components found in the planet’s atmosphere and regolith for an ascension vehicle to return a potential sample return or crew return vehicle from Mars. The Atmosphere Processing Module (APM), a subunit of the pathfinder, uses cryocoolers to isolate and collect carbon dioxide from Mars simulant gas. The carbon dioxide is fed with hydrogen into a Sabatier reactor where methane is produced. The APM is currently undergoing the final stages of testing at Kennedy Space Center prior to process integration testing with the other subunits of the pathfinder. The automation software for the APM cryocoolers was tested and found to perform nominally. The catalyst used for the Sabatier reactor was investigated to determine the factors contributing to catalyst failure. The results from the catalyst testing require further analysis, but it appears that the rapid change in temperature during reactor start up or the elevated operating temperature is responsible for the changes observed in the catalyst.

Evaluation of mouse red blood cell and platelet counting with an automated hematology analyzer.

PubMed

Fukuda, Teruko; Asou, Eri; Nogi, Kimiko; Goto, Kazuo

2017-10-07

An evaluation of mouse red blood cell (RBC) and platelet (PLT) counting with an automated hematology analyzer was performed with three strains of mice, C57BL/6 (B6), BALB/c (BALB) and DBA/2 (D2). There were no significant differences in RBC and PLT counts between manual and automated optical methods in any of the samples, except for D2 mice. For D2, RBC counts obtained using the manual method were significantly lower than those obtained using the automated optical method (P<0.05), and PLT counts obtained using the manual method were higher than those obtained using the automated optical method (P<0.05). An automated hematology analyzer can be used for RBC and PLT counting; however, an appropriate method should be selected when D2 mice samples are used.

An automated atmospheric sampling system operating on 747 airliners

NASA Technical Reports Server (NTRS)

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

1976-01-01

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

A methodology to determine the level of automation to improve the production process and reduce the ergonomics index

NASA Astrophysics Data System (ADS)

Chan-Amaya, Alejandro; Anaya-Pérez, María Elena; Benítez-Baltazar, Víctor Hugo

2017-08-01

Companies are constantly looking for improvements in productivity to increase their competitiveness. The use of automation technologies is a tool that have been proven to be effective to achieve this. There are companies that are not familiar with the process to acquire automation technologies, therefore, they abstain from investments and thereby miss the opportunity to take advantage of it. The present document proposes a methodology to determine the level of automation appropriate for the production process and thus minimize automation and improve production taking in consideration the ergonomics factor.

Rapid-Viability PCR Method for Detection of Live, Virulent Bacillus anthracis in Environmental Samples ▿

PubMed Central

Létant, Sonia E.; Murphy, Gloria A.; Alfaro, Teneile M.; Avila, Julie R.; Kane, Staci R.; Raber, Ellen; Bunt, Thomas M.; Shah, Sanjiv R.

2011-01-01

In the event of a biothreat agent release, hundreds of samples would need to be rapidly processed to characterize the extent of contamination and determine the efficacy of remediation activities. Current biological agent identification and viability determination methods are both labor- and time-intensive such that turnaround time for confirmed results is typically several days. In order to alleviate this issue, automated, high-throughput sample processing methods were developed in which real-time PCR analysis is conducted on samples before and after incubation. The method, referred to as rapid-viability (RV)-PCR, uses the change in cycle threshold after incubation to detect the presence of live organisms. In this article, we report a novel RV-PCR method for detection of live, virulent Bacillus anthracis, in which the incubation time was reduced from 14 h to 9 h, bringing the total turnaround time for results below 15 h. The method incorporates a magnetic bead-based DNA extraction and purification step prior to PCR analysis, as well as specific real-time PCR assays for the B. anthracis chromosome and pXO1 and pXO2 plasmids. A single laboratory verification of the optimized method applied to the detection of virulent B. anthracis in environmental samples was conducted and showed a detection level of 10 to 99 CFU/sample with both manual and automated RV-PCR methods in the presence of various challenges. Experiments exploring the relationship between the incubation time and the limit of detection suggest that the method could be further shortened by an additional 2 to 3 h for relatively clean samples. PMID:21764960

An on-line potentiometric sequential injection titration process analyser for the determination of acetic acid.

PubMed

van Staden, J F; Mashamba, Mulalo G; Stefan, Raluca I

2002-09-01

An on-line potentiometric sequential injection titration process analyser for the determination of acetic acid is proposed. A solution of 0.1 mol L(-1) sodium chloride is used as carrier. Titration is achieved by aspirating acetic acid samples between two strong base-zone volumes into a holding coil and by channelling the stack of well-defined zones with flow reversal through a reaction coil to a potentiometric sensor where the peak widths were measured. A linear relationship between peak width and logarithm of the acid concentration was obtained in the range 1-9 g/100 mL. Vinegar samples were analysed without any sample pre-treatment. The method has a relative standard deviation of 0.4% with a sample frequency of 28 samples per hour. The results revealed good agreement between the proposed sequential injection and an automated batch titration method.

An Energy Efficient Adaptive Sampling Algorithm in a Sensor Network for Automated Water Quality Monitoring.

PubMed

Shu, Tongxin; Xia, Min; Chen, Jiahong; Silva, Clarence de

2017-11-05

Power management is crucial in the monitoring of a remote environment, especially when long-term monitoring is needed. Renewable energy sources such as solar and wind may be harvested to sustain a monitoring system. However, without proper power management, equipment within the monitoring system may become nonfunctional and, as a consequence, the data or events captured during the monitoring process will become inaccurate as well. This paper develops and applies a novel adaptive sampling algorithm for power management in the automated monitoring of the quality of water in an extensive and remote aquatic environment. Based on the data collected on line using sensor nodes, a data-driven adaptive sampling algorithm (DDASA) is developed for improving the power efficiency while ensuring the accuracy of sampled data. The developed algorithm is evaluated using two distinct key parameters, which are dissolved oxygen (DO) and turbidity. It is found that by dynamically changing the sampling frequency, the battery lifetime can be effectively prolonged while maintaining a required level of sampling accuracy. According to the simulation results, compared to a fixed sampling rate, approximately 30.66% of the battery energy can be saved for three months of continuous water quality monitoring. Using the same dataset to compare with a traditional adaptive sampling algorithm (ASA), while achieving around the same Normalized Mean Error (NME), DDASA is superior in saving 5.31% more battery energy.

An Energy Efficient Adaptive Sampling Algorithm in a Sensor Network for Automated Water Quality Monitoring

PubMed Central

Shu, Tongxin; Xia, Min; Chen, Jiahong; de Silva, Clarence

2017-01-01

Power management is crucial in the monitoring of a remote environment, especially when long-term monitoring is needed. Renewable energy sources such as solar and wind may be harvested to sustain a monitoring system. However, without proper power management, equipment within the monitoring system may become nonfunctional and, as a consequence, the data or events captured during the monitoring process will become inaccurate as well. This paper develops and applies a novel adaptive sampling algorithm for power management in the automated monitoring of the quality of water in an extensive and remote aquatic environment. Based on the data collected on line using sensor nodes, a data-driven adaptive sampling algorithm (DDASA) is developed for improving the power efficiency while ensuring the accuracy of sampled data. The developed algorithm is evaluated using two distinct key parameters, which are dissolved oxygen (DO) and turbidity. It is found that by dynamically changing the sampling frequency, the battery lifetime can be effectively prolonged while maintaining a required level of sampling accuracy. According to the simulation results, compared to a fixed sampling rate, approximately 30.66% of the battery energy can be saved for three months of continuous water quality monitoring. Using the same dataset to compare with a traditional adaptive sampling algorithm (ASA), while achieving around the same Normalized Mean Error (NME), DDASA is superior in saving 5.31% more battery energy. PMID:29113087

CFD Process Pre- and Post-processing Automation in Support of Space Propulsion

NASA Technical Reports Server (NTRS)

Dorney, Suzanne M.

2003-01-01

The use of Computational Fluid Dynamics or CFD has become standard practice in the design and analysis of the major components used for space propulsion. In an attempt to standardize and improve the CFD process a series of automated tools have been developed. Through the use of these automated tools the application of CFD to the design cycle has been improved and streamlined. This paper presents a series of applications in which deficiencies were identified in the CFD process and corrected through the development of automated tools.

Comparability of automated human induced pluripotent stem cell culture: a pilot study.

PubMed

Archibald, Peter R T; Chandra, Amit; Thomas, Dave; Chose, Olivier; Massouridès, Emmanuelle; Laâbi, Yacine; Williams, David J

2016-12-01

Consistent and robust manufacturing is essential for the translation of cell therapies, and the utilisation automation throughout the manufacturing process may allow for improvements in quality control, scalability, reproducibility and economics of the process. The aim of this study was to measure and establish the comparability between alternative process steps for the culture of hiPSCs. Consequently, the effects of manual centrifugation and automated non-centrifugation process steps, performed using TAP Biosystems' CompacT SelecT automated cell culture platform, upon the culture of a human induced pluripotent stem cell (hiPSC) line (VAX001024c07) were compared. This study, has demonstrated that comparable morphologies and cell diameters were observed in hiPSCs cultured using either manual or automated process steps. However, non-centrifugation hiPSC populations exhibited greater cell yields, greater aggregate rates, increased pluripotency marker expression, and decreased differentiation marker expression compared to centrifugation hiPSCs. A trend for decreased variability in cell yield was also observed after the utilisation of the automated process step. This study also highlights the detrimental effect of the cryopreservation and thawing processes upon the growth and characteristics of hiPSC cultures, and demonstrates that automated hiPSC manufacturing protocols can be successfully transferred between independent laboratories.

The automated system for technological process of spacecraft's waveguide paths soldering

NASA Astrophysics Data System (ADS)

Tynchenko, V. S.; Murygin, A. V.; Emilova, O. A.; Bocharov, A. N.; Laptenok, V. D.

2016-11-01

The paper solves the problem of automated process control of space vehicles waveguide paths soldering by means of induction heating. The peculiarities of the induction soldering process are analyzed and necessity of information-control system automation is identified. The developed automated system makes the control of the product heating process, by varying the power supplied to the inductor, on the basis of information about the soldering zone temperature, and stabilizing the temperature in a narrow range above the melting point of the solder but below the melting point of the waveguide. This allows the soldering process automating to improve the quality of the waveguides and eliminate burn-troughs. The article shows a block diagram of a software system consisting of five modules, and describes the main algorithm of its work. Also there is a description of the waveguide paths automated soldering system operation, for explaining the basic functions and limitations of the system. The developed software allows setting of the measurement equipment, setting and changing parameters of the soldering process, as well as view graphs of temperatures recorded by the system. There is shown the results of experimental studies that prove high quality of soldering process control and the system applicability to the tasks of automation.

Computer-Assisted Automated Scoring of Polysomnograms Using the Somnolyzer System

PubMed Central

Punjabi, Naresh M.; Shifa, Naima; Dorffner, Georg; Patil, Susheel; Pien, Grace; Aurora, Rashmi N.

2015-01-01

Study Objectives: Manual scoring of polysomnograms is a time-consuming and tedious process. To expedite the scoring of polysomnograms, several computerized algorithms for automated scoring have been developed. The overarching goal of this study was to determine the validity of the Somnolyzer system, an automated system for scoring polysomnograms. Design: The analysis sample comprised of 97 sleep studies. Each polysomnogram was manually scored by certified technologists from four sleep laboratories and concurrently subjected to automated scoring by the Somnolyzer system. Agreement between manual and automated scoring was examined. Sleep staging and scoring of disordered breathing events was conducted using the 2007 American Academy of Sleep Medicine criteria. Setting: Clinical sleep laboratories. Measurements and Results: A high degree of agreement was noted between manual and automated scoring of the apnea-hypopnea index (AHI). The average correlation between the manually scored AHI across the four clinical sites was 0.92 (95% confidence interval: 0.90–0.93). Similarly, the average correlation between the manual and Somnolyzer-scored AHI values was 0.93 (95% confidence interval: 0.91–0.96). Thus, interscorer correlation between the manually scored results was no different than that derived from manual and automated scoring. Substantial concordance in the arousal index, total sleep time, and sleep efficiency between manual and automated scoring was also observed. In contrast, differences were noted between manually and automated scored percentages of sleep stages N1, N2, and N3. Conclusion: Automated analysis of polysomnograms using the Somnolyzer system provides results that are comparable to manual scoring for commonly used metrics in sleep medicine. Although differences exist between manual versus automated scoring for specific sleep stages, the level of agreement between manual and automated scoring is not significantly different than that between any two human scorers. In light of the burden associated with manual scoring, automated scoring platforms provide a viable complement of tools in the diagnostic armamentarium of sleep medicine. Citation: Punjabi NM, Shifa N, Dorffner G, Patil S, Pien G, Aurora RN. Computer-assisted automated scoring of polysomnograms using the Somnolyzer system. SLEEP 2015;38(10):1555–1566. PMID:25902809

Bioprocess automation on a Mini Pilot Plant enables fast quantitative microbial phenotyping.

PubMed

Unthan, Simon; Radek, Andreas; Wiechert, Wolfgang; Oldiges, Marco; Noack, Stephan

2015-03-11

The throughput of cultivation experiments in bioprocess development has drastically increased in recent years due to the availability of sophisticated microliter scale cultivation devices. However, as these devices still require time-consuming manual work, the bottleneck was merely shifted to media preparation, inoculation and finally the analyses of cultivation samples. A first step towards solving these issues was undertaken in our former study by embedding a BioLector in a robotic workstation. This workstation already allowed for the optimization of heterologous protein production processes, but remained limited when aiming for the characterization of small molecule producer strains. In this work, we extended our workstation to a versatile Mini Pilot Plant (MPP) by integrating further robotic workflows and microtiter plate assays that now enable a fast and accurate phenotyping of a broad range of microbial production hosts. A fully automated harvest procedure was established, which repeatedly samples up to 48 wells from BioLector cultivations in response to individually defined trigger conditions. The samples are automatically clarified by centrifugation and finally frozen for subsequent analyses. Sensitive metabolite assays in 384-well plate scale were integrated on the MPP for the direct determination of substrate uptake (specifically D-glucose and D-xylose) and product formation (specifically amino acids). In a first application, we characterized a set of Corynebacterium glutamicum L-lysine producer strains and could rapidly identify a unique strain showing increased L-lysine titers, which was subsequently confirmed in lab-scale bioreactor experiments. In a second study, we analyzed the substrate uptake kinetics of a previously constructed D-xylose-converting C. glutamicum strain during cultivation on mixed carbon sources in a fully automated experiment. The presented MPP is designed to face the challenges typically encountered during early-stage bioprocess development. Especially the bottleneck of sample analyses from fast and parallelized microtiter plate cultivations can be solved using cutting-edge robotic automation. As robotic workstations become increasingly attractive for biotechnological research, we expect our setup to become a template for future bioprocess development.

The UK Biobank sample handling and storage protocol for the collection, processing and archiving of human blood and urine.

PubMed

Elliott, Paul; Peakman, Tim C

2008-04-01

UK Biobank is a large prospective study in the UK to investigate the role of genetic factors, environmental exposures and lifestyle in the causes of major diseases of late and middle age. Extensive data and biological samples are being collected from 500,000 participants aged between 40 and 69 years. The biological samples that are collected and how they are processed and stored will have a major impact on the future scientific usefulness of the UK Biobank resource. The aim of the UK Biobank sample handling and storage protocol is to specify methods for the collection and storage of participant samples that give maximum scientific return within the available budget. Processing or storage methods that, as far as can be predicted, will preclude current or future assays have been avoided. The protocol was developed through a review of the literature on sample handling and processing, wide consultation within the academic community and peer review. Protocol development addressed which samples should be collected, how and when they should be processed and how the processed samples should be stored to ensure their long-term integrity. The recommended protocol was extensively tested in a series of validation studies. UK Biobank collects about 45 ml blood and 9 ml of urine with minimal local processing from each participant using the vacutainer system. A variety of preservatives, anti-coagulants and clot accelerators is used appropriate to the expected end use of the samples. Collection of other material (hair, nails, saliva and faeces) was also considered but rejected for the full cohort. Blood and urine samples from participants are transported overnight by commercial courier to a central laboratory where they are processed and aliquots of urine, plasma, serum, white cells and red cells stored in ultra-low temperature archives. Aliquots of whole blood are also stored for potential future production of immortalized cell lines. A standard panel of haematology assays is completed on whole blood from all participants, since such assays need to be conducted on fresh samples (whereas other assays can be done on stored samples). By the end of the recruitment phase, 15 million sample aliquots will be stored in two geographically separate archives: 9.5 million in a -80 degrees C automated archive and 5.5 million in a manual liquid nitrogen archive at -180 degrees C. Because of the size of the study and the numbers of samples obtained from participants, the protocol stipulates a highly automated approach for the processing and storage of samples. Implementation of the processes, technology, systems and facilities has followed best practices used in manufacturing industry to reduce project risk and to build in quality and robustness. The data produced from sample collection, processing and storage are highly complex and are managed by a commercially available LIMS system fully integrated with the entire process. The sample handling and storage protocol adopted by UK Biobank provides quality assured and validated methods that are feasible within the available funding and reflect the size and aims of the project. Experience from recruiting and processing the first 40,000 participants to the study demonstrates that the adopted methods and technologies are fit-for-purpose and robust.

Life Sciences Research Facility automation requirements and concepts for the Space Station

NASA Technical Reports Server (NTRS)

Rasmussen, Daryl N.

1986-01-01

An evaluation is made of the methods and preliminary results of a study on prospects for the automation of the NASA Space Station's Life Sciences Research Facility. In order to remain within current Space Station resource allocations, approximately 85 percent of planned life science experiment tasks must be automated; these tasks encompass specimen care and feeding, cage and instrument cleaning, data acquisition and control, sample analysis, waste management, instrument calibration, materials inventory and management, and janitorial work. Task automation will free crews for specimen manipulation, tissue sampling, data interpretation and communication with ground controllers, and experiment management.

Integrated Microfluidic Devices for Automated Microarray-Based Gene Expression and Genotyping Analysis

NASA Astrophysics Data System (ADS)

Liu, Robin H.; Lodes, Mike; Fuji, H. Sho; Danley, David; McShea, Andrew

Microarray assays typically involve multistage sample processing and fluidic handling, which are generally labor-intensive and time-consuming. Automation of these processes would improve robustness, reduce run-to-run and operator-to-operator variation, and reduce costs. In this chapter, a fully integrated and self-contained microfluidic biochip device that has been developed to automate the fluidic handling steps for microarray-based gene expression or genotyping analysis is presented. The device consists of a semiconductor-based CustomArray® chip with 12,000 features and a microfluidic cartridge. The CustomArray was manufactured using a semiconductor-based in situ synthesis technology. The micro-fluidic cartridge consists of microfluidic pumps, mixers, valves, fluid channels, and reagent storage chambers. Microarray hybridization and subsequent fluidic handling and reactions (including a number of washing and labeling steps) were performed in this fully automated and miniature device before fluorescent image scanning of the microarray chip. Electrochemical micropumps were integrated in the cartridge to provide pumping of liquid solutions. A micromixing technique based on gas bubbling generated by electrochemical micropumps was developed. Low-cost check valves were implemented in the cartridge to prevent cross-talk of the stored reagents. Gene expression study of the human leukemia cell line (K562) and genotyping detection and sequencing of influenza A subtypes have been demonstrated using this integrated biochip platform. For gene expression assays, the microfluidic CustomArray device detected sample RNAs with a concentration as low as 0.375 pM. Detection was quantitative over more than three orders of magnitude. Experiment also showed that chip-to-chip variability was low indicating that the integrated microfluidic devices eliminate manual fluidic handling steps that can be a significant source of variability in genomic analysis. The genotyping results showed that the device identified influenza A hemagglutinin and neuraminidase subtypes and sequenced portions of both genes, demonstrating the potential of integrated microfluidic and microarray technology for multiple virus detection. The device provides a cost-effective solution to eliminate labor-intensive and time-consuming fluidic handling steps and allows microarray-based DNA analysis in a rapid and automated fashion.

[Algorithm for the automated processing of rheosignals].

PubMed

Odinets, G S

1988-01-01

Algorithm for rheosignals recognition for a microprocessing device with a representation apparatus and with automated and manual cursor control was examined. The algorithm permits to automate rheosignals registrating and processing taking into account their changeability.

Instrument Control (iC) – An Open-Source Software to Automate Test Equipment

PubMed Central

Pernstich, K. P.

2012-01-01

It has become common practice to automate data acquisition from programmable instrumentation, and a range of different software solutions fulfill this task. Many routine measurements require sequential processing of certain tasks, for instance to adjust the temperature of a sample stage, take a measurement, and repeat that cycle for other temperatures. This paper introduces an open-source Java program that processes a series of text-based commands that define the measurement sequence. These commands are in an intuitive format which provides great flexibility and allows quick and easy adaptation to various measurement needs. For each of these commands, the iC-framework calls a corresponding Java method that addresses the specified instrument to perform the desired task. The functionality of iC can be extended with minimal programming effort in Java or Python, and new measurement equipment can be addressed by defining new commands in a text file without any programming. PMID:26900522

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.

Instrument Control (iC) - An Open-Source Software to Automate Test Equipment.

PubMed

Pernstich, K P

2012-01-01

It has become common practice to automate data acquisition from programmable instrumentation, and a range of different software solutions fulfill this task. Many routine measurements require sequential processing of certain tasks, for instance to adjust the temperature of a sample stage, take a measurement, and repeat that cycle for other temperatures. This paper introduces an open-source Java program that processes a series of text-based commands that define the measurement sequence. These commands are in an intuitive format which provides great flexibility and allows quick and easy adaptation to various measurement needs. For each of these commands, the iC-framework calls a corresponding Java method that addresses the specified instrument to perform the desired task. The functionality of iC can be extended with minimal programming effort in Java or Python, and new measurement equipment can be addressed by defining new commands in a text file without any programming.

Flexible End2End Workflow Automation of Hit-Discovery Research.

PubMed

Holzmüller-Laue, Silke; Göde, Bernd; Thurow, Kerstin

2014-08-01

The article considers a new approach of more complex laboratory automation at the workflow layer. The authors purpose the automation of end2end workflows. The combination of all relevant subprocesses-whether automated or manually performed, independently, and in which organizational unit-results in end2end processes that include all result dependencies. The end2end approach focuses on not only the classical experiments in synthesis or screening, but also on auxiliary processes such as the production and storage of chemicals, cell culturing, and maintenance as well as preparatory activities and analyses of experiments. Furthermore, the connection of control flow and data flow in the same process model leads to reducing of effort of the data transfer between the involved systems, including the necessary data transformations. This end2end laboratory automation can be realized effectively with the modern methods of business process management (BPM). This approach is based on a new standardization of the process-modeling notation Business Process Model and Notation 2.0. In drug discovery, several scientific disciplines act together with manifold modern methods, technologies, and a wide range of automated instruments for the discovery and design of target-based drugs. The article discusses the novel BPM-based automation concept with an implemented example of a high-throughput screening of previously synthesized compound libraries. © 2014 Society for Laboratory Automation and Screening.

IsoMS: automated processing of LC-MS data generated by a chemical isotope labeling metabolomics platform.

PubMed

Zhou, Ruokun; Tseng, Chiao-Li; Huan, Tao; Li, Liang

2014-05-20

A chemical isotope labeling or isotope coded derivatization (ICD) metabolomics platform uses a chemical derivatization method to introduce a mass tag to all of the metabolites having a common functional group (e.g., amine), followed by LC-MS analysis of the labeled metabolites. To apply this platform to metabolomics studies involving quantitative analysis of different groups of samples, automated data processing is required. Herein, we report a data processing method based on the use of a mass spectral feature unique to the chemical labeling approach, i.e., any differential-isotope-labeled metabolites are detected as peak pairs with a fixed mass difference in a mass spectrum. A software tool, IsoMS, has been developed to process the raw data generated from one or multiple LC-MS runs by peak picking, peak pairing, peak-pair filtering, and peak-pair intensity ratio calculation. The same peak pairs detected from multiple samples are then aligned to produce a CSV file that contains the metabolite information and peak ratios relative to a control (e.g., a pooled sample). This file can be readily exported for further data and statistical analysis, which is illustrated in an example of comparing the metabolomes of human urine samples collected before and after drinking coffee. To demonstrate that this method is reliable for data processing, five (13)C2-/(12)C2-dansyl labeled metabolite standards were analyzed by LC-MS. IsoMS was able to detect these metabolites correctly. In addition, in the analysis of a (13)C2-/(12)C2-dansyl labeled human urine, IsoMS detected 2044 peak pairs, and manual inspection of these peak pairs found 90 false peak pairs, representing a false positive rate of 4.4%. IsoMS for Windows running R is freely available for noncommercial use from www.mycompoundid.org/IsoMS.

Some aspects of analytical chemistry as applied to water quality assurance techniques for reclaimed water: The potential use of X-ray fluorescence spectrometry for automated on-line fast real-time simultaneous multi-component analysis of inorganic pollutants in reclaimed water

NASA Technical Reports Server (NTRS)

Ling, A. C.; Macpherson, L. H.; Rey, M.

1981-01-01

The potential use of isotopically excited energy dispersive X-ray fluorescence (XRF) spectrometry for automated on line fast real time (5 to 15 minutes) simultaneous multicomponent (up to 20) trace (1 to 10 parts per billion) analysis of inorganic pollutants in reclaimed water was examined. Three anionic elements (chromium 6, arsenic and selenium) were studied. The inherent lack of sensitivity of XRF spectrometry for these elements mandates use of a preconcentration technique and various methods were examined, including: several direct and indirect evaporation methods; ion exchange membranes; selective and nonselective precipitation; and complexation processes. It is shown tha XRF spectrometry itself is well suited for automated on line quality assurance, and can provide a nondestructive (and thus sample storage and repeat analysis capabilities) and particularly convenient analytical method. Further, the use of an isotopically excited energy dispersive unit (50 mCi Cd-109 source) coupled with a suitable preconcentration process can provide sufficient sensitivity to achieve the current mandated minimum levels of detection without the need for high power X-ray generating tubes.

An Improved Method for Measuring Quantitative Resistance to the Wheat Pathogen Zymoseptoria tritici Using High-Throughput Automated Image Analysis.

PubMed

Stewart, Ethan L; Hagerty, Christina H; Mikaberidze, Alexey; Mundt, Christopher C; Zhong, Ziming; McDonald, Bruce A

2016-07-01

Zymoseptoria tritici causes Septoria tritici blotch (STB) on wheat. An improved method of quantifying STB symptoms was developed based on automated analysis of diseased leaf images made using a flatbed scanner. Naturally infected leaves (n = 949) sampled from fungicide-treated field plots comprising 39 wheat cultivars grown in Switzerland and 9 recombinant inbred lines (RIL) grown in Oregon were included in these analyses. Measures of quantitative resistance were percent leaf area covered by lesions, pycnidia size and gray value, and pycnidia density per leaf and lesion. These measures were obtained automatically with a batch-processing macro utilizing the image-processing software ImageJ. All phenotypes in both locations showed a continuous distribution, as expected for a quantitative trait. The trait distributions at both sites were largely overlapping even though the field and host environments were quite different. Cultivars and RILs could be assigned to two or more statistically different groups for each measured phenotype. Traditional visual assessments of field resistance were highly correlated with quantitative resistance measures based on image analysis for the Oregon RILs. These results show that automated image analysis provides a promising tool for assessing quantitative resistance to Z. tritici under field conditions.

Towards automated segmentation of cells and cell nuclei in nonlinear optical microscopy.

PubMed

Medyukhina, Anna; Meyer, Tobias; Schmitt, Michael; Romeike, Bernd F M; Dietzek, Benjamin; Popp, Jürgen

2012-11-01

Nonlinear optical (NLO) imaging techniques based e.g. on coherent anti-Stokes Raman scattering (CARS) or two photon excited fluorescence (TPEF) show great potential for biomedical imaging. In order to facilitate the diagnostic process based on NLO imaging, there is need for an automated calculation of quantitative values such as cell density, nucleus-to-cytoplasm ratio, average nuclear size. Extraction of these parameters is helpful for the histological assessment in general and specifically e.g. for the determination of tumor grades. This requires an accurate image segmentation and detection of locations and boundaries of cells and nuclei. Here we present an image processing approach for the detection of nuclei and cells in co-registered TPEF and CARS images. The algorithm developed utilizes the gray-scale information for the detection of the nuclei locations and the gradient information for the delineation of the nuclear and cellular boundaries. The approach reported is capable for an automated segmentation of cells and nuclei in multimodal TPEF-CARS images of human brain tumor samples. The results are important for the development of NLO microscopy into a clinically relevant diagnostic tool. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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 dissolved concentration of Fe and Mn in the ground and streamwater samples stored in low density polyethylene (LDPE) sample bags decreased by 89% and 97%, respectively. In some cases of groundwater, the concentration of Ca decreased by 25%, due to degassing of CO2. However, DOC of the samples in LDPE bags without filtration increased up to 50% in 2 weeks, suggesting contamination from the bag. Performance of the new design was evaluated using the Fe-Mn-spiked Rivendell samples and environmental water samples collected from 1) Rivendell, 2) the Strawberry Creek located at the University of California, Berkeley campus, and 3) the San Francisco Bay. The samples were filtered using the developed method and stored in room temperature in 2 - 3 weeks without further treatment. The method improved the sample integrity significantly; the average recovery rates of Fe, Mn, DOC, and Ca were 92%, 98%, 90%, and 97%, respectively.

Gas pressure assisted microliquid-liquid extraction coupled online to direct infusion mass spectrometry: a new automated screening platform for bioanalysis.

PubMed

Raterink, Robert-Jan; Witkam, Yoeri; Vreeken, Rob J; Ramautar, Rawi; Hankemeier, Thomas

2014-10-21

In the field of bioanalysis, there is an increasing demand for miniaturized, automated, robust sample pretreatment procedures that can be easily connected to direct-infusion mass spectrometry (DI-MS) in order to allow the high-throughput screening of drugs and/or their metabolites in complex body fluids like plasma. Liquid-Liquid extraction (LLE) is a common sample pretreatment technique often used for complex aqueous samples in bioanalysis. Despite significant developments that have been made in automated and miniaturized LLE procedures, fully automated LLE techniques allowing high-throughput bioanalytical studies on small-volume samples using direct infusion mass spectrometry, have not been matured yet. Here, we introduce a new fully automated micro-LLE technique based on gas-pressure assisted mixing followed by passive phase separation, coupled online to nanoelectrospray-DI-MS. Our method was characterized by varying the gas flow and its duration through the solvent mixture. For evaluation of the analytical performance, four drugs were spiked to human plasma, resulting in highly acceptable precision (RSD down to 9%) and linearity (R(2) ranging from 0.990 to 0.998). We demonstrate that our new method does not only allow the reliable extraction of analytes from small sample volumes of a few microliters in an automated and high-throughput manner, but also performs comparable or better than conventional offline LLE, in which the handling of small volumes remains challenging. Finally, we demonstrate the applicability of our method for drug screening on dried blood spots showing excellent linearity (R(2) of 0.998) and precision (RSD of 9%). In conclusion, we present the proof of principe of a new high-throughput screening platform for bioanalysis based on a new automated microLLE method, coupled online to a commercially available nano-ESI-DI-MS.

Influence of sample preparation and reliability of automated numerical refocusing in stain-free analysis of dissected tissues with quantitative phase digital holographic microscopy

NASA Astrophysics Data System (ADS)

Kemper, Björn; Lenz, Philipp; Bettenworth, Dominik; Krausewitz, Philipp; Domagk, Dirk; Ketelhut, Steffi

2015-05-01

Digital holographic microscopy (DHM) has been demonstrated to be a versatile tool for high resolution non-destructive quantitative phase imaging of surfaces and multi-modal minimally-invasive monitoring of living cell cultures in-vitro. DHM provides quantitative monitoring of physiological processes through functional imaging and structural analysis which, for example, gives new insight into signalling of cellular water permeability and cell morphology changes due to toxins and infections. Also the analysis of dissected tissues quantitative DHM phase contrast prospects application fields by stain-free imaging and the quantification of tissue density changes. We show that DHM allows imaging of different tissue layers with high contrast in unstained tissue sections. As the investigation of fixed samples represents a very important application field in pathology, we also analyzed the influence of the sample preparation. The retrieved data demonstrate that the quality of quantitative DHM phase images of dissected tissues depends strongly on the fixing method and common staining agents. As in DHM the reconstruction is performed numerically, multi-focus imaging is achieved from a single digital hologram. Thus, we evaluated the automated refocussing feature of DHM for application on different types of dissected tissues and revealed that on moderately stained samples highly reproducible holographic autofocussing can be achieved. Finally, it is demonstrated that alterations of the spatial refractive index distribution in murine and human tissue samples represent a reliable absolute parameter that is related of different degrees of inflammation in experimental colitis and Crohn's disease. This paves the way towards the usage of DHM in digital pathology for automated histological examinations and further studies to elucidate the translational potential of quantitative phase microscopy for the clinical management of patients, e.g., with inflammatory bowel disease.

National Forum on the Future of Automated Materials Processing in US Industry: The Role of Sensors. Report of a workshop (1st) held at Santa Barbara, California on December 16-17, 1985

NASA Astrophysics Data System (ADS)

Yolken, H. T.; Mehrabian, R.

1985-12-01

These are the proceedings of the workshop A National Forum on the Future of Automated Materials Processing in U.S. Industry - The Role of Sensors. This is the first of two workshops to be sponsored by the Industrial Research Institute and the White House Office of Science and Technology Policy, Committee on Materials Working Group on Automation of Materials Processing. The second workshop will address the other two key components required for automated materials processing, process models and artificial intelligence coupled with computer integration of the system. The objective of these workshops is to identify and assess important issues afecting the competitive position of U.S. industry related to its ability to automate production processes for basic and advanced materials and to develop approaches for improved capability through cooperative R&D and associated efforts.

Laboratory Automation and Intra-Laboratory Turnaround Time: Experience at the University Hospital Campus Bio-Medico of Rome.

PubMed

Angeletti, Silvia; De Cesaris, Marina; Hart, Jonathan George; Urbano, Michele; Vitali, Massimiliano Andrea; Fragliasso, Fulvio; Dicuonzo, Giordano

2015-12-01

Intra-laboratory turnaround time (TAT) is a key indicator of laboratory performance. Improving TAT is a complex task requiring staff education, equipment acquisition, and adequate TAT monitoring. The aim of the present study was to evaluate the intra-laboratory TAT after laboratory automation implementation (June 2013-June 2014) and to compare it to that in the preautomation period (July 2012-May 2013). Intra-laboratory TAT was evaluated both as the mean TAT registered and the percentage of outlier (OP) exams. The mean TAT was 36, 38, and 34 min during the study periods, respectively. These values respected the goal TAT established at 45 min. The OP, calculated at 45 min as well as at 60 min, decreased from 26 to 21 and from 11 to 5, respectively. From a focused analysis on blood count cell, troponin I, and prothrombin (PT) test, TAT improvement was more evident for tests requiring longer preanalytical process. The follow-up of TAT from June 2013 to June 2014 revealed the reduction of the mean TAT as well as of the OP exams after automation implementation and that automation more strongly affects the test in the preanalytical phase including centrifugation of the sample, such as troponin I and PT. © 2015 Society for Laboratory Automation and Screening.

A Comparative Experimental Study on the Use of Machine Learning Approaches for Automated Valve Monitoring Based on Acoustic Emission Parameters

NASA Astrophysics Data System (ADS)

Ali, Salah M.; Hui, K. H.; Hee, L. M.; Salman Leong, M.; Al-Obaidi, M. A.; Ali, Y. H.; Abdelrhman, Ahmed M.

2018-03-01

Acoustic emission (AE) analysis has become a vital tool for initiating the maintenance tasks in many industries. However, the analysis process and interpretation has been found to be highly dependent on the experts. Therefore, an automated monitoring method would be required to reduce the cost and time consumed in the interpretation of AE signal. This paper investigates the application of two of the most common machine learning approaches namely artificial neural network (ANN) and support vector machine (SVM) to automate the diagnosis of valve faults in reciprocating compressor based on AE signal parameters. Since the accuracy is an essential factor in any automated diagnostic system, this paper also provides a comparative study based on predictive performance of ANN and SVM. AE parameters data was acquired from single stage reciprocating air compressor with different operational and valve conditions. ANN and SVM diagnosis models were subsequently devised by combining AE parameters of different conditions. Results demonstrate that ANN and SVM models have the same results in term of prediction accuracy. However, SVM model is recommended to automate diagnose the valve condition in due to the ability of handling a high number of input features with low sampling data sets.

Automated Discovery and Modeling of Sequential Patterns Preceding Events of Interest

NASA Technical Reports Server (NTRS)

Rohloff, Kurt

2010-01-01

The integration of emerging data manipulation technologies has enabled a paradigm shift in practitioners' abilities to understand and anticipate events of interest in complex systems. Example events of interest include outbreaks of socio-political violence in nation-states. Rather than relying on human-centric modeling efforts that are limited by the availability of SMEs, automated data processing technologies has enabled the development of innovative automated complex system modeling and predictive analysis technologies. We introduce one such emerging modeling technology - the sequential pattern methodology. We have applied the sequential pattern methodology to automatically identify patterns of observed behavior that precede outbreaks of socio-political violence such as riots, rebellions and coups in nation-states. The sequential pattern methodology is a groundbreaking approach to automated complex system model discovery because it generates easily interpretable patterns based on direct observations of sampled factor data for a deeper understanding of societal behaviors that is tolerant of observation noise and missing data. The discovered patterns are simple to interpret and mimic human's identifications of observed trends in temporal data. Discovered patterns also provide an automated forecasting ability: we discuss an example of using discovered patterns coupled with a rich data environment to forecast various types of socio-political violence in nation-states.

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.

A methodology for the semi-automatic digital image analysis of fragmental impactites

NASA Astrophysics Data System (ADS)

Chanou, A.; Osinski, G. R.; Grieve, R. A. F.

2014-04-01

A semi-automated digital image analysis method is developed for the comparative textural study of impact melt-bearing breccias. This method uses the freeware software ImageJ developed by the National Institute of Health (NIH). Digital image analysis is performed on scans of hand samples (10-15 cm across), based on macroscopic interpretations of the rock components. All image processing and segmentation are done semi-automatically, with the least possible manual intervention. The areal fraction of components is estimated and modal abundances can be deduced, where the physical optical properties (e.g., contrast, color) of the samples allow it. Other parameters that can be measured include, for example, clast size, clast-preferred orientations, average box-counting dimension or fragment shape complexity, and nearest neighbor distances (NnD). This semi-automated method allows the analysis of a larger number of samples in a relatively short time. Textures, granulometry, and shape descriptors are of considerable importance in rock characterization. The methodology is used to determine the variations of the physical characteristics of some examples of fragmental impactites.

Fully automated processing of fMRI data in SPM: from MRI scanner to PACS.

PubMed

Maldjian, Joseph A; Baer, Aaron H; Kraft, Robert A; Laurienti, Paul J; Burdette, Jonathan H

2009-01-01

Here we describe the Wake Forest University Pipeline, a fully automated method for the processing of fMRI data using SPM. The method includes fully automated data transfer and archiving from the point of acquisition, real-time batch script generation, distributed grid processing, interface to SPM in MATLAB, error recovery and data provenance, DICOM conversion and PACS insertion. It has been used for automated processing of fMRI experiments, as well as for the clinical implementation of fMRI and spin-tag perfusion imaging. The pipeline requires no manual intervention, and can be extended to any studies requiring offline processing.

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.

Remotely Controlled Mixers for Light Microscopy Module (LMM) Colloid Samples

NASA Technical Reports Server (NTRS)

Kurk, Michael A. (Andy)

2015-01-01

Developed by NASA Glenn Research Center, the LMM aboard the International Space Station (ISS) is enabling multiple biomedical science experiments. Techshot, Inc., has developed a series of colloid specialty cell systems (C-SPECS) for use in the colloid science experiment module on the LMM. These low-volume mixing devices will enable uniform particle density and remotely controlled repetition of LMM colloid experiments. By automating the experiment process, C-SPECS allow colloid samples to be processed more quickly. In addition, C-SPECS will minimize the time the crew will need to spend on colloid experiments as well as eliminate the need for multiple and costly colloid samples, which are expended after a single examination. This high-throughput capability will lead to more efficient and productive use of the LMM. As commercial launch vehicles begin routine visits to the ISS, C-SPECS could become a significant means to process larger quantities of high-value materials for commercial customers.

More steps towards process automation for optical fabrication

NASA Astrophysics Data System (ADS)

Walker, David; Yu, Guoyu; Beaucamp, Anthony; Bibby, Matt; Li, Hongyu; McCluskey, Lee; Petrovic, Sanja; Reynolds, Christina

2017-06-01

In the context of Industrie 4.0, we have previously described the roles of robots in optical processing, and their complementarity with classical CNC machines, providing both processing and automation functions. After having demonstrated robotic moving of parts between a CNC polisher and metrology station, and auto-fringe-acquisition, we have moved on to automate the wash-down operation. This is part of a wider strategy we describe in this paper, leading towards automating the decision-making operations required before and throughout an optical manufacturing cycle.

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...

Paint Analysis

NASA Technical Reports Server (NTRS)

1994-01-01

Lewis Research Center (LEW) has assisted The Cleveland Museum of Art (CMA) in analyzing the museum's paintings. Because of the many layers of paint that are often involved, this is a complex process. The cross-section of a paint chip must be scanned with a microscope to determine whether a paint layer is original or a restoration. The paint samples, however, are rarely flat enough for high magnification viewing and are frequently scratched. LEW devised an automated method that produces intact, flat, polished paint cross-sections. A sophisticated microprocessor-controlled grinding and polishing machine was manually employed in preparation of exotic samples for aerospace research was a readily adaptable technique. It produced perfectly flat samples with clearly defined layers. The process has been used successfully on a number of paintings, and LEW and CMA are considering additional applications.

Automated Subsystem Control for Life Support System (ASCLSS)

NASA Technical Reports Server (NTRS)

Block, Roger F.

1987-01-01

The Automated Subsystem Control for Life Support Systems (ASCLSS) program has successfully developed and demonstrated a generic approach to the automation and control of space station subsystems. The automation system features a hierarchical and distributed real-time control architecture which places maximum controls authority at the lowest or process control level which enhances system autonomy. The ASCLSS demonstration system pioneered many automation and control concepts currently being considered in the space station data management system (DMS). Heavy emphasis is placed on controls hardware and software commonality implemented in accepted standards. The approach demonstrates successfully the application of real-time process and accountability with the subsystem or process developer. The ASCLSS system completely automates a space station subsystem (air revitalization group of the ASCLSS) which moves the crew/operator into a role of supervisory control authority. The ASCLSS program developed over 50 lessons learned which will aide future space station developers in the area of automation and controls..

Improvements to the Processing and Characterization of Needled Composite Laminates

DTIC Science & Technology

2014-01-01

the automated processing equipment are shown and discussed. The modifications allow better spatial control at the penetration sites and the ability... automated processing equipment are shown and discussed. The modifications allow better spatial control at the penetration sites and the ability to...semi- automated processing equipment, commercial off-the-shelf (COTS) needles and COTS aramid mat designed for other applications. Needled material

Knowledge Representation Artifacts for Use in Sensemaking Support Systems

DTIC Science & Technology

2015-03-12

and manual processing must be replaced by automated processing wherever it makes sense and is possible. Clearly, given the data and cognitive...knowledge-centric view to situation analysis and decision-making as previously discussed, has lead to the development of several automated processing components...for use in sensemaking support systems [6-11]. In turn, automated processing has required the development of appropriate knowledge

Command and Control Common Semantic Core Required to Enable Net-centric Operations

DTIC Science & Technology

2008-05-20

automated processing capability. A former US Marine Corps component C4 director during Operation Iraqi Freedom identified the problems of 1) uncertainty...interoperability improvements to warfighter community processes, thanks to ubiquitous automated processing , are likely high and somewhat easier to quantify. A...synchronized with the actions of other partners / warfare communities. This requires high- quality information, rapid sharing and automated processing – which

The Automated Office.

ERIC Educational Resources Information Center

Naclerio, Nick

1979-01-01

Clerical personnel may be able to climb career ladders as a result of office automation and expanded job opportunities in the word processing area. Suggests opportunities in an automated office system and lists books and periodicals on word processing for counselors and teachers. (MF)

Rapid Protein Global Fold Determination Using Ultrasparse Sampling, High-Dynamic Range Artifact Suppression, and Time-Shared NOESY

PubMed Central

Coggins, Brian E.; Werner-Allen, Jonathan W.; Yan, Anthony; Zhou, Pei

2012-01-01

In structural studies of large proteins by NMR, global fold determination plays an increasingly important role in providing a first look at a target’s topology and reducing assignment ambiguity in NOESY spectra of fully-protonated samples. In this work, we demonstrate the use of ultrasparse sampling, a new data processing algorithm, and a 4-D time-shared NOESY experiment (1) to collect all NOEs in 2H/13C/15N-labeled protein samples with selectively-protonated amide and ILV methyl groups at high resolution in only four days, and (2) to calculate global folds from this data using fully automated resonance assignment. The new algorithm, SCRUB, incorporates the CLEAN method for iterative artifact removal, but applies an additional level of iteration, permitting real signals to be distinguished from noise and allowing nearly all artifacts generated by real signals to be eliminated. In simulations with 1.2% of the data required by Nyquist sampling, SCRUB achieves a dynamic range over 10000:1 (250× better artifact suppression than CLEAN) and completely quantitative reproduction of signal intensities, volumes, and lineshapes. Applied to 4-D time-shared NOESY data, SCRUB processing dramatically reduces aliasing noise from strong diagonal signals, enabling the identification of weak NOE crosspeaks with intensities 100× less than diagonal signals. Nearly all of the expected peaks for interproton distances under 5 Å were observed. The practical benefit of this method is demonstrated with structure calculations for 23 kDa and 29 kDa test proteins using the automated assignment protocol of CYANA, in which unassigned 4-D time-shared NOESY peak lists produce accurate and well-converged global fold ensembles, whereas 3-D peak lists either fail to converge or produce significantly less accurate folds. The approach presented here succeeds with an order of magnitude less sampling than required by alternative methods for processing sparse 4-D data. PMID:22946863

An Intelligent Automation Platform for Rapid Bioprocess Design

PubMed Central

Wu, Tianyi

2014-01-01

Bioprocess development is very labor intensive, requiring many experiments to characterize each unit operation in the process sequence to achieve product safety and process efficiency. Recent advances in microscale biochemical engineering have led to automated experimentation. A process design workflow is implemented sequentially in which (1) a liquid-handling system performs high-throughput wet lab experiments, (2) standalone analysis devices detect the data, and (3) specific software is used for data analysis and experiment design given the user’s inputs. We report an intelligent automation platform that integrates these three activities to enhance the efficiency of such a workflow. A multiagent intelligent architecture has been developed incorporating agent communication to perform the tasks automatically. The key contribution of this work is the automation of data analysis and experiment design and also the ability to generate scripts to run the experiments automatically, allowing the elimination of human involvement. A first-generation prototype has been established and demonstrated through lysozyme precipitation process design. All procedures in the case study have been fully automated through an intelligent automation platform. The realization of automated data analysis and experiment design, and automated script programming for experimental procedures has the potential to increase lab productivity. PMID:24088579

An Automated Method for High-Definition Transcranial Direct Current Stimulation Modeling*

PubMed Central

Huang, Yu; Su, Yuzhuo; Rorden, Christopher; Dmochowski, Jacek; Datta, Abhishek; Parra, Lucas C.

2014-01-01

Targeted transcranial stimulation with electric currents requires accurate models of the current flow from scalp electrodes to the human brain. Idiosyncratic anatomy of individual brains and heads leads to significant variability in such current flows across subjects, thus, necessitating accurate individualized head models. Here we report on an automated processing chain that computes current distributions in the head starting from a structural magnetic resonance image (MRI). The main purpose of automating this process is to reduce the substantial effort currently required for manual segmentation, electrode placement, and solving of finite element models. In doing so, several weeks of manual labor were reduced to no more than 4 hours of computation time and minimal user interaction, while current-flow results for the automated method deviated by less than 27.9% from the manual method. Key facilitating factors are the addition of three tissue types (skull, scalp and air) to a state-of-the-art automated segmentation process, morphological processing to correct small but important segmentation errors, and automated placement of small electrodes based on easily reproducible standard electrode configurations. We anticipate that such an automated processing will become an indispensable tool to individualize transcranial direct current stimulation (tDCS) therapy. PMID:23367144

Geena 2, improved automated analysis of MALDI/TOF mass spectra.

PubMed

Romano, Paolo; Profumo, Aldo; Rocco, Mattia; Mangerini, Rosa; Ferri, Fabio; Facchiano, Angelo

2016-03-02

Mass spectrometry (MS) is producing high volumes of data supporting oncological sciences, especially for translational research. Most of related elaborations can be carried out by combining existing tools at different levels, but little is currently available for the automation of the fundamental steps. For the analysis of MALDI/TOF spectra, a number of pre-processing steps are required, including joining of isotopic abundances for a given molecular species, normalization of signals against an internal standard, background noise removal, averaging multiple spectra from the same sample, and aligning spectra from different samples. In this paper, we present Geena 2, a public software tool for the automated execution of these pre-processing steps for MALDI/TOF spectra. Geena 2 has been developed in a Linux-Apache-MySQL-PHP web development environment, with scripts in PHP and Perl. Input and output are managed as simple formats that can be consumed by any database system and spreadsheet software. Input data may also be stored in a MySQL database. Processing methods are based on original heuristic algorithms which are introduced in the paper. Three simple and intuitive web interfaces are available: the Standard Search Interface, which allows a complete control over all parameters, the Bright Search Interface, which leaves to the user the possibility to tune parameters for alignment of spectra, and the Quick Search Interface, which limits the number of parameters to a minimum by using default values for the majority of parameters. Geena 2 has been utilized, in conjunction with a statistical analysis tool, in three published experimental works: a proteomic study on the effects of long-term cryopreservation on the low molecular weight fraction of serum proteome, and two retrospective serum proteomic studies, one on the risk of developing breat cancer in patients affected by gross cystic disease of the breast (GCDB) and the other for the identification of a predictor of breast cancer mortality following breast cancer surgery, whose results were validated by ELISA, a completely alternative method. Geena 2 is a public tool for the automated pre-processing of MS data originated by MALDI/TOF instruments, with a simple and intuitive web interface. It is now under active development for the inclusion of further filtering options and for the adoption of standard formats for MS spectra.

Development Status: Automation Advanced Development Space Station Freedom Electric Power System

NASA Technical Reports Server (NTRS)

Dolce, James L.; Kish, James A.; Mellor, Pamela A.

1990-01-01

Electric power system automation for Space Station Freedom is intended to operate in a loop. Data from the power system is used for diagnosis and security analysis to generate Operations Management System (OMS) requests, which are sent to an arbiter, which sends a plan to a commander generator connected to the electric power system. This viewgraph presentation profiles automation software for diagnosis, scheduling, and constraint interfaces, and simulation to support automation development. The automation development process is diagrammed, and the process of creating Ada and ART versions of the automation software is described.

Design and Elementary Evaluation of a Highly-Automated Fluorescence-Based Instrument System for On-Site Detection of Food-Borne Pathogens

PubMed Central

Lu, Zhan; Zhang, Jianyi; Xu, Lizhou; Li, Yanbin; Chen, Siyu; Ye, Zunzhong; Wang, Jianping

2017-01-01

A simple, highly-automated instrument system used for on-site detection of foodborne pathogens based on fluorescence was designed, fabricated, and preliminarily tested in this paper. A corresponding method has been proved effective in our previous studies. This system utilizes a light-emitting diode (LED) to excite fluorescent labels and a spectrometer to record the fluorescence signal from samples. A rotation stage for positioning and switching samples was innovatively designed for high-throughput detection, ten at most in one single run. We also developed software based on LabVIEW for data receiving, processing, and the control of the whole system. In the test of using a pure quantum dot (QD) solution as a standard sample, detection results from this home-made system were highly-relevant with that from a well-commercialized product and even slightly better reproducibility was found. And in the test of three typical kinds of food-borne pathogens, fluorescence signals recorded by this system are highly proportional to the variation of the sample concentration, with a satisfied limit of detection (LOD) (nearly 102–103 CFU·mL−1 in food samples). Additionally, this instrument system is low-cost and easy-to-use, showing a promising potential for on-site rapid detection of food-borne pathogens. PMID:28241478

Design and Elementary Evaluation of a Highly-Automated Fluorescence-Based Instrument System for On-Site Detection of Food-Borne Pathogens.

PubMed

Lu, Zhan; Zhang, Jianyi; Xu, Lizhou; Li, Yanbin; Chen, Siyu; Ye, Zunzhong; Wang, Jianping

2017-02-23

A simple, highly-automated instrument system used for on-site detection of foodborne pathogens based on fluorescence was designed, fabricated, and preliminarily tested in this paper. A corresponding method has been proved effective in our previous studies. This system utilizes a light-emitting diode (LED) to excite fluorescent labels and a spectrometer to record the fluorescence signal from samples. A rotation stage for positioning and switching samples was innovatively designed for high-throughput detection, ten at most in one single run. We also developed software based on LabVIEW for data receiving, processing, and the control of the whole system. In the test of using a pure quantum dot (QD) solution as a standard sample, detection results from this home-made system were highly-relevant with that from a well-commercialized product and even slightly better reproducibility was found. And in the test of three typical kinds of food-borne pathogens, fluorescence signals recorded by this system are highly proportional to the variation of the sample concentration, with a satisfied limit of detection (LOD) (nearly 10²-10³ CFU·mL -1 in food samples). Additionally, this instrument system is low-cost and easy-to-use, showing a promising potential for on-site rapid detection of food-borne pathogens.

Containerless automated processing of intermetallic compounds and composites

NASA Technical Reports Server (NTRS)

Johnson, D. R.; Joslin, S. M.; Reviere, R. D.; Oliver, B. F.; Noebe, R. D.

1993-01-01

An automated containerless processing system has been developed to directionally solidify high temperature materials, intermetallic compounds, and intermetallic/metallic composites. The system incorporates a wide range of ultra-high purity chemical processing conditions. The utilization of image processing for automated control negates the need for temperature measurements for process control. The list of recent systems that have been processed includes Cr, Mo, Mn, Nb, Ni, Ti, V, and Zr containing aluminides. Possible uses of the system, process control approaches, and properties and structures of recently processed intermetallics are reviewed.

Virtual automation.

PubMed

Casis, E; Garrido, A; Uranga, B; Vives, A; Zufiaurre, C

2001-01-01

Total laboratory automation (TLA) can be substituted in mid-size laboratories by a computer sample workflow control (virtual automation). Such a solution has been implemented in our laboratory using PSM, software developed in cooperation with Roche Diagnostics (Barcelona, Spain), to this purpose. This software is connected to the online analyzers and to the laboratory information system and is able to control and direct the samples working as an intermediate station. The only difference with TLA is the replacement of transport belts by personnel of the laboratory. The implementation of this virtual automation system has allowed us the achievement of the main advantages of TLA: workload increase (64%) with reduction in the cost per test (43%), significant reduction in the number of biochemistry primary tubes (from 8 to 2), less aliquoting (from 600 to 100 samples/day), automation of functional testing, drastic reduction of preanalytical errors (from 11.7 to 0.4% of the tubes) and better total response time for both inpatients (from up to 48 hours to up to 4 hours) and outpatients (from up to 10 days to up to 48 hours). As an additional advantage, virtual automation could be implemented without hardware investment and significant headcount reduction (15% in our lab).

Automated Fast Screening Method for Cocaine Identification in Seized Drug Samples Using a Portable Fourier Transform Infrared (FT-IR) Instrument.

PubMed

Mainali, Dipak; Seelenbinder, John

2016-05-01

Quick and presumptive identification of seized drug samples without destroying evidence is necessary for law enforcement officials to control the trafficking and abuse of drugs. This work reports an automated screening method to detect the presence of cocaine in seized samples using portable Fourier transform infrared (FT-IR) spectrometers. The method is based on the identification of well-defined characteristic vibrational frequencies related to the functional group of the cocaine molecule and is fully automated through the use of an expert system. Traditionally, analysts look for key functional group bands in the infrared spectra and characterization of the molecules present is dependent on user interpretation. This implies the need for user expertise, especially in samples that likely are mixtures. As such, this approach is biased and also not suitable for non-experts. The method proposed in this work uses the well-established "center of gravity" peak picking mathematical algorithm and combines it with the conditional reporting feature in MicroLab software to provide an automated method that can be successfully employed by users with varied experience levels. The method reports the confidence level of cocaine present only when a certain number of cocaine related peaks are identified by the automated method. Unlike library search and chemometric methods that are dependent on the library database or the training set samples used to build the calibration model, the proposed method is relatively independent of adulterants and diluents present in the seized mixture. This automated method in combination with a portable FT-IR spectrometer provides law enforcement officials, criminal investigators, or forensic experts a quick field-based prescreening capability for the presence of cocaine in seized drug samples. © The Author(s) 2016.

Information Fusion for Feature Extraction and the Development of Geospatial Information

DTIC Science & Technology

2004-07-01

of automated processing . 2. Requirements for Geospatial Information Accurate, timely geospatial information is critical for many military...this evaluation illustrates some of the difficulties in comparing manual and automated processing results (figure 5). The automated delineation of

Artificial intelligence applied to the automatic analysis of absorption spectra. Objective measurement of the fine structure constant

NASA Astrophysics Data System (ADS)

Bainbridge, Matthew B.; Webb, John K.

2017-06-01

A new and automated method is presented for the analysis of high-resolution absorption spectra. Three established numerical methods are unified into one `artificial intelligence' process: a genetic algorithm (Genetic Voigt Profile FIT, gvpfit); non-linear least-squares with parameter constraints (vpfit); and Bayesian model averaging (BMA). The method has broad application but here we apply it specifically to the problem of measuring the fine structure constant at high redshift. For this we need objectivity and reproducibility. gvpfit is also motivated by the importance of obtaining a large statistical sample of measurements of Δα/α. Interactive analyses are both time consuming and complex and automation makes obtaining a large sample feasible. In contrast to previous methodologies, we use BMA to derive results using a large set of models and show that this procedure is more robust than a human picking a single preferred model since BMA avoids the systematic uncertainties associated with model choice. Numerical simulations provide stringent tests of the whole process and we show using both real and simulated spectra that the unified automated fitting procedure out-performs a human interactive analysis. The method should be invaluable in the context of future instrumentation like ESPRESSO on the VLT and indeed future ELTs. We apply the method to the zabs = 1.8389 absorber towards the zem = 2.145 quasar J110325-264515. The derived constraint of Δα/α = 3.3 ± 2.9 × 10-6 is consistent with no variation and also consistent with the tentative spatial variation reported in Webb et al. and King et al.

45 CFR 309.145 - What costs are allowable for Tribal IV-D programs carried out under § 309.65(a) of this part?

Code of Federal Regulations, 2010 CFR

2010-10-01

.... (h) Automated data processing computer systems, including: (1) Planning efforts in the identification, evaluation, and selection of an automated data processing computer system solution meeting the program... existing automated data processing computer system to support Tribal IV-D program operations, and...

45 CFR 309.145 - What costs are allowable for Tribal IV-D programs carried out under § 309.65(a) of this part?

Code of Federal Regulations, 2013 CFR

2013-10-01

.... (h) Automated data processing computer systems, including: (1) Planning efforts in the identification, evaluation, and selection of an automated data processing computer system solution meeting the program... existing automated data processing computer system to support Tribal IV-D program operations, and...

45 CFR 309.145 - What costs are allowable for Tribal IV-D programs carried out under § 309.65(a) of this part?

Code of Federal Regulations, 2014 CFR

2014-10-01

.... (h) Automated data processing computer systems, including: (1) Planning efforts in the identification, evaluation, and selection of an automated data processing computer system solution meeting the program... existing automated data processing computer system to support Tribal IV-D program operations, and...

45 CFR 309.145 - What costs are allowable for Tribal IV-D programs carried out under § 309.65(a) of this part?

Code of Federal Regulations, 2012 CFR

2012-10-01

.... (h) Automated data processing computer systems, including: (1) Planning efforts in the identification, evaluation, and selection of an automated data processing computer system solution meeting the program... existing automated data processing computer system to support Tribal IV-D program operations, and...

45 CFR 309.145 - What costs are allowable for Tribal IV-D programs carried out under § 309.65(a) of this part?

Code of Federal Regulations, 2011 CFR

2011-10-01

.... (h) Automated data processing computer systems, including: (1) Planning efforts in the identification, evaluation, and selection of an automated data processing computer system solution meeting the program... existing automated data processing computer system to support Tribal IV-D program operations, and...

Microbiology of beef carcasses before and after slaughterline automation.

PubMed Central

Whelehan, O. P.; Hudson, W. R.; Roberts, T. A.

1986-01-01

The bacterial status of beef carcasses at a commercial abattoir was monitored before and after slaughterline automation. Bacterial counts did not differ significantly overall (P greater than 0.05) between the original manual line and the automated line for either morning or afternoon slaughter. On the manual line counts in the morning were lower than those from carcasses slaughtered in the afternoon, but on the automated line there was no difference between morning and afternoon counts. Due to highly significant line X sample site interaction for both morning and afternoon counts, overall differences among sample sites were not found by analysis of variance. However, principal components analysis revealed a significant shift in bacterial contamination among some sites due to slaughterline changes. The incidence of Enterobacteriaceae increased marginally following automation. PMID:3701039

Automated workflows for modelling chemical fate, kinetics and toxicity.

PubMed

Sala Benito, J V; Paini, Alicia; Richarz, Andrea-Nicole; Meinl, Thorsten; Berthold, Michael R; Cronin, Mark T D; Worth, Andrew P

2017-12-01

Automation is universal in today's society, from operating equipment such as machinery, in factory processes, to self-parking automobile systems. While these examples show the efficiency and effectiveness of automated mechanical processes, automated procedures that support the chemical risk assessment process are still in their infancy. Future human safety assessments will rely increasingly on the use of automated models, such as physiologically based kinetic (PBK) and dynamic models and the virtual cell based assay (VCBA). These biologically-based models will be coupled with chemistry-based prediction models that also automate the generation of key input parameters such as physicochemical properties. The development of automated software tools is an important step in harmonising and expediting the chemical safety assessment process. In this study, we illustrate how the KNIME Analytics Platform can be used to provide a user-friendly graphical interface for these biokinetic models, such as PBK models and VCBA, which simulates the fate of chemicals in vivo within the body and in vitro test systems respectively. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Adaptive automation of human-machine system information-processing functions.

PubMed

Kaber, David B; Wright, Melanie C; Prinzel, Lawrence J; Clamann, Michael P

2005-01-01

The goal of this research was to describe the ability of human operators to interact with adaptive automation (AA) applied to various stages of complex systems information processing, defined in a model of human-automation interaction. Forty participants operated a simulation of an air traffic control task. Automated assistance was adaptively applied to information acquisition, information analysis, decision making, and action implementation aspects of the task based on operator workload states, which were measured using a secondary task. The differential effects of the forms of automation were determined and compared with a manual control condition. Results of two 20-min trials of AA or manual control revealed a significant effect of the type of automation on performance, particularly during manual control periods as part of the adaptive conditions. Humans appear to better adapt to AA applied to sensory and psychomotor information-processing functions (action implementation) than to AA applied to cognitive functions (information analysis and decision making), and AA is superior to completely manual control. Potential applications of this research include the design of automation to support air traffic controller information processing.

An automated, open-source pipeline for mass production of digital elevation models (DEMs) from very-high-resolution commercial stereo satellite imagery

NASA Astrophysics Data System (ADS)

Shean, David E.; Alexandrov, Oleg; Moratto, Zachary M.; Smith, Benjamin E.; Joughin, Ian R.; Porter, Claire; Morin, Paul

2016-06-01

We adapted the automated, open source NASA Ames Stereo Pipeline (ASP) to generate digital elevation models (DEMs) and orthoimages from very-high-resolution (VHR) commercial imagery of the Earth. These modifications include support for rigorous and rational polynomial coefficient (RPC) sensor models, sensor geometry correction, bundle adjustment, point cloud co-registration, and significant improvements to the ASP code base. We outline a processing workflow for ˜0.5 m ground sample distance (GSD) DigitalGlobe WorldView-1 and WorldView-2 along-track stereo image data, with an overview of ASP capabilities, an evaluation of ASP correlator options, benchmark test results, and two case studies of DEM accuracy. Output DEM products are posted at ˜2 m with direct geolocation accuracy of <5.0 m CE90/LE90. An automated iterative closest-point (ICP) co-registration tool reduces absolute vertical and horizontal error to <0.5 m where appropriate ground-control data are available, with observed standard deviation of ˜0.1-0.5 m for overlapping, co-registered DEMs (n = 14, 17). While ASP can be used to process individual stereo pairs on a local workstation, the methods presented here were developed for large-scale batch processing in a high-performance computing environment. We are leveraging these resources to produce dense time series and regional mosaics for the Earth's polar regions.

Automation and Intensity Modulated Radiation Therapy for Individualized High-Quality Tangent Breast Treatment Plans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Purdie, Thomas G., E-mail: Tom.Purdie@rmp.uhn.on.ca; Department of Radiation Oncology, University of Toronto, Toronto, Ontario; Techna Institute, University Health Network, Toronto, Ontario

Purpose: To demonstrate the large-scale clinical implementation and performance of an automated treatment planning methodology for tangential breast intensity modulated radiation therapy (IMRT). Methods and Materials: Automated planning was used to prospectively plan tangential breast IMRT treatment for 1661 patients between June 2009 and November 2012. The automated planning method emulates the manual steps performed by the user during treatment planning, including anatomical segmentation, beam placement, optimization, dose calculation, and plan documentation. The user specifies clinical requirements of the plan to be generated through a user interface embedded in the planning system. The automated method uses heuristic algorithms to definemore » and simplify the technical aspects of the treatment planning process. Results: Automated planning was used in 1661 of 1708 patients receiving tangential breast IMRT during the time interval studied. Therefore, automated planning was applicable in greater than 97% of cases. The time for treatment planning using the automated process is routinely 5 to 6 minutes on standard commercially available planning hardware. We have shown a consistent reduction in plan rejections from plan reviews through the standard quality control process or weekly quality review multidisciplinary breast rounds as we have automated the planning process for tangential breast IMRT. Clinical plan acceptance increased from 97.3% using our previous semiautomated inverse method to 98.9% using the fully automated method. Conclusions: Automation has become the routine standard method for treatment planning of tangential breast IMRT at our institution and is clinically feasible on a large scale. The method has wide clinical applicability and can add tremendous efficiency, standardization, and quality to the current treatment planning process. The use of automated methods can allow centers to more rapidly adopt IMRT and enhance access to the documented improvements in care for breast cancer patients, using technologies that are widely available and already in clinical use.« less

Automation and intensity modulated radiation therapy for individualized high-quality tangent breast treatment plans.

PubMed

Purdie, Thomas G; Dinniwell, Robert E; Fyles, Anthony; Sharpe, Michael B

2014-11-01

To demonstrate the large-scale clinical implementation and performance of an automated treatment planning methodology for tangential breast intensity modulated radiation therapy (IMRT). Automated planning was used to prospectively plan tangential breast IMRT treatment for 1661 patients between June 2009 and November 2012. The automated planning method emulates the manual steps performed by the user during treatment planning, including anatomical segmentation, beam placement, optimization, dose calculation, and plan documentation. The user specifies clinical requirements of the plan to be generated through a user interface embedded in the planning system. The automated method uses heuristic algorithms to define and simplify the technical aspects of the treatment planning process. Automated planning was used in 1661 of 1708 patients receiving tangential breast IMRT during the time interval studied. Therefore, automated planning was applicable in greater than 97% of cases. The time for treatment planning using the automated process is routinely 5 to 6 minutes on standard commercially available planning hardware. We have shown a consistent reduction in plan rejections from plan reviews through the standard quality control process or weekly quality review multidisciplinary breast rounds as we have automated the planning process for tangential breast IMRT. Clinical plan acceptance increased from 97.3% using our previous semiautomated inverse method to 98.9% using the fully automated method. Automation has become the routine standard method for treatment planning of tangential breast IMRT at our institution and is clinically feasible on a large scale. The method has wide clinical applicability and can add tremendous efficiency, standardization, and quality to the current treatment planning process. The use of automated methods can allow centers to more rapidly adopt IMRT and enhance access to the documented improvements in care for breast cancer patients, using technologies that are widely available and already in clinical use. Copyright © 2014 Elsevier Inc. All rights reserved.

Trust in automation: designing for appropriate reliance.

PubMed

Lee, John D; See, Katrina A

2004-01-01

Automation is often problematic because people fail to rely upon it appropriately. Because people respond to technology socially, trust influences reliance on automation. In particular, trust guides reliance when complexity and unanticipated situations make a complete understanding of the automation impractical. This review considers trust from the organizational, sociological, interpersonal, psychological, and neurological perspectives. It considers how the context, automation characteristics, and cognitive processes affect the appropriateness of trust. The context in which the automation is used influences automation performance and provides a goal-oriented perspective to assess automation characteristics along a dimension of attributional abstraction. These characteristics can influence trust through analytic, analogical, and affective processes. The challenges of extrapolating the concept of trust in people to trust in automation are discussed. A conceptual model integrates research regarding trust in automation and describes the dynamics of trust, the role of context, and the influence of display characteristics. Actual or potential applications of this research include improved designs of systems that require people to manage imperfect automation.

Screening for anabolic steroids in urine of forensic cases using fully automated solid phase extraction and LC-MS-MS.

PubMed

Andersen, David W; Linnet, Kristian

2014-01-01

A screening method for 18 frequently measured exogenous anabolic steroids and the testosterone/epitestosterone (T/E) ratio in forensic cases has been developed and validated. The method involves a fully automated sample preparation including enzyme treatment, addition of internal standards and solid phase extraction followed by analysis by liquid chromatography-tandem mass spectrometry (LC-MS-MS) using electrospray ionization with adduct formation for two compounds. Urine samples from 580 forensic cases were analyzed to determine the T/E ratio and occurrence of exogenous anabolic steroids. Extraction recoveries ranged from 77 to 95%, matrix effects from 48 to 78%, overall process efficiencies from 40 to 54% and the lower limit of identification ranged from 2 to 40 ng/mL. In the 580 urine samples analyzed from routine forensic cases, 17 (2.9%) were found positive for one or more anabolic steroids. Only seven different steroids including testosterone were found in the material, suggesting that only a small number of common steroids are likely to occur in a forensic context. The steroids were often in high concentrations (>100 ng/mL), and a combination of steroids and/or other drugs of abuse were seen in the majority of cases. The method presented serves as a fast and automated screening procedure, proving the suitability of LC-MS-MS for analyzing anabolic steroids. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

LC-MS/MS Peptide Mapping with Automated Data Processing for Routine Profiling of N-Glycans in Immunoglobulins

NASA Astrophysics Data System (ADS)

Shah, Bhavana; Jiang, Xinzhao Grace; Chen, Louise; Zhang, Zhongqi

2014-06-01

Protein N-Glycan analysis is traditionally performed by high pH anion exchange chromatography (HPAEC), reversed phase liquid chromatography (RPLC), or hydrophilic interaction liquid chromatography (HILIC) on fluorescence-labeled glycans enzymatically released from the glycoprotein. These methods require time-consuming sample preparations and do not provide site-specific glycosylation information. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) peptide mapping is frequently used for protein structural characterization and, as a bonus, can potentially provide glycan profile on each individual glycosylation site. In this work, a recently developed glycopeptide fragmentation model was used for automated identification, based on their MS/MS, of N-glycopeptides from proteolytic digestion of monoclonal antibodies (mAbs). Experimental conditions were optimized to achieve accurate profiling of glycoforms. Glycan profiles obtained from LC-MS/MS peptide mapping were compared with those obtained from HPAEC, RPLC, and HILIC analyses of released glycans for several mAb molecules. Accuracy, reproducibility, and linearity of the LC-MS/MS peptide mapping method for glycan profiling were evaluated. The LC-MS/MS peptide mapping method with fully automated data analysis requires less sample preparation, provides site-specific information, and may serve as an alternative method for routine profiling of N-glycans on immunoglobulins as well as other glycoproteins with simple N-glycans.

Automated protein identification by the combination of MALDI MS and MS/MS spectra from different instruments.

PubMed

Levander, Fredrik; James, Peter

2005-01-01

The identification of proteins separated on two-dimensional gels is most commonly performed by trypsin digestion and subsequent matrix-assisted laser desorption ionization (MALDI) with time-of-flight (TOF). Recently, atmospheric pressure (AP) MALDI coupled to an ion trap (IT) has emerged as a convenient method to obtain tandem mass spectra (MS/MS) from samples on MALDI target plates. In the present work, we investigated the feasibility of using the two methodologies in line as a standard method for protein identification. In this setup, the high mass accuracy MALDI-TOF spectra are used to calibrate the peptide precursor masses in the lower mass accuracy AP-MALDI-IT MS/MS spectra. Several software tools were developed to automate the analysis process. Two sets of MALDI samples, consisting of 142 and 421 gel spots, respectively, were analyzed in a highly automated manner. In the first set, the protein identification rate increased from 61% for MALDI-TOF only to 85% for MALDI-TOF combined with AP-MALDI-IT. In the second data set the increase in protein identification rate was from 44% to 58%. AP-MALDI-IT MS/MS spectra were in general less effective than the MALDI-TOF spectra for protein identification, but the combination of the two methods clearly enhanced the confidence in protein identification.

Efficient low-power wireless communication setup for an autonomous soil moisture sensor

NASA Astrophysics Data System (ADS)

Surducan, Vasile; Surducan, Emanoil

2017-12-01

During July 2016 - September 2017, a micro-irrigation system was set up and tested in field and greenhouse-like conditions, using eight inexpensive soil moisture sensors designed and manufactured in our institute. Each sensor was powered by accumulators charged by an (8 × 14) cm2 solar panel. The energy budget was carefully managed to allow long operating time for both the moisture sensor and the irrigation automation. We present here the hardware-software setup implemented in our proprietary moisture sensor for wireless communication, using Bluetooth Low Energy modules (BLE). The autonomy of the system may reach 4-5 cloudy days without the need of recharging the accumulators from the sun. Over the entire operating period, the moisture sensors send data wirelessly every sampling time (15 to 30 minutes) following water drips on the soil for the next 30 seconds, pushed by a low power micro pump. The micro-irrigation process is repeated every sampling time, until the soil moisture threshold is reached. In between the operating states, the sensor and watering automation go to sleep. The software algorithm ensures low energy (max. 2.8 mWh) consumption for the moisture sensor and 20 mWh for the irrigation automation, substantially increasing the accumulators discharge cycle.

Development of an automated pre-sampling plan for construction projects : final report.

DOT National Transportation Integrated Search

1983-03-01

The development of an automated pre-sampling plan was undertaken to free the district construction personnel from the cumbersome and time-consuming task of preparing such plans manually. A computer program was written and linked to a data file which ...

Automated manufacturing process for DEAP stack-actuators

NASA Astrophysics Data System (ADS)

Tepel, Dominik; Hoffstadt, Thorben; Maas, Jürgen

2014-03-01

Dielectric elastomers (DE) are thin polymer films belonging to the class of electroactive polymers (EAP), which are coated with compliant and conductive electrodes on each side. Due to the influence of an electrical field, dielectric elastomers perform a large amount of deformation. In this contribution a manufacturing process of automated fabricated stack-actuators based on dielectric electroactive polymers (DEAP) are presented. First of all the specific design of the considered stack-actuator is explained and afterwards the development, construction and realization of an automated manufacturing process is presented in detail. By applying this automated process, stack-actuators with reproducible and homogeneous properties can be manufactured. Finally, first DEAP actuator modules fabricated by the mentioned process are validated experimentally.

Can a combination of average of normals and "real time" External Quality Assurance replace Internal Quality Control?

PubMed

Badrick, Tony; Graham, Peter

2018-03-28

Internal Quality Control and External Quality Assurance are separate but related processes that have developed independently in laboratory medicine over many years. They have different sample frequencies, statistical interpretations and immediacy. Both processes have evolved absorbing new understandings of the concept of laboratory error, sample material matrix and assay capability. However, we do not believe at the coalface that either process has led to much improvement in patient outcomes recently. It is the increasing reliability and automation of analytical platforms along with improved stability of reagents that has reduced systematic and random error, which in turn has minimised the risk of running less frequent IQC. We suggest that it is time to rethink the role of both these processes and unite them into a single approach using an Average of Normals model supported by more frequent External Quality Assurance samples. This new paradigm may lead to less confusion for laboratory staff and quicker responses to and identification of out of control situations.

An Automated Energy Detection Algorithm Based on Morphological and Statistical Processing Techniques

DTIC Science & Technology

2018-01-09

ARL-TR-8272 ● JAN 2018 US Army Research Laboratory An Automated Energy Detection Algorithm Based on Morphological and...is no longer needed. Do not return it to the originator. ARL-TR-8272 ● JAN 2018 US Army Research Laboratory An Automated Energy ...4. TITLE AND SUBTITLE An Automated Energy Detection Algorithm Based on Morphological and Statistical Processing Techniques 5a. CONTRACT NUMBER

Instrument to collect fogwater for chemical analysis

NASA Astrophysics Data System (ADS)

Jacob, Daniel J.; Waldman, Jed M.; Haghi, Mehrdad; Hoffmann, Michael R.; Flagan, Richard C.

1985-06-01

An instrument is presented which collects large samples of ambient fogwater by impaction of droplets on a screen. The collection efficiency of the instrument is determined as a function of droplet size, and it is shown that fog droplets in the range 3-100-μm diameter are efficiently collected. No significant evaporation or condensation occurs at any stage of the collection process. Field testing indicates that samples collected are representative of the ambient fogwater. The instrument may easily be automated, and is suitable for use in routine air quality monitoring programs.

Oxygen-controlled automated neural differentiation of mouse embryonic stem cells.

PubMed

Mondragon-Teran, Paul; Tostoes, Rui; Mason, Chris; Lye, Gary J; Veraitch, Farlan S

2013-03-01

Automation and oxygen tension control are two tools that provide significant improvements to the reproducibility and efficiency of stem cell production processes. the aim of this study was to establish a novel automation platform capable of controlling oxygen tension during both the cell-culture and liquid-handling steps of neural differentiation processes. We built a bespoke automation platform, which enclosed a liquid-handling platform in a sterile, oxygen-controlled environment. An airtight connection was used to transfer cell culture plates to and from an automated oxygen-controlled incubator. Our results demonstrate that our system yielded comparable cell numbers, viabilities, metabolism profiles and differentiation efficiencies when compared with traditional manual processes. Interestingly, eliminating exposure to ambient conditions during the liquid-handling stage resulted in significant improvements in the yield of MAP2-positive neural cells, indicating that this level of control can improve differentiation processes. This article describes, for the first time, an automation platform capable of maintaining oxygen tension control during both the cell-culture and liquid-handling stages of a 2D embryonic stem cell differentiation process.

Automated Forensic Animal Family Identification by Nested PCR and Melt Curve Analysis on an Off-the-Shelf Thermocycler Augmented with a Centrifugal Microfluidic Disk Segment.

PubMed

Keller, Mark; Naue, Jana; Zengerle, Roland; von Stetten, Felix; Schmidt, Ulrike

2015-01-01

Nested PCR remains a labor-intensive and error-prone biomolecular analysis. Laboratory workflow automation by precise control of minute liquid volumes in centrifugal microfluidic Lab-on-a-Chip systems holds great potential for such applications. However, the majority of these systems require costly custom-made processing devices. Our idea is to augment a standard laboratory device, here a centrifugal real-time PCR thermocycler, with inbuilt liquid handling capabilities for automation. We have developed a microfluidic disk segment enabling an automated nested real-time PCR assay for identification of common European animal groups adapted to forensic standards. For the first time we utilize a novel combination of fluidic elements, including pre-storage of reagents, to automate the assay at constant rotational frequency of an off-the-shelf thermocycler. It provides a universal duplex pre-amplification of short fragments of the mitochondrial 12S rRNA and cytochrome b genes, animal-group-specific main-amplifications, and melting curve analysis for differentiation. The system was characterized with respect to assay sensitivity, specificity, risk of cross-contamination, and detection of minor components in mixtures. 92.2% of the performed tests were recognized as fluidically failure-free sample handling and used for evaluation. Altogether, augmentation of the standard real-time thermocycler with a self-contained centrifugal microfluidic disk segment resulted in an accelerated and automated analysis reducing hands-on time, and circumventing the risk of contamination associated with regular nested PCR protocols.

[The actual possibilities of robotic microscopy in analysis automation and laboratory telemedicine].

PubMed

Medovyĭ, V S; Piatnitskiĭ, A M; Sokolinskiĭ, B Z; Balugian, R Sh

2012-10-01

The article discusses the possibilities of automation microscopy complexes manufactured by Cellavision and MEKOS to perform the medical analyses of blood films and other biomaterials. The joint work of the complex and physician in the regimen of automatic load stages, screening, sampling and sorting on types with simple morphology, visual sorting of sub-sample with complex morphology provides significant increase of method sensitivity, load decrease and enhancement of physician work conditions. The information technologies, the virtual slides and laboratory telemedicine included permit to develop the representative samples of rare types and pathologies to promote automation methods and medical research targets.

Combined Falling Drop/Open Port Sampling Interface System for Automated Flow Injection Mass Spectrometry

DOE PAGES

Van Berkel, Gary J.; Kertesz, Vilmos; Orcutt, Matt; ...

2017-11-07

The aim of this work was to demonstrate and to evaluate the analytical performance of a combined falling drop/open port sampling interface (OPSI) system as a simple noncontact, no-carryover, automated system for flow injection analysis with mass spectrometry. The falling sample drops were introduced into the OPSI using a widely available autosampler platform utilizing low cost disposable pipet tips and conventional disposable microtiter well plates. The volume of the drops that fell onto the OPSI was in the 7–15 μL range with an injected sample volume of several hundred nanoliters. Sample drop height, positioning of the internal capillary on themore » sampling end of the probe, and carrier solvent flow rate were optimized for maximum signal. Sample throughput, signal reproducibility, matrix effects, and quantitative analysis capability of the system were established using the drug molecule propranolol and its isotope labeled internal standard in water, unprocessed river water and two commercially available buffer matrices. A sample-to-sample throughput of ~45 s with a ~4.5 s base-to-base flow injection peak profile was obtained in these experiments. In addition, quantitation with minimally processed rat plasma samples was demonstrated with three different statin drugs (atorvastatin, rosuvastatin, and fluvastatin). Direct characterization capability of unprocessed samples was demonstrated by the analysis of neat vegetable oils. Employing the autosampler system for spatially resolved liquid extraction surface sampling exemplified by the analysis of propranolol and its hydroxypropranolol glucuronide phase II metabolites from a rat thin tissue section was also illustrated.« less

Combined Falling Drop/Open Port Sampling Interface System for Automated Flow Injection Mass Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Berkel, Gary J.; Kertesz, Vilmos; Orcutt, Matt

The aim of this work was to demonstrate and to evaluate the analytical performance of a combined falling drop/open port sampling interface (OPSI) system as a simple noncontact, no-carryover, automated system for flow injection analysis with mass spectrometry. The falling sample drops were introduced into the OPSI using a widely available autosampler platform utilizing low cost disposable pipet tips and conventional disposable microtiter well plates. The volume of the drops that fell onto the OPSI was in the 7–15 μL range with an injected sample volume of several hundred nanoliters. Sample drop height, positioning of the internal capillary on themore » sampling end of the probe, and carrier solvent flow rate were optimized for maximum signal. Sample throughput, signal reproducibility, matrix effects, and quantitative analysis capability of the system were established using the drug molecule propranolol and its isotope labeled internal standard in water, unprocessed river water and two commercially available buffer matrices. A sample-to-sample throughput of ~45 s with a ~4.5 s base-to-base flow injection peak profile was obtained in these experiments. In addition, quantitation with minimally processed rat plasma samples was demonstrated with three different statin drugs (atorvastatin, rosuvastatin, and fluvastatin). Direct characterization capability of unprocessed samples was demonstrated by the analysis of neat vegetable oils. Employing the autosampler system for spatially resolved liquid extraction surface sampling exemplified by the analysis of propranolol and its hydroxypropranolol glucuronide phase II metabolites from a rat thin tissue section was also illustrated.« less

Augmenting team cognition in human-automation teams performing in complex operational environments.

PubMed

Cuevas, Haydee M; Fiore, Stephen M; Caldwell, Barrett S; Strater, Laura

2007-05-01

There is a growing reliance on automation (e.g., intelligent agents, semi-autonomous robotic systems) to effectively execute increasingly cognitively complex tasks. Successful team performance for such tasks has become even more dependent on team cognition, addressing both human-human and human-automation teams. Team cognition can be viewed as the binding mechanism that produces coordinated behavior within experienced teams, emerging from the interplay between each team member's individual cognition and team process behaviors (e.g., coordination, communication). In order to better understand team cognition in human-automation teams, team performance models need to address issues surrounding the effect of human-agent and human-robot interaction on critical team processes such as coordination and communication. Toward this end, we present a preliminary theoretical framework illustrating how the design and implementation of automation technology may influence team cognition and team coordination in complex operational environments. Integrating constructs from organizational and cognitive science, our proposed framework outlines how information exchange and updating between humans and automation technology may affect lower-level (e.g., working memory) and higher-level (e.g., sense making) cognitive processes as well as teams' higher-order "metacognitive" processes (e.g., performance monitoring). Issues surrounding human-automation interaction are discussed and implications are presented within the context of designing automation technology to improve task performance in human-automation teams.

Film/Adhesive Processing Module for Fiber-Placement Processing of Composites

NASA Technical Reports Server (NTRS)

Hulcher, A. Bruce

2007-01-01

An automated apparatus has been designed and constructed that enables the automated lay-up of composite structures incorporating films, foils, and adhesives during the automated fiber-placement process. This apparatus, denoted a film module, could be used to deposit materials in film or thin sheet form either simultaneously when laying down the fiber composite article or in an independent step.

Automated extraction for the analysis of 11-nor-delta9-tetrahydrocannabinol-9-carboxylic acid (THCCOOH) in urine using a six-head probe Hamilton Microlab 2200 system and gas chromatography-mass spectrometry.

PubMed

Whitter, P D; Cary, P L; Leaton, J I; Johnson, J E

1999-01-01

An automated extraction scheme for the analysis of 11 -nor-delta9-tetrahydrocannabinol-9-carboxylic acid using the Hamilton Microlab 2200, which was modified for gravity-flow solid-phase extraction, has been evaluated. The Hamilton was fitted with a six-head probe, a modular valve positioner, and a peristaltic pump. The automated method significantly increased sample throughput, improved assay consistency, and reduced the time spent performing the extraction. Extraction recovery for the automated method was > 90%. The limit of detection, limit of quantitation, and upper limit of linearity were equivalent to the manual method: 1.5, 3.0, and 300 ng/mL, respectively. Precision at the 15-ng/mL cut-off was as follows: mean = 14.4, standard deviation = 0.5, coefficient of variation = 3.5%. Comparison of 38 patient samples, extracted by the manual and automated extraction methods, demonstrated the following correlation statistics: r = .991, slope 1.029, and y-intercept -2.895. Carryover was < 0.3% at 1000 ng/mL. Aliquoting/extraction time for the automated method (48 urine samples) was 50 min, and the manual procedure required approximately 2.5 h. The automated aliquoting/extraction method on the Hamilton Microlab 2200 and its use in forensic applications are reviewed.

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 the phenology, solar-view geometry, and atmospheric condition etc. factors but not actual landcover difference. Finally, we will compare the classification results from screened and unscreened training samples to assess the improvement achieved by cleaning up the training samples. Keywords:

Agile based "Semi-"Automated Data ingest process : ORNL DAAC example

NASA Astrophysics Data System (ADS)

Santhana Vannan, S. K.; Beaty, T.; Cook, R. B.; Devarakonda, R.; Hook, L.; Wei, Y.; Wright, D.

2015-12-01

The ORNL DAAC archives and publishes data and information relevant to biogeochemical, ecological, and environmental processes. The data archived at the ORNL DAAC must be well formatted, self-descriptive, and documented, as well as referenced in a peer-reviewed publication. The ORNL DAAC ingest team curates diverse data sets from multiple data providers simultaneously. To streamline the ingest process, the data set submission process at the ORNL DAAC has been recently updated to use an agile process and a semi-automated workflow system has been developed to provide a consistent data provider experience and to create a uniform data product. The goals of semi-automated agile ingest process are to: 1.Provide the ability to track a data set from acceptance to publication 2. Automate steps that can be automated to improve efficiencies and reduce redundancy 3.Update legacy ingest infrastructure 4.Provide a centralized system to manage the various aspects of ingest. This talk will cover the agile methodology, workflow, and tools developed through this system.

Automation Bias: Decision Making and Performance in High-Tech Cockpits

NASA Technical Reports Server (NTRS)

Mosier, Kathleen L.; Skitka, Linda J.; Heers, Susan; Burdick, Mark; Rosekind, Mark R. (Technical Monitor)

1997-01-01

Automated aids and decision support tools are rapidly becoming indispensible tools in high-technology cockpits, and are assuming increasing control of "cognitive" flight tasks, such as calculating fuel-efficient routes, navigating, or detecting and diagnosing system malfunctions and abnormalities. This study was designed to investigate "automation bias," a recently documented factor in the use of automated aids and decision support systems. The term refers to omission and commission errors resulting from the use of automated cues as a heuristic replacement for vigilant information seeking and processing. Glass-cockpit pilots flew flight scenarios involving automation "events," or opportunities for automation-related omission and commission errors. Pilots who perceived themselves as "accountable" for their performance and strategies of interaction with the automation were more likely to double-check automated functioning against other cues, and less likely to commit errors. Pilots were also likely to erroneously "remember" the presence of expected cues when describing their decision-making processes.

An integratable microfluidic cartridge for forensic swab samples lysis.

PubMed

Yang, Jianing; Brooks, Carla; Estes, Matthew D; Hurth, Cedric M; Zenhausern, Frederic

2014-01-01

Fully automated rapid forensic DNA analysis requires integrating several multistep processes onto a single microfluidic platform, including substrate lysis, extraction of DNA from the released lysate solution, multiplexed PCR amplification of STR loci, separation of PCR products by capillary electrophoresis, and analysis for allelic peak calling. Over the past several years, most of the rapid DNA analysis systems developed started with the reference swab sample lysate and involved an off-chip lysis of collected substrates. As a result of advancement in technology and chemistry, addition of a microfluidic module for swab sample lysis has been achieved in a few of the rapid DNA analysis systems. However, recent reports on integrated rapid DNA analysis systems with swab-in and answer-out capability lack any quantitative and qualitative characterization of the swab-in sample lysis module, which is important for downstream forensic sample processing. Maximal collection and subsequent recovery of the biological material from the crime scene is one of the first and critical steps in forensic DNA technology. Herein we present the design, fabrication and characterization of an integratable swab lysis cartridge module and the test results obtained from different types of commonly used forensic swab samples, including buccal, saliva, and blood swab samples, demonstrating the compatibility with different downstream DNA extraction chemistries. This swab lysis cartridge module is easy to operate, compatible with both forensic and microfluidic requirements, and ready to be integrated with our existing automated rapid forensic DNA analysis system. Following the characterization of the swab lysis module, an integrated run from buccal swab sample-in to the microchip CE electropherogram-out was demonstrated on the integrated prototype instrument. Therefore, in this study, we demonstrate that this swab lysis cartridge module is: (1) functionally, comparable with routine benchtop lysis, (2) compatible with various types of swab samples and chemistries, and (3) integratable to achieve a micro total analysis system (μTAS) for rapid DNA analysis. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

45 CFR 310.5 - What options are available for Computerized Tribal IV-D Systems and office automation?

Code of Federal Regulations, 2010 CFR

2010-10-01

... to conduct automated data processing and recordkeeping activities through Office Automation... IV-D Systems and office automation? 310.5 Section 310.5 Public Welfare Regulations Relating to Public... AUTOMATION Requirements for Computerized Tribal IV-D Systems and Office Automation § 310.5 What options are...

An Automation Survival Guide for Media Centers.

ERIC Educational Resources Information Center

Whaley, Roger E.

1989-01-01

Reviews factors that should affect the decision to automate a school media center and offers suggestions for the automation process. Topics discussed include getting the library collection ready for automation, deciding what automated functions are needed, evaluating software vendors, selecting software, and budgeting. (CLB)

Human Papillomavirus (HPV) Genotyping: Automation and Application in Routine Laboratory Testing

PubMed Central

Torres, M; Fraile, L; Echevarria, JM; Hernandez Novoa, B; Ortiz, M

2012-01-01

A large number of assays designed for genotyping human papillomaviruses (HPV) have been developed in the last years. They perform within a wide range of analytical sensitivity and specificity values for the different viral types, and are used either for diagnosis, epidemiological studies, evaluation of vaccines and implementing and monitoring of vaccination programs. Methods for specific genotyping of HPV-16 and HPV-18 are also useful for the prevention of cervical cancer in screening programs. Some commercial tests are, in addition, fully or partially automated. Automation of HPV genotyping presents advantages such as the simplicity of the testing procedure for the operator, the ability to process a large number of samples in a short time, and the reduction of human errors from manual operations, allowing a better quality assurance and a reduction of cost. The present review collects information about the current HPV genotyping tests, with special attention to practical aspects influencing their use in clinical laboratories. PMID:23248734

SYRIAC: The systematic review information automated collection system a data warehouse for facilitating automated biomedical text classification.

PubMed

Yang, Jianji J; Cohen, Aaron M; Cohen, Aaron; McDonagh, Marian S

2008-11-06

Automatic document classification can be valuable in increasing the efficiency in updating systematic reviews (SR). In order for the machine learning process to work well, it is critical to create and maintain high-quality training datasets consisting of expert SR inclusion/exclusion decisions. This task can be laborious, especially when the number of topics is large and source data format is inconsistent.To approach this problem, we build an automated system to streamline the required steps, from initial notification of update in source annotation files to loading the data warehouse, along with a web interface to monitor the status of each topic. In our current collection of 26 SR topics, we were able to standardize almost all of the relevance judgments and recovered PMIDs for over 80% of all articles. Of those PMIDs, over 99% were correct in a manual random sample study. Our system performs an essential function in creating training and evaluation data sets for SR text mining research.

SYRIAC: The SYstematic Review Information Automated Collection System A Data Warehouse for Facilitating Automated Biomedical Text Classification

PubMed Central

Yang, Jianji J.; Cohen, Aaron M.; McDonagh, Marian S.

2008-01-01

Automatic document classification can be valuable in increasing the efficiency in updating systematic reviews (SR). In order for the machine learning process to work well, it is critical to create and maintain high-quality training datasets consisting of expert SR inclusion/exclusion decisions. This task can be laborious, especially when the number of topics is large and source data format is inconsistent. To approach this problem, we build an automated system to streamline the required steps, from initial notification of update in source annotation files to loading the data warehouse, along with a web interface to monitor the status of each topic. In our current collection of 26 SR topics, we were able to standardize almost all of the relevance judgments and recovered PMIDs for over 80% of all articles. Of those PMIDs, over 99% were correct in a manual random sample study. Our system performs an essential function in creating training and evaluation datasets for SR text mining research. PMID:18999194

High-speed autoverifying technology for printed wiring boards

NASA Astrophysics Data System (ADS)

Ando, Moritoshi; Oka, Hiroshi; Okada, Hideo; Sakashita, Yorihiro; Shibutani, Nobumi

1996-10-01

We have developed an automated pattern verification technique. The output of an automated optical inspection system contains many false alarms. Verification is needed to distinguish between minor irregularities and serious defects. In the past, this verification was usually done manually, which led to unsatisfactory product quality. The goal of our new automated verification system is to detect pattern features on surface mount technology boards. In our system, we employ a new illumination method, which uses multiple colors and multiple direction illumination. Images are captured with a CCD camera. We have developed a new algorithm that uses CAD data for both pattern matching and pattern structure determination. This helps to search for patterns around a defect and to examine defect definition rules. These are processed with a high speed workstation and a hard-wired circuits. The system can verify a defect within 1.5 seconds. The verification system was tested in a factory. It verified 1,500 defective samples and detected all significant defects with only a 0.1 percent of error rate (false alarm).

Compact and light-weight automated semen analysis platform using lensfree on-chip microscopy.

PubMed

Su, Ting-Wei; Erlinger, Anthony; Tseng, Derek; Ozcan, Aydogan

2010-10-01

We demonstrate a compact and lightweight platform to conduct automated semen analysis using a lensfree on-chip microscope. This holographic on-chip imaging platform weighs ∼46 g, measures ∼4.2 × 4.2 × 5.8 cm, and does not require any lenses, lasers or other bulky optical components to achieve phase and amplitude imaging of sperms over ∼24 mm(2) field-of-view with an effective numerical aperture of ∼0.2. Using this wide-field lensfree on-chip microscope, semen samples are imaged for ∼10 s, capturing a total of ∼20 holographic frames. Digital subtraction of these consecutive lensfree frames, followed by appropriate processing of the reconstructed images, enables automated quantification of the count, the speed and the dynamic trajectories of motile sperms, while summation of the same frames permits counting of immotile sperms. Such a compact and lightweight automated semen analysis platform running on a wide-field lensfree on-chip microscope could be especially important for fertility clinics, personal male fertility tests, as well as for field use in veterinary medicine such as in stud farming and animal breeding applications.

Tests of Spectral Cloud Classification Using DMSP Fine Mode Satellite Data.

DTIC Science & Technology

1980-06-02

processing techniques of potential value. Fourier spectral analysis was identified as the most promising technique to upgrade automated processing of...these measurements on the Earth’s surface is 0. 3 n mi. 3. Pickett, R.M., and Blackman, E.S. (1976) Automated Processing of Satellite Imagery Data at Air...and Pickett. R. Al. (1977) Automated Processing of Satellite Imagery Data at the Air Force Global Weather Central: Demonstrations of Spectral Analysis

Fast and accurate determination of arsenobetaine in fish tissues using accelerated solvent extraction and HPLC-ICP-MS determination.

PubMed

Wahlen, Raimund

2004-04-01

A high-performance liquid chromatography-inductively coupled plasma-mass spectrometry (HPLC-ICP-MS) method has been developed for the fast and accurate analysis of arsenobetaine (AsB) in fish samples extracted by accelerated solvent extraction. The combined extraction and analysis approach is validated using certified reference materials for AsB in fish and during a European intercomparison exercise with a blind sample. Up to six species of arsenic (As) can be separated and quantitated in the extracts within a 10-min isocratic elution. The method is optimized so as to minimize time-consuming sample preparation steps and allow for automated extraction and analysis of large sample batches. A comparison of standard addition and external calibration show no significant difference in the results obtained, which indicates that the LC-ICP-MS method is not influenced by severe matrix effects. The extraction procedure can process up to 24 samples in an automated manner, yet the robustness of the developed HPLC-ICP-MS approach is highlighted by the capability to run more than 50 injections per sequence, which equates to a total run-time of more than 12 h. The method can therefore be used to rapidly and accurately assess the proportion of nontoxic AsB in fish samples with high total As content during toxicological screening studies.

Can the Roche hemolysis index be used for automated determination of cell-free hemoglobin? A comparison to photometric assays.

PubMed

Petrova, Darinka Todorova; Cocisiu, Gabriela Ariadna; Eberle, Christoph; Rhode, Karl-Heinz; Brandhorst, Gunnar; Walson, Philip D; Oellerich, Michael

2013-09-01

The aim of this study was to develop a novel method for automated quantification of cell-free hemoglobin (fHb) based on the HI (Roche Diagnostics). The novel fHb method based on the HI was correlated with fHb measured using the triple wavelength methods of both Harboe [fHb, g/L = (0.915 * HI + 2.634)/100] and Fairbanks et al. [fHb, g/L = (0.917 * HI + 2.131)/100]. fHb concentrations were estimated from the HI using the Roche Modular automated platform in self-made and commercially available quality controls, as well as samples from a proficiency testing scheme (INSTAND). The fHb using Roche automated HI results were then compared to results obtained using the traditional spectrophotometric assays for one hundred plasma samples with varying degrees of hemolysis, lipemia and/or bilirubinemia. The novel method using automated HI quantification on the Roche Modular clinical chemistry platform correlated well with results using the classical methods in the 100 patient samples (Harboe: r = 0.9284; Fairbanks et al.: r = 0.9689) and recovery was good for self-made controls. However, commercially available quality controls showed poor recovery due to an unidentified matrix problem. The novel method produced reliable determination of fHb in samples without interferences. However, poor recovery using commercially available fHb quality control samples currently greatly limits its usefulness. © 2013.

Armored Combat Vehicles Science and Technology Plan

DTIC Science & Technology

1982-11-01

APPLICATION OF SENSORS Investigate the seismic, acoustic, and electromagnetic signatures of military and intruder -type targets and the theoretical aspects...a prototype sampling system which has the capability to monitor ambieut air both outside and inside vehicles and provide an early warning to the crew...and through various processing modules provide automated functions for simultaneous tracking of targets and automitic recognition, 74 f’," SENSING

Development of an Automated DNA Detection System Using an Electrochemical DNA Chip Technology

NASA Astrophysics Data System (ADS)

Hongo, Sadato; Okada, Jun; Hashimoto, Koji; Tsuji, Koichi; Nikaido, Masaru; Gemma, Nobuhiro

A new compact automated DNA detection system Genelyzer™ has been developed. After injecting a sample solution into a cassette with a built-in electrochemical DNA chip, processes from hybridization reaction to detection and analysis are all operated fully automatically. In order to detect a sample DNA, electrical currents from electrodes due to an oxidization reaction of electrochemically active intercalator molecules bound to hybridized DNAs are detected. The intercalator is supplied as a reagent solution by a fluid supply unit of the system. The feasibility test proved that the simultaneous typing of six single nucleotide polymorphisms (SNPs) associated with a rheumatoid arthritis (RA) was carried out within two hours and that all the results were consistent with those by conventional typing methods. It is expected that this system opens a new way to a DNA testing such as a test for infectious diseases, a personalized medicine, a food inspection, a forensic application and any other applications.

The laboratory of the 1990s—Planning for total automation

PubMed Central

Brunner, Linda A.

1992-01-01

The analytical laboratory of the 1990s must be able to meet and accommodate the rapid evolution of modern-day technology. One such area is laboratory automation. Total automation may be seen as the coupling of computerized sample tracking, electronic documentation and data reduction with automated sample handling, preparation and analysis, resulting in a complete analytical procedure with minimal human involvement. Requirements may vary from one laboratory or facility to another, so the automation has to be flexible enough to cover a wide range of applications, and yet fit into specific niches depending on individual needs. Total automation must be planned for, well in advance, if the endeavour is to be a success. Space, laboratory layout, proper equipment, and the availability and access to necessary utilities must be taken into account. Adequate training and experience of the personnel working with the technology must also be ensured. In addition, responsibilities of installation, programming maintenance and operation have to be addressed. Proper time management and the efficient implementation and use of total automation are also crucial to successful operations. This paper provides insights into laboratory organization and requirements, as well as discussing the management issues that must be faced when automating laboratory procedures. PMID:18924925

NASA Global Atmospheric Sampling Program (GASP) data report for tape VL0006

NASA Technical Reports Server (NTRS)

Gauntner, D. J.; Holdeman, J. D.; Humenik, F. M.

1977-01-01

The NASA Global Atmospheric Sampling Program (GASP) is obtaining measurements of atmospheric trace constituents in the upper troposphere and lower stratosphere using fully automated air sampling systems on board several commercial B-747 aircraft in routine airline service. Atmospheric ozone, and related flight and meteorological data were obtained during 245 flights of a Qantas Airways of Australia B-747 and two Pan American World Airways B-747s from July 1976 through September 1976. In addition, whole air samples, obtained during three flights, were analyzed for trichlorofluoromethane, and filter samples, obtained during four flights, were analyzed for sulfates, nitrates, fluorides, and chlorides. Flight routes and dates, instrumentation, data processing procedures, data tape specifications, and selected analyses are discussed.

Magnetic separations in biotechnology.

PubMed

Borlido, L; Azevedo, A M; Roque, A C A; Aires-Barros, M R

2013-12-01

Magnetic separations are probably one of the most versatile separation processes in biotechnology as they are able to purify cells, viruses, proteins and nucleic acids directly from crude samples. The fast and gentle process in combination with its easy scale-up and automation provide unique advantages over other separation techniques. In the midst of this process are the magnetic adsorbents tailored for the envisioned target and whose complex synthesis spans over multiple fields of science. In this context, this article reviews both the synthesis and tailoring of magnetic adsorbents for bioseparations as well as their ultimate application. Copyright © 2013 Elsevier Inc. All rights reserved.

Enhanced clinical-scale manufacturing of TCR transduced T-cells using closed culture system modules.

PubMed

Jin, Jianjian; Gkitsas, Nikolaos; Fellowes, Vicki S; Ren, Jiaqiang; Feldman, Steven A; Hinrichs, Christian S; Stroncek, David F; Highfill, Steven L

2018-01-24

Genetic engineering of T-cells to express specific T cell receptors (TCR) has emerged as a novel strategy to treat various malignancies. More widespread utilization of these types of therapies has been somewhat constrained by the lack of closed culture processes capable of expanding sufficient numbers of T-cells for clinical application. Here, we evaluate a process for robust clinical grade manufacturing of TCR gene engineered T-cells. TCRs that target human papillomavirus E6 and E7 were independently tested. A 21 day process was divided into a transduction phase (7 days) and a rapid expansion phase (14 days). This process was evaluated using two healthy donor samples and four samples obtained from patients with epithelial cancers. The process resulted in ~ 2000-fold increase in viable nucleated cells and high transduction efficiencies (64-92%). At the end of culture, functional assays demonstrated that these cells were potent and specific in their ability to kill tumor cells bearing target and secrete large quantities of interferon and tumor necrosis factor. Both phases of culture were contained within closed or semi-closed modules, which include automated density gradient separation and cell culture bags for the first phase and closed GREX culture devices and wash/concentrate systems for the second phase. Large-scale manufacturing using modular systems and semi-automated devices resulted in highly functional clinical-grade TCR transduced T-cells. This process is now in use in actively accruing clinical trials and the NIH Clinical Center and can be utilized at other cell therapy manufacturing sites that wish to scale-up and optimize their processing using closed systems.

Comparison of supervised machine learning algorithms for waterborne pathogen detection using mobile phone fluorescence microscopy

NASA Astrophysics Data System (ADS)

Ceylan Koydemir, Hatice; Feng, Steve; Liang, Kyle; Nadkarni, Rohan; Benien, Parul; Ozcan, Aydogan

2017-06-01

Giardia lamblia is a waterborne parasite that affects millions of people every year worldwide, causing a diarrheal illness known as giardiasis. Timely detection of the presence of the cysts of this parasite in drinking water is important to prevent the spread of the disease, especially in resource-limited settings. Here we provide extended experimental testing and evaluation of the performance and repeatability of a field-portable and cost-effective microscopy platform for automated detection and counting of Giardia cysts in water samples, including tap water, non-potable water, and pond water. This compact platform is based on our previous work, and is composed of a smartphone-based fluorescence microscope, a disposable sample processing cassette, and a custom-developed smartphone application. Our mobile phone microscope has a large field of view of 0.8 cm2 and weighs only 180 g, excluding the phone. A custom-developed smartphone application provides a user-friendly graphical interface, guiding the users to capture a fluorescence image of the sample filter membrane and analyze it automatically at our servers using an image processing algorithm and training data, consisting of >30,000 images of cysts and >100,000 images of other fluorescent particles that are captured, including, e.g. dust. The total time that it takes from sample preparation to automated cyst counting is less than an hour for each 10 ml of water sample that is tested. We compared the sensitivity and the specificity of our platform using multiple supervised classification models, including support vector machines and nearest neighbors, and demonstrated that a bootstrap aggregating (i.e. bagging) approach using raw image file format provides the best performance for automated detection of Giardia cysts. We evaluated the performance of this machine learning enabled pathogen detection device with water samples taken from different sources (e.g. tap water, non-potable water, pond water) and achieved a limit of detection of 12 cysts per 10 ml, an average cyst capture efficiency of 79%, and an accuracy of 95%. Providing rapid detection and quantification of waterborne pathogens without the need for a microbiology expert, this field-portable imaging and sensing platform running on a smartphone could be very useful for water quality monitoring in resource-limited settings.

Protocol: high throughput silica-based purification of RNA from Arabidopsis seedlings in a 96-well format

PubMed Central

2011-01-01

The increasing popularity of systems-based approaches to plant research has resulted in a demand for high throughput (HTP) methods to be developed. RNA extraction from multiple samples in an experiment is a significant bottleneck in performing systems-level genomic studies. Therefore we have established a high throughput method of RNA extraction from Arabidopsis thaliana to facilitate gene expression studies in this widely used plant model. We present optimised manual and automated protocols for the extraction of total RNA from 9-day-old Arabidopsis seedlings in a 96 well plate format using silica membrane-based methodology. Consistent and reproducible yields of high quality RNA are isolated averaging 8.9 μg total RNA per sample (~20 mg plant tissue). The purified RNA is suitable for subsequent qPCR analysis of the expression of over 500 genes in triplicate from each sample. Using the automated procedure, 192 samples (2 × 96 well plates) can easily be fully processed (samples homogenised, RNA purified and quantified) in less than half a day. Additionally we demonstrate that plant samples can be stored in RNAlater at -20°C (but not 4°C) for 10 months prior to extraction with no significant effect on RNA yield or quality. Additionally, disrupted samples can be stored in the lysis buffer at -20°C for at least 6 months prior to completion of the extraction procedure providing a flexible sampling and storage scheme to facilitate complex time series experiments. PMID:22136293

Protocol: high throughput silica-based purification of RNA from Arabidopsis seedlings in a 96-well format.

PubMed

Salvo-Chirnside, Eliane; Kane, Steven; Kerr, Lorraine E

2011-12-02

The increasing popularity of systems-based approaches to plant research has resulted in a demand for high throughput (HTP) methods to be developed. RNA extraction from multiple samples in an experiment is a significant bottleneck in performing systems-level genomic studies. Therefore we have established a high throughput method of RNA extraction from Arabidopsis thaliana to facilitate gene expression studies in this widely used plant model. We present optimised manual and automated protocols for the extraction of total RNA from 9-day-old Arabidopsis seedlings in a 96 well plate format using silica membrane-based methodology. Consistent and reproducible yields of high quality RNA are isolated averaging 8.9 μg total RNA per sample (~20 mg plant tissue). The purified RNA is suitable for subsequent qPCR analysis of the expression of over 500 genes in triplicate from each sample. Using the automated procedure, 192 samples (2 × 96 well plates) can easily be fully processed (samples homogenised, RNA purified and quantified) in less than half a day. Additionally we demonstrate that plant samples can be stored in RNAlater at -20°C (but not 4°C) for 10 months prior to extraction with no significant effect on RNA yield or quality. Additionally, disrupted samples can be stored in the lysis buffer at -20°C for at least 6 months prior to completion of the extraction procedure providing a flexible sampling and storage scheme to facilitate complex time series experiments.

Space station automation study: Automation requirements derived from space manufacturing concepts. Volume 1: Executive summary

NASA Technical Reports Server (NTRS)

1984-01-01

The electroepitaxial process and the Very Large Scale Integration (VLSI) circuits (chips) facilities were chosen because each requires a very high degree of automation, and therefore involved extensive use of teleoperators, robotics, process mechanization, and artificial intelligence. Both cover a raw materials process and a sophisticated multi-step process and are therfore highly representative of the kinds of difficult operation, maintenance, and repair challenges which can be expected for any type of space manufacturing facility. Generic areas were identified which will require significant further study. The initial design will be based on terrestrial state-of-the-art hard automation. One hundred candidate missions were evaluated on the basis of automation portential and availability of meaning ful knowldege. The design requirements and unconstrained design concepts developed for the two missions are presented.

Automation of serum (1→3)-beta-D-glucan testing allows reliable and rapid discrimination of patients with and without candidemia.

PubMed

Prüller, Florian; Wagner, Jasmin; Raggam, Reinhard B; Hoenigl, Martin; Kessler, Harald H; Truschnig-Wilders, Martie; Krause, Robert

2014-07-01

Testing for (1→3)-beta-D-glucan (BDG) is used for detection of invasive fungal infection. However, current assays lack automation and the ability to conduct rapid single-sample testing. The Fungitell assay was adopted for automation and evaluated using clinical samples from patients with culture-proven candidemia and from culture-negative controls in duplicate. A comparison with the standard assay protocol was made in order to establish analytical specifications. With the automated protocol, the analytical measuring range was 8-2500 pg/ml of BDG, and precision testing resulted in coefficients of variation that ranged from 3.0% to 5.5%. Samples from 15 patients with culture-proven candidemia and 94 culture-negative samples were evaluated. All culture-proven samples showed BDG values >80 pg/ml (mean 1247 pg/ml; range, 116-2990 pg/ml), which were considered positive. Of the 94 culture-negative samples, 92 had BDG values <60 pg/ml (mean, 28 pg/ml), which were considered to be negative, and 2 samples were false-positive (≥80 pg/ml; up to 124 pg/ml). Results could be obtained within 45 min and showed excellent agreement with results obtained with the standard assay protocol. The automated Fungitell assay proved to be reliable and rapid for diagnosis of candidemia. It was demonstrated to be feasible and cost efficient for both single-sample and large-scale testing of serum BDG. Its 1-h time-to-result will allow better support for clinicians in the management of antifungal therapy. © The Author 2014. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A compendium of controlled diffusion blades generated by an automated inverse design procedure

NASA Technical Reports Server (NTRS)

Sanz, Jose M.

1989-01-01

A set of sample cases was produced to test an automated design procedure developed at the NASA Lewis Research Center for the design of controlled diffusion blades. The range of application of the automated design procedure is documented. The results presented include characteristic compressor and turbine blade sections produced with the automated design code as well as various other airfoils produced with the base design method prior to the incorporation of the automated procedure.

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.

Single-run determination of polybrominated diphenyl ethers (PBDEs) di- to deca-brominated in fish meal, fish oil and fish feed by isotope dilution: application of automated sample purification and gas chromatography/ion trap tandem mass spectrometry (GC/ITMS).

PubMed

Blanco, Sonia Lucía; Vieites, Juan M

2010-07-05

The present paper describes the application of automated cleanup and fractionation procedures of the Power Prep system (Fluid Management Systems) for the determination of polybrominated diphenyl ethers (PBDEs) in feeding stuffs and fish meal and oil. Gas chromatography (GC) separation followed by ion trap tandem mass spectrometry detection in EI mode (ITMS) allowed the analysis of di- to deca-BDEs in the samples matrices used in fish aquaculture. The method developed enabled the determination of 26 native PBDE congeners and 11 (13)C(12)-labelled congeners, including deca-BDE 209, in a single-run analysis, using isotope dilution. The automated cleanup, consisting of a succession of multilayer silica and basic alumina columns previously applied by Wyrzykowska et al. (2009) [28] in combustion flue gas, was successfully applied in our complex matrices. The method allowed an increase in productivity, i.e. lower time was required to process samples, and simultaneous purification of several samples was achieved at a time, reducing analyst dedication and human error input. Average recoveries of 43-96% were obtained. GC/ITMS can overcome the complexity originating from the sample matrix, eliminating matrix effects by tandem MS, to enable the detection of congeners penta- to nona-BDEs where interferent masses were present. The provisional detection limits, estimated in the samples, were 5-30 pg for di-, tri-, tetra-, and penta-BDEs, 20-65 pg for hexa-, hepta-, octa- and nona-BDEs, and 105 pg for deca-BDE. Reduction of deca-BDE 209 blank values is of concern to ongoing research. Good accuracy was obtained by application of the whole procedure, representing an efficient, low-cost and fast alternative for routine analyses. Copyright 2010 Elsevier B.V. All rights reserved.

Improved compliance by BPM-driven workflow automation.

PubMed

Holzmüller-Laue, Silke; Göde, Bernd; Fleischer, Heidi; Thurow, Kerstin

2014-12-01

Using methods and technologies of business process management (BPM) for the laboratory automation has important benefits (i.e., the agility of high-level automation processes, rapid interdisciplinary prototyping and implementation of laboratory tasks and procedures, and efficient real-time process documentation). A principal goal of the model-driven development is the improved transparency of processes and the alignment of process diagrams and technical code. First experiences of using the business process model and notation (BPMN) show that easy-to-read graphical process models can achieve and provide standardization of laboratory workflows. The model-based development allows one to change processes quickly and an easy adaption to changing requirements. The process models are able to host work procedures and their scheduling in compliance with predefined guidelines and policies. Finally, the process-controlled documentation of complex workflow results addresses modern laboratory needs of quality assurance. BPMN 2.0 as an automation language to control every kind of activity or subprocess is directed to complete workflows in end-to-end relationships. BPMN is applicable as a system-independent and cross-disciplinary graphical language to document all methods in laboratories (i.e., screening procedures or analytical processes). That means, with the BPM standard, a communication method of sharing process knowledge of laboratories is also available. © 2014 Society for Laboratory Automation and Screening.

Problems of Automation and Management Principles Information Flow in Manufacturing

NASA Astrophysics Data System (ADS)

Grigoryuk, E. N.; Bulkin, V. V.

2017-07-01

Automated control systems of technological processes are complex systems that are characterized by the presence of elements of the overall focus, the systemic nature of the implemented algorithms for the exchange and processing of information, as well as a large number of functional subsystems. The article gives examples of automatic control systems and automated control systems of technological processes held parallel between them by identifying strengths and weaknesses. Other proposed non-standard control system of technological process.

Automated array assembly, phase 2

NASA Technical Reports Server (NTRS)

Carbajal, B. G.

1979-01-01

Tasks of scaling up the tandem junction cell (TJC) from 2 cm x 2 cm to 6.2 cm and the assembly of several modules using these large area TJC's are described. The scale-up of the TJC was based on using the existing process and doing the necessary design activities to increase the cell area to an acceptably large area. The design was carried out using available device models. The design was verified and sample large area TJCs were fabricated. Mechanical and process problems occurred causing a schedule slippage that resulted in contract expiration before enough large-area TJCs were fabricated to populate the sample tandem junction modules (TJM). A TJM design was carried out in which the module interconnects served to augment the current collecting buses on the cell. No sample TJMs were assembled due to a shortage of large-area TJCs.

Automatic identification of variables in epidemiological datasets using logic regression.

PubMed

Lorenz, Matthias W; Abdi, Negin Ashtiani; Scheckenbach, Frank; Pflug, Anja; Bülbül, Alpaslan; Catapano, Alberico L; Agewall, Stefan; Ezhov, Marat; Bots, Michiel L; Kiechl, Stefan; Orth, Andreas

2017-04-13

For an individual participant data (IPD) meta-analysis, multiple datasets must be transformed in a consistent format, e.g. using uniform variable names. When large numbers of datasets have to be processed, this can be a time-consuming and error-prone task. Automated or semi-automated identification of variables can help to reduce the workload and improve the data quality. For semi-automation high sensitivity in the recognition of matching variables is particularly important, because it allows creating software which for a target variable presents a choice of source variables, from which a user can choose the matching one, with only low risk of having missed a correct source variable. For each variable in a set of target variables, a number of simple rules were manually created. With logic regression, an optimal Boolean combination of these rules was searched for every target variable, using a random subset of a large database of epidemiological and clinical cohort data (construction subset). In a second subset of this database (validation subset), this optimal combination rules were validated. In the construction sample, 41 target variables were allocated on average with a positive predictive value (PPV) of 34%, and a negative predictive value (NPV) of 95%. In the validation sample, PPV was 33%, whereas NPV remained at 94%. In the construction sample, PPV was 50% or less in 63% of all variables, in the validation sample in 71% of all variables. We demonstrated that the application of logic regression in a complex data management task in large epidemiological IPD meta-analyses is feasible. However, the performance of the algorithm is poor, which may require backup strategies.

Implementation and Evaluation of a Fully Automated Multiplex Real-Time PCR Assay on the BD Max Platform to Detect and Differentiate Herpesviridae from Cerebrospinal Fluids

PubMed Central

Köller, Thomas; Kurze, Daniel; Lange, Mirjam; Scherdin, Martin; Podbielski, Andreas; Warnke, Philipp

2016-01-01

A fully automated multiplex real-time PCR assay—including a sample process control and a plasmid based positive control—for the detection and differentiation of herpes simplex virus 1 (HSV1), herpes simplex virus 2 (HSV2) and varicella-zoster virus (VZV) from cerebrospinal fluids (CSF) was developed on the BD Max platform. Performance was compared to an established accredited multiplex real time PCR protocol utilizing the easyMAG and the LightCycler 480/II, both very common devices in viral molecular diagnostics. For clinical validation, 123 CSF specimens and 40 reference samples from national interlaboratory comparisons were examined with both methods, resulting in 97.6% and 100% concordance for CSF and reference samples, respectively. Utilizing the BD Max platform revealed sensitivities of 173 (CI 95%, 88–258) copies/ml for HSV1, 171 (CI 95%, 148–194) copies/ml for HSV2 and 84 (CI 95%, 5–163) copies/ml for VZV. Cross reactivity could be excluded by checking 25 common viral, bacterial and fungal human pathogens. Workflow analyses displayed shorter test duration as well as remarkable fewer and easier preparation steps with the potential to reduce error rates occurring when manually assessing patient samples. This protocol allows for a fully automated PCR assay on the BD Max platform for the simultaneously detection of herpesviridae from CSF specimens. Singular or multiple infections due to HSV1, HSV2 and VZV can reliably be differentiated with good sensitivities. Control parameters are included within the assay, thereby rendering its suitability for current quality management requirements. PMID:27092772

Public Library Automation Report: 1984.

ERIC Educational Resources Information Center

Gotanda, Masae

Data processing was introduced to public libraries in Hawaii in 1973 with a feasibility study which outlined the candidate areas for automation. Since then, the Office of Library Services has automated the order procedures for one of the largest book processing centers for public libraries in the country; created one of the first COM…

Quantitative comparison and evaluation of software packages for assessment of abdominal adipose tissue distribution by magnetic resonance imaging.

PubMed

Bonekamp, S; Ghosh, P; Crawford, S; Solga, S F; Horska, A; Brancati, F L; Diehl, A M; Smith, S; Clark, J M

2008-01-01

To examine five available software packages for the assessment of abdominal adipose tissue with magnetic resonance imaging, compare their features and assess the reliability of measurement results. Feature evaluation and test-retest reliability of softwares (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision) used in manual, semi-automated or automated segmentation of abdominal adipose tissue. A random sample of 15 obese adults with type 2 diabetes. Axial T1-weighted spin echo images centered at vertebral bodies of L2-L3 were acquired at 1.5 T. Five software packages were evaluated (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision), comparing manual, semi-automated and automated segmentation approaches. Images were segmented into cross-sectional area (CSA), and the areas of visceral (VAT) and subcutaneous adipose tissue (SAT). Ease of learning and use and the design of the graphical user interface (GUI) were rated. Intra-observer accuracy and agreement between the software packages were calculated using intra-class correlation. Intra-class correlation coefficient was used to obtain test-retest reliability. Three of the five evaluated programs offered a semi-automated technique to segment the images based on histogram values or a user-defined threshold. One software package allowed manual delineation only. One fully automated program demonstrated the drawbacks of uncritical automated processing. The semi-automated approaches reduced variability and measurement error, and improved reproducibility. There was no significant difference in the intra-observer agreement in SAT and CSA. The VAT measurements showed significantly lower test-retest reliability. There were some differences between the software packages in qualitative aspects, such as user friendliness. Four out of five packages provided essentially the same results with respect to the inter- and intra-rater reproducibility. Our results using SliceOmatic, Analyze or NIHImage were comparable and could be used interchangeably. Newly developed fully automated approaches should be compared to one of the examined software packages.

Quantitative comparison and evaluation of software packages for assessment of abdominal adipose tissue distribution by magnetic resonance imaging

PubMed Central

Bonekamp, S; Ghosh, P; Crawford, S; Solga, SF; Horska, A; Brancati, FL; Diehl, AM; Smith, S; Clark, JM

2009-01-01

Objective To examine five available software packages for the assessment of abdominal adipose tissue with magnetic resonance imaging, compare their features and assess the reliability of measurement results. Design Feature evaluation and test–retest reliability of softwares (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision) used in manual, semi-automated or automated segmentation of abdominal adipose tissue. Subjects A random sample of 15 obese adults with type 2 diabetes. Measurements Axial T1-weighted spin echo images centered at vertebral bodies of L2–L3 were acquired at 1.5 T. Five software packages were evaluated (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision), comparing manual, semi-automated and automated segmentation approaches. Images were segmented into cross-sectional area (CSA), and the areas of visceral (VAT) and subcutaneous adipose tissue (SAT). Ease of learning and use and the design of the graphical user interface (GUI) were rated. Intra-observer accuracy and agreement between the software packages were calculated using intra-class correlation. Intra-class correlation coefficient was used to obtain test–retest reliability. Results Three of the five evaluated programs offered a semi-automated technique to segment the images based on histogram values or a user-defined threshold. One software package allowed manual delineation only. One fully automated program demonstrated the drawbacks of uncritical automated processing. The semi-automated approaches reduced variability and measurement error, and improved reproducibility. There was no significant difference in the intra-observer agreement in SAT and CSA. The VAT measurements showed significantly lower test–retest reliability. There were some differences between the software packages in qualitative aspects, such as user friendliness. Conclusion Four out of five packages provided essentially the same results with respect to the inter- and intra-rater reproducibility. Our results using SliceOmatic, Analyze or NIHImage were comparable and could be used interchangeably. Newly developed fully automated approaches should be compared to one of the examined software packages. PMID:17700582

Development of an automated fuzing station for the future armored resupply vehicle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chesser, J.B.; Jansen, J.F.; Lloyd, P.D.

1995-03-01

The US Army is developing the Advanced Field Artillery System (SGSD), a next generation armored howitzer. The Future Armored Resupply Vehicle (FARV) will be its companion ammunition resupply vehicle. The FARV with automate the supply of ammunition and fuel to the AFAS which will increase capabilities over the current system. One of the functions being considered for automation is ammunition processing. Oak Ridge National Laboratory is developing equipment to demonstrate automated ammunition processing. One of the key operations to be automated is fuzing. The projectiles are initially unfuzed, and a fuze must be inserted and threaded into the projectile asmore » part of the processing. A constraint on the design solution is that the ammunition cannot be modified to simplify automation. The problem was analyzed to determine the alignment requirements. Using the results of the analysis, ORNL designed, built, and tested a test stand to verify the selected design solution.« less

PLACE: an open-source python package for laboratory automation, control, and experimentation.

PubMed

Johnson, Jami L; Tom Wörden, Henrik; van Wijk, Kasper

2015-02-01

In modern laboratories, software can drive the full experimental process from data acquisition to storage, processing, and analysis. The automation of laboratory data acquisition is an important consideration for every laboratory. When implementing a laboratory automation scheme, important parameters include its reliability, time to implement, adaptability, and compatibility with software used at other stages of experimentation. In this article, we present an open-source, flexible, and extensible Python package for Laboratory Automation, Control, and Experimentation (PLACE). The package uses modular organization and clear design principles; therefore, it can be easily customized or expanded to meet the needs of diverse laboratories. We discuss the organization of PLACE, data-handling considerations, and then present an example using PLACE for laser-ultrasound experiments. Finally, we demonstrate the seamless transition to post-processing and analysis with Python through the development of an analysis module for data produced by PLACE automation. © 2014 Society for Laboratory Automation and Screening.

Comprehensive automation of the solid phase extraction gas chromatographic mass spectrometric analysis (SPE-GC/MS) of opioids, cocaine, and metabolites from serum and other matrices.

PubMed

Lerch, Oliver; Temme, Oliver; Daldrup, Thomas

2014-07-01

The analysis of opioids, cocaine, and metabolites from blood serum is a routine task in forensic laboratories. Commonly, the employed methods include many manual or partly automated steps like protein precipitation, dilution, solid phase extraction, evaporation, and derivatization preceding a gas chromatography (GC)/mass spectrometry (MS) or liquid chromatography (LC)/MS analysis. In this study, a comprehensively automated method was developed from a validated, partly automated routine method. This was possible by replicating method parameters on the automated system. Only marginal optimization of parameters was necessary. The automation relying on an x-y-z robot after manual protein precipitation includes the solid phase extraction, evaporation of the eluate, derivatization (silylation with N-methyl-N-trimethylsilyltrifluoroacetamide, MSTFA), and injection into a GC/MS. A quantitative analysis of almost 170 authentic serum samples and more than 50 authentic samples of other matrices like urine, different tissues, and heart blood on cocaine, benzoylecgonine, methadone, morphine, codeine, 6-monoacetylmorphine, dihydrocodeine, and 7-aminoflunitrazepam was conducted with both methods proving that the analytical results are equivalent even near the limits of quantification (low ng/ml range). To our best knowledge, this application is the first one reported in the literature employing this sample preparation system.

Automated multi-lesion detection for referable diabetic retinopathy in indigenous health care.

PubMed

Pires, Ramon; Carvalho, Tiago; Spurling, Geoffrey; Goldenstein, Siome; Wainer, Jacques; Luckie, Alan; Jelinek, Herbert F; Rocha, Anderson

2015-01-01

Diabetic Retinopathy (DR) is a complication of diabetes mellitus that affects more than one-quarter of the population with diabetes, and can lead to blindness if not discovered in time. An automated screening enables the identification of patients who need further medical attention. This study aimed to classify retinal images of Aboriginal and Torres Strait Islander peoples utilizing an automated computer-based multi-lesion eye screening program for diabetic retinopathy. The multi-lesion classifier was trained on 1,014 images from the São Paulo Eye Hospital and tested on retinal images containing no DR-related lesion, single lesions, or multiple types of lesions from the Inala Aboriginal and Torres Strait Islander health care centre. The automated multi-lesion classifier has the potential to enhance the efficiency of clinical practice delivering diabetic retinopathy screening. Our program does not necessitate image samples for training from any specific ethnic group or population being assessed and is independent of image pre- or post-processing to identify retinal lesions. In this Aboriginal and Torres Strait Islander population, the program achieved 100% sensitivity and 88.9% specificity in identifying bright lesions, while detection of red lesions achieved a sensitivity of 67% and specificity of 95%. When both bright and red lesions were present, 100% sensitivity with 88.9% specificity was obtained. All results obtained with this automated screening program meet WHO standards for diabetic retinopathy screening.

Automated Multi-Lesion Detection for Referable Diabetic Retinopathy in Indigenous Health Care

PubMed Central

Pires, Ramon; Carvalho, Tiago; Spurling, Geoffrey; Goldenstein, Siome; Wainer, Jacques; Luckie, Alan; Jelinek, Herbert F.; Rocha, Anderson

2015-01-01

Diabetic Retinopathy (DR) is a complication of diabetes mellitus that affects more than one-quarter of the population with diabetes, and can lead to blindness if not discovered in time. An automated screening enables the identification of patients who need further medical attention. This study aimed to classify retinal images of Aboriginal and Torres Strait Islander peoples utilizing an automated computer-based multi-lesion eye screening program for diabetic retinopathy. The multi-lesion classifier was trained on 1,014 images from the São Paulo Eye Hospital and tested on retinal images containing no DR-related lesion, single lesions, or multiple types of lesions from the Inala Aboriginal and Torres Strait Islander health care centre. The automated multi-lesion classifier has the potential to enhance the efficiency of clinical practice delivering diabetic retinopathy screening. Our program does not necessitate image samples for training from any specific ethnic group or population being assessed and is independent of image pre- or post-processing to identify retinal lesions. In this Aboriginal and Torres Strait Islander population, the program achieved 100% sensitivity and 88.9% specificity in identifying bright lesions, while detection of red lesions achieved a sensitivity of 67% and specificity of 95%. When both bright and red lesions were present, 100% sensitivity with 88.9% specificity was obtained. All results obtained with this automated screening program meet WHO standards for diabetic retinopathy screening. PMID:26035836

Software for Partly Automated Recognition of Targets

NASA Technical Reports Server (NTRS)

Opitz, David; Blundell, Stuart; Bain, William; Morris, Matthew; Carlson, Ian; Mangrich, Mark; Selinsky, T.

2002-01-01

The Feature Analyst is a computer program for assisted (partially automated) recognition of targets in images. This program was developed to accelerate the processing of high-resolution satellite image data for incorporation into geographic information systems (GIS). This program creates an advanced user interface that embeds proprietary machine-learning algorithms in commercial image-processing and GIS software. A human analyst provides samples of target features from multiple sets of data, then the software develops a data-fusion model that automatically extracts the remaining features from selected sets of data. The program thus leverages the natural ability of humans to recognize objects in complex scenes, without requiring the user to explain the human visual recognition process by means of lengthy software. Two major subprograms are the reactive agent and the thinking agent. The reactive agent strives to quickly learn the user's tendencies while the user is selecting targets and to increase the user's productivity by immediately suggesting the next set of pixels that the user may wish to select. The thinking agent utilizes all available resources, taking as much time as needed, to produce the most accurate autonomous feature-extraction model possible.

A modular assembling platform for manufacturing of microsystems by optical tweezers

NASA Astrophysics Data System (ADS)

Ksouri, Sarah Isabelle; Aumann, Andreas; Ghadiri, Reza; Prüfer, Michael; Baer, Sebastian; Ostendorf, Andreas

2013-09-01

Due to the increased complexity in terms of materials and geometries for microsystems new assembling techniques are required. Assembling techniques from the semiconductor industry are often very specific and cannot fulfill all specifications in more complex microsystems. Therefore, holographic optical tweezers are applied to manipulate structures in micrometer range with highest flexibility and precision. As is well known non-spherical assemblies can be trapped and controlled by laser light and assembled with an additional light modulator application, where the incident laser beam is rearranged into flexible light patterns in order to generate multiple spots. The complementary building blocks are generated by a two-photon-polymerization process. The possibilities of manufacturing arbitrary microstructures and the potential of optical tweezers lead to the idea of combining manufacturing techniques with manipulation processes to "microrobotic" processes. This work presents the manipulation of generated complex microstructures with optical tools as well as a storage solution for 2PP assemblies. A sample holder has been developed for the manual feeding of 2PP building blocks. Furthermore, a modular assembling platform has been constructed for an `all-in-one' 2PP manufacturing process as a dedicated storage system. The long-term objective is the automation process of feeding and storage of several different 2PP micro-assemblies to realize an automated assembly process.

21 CFR 864.5600 - Automated hematocrit instrument.

Code of Federal Regulations, 2012 CFR

2012-04-01

... measures the packed red cell volume of a blood sample to distinguish normal from abnormal states, such as anemia and erythrocytosis (an increase in the number of red cells). (b) Classification. Class II... § 864.5600 Automated hematocrit instrument. (a) Identification. An automated hematocrit instrument is a...

21 CFR 864.5600 - Automated hematocrit instrument.

Code of Federal Regulations, 2011 CFR

2011-04-01

... measures the packed red cell volume of a blood sample to distinguish normal from abnormal states, such as anemia and erythrocytosis (an increase in the number of red cells). (b) Classification. Class II... § 864.5600 Automated hematocrit instrument. (a) Identification. An automated hematocrit instrument is a...

21 CFR 864.5600 - Automated hematocrit instrument.

Code of Federal Regulations, 2014 CFR

2014-04-01

... measures the packed red cell volume of a blood sample to distinguish normal from abnormal states, such as anemia and erythrocytosis (an increase in the number of red cells). (b) Classification. Class II... § 864.5600 Automated hematocrit instrument. (a) Identification. An automated hematocrit instrument is a...

21 CFR 864.5600 - Automated hematocrit instrument.

Code of Federal Regulations, 2013 CFR

2013-04-01

... measures the packed red cell volume of a blood sample to distinguish normal from abnormal states, such as anemia and erythrocytosis (an increase in the number of red cells). (b) Classification. Class II... § 864.5600 Automated hematocrit instrument. (a) Identification. An automated hematocrit instrument is a...

21 CFR 864.5600 - Automated hematocrit instrument.

Code of Federal Regulations, 2010 CFR

2010-04-01

... measures the packed red cell volume of a blood sample to distinguish normal from abnormal states, such as anemia and erythrocytosis (an increase in the number of red cells). (b) Classification. Class II... § 864.5600 Automated hematocrit instrument. (a) Identification. An automated hematocrit instrument is a...

Automated Processing of 2-D Gel Electrophoretograms of Genomic DNA for Hunting Pathogenic DNA Molecular Changes.

PubMed

Takahashi; Nakazawa; Watanabe; Konagaya

1999-01-01

We have developed the automated processing algorithms for 2-dimensional (2-D) electrophoretograms of genomic DNA based on RLGS (Restriction Landmark Genomic Scanning) method, which scans the restriction enzyme recognition sites as the landmark and maps them onto a 2-D electrophoresis gel. Our powerful processing algorithms realize the automated spot recognition from RLGS electrophoretograms and the automated comparison of a huge number of such images. In the final stage of the automated processing, a master spot pattern, on which all the spots in the RLGS images are mapped at once, can be obtained. The spot pattern variations which seemed to be specific to the pathogenic DNA molecular changes can be easily detected by simply looking over the master spot pattern. When we applied our algorithms to the analysis of 33 RLGS images derived from human colon tissues, we successfully detected several colon tumor specific spot pattern changes.

Complacency and bias in human use of automation: an attentional integration.

PubMed

Parasuraman, Raja; Manzey, Dietrich H

2010-06-01

Our aim was to review empirical studies of complacency and bias in human interaction with automated and decision support systems and provide an integrated theoretical model for their explanation. Automation-related complacency and automation bias have typically been considered separately and independently. Studies on complacency and automation bias were analyzed with respect to the cognitive processes involved. Automation complacency occurs under conditions of multiple-task load, when manual tasks compete with the automated task for the operator's attention. Automation complacency is found in both naive and expert participants and cannot be overcome with simple practice. Automation bias results in making both omission and commission errors when decision aids are imperfect. Automation bias occurs in both naive and expert participants, cannot be prevented by training or instructions, and can affect decision making in individuals as well as in teams. While automation bias has been conceived of as a special case of decision bias, our analysis suggests that it also depends on attentional processes similar to those involved in automation-related complacency. Complacency and automation bias represent different manifestations of overlapping automation-induced phenomena, with attention playing a central role. An integrated model of complacency and automation bias shows that they result from the dynamic interaction of personal, situational, and automation-related characteristics. The integrated model and attentional synthesis provides a heuristic framework for further research on complacency and automation bias and design options for mitigating such effects in automated and decision support systems.

CERES AuTomAted job Loading SYSTem (CATALYST): An automated workflow manager for satellite data production

NASA Astrophysics Data System (ADS)

Gleason, J. L.; Hillyer, T. N.; Wilkins, J.

2012-12-01

The CERES Science Team integrates data from 5 CERES instruments onboard the Terra, Aqua and NPP missions. The processing chain fuses CERES observations with data from 19 other unique sources. The addition of CERES Flight Model 5 (FM5) onboard NPP, coupled with ground processing system upgrades further emphasizes the need for an automated job-submission utility to manage multiple processing streams concurrently. The operator-driven, legacy-processing approach relied on manually staging data from magnetic tape to limited spinning disk attached to a shared memory architecture system. The migration of CERES production code to a distributed, cluster computing environment with approximately one petabyte of spinning disk containing all precursor input data products facilitates the development of a CERES-specific, automated workflow manager. In the cluster environment, I/O is the primary system resource in contention across jobs. Therefore, system load can be maximized with a throttling workload manager. This poster discusses a Java and Perl implementation of an automated job management tool tailored for CERES processing.

Testing of a Microfluidic Sampling System for High Temperature Electrochemical MC&A

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pereira, Candido; Nichols, Kevin

2013-11-27

This report describes the preliminary validation of a high-temperature microfluidic chip system for sampling of electrochemical process salt. Electroanalytical and spectroscopic techniques are attractive candidates for improvement through high-throughput sample analysis via miniaturization. Further, microfluidic chip systems are amenable to micro-scale chemical processing such as rapid, automated sample purification to improve sensor performance. The microfluidic chip was tested to determine the feasibility of the system for high temperature applications and conditions under which microfluidic systems can be used to generate salt droplets at process temperature to support development of material balance and control systems in a used fuel treatment facility.more » In FY13, the project focused on testing a quartz microchip device with molten salts at near process temperatures. The equipment was installed in glove box and tested up to 400°C using commercial thermal transfer fluids as the carrier phase. Preliminary tests were carried out with a low-melting halide salt to initially characterize the properties of this novel liquid-liquid system and to investigate the operating regimes for inducing droplet flow within candidate carrier fluids. Initial results show that the concept is viable for high temperature sampling but further development is required to optimize the system to operate with process relevant molten salts.« less

Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data

PubMed Central

Jaitly, Navdeep; Mayampurath, Anoop; Littlefield, Kyle; Adkins, Joshua N; Anderson, Gordon A; Smith, Richard D

2009-01-01

Background Data generated from liquid chromatography coupled to high-resolution mass spectrometry (LC-MS)-based studies of a biological sample can contain large amounts of biologically significant information in the form of proteins, peptides, and metabolites. Interpreting this data involves inferring the masses and abundances of biomolecules injected into the instrument. Because of the inherent complexity of mass spectral patterns produced by these biomolecules, the analysis is significantly enhanced by using visualization capabilities to inspect and confirm results. In this paper we describe Decon2LS, an open-source software package for automated processing and visualization of high-resolution MS data. Drawing extensively on algorithms developed over the last ten years for ICR2LS, Decon2LS packages the algorithms as a rich set of modular, reusable processing classes for performing diverse functions such as reading raw data, routine peak finding, theoretical isotope distribution modelling, and deisotoping. Because the source code is openly available, these functionalities can now be used to build derivative applications in relatively fast manner. In addition, Decon2LS provides an extensive set of visualization tools, such as high performance chart controls. Results With a variety of options that include peak processing, deisotoping, isotope composition, etc, Decon2LS supports processing of multiple raw data formats. Deisotoping can be performed on an individual scan, an individual dataset, or on multiple datasets using batch processing. Other processing options include creating a two dimensional view of mass and liquid chromatography (LC) elution time features, generating spectrum files for tandem MS data, creating total intensity chromatograms, and visualizing theoretical peptide profiles. Application of Decon2LS to deisotope different datasets obtained across different instruments yielded a high number of features that can be used to identify and quantify peptides in the biological sample. Conclusion Decon2LS is an efficient software package for discovering and visualizing features in proteomics studies that require automated interpretation of mass spectra. Besides being easy to use, fast, and reliable, Decon2LS is also open-source, which allows developers in the proteomics and bioinformatics communities to reuse and refine the algorithms to meet individual needs. Decon2LS source code, installer, and tutorials may be downloaded free of charge at . PMID:19292916

Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data.

PubMed

Jaitly, Navdeep; Mayampurath, Anoop; Littlefield, Kyle; Adkins, Joshua N; Anderson, Gordon A; Smith, Richard D

2009-03-17

Data generated from liquid chromatography coupled to high-resolution mass spectrometry (LC-MS)-based studies of a biological sample can contain large amounts of biologically significant information in the form of proteins, peptides, and metabolites. Interpreting this data involves inferring the masses and abundances of biomolecules injected into the instrument. Because of the inherent complexity of mass spectral patterns produced by these biomolecules, the analysis is significantly enhanced by using visualization capabilities to inspect and confirm results. In this paper we describe Decon2LS, an open-source software package for automated processing and visualization of high-resolution MS data. Drawing extensively on algorithms developed over the last ten years for ICR2LS, Decon2LS packages the algorithms as a rich set of modular, reusable processing classes for performing diverse functions such as reading raw data, routine peak finding, theoretical isotope distribution modelling, and deisotoping. Because the source code is openly available, these functionalities can now be used to build derivative applications in relatively fast manner. In addition, Decon2LS provides an extensive set of visualization tools, such as high performance chart controls. With a variety of options that include peak processing, deisotoping, isotope composition, etc, Decon2LS supports processing of multiple raw data formats. Deisotoping can be performed on an individual scan, an individual dataset, or on multiple datasets using batch processing. Other processing options include creating a two dimensional view of mass and liquid chromatography (LC) elution time features, generating spectrum files for tandem MS data, creating total intensity chromatograms, and visualizing theoretical peptide profiles. Application of Decon2LS to deisotope different datasets obtained across different instruments yielded a high number of features that can be used to identify and quantify peptides in the biological sample. Decon2LS is an efficient software package for discovering and visualizing features in proteomics studies that require automated interpretation of mass spectra. Besides being easy to use, fast, and reliable, Decon2LS is also open-source, which allows developers in the proteomics and bioinformatics communities to reuse and refine the algorithms to meet individual needs.Decon2LS source code, installer, and tutorials may be downloaded free of charge at http://http:/ncrr.pnl.gov/software/.

Basic forest cover mapping using digitized remote sensor data and automated data processing techniques

NASA Technical Reports Server (NTRS)

Coggeshall, M. E.; Hoffer, R. M.

1973-01-01

Remote sensing equipment and automatic data processing techniques were employed as aids in the institution of improved forest resource management methods. On the basis of automatically calculated statistics derived from manually selected training samples, the feature selection processor of LARSYS selected, upon consideration of various groups of the four available spectral regions, a series of channel combinations whose automatic classification performances (for six cover types, including both deciduous and coniferous forest) were tested, analyzed, and further compared with automatic classification results obtained from digitized color infrared photography.

A Fully Automated Microfluidic Femtosecond Laser Axotomy Platform for Nerve Regeneration Studies in C. elegans

PubMed Central

Gokce, Sertan Kutal; Guo, Samuel X.; Ghorashian, Navid; Everett, W. Neil; Jarrell, Travis; Kottek, Aubri; Bovik, Alan C.; Ben-Yakar, Adela

2014-01-01

Femtosecond laser nanosurgery has been widely accepted as an axonal injury model, enabling nerve regeneration studies in the small model organism, Caenorhabditis elegans. To overcome the time limitations of manual worm handling techniques, automation and new immobilization technologies must be adopted to improve throughput in these studies. While new microfluidic immobilization techniques have been developed that promise to reduce the time required for axotomies, there is a need for automated procedures to minimize the required amount of human intervention and accelerate the axotomy processes crucial for high-throughput. Here, we report a fully automated microfluidic platform for performing laser axotomies of fluorescently tagged neurons in living Caenorhabditis elegans. The presented automation process reduces the time required to perform axotomies within individual worms to ∼17 s/worm, at least one order of magnitude faster than manual approaches. The full automation is achieved with a unique chip design and an operation sequence that is fully computer controlled and synchronized with efficient and accurate image processing algorithms. The microfluidic device includes a T-shaped architecture and three-dimensional microfluidic interconnects to serially transport, position, and immobilize worms. The image processing algorithms can identify and precisely position axons targeted for ablation. There were no statistically significant differences observed in reconnection probabilities between axotomies carried out with the automated system and those performed manually with anesthetics. The overall success rate of automated axotomies was 67.4±3.2% of the cases (236/350) at an average processing rate of 17.0±2.4 s. This fully automated platform establishes a promising methodology for prospective genome-wide screening of nerve regeneration in C. elegans in a truly high-throughput manner. PMID:25470130

The effects of total laboratory automation on the management of a clinical chemistry laboratory. Retrospective analysis of 36 years.

PubMed

Sarkozi, Laszlo; Simson, Elkin; Ramanathan, Lakshmi

2003-03-01

Thirty-six years of data and history of laboratory practice at our institution has enabled us to follow the effects of analytical automation, then recently pre-analytical and post-analytical automation on productivity, cost reduction and enhanced quality of service. In 1998, we began the operation of a pre- and post-analytical automation system (robotics), together with an advanced laboratory information system to process specimens prior to analysis, deliver them to various automated analytical instruments, specimen outlet racks and finally to refrigerated stockyards. By the end of 3 years of continuous operation, we compared the chemistry part of the system with the prior 33 years and quantitated the financial impact of the various stages of automation. Between 1965 and 2000, the Consumer Price Index increased by a factor of 5.5 in the United States. During the same 36 years, at our institution's Chemistry Department the productivity (indicated as the number of reported test results/employee/year) increased from 10,600 to 104,558 (9.3-fold). When expressed in constant 1965 dollars, the total cost per test decreased from 0.79 dollars to 0.15 dollars. Turnaround time for availability of results on patient units decreased to the extent that Stat specimens requiring a turnaround time of <1 h do not need to be separately prepared or prioritized on the system. Our experience shows that the introduction of a robotics system for perianalytical automation has brought a large improvement in productivity together with decreased operational cost. It enabled us to significantly increase our workload together with a reduction of personnel. In addition, stats are handled easily and there are benefits such as safer working conditions and improved sample identification, which are difficult to quantify at this stage.

Data Processing and First Products from the Hyperspectral Imager for the Coastal Ocean (HICO) on the International Space Station

DTIC Science & Technology

2010-04-01

NRL Stennis Space Center (NRL-SSC) for further processing using the NRL SSC Automated Processing System (APS). APS was developed for processing...have not previously developed automated processing for 73 hyperspectral ocean color data. The hyperspectral processing branch includes several

Online extraction LC-MS/MS method for the simultaneous quantitative confirmation of urine drugs of abuse and metabolites: amphetamines, opiates, cocaine, cannabis, benzodiazepines and methadone.

PubMed

de Jager, Andrew D; Bailey, Neville L

2011-09-01

A rapid LC-MS/MS method for confirmatory testing of five major categories of drugs of abuse (amphetamine-type substances, opiates, cocaine, cannabis metabolites and benzodiazepines) in urine has been developed. All drugs of abuse mandated by the Australian/New Zealand Standard AS/NZS 4308:2008 are quantified in a single chromatographic run. Urine samples are diluted with a mixture of isotope labelled internal standards. An on-line trap-and-flush approach, followed by LC-ESI-MS/MS has been successfully used to process samples in a functioning drugs of abuse laboratory. Following injection of diluted urine samples, compounds retained on the trap cartridge are flushed onto a reverse-phase C18 HPLC column (5-μm particle size) with embedded hydrophylic functionality. A total chromatographic run-time of 15 min is required for adequate resolution. Automated quantitation software algorithms have been developed in-house using XML scripting to partially automate the identification of positive samples, taking into account ion ratio (IR) and retention times (Rt). The sensitivity of the assay was found to be adequate for the quantitation of drugs in urine at and below the confirmation cut-off concentrations prescribed by AS/NZS 4308:2008. Copyright © 2011 Elsevier B.V. All rights reserved.

Use of a Novel Fluidics Microbead Trap/Flow-cell Enhances Speed and Sensitivity of Bead-Based Bioassays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ozanich, Rich M.; Antolick, Kathryn C.; Bruckner-Lea, Cindy J.

2007-09-15

Automated devices and methods for biological sample preparation often utilize surface functionalized microbeads (superparamagnetic or non-magnetic) to allow capture, purification and pre-concentration of trace amounts of proteins, cells, or nucleic acids (DNA/RNA) from complex samples. We have developed unique methods and hardware for trapping either magnetic or non-magnetic functionalized beads that allow samples and reagents to be efficiently perfused over a micro-column of beads. This approach yields enhanced mass transport and up to 5-fold improvements in assay sensitivity or speed, dramatically improving assay capability relative to assays conducted in more traditional “batch modes” (i.e., in tubes or microplate wells). Summarymore » results are given that highlight the analytical performance improvements obtained for automated microbead processing systems utilizing novel microbead trap/flow-cells for various applications, including: 1) simultaneous capture of multiple cytokines using an antibody-coupled polystyrene bead assay with subsequent flow cytometry detection; 2) capture of nucleic acids using oligonucleotide coupled polystyrene beads with flow cytometry detection; and 3) capture of Escherichia coli 0157:H7 (E. coli) from 50 mL sample volumes using antibody-coupled superparamagnetic microbeads with subsequent culturing to assess capture efficiency.« less