Science.gov

Sample records for device-independent real-time identification

  1. Real-time flutter identification

    NASA Technical Reports Server (NTRS)

    Roy, R.; Walker, R.

    1985-01-01

    The techniques and a FORTRAN 77 MOdal Parameter IDentification (MOPID) computer program developed for identification of the frequencies and damping ratios of multiple flutter modes in real time are documented. Physically meaningful model parameterization was combined with state of the art recursive identification techniques and applied to the problem of real time flutter mode monitoring. The performance of the algorithm in terms of convergence speed and parameter estimation error is demonstrated for several simulated data cases, and the results of actual flight data analysis from two different vehicles are presented. It is indicated that the algorithm is capable of real time monitoring of aircraft flutter characteristics with a high degree of reliability.

  2. Species identification in meat products using real-time PCR.

    PubMed

    Jonker, K M; Tilburg, J J H C; Hagele, G H; de Boer, E

    2008-05-01

    One of the most convenient methods for the identification of animal species in processed meat products is the examination of DNA sequences. Real-time polymerase chain reaction (qPCR) techniques are particularly suitable because even small fragments of DNA formed during heat processing of the meat can be amplified and identified. A real-time PCR method has been developed and evaluated for the identification of processed meat products. In test mixtures containing beef, pork, horse, mutton, chicken and turkey, it was possible to identify these species down to a level of 0.05%. By adjusting the number of cycles, it was possible to detect levels as low as 0.01% of these species. Cross-reactivity between these species was not found, except for pure horsemeat (250 ng DNA) in the assay for turkey meat. Cross-reactivity of deer, roe, ostrich, kangaroo, goat, domestic duck, mallard, goose, pigeon, guinea fowl, quail and pheasant was also investigated and it was found that amounts as high as 250 ng DNA of these species in the reaction vial did not result in (false) positive signals except for amounts higher than 125 ng deer DNA and higher than 50 ng pigeon DNA in the determination of chicken and beef, respectively. More than 150 meat samples were examined using DNA hybridization and real-time PCR. A comparison of the results showed a better performance of the real-time procedure compared to DNA hybridization.

  3. Real-time bioacoustics monitoring and automated species identification

    PubMed Central

    Corrada-Bravo, Carlos; Campos-Cerqueira, Marconi; Milan, Carlos; Vega, Giovany; Alvarez, Rafael

    2013-01-01

    Traditionally, animal species diversity and abundance is assessed using a variety of methods that are generally costly, limited in space and time, and most importantly, they rarely include a permanent record. Given the urgency of climate change and the loss of habitat, it is vital that we use new technologies to improve and expand global biodiversity monitoring to thousands of sites around the world. In this article, we describe the acoustical component of the Automated Remote Biodiversity Monitoring Network (ARBIMON), a novel combination of hardware and software for automating data acquisition, data management, and species identification based on audio recordings. The major components of the cyberinfrastructure include: a solar powered remote monitoring station that sends 1-min recordings every 10 min to a base station, which relays the recordings in real-time to the project server, where the recordings are processed and uploaded to the project website (arbimon.net). Along with a module for viewing, listening, and annotating recordings, the website includes a species identification interface to help users create machine learning algorithms to automate species identification. To demonstrate the system we present data on the vocal activity patterns of birds, frogs, insects, and mammals from Puerto Rico and Costa Rica. PMID:23882441

  4. Real-time machine tool chatter identification and control system

    NASA Astrophysics Data System (ADS)

    Zhang, Shilong

    1997-05-01

    Chatter in machining processes is one of the most important factors limiting production rates. In order to suppress machine tool chatter during orthogonal cutting processes, a real time active chatter controller is designed and implemented that is able to adopt to the continuously changing machining parameters. An electro-hydraulic servo system is used to control the movement of the cutting tool. The cutting force, workpiece acceleration, and tool displacement are measured in real time. The transfer function of the workpiece is estimated by using the cutting force and the acceleration of the workpiece. All the digital signal acquisition and processing tasks are performed by a digital signal processor (MicroStar DAP3200a/415). The digital controller is designed such that the servo/actuator dynamics is adjusted to match the workpiece dynamics to suppress chatter. To make the controller adaptive to the changing dynamics of the workpiece, a recursive least square technique is used to identify the workpiece dynamics in real time. The estimated workpiece dynamics parameters are then used in the digital controller to calculate a new servo output, thus controlling the tool movement. Simulations show that chatter can be suppressed successfully by using this method. Experiments agree well with simulations.

  5. Development of a wearable motion detector for telemonitoring and real-time identification of physical activity.

    PubMed

    Yang, Che-Chang; Hsu, Yeh-Liang

    2009-01-01

    Characteristics of physical activity are indicative of one's mobility level, latent chronic diseases, and aging process. Current research has been oriented to provide quantitative assessment of physical activity with ambulatory monitoring approaches. This study presents the design of a portable microprocessor-based accelerometry measuring device to implement real-time physical activity identification. An algorithm was developed to process real-time tri-axial acceleration signals produced by human movement to identify targeted still postures, postural transitions, and dynamic movements. Fall detection was also featured in this algorithm to meet the increasing needs of elderly care in free-living environments. High identification accuracy was obtained in performance evaluation. This device is technically viable for telemonitoring and real-time identification of physical activity, while providing sufficient information to evaluate a person's activity of daily living and her/his status of physical mobility. Limitations regarding real-time processing and implementation of the system for telemonitoring in the home environment were also observed.

  6. Multiplex real-time PCR for identification of canine parvovirus antigenic types.

    PubMed

    Kaur, Gurpreet; Chandra, Mudit; Dwivedi, P N; Narang, Deepti

    2016-07-01

    Canine parvovirus (CPV) is an important disease causing gastroenteritis and/or haemorrhagic gastroenteritis in dogs. There are four antigenic types of CPV reported worldwide viz. CPV 2, CPV 2a, CPV 2b and CPV 2c. The diagnosis of CPV with the identification of the antigen type responsible remains problematic. In the present study, identification as well as antigenic typing of CPV was done using a de novo multiplex real time PCR to combat the problem of antigenic type identification. From the study it could be concluded that the here developed multiplex real time PCR assay could be used for rapid detection of CPV as well as typing of its three antigenic types.

  7. Flight Investigation of Prescribed Simultaneous Independent Surface Excitations for Real-Time Parameter Identification

    NASA Technical Reports Server (NTRS)

    Moes, Timothy R.; Smith, Mark S.; Morelli, Eugene A.

    2003-01-01

    Near real-time stability and control derivative extraction is required to support flight demonstration of Intelligent Flight Control System (IFCS) concepts being developed by NASA, academia, and industry. Traditionally, flight maneuvers would be designed and flown to obtain stability and control derivative estimates using a postflight analysis technique. The goal of the IFCS concept is to be able to modify the control laws in real time for an aircraft that has been damaged in flight. In some IFCS implementations, real-time parameter identification (PID) of the stability and control derivatives of the damaged aircraft is necessary for successfully reconfiguring the control system. This report investigates the usefulness of Prescribed Simultaneous Independent Surface Excitations (PreSISE) to provide data for rapidly obtaining estimates of the stability and control derivatives. Flight test data were analyzed using both equation-error and output-error PID techniques. The equation-error PID technique is known as Fourier Transform Regression (FTR) and is a frequency-domain real-time implementation. Selected results were compared with a time-domain output-error technique. The real-time equation-error technique combined with the PreSISE maneuvers provided excellent derivative estimation in the longitudinal axis. However, the PreSISE maneuvers as presently defined were not adequate for accurate estimation of the lateral-directional derivatives.

  8. A Novel Multiplex Real-Time PCR for the Identification of Mycobacteria Associated with Zoonotic Tuberculosis

    PubMed Central

    Reddington, Kate; O'Grady, Justin; Dorai-Raj, Siobhan; Niemann, Stefan; van Soolingen, Dick; Barry, Thomas

    2011-01-01

    Background Tuberculosis (TB) is the leading cause of death worldwide from a single infectious agent. An ability to detect the Mycobacterium tuberculosis complex (MTC) in clinical material while simultaneously differentiating its members is considered important. This allows for the gathering of epidemiological information pertaining to the prevalence, transmission and geographical distribution of the MTC, including those MTC members associated with zoonotic TB infection in humans. Also differentiating between members of the MTC provides the clinician with inherent MTC specific drug susceptibility profiles to guide appropriate chemotherapy. Methodology/Principal Findings The aim of this study was to develop a multiplex real-time PCR assay using novel molecular targets to identify and differentiate between the phylogenetically closely related M. bovis, M. bovis BCG and M. caprae. The lpqT gene was explored for the collective identification of M. bovis, M. bovis BCG and M. caprae, the lepA gene was targeted for the specific identification of M. caprae and a Region of Difference 1 (RD1) assay was incorporated in the test to differentiate M. bovis BCG. The multiplex real-time PCR assay was evaluated on 133 bacterial strains and was determined to be 100% specific for the members of the MTC targeted. Conclusions/Significance The multiplex real-time PCR assay developed in this study is the first assay described for the identification and simultaneous differentiation of M. bovis, M. bovis BCG and M. caprae in one internally controlled reaction. Future validation of this multiplex assay should demonstrate its potential in the rapid and accurate diagnosis of TB caused by these three mycobacteria. Furthermore, the developed assay may be used in conjunction with a recently described multiplex real-time PCR assay for identification of the MTC and simultaneous differentiation of M. tuberculosis, M. canettii resulting in an ability to differentiate five of the eight members of the

  9. Floor Covering and Surface Identification for Assistive Mobile Robotic Real-Time Room Localization Application

    PubMed Central

    Gillham, Michael; Howells, Gareth; Spurgeon, Sarah; McElroy, Ben

    2013-01-01

    Assistive robotic applications require systems capable of interaction in the human world, a workspace which is highly dynamic and not always predictable. Mobile assistive devices face the additional and complex problem of when and if intervention should occur; therefore before any trajectory assistance is given, the robotic device must know where it is in real-time, without unnecessary disruption or delay to the user requirements. In this paper, we demonstrate a novel robust method for determining room identification from floor features in a real-time computational frame for autonomous and assistive robotics in the human environment. We utilize two inexpensive sensors: an optical mouse sensor for straightforward and rapid, texture or pattern sampling, and a four color photodiode light sensor for fast color determination. We show how data relating floor texture and color obtained from typical dynamic human environments, using these two sensors, compares favorably with data obtained from a standard webcam. We show that suitable data can be extracted from these two sensors at a rate 16 times faster than a standard webcam, and that these data are in a form which can be rapidly processed using readily available classification techniques, suitable for real-time system application. We achieved a 95% correct classification accuracy identifying 133 rooms' flooring from 35 classes, suitable for fast coarse global room localization application, boundary crossing detection, and additionally some degree of surface type identification. PMID:24351647

  10. Floor covering and surface identification for assistive mobile robotic real-time room localization application.

    PubMed

    Gillham, Michael; Howells, Gareth; Spurgeon, Sarah; McElroy, Ben

    2013-01-01

    Assistive robotic applications require systems capable of interaction in the human world, a workspace which is highly dynamic and not always predictable. Mobile assistive devices face the additional and complex problem of when and if intervention should occur; therefore before any trajectory assistance is given, the robotic device must know where it is in real-time, without unnecessary disruption or delay to the user requirements. In this paper, we demonstrate a novel robust method for determining room identification from floor features in a real-time computational frame for autonomous and assistive robotics in the human environment. We utilize two inexpensive sensors: an optical mouse sensor for straightforward and rapid, texture or pattern sampling, and a four color photodiode light sensor for fast color determination. We show how data relating floor texture and color obtained from typical dynamic human environments, using these two sensors, compares favorably with data obtained from a standard webcam. We show that suitable data can be extracted from these two sensors at a rate 16 times faster than a standard webcam, and that these data are in a form which can be rapidly processed using readily available classification techniques, suitable for real-time system application. We achieved a 95% correct classification accuracy identifying 133 rooms' flooring from 35 classes, suitable for fast coarse global room localization application, boundary crossing detection, and additionally some degree of surface type identification. PMID:24351647

  11. Real-time automatic target identification system for air-to-ground targeting

    NASA Astrophysics Data System (ADS)

    Nicholas, Mike; Wood, Jonathan; Nothard, Jo

    2005-10-01

    Future targeting systems, for manned or unmanned combat aircraft, aim to provide increased mission success and platform survivability by successfully detecting and identifying even difficult targets at very long ranges. One of the key enabling technologies for such systems is robust automatic target identification (ATI), operating on high resolution electro-optic sensor imagery. QinetiQ have developed a real time ATI processor which will be demonstrated with infrared imagery from the Wescam MX15 in airborne trials in summer 2005. This paper describes some of the novel ATI algorithms, the challenges overcome to port the ATI from the laboratory onto a real time system and offers an assessment of likely airborne performance based on analysis of synthetic image sequences.

  12. New Products for Near Real-Time Enhanced Landslide Identification and Precipitation Monitoring

    NASA Astrophysics Data System (ADS)

    Roberts-Pierel, J.; Ahamed, A.; Fayne, J.; Rumsey, A.

    2015-12-01

    Nepal and the Himalayan region are hotspots for landslide activity due to mountainous topography, complex terrain, and monsoon rains. Current research in landslide modeling and detection generally requires high resolution imagery with software aided classification or manual digitization by analysts. These methods are plagued by low spatial and temporal accuracy. Addressing issues in conventional measurement, this study combined optical data from Landsat 8, a Digital Elevation Model (DEM) generated from Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER), and precipitation data from the Global Precipitation Measurement Mission (GPM) to create two products. The Sudden Landslide Identification Product (SLIP) uses Landsat 8 and the ASTER DEM to identify landslides in near real-time, and provides damage assessments by mapping landslides triggered by precipitation. Detecting Real-time Increased Precipitation (DRIP) monitors precipitation levels extracted from the GPM-IMERG 30-minute product to create alerts in near real-time when current rainfall levels exceed regional threshold values. After a landslide detection is made by SLIP, historical rainfall data from DRIP is analyzed to estimate a date for the detected landslide. Together, DRIP and SLIP will be used by local and regional organizations in Nepal such as the International Centre for Integrated Mountain Development (ICIMOD), as well as the international scientific community to protect lives, preserve infrastructure, and manage local ecosystems.

  13. Messenger RNA profiling: a novel method for body fluid identification by real-time PCR.

    PubMed

    Nussbaumer, Christa; Gharehbaghi-Schnell, Elisabeth; Korschineck, Irina

    2006-03-10

    Conventional methods for the identification of different body fluids like blood, semen and saliva from biological stains involve immunological or enzymatic detection of certain proteins. In this study, we investigated potential RNA markers with the aim of developing Real-Time polymerase chain reaction (PCR) based methods to allow differentiation between several body fluids. Total RNA samples from artificially stained swabs and from various pieces of evidence from case work were extracted, amplified and analyzed with several RNA markers. Three assays detecting the body fluids of interest were selected: hemoglobin-alpha locus 1 (HBA), kallikrein 3 (KLK) and mucin 4 (MUC). With this approach, we demonstrate that specific Real-Time PCR assays are useful in identifying the source of the biological stain. Furthermore, RNA profiling of various body fluids was even possible on samples stored over a long period of time at ambient temperature. The stability and sensitivity of the applied method outlines a novel application for Real-Time PCR within the forensic field.

  14. Status of FARTECH's Multi-Sensor Real-Time Resistive Wall Mode Identification Project

    NASA Astrophysics Data System (ADS)

    Kim, J. S.; Edgell, D. H.; Bogatu, I. N.; Kim, Y. B.; Humphreys, D. A.; Walker, M. L.; Leuer, J. A.; Turnbull, A. D.

    2002-11-01

    Early detection of resistive wall mode (RWM) identification (ID) is possible utilizing multiple sensors to enhance the signal-to-noise ratio, and mode structure recognition with a pre-modeled numerical structure, assuming similar equilibria to be reproduced. Magnetic probes, and internal and external saddle loops are currently used. The predicted structures are modeled via FARVAC(D.H. Edgell, FARTECH, Inc. Report FT020523, May (2002).) and VACUUM using the GATO linear RWM mode. The RWM structures are then matched to the experimental data in real-time. For better algorithm and understanding of the modes, other sensors such as soft x-ray data are being incorporated in the program. In addition, an equilibrium and stability code is being developed for basic understanding of the RWM physics such as RWM rotation and dissipation. Systematic implementation and communication of our mode identification to the DIII-D PCS are being developed and tested.

  15. Real-Time PCR Assay for the Identification of the Brown Marmorated Stink Bug (Halyomorpha halys)

    PubMed Central

    Dhami, Manpreet K.; Dsouza, Melissa; Waite, David W.; Anderson, Diane; Li, Dongmei

    2016-01-01

    The brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae), is a gregarious crop pest that has rapidly spread across the world in the last two decades. It is an excellent hitchhiker species, especially as an over-wintering adult. During this period it is often associated with non-biological commodities such as shipping containers and machinery that travel long distances. Inadequate identification keys and similarity to common species has assisted its spread across Europe, while accurate identification from immature stages or eggs is not possible. We developed a real-time TaqMan PCR assay for the accurate and sensitive detection of the brown marmorated stink bug from all life stages. The assay performance against required diagnostic criterion and within a quarantine framework are described. PMID:26955631

  16. REAL-TIME IDENTIFICATION AND CHARACTERIZATION OF ASBESTOS AND CONCRETE MATERIALS WITH RADIOACTIVE CONTAMINATION

    SciTech Connect

    XU, X. George; Zhang, X.C.

    2002-05-10

    Concrete and asbestos-containing materials were widely used in DOE building construction in the 1940s and 1950s. Over the years, many of these porous materials have been contaminated with radioactive sources, on and below the surface. To improve current practice in identifying hazardous materials and in characterizing radioactive contamination, an interdisciplinary team from Rensselaer has conducted research in two aspects: (1) to develop terahertz time-domain spectroscopy and imaging system that can be used to analyze environmental samples such as asbestos in the field, and (2) to develop algorithms for characterizing the radioactive contamination depth profiles in real-time in the field using gamma spectroscopy. The basic research focused on the following: (1) mechanism of generating of broadband pulsed radiation in terahertz region, (2) optimal free-space electro-optic sampling for asbestos, (3) absorption and transmission mechanisms of asbestos in THz region, (4) the role of asbestos sample conditions on the temporal and spectral distributions, (5) real-time identification and mapping of asbestos using THz imaging, (7) Monte Carlo modeling of distributed contamination from diffusion of radioactive materials into porous concrete and asbestos materials, (8) development of unfolding algorithms for gamma spectroscopy, and (9) portable and integrated spectroscopy systems for field testing in DOE. Final results of the project show that the combination of these innovative approaches has the potential to bring significant improvement in future risk reduction and cost/time saving in DOE's D and D activities.

  17. A robust approach to battery fuel gauging, part I: Real time model identification

    NASA Astrophysics Data System (ADS)

    Balasingam, B.; Avvari, G. V.; Pattipati, B.; Pattipati, K. R.; Bar-Shalom, Y.

    2014-12-01

    In this paper, the first of a series of papers on battery fuel gauge (BFG), we present a real time parameter estimation strategy for robust state of charge (SOC) tracking. The proposed parameter estimation scheme has the following novel features: it models hysteresis as an error in the open circuit voltage (OCV) and employs a combination of real time, linear parameter estimation and SOC tracking technique to compensate for it. This obviates the need for modeling of hysteresis as a function of SOC and load current. We identify the presence of correlated noise that has been so far ignored in the literature and use it to enhance the accuracy of model identification. As a departure from the conventional "one model fits all" strategy, we identify four different equivalent models of the battery that represent four modes of typical battery operation and develop the framework for seamless SOC tracking by switching. The proposed parameter approach enables a robust initialization/re-initialization strategy for continuous operation of the BFG. The performance of the online parameter estimation scheme was first evaluated through simulated data. Then, the proposed algorithm was validated using hardware-in-the-loop (HIL) data collected from commercially available Li-ion batteries.

  18. A novel algorithm for real-time adaptive signal detection and identification

    SciTech Connect

    Sleefe, G.E.; Ladd, M.D.; Gallegos, D.E.; Sicking, C.W.; Erteza, I.A.

    1998-04-01

    This paper describes a novel digital signal processing algorithm for adaptively detecting and identifying signals buried in noise. The algorithm continually computes and updates the long-term statistics and spectral characteristics of the background noise. Using this noise model, a set of adaptive thresholds and matched digital filters are implemented to enhance and detect signals that are buried in the noise. The algorithm furthermore automatically suppresses coherent noise sources and adapts to time-varying signal conditions. Signal detection is performed in both the time-domain and the frequency-domain, thereby permitting the detection of both broad-band transients and narrow-band signals. The detection algorithm also provides for the computation of important signal features such as amplitude, timing, and phase information. Signal identification is achieved through a combination of frequency-domain template matching and spectral peak picking. The algorithm described herein is well suited for real-time implementation on digital signal processing hardware. This paper presents the theory of the adaptive algorithm, provides an algorithmic block diagram, and demonstrate its implementation and performance with real-world data. The computational efficiency of the algorithm is demonstrated through benchmarks on specific DSP hardware. The applications for this algorithm, which range from vibration analysis to real-time image processing, are also discussed.

  19. A fluorescence-based quantitative real-time PCR assay for accurate Pocillopora damicornis species identification

    NASA Astrophysics Data System (ADS)

    Thomas, Luke; Stat, Michael; Evans, Richard D.; Kennington, W. Jason

    2016-09-01

    Pocillopora damicornis is one of the most extensively studied coral species globally, but high levels of phenotypic plasticity within the genus make species identification based on morphology alone unreliable. As a result, there is a compelling need to develop cheap and time-effective molecular techniques capable of accurately distinguishing P. damicornis from other congeneric species. Here, we develop a fluorescence-based quantitative real-time PCR (qPCR) assay to genotype a single nucleotide polymorphism that accurately distinguishes P. damicornis from other morphologically similar Pocillopora species. We trial the assay across colonies representing multiple Pocillopora species and then apply the assay to screen samples of Pocillopora spp. collected at regional scales along the coastline of Western Australia. This assay offers a cheap and time-effective alternative to Sanger sequencing and has broad applications including studies on gene flow, dispersal, recruitment and physiological thresholds of P. damicornis.

  20. Development of a real-time PCR method for the identification of Atlantic mackerel (Scomber scombrus).

    PubMed

    Velasco, Amaya; Sánchez, Ana; Martínez, Icíar; Santaclara, Francisco J; Pérez-Martín, Ricardo I; Sotelo, Carmen G

    2013-12-01

    A Real Time-PCR method based on TaqMan technology for the identification of Scomber scombrus has been developed. A system of specific primers and a Minor Groove Binding (MGB) TaqMan probe based on sequences of the mitochondrial cytochrome b region was designed. The method was successfully tested in 81 specimens of S. scombrus and related species and validated in 26 different commercial samples. An average Threshold Cycle (Ct) value of 15.3 was obtained with S. scombrus DNA. With the other species tested fluorescence signal was not detected or Ct was significantly higher (P<0.001). The efficiency of the assay was estimated to be 92.41%, with 100% specificity, and no cross reactivity was detected with any other species. These results reveal that the developed method is a rapid and efficient tool to unequivocally identify S. scombrus and may aid in the prevention of fraud or mislabelling in mackerel products.

  1. Real-time aircraft structural damage identification with flight condition variations

    NASA Astrophysics Data System (ADS)

    Lew, Jiann-Shiun; Loh, Chin-Hsiung

    2012-04-01

    This paper presents a real-time structural damage identification method for aircraft with flight condition variations. The proposed approach begins by identifying the dynamic models under various test conditions from time-domain input/output data. A singular value decomposition technique is then used to characterize and quantify the parameter uncertainties from the identified models. The uncertainty coordinates, corresponding to the identified principal directions, of the identified models are computed, and the residual errors between the identified uncertainty coordinates and the estimated uncertainty coordinates of the health structure are used to identify damage status. A correlation approach is applied to identify damage type and intensity, based on the difference between the identified parameters and the estimated parameters of the healthy structure. The proposed approach is demonstrated by application to the Benchmark Active Controls Technology (BACT) wind-tunnel model.

  2. Species identification of Cannabis sativa using real-time quantitative PCR (qPCR).

    PubMed

    Johnson, Christopher E; Premasuthan, Amritha; Satkoski Trask, Jessica; Kanthaswamy, Sree

    2013-03-01

    Most narcotics-related cases in the United States involve Cannabis sativa. Material is typically identified based on the cystolithic hairs on the leaves and with chemical tests to identify of the presence of cannabinoids. Suspect seeds are germinated into a viable plant so that morphological and chemical tests can be conducted. Seed germination, however, causes undue analytical delays. DNA analyses that involve the chloroplast and nuclear genomes have been developed for identification of C. sativa materials, but they require several nanograms of template DNA. Using the trnL 3' exon-trnF intragenic spacer regions within the C. sativa chloroplast, we have developed a real-time quantitative PCR assay that is capable of identifying picogram amounts of chloroplast DNA for species determination of suspected C. sativa material. This assay provides forensic science laboratories with a quick and reliable method to identify an unknown sample as C. sativa.

  3. Development and evaluation of real-time PCR assays for bloodmeal identification in Culicoides midges.

    PubMed

    VAN DER Saag, M R; Gu, X; Ward, M P; Kirkland, P D

    2016-06-01

    Culicoides (Diptera: Ceratopogonidae) midges are the biological vectors of a number of arboviruses of veterinary importance. However, knowledge relating to the basic biology of some species, including their host-feeding preferences, is limited. Identification of host-feeding preferences in haematophagous insects can help to elucidate the transmission dynamics of the arboviruses they may transmit. In this study, a series of semi-quantitative real-time polymerase chain reaction (qPCR) assays to identify the vertebrate host sources of bloodmeals of Culicoides midges was developed. Two pan-reactive species group and seven species-specific qPCR assays were developed and evaluated. The assays are quick to perform and less expensive than nucleic acid sequencing of bloodmeals. Using these assays, it was possible to rapidly test nearly 700 blood-fed midges of various species from several geographic locations in Australia. PMID:26854008

  4. Detection of dermcidin for sweat identification by real-time RT-PCR and ELISA.

    PubMed

    Sakurada, Koichi; Akutsu, Tomoko; Fukushima, Hisayo; Watanabe, Ken; Yoshino, Mineo

    2010-01-30

    We evaluated the performance of real-time RT-PCR and ELISA assays for detection of dermcidin (DCD) in sweat and body-fluid stains. DCD, a small antibiotic peptide secreted into human sweat, was detected by real-time RT-PCR in 7-day-old stains containing as small as 10 microL of sweat, and the assay showed high specificity when testing 7-day-old stains containing 30 microL of other body-fluid. ELISA using anti-human dermcidin mouse monoclonal antibody detected DCD sweat diluted up to approximately 10,000-fold and could specifically detect DCD in 10 microL of body-fluid stains. The performance of the two assays was tested during winter on samples that simulated forensic case samples: an undershirt and a sock worn for 20 h, a handkerchief used to wipe the brow several times within 12h, a cap and a cotton glove worn for 4h, and a white robe worn at intervals for 2 years. The result showed that the former assay detected DCD in all sites of the undershirt examined (armpit, back, and breast), and the latter gave a relatively high OD value in the armpit among the three sites. For the socks, although the latter assay gave very high OD values in both the center and toe of the foot sole, the former could not detect DCD in both of them. These results indicate that highly damp conditions, such as inside a shoe, might promote the degradation of mRNA in samples such as socks. In the other case samples, sweat was adequately detected by both assays. This study is the first demonstration of the use of real-time RT-PCR to sensitively identify sweat among body-fluid stains, and it confirmed that dermcidin was an excellent marker for sweat identification. In addition, the usefulness of ELISA was also verified. Positive sweat identification using these assays is expected to assist forensic practice.

  5. Identification of five highly priced tuna species by quantitative real-time polymerase chain reaction.

    PubMed

    Liu, Shasha; Xu, Kunhua; Wu, Zhigang; Xie, Xiao; Feng, Junli

    2016-09-01

    Tunas are economically important fishery worldwide, and are often used for commercial processed production. For effective fishery management and protection of consumers' rights, it is important to develop a molecular method to identify species in canned tuna products rapidly and reliably. Here, we have developed a duplex quantitative real-time PCR (qPCR) for identification of five highly priced tuna species (Thunnus maccoyii, Thunnus obesus, Thunnus albacares, Thunnus alalunga and Katsuwonus pelamis) from processed as well as fresh fish. After amplification and sequencing of seven genetic markers commonly used for species identification, 16S rDNA and control region (CR) of mitochondrial DNA were selected as the reference gene markers for genus Thunnus and tuna species identification, respectively. Subsequently, a 73 bp fragment of 16S rDNA and 85-99 bp fragment of CR were simultaneously amplified from each target species by qPCR. The qPCR efficiency of each reaction was calculated according to the standard curves, and the method was validated by amplification DNA extracted from single or mixed tuna specimen. The developed duplex qPCR system was applied to authenticate species of 14 commercial tuna products successfully, which demonstrated it was really a useful and academic technique to identify highly priced tuna species. PMID:25714139

  6. The development of a near-real time hail damage swath identification algorithm for vegetation

    NASA Astrophysics Data System (ADS)

    Bell, Jordan R.

    The central United States is primarily covered in agricultural lands with a growing season that peaks during the same time as the region's climatological maximum for severe weather. These severe thunderstorms can bring large hail that can cause extensive areas of crop damage, which can be difficult to survey from the ground. Satellite remote sensing can help with the identification of these damaged areas. This study examined three techniques for identifying damage using satellite imagery that could be used in the development of a near-real time algorithm formulated for the detection of damage to agriculture caused by hail. The three techniques: a short term Normalized Difference Vegetation Index (NDVI) change product, a modified Vegetation Health Index (mVHI) that incorporates both NDVI and land surface temperature (LST), and a feature detection technique based on NDVI and LST anomalies were tested on a single training case and five case studies. Skill scores were computed for each of the techniques during the training case and each case study. Among the best-performing case studies, the probability of detection (POD) for the techniques ranged from 0.527 - 0.742. Greater skill was noted for environments that occurred later in the growing season over areas where the land cover was consistently one or two types of uniform vegetation. The techniques struggled in environments where the land cover was not able to provide uniform vegetation, resulting in POD of 0.067 - 0.223. The feature detection technique was selected to be used for the near-real-time algorithm, based on the consistent performance throughout the entire growing season.

  7. Identification of four squid species by quantitative real-time polymerase chain reaction.

    PubMed

    Ye, Jian; Feng, Junli; Liu, Shasha; Zhang, Yanping; Jiang, Xiaona; Dai, Zhiyuan

    2016-02-01

    Squids are distributed worldwide, including many species of commercial importance, and they are often made into varieties of flavor foods. The rapid identification methods for squid species especially their processed products, however, have not been well developed. In this study, quantitative real-time PCR (qPCR) systems based on specific primers and TaqMan probes have been established for rapid and accurate identification of four common squid species (Ommastrephes bartramii, Dosidicus gigas, Illex argentinus, Todarodes pacificus) in Chinese domestic market. After analyzing mitochondrial genes reported in GenBank, the mitochondrial cytochrome b (Cytb) gene was selected for O. bartramii detection, cytochrome c oxidase subunit I (COI) gene for D. gigas and T. Pacificus detection, ATPase subunit 6 (ATPase 6) gene for I. Argentinus detection, and 12S ribosomal RNA (12S rDNA) gene for designing Ommastrephidae-specific primers and probe. As a result, all the TaqMan systems are of good performance, and efficiency of each reaction was calculated by making standard curves. This method could detect target species either in single or mixed squid specimen, and it was applied to identify 12 squid processed products successfully. Thus, it would play an important role in fulfilling labeling regulations and squid fishery control.

  8. Development of real-time PCR assay for genetic identification of the mottled skate, Beringraja pulchra.

    PubMed

    Hwang, In Kwan; Lee, Hae Young; Kim, Min-Hee; Jo, Hyun-Su; Choi, Dong-Ho; Kang, Pil-Won; Lee, Yang-Han; Cho, Nam-Soo; Park, Ki-Won; Chae, Ho Zoon

    2015-10-01

    The mottled skate, Beringraja pulchra is one of the commercially important fishes in the market today. However, B. pulchra identification methods have not been well developed. The current study reports a novel real-time PCR method based on TaqMan technology developed for the genetic identification of B. pulchra. The mitochondrial cytochrome oxidase subunit 1 (COI) nucleotide sequences of 29 B. pulchra, 157 skates and rays reported in GenBank DNA database were comparatively analyzed and the COI sequences specific to B. pulchra was identified. Based on this information, a system of specific primers and Minor Groove Binding (MGB) TaqMan probe were designed. The assay successfully discriminated in 29 specimens of B. pulchra and 27 commercial samples with unknown species identity. For B. pulchra DNA, an average Threshold Cycle (Ct) value of 19.1±0.1 was obtained. Among 27 commercial samples, two samples showed average Ct values 19.1±0.0 and 26.7±0.1, respectively and were confirmed to be B. pulchra based on sequencing. The other samples tested showed undetectable or extremely weak signals for the target fragment, which was also consistent with the sequencing results. These results reveal that the method developed is a rapid and efficient tool to identify B. pulchra and might prevent fraud or mislabeling during the distribution of B. pulchra products.

  9. Parametric identification of a servo-hydraulic actuator for real-time hybrid simulation

    NASA Astrophysics Data System (ADS)

    Qian, Yili; Ou, Ge; Maghareh, Amin; Dyke, Shirley J.

    2014-10-01

    In a typical Real-time Hybrid Simulation (RTHS) setup, servo-hydraulic actuators serve as interfaces between the computational and physical substructures. Time delay introduced by actuator dynamics and complex interaction between the actuators and the specimen has detrimental effects on the stability and accuracy of RTHS. Therefore, a good understanding of servo-hydraulic actuator dynamics is a prerequisite for controller design and computational simulation of RTHS. This paper presents an easy-to-use parametric identification procedure for RTHS users to obtain re-useable actuator parameters for a range of payloads. The critical parameters in a linearized servo-hydraulic actuator model are optimally obtained from genetic algorithms (GA) based on experimental data collected from various specimen mass/stiffness combinations loaded to the target actuator. The actuator parameters demonstrate convincing convergence trend in GA. A key feature of this parametric modeling procedure is its re-usability under different testing scenarios, including different specimen mechanical properties and actuator inner-loop control gains. The models match well with experimental results. The benefit of the proposed parametric identification procedure has been demonstrated by (1) designing an H∞ controller with the identified system parameters that significantly improves RTHS performance; and (2) establishing an analysis and computational simulation of a servo-hydraulic system that help researchers interpret system instability and improve design of experiments.

  10. Development of a Near-Real Time Hail Damage Swath Identification Algorithm for Vegetation

    NASA Technical Reports Server (NTRS)

    Bell, Jordan R.; Molthan, Andrew L.; Schultz, Lori A.; McGrath, Kevin M.; Burks, Jason E.

    2015-01-01

    The Midwest is home to one of the world's largest agricultural growing regions. Between the time period of late May through early September, and with irrigation and seasonal rainfall these crops are able to reach their full maturity. Using moderate to high resolution remote sensors, the monitoring of the vegetation can be achieved using the red and near-infrared wavelengths. These wavelengths allow for the calculation of vegetation indices, such as Normalized Difference Vegetation Index (NDVI). The vegetation growth and greenness, in this region, grows and evolves uniformly as the growing season progresses. However one of the biggest threats to Midwest vegetation during the time period is thunderstorms that bring large hail and damaging winds. Hail and wind damage to crops can be very expensive to crop growers and, damage can be spread over long swaths associated with the tracks of the damaging storms. Damage to the vegetation can be apparent in remotely sensed imagery and is visible from space after storms slightly damage the crops, allowing for changes to occur slowly over time as the crops wilt or more readily apparent if the storms strip material from the crops or destroy them completely. Previous work on identifying these hail damage swaths used manual interpretation by the way of moderate and higher resolution satellite imagery. With the development of an automated and near-real time hail swath damage identification algorithm, detection can be improved, and more damage indicators be created in a faster and more efficient way. The automated detection of hail damage swaths will examine short-term, large changes in the vegetation by differencing near-real time eight day NDVI composites and comparing them to post storm imagery from the Moderate Resolution Imaging Spectroradiometer (MODIS) aboard Terra and Aqua and Visible Infrared Imaging Radiometer Suite (VIIRS) aboard Suomi NPP. In addition land surface temperatures from these instruments will be examined as

  11. Validation of a real-time PCR assay for the molecular identification of Mycobacterium tuberculosis.

    PubMed

    Sales, Mariana L; Fonseca Júnior, Antônio Augusto; Orzil, Lívia; Alencar, Andrea Padilha; Silva, Marcio Roberto; Issa, Marina Azevedo; Soares Filho, Paulo Martins; Lage, Andrey Pereira; Heinemann, Marcos Bryan

    2014-01-01

    Mycobacterium tuberculosis is the major cause of tuberculosis in humans. This bacillus gained prominence with the occurrence of HIV, presenting itself as an important opportunistic infection associated with acquired immunodeficiency syndrome (AIDS). The current study aimed to develop a real-time PCR using Eva Green technology for molecular identification of M. tuberculosis isolates. The primers were designed to Rv1510 gene. Ninety nine samples of M. tuberculosis and sixty samples of M. bovis were tested and no sample of the bovine bacillus was detected by the qPCR. Statistical tests showed no difference between the qPCR and biochemical tests used to identify the Mycobacterium tuberculosis. The correlation between tests was perfect with Kappa index of 1.0 (p < 0.001, CI = 0.84 - 1.0). The diagnostic sensitivity and specificity were 100% (CI = 95.94% - 100%) and 100% (CI = 93.98% - 100%). This qPCR was developed with the goal of diagnosing the bacillus M. tuberculosis in samples of bacterial suspension. TB reference laboratories (health and agriculture sectors), public health programs and epidemiological studies probably may benefit from such method.

  12. Demonstration of real-time automatic target identification from a surrogate UAV

    NASA Astrophysics Data System (ADS)

    Randall, Peter; Wood, Jonathan; Nothard, Jo; Cowell, Jason; Smart, Karen; Pearce, Dan

    2006-05-01

    Airborne surveillance and targeting sensors are capable of generating large quantities of imagery, making it difficult for the user to find the targets of interest. Automatic target identification (ATI) can assist this process by searching for target-like objects and classifying them, thus reducing workload. ATI algorithms, developed in the laboratory by QinetiQ, have been implemented in real-time on ruggedised processing capable of flight. A series of airborne tests has been carried out to assess the performance of the ATI under real world conditions, using a Wescam EO/IR turret as the source of imagery. The tests included examples of military vehicles in urban and rural scenarios, with varying degrees of hide and concealment. Tests were conducted in different weather conditions to assess the robustness of the sensor and ATI combination. This paper discusses the tests carried out and the performance of the ATI achieved as a function of the test parameters. Conclusions are drawn as to the current state of ATI and its applicability to military requirements.

  13. RAPHIDOPHYCEAE [CHADEFAUD EX SILVA] SYSTEMATICS AND RAPID IDENTIFICATION: SEQUENCE ANALYSES AND REAL-TIME PCR ASSAYS

    PubMed Central

    Bowers, Holly A.; Tomas, Carmelo; Tengs, Torstein; Kempton, Jason W.; Lewitus, Alan J.; Oldach, David W.

    2010-01-01

    Species within the class Raphidophyceae were associated with fish kill events in Japanese, European, Canadian, and U.S. coastal waters. Fish mortality was attributable to gill damage with exposure to reactive oxygen species (peroxide, superoxide, and hydroxide radicals), neurotoxins, physical clogging, and hemolytic substances. Morphological identification of these organisms in environmental water samples is difficult, particularly when fixatives are used. Because of this difficulty and the continued global emergence of these species in coastal estuarine waters, we initiated the development and validation of a suite of real-time polymerase chain reaction (PCR) assays. Sequencing was used to generate complete data sets for nuclear encoded small-subunit ribosomal RNA (SSU rRNA; 18S); internal transcribed spacers 1 and 2, 5.8S; and plastid encoded SSU rRNA (16S) for confirmed raphidophyte cultures from various geographic locations. Sequences for several Chattonella species (C. antiqua, C. marina, C. ovata, C. subsalsa, and C. verruculosa), Heterosigma akashiwo, and Fibrocapsa japonica were generated and used to design rapid and specific PCR assays for several species including C. verruculosa Hara et Chihara, C. subsalsa Biecheler, the complex comprised of C. marina Hara et Chihara, C. antiqua Ono and C. ovata, H. akashiwo Ono, and F. japonica Toriumi et Takano using appropriate loci. With this comprehensive data set, we were also able to perform phylogenetic analyses to determine the relationship between these species. PMID:20411032

  14. Identification of reference genes for real-time quantitative PCR experiments in the liverwort Marchantia polymorpha.

    PubMed

    Saint-Marcoux, Denis; Proust, Hélène; Dolan, Liam; Langdale, Jane A

    2015-01-01

    Real-time quantitative polymerase chain reaction (qPCR) has become widely used as a method to compare gene transcript levels across different conditions. However, selection of suitable reference genes to normalize qPCR data is required for accurate transcript level analysis. Recently, Marchantia polymorpha has been adopted as a model for the study of liverwort development and land plant evolution. Identification of appropriate reference genes has therefore become a necessity for gene expression studies. In this study, transcript levels of eleven candidate reference genes have been analyzed across a range of biological contexts that encompass abiotic stress, hormone treatment and different developmental stages. The consistency of transcript levels was assessed using both geNorm and NormFinder algorithms, and a consensus ranking of the different candidate genes was then obtained. MpAPT and MpACT showed relatively constant transcript levels across all conditions tested whereas the transcript levels of other candidate genes were clearly influenced by experimental conditions. By analyzing transcript levels of phosphate and nitrate starvation reporter genes, we confirmed that MpAPT and MpACT are suitable reference genes in M. polymorpha and also demonstrated that normalization with an inappropriate gene can lead to erroneous analysis of qPCR data. PMID:25798897

  15. Real-time identification of vehicle motion-modes using neural networks

    NASA Astrophysics Data System (ADS)

    Wang, Lifu; Zhang, Nong; Du, Haiping

    2015-01-01

    A four-wheel ground vehicle has three body-dominated motion-modes, that is, bounce, roll, and pitch motion-modes. Real-time identification of these motion-modes can make vehicle suspensions, in particular, active suspensions, target on the dominant motion-mode and apply appropriate control strategies to improve its performance with less power consumption. Recently, a motion-mode energy method (MEM) was developed to identify the vehicle body motion-modes. However, this method requires the measurement of full vehicle states and road inputs, which are not always available in practice. This paper proposes an alternative approach to identify vehicle primary motion-modes with acceptable accuracy by employing neural networks (NNs). The effectiveness of the trained NNs is verified on a 10-DOF full-car model under various types of excitation inputs. The results confirm that the proposed method is effective in determining vehicle primary motion-modes with comparable accuracy to the MEM method. Experimental data is further used to validate the proposed method.

  16. Validation of a real-time PCR assay for the molecular identification of Mycobacterium tuberculosis

    PubMed Central

    Sales, Mariana L.; Fonseca, Antônio Augusto; Orzil, Lívia; Alencar, Andrea Padilha; Silva, Marcio Roberto; Issa, Marina Azevedo; Filho, Paulo Martins Soares; Lage, Andrey Pereira; Heinemann, Marcos Bryan

    2014-01-01

    Mycobacterium tuberculosis is the major cause of tuberculosis in humans. This bacillus gained prominence with the occurrence of HIV, presenting itself as an important opportunistic infection associated with acquired immunodeficiency syndrome (AIDS). The current study aimed to develop a real-time PCR using Eva Green technology for molecular identification of M. tuberculosis isolates. The primers were designed to Rv1510 gene. Ninety nine samples of M. tuberculosis and sixty samples of M. bovis were tested and no sample of the bovine bacillus was detected by the qPCR. Statistical tests showed no difference between the qPCR and biochemical tests used to identify the Mycobacterium tuberculosis. The correlation between tests was perfect with Kappa index of 1.0 (p < 0.001, CI = 0.84 – 1.0). The diagnostic sensitivity and specificity were 100% (CI = 95.94% – 100%) and 100% (CI = 93.98% – 100%). This qPCR was developed with the goal of diagnosing the bacillus M. tuberculosis in samples of bacterial suspension. TB reference laboratories (health and agriculture sectors), public health programs and epidemiological studies probably may benefit from such method. PMID:25763042

  17. Development of a Real-Time PCR for Identification of Brachyspira Species in Human Colonic Biopsies

    PubMed Central

    Westerman, Laurens J.; Stel, Herbert V.; Schipper, Marguerite E. I.; Bakker, Leendert J.; Neefjes-Borst, Eskelina A.; van den Brande, Jan H. M.; Boel, Edwin C. H.; Seldenrijk, Kees A.; Siersema, Peter D.; Bonten, Marc J. M.; Kusters, Johannes G.

    2012-01-01

    Background Brachyspira species are fastidious anaerobic microorganisms, that infect the colon of various animals. The genus contains both important pathogens of livestock as well as commensals. Two species are known to infect humans: B. aalborgi and B. pilosicoli. There is some evidence suggesting that the veterinary pathogenic B. pilosicoli is a potential zoonotic agent, however, since diagnosis in humans is based on histopathology of colon biopsies, species identification is not routinely performed in human materials. Methods The study population comprised 57 patients with microscopic evidence of Brachyspira infection and 26 patients with no histopathological evidence of Brachyspira infection. Concomitant faecal samples were available from three infected patients. Based on publically available 16S rDNA gene sequences of all Brachyspira species, species-specific primer sets were designed. DNA was extracted and tested by real-time PCR and 16S rDNA was sequenced. Results Sensitivity and specificity for identification of Brachyspira species in colon biopsies was 100% and 87.7% respectively. Sequencing revealed B. pilosicoli in 15.4% of patients, B. aalborgi in 76.9% and a third species, tentatively named “Brachyspira hominis”, in 26.2%. Ten patients (12.3%) had a double and two (3.1%) a triple infection. The presence of Brachyspira pilosicoli was significantly associated with inflammatory changes in the colon-biopsy (p = 0.028). Conclusions This newly designed PCR allows for sub-differentiation of Brachyspira species in patient material and thus allows large-scaled surveillance studies to elucidate the pathogenicity of human Brachyspira infections. One-third of affected patients appeared to be infected with a novel species. PMID:23284968

  18. Multiplex real-time PCR assays for the identification of the potato cyst and tobacco cyst nematodes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    TaqMan primer-probe sets were developed for the detection and identification of potato cyst nematodes (PCN) Globodera pallida and G. rostochiensis using two-tube, multiplex real-time PCR. One tube contained a primer-probe set specific for G. pallida (pale cyst nematode) multiplexed with another prim...

  19. [Development of a real-time polymerase chain reaction method for the identification of Candida species].

    PubMed

    Ağca, Harun; Dalyan Cilo, Burcu; Özmerdiven, Gülşah Ece; Sağlam, Sezcan; Ener, Beyza

    2015-01-01

    Candida species are one of the major causes of nosocomial infections and are the fourth most common agent involved in bloodstream infections. The impact of non-albicans Candida species is increasing, however C.albicans is still the most common species. Since the antifungal susceptibility pattern among Candida spp. may be different, rapid diagnosis and identification of non-albicans Candida spp. are important for the determination of antifungal agents that will be used for treatment. The aim of the study was to describe a real-time polymerase chain reaction (Rt-PCR) assay that rapidly detects, identifies and quantitates Candida species from blood culture samples. A total of 50 consecutive positive blood culture bottles (BACTEC, Beckton Dickinson, USA) identified at our laboratory between June-November 2013, were included in the study. Reference strains of Candida spp. (C.albicans ATCC 10231, C.glabrata ATCC 90030, C.tropicalis ATCC 1021, C.krusei ATCC 6258, C.parapsilosis ATCC 22019 and C. dubliniensis CD36) grown on Sabouraud dextrose agar were used for quality control. BACTEC bottles that were positive for Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus were also studied to search the cross-reactivity. A commercial kit (Zymo Research, USA) was used for DNA extraction. Real-time PCR was performed on LightCycler 480 (Roche, Germany) with primers and probes specific for 18S rRNA of Candida species. Twenty microlitres of the reaction mix contained 2 μl of extracted DNA, 2 μl of LightCycler Fast Start DNA Master Probe (Roche Diagnostics, Germany), 2 μl of MgCl(2) (5 mmol), 2 μl of 10x PCR buffer (Roche Diagnostics, Germany), 0.5 μl of each primer (0.01 nmol/μl) and 1 μl of each probe (0.1 μmol/μl) (TibMolBiol, Germany). Amplification was performed using the following conditions; 95°C for 10 mins and 50 cycles of denaturation at 95°C for 10 secs, annealing at 62°C for 10 secs and polymerisation at 72°C for 20 secs. A melting curve was

  20. [Development of a real-time polymerase chain reaction method for the identification of Candida species].

    PubMed

    Ağca, Harun; Dalyan Cilo, Burcu; Özmerdiven, Gülşah Ece; Sağlam, Sezcan; Ener, Beyza

    2015-01-01

    Candida species are one of the major causes of nosocomial infections and are the fourth most common agent involved in bloodstream infections. The impact of non-albicans Candida species is increasing, however C.albicans is still the most common species. Since the antifungal susceptibility pattern among Candida spp. may be different, rapid diagnosis and identification of non-albicans Candida spp. are important for the determination of antifungal agents that will be used for treatment. The aim of the study was to describe a real-time polymerase chain reaction (Rt-PCR) assay that rapidly detects, identifies and quantitates Candida species from blood culture samples. A total of 50 consecutive positive blood culture bottles (BACTEC, Beckton Dickinson, USA) identified at our laboratory between June-November 2013, were included in the study. Reference strains of Candida spp. (C.albicans ATCC 10231, C.glabrata ATCC 90030, C.tropicalis ATCC 1021, C.krusei ATCC 6258, C.parapsilosis ATCC 22019 and C. dubliniensis CD36) grown on Sabouraud dextrose agar were used for quality control. BACTEC bottles that were positive for Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus were also studied to search the cross-reactivity. A commercial kit (Zymo Research, USA) was used for DNA extraction. Real-time PCR was performed on LightCycler 480 (Roche, Germany) with primers and probes specific for 18S rRNA of Candida species. Twenty microlitres of the reaction mix contained 2 μl of extracted DNA, 2 μl of LightCycler Fast Start DNA Master Probe (Roche Diagnostics, Germany), 2 μl of MgCl(2) (5 mmol), 2 μl of 10x PCR buffer (Roche Diagnostics, Germany), 0.5 μl of each primer (0.01 nmol/μl) and 1 μl of each probe (0.1 μmol/μl) (TibMolBiol, Germany). Amplification was performed using the following conditions; 95°C for 10 mins and 50 cycles of denaturation at 95°C for 10 secs, annealing at 62°C for 10 secs and polymerisation at 72°C for 20 secs. A melting curve was

  1. Multiplex Real-Time PCR Method for Simultaneous Identification and Toxigenic Type Characterization of Clostridium difficile From Stool Samples

    PubMed Central

    Alam, Mohammad J.; Tisdel, Naradah L.; Shah, Dhara N.; Yapar, Mehmet; Lasco, Todd M.; Garey, Kevin W.

    2015-01-01

    Background The aim of this study was to develop and validate a multiplex real-time PCR assay for simultaneous identification and toxigenic type characterization of Clostridium difficile. Methods The multiplex real-time PCR assay targeted and simultaneously detected triose phosphate isomerase (tpi) and binary toxin (cdtA) genes, and toxin A (tcdA) and B (tcdB) genes in the first and sec tubes, respectively. The results of multiplex real-time PCR were compared to those of the BD GeneOhm Cdiff assay, targeting the tcdB gene alone. The toxigenic culture was used as the reference, where toxin genes were detected by multiplex real-time PCR. Results A total of 351 stool samples from consecutive patients were included in the study. Fifty-five stool samples (15.6%) were determined to be positive for the presence of C. difficile by using multiplex real-time PCR. Of these, 48 (87.2%) were toxigenic (46 tcdA and tcdB-positive, two positive for only tcdB) and 11 (22.9%) were cdtA-positive. The sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV) of the multiplex real-time PCR compared with the toxigenic culture were 95.6%, 98.6%, 91.6%, and 99.3%, respectively. The analytical sensitivity of the multiplex real-time PCR assay was determined to be 103colonyforming unit (CFU)/g spiked stool sample and 0.0625 pg genomic DNA from culture. Analytical specificity determined by using 15 enteric and non-clostridial reference strains was 100%. Conclusions The multiplex real-time PCR assay accurately detected C. difficile isolates from diarrheal stool samples and characterized its toxin genes in a single PCR run. PMID:25932438

  2. SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy

    PubMed Central

    Tang, Yunqing; Dai, Luru; Zhang, Xiaoming; Li, Junbai; Hendriks, Johnny; Fan, Xiaoming; Gruteser, Nadine; Meisenberg, Annika; Baumann, Arnd; Katranidis, Alexandros; Gensch, Thomas

    2015-01-01

    Single molecule localization based super-resolution fluorescence microscopy offers significantly higher spatial resolution than predicted by Abbe’s resolution limit for far field optical microscopy. Such super-resolution images are reconstructed from wide-field or total internal reflection single molecule fluorescence recordings. Discrimination between emission of single fluorescent molecules and background noise fluctuations remains a great challenge in current data analysis. Here we present a real-time, and robust single molecule identification and localization algorithm, SNSMIL (Shot Noise based Single Molecule Identification and Localization). This algorithm is based on the intrinsic nature of noise, i.e., its Poisson or shot noise characteristics and a new identification criterion, QSNSMIL, is defined. SNSMIL improves the identification accuracy of single fluorescent molecules in experimental or simulated datasets with high and inhomogeneous background. The implementation of SNSMIL relies on a graphics processing unit (GPU), making real-time analysis feasible as shown for real experimental and simulated datasets. PMID:26098742

  3. Identification of nasal blood by real-time RT-PCR.

    PubMed

    Sakurada, Koichi; Akutsu, Tomoko; Watanabe, Ken; Yoshino, Mineo

    2012-07-01

    A new approach for the identification of body fluid stains by comparing specific mRNA expression levels has been extensively studied in recent years. Here, we examine whether nasal blood, which is regarded as one of the most difficult types of blood to identify, can be identified by comparing mRNA expression levels of target genes specific to saliva, nasal secretion, and blood. The saliva-specific statherin gene (STATH) was found to be expressed at high levels in not only saliva (dCt value: 1.32±1.39, n=5), but also nasal secretions (dCt value: 0.90±1.14, n=5), while the histatin gene (HTN3) was only expressed at high levels in saliva (dCt value: 1.08±2.35, n=5). We also confirmed that the hemoglobin-beta gene (HBB) showed high expression levels in blood (dCt value: -9.51±0.40, n=5). Four nasal blood stains were found to highly express STATH (dCt value: 5.65±3.98) and HBB (dCt value: -8.79±1.67) but not HTN3, suggesting that the stain samples contained both nasal secretions and blood and can therefore be identified as nasal blood stains. Although menstrual blood showed the same expression pattern as nasal blood, the menstrual blood-specific protein matrix metallopeptidase 7 (MMP7) was not expressed in all nasal blood stain samples. Therefore, its expression levels could be used to discriminate between nasal and menstrual blood. In conclusion, real-time RT-PCR was able to identify nasal blood, although the stability of gene expression in nasal blood stains was low over time, suggesting that this assay may not be effective for older stains. Future work should examine the usefulness of this assay under various environmental conditions.

  4. Development of a Near Real-Time Hail Damage Swath Identification Algorithm for Vegetation

    NASA Technical Reports Server (NTRS)

    Bell, Jordan R.; Molthan, Andrew L.; Schultz, Kori A.; McGrath, Kevin M.; Burks, Jason E.

    2015-01-01

    Every year in the Midwest and Great Plains, widespread greenness forms in conjunction with the latter part of the spring-summer growing season. This prevalent greenness forms as a result of the high concentration of agricultural areas having their crops reach their maturity before the fall harvest. This time of year also coincides with an enhanced hail frequency for the Great Plains (Cintineo et al. 2012). These severe thunderstorms can bring damaging winds and large hail that can result in damage to the surface vegetation. The spatial extent of the damage can relatively small concentrated area or be a vast swath of damage that is visible from space. These large areas of damage have been well documented over the years. In the late 1960s aerial photography was used to evaluate crop damage caused by hail. As satellite remote sensing technology has evolved, the identification of these hail damage streaks has increased. Satellites have made it possible to view these streaks in additional spectrums. Parker et al. (2005) documented two streaks using the Moderate Resolution Imaging Spectroradiometer (MODIS) that occurred in South Dakota. He noted the potential impact that these streaks had on the surface temperature and associated surface fluxes that are impacted by a change in temperature. Gallo et al. (2012) examined at the correlation between radar signatures and ground observations from storms that produced a hail damage swath in Central Iowa also using MODIS. Finally, Molthan et al. (2013) identified hail damage streaks through MODIS, Landsat-7, and SPOT observations of different resolutions for the development of a potential near-real time applications. The manual analysis of hail damage streaks in satellite imagery is both tedious and time consuming, and may be inconsistent from event to event. This study focuses on development of an objective and automatic algorithm to detect these areas of damage in a more efficient and timely manner. This study utilizes the

  5. [Identification for genetically modified maize T14/T25 with real time fluorescent PCR method].

    PubMed

    Cao, Ji-Juan; Qin, Wen; Zhu, Shui-Fang; Cao, Yuan-Yin

    2004-09-01

    To identify genetically modified (GM) maize T14/T25 lines, a real-time fluorescent PCR (RTF PCR) assay was performed in this study. Primers and Taqman probes specific for inserted genes in the T14/T25 were used to conduct the real-time fluorescent (RTF) PCR and PCR assays. The RTF PCR method was established to detect and identify GM maize lines. The results show that the TaqMan probe could identify T14/T25 maize used, while other GM and NO-GM maize didn't be detected. The RTF PCR could be a new method for detecting other genetically modified organism.

  6. [Identification of human pathogenic variola and monkeypox viruses by real-time polymerase chain reaction].

    PubMed

    Kostina, E V; Gavrilova, E V; Riabinin, V A; Shchelkunov, S N; Siniakov, A N

    2009-01-01

    A kit of specific oligonucleotide primers and hybridization probes has been proposed to detect orthopoxviruses (OPV) and to discriminate human pathogenic viruses, such as variola virus and monkey virus by real-time polymerase chain reaction (PCR). For real-time PCR, the following pairs of fluorophore and a fluorescence quencher were used: TAMRA-BHQ2 for genus-specific probes and FAM-BHQ1 for species-specific ones (variola virus, monkeypox virus, ectomelia virus). The specificity of this assay was tested on 38 strains of 6 OPV species and it was 100%.

  7. Duplex real-time PCR assay for rapid identification of Staphylococcus aureus isolates from dairy cow milk.

    PubMed

    Pilla, Rachel; Snel, Gustavo G M; Malvisi, Michela; Piccinini, Renata

    2013-05-01

    Staphylococcus aureus isolates from dairy cow mastitis are not always consistent with the characteristic morphology described, and molecular investigation is often needed. The aim of the study was to develop a duplex real-time PCR assay for rapid identification of Staph. aureus isolates, targeting both nuc and Sa442. Overall, 140 isolates collected from dairy cow mastitis in 90 different herds, were tested. All strains had been identified using morphological and biochemical characteristics. DNA from each strain was amplified in real-time PCR assay, to detect nuc or Sa442. Thereafter, a duplex real-time PCR assay was performed, and specificity of the amplified products was assessed by high resolution melting curve analysis. Out of 124 Staph. aureus isolates, 33 did not show the typical morphology or enzymic activity; in 118 strains, the two melt-curve peaks consistent with nuc and Sa442 were revealed, while 2 isolates showed only the peak consistent with Sa442. Four isolates bacteriologically identified as Staph. aureus, were PCR-negative and were further identified as Staph. pseudintermedius by sequencing. Staph. pseudintermedius and coagulase-negative staphylococci did not carry nuc or Sa442. The results showed the correct identification of all isolates, comprehending also coagulase-or nuc-negative Staph. aureus, while other coagulase-positive Staphylococci were correctly identified as non-Staph. aureus. Both sensitivity and specificity were 100%. High resolution melting analysis allowed easy detection of unspecific products. Finally, the duplex real-time PCR was applied directly to 40 milk samples, to detect infected mammary quarters. The assay confirmed the results of bacteriological analysis, on Staph. aureus-positive or-negative samples. Therefore, the proposed duplex real-time PCR could be used in laboratory routine as a cost-effective and powerful tool for high-throughput identification of atypical Staph. aureus isolates causing dairy cow mastitis. Also, it

  8. Identification of Histoplasma capsulatum from culture extracts by real-time PCR.

    PubMed

    Martagon-Villamil, Jose; Shrestha, Nabin; Sholtis, Mary; Isada, Carlos M; Hall, Gerri S; Bryne, Terry; Lodge, Barbara A; Reller, L Barth; Procop, Gary W

    2003-03-01

    We designed and tested a real-time LightCycler PCR assay for Histoplasma capsulatum that correctly identified the 34 H. capsulatum isolates in a battery of 107 fungal isolates tested and also detected H. capsulatum in clinical specimens from three patients that were culture positive for this organism. PMID:12624071

  9. Development of a real-time PCR method (Taqman) for rapid identification and quantification of Prorocentrum donghaiense

    NASA Astrophysics Data System (ADS)

    Yuan, Jian; Mi, Tiezhu; Zhen, Yu; Yu, Zhigang

    2012-09-01

    Prorocentrum donghaiense is a dinoflagellate that is widely distributed in the East China Sea and has become increasingly involved in Harmful Algal Blooms (HABs). Therefore, it is necessary to study this dinoflagellate to monitor HABs. In this study, 13 pairs of primers specific to P. donghaiense (within its internal transcribed spacer (ITS) regions) were designed for SYBR Green I real-time PCR. As the SYBR Green I real-time PCR could not identify P. donghaiense in a specific manner, a Taqman real-time PCR method was developed by designing a set of specific primers and a Taqman probe. A 10-fold serial dilution of recombinant plasmid containing ITS regions of P. donghaiense was prepared as standard samples and the standard curve was established. Additionally, we quantified the genomic DNA in P. donghaiense cells and utilized this DNA to prepare another 10-fold serial dilution of standard sample and accordingly set up the standard curve. The mathematic correlation between the cell number and its corresponding plasmid copy number was also established. In order to test the efficiency of the real-time PCR method, laboratory samples and P. donghaiense HAB field samples were employed for identification and quantitative analysis. As to laboratory samples, as few as 102 cells of P. donghaiense could be quantified precisely utilizing both centrifugation and filtration techniques. The quantification results from field samples by real-time PCR were highly similar to those by light microscopy. In conclusion, the real-time PCR could be applied to identify and quantify P. donghaiense in HABs.

  10. Simple Real-Time PCR and Amplicon Sequencing Method for Identification of Plasmodium Species in Human Whole Blood.

    PubMed

    Lefterova, Martina I; Budvytiene, Indre; Sandlund, Johanna; Färnert, Anna; Banaei, Niaz

    2015-07-01

    Malaria is the leading identifiable cause of fever in returning travelers. Accurate Plasmodium species identification has therapy implications for P. vivax and P. ovale, which have dormant liver stages requiring primaquine. Compared to microscopy, nucleic acid tests have improved specificity for species identification and higher sensitivity for mixed infections. Here, we describe a SYBR green-based real-time PCR assay for Plasmodium species identification from whole blood, which uses a panel of reactions to detect species-specific non-18S rRNA gene targets. A pan-Plasmodium 18S rRNA target is also amplified to allow species identification or confirmation by sequencing if necessary. An evaluation of assay accuracy, performed on 76 clinical samples (56 positives using thin smear microscopy as the reference method and 20 negatives), demonstrated clinical sensitivities of 95.2% for P. falciparum (20/21 positives detected) and 100% for the Plasmodium genus (52/52), P. vivax (20/20), P. ovale (9/9), and P. malariae (6/6). The sensitivity of the P. knowlesi-specific PCR was evaluated using spiked whole blood samples (100% [10/10 detected]). The specificities of the real-time PCR primers were 94.2% for P. vivax (49/52) and 100% for P. falciparum (51/51), P. ovale (62/62), P. malariae (69/69), and P. knowlesi (52/52). Thirty-three specimens were used to test species identification by sequencing the pan-Plasmodium 18S rRNA PCR product, with correct identification in all cases. The real-time PCR assay also identified two samples with mixed P. falciparum and P. ovale infection, which was confirmed by sequencing. The assay described here can be integrated into a malaria testing algorithm in low-prevalence areas, allowing definitive Plasmodium species identification shortly after malaria diagnosis by microscopy.

  11. Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION(TM) sequencing.

    PubMed

    Cao, Minh Duc; Ganesamoorthy, Devika; Elliott, Alysha G; Zhang, Huihui; Cooper, Matthew A; Coin, Lachlan J M

    2016-07-26

    The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This has great potential to shorten the sample-to-results time and is likely to have benefits such as rapid diagnosis of bacterial infection and identification of drug resistance. However, there are few tools available for streaming analysis of real-time sequencing data. Here, we present a framework for streaming analysis of MinION real-time sequence data, together with probabilistic streaming algorithms for species typing, strain typing and antibiotic resistance profile identification. Using four culture isolate samples, as well as a mixed-species sample, we demonstrate that bacterial species and strain information can be obtained within 30 min of sequencing and using about 500 reads, initial drug-resistance profiles within two hours, and complete resistance profiles within 10 h. While strain identification with multi-locus sequence typing required more than 15x coverage to generate confident assignments, our novel gene-presence typing could detect the presence of a known strain with 0.5x coverage. We also show that our pipeline can process over 100 times more data than the current throughput of the MinION on a desktop computer.

  12. Real-Time Identification and Characterization of Asbestos and Concrete Materials with Radioactive Contamination

    SciTech Connect

    Xu, George; Zhang, Xi-Cheng

    1999-06-01

    Concrete and asbestos-containing materials were widely used in U.S. Department of Energy (DOE) building construction in the 1940s and 1950s. Over the years, many of these porous building materials have been contaminated with radioactive sources, on and below the surface. This intractable radioactive-and-hazardous- asbestos mixed-waste-stream has created a tremendous challenge to DOE decontamination and decommissioning (D&D) project managers. The current practice to identify asbestos and to characterize radioactive contamination depth profiles involve bore sampling, and is inefficient, costly, and unsafe. A three-year research project was started on 10/1/98 at Rensselaer with the following ultimate goals: (1) development of novel non-destructive methods for identifying the hazardous asbestos in real-time and in-situ, and (2) development of new algorithms and apparatus for characterizing the radioactive contamination depth profile in real-time and in-situ.

  13. Real-Time Identification and Characterization of Asbestos and Concrete Materials with Radioactive Contamination

    SciTech Connect

    Xu, George; Zhang, Xi-Cheng

    2000-06-01

    Concrete and asbestos-containing materials were widely used in U.S. Department of Energy (DOE) building construction in the 1940s and 1950s. Over the years, many of these porous building materials have been contaminated with radioactive sources, on and below the surface. This intractable radioactive-and-hazardous-asbestos mixed-waste stream has created a tremendous challenge to DOE decontamination and decommissioning (D&D) project managers. The current practice to identify asbestos and to characterize radioactive contamination depth profiles in based solely on bore sampling, which is inefficient, costly, and unsafe. A three-year research project was started 1998 at Rensselaer with the following ultimate goals: (1) development of novel non-destructive methods for identifying the hazardous asbestos in real-time and in-situ, and (2) development of new algorithms and apparatus for characterizing the radioactive contamination depth profile in real-time and in-situ.

  14. A Real-Time PCR Array for Hierarchical Identification of Francisella Isolates

    PubMed Central

    Svensson, Kerstin; Granberg, Malin; Karlsson, Linda; Neubauerova, Vera; Forsman, Mats; Johansson, Anders

    2009-01-01

    A robust, rapid and flexible real-time PCR assay for hierarchical genetic typing of clinical and environmental isolates of Francisella is presented. Typing markers were found by multiple genome and gene comparisons, from which 23 canonical single nucleotide polymorphisms (canSNPs) and 11 canonical insertion-deletion mutations (canINDELs) were selected to provide phylogenetic guidelines for classification from genus to isolate level. The specificity of the developed assay, which uses 68 wells of a 96-well real-time PCR format with a detection limit of 100 pg DNA, was assessed using 62 Francisella isolates of diverse genetic and geographical origins. It was then successfully used for typing 14 F. tularensis subsp. holarctica isolates obtained from tularemia patients in Sweden in 2008 and five more genetically diverse Francisella isolates of global origins. When applied to human ulcer specimens for direct pathogen detection the results were incomplete due to scarcity of DNA, but sufficient markers were identified to detect fine-resolution differences among F. tularensis subsp. holarctica isolates causing infection in the patients. In contrast to other real-time PCR assays for Francisella, which are typically designed for specific detection of a species, subspecies, or strain, this type of assay can be easily tailored to provide appropriate phylogenetic and/or geographical resolution to meet the objectives of the analysis. PMID:20027310

  15. Evaluation of multiple genomic targets for identification and confirmation of Mycobacterium avium subsp. paratuberculosis isolates using real-time PCR.

    PubMed

    Rajeev, Sreekumari; Zhang, Yan; Sreevatsan, Srinand; Motiwala, Alifiya S; Byrum, Beverly

    2005-02-25

    Specificity of six previously published Mycobacterium avium subsp. paratuberculosis (MAP) genomic loci, including 10, 38, 56, 93, 251, and 252 were evaluated in this study. Target 251 which was identified as MAP-specific was further evaluated in 210 MAP isolates, 14 non-MAP mycobacterial species, 7 atypical mycobacterial isolates, and 9 other bacterial species using real-time PCR. A previously published IS900 primer and probe combination was used as a positive control along with a universal ribosomal DNA gene sequence (UVA) as an internal control to evaluate PCR inhibition. All MAP isolates were positive with IS900, 251, and UVA by real-time PCR. All non-MAP mycobacterial species except one atypical mycobacterial isolate and other bacterial species used in this study were negative for IS900. All of these species were negative for 251. The atypical mycobacterial isolate, positive for IS900 and UVA, was negative for 251. A combination of IS900 and 251 PCR is ideal for sensitive and specific confirmation of MAP isolates from conventional fecal cultures. This study also evaluated the specificity of 251 real-time PCR, on broth cultures from 50 known bovine fecal samples. Acid fast staining followed by IS900 and 251 real-time PCR can be used for accurate identification and confirmation of MAP from broth cultures.

  16. HUMAN FECAL SOURCE IDENTIFICATION: REAL-TIME QUANTITATIVE PCR METHOD STANDARDIZATION - abstract

    EPA Science Inventory

    Method standardization or the formal development of a protocol that establishes uniform performance benchmarks and practices is necessary for widespread adoption of a fecal source identification approach. Standardization of a human-associated fecal identification method has been...

  17. Human Fecal Source Identification: Real-Time Quantitative PCR Method Standardization

    EPA Science Inventory

    Method standardization or the formal development of a protocol that establishes uniform performance benchmarks and practices is necessary for widespread adoption of a fecal source identification approach. Standardization of a human-associated fecal identification method has been...

  18. Real-time full-motion color Flash lidar for target detection and identification

    NASA Astrophysics Data System (ADS)

    Nelson, Roy; Coppock, Eric; Craig, Rex; Craner, Jeremy; Nicks, Dennis; von Niederhausern, Kurt

    2015-05-01

    Greatly improved understanding of areas and objects of interest can be gained when real time, full-motion Flash LiDAR is fused with inertial navigation data and multi-spectral context imagery. On its own, full-motion Flash LiDAR provides the opportunity to exploit the z dimension for improved intelligence vs. 2-D full-motion video (FMV). The intelligence value of this data is enhanced when it is combined with inertial navigation data to produce an extended, georegistered data set suitable for a variety of analysis. Further, when fused with multispectral context imagery the typical point cloud now becomes a rich 3-D scene which is intuitively obvious to the user and allows rapid cognitive analysis with little or no training. Ball Aerospace has developed and demonstrated a real-time, full-motion LIDAR system that fuses context imagery (VIS to MWIR demonstrated) and inertial navigation data in real time, and can stream these information-rich geolocated/fused 3-D scenes from an airborne platform. In addition, since the higher-resolution context camera is boresighted and frame synchronized to the LiDAR camera and the LiDAR camera is an array sensor, techniques have been developed to rapidly interpolate the LIDAR pixel values creating a point cloud that has the same resolution as the context camera, effectively creating a high definition (HD) LiDAR image. This paper presents a design overview of the Ball TotalSight™ LIDAR system along with typical results over urban and rural areas collected from both rotary and fixed-wing aircraft. We conclude with a discussion of future work.

  19. Loss-pattern identification in near-real-time accounting systems

    SciTech Connect

    Argentesi, F.; Hafer, J.F.; Markin, J.T.; Shipley, J.P.

    1982-01-01

    To maximize the benefits from an advanced safeguards technique such as near-real-time accounting (NRTA), sophisticated methods of analyzing sequential materials accounting data are necessary. The methods must be capable of controlling the overall false-alarm rate while assuring good power of detection against all possible diversion scenarios. A method drawn from the field of pattern recognition and related to the alarm-sequence chart appears to be promising. Power curves based on Monte Carlo calculations illustrate the improvements over more conventional methods. 3 figures, 2 tables.

  20. Real-time PCR assays compared to culture-based approaches for identification of aerobic bacteria in chronic wounds.

    PubMed

    Melendez, J H; Frankel, Y M; An, A T; Williams, L; Price, L B; Wang, N-Y; Lazarus, G S; Zenilman, J M

    2010-12-01

    Chronic wounds cause substantial morbidity and disability. Infection in chronic wounds is clinically defined by routine culture methods that can take several days to obtain a final result, and may not fully describe the community of organisms or biome within these wounds. Molecular diagnostic approaches offer promise for a more rapid and complete assessment. We report the development of a suite of real-time PCR assays for rapid identification of bacteria directly from tissue samples. The panel of assays targets 14 common, clinically relevant, aerobic pathogens and demonstrates a high degree of sensitivity and specificity using a panel of organisms commonly associated with chronic wound infection. Thirty-nine tissue samples from 29 chronic wounds were evaluated and the results compared with those obtained by culture. As revealed by culture and PCR, the most common organisms were methicillin-resistant Staphylococcus aureus (MRSA) followed by Streptococcus agalactiae (Group B streptococcus) and Pseudomonas aeruginosa. The sensitivities of the PCR assays were 100% and 90% when quantitative and qualitative culture results were used as the reference standard, respectively. The assays allowed the identification of bacterial DNA from ten additional organisms that were not revealed by quantitative or qualitative cultures. Under optimal conditions, the turnaround time for PCR results is as short as 4-6 h. Real-time PCR is a rapid and inexpensive approach that can be easily introduced into clinical practice for detection of organisms directly from tissue samples. Characterization of the anaerobic microflora by real-time PCR of chronic wounds is warranted.

  1. Processor core for real time background identification of HD video based on OpenCV Gaussian mixture model algorithm

    NASA Astrophysics Data System (ADS)

    Genovese, Mariangela; Napoli, Ettore

    2013-05-01

    The identification of moving objects is a fundamental step in computer vision processing chains. The development of low cost and lightweight smart cameras steadily increases the request of efficient and high performance circuits able to process high definition video in real time. The paper proposes two processor cores aimed to perform the real time background identification on High Definition (HD, 1920 1080 pixel) video streams. The implemented algorithm is the OpenCV version of the Gaussian Mixture Model (GMM), an high performance probabilistic algorithm for the segmentation of the background that is however computationally intensive and impossible to implement on general purpose CPU with the constraint of real time processing. In the proposed paper, the equations of the OpenCV GMM algorithm are optimized in such a way that a lightweight and low power implementation of the algorithm is obtained. The reported performances are also the result of the use of state of the art truncated binary multipliers and ROM compression techniques for the implementation of the non-linear functions. The first circuit has commercial FPGA devices as a target and provides speed and logic resource occupation that overcome previously proposed implementations. The second circuit is oriented to an ASIC (UMC-90nm) standard cell implementation. Both implementations are able to process more than 60 frames per second in 1080p format, a frame rate compatible with HD television.

  2. A novel application of real-time RT-LAMP for body fluid identification: using HBB detection as the model.

    PubMed

    Su, Chih-Wen; Li, Chiao-Yun; Lee, James Chun-I; Ji, Dar-Der; Li, Shu-Ying; Daniel, Barbara; Syndercombe-Court, Denise; Linacre, Adrian; Hsieh, Hsing-Mei

    2015-06-01

    We report on a novel application of real-time reverse transcription-loop-mediated isothermal amplification (real-time RT-LAMP) to identify the presence of a specific body fluid using blood as a proof-of-concept model. By comparison with recently developed methods of body fluid identification, the RT-LAMP assay is rapid and requires only one simple heating-block maintained at a single temperature, circumventing the need for dedicated equipment. RNA was extracted from different body fluids (blood, semen, saliva, menstrual blood, sweat, and urine) for use in real-time RT-LAMP reaction. The 18S rRNA locus was used as the internal control and hemoglobin beta (HBB) as the blood-specific marker. Reverse transcription and LAMP reaction were performed in the same tube using a turbidimeter for real-time monitoring the reaction products within a threshold of 60 min. HBB LAMP products were only detected in blood and not in any of the other body fluid, but products from the 18S rRNA gene were detected in all the tested body fluids as expected. The limit of detection was a minimum of 10(-5) ng total RNA for detection of both 18S rRNA and HBB. Augmenting the detection of RT-LAMP products was performed by separation of the products using gel electrophoresis and collecting the fluorescence of calcein. The data collected indicated complete concordance with the body fluid tested regardless of the method of detection used. This is the first application of real-time RT-LAMP to detect body fluid specific RNA and indicates the use of this method in forensic biology.

  3. Real-Time Parameter Estimation Method Applied to a MIMO Process and its Comparison with an Offline Identification Method

    SciTech Connect

    Kaplanoglu, Erkan; Safak, Koray K.; Varol, H. Selcuk

    2009-01-12

    An experiment based method is proposed for parameter estimation of a class of linear multivariable systems. The method was applied to a pressure-level control process. Experimental time domain input/output data was utilized in a gray-box modeling approach. Prior knowledge of the form of the system transfer function matrix elements is assumed to be known. Continuous-time system transfer function matrix parameters were estimated in real-time by the least-squares method. Simulation results of experimentally determined system transfer function matrix compare very well with the experimental results. For comparison and as an alternative to the proposed real-time estimation method, we also implemented an offline identification method using artificial neural networks and obtained fairly good results. The proposed methods can be implemented conveniently on a desktop PC equipped with a data acquisition board for parameter estimation of moderately complex linear multivariable systems.

  4. Identification of Legionella Pneumophila in Intubated Patients With TaqMan Real Time PCR

    PubMed Central

    Divan Khosroshahi, Nader; Naserpour Farivar, Taghi; Johari, Pouran

    2015-01-01

    Background: Legionellaceae contains Legionella genus with over 52 species and 64 serogroups. It is one of the most important causes of respiratory disease in human. More than 30% of hospital-acquired pneumonia is caused by Legionella. Ventilator-associated pneumonia (VAP) is an infection acquired in hospital wards, particularly in intensive care unit (ICU). This disease approximately affects 9% to 20% of intubated patients. Mortality in these patients varies between 8% and 76%. Legionella is one of the important factors for infection in intubated patients. Objectives: The present study was aimed to investigate the use of molecular methods in diagnosis of infection caused by Legionella pneumophila. Materials and Methods: In this study, 109 samples of lung secretions collected from intubated patients admitted to ICU wards of four university hospitals in a three-month period were examined. Cultivation and Real time Polymerase Chain Reaction (PCR) methods were used to assess L. pneumophila colonization in these samples. Results: Eleven samples had positive results using real time PCR analysis of 16s rRNA gene fragments specific for L. pneumophila, but according to culture method on specific buffered charcoal-yeast extract medium (BCYE), no positive cases were detected. Of the total positive cases, six were males, one female and four infants. The seven adults aged 40-65 years. Conclusions: Using molecular methods in diagnosis of infection caused by L. pneumophila has a great value because of its high specificity and rapid diagnosis potency. PMID:25834717

  5. Identification of lactic acid bacteria isolated from wine using real-time PCR.

    PubMed

    Kántor, Attila; Kluz, Maciej; Puchalski, Czeslaw; Terentjeva, Margarita; Kačániová, Miroslava

    2016-01-01

    Different lactic acid bacteria strains have been shown to cause wine spoilage, including the generation of substances undesirable for the health of wine consumers. The aim of this study was to investigate the occurrence of selected species of heterofermentative lactobacilli, specifically Lactobacillus brevis, Lactobacillus hilgardii, and Lactobacillus plantarum in six different Slovak red wines following the fermentation process. In order to identify the dominant Lactobacillus strain using quantitative (real time) polymerized chain reaction (qPCR) method, pure lyophilized bacterial cultures from the Czech Collection of Microorganisms were used. Six different red wine samples following malolactic fermentation were obtained from selected wineries. After collection, the samples were subjected to a classic plate dilution method for enumeration of lactobacilli cells. Real-time PCR was performed after DNA extraction from pure bacterial strains and wine samples. We used SYBR® Green master mix reagents for measuring the fluorescence in qPCR. The number of lactobacilli ranged from 3.60 to 5.02 log CFU mL(-1). Specific lactobacilli strains were confirmed by qPCR in all wine samples. The number of lactobacilli ranged from 10(3) to 10(6) CFU mL(-1). A melting curve with different melting temperatures (T(m)) of DNA amplicons was obtained after PCR for the comparison of T(m) of control and experimental portions, revealing that the most common species in wine samples was Lactobacillus plantarum with a T(m) of 84.64°C.

  6. Snow avalanche detection and identification for near real-time application

    NASA Astrophysics Data System (ADS)

    Havens, S.; Johnson, J. B.; Marshall, H.; Nicholson, B.; Trisca, G. O.

    2013-12-01

    A near real-time avalanche detection system will provide highway avalanche forecasters with a tool to remotely monitor major avalanche paths and provide information about regional avalanche activity and timing. For the last three winters, a network of infrasound arrays has been remotely monitoring both avalanche and non-avalanche events along a 10 mile section of Highway 21 in Idaho. To provide the best results to avalanche forecasters, the system must be robust and detect all major avalanche events of interest that affect the highway. Over the last three winters, the infrasound arrays recorded multiple avalanche cycles and we explore different methods of event detection for both large dry avalanches (strong infrasound signal) and small wet avalanches (weak infrasound signal). We compare the F-statistic and cross-correlation techniques (i.e. PMCC) to determine the most robust method and develop computationally efficient algorithms to implement in near-real time using parallel processing and GPU computing. Once an event has been detected, we use the artificial intelligence method of recursive neural networks to classify based on similar characteristics to past known signals.

  7. Rapid identification of Campylobacter jejuni from poultry carcasses and slaughtering environment samples by real-time PCR.

    PubMed

    Ivanova, Mirena; Singh, Randhir; Dharmasena, Muthu; Gong, Chao; Krastanov, Albert; Jiang, Xiuping

    2014-06-01

    The objective of this study was to develop a real-time PCR assay for rapid identification of Campylobacter jejuni and to apply the method in analyzing samples from poultry processing. A C. jejuni-specific primer set targeting a portion of the C. jejuni hippuricase gene was developed. The specificity of the newly designed primer pair was verified using 5 C. jejuni strains and 20 other bacterial strains. Sensitivity was determined to be as low as 1 genome copy per reaction. A total of 73 samples were collected at different sites along the processing line during 2 visits to a poultry slaughterhouse and were examined by direct plating onto modified charcoal cefoperazone deoxycholate agar or after enrichment in Bolton broth followed by plating on modified charcoal cefoperazone deoxycholate agar. The newly developed real-time PCR assay was used to identify the presumptive colonies as belonging to C. jejuni. A real-time PCR assay targeting 16S ribosomal RNA was also applied to determine Campylobacter spp. prevalence. Results from the real-time PCR analysis indicated considerable variability in Campylobacter contamination, with incidence rates of 72.7 and 27.6% for sampling days A and B, respectively. Campylobacter was isolated from 100% of prescalded and preeviscerated carcasses on sampling day A. In contrast, on sampling day B, the highest number of Campylobacter-positive carcasses was recovered after evisceration (60%). The chilling process significantly reduced (P < 0.05) Campylobacter population, but the percentage of positive samples on sampling day A increased to 80%. All samples collected from the processing environment, except scalding tank 3 and the prechiller and chiller tanks, were 100% positive on day A, whereas no campylobacters were isolated from machinery on sampling day B. Our results revealed the widespread of C. jejuni in poultry processing and proved that the newly developed real-time PCR assay is a simple, specific, and inexpensive method for rapid C

  8. Real-time automated failure identification in the Control Center Complex (CCC)

    NASA Technical Reports Server (NTRS)

    Kirby, Sarah; Lauritsen, Janet; Pack, Ginger; Ha, Anhhoang; Jowers, Steven; Mcnenny, Robert; Truong, The; Dell, James

    1993-01-01

    A system which will provide real-time failure management support to the Space Station Freedom program is described. The system's use of a simplified form of model based reasoning qualifies it as an advanced automation system. However, it differs from most such systems in that it was designed from the outset to meet two sets of requirements. First, it must provide a useful increment to the fault management capabilities of the Johnson Space Center (JSC) Control Center Complex (CCC) Fault Detection Management system. Second, it must satisfy CCC operational environment constraints such as cost, computer resource requirements, verification, and validation, etc. The need to meet both requirement sets presents a much greater design challenge than would have been the case had functionality been the sole design consideration. The choice of technology, discussing aspects of that choice and the process for migrating it into the control center is overviewed.

  9. Performance of a real-time PCR assay for the rapid identification of Mycobacterium species.

    PubMed

    Wang, Hye-young; Kim, Hyunjung; Kim, Sunghyun; Kim, Do-kyoon; Cho, Sang-Nae; Lee, Hyeyoung

    2015-01-01

    Mycobacteria cause a variety of illnesses that differ in severity and public health implications. The differentiation of Mycobacterium tuberculosis (MTB) from nontuberculous mycobacteria (NTM) is of primary importance for infection control and choice of antimicrobial therapy. The diagnosis of diseases caused by NTM is difficult because NTM species are prevalent in the environment and because they have fastidious properties. In the present study, we evaluated 279 clinical isolates grown in liquid culture provided by The Catholic University of Korea, St. Vincent's Hospital using real-time PCR based on mycobacterial rpoB gene sequences. The positive rate of real-time PCR assay accurately discriminated 100% (195/195) and 100% (84/84) between MTB and NTM species. Comparison of isolates identified using the MolecuTech REBA Myco-ID(®) and Real Myco-ID® were completely concordant except for two samples. Two cases that were identified as mixed infection (M. intracellulare-M. massiliense and M. avium-M. massiliense co-infection) by PCRREBA assay were only detected using M. abscessus-specific probes by Real Myco-ID(®). Among a total of 84 cases, the most frequently identified NTM species were M. intracellulare (n=38, 45.2%), M. avium (n=18, 23.7%), M. massiliense (n=10, 13.2%), M. fortuitum (n=5, 6%), M. abscessus (n=3, 3.9%), M. gordonae (n=3, 3.9%), M. kansasii (n=2, 2.4%), M. mucogenicum (n=2, 2.4%), and M. chelonae (n= 1, 1.2%). Real Myco-ID(®) is an efficient tool for the rapid detection of NTM species as well as MTB and sensitive and specific and comparable to conventional methods.

  10. Accurate identification of Candida parapsilosis (sensu lato) by use of mitochondrial DNA and real-time PCR.

    PubMed

    Souza, Ana Carolina R; Ferreira, Renata C; Gonçalves, Sarah S; Quindós, Guillermo; Eraso, Elena; Bizerra, Fernando C; Briones, Marcelo R S; Colombo, Arnaldo L

    2012-07-01

    Candida parapsilosis is the Candida species isolated the second most frequently from blood cultures in South America and some European countries, such as Spain. Since 2005, this species has been considered a complex of 3 closely related species: C. parapsilosis, Candida metapsilosis, and Candida orthopsilosis. Here, we describe a real-time TaqMan-MGB PCR assay, using mitochondrial DNA (mtDNA) as the target, which readily distinguishes these 3 species. We first used comparative genomics to locate syntenic regions between these 3 mitochondrial genomes and then selected NADH5 as the target for the real-time PCR assay. Probes were designed to include a combination of different single-nucleotide polymorphisms that are able to differentiate each species within the C. parapsilosis complex. This new methodology was first tested using mtDNA and then genomic DNA from 4 reference and 5 clinical strains. For assay validation, a total of 96 clinical isolates and 4 American Type Culture Collection (ATCC) isolates previously identified by internal transcribed spacer (ITS) ribosomal DNA (rDNA) sequencing were tested. Real-time PCR using genomic DNA was able to differentiate the 3 species with 100% accuracy. No amplification was observed when DNA from other species was used as the template. We observed 100% congruence with ITS rDNA sequencing identification, including for 30 strains used in blind testing. This novel method allows a quick and accurate intracomplex identification of C. parapsilosis and saves time compared with sequencing, which so far has been considered the "gold standard" for Candida yeast identification. In addition, this assay provides a useful tool for epidemiological and clinical studies of these emergent species.

  11. A multi-target real-time PCR assay for rapid identification of meningitis-associated microorganisms.

    PubMed

    Favaro, Marco; Savini, Vincenzo; Favalli, Cartesio; Fontana, Carla

    2013-01-01

    A central nervous system (CNS) infection, such as meningitis, is a serious and life-threatening condition. Bacterial meningitis can be severe and may result in brain damage, disability or even death. Rapid diagnosis of CNS infections and identification of the pathogenic microorganisms are needed to improve the patient outcome. Bacterial culture of a patient's cerebrospinal fluid (CSF) is currently considered the "gold standard" for diagnosing bacterial meningitis. From the CSF cultures researchers can assess the in vitro susceptibility of the causative microorganism to determine the best antibiotic treatment. However, many of the culture assays, such as microscopy and the latex agglutination test are not sensitive. To enhance pathogen detection in CSF samples we developed a multi-target real-time PCR assay that can rapidly identify six different microorganisms: Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, Streptococcus agalactiae, Listeria monocytogenes and Cryptococcus neoformans. In this study we applied this PCR analysis to 296 CSF samples from patients who were suspected of having meningitis. Of the 296 samples that were examined, 59 samples were positive according to the CSF culture and/or molecular assays. Forty-six CSF samples were positive for both the CSF culture and our real-time PCR assay, while 13 samples were positive for the real-time PCR but negative for the traditional assays. This discrepancy may have been caused by the fact that these samples were collected from 23 patients who were treated with antimicrobials before CSF sampling.

  12. Taqman real-time quantitative PCR for identification of western flower thrip (Frankliniella occidentalis) for plant quarantine

    PubMed Central

    Huang, K. S.; Lee, S. E.; Yeh, Y.; Shen, G. S.; Mei, E.; Chang, C. M.

    2010-01-01

    Western flower thrip (Frankliniella occidentalis) is a major global pest of agricultural products. It directly damages crops through feeding, oviposition activity or transmission of several plant viruses. We describe a Taqman real-time quantitative PCR detection system, which can rapidly identify F. occidentalis from thrips larvae to complement the traditional morphological identification. The data showed that our detection system targeted on the ribosomal RNA gene regions of F. occidentalis has high sensitivity and specificity. The rapid method can be used for on-site testing of samples at ports-of-entry in the future. PMID:20129946

  13. Feature-level signal processing for near-real-time odor identification

    NASA Astrophysics Data System (ADS)

    Roppel, Thaddeus A.; Padgett, Mary Lou; Waldemark, Joakim T. A.; Wilson, Denise M.

    1998-09-01

    Rapid detection and classification of odor is of particular interest in applications such as manufacturing of consumer items, food processing, drug and explosives detection, and battlefield situation assessment. Various detection and classification techniques are under investigation so that end users can have access to useful information from odor sensor arrays in near-real-time. Feature-level data clustering and classification techniques are proposed that are (1) parallelizable to permit efficient hardware implementation, (2) adaptable to readily incorporate new data classes, (3) capable of gracefully handling outlier data points and failed sensor conditions, and (4) can provide confidence intervals and/or a traceable decision record along with each classification to permit validation and verification. Results from using specific techniques will be presented and compared. The techniques studied include principal components analysis, automated outlier determination, radial basis functions (RBF), multi-layer perceptrons (MLP), and pulse-coupled neural networks (PCNN). The results reported here are based on data from a testbed in which a gas sensor array is exposed to odor samples on a continuous basis. We have reported previously that more detailed and faster discrimination can be obtained by using sensor transient response in addition to steady state response. As the size of the data set grows we are able to more accurately model performance of a sensor array under realistic conditions.

  14. Evaluation of a co-extraction method for real-time PCR-based body fluid identification and DNA typing.

    PubMed

    Watanabe, Ken; Iwashima, Yasuki; Akutsu, Tomoko; Sekiguchi, Kazumasa; Sakurada, Koichi

    2014-01-01

    Body fluid identification and individual identification are an important series of tests in usual criminal investigations. Recent reports have demonstrated a new approach using DNA/RNA co-extraction methods in which RNA for body fluid identification and DNA for short tandem repeat (STR) typing are extracted simultaneously from the same sample. This study evaluated a standard co-extraction kit, the AllPrep® DNA/RNA Mini Kit, in order to demonstrate the availability of the co-extraction procedure for those real-time polymerase chain reaction-based body fluid identification methods that we have validated previously. We demonstrated that the use of the Allprep Kit, for which we adjusted the lysis temperature to 56°C to improve extraction efficiency, can simultaneously extract sufficient RNA and DNA for body fluid identification and STR analysis; however, a longer incubation at a high temperature slightly affected the ΔCt value of each target gene and appeared to be not as effective for DNA extraction from old stains as from 1-day-old stains. This method is promising for future forensic investigations because the use of this kit can reduce sample consumption for body fluid identification and DNA typing.

  15. Detection of orthopoxvirus DNA by real-time PCR and identification of variola virus DNA by melting analysis.

    PubMed

    Nitsche, Andreas; Ellerbrok, Heinz; Pauli, Georg

    2004-03-01

    Although variola virus was eradicated by the World Health Organization vaccination program in the 1970s, the diagnosis of smallpox infection has attracted great interest in the context of a possible deliberate release of variola virus in bioterrorist attacks. Obviously, fast and reliable diagnostic tools are required to detect variola virus and to distinguish it from orthopoxviruses that have identical morphological characteristics, including vaccinia virus. The advent of real-time PCR for the clinical diagnosis of viral infections has facilitated the detection of minute amounts of viral nucleic acids in a fast, safe, and precise manner, including the option to quantify and to genotype the target reliably. In this study a complete set of four hybridization probe-based real-time PCR assays for the specific detection of orthopoxvirus DNA is presented. Melting analysis following PCR enables the identification of variola virus by the PCR product's characteristic melting temperature, permitting the discrimination of variola virus from other orthopoxviruses. In addition, an assay for the specific amplification of variola virus DNA is presented. All assays can be performed simultaneously in the same cycler, and results of a PCR run are obtained in less than 1 h. The application of more than one assay for the same organism significantly contributes to the diagnostic reliability, reducing the risk of false-negative results due to unknown sequence variations. In conclusion, the assays presented will improve the speed and reliability of orthopoxvirus diagnostics and variola virus identification.

  16. High-throughput gender identification of Accipitridae eagles with real-time PCR using TaqMan probes.

    PubMed

    Chang, H-W; Gu, D-L; Su, S-H; Chang, C-C; Cheng, C-A; Huang, H-W; Yao, C-T; Chou, T-C; Chuang, L-Y; Cheng, C-C

    2008-07-01

    The objective was to develop high-throughput gender identification of eagles. Based on BLAST and alignment analyses, the CHD-Z and CHD-W sequences of nine species of eagles were highly homologous with Spilornis cheela hoya (S. c. hoya); therefore, TaqMan probes were designed to target their CHD-ZW-common and CHD-W-specific regions. In S. c. hoya, genders were identified using TaqMan-based, real-time PCR (amplified by P2/P8 primers); this method was validated with anatomically confirmed controls (one of each gender). Both genders had high intensities of the HEX-labeled (CHD-ZW-common) probe, whereas only females had high intensity of the FAM-labeled (CHD-W-specific) probe. The sequence of the CHD-W-specific probe designed for S. c. hoya was completely homologous with the CHD-W-specific region in Circaetus gallicus, Gyps indicus, and Gyps bengalensis, and was only one nucleotide different from those of Accipiter nisus, Spizaetus nipalensis, Aquila chrysaetos, Circus spilonotus, and Milvus migrans. For the CHD-ZW-common probe, all species listed were completely conserved. Using real-time PCR software, we established auto-calling of the genders of 15 individuals of S. c. hoya. In conclusion, this method provided accurate, high-throughput gender identification for S. c. hoya, and has considerable potential for identifying the gender of several related species of eagles. PMID:18440628

  17. Performance of an in-house real-time polymerase chain reaction for identification of Mycobacterium tuberculosis isolates in laboratory routine diagnosis from a high burden setting

    PubMed Central

    Gallo, Juliana Failde; Pinhata, Juliana Maira Watanabe; Chimara, Erica; Gonçalves, Maria Gisele; Fukasawa, Lucila Okuyama; de Oliveira, Rosangela Siqueira

    2016-01-01

    Abstract Brazil is one of the high burden countries for tuberculosis, and a rapid diagnosis is essential for effective control of the disease. In the present study, an in-house real-time polymerase chain reaction (PCR) assay targeting the mpt64 gene for identification of Mycobacterium tuberculosis complex isolates was evaluated under routine diagnosis conditions in a reference laboratory. From May 2011 to July 2012, 1,520 isolates of mycobacteria were prospectively submitted for phenotypic and/or PRA-hsp65 identification and to real-time PCR. The mpt64 real-time PCR showed 99.7% sensitivity and 96% specificity and detected 79.4% of the cases missed by phenotypic and PRA-hsp65 identification. The in-house real-time PCR assay showed high sensitivity and specificity and was successfully implemented in the routine diagnosis of tuberculosis in a reference laboratory from a high burden setting. PMID:27598243

  18. Performance of an in-house real-time polymerase chain reaction for identification of Mycobacterium tuberculosis isolates in laboratory routine diagnosis from a high burden setting.

    PubMed

    Gallo, Juliana Failde; Pinhata, Juliana Maira Watanabe; Chimara, Erica; Gonçalves, Maria Gisele; Fukasawa, Lucila Okuyama; Oliveira, Rosangela Siqueira de

    2016-09-01

    Brazil is one of the high burden countries for tuberculosis, and a rapid diagnosis is essential for effective control of the disease. In the present study, an in-house real-time polymerase chain reaction (PCR) assay targeting the mpt64 gene for identification of Mycobacterium tuberculosis complex isolates was evaluated under routine diagnosis conditions in a reference laboratory. From May 2011 to July 2012, 1,520 isolates of mycobacteria were prospectively submitted for phenotypic and/or PRA-hsp65 identification and to real-time PCR. The mpt64 real-time PCR showed 99.7% sensitivity and 96% specificity and detected 79.4% of the cases missed by phenotypic and PRA-hsp65 identification. The in-house real-time PCR assay showed high sensitivity and specificity and was successfully implemented in the routine diagnosis of tuberculosis in a reference laboratory from a high burden setting.

  19. Multigate transcranial Doppler ultrasound system with real-time embolic signal identification and archival.

    PubMed

    Fan, Lingke; Boni, Enrico; Tortoli, Piero; Evans, David H

    2006-10-01

    An integrated system for acquisition and processing of intracranial and extracranial Doppler signals and automatic embolic signal detection has been developed. The hardware basis of the system is a purpose-built acquisition/processing board that includes a multigate Doppler unit controlled through a computer. The signal-processing engine of the system contains a fast Fourier transform (FFT)-based, spectral-analysis unit and an embolic signal-detection unit using expert system reasoning theory. The system is designed so that up to four receive gates from a single transducer can be used to provide useful reasoning information to the embolic signal-detection unit. Alternatively, two transducers can be used simultaneously, either for bilateral transcranial Doppler (TCD) investigations or for simultaneous intra- and extracranial investigation of different arteries. The structure of the software will allow the future implementation of embolus detection algorithms that use the information from all four channels when a single transducer is used, or of independent embolus detection in two sets of two channels when two transducers are used. The user-friendly system has been tested in-vitro, and it has demonstrated a 93.6% sensitivity for micro-embolic signal (MES) identification. Preliminary in-vivo results also are encouraging. PMID:17036793

  20. Fast Identification of 1,3-Dimethylamylamine Using Direct Analysis in Real Time-QToF-MS.

    PubMed

    Avula, Bharathi; Smillie, Troy J; Wang, Yan-Hong; Zweigenbaum, Jerry; ElSohly, Mahmoud A; Khan, Ikhlas A

    2015-01-01

    The central nervous system stimulant 1,3-dimethylamylamine (DMAA) has been found in preworkout products and dietary supplements. A fast direct analysis in real time-quadrupole time of flight-MS method was used for identification of DMAA in dietary supplements and to determine if this compound is present in geranium (Pelargonium graveolens) plants or oil. This method involved the use of [M+H]+ ions in the positive mode based on the exact mass of DMAA. The results of this investigation showed that DMAA was not detected from authentic samples of P. graveolens plant material or pelargonium oil or in multiple samples of commercially available pelargonium oil. DMAA was detected in three samples of dietary supplements. The LOD of DMAA was found to be 10 ng/mL.

  1. Fast Identification of 1,3-Dimethylamylamine Using Direct Analysis in Real Time-QToF-MS.

    PubMed

    Avula, Bharathi; Smillie, Troy J; Wang, Yan-Hong; Zweigenbaum, Jerry; ElSohly, Mahmoud A; Khan, Ikhlas A

    2015-01-01

    The central nervous system stimulant 1,3-dimethylamylamine (DMAA) has been found in preworkout products and dietary supplements. A fast direct analysis in real time-quadrupole time of flight-MS method was used for identification of DMAA in dietary supplements and to determine if this compound is present in geranium (Pelargonium graveolens) plants or oil. This method involved the use of [M+H]+ ions in the positive mode based on the exact mass of DMAA. The results of this investigation showed that DMAA was not detected from authentic samples of P. graveolens plant material or pelargonium oil or in multiple samples of commercially available pelargonium oil. DMAA was detected in three samples of dietary supplements. The LOD of DMAA was found to be 10 ng/mL. PMID:26086254

  2. Identification of the five human Plasmodium species including P. knowlesi by real-time polymerase chain reaction.

    PubMed

    Oddoux, O; Debourgogne, A; Kantele, A; Kocken, C H; Jokiranta, T S; Vedy, S; Puyhardy, J M; Machouart, M

    2011-04-01

    Recently, Plasmodium knowlesi has been recognised as the fifth Plasmodium species causing malaria in humans. Hundreds of human cases infected with this originally simian Plasmodium species have been described in Asian countries and increasing numbers are reported in Europe from travellers. The growing impact of tourism and economic development in South and Southeast Asia are expected to subsequently lead to a further increase in cases both among locals and among travellers. P. knowlesi is easily misidentified in microscopy as P. malariae or P. falciparum. We developed new primers for the rapid and specific detection of this species by low-cost real-time polymerase chain reaction (PCR) and added this method to an already existing panel of primers used for the molecular identification of the other four species in one reaction. Reference laboratories should now be able to identify undisputably and rapidly P. knowlesi, as it is a potentially fatal pathogen.

  3. Plant seed species identification from chemical fingerprints: a high-throughput application of direct analysis in real time mass spectrometry.

    PubMed

    Lesiak, Ashton D; Cody, Robert B; Dane, A John; Musah, Rabi A

    2015-09-01

    Plant species identification based on the morphological features of plant parts is a well-established science in botany. However, species identification from seeds has largely been unexplored, despite the fact that the seeds contain all of the genetic information that distinguishes one plant from another. Using seeds of genus Datura plants, we show here that the mass spectrum-derived chemical fingerprints for seeds of the same species are similar. On the other hand, seeds from different species within the same genus display distinct chemical signatures, even though they may contain similar characteristic biomarkers. The intraspecies chemical signature similarities on the one hand, and interspecies fingerprint differences on the other, can be processed by multivariate statistical analysis methods to enable rapid species-level identification and differentiation. The chemical fingerprints can be acquired rapidly and in a high-throughput manner by direct analysis in real time mass spectrometry (DART-MS) analysis of the seeds in their native form, without use of a solvent extract. Importantly, knowledge of the identity of the detected molecules is not required for species level identification. However, confirmation of the presence within the seeds of various characteristic tropane and other alkaloids, including atropine, scopolamine, scopoline, tropine, tropinone, and tyramine, was accomplished by comparison of the in-source collision-induced dissociation (CID) fragmentation patterns of authentic standards, to the fragmentation patterns observed in the seeds when analyzed under similar in-source CID conditions. The advantages, applications, and implications of the chemometric processing of DART-MS derived seed chemical signatures for species level identification and differentiation are discussed.

  4. Culture-independent identification and quantification of Gallibacterium anatis (G. anatis) by real-time quantitative PCR.

    PubMed

    Wang, Chong; Robles, Francisco; Ramirez, Saul; Riber, Anja Brinch; Bojesen, Anders Miki

    2016-10-01

    Gallibacterium is a genus within the family Pasteurellaceae characterized by a high level of phenotypic and genetic diversity. No diagnostic method has yet been described, which allows species-specific identification of Gallibacterium anatis. The aim of this study was to develop a real-time quantitative PCR (qPCR) method allowing species-specific identification and quantification of G. anatis. A G. anatis specific DNA sequence was identified in the gyrase subunit B gene (gyrB) and used to design a TaqMan probe and corresponding primers. The specificity of the assay was tested on 52 bacterial strains. Twenty-two of the strains represented all of the presently available 13 phenotypic variants of G. anatis originating from different geographical locations. Nine strains represented each of the additional six Gallibacterium species and 21 strains represented other poultry associated bacterial species of the families Pasteurellaceae, Enterobacteriaceae and Flavobacteriaceae. Regarding specificity none of non-G. anatis strains tested positive with the proposed assay. To test and compare the qPCR method's ability to detect G. anatis from field samples, the sensitivity was compared to a previously published conventional PCR method and culture-based identification, respectively. The detection rates were 97%, 78% and 34% for the current qPCR, the conventional PCR and the culture-based identification method, respectively. The qPCR assay was able to detect the gene gyrB in serial dilutions of 10(8) colony forming units (CFU)/ml to as low as 10(0) CFU/ml copies. The proposed qPCR method is thus highly specific, sensitive and reproducible. In conclusion, we have developed a qPCR method that allows species-specific identification of G. anatis.

  5. Rapid molecular identification of Listeria species by use of real-time PCR and high-resolution melting analysis.

    PubMed

    Jin, Dazhi; Luo, Yun; Zhang, Zheng; Fang, Weijia; Ye, Julian; Wu, Fang; Ding, Gangqiang

    2012-05-01

    Identification of Listeria species via a molecular method is critical for food safety and clinical diagnosis. In this study, an assay integrating real-time quantitative PCR (Q-PCR) with high-resolution melting (HRM) curve analysis was developed and assessed for rapid identification of six Listeria species. The ssrA gene, which encodes a transfer-messenger RNA (tmRNA) is conserved and common to all bacterial phyla, contains a variable domain in Listeria spp. Therefore, Q-PCR and a HRM profile were applied to characterize this gene. Fifty-three Listeria species and 45 non-Listeria species were detected using one primer set, with an accuracy of 100% in reference to conventional methods. There was a 93.3% correction rate to 30 artificially contaminated samples. Thus, Q-PCR with melting profiling analysis proved able to identify Listeria species accurately. Consequently, this study demonstrates that the assay we developed is a functional tool for rapidly identifying six Listeria species, and has the potential for discriminating novel species food safety and epidemiological research.

  6. Detection and identification of Rift Valley fever virus in mosquito vectors by quantitative real-time PCR.

    PubMed

    Mwaengo, D; Lorenzo, G; Iglesias, J; Warigia, M; Sang, R; Bishop, R P; Brun, A

    2012-10-01

    Diagnostic methods allowing for rapid identification of pathogens are crucial for controlling and preventing dissemination after disease outbreaks as well as for use in surveillance programs. For arboviruses, detection of the presence of virus in their arthropod hosts is important for monitoring of viral activity and quantitative information is useful for modeling of transmission dynamics. In this study, molecular detection of Rift Valley fever virus (RVFV) in mosquito samples from the 2006 to 2007 East African outbreaks was performed using quantitative real-time PCR assay (qRT-PCR). Specific RVFV sequence-based primer/fluorogenic (TaqMan) probe sets were derived from the L and S RNA segments of the virus. Both primer-probe L and S segment-based combinations detected genomic RVFV sequences, with generally comparable levels of sensitivity. Viral loads from three mosquito species, Aedes mcintoshi, Aedes ochraceus and Mansonia uniformis were estimated and significant differences of between 5- and 1000-fold were detected between Ae. mcintoshi and M. uniformis using both the L and S primer-probe-based assays. The genetic relationships of the viral sequences in mosquito samples were established by partial M segment sequencing and assigned to the two previously described viral lineages defined by analysis of livestock isolates obtained during the 2006-2007 outbreak, confirming that similar viruses were present in both the vector and mammalian host. The data confirms the utility of qRT-PCR for identification and initial quantification of virus in mosquito samples during RVFV outbreaks.

  7. Identification and validation of reference genes for quantitative real-time polymerase chain reaction in Cimex lectularius.

    PubMed

    Mamidala, Praveen; Rajarapu, Swapna P; Jones, Susan C; Mittapalli, Omprakash

    2011-07-01

    Quantitative real-time polymerase chain reaction (qRT-PCR) has emerged as robust methodology for gene expression studies, but reference genes are crucial for accurate normalization. Commonly used reference genes are housekeeping genes that are thought to be nonregulated; however, their expression can be unstable across different experimental conditions. We report the identification and validation of suitable reference genes in the bed bug, Cimex lectularius, by using qRT-PCR. The expression stability of eight reference genes in different tissues (abdominal cuticle, midgut, Malpighian tubules, and ovary) and developmental stages (early instar nymphs, late instar nymphs, and adults) of pesticide-susceptible and pesticide-exposed C. lectularius were analyzed using geNorm, NormFinder, and BestKeeper. Overall expression analysis of the eight reference genes revealed significant variation among samples, indicating the necessity of validating suitable reference genes for accurate quantification of mRNA transcripts. Ribosomal protein (RPL18) exhibited the most stable gene expression across all the tissue and developmental-stage samples; a-tubulin revealed the least stability across all of the samples examined. Thus, we recommend RPL18 as a suitable reference gene for normalization in gene expression studies of C. lectularius. PMID:21845960

  8. Multi-probe real-time PCR identification of four common Candida species in blood culture broth.

    PubMed

    Foongladda, Suporn; Mongkol, Nanthanida; Petlum, Pornphan; Chayakulkeeree, Methee

    2014-06-01

    We developed a single-tube real-time polymerase chain reaction (PCR) assay with multiple hybridization probes for detecting Candida albicans, C. tropicalis, C. glabrata, and C. parapsilosis. Primers were designed to amplify 18S rRNA gene of the genus Candida, and DNA probes were designed to hybridize two areas of the amplicons. The amplification curves and specific melting peaks of the probes hybridized with PCR product were used for definite species identifications. The reaction specificity was 100 % when evaluating the assay using DNA samples from 21 isolates of fungal and bacterial species. The assay was further evaluated in 129 fungal blood culture broth samples which were culture positive for fungus. Of the 129 samples, 119 were positively identified as: C. albicans (39), C. tropicalis (30), C. parapsilosis (23), C. glabrata (20), Candida spp. (5), and two samples containing mixed C. glabrata/C. albicans and C. glabrata/C. tropicalis. The five Candida spp. were identified by sequencing analysis as C. krusei, C. dubliniensis, C. aquaetextoris, and two isolates of C. athensensis. Of the ten samples which showed negative PCR results, six were Cryptococcus neoformans, and the others were Trichosporon sp., Rhodotorula sp., Fusarium sp., and Penicillium marneffei. Our findings show that the assay was highly effective in identifying the four medically important Candida species. The results can be available within 3 h after positivity of a blood culture broth sample.

  9. Accurate and rapid identification of the Burkholderia pseudomallei near-neighbour, Burkholderia ubonensis, using real-time PCR.

    PubMed

    Price, Erin P; Sarovich, Derek S; Webb, Jessica R; Ginther, Jennifer L; Mayo, Mark; Cook, James M; Seymour, Meagan L; Kaestli, Mirjam; Theobald, Vanessa; Hall, Carina M; Busch, Joseph D; Foster, Jeffrey T; Keim, Paul; Wagner, David M; Tuanyok, Apichai; Pearson, Talima; Currie, Bart J

    2013-01-01

    Burkholderia ubonensis is an environmental bacterium belonging to the Burkholderia cepacia complex (Bcc), a group of genetically related organisms that are associated with opportunistic but generally nonfatal infections in healthy individuals. In contrast, the near-neighbour species Burkholderia pseudomallei causes melioidosis, a disease that can be fatal in up to 95% of cases if left untreated. B. ubonensis is frequently misidentified as B. pseudomallei from soil samples using selective culturing on Ashdown's medium, reflecting both the shared environmental niche and morphological similarities of these species. Additionally, B. ubonensis shows potential as an important biocontrol agent in B. pseudomallei-endemic regions as certain strains possess antagonistic properties towards B. pseudomallei. Current methods for characterising B. ubonensis are laborious, time-consuming and costly, and as such this bacterium remains poorly studied. The aim of our study was to develop a rapid and inexpensive real-time PCR-based assay specific for B. ubonensis. We demonstrate that a novel B. ubonensis-specific assay, Bu550, accurately differentiates B. ubonensis from B. pseudomallei and other species that grow on selective Ashdown's agar. We anticipate that Bu550 will catalyse research on B. ubonensis by enabling rapid identification of this organism from Ashdown's-positive colonies that are not B. pseudomallei.

  10. Quantitative real-time PCR (qPCR) assay for human-dog-cat species identification and nuclear DNA quantification.

    PubMed

    Kanthaswamy, S; Premasuthan, A; Ng, J; Satkoski, J; Goyal, V

    2012-03-01

    In the United States, human forensic evidence collected from crime scenes is usually comingled with biomaterial of canine and feline origins. Knowledge of the concentration of nuclear DNA extracted from a crime scene biological sample and the species from which the sample originated is essential for DNA profiling. The ability to accurately detect and quantify target DNA in mixed-species samples is crucial when target DNA may be overwhelmed by non-target DNA. We have designed and evaluated a species-specific (human, dog and cat) nuclear DNA identification assay based on the TaqMan(®) quantitative real-time PCR (qPCR) technology that can simultaneously detect and measure minute quantities of DNA specific to either humans, dogs and/or cats. The fluorogenic triplex assay employs primers and hydrolysis probes that target the human TH01 locus as well as the dog and cat Melanocortin 1 Receptor (MC1R) sequences in a species-specific manner. We also demonstrate that the assay is a highly sensitive, reliable and robust method for identifying and quantifying mixed-species templates of human-dog-cat origin with as little as 0.4 pg of human and cat nuclear DNA, respectively, and 4.0 pg of dog nuclear DNA.

  11. Novel real-time PCR method based on growth hormone gene for identification of Salmonidae ingredient in food.

    PubMed

    Li, Xiang; Li, Jinbo; Zhang, Shuya; He, Yuping; Pan, Liangwen

    2013-05-29

    To avoid fraudulent substitutions in fish markets, the proper methods are needed to test the authenticity of the ingredients. As a preferable methodology, a quantitative real-time polymerase chain reaction (qPCR) method was used in this study to identify species from the Salmonidae family based on the salmon growth hormone gene. Fish samples of six genera from the Salmonidae family were tested to identify the specificity, sensitivity, and applicability of the established method. Results showed that the method was highly specific for salmonid detection. Ct values were obtained only from 31 Salmonidae fish species samples. The relative and absolute limits of detection were 0.01% and 25 pg of genomic DNA, respectively, which could meet with the requirements of routine detections. To test the applicability of the method, the content of salmonid ingredients in 16 commercial food products was quantified from standard curves constructed from DNA of two Salmonidae species. The results revealed that the salmonid ingredient was detected in 12 samples, indicating that 25% of the labels are inauthentic. These results demonstrate that the developed qPCR method is suitable for identification of Salmonidae ingredients. PMID:23600678

  12. Development of a real-time PCR assay for identification and quantification of the fish pathogen Francisella noatunensis subsp. orientalis.

    PubMed

    Soto, Esteban; Bowles, Kimberly; Fernandez, Denise; Hawke, John P

    2010-04-01

    Members of the genus Francisella are small Gram-negative facultative intracellular bacteria that cause francisellosis in a wide variety of fish species worldwide. F. noatunensis subsp. orientalis has been recently described as a warm-water pathogen of tilapia Oreochromis spp. In this study, a quantitative real-time polymerase chain reaction (qPCR) TaqMan probe assay was developed to rapidly and accurately detect and quantify F. noatunensis subsp. orientalis from fish tissue. The target region of the assay was the F. tularensis iglC gene homologue previously found in F. noatunensis subsp. orientalis. Probe specificity was confirmed by the lack of signal and cross-reactivity with 12 common fish pathogens, 2 subspecies of F. tularensis, F. noatunensis subsp. noatunensis, and tilapia tissue. The range of linearity was determined to be 50 fg to 1.4 mg, and the lower limit of detection was 50 fg of DNA (equivalent to approximately 25 genome equivalents) per reaction. A similar sensitivity was observed with DNA extracted from a mixture of F. noatunensis subsp. orientalis and fish tissue. The assay was also able to detect and quantify F. noatunensis subsp. orientalis from the spleens of experimentally infected tilapia. No signal was observed in the control groups. In conclusion, we have developed a highly sensitive and specific assay that can be used for the specific identification and quantification of F. noatunensis subsp. orientalis. PMID:20481087

  13. Real-time PCR-based identification of Borrelia burgdorferi sensu lato species in ticks collected from humans in Romania.

    PubMed

    Briciu, Violeta T; Meyer, Fabian; Sebah, Daniela; Tăţulescu, Doina F; Coroiu, Georgiana; Lupşe, Mihaela; Carstina, Dumitru; Mihalca, Andrei D; Hizo-Teufel, Cecilia; Klier, Christiane; Huber, Ingrid; Fingerle, Volker

    2014-09-01

    The aims of our study were to determine (i) which tick species bite humans in Romania and (ii) the prevalence of Borrelia (B.) burgdorferi genospecies in these ticks. All ticks collected from patients who presented to the Clinic of Infectious Diseases Cluj Napoca in spring/summer 2010 were morphologically identified by an entomologist and tested for B. burgdorferi genospecies prevalence by a real-time PCR assay targeting the hbb gene and melting curve analysis. Out of 532 ticks, 518 were Ixodes ricinus, 10 Dermacentor marginatus, and 3 Haemaphysalis spp. ticks, and one unidentified tick due to destruction. Since evaluation of the hbb PCR revealed that it was not possible to differentiate between B. spielmanii/B. valaisiana and B. garinii/B. bavariensis, sequencing of an 800-bp fragment of the ospA gene was performed in these cases. Out of 389 investigated ticks, 43 were positive by hbb PCR for B. burgdorferi sensu lato. The positive samples were 42 Ixodes ricinus (11.1% B. burgdorferi sensu lato prevalence) and the one unidentified tick. Species identification revealed the presence of mainly B. afzelii, but also of B. garinii, B. burgdorferi sensu stricto, B. valaisiana, and B. lusitaniae. In 4 samples, differentiation between B. spielmanii/B. valaisiana was impossible. Our study shows that the most relevant human pathogenic B. burgdorferi genospecies - predominantly B. afzelii - are present in ticks collected from Romanian patients.

  14. Identification of the country of growth of Sophora flavescens using direct analysis in real time mass spectrometry (DART-MS).

    PubMed

    Fukuda, Eriko; Uesawa, Yoshihiro; Baba, Masaki; Suzuki, Ryuichiro; Fukuda, Tatsuo; Shirataki, Yoshiaki; Okada, Yoshihito

    2014-11-01

    In order to identify the country of growth of Sophora flavescens by chemical fingerprinting, extracts of plants grown in China and Japan were analyzed using direct analysis in real time mass spectrometry (DART)-MS. The peaks characteristic of each country of growth were statistically analyzed using a volcano plot to summarize the relationship between the p-values of a statistical test and the magnitude of the difference in the peak intensities of the samples in the groups. Peaks with ap value < 0.05 in the t-test and a ≥ 2 absolute difference were defined as characteristic. Peaks characteristic of Chinese S. flavescens were found at m/z 439 and 440. In contrast, peaks characteristic of Japanese S. flavescens were found at m/z 313, 423, 437 and 441. The intensity of the selected peaks was similar in Japanese samples, whereas the m/z 439 peak had a significantly higher intensity than the other peaks in Chinese samples. Therefore, differences in selected peak patterns may allow identification of the country of growth of S. flavescens.

  15. Novel real-time PCR method based on growth hormone gene for identification of Salmonidae ingredient in food.

    PubMed

    Li, Xiang; Li, Jinbo; Zhang, Shuya; He, Yuping; Pan, Liangwen

    2013-05-29

    To avoid fraudulent substitutions in fish markets, the proper methods are needed to test the authenticity of the ingredients. As a preferable methodology, a quantitative real-time polymerase chain reaction (qPCR) method was used in this study to identify species from the Salmonidae family based on the salmon growth hormone gene. Fish samples of six genera from the Salmonidae family were tested to identify the specificity, sensitivity, and applicability of the established method. Results showed that the method was highly specific for salmonid detection. Ct values were obtained only from 31 Salmonidae fish species samples. The relative and absolute limits of detection were 0.01% and 25 pg of genomic DNA, respectively, which could meet with the requirements of routine detections. To test the applicability of the method, the content of salmonid ingredients in 16 commercial food products was quantified from standard curves constructed from DNA of two Salmonidae species. The results revealed that the salmonid ingredient was detected in 12 samples, indicating that 25% of the labels are inauthentic. These results demonstrate that the developed qPCR method is suitable for identification of Salmonidae ingredients.

  16. Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods.

    PubMed

    Shanks, Orin C; Kelty, Catherine A; Oshiro, Robin; Haugland, Richard A; Madi, Tania; Brooks, Lauren; Field, Katharine G; Sivaganesan, Mano

    2016-05-01

    There is growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for water quality management. The transition from a research tool to a standardized protocol requires a high degree of confidence in data quality across laboratories. Data quality is typically determined through a series of specifications that ensure good experimental practice and the absence of bias in the results due to DNA isolation and amplification interferences. However, there is currently a lack of consensus on how best to evaluate and interpret human fecal source identification qPCR experiments. This is, in part, due to the lack of standardized protocols and information on interlaboratory variability under conditions for data acceptance. The aim of this study is to provide users and reviewers with a complete series of conditions for data acceptance derived from a multiple laboratory data set using standardized procedures. To establish these benchmarks, data from HF183/BacR287 and HumM2 human-associated qPCR methods were generated across 14 laboratories. Each laboratory followed a standardized protocol utilizing the same lot of reference DNA materials, DNA isolation kits, amplification reagents, and test samples to generate comparable data. After removal of outliers, a nested analysis of variance (ANOVA) was used to establish proficiency metrics that include lab-to-lab, replicate testing within a lab, and random error for amplification inhibition and sample processing controls. Other data acceptance measurements included extraneous DNA contamination assessments (no-template and extraction blank controls) and calibration model performance (correlation coefficient, amplification efficiency, and lower limit of quantification). To demonstrate the implementation of the proposed standardized protocols and data acceptance criteria, comparable data from two additional laboratories were reviewed. The data acceptance criteria

  17. Acetobacter malorum and Acetobacter cerevisiae identification and quantification by Real-Time PCR with TaqMan-MGB probes.

    PubMed

    Valera, Maria José; Torija, Maria Jesús; Mas, Albert; Mateo, Estibaliz

    2013-10-01

    The identification and quantification of Acetobacter malorum and Acetobacter cerevisiae in wine and vinegar were performed using the Real-Time PCR (RT-PCR) with two TaqMan-MGB probes designed to amplify the internal transcribed spacer (ITS) region between the 16S-23S rRNA genes. The primers and probes were highly specific, with a detection limit of 10² cells/ml for both species, and the efficiency of the technique was >80%. The RT-PCR technique with these two new TaqMan-MGB probes, together with the five (Acetobacter aceti, Acetobacter pasteurianus, Gluconobacter oxydans, Gluconacetobacter hansenii and Gluconacetobacter europaeus) that are already available (Torija et al., 2010), were validated on known concentrations of Acetic Acid Bacteria (AAB) grown in glucose medium (GY) and in inoculated matrices of wine and vinegar. Furthermore, this technique was applied to evaluate the AAB population in real wine samples collected in the Canary Islands. PCR enrichment performed prior to RT-PCR increased the accuracy of quantification and produced results similar to those detected with SYBR-Green. In real wine samples, the total AAB enumeration ranged from 9 × 10² to 10⁶ cells/ml, and the seven AAB species tested were detected in more than one sample. However, AAB recovery on plates was poor; the isolates obtained on plates were A. malorum, G. oxydans, A. cerevisiae and A. pasteurianus species. RT-PCR with TaqMan-MGB probes is an accurate, specific and fast method for the identification and quantification of AAB species commonly found in wine and vinegar.

  18. Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods

    PubMed Central

    Kelty, Catherine A.; Oshiro, Robin; Haugland, Richard A.; Madi, Tania; Brooks, Lauren; Field, Katharine G.; Sivaganesan, Mano

    2016-01-01

    There is growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for water quality management. The transition from a research tool to a standardized protocol requires a high degree of confidence in data quality across laboratories. Data quality is typically determined through a series of specifications that ensure good experimental practice and the absence of bias in the results due to DNA isolation and amplification interferences. However, there is currently a lack of consensus on how best to evaluate and interpret human fecal source identification qPCR experiments. This is, in part, due to the lack of standardized protocols and information on interlaboratory variability under conditions for data acceptance. The aim of this study is to provide users and reviewers with a complete series of conditions for data acceptance derived from a multiple laboratory data set using standardized procedures. To establish these benchmarks, data from HF183/BacR287 and HumM2 human-associated qPCR methods were generated across 14 laboratories. Each laboratory followed a standardized protocol utilizing the same lot of reference DNA materials, DNA isolation kits, amplification reagents, and test samples to generate comparable data. After removal of outliers, a nested analysis of variance (ANOVA) was used to establish proficiency metrics that include lab-to-lab, replicate testing within a lab, and random error for amplification inhibition and sample processing controls. Other data acceptance measurements included extraneous DNA contamination assessments (no-template and extraction blank controls) and calibration model performance (correlation coefficient, amplification efficiency, and lower limit of quantification). To demonstrate the implementation of the proposed standardized protocols and data acceptance criteria, comparable data from two additional laboratories were reviewed. The data acceptance criteria

  19. Rapid and accurate identification of Mycobacterium tuberculosis complex and common non-tuberculous mycobacteria by multiplex real-time PCR targeting different housekeeping genes.

    PubMed

    Nasr Esfahani, Bahram; Rezaei Yazdi, Hadi; Moghim, Sharareh; Ghasemian Safaei, Hajieh; Zarkesh Esfahani, Hamid

    2012-11-01

    Rapid and accurate identification of mycobacteria isolates from primary culture is important due to timely and appropriate antibiotic therapy. Conventional methods for identification of Mycobacterium species based on biochemical tests needs several weeks and may remain inconclusive. In this study, a novel multiplex real-time PCR was developed for rapid identification of Mycobacterium genus, Mycobacterium tuberculosis complex (MTC) and the most common non-tuberculosis mycobacteria species including M. abscessus, M. fortuitum, M. avium complex, M. kansasii, and the M. gordonae in three reaction tubes but under same PCR condition. Genetic targets for primer designing included the 16S rDNA gene, the dnaJ gene, the gyrB gene and internal transcribed spacer (ITS). Multiplex real-time PCR was setup with reference Mycobacterium strains and was subsequently tested with 66 clinical isolates. Results of multiplex real-time PCR were analyzed with melting curves and melting temperature (T (m)) of Mycobacterium genus, MTC, and each of non-tuberculosis Mycobacterium species were determined. Multiplex real-time PCR results were compared with amplification and sequencing of 16S-23S rDNA ITS for identification of Mycobacterium species. Sensitivity and specificity of designed primers were each 100 % for MTC, M. abscessus, M. fortuitum, M. avium complex, M. kansasii, and M. gordonae. Sensitivity and specificity of designed primer for genus Mycobacterium was 96 and 100 %, respectively. According to the obtained results, we conclude that this multiplex real-time PCR with melting curve analysis and these novel primers can be used for rapid and accurate identification of genus Mycobacterium, MTC, and the most common non-tuberculosis Mycobacterium species.

  20. Identification of individual herbal drugs in tea mixtures using restriction analysis of ITS DNA and real-time PCR.

    PubMed

    Slanc, P; Ravnikar, M; Strukelj, B

    2006-11-01

    We have studied a sedative tea made of Valerianae radix (Valeriana officinalis L.), Lupuli strobuli (Humulus lupulus L.), Melissae folium (Melissa officinalis L.) and Menthae piperitae folium (Mentha piperita L.). In order to identify the constituent drugs a method was established involving amplification of the internal transcribed spacers (ITS) region of nuclear ribosomal DNA on the basis of restriction analysis and real-time PCR. ITS regions of individual drugs were amplified and sequenced. Restriction analysis was performed with selected restriction endonucleases Nae I, PshA I and Xcm I. Real-time PCR was carried out, using primers specifically designed for each individual herbal drug. Real-time PCR proved to be a method for identifying individual herbal drugs in a tea mixture with a single DNA extraction in a single PCR run, since its limit of detection is lower than that for restriction analysis. PMID:17152982

  1. Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods

    EPA Science Inventory

    There is a growing interest in the application of human-associated fecal sourceidentification quantitative real-time PCR (qPCR) technologies for water quality management. The transition from a research tool to a standardized protocol requires a high degree of confidence in data q...

  2. Application of relative quantification TaqMan real-time polymerase chain reaction technology for the identification and quantification of Thunnus alalunga and Thunnus albacares.

    PubMed

    Lopez, Itziar; Pardo, Miguel Angel

    2005-06-01

    A novel one-step methodology based on real-time Polymerase Chain Reaction (PCR) technology has been developed for the identification of two of the most valuable tuna species. Nowadays, species identification of seafood products has a major concern due to the importing to Europe of new species from other countries. To achieve this aim, two specific TaqMan systems were devised to identify Thunnus alalunga and Thunnus albacares. Another system specific to Scombroidei species was devised as a consensus system. In addition, a relative quantification methodology was carried out to quantify T. alalunga and T. albacares in mixtures after the relative amount of the target was compared with the consensus. This relative quantification methodology does not require a known amount of standard, allowing the analysis of many more samples together and saving costs and time. The utilization of real-time PCR does not require sample handling, preventing contamination and resulting in much faster and higher throughput results. PMID:15913324

  3. A quantitative real-time PCR assay for the identification and enumeration of Alexandrium cysts in marine sediments

    PubMed Central

    Erdner, D.L.; Percy, L.; Keafer, B.; Lewis, J.; Anderson, D.M.

    2009-01-01

    Harmful algal blooms (HABs) are a global problem that affects both human and ecosystem health. One of the most serious and widespread HAB poisoning syndromes is paralytic shellfish poisoning, commonly caused by Alexandrium spp. dinoflagellates. Like many toxic dinoflagellates, Alexandrium produces resistant resting cysts as part of its life cycle. These cysts play a key role in bloom initiation and decline, as well as dispersal and colonization of new areas. Information on cyst numbers and identity is essential for understanding and predicting blooms, yet comprehensive cyst surveys are extremely time- and labor-intensive. Here we describe the development and validation of a quantitative real-time PCR (qPCR) technique for the enumeration of cysts of A. tamarense of the toxic North American/Group I ribotype. The method uses a cloned fragment of the large subunit ribosomal RNA gene as a standard for cyst quantification, with an experimentally determined conversion factor of 28,402±6152 LSU ribosomal gene copies per cyst. Tests of DNA extraction and PCR efficiency show that mechanical breakage is required for adequate cyst lysis, and that it was necessary to dilute our DNA extracts 50-fold in order to abolish PCR inhibition from compounds co-extracted from the sediment. The resulting assay shows a linear response over 6 orders of magnitude and can reliably quantify ≥10cysts/cc sediment. For method validation, 129 natural sediment samples were split and analyzed in parallel, using both the qPCR and primulin-staining techniques. Overall, there is a significant correlation (p<0.001) between the cyst abundances determined by the two methods, although the qPCR counts tend to be lower than the primulin values. This underestimation is less pronounced in those samples collected from the top 1 cm of sediment, and more pronounced in those derived from the next 1–3 cm of the core. These differences may be due to the condition of the cysts in the different layers, as the top

  4. A quantitative real-time PCR assay for the identification and enumeration of Alexandrium cysts in marine sediments

    NASA Astrophysics Data System (ADS)

    Erdner, D. L.; Percy, L.; Keafer, B.; Lewis, J.; Anderson, D. M.

    2010-02-01

    Harmful algal blooms (HABs) are a global problem that affects both human and ecosystem health. One of the most serious and widespread HAB poisoning syndromes is paralytic shellfish poisoning, commonly caused by Alexandrium spp. dinoflagellates. Like many toxic dinoflagellates, Alexandrium produces resistant resting cysts as part of its life cycle. These cysts play a key role in bloom initiation and decline, as well as dispersal and colonization of new areas. Information on cyst numbers and identity is essential for understanding and predicting blooms, yet comprehensive cyst surveys are extremely time- and labor-intensive. Here we describe the development and validation of a quantitative real-time PCR (qPCR) technique for the enumeration of cysts of A. tamarense of the toxic North American/Group I ribotype. The method uses a cloned fragment of the large subunit ribosomal RNA gene as a standard for cyst quantification, with an experimentally determined conversion factor of 28,402±6152 LSU ribosomal gene copies per cyst. Tests of DNA extraction and PCR efficiency show that mechanical breakage is required for adequate cyst lysis, and that it was necessary to dilute our DNA extracts 50-fold in order to abolish PCR inhibition from compounds co-extracted from the sediment. The resulting assay shows a linear response over 6 orders of magnitude and can reliably quantify ≥10 cysts/cm 3 sediment. For method validation, 129 natural sediment samples were split and analyzed in parallel, using both the qPCR and primulin-staining techniques. Overall, there is a significant correlation ( p<0.001) between the cyst abundances determined by the two methods, although the qPCR counts tend to be lower than the primulin values. This underestimation is less pronounced in those samples collected from the top 1 cm of sediment, and more pronounced in those derived from the next 1-3 cm of the core. These differences may be due to the condition of the cysts in the different layers, as the

  5. A quick method for species identification of Japanese eel (Anguilla japonica) using real-time PCR: an onboard application for use during sampling surveys.

    PubMed

    Watanabe, Shun; Minegishi, Yuki; Yoshinaga, Tatsuki; Aoyama, Jun; Tsukamoto, Katsumi

    2004-01-01

    To compensate for the limited number of morphological characteristics of fish eggs and larvae, we established a convenient and robust method of species identification for eggs of the Japanese eel (Anguilla japonica) using a real-time polymerase chain reaction (PCR) that can be performed onboard research ships at sea. A total of about 1.2 kbp of the mitochondrial 16S ribosomal RNA gene sequences from all species of Anguilla and 3 other anguilliform species were compared to design specific primer pairs and a probe for A. japonica. This real-time PCR amplification was conducted for a total of 44 specimens including A. japonica, A. marmorata, A. bicolor pacifica, and 6 other anguilliform species. Immediate PCR amplification was only observed in A. japonica. We then tested this method under onboard conditions and obtained the same result as had been produced in the laboratory. These results suggest that real-time PCR can be a powerful tool for detecting Japanese eel eggs and newly hatched larvae immediately after onboard sampling during research cruises and will allow targeted sampling efforts to occur rapidly in response to any positive onboard identification of the eggs and larvae of this species.

  6. Identification and quantitative detection of Legionella spp. in various aquatic environments by real-time PCR assay.

    PubMed

    Kao, Po-Min; Tung, Min-Che; Hsu, Bing-Mu; Chiu, Yi-Chou; She, Cheng-Yu; Shen, Shu-Min; Huang, Yu-Li; Huang, Wen-Chien

    2013-09-01

    In this study, a SYBR green quantitative real-time PCR was developed to quantify and detect the Legionella spp. in various environmental water samples. The water samples were taken from watershed, water treatment plant, and thermal spring area in Taiwan. Legionella was detected in 13.6 % (24/176), and the detection rate for river water, raw drinking water, and thermal spring water was 10, 21.4, and 16.6 %, respectively. Using real-time PCR, concentration of Legionella spp. in detected samples ranged between 9.75 × 10(4) and 3.47 × 10(5) cells/L in river water, 6.92 × 10(4) and 4.29 × 10(5) cells/L in raw drinking water, and 5.71 × 10(4) and 2.12 × 10(6) cells/L for thermal spring water samples. The identified species included Legionella pneumophila (20.8 %), Legionella jordanis (4.2 %), Legionella nautarum (4.2 %), Legionella sp. (4.2 %), and uncultured Legionella sp. (66.6 %). The presence of L. pneumophila in aquatic environments suggested a potential public health threat that must be further examined.

  7. Real-time PCR assays for detection of Brucella spp. and the identification of genotype ST27 in bottlenose dolphins (Tursiops truncatus).

    PubMed

    Wu, Qingzhong; McFee, Wayne E; Goldstein, Tracey; Tiller, Rebekah V; Schwacke, Lori

    2014-05-01

    Rapid detection of Brucella spp. in marine mammals is challenging. Microbiologic culture is used for definitive diagnosis of brucellosis, but is time consuming, has low sensitivity and can be hazardous to laboratory personnel. Serological methods can aid in diagnosis, but may not differentiate prior exposure versus current active infection and may cross-react with unrelated Gram-negative bacteria. This study reports a real-time PCR assay for the detection of Brucella spp. and application to screen clinical samples from bottlenose dolphins stranded along the coast of South Carolina, USA. The assay was found to be 100% sensitive for the Brucella strains tested, and the limit of detection was 0.27fg of genomic DNA from Brucella ceti B1/94 per PCR volume. No amplification was detected for the non-Brucella pathogens tested. Brucella DNA was detected in 31% (55/178) of clinical samples tested. These studies indicate that the real-time PCR assay is highly sensitive and specific for the detection of Brucella spp. in bottlenose dolphins. We also developed a second real-time PCR assay for rapid identification of Brucella ST27, a genotype that is associated with human zoonotic infection. Positive results were obtained for Brucella strains which had been identified as ST27 by multilocus sequence typing. No amplification was found for other Brucella strains included in this study. ST27 was identified in 33% (18/54) of Brucella spp. DNA-positive clinical samples. To our knowledge, this is the first report on the use of a real-time PCR assay for identification of Brucella genotype ST27 in marine mammals. PMID:24632518

  8. Real-time PCR assays for detection of Brucella spp. and the identification of genotype ST27 in bottlenose dolphins (Tursiops truncatus).

    PubMed

    Wu, Qingzhong; McFee, Wayne E; Goldstein, Tracey; Tiller, Rebekah V; Schwacke, Lori

    2014-05-01

    Rapid detection of Brucella spp. in marine mammals is challenging. Microbiologic culture is used for definitive diagnosis of brucellosis, but is time consuming, has low sensitivity and can be hazardous to laboratory personnel. Serological methods can aid in diagnosis, but may not differentiate prior exposure versus current active infection and may cross-react with unrelated Gram-negative bacteria. This study reports a real-time PCR assay for the detection of Brucella spp. and application to screen clinical samples from bottlenose dolphins stranded along the coast of South Carolina, USA. The assay was found to be 100% sensitive for the Brucella strains tested, and the limit of detection was 0.27fg of genomic DNA from Brucella ceti B1/94 per PCR volume. No amplification was detected for the non-Brucella pathogens tested. Brucella DNA was detected in 31% (55/178) of clinical samples tested. These studies indicate that the real-time PCR assay is highly sensitive and specific for the detection of Brucella spp. in bottlenose dolphins. We also developed a second real-time PCR assay for rapid identification of Brucella ST27, a genotype that is associated with human zoonotic infection. Positive results were obtained for Brucella strains which had been identified as ST27 by multilocus sequence typing. No amplification was found for other Brucella strains included in this study. ST27 was identified in 33% (18/54) of Brucella spp. DNA-positive clinical samples. To our knowledge, this is the first report on the use of a real-time PCR assay for identification of Brucella genotype ST27 in marine mammals.

  9. Determination of breath isoprene allows the identification of the expiratory fraction of the propofol breath signal during real-time propofol breath monitoring.

    PubMed

    Hornuss, Cyrill; Dolch, Michael E; Janitza, Silke; Souza, Kimberly; Praun, Siegfried; Apfel, Christian C; Schelling, Gustav

    2013-10-01

    Real-time measurement of propofol in the breath may be used for routine clinical monitoring. However, this requires unequivocal identification of the expiratory phase of the respiratory propofol signal as only expiratory propofol reflects propofol blood concentrations. Determination of CO2 breath concentrations is the current gold standard for the identification of expiratory gas but usually requires additional equipment. Human breath also contains isoprene, a volatile organic compound with low inspiratory breath concentration and an expiratory concentration plateau. We investigated whether breath isoprene could be used similarly to CO2 to identify the expiratory fraction of the propofol breath signal. We investigated real-time breath data obtained from 40 study subjects during routine anesthesia. Propofol, isoprene, and CO2 breath concentrations were determined by a combined ion molecule reaction/electron impact mass spectrometry system. The expiratory propofol signal was identified according to breath CO2 and isoprene concentrations and presented as median of intervals of 30 s duration. Bland-Altman analysis was applied to detect differences (bias) in the expiratory propofol signal extracted by the two identification methods. We investigated propofol signals in a total of 3,590 observation intervals of 30 s duration in the 40 study subjects. In 51.4 % of the intervals (1,844/3,590) both methods extracted the same results for expiratory propofol signal. Overall bias between the two data extraction methods was -0.12 ppb. The lower and the upper limits of the 95 % CI were -0.69 and 0.45 ppb. Determination of isoprene breath concentrations allows the identification of the expiratory propofol signal during real-time breath monitoring.

  10. Development of a qualitative real-time PCR method to detect 19 targets for identification of genetically modified organisms.

    PubMed

    Peng, Cheng; Wang, Pengfei; Xu, Xiaoli; Wang, Xiaofu; Wei, Wei; Chen, Xiaoyun; Xu, Junfeng

    2016-01-01

    As the amount of commercially available genetically modified organisms (GMOs) grows recent years, the diversity of target sequences for molecular detection techniques are eagerly needed. Considered as the gold standard for GMO analysis, the real-time PCR technology was optimized to produce a high-throughput GMO screening method. With this method we can detect 19 transgenic targets. The specificity of the assays was demonstrated to be 100 % by the specific amplification of DNA derived from reference material from 20 genetically modified crops and 4 non modified crops. Furthermore, most assays showed a very sensitive detection, reaching the limit of ten copies. The 19 assays are the most frequently used genetic elements present in GM crops and theoretically enable the screening of the known GMO described in Chinese markets. Easy to use, fast and cost efficient, this method approach fits the purpose of GMO testing laboratories.

  11. An Integrated Flow Cytometry-Based System for Real-Time, High Sensitivity Bacterial Detection and Identification

    PubMed Central

    Buzatu, Dan A.; Moskal, Ted J.; Williams, Anna J.; Cooper, Willie Mae; Mattes, William B.; Wilkes, Jon G.

    2014-01-01

    Foodborne illnesses occur in both industrialized and developing countries, and may be increasing due to rapidly evolving food production practices. Yet some primary tools used to assess food safety are decades, if not centuries, old. To improve the time to result for food safety assessment a sensitive flow cytometer based system to detect microbial contamination was developed. By eliminating background fluorescence and improving signal to noise the assays accurately measure bacterial load or specifically identify pathogens. These assays provide results in minutes or, if sensitivity to one cell in a complex matrix is required, after several hours enrichment. Conventional assessments of food safety require 48 to 56 hours. The assays described within are linear over 5 orders of magnitude with results identical to culture plates, and report live and dead microorganisms. This system offers a powerful approach to real-time assessment of food safety, useful for industry self-monitoring and regulatory inspection. PMID:24718659

  12. Development of a qualitative real-time PCR method to detect 19 targets for identification of genetically modified organisms.

    PubMed

    Peng, Cheng; Wang, Pengfei; Xu, Xiaoli; Wang, Xiaofu; Wei, Wei; Chen, Xiaoyun; Xu, Junfeng

    2016-01-01

    As the amount of commercially available genetically modified organisms (GMOs) grows recent years, the diversity of target sequences for molecular detection techniques are eagerly needed. Considered as the gold standard for GMO analysis, the real-time PCR technology was optimized to produce a high-throughput GMO screening method. With this method we can detect 19 transgenic targets. The specificity of the assays was demonstrated to be 100 % by the specific amplification of DNA derived from reference material from 20 genetically modified crops and 4 non modified crops. Furthermore, most assays showed a very sensitive detection, reaching the limit of ten copies. The 19 assays are the most frequently used genetic elements present in GM crops and theoretically enable the screening of the known GMO described in Chinese markets. Easy to use, fast and cost efficient, this method approach fits the purpose of GMO testing laboratories. PMID:27386337

  13. Development of Candida-Specific Real-Time PCR Assays for the Detection and Identification of Eight Medically Important Candida Species.

    PubMed

    Zhang, Jing; Hung, Guo-Chiuan; Nagamine, Kenjiro; Li, Bingjie; Tsai, Shien; Lo, Shyh-Ching

    2016-01-01

    Culture-based identification methods have been the gold standard for the diagnosis of fungal infection. Currently, molecular technologies such as real-time PCR assays with short turnaround time can provide desirable alternatives for the rapid detection of Candida microbes. However, most of the published PCR primer sets are not Candida specific and likely to amplify DNA from common environmental contaminants, such as Aspergillus microbes. In this study, we designed pan-Candida primer sets based on the ribosomal DNA-coding regions conserved within Candida but distinct from those of Aspergillus and Penicillium. We demonstrate that the final two selected pan-Candida primer sets would not amplify Aspergillus DNA and could be used to differentiate eight medically important Candida pathogens in real-time PCR assays based on their melting profiles, with a sensitivity of detection as low as 10 fg of Candida genomic DNA. Moreover, we further evaluated and selected species-specific primer sets covering Candida albicans, Candida glabrata, Candida tropicalis, and Candida dubliniensis and show that they had high sensitivity and specificity. These real-time PCR primer sets could potentially be assembled into a single PCR array for the rapid detection of Candida species in various clinical settings, such as corneal transplantation. PMID:27103821

  14. Evaluation of three real-time PCR assays for differential identification of Mycobacterium tuberculosis complex and nontuberculous mycobacteria species in liquid culture media.

    PubMed

    Jung, Yu Jung; Kim, Ji-Youn; Song, Dong Joon; Koh, Won-Jung; Huh, Hee Jae; Ki, Chang-Seok; Lee, Nam Yong

    2016-06-01

    We evaluated the analytical performance of M. tuberculosis complex (MTBC)/nontuberculous mycobacteria (NTM) PCR assays for differential identification of MTBC and NTM using culture-positive liquid media. Eighty-five type strains and 100 consecutive mycobacterial liquid media cultures (MGIT 960 system) were analyzed by a conventional PCR assay (MTB-ID(®) V3) and three real-time PCR assays (AdvanSure™ TB/NTM real-time PCR, AdvanSure; GENEDIA(®) MTB/NTM Detection Kit, Genedia; Real-Q MTB & NTM kit, Real-Q). The accuracy rates for reference strains were 89.4%, 100%, 98.8%, and 98.8% for the MTB-ID V3, AdvanSure, Genedia, and Real-Q assays, respectively. Cross-reactivity in the MTB-ID V3 assay was mainly attributable to non-mycobacterium Corynebacterineae species. The diagnostic performance was determined using clinical isolates grown in liquid media, and the overall sensitivities for all PCR assays were higher than 95%. In conclusion, the three real-time PCR assays showed better performance in discriminating mycobacterium species and non-mycobacterium Corynebacterineae species than the conventional PCR assay.

  15. Identification of Reference Genes for Quantitative Real Time PCR Assays in Aortic Tissue of Syrian Hamsters with Bicuspid Aortic Valve

    PubMed Central

    Rueda-Martínez, Carmen; Fernández, M. Carmen; Soto-Navarrete, María Teresa; Jiménez-Navarro, Manuel; Durán, Ana Carmen; Fernández, Borja

    2016-01-01

    Bicuspid aortic valve (BAV) is the most frequent congenital cardiac malformation in humans, and appears frequently associated with dilatation of the ascending aorta. This association is likely the result of a common aetiology. Currently, a Syrian hamster strain with a relatively high (∼40%) incidence of BAV constitutes the only spontaneous animal model of BAV disease. The characterization of molecular alterations in the aorta of hamsters with BAV may serve to identify pathophysiological mechanisms and molecular markers of disease in humans. In this report, we evaluate the expression of ten candidate reference genes in aortic tissue of hamsters in order to identify housekeeping genes for normalization using quantitative real time PCR (RT-qPCR) assays. A total of 51 adult (180–240 days old) and 56 old (300–440 days old) animals were used. They belonged to a control strain of hamsters with normal, tricuspid aortic valve (TAV; n = 30), or to the affected strain of hamsters with TAV (n = 45) or BAV (n = 32). The expression stability of the candidate reference genes was determined by RT-qPCR using three statistical algorithms, GeNorm, NormFinder and Bestkeeper. The expression analyses showed that the most stable reference genes for the three algorithms employed were Cdkn1β, G3pdh and Polr2a. We propose the use of Cdkn1β, or both Cdkn1β and G3pdh as reference genes for mRNA expression analyses in Syrian hamster aorta. PMID:27711171

  16. Development of a real-time PCR Assay for identification of Coccidioides immitis by use of the BD Max system.

    PubMed

    Mitchell, Marilyn; Dizon, Dominic; Libke, Robert; Peterson, Michael; Slater, David; Dhillon, Akashdeep

    2015-03-01

    Rapid real-time PCR (RT-PCR) can be performed in a community hospital setting to identify Coccidioides species using the new Becton Dickinson molecular instrument BD Max. Following sample preparation, DNA extraction and PCR were performed on the BD Max using the BD Max extraction kit ExK-DNA-1 test strip and a master mix prepared by BioGX (Birmingham, AL). Sample preparation took 2 h, and testing on the BD Max took an additional 2 h. Method sensitivity and specificity were evaluated along with the limits of detection to confirm that this convenient method would provide medically useful information. Using serial dilutions, the lower limit of detection was determined to be 1 CFU/μl. Testing with this method was validated using samples from various body sites, including bronchial alveolar lavage (BAL) fluid; sputum and lung tissue samples; and pleural and spinal fluids. Safety protocols were established, and specimen preparation processes were developed for the various types of specimens. The range for the cycle threshold (CT) indicating adequate fluorescent signal to signify a positive result was established along with the acceptable range for the internal standard. Positive controls run with each batch were prepared by spiking a pooled BAL fluid specimen with a known dilution of Coccidioides immitis organism. Our experience with testing >330 patient samples shows that clinically relevant information can be available within 4 h using an RT-PCR method on the BD Max to identify Coccidioides spp., with sensitivity equivalent to culture. PMID:25588654

  17. Identification of Dobrava, Hantaan, Seoul, and Puumala viruses by one-step real-time RT-PCR.

    PubMed

    Aitichou, Mohamed; Saleh, Sharron S; McElroy, Anita K; Schmaljohn, C; Ibrahim, M Sofi

    2005-03-01

    We developed four assays for specifically identifying Dobrava (DOB), Hantaan (HTN), Puumala (PUU), and Seoul (SEO) viruses. The assays are based on the real-time one-step reverse transcriptase polymerase chain reaction (RT-PCR) with the small segment used as the target sequence. The detection limits of DOB, HTN, PUU, and SEO assays were 25, 25, 25, and 12.5 plaque-forming units, respectively. The assays were evaluated in blinded experiments, each with 100 samples that contained Andes, Black Creek Canal, Crimean-Congo hemorrhagic fever, Rift Valley fever and Sin Nombre viruses in addition to DOB, HTN, PUU and SEO viruses. The sensitivity levels of the DOB, HTN, PUU, and SEO assays were 98%, 96%, 92% and 94%, respectively. The specificity of DOB, HTN and SEO assays was 100% and the specificity of the PUU assay was 98%. Because of the high levels of sensitivity, specificity, and reproducibility, we believe that these assays can be useful for diagnosing and differentiating these four Old-World hantaviruses.

  18. A real-time PCR-based semi-quantitative breakpoint to aid in molecular identification of urinary tract infections.

    PubMed

    Hansen, Wendy L J; van der Donk, Christina F M; Bruggeman, Cathrien A; Stobberingh, Ellen E; Wolffs, Petra F G

    2013-01-01

    This study presents a novel approach to aid in diagnosis of urinary tract infections (UTIs). A real-time PCR assay was used to screen for culture-positive urinary specimens and to identify the causative uropathogen. Semi-quantitative breakpoints were used to screen for significant bacteriuria (presence of ≥ 10(5) CFU/ml of uropathogens) or low-level bacteriuria (containing between 10(3) and 10(4) CFU/ml of uropathogens). The 16S rDNA-based assay could identify the most prevalent uropathogens using probes for Escherichia coli, Pseudomonas species, Pseudomonas aeruginosa, Staphylococcus species, Staphylococcus aureus, Enterococcus species and Streptococcus species. 330 urinary specimens were analysed and results were compared with conventional urine culture. Using a PCR Ct value of 25 as semi-quantitative breakpoint for significant bacteriuria resulted in a sensitivity and specificity of 97% and 80%, respectively. In 78% of the samples with monomicrobial infections the assay contained probes to detect the bacteria present in the urine specimens and 99% of these uropathogens was correctly identified. Concluding, this proof-of-concept approach demonstrates that the assay can distinguish bacteriuria from no bacteriuria as well as detect the involved uropathogen within 4 hours after sampling, allowing adequate therapy decisions within the same day as well as drastically reduce consequent urine culturing.

  19. Identification and Validation of Reference Genes for Quantitative Real-Time PCR Normalization and Its Applications in Lycium

    PubMed Central

    Zeng, Shaohua; Liu, Yongliang; Wu, Min; Liu, Xiaomin; Shen, Xiaofei; Liu, Chunzhao; Wang, Ying

    2014-01-01

    Lycium barbarum and L. ruthenicum are extensively used as traditional Chinese medicinal plants. Next generation sequencing technology provides a powerful tool for analyzing transcriptomic profiles of gene expression in non-model species. Such gene expression can then be confirmed with quantitative real-time polymerase chain reaction (qRT-PCR). Therefore, use of systematically identified suitable reference genes is a prerequisite for obtaining reliable gene expression data. Here, we calculated the expression stability of 18 candidate reference genes across samples from different tissues and grown under salt stress using geNorm and NormFinder procedures. The geNorm-determined rank of reference genes was similar to those defined by NormFinder with some differences. Both procedures confirmed that the single most stable reference gene was ACNTIN1 for L. barbarum fruits, H2B1 for L. barbarum roots, and EF1α for L. ruthenicum fruits. PGK3, H2B2, and PGK3 were identified as the best stable reference genes for salt-treated L. ruthenicum leaves, roots, and stems, respectively. H2B1 and GAPDH1+PGK1 for L. ruthenicum and SAMDC2+H2B1 for L. barbarum were the best single and/or combined reference genes across all samples. Finally, expression of salt-responsive gene NAC, fruit ripening candidate gene LrPG, and anthocyanin genes were investigated to confirm the validity of the selected reference genes. Suitable reference genes identified in this study provide a foundation for accurately assessing gene expression and further better understanding of novel gene function to elucidate molecular mechanisms behind particular biological/physiological processes in Lycium. PMID:24810586

  20. Identification of new leishmanicidal peptide lead structures by automated real-time monitoring of changes in intracellular ATP.

    PubMed Central

    Luque-Ortega, J Román; Saugar, José M; Chiva, Cristina; Andreu, David; Rivas, Luis

    2003-01-01

    Leishmanicidal drugs interacting stoichiometrically with parasite plasma membrane lipids, thus promoting permeability, have raised significant expectations for Leishmania chemotherapy due to their nil or very low induction of resistance. Inherent in this process is a decrease in intracellular ATP, either wasted by ionic pumps to restore membrane potential or directly leaked through larger membrane lesions caused by the drug. We have adapted a luminescence method for fast automated real-time monitoring of this process, using Leishmania donovani promastigotes transfected with a cytoplasmic luciferase form, previously tested for anti-mitochondrial drugs. The system was first assayed against a set of well-known membrane-active drugs [amphotericin B, nystatin, cecropin A-melittin peptide CA(1-8)M(1-18)], plus two ionophoric polyethers (narasin and salinomycin) not previously tested on Leishmania, then used to screen seven new cecropin A-melittin hybrid peptides. All membrane-active compounds showed a good correlation between inhibition of luminescence and leishmanicidal activity. Induction of membrane permeability was demonstrated by dissipation of membrane potential, SYTOX trade mark Green influx and membrane damage assessed by electron microscopy, except for the polyethers, where ATP decrease was due to inhibition of its mitochondrial synthesis. Five of the test peptides showed an ED50 around 1 microM on promastigotes. These peptides, with equal or better activity than 26-residue-long CA(1-8)M(1-18), are the shortest leishmanicidal peptides described so far, and validate our luminescence assay as a fast and cheap screening tool for membrane-active compounds. PMID:12864731

  1. Visualizing the store-operated channel complex assembly in real time: identification of SERCA2 as a new member.

    PubMed

    Sampieri, Alicia; Zepeda, Angelica; Asanov, Alexander; Vaca, Luis

    2009-05-01

    Depletion of intracellular calcium stores leads to the activation of calcium influx via the so-called store-operated channels (SOCs). Recent evidence positions Orai proteins as the putative channels responsible for this process. The stromal interacting molecule (STIM1) has been recently identified as the calcium sensor located at the endoplasmic reticulum (ER), and responsible for communicating the deplete state of calcium stores to Orai at the plasma membrane (PM). However, recent experimental findings suggest that Orai and STIM1 are only part of a larger molecular complex required to modulate store-operated calcium entry (SOCE). In the present study we describe the assembly of the several of the components from the SOC complex in real-time, utilizing a novel imaging method. Using FRET imaging we show that under resting conditions (with calcium stores replenished) STIM1 travels continuously through the ER associated to the microtubule tracking protein, EB1. Upon depletion of the ER STIM1 dissociates from EB1 and aggregates into macromolecular complexes at the ER which includes the microsomal calcium ATPase. This association follows the assembly of Orai into macromolecular aggregates at the PM. We show that STIM1-Orai association follows a similar time course as that of Orai aggregation at the PM. During this last step of the process, calcium-selective, whole-cell inward currents developed, simultaneously. We show that this process is fully reversible. Replenishing intracellular calcium stores induces STIM1-Orai complex dissociation and shuts down inward currents. Under these conditions STIM1 re-associates to EB1, and reinitiates its travel through the ER.

  2. Development of a real-time PCR assay (SYBR Green I) for rapid identification and quantification of scyphomedusae Aurelia sp.1 planulae

    NASA Astrophysics Data System (ADS)

    Wang, Jianyan; Zhen, Yu; Mi, Tiezhu; Yu, Zhigang; Wang, Guoshan

    2015-07-01

    The complicated life cycle of Aurelia spp., comprising benthic asexually-reproducing polyps and sexually-reproducing medusae, makes it hard for researchers to identify and track them, especially for early stage individuals, such as planulae. To solve this problem, we developed a real-time PCR assay (SYBR Green I) to identify planulae in both cultured and natural seawater samples. Species-specific primers targeting Aurelia sp.1 mitochondrial 16S rDNA (mt 16S rDNA) regions were designed. Using a calibration curve constructed with plasmids containing the Aurelia sp.1 mt 16S rDNA fragment and a standard curve for planulae, the absolute number of mt 16S rDNA copies per planula was determined and from that the total number of planulae per sample was estimated. For the field samples, a 100-fold dilution of the sample DNA combined with a final concentration of 0.2 μg/μL BSA in the PCR reaction mixture was used to remove real-time PCR inhibitors. Samples collected in Jiaozhou Bay from July to September 2012 were subsequently analyzed using this assay. Peak Aurelia sp.1 planula abundance occurred in July 2012 at stations near Hongdao Island and Qingdao offshore; abundances were very low in August and September. The real-time PCR assay (SYBR Green I) developed here negates the need for traditional microscopic identification, which is laborious and time-consuming, and can detect and quantify jellyfish planulae in field plankton samples rapidly and specifically.

  3. A centrifugal direct recombinase polymerase amplification (direct-RPA) microdevice for multiplex and real-time identification of food poisoning bacteria.

    PubMed

    Choi, Goro; Jung, Jae Hwan; Park, Byung Hyun; Oh, Seung Jun; Seo, Ji Hyun; Choi, Jong Seob; Kim, Do Hyun; Seo, Tae Seok

    2016-06-21

    In this study, we developed a centrifugal direct recombinase polymerase amplification (direct-RPA) microdevice for multiplex and real-time identification of food poisoning bacteria contaminated milk samples. The microdevice was designed to contain identical triplicate functional units and each unit has four reaction chambers, thereby making it possible to perform twelve direct-RPA reactions simultaneously. The integrated microdevice consisted of two layers: RPA reagents were injected in the top layer, while spiked milk samples with food poisoning bacteria were loaded into sample reservoirs in the bottom layer. For multiplex bacterial detection, the target gene-specific primers and probes were dried in each reaction chamber. The introduced samples and reagents could be equally aliquoted and dispensed into each reaction chamber by centrifugal force, and then the multiplex direct-RPA reaction was executed. The target genes of bacteria spiked in milk could be amplified at 39 °C without a DNA extraction step by using the direct-RPA cocktails, which were a combination of a direct PCR buffer and RPA enzymes. As the target gene amplification proceeded, the increased fluorescence signals coming from the reaction chambers were recorded in real-time at an interval of 2 min. The entire process, including the sample distribution, the direct-RPA reaction, and the real-time analysis, was accomplished with a custom-made portable genetic analyzer and a miniaturized optical detector. Monoplex, duplex, and triplex food poisoning bacteria (Salmonella enterica, Escherichia coli O157:H7, and Vibrio parahaemolyticus) detection was successfully performed with a detection sensitivity of 4 cells per 3.2 μL of milk samples within 30 min. By implementing the direct-PRA on the miniaturized centrifugal microsystem, the on-site food poisoning bacteria analysis would be feasible with high speed, sensitivity, and multiplicity.

  4. Flight Testing and Real-Time System Identification Analysis of a UH-60A Black Hawk Helicopter with an Instrumented External Sling Load

    NASA Technical Reports Server (NTRS)

    McCoy, Allen H.

    1998-01-01

    Helicopter external air transportation plays an important role in today's world. For both military and civilian helicopters, external sling load operations offer an efficient and expedient method of handling heavy, oversized cargo. With the ability to reach areas otherwise inaccessible by ground transportation, helicopter external load operations are conducted in industries such as logging, construction, and fire fighting, as well as in support of military tactical transport missions. Historically, helicopter and load combinations have been qualified through flight testing, requiring considerable time and cost. With advancements in simulation and flight test techniques there is potential to substantially reduce costs and increase the safety of helicopter sling load certification. Validated simulation tools make possible accurate prediction of operational flight characteristics before initial flight tests. Real time analysis of test data improves the safety and efficiency of the testing programs. To advance these concepts, the U.S. Army and NASA, in cooperation with the Israeli Air Force and Technion, under a Memorandum of Agreement, seek to develop and validate a numerical model of the UH-60 with sling load and demonstrate a method of near real time flight test analysis. This thesis presents results from flight tests of a U.S. Army Black Hawk helicopter with various external loads. Tests were conducted as the U.S. first phase of this MOA task. The primary load was a container express box (CONEX) which contained a compact instrumentation package. The flights covered the airspeed range from hover to 70 knots. Primary maneuvers were pitch and roll frequency sweeps, steps, and doublets. Results of the test determined the effect of the suspended load on both the aircraft's handling qualities and its control system's stability margins. Included were calculations of the stability characteristics of the load's pendular motion. Utilizing CIFER(R) software, a method for near-real

  5. A centrifugal direct recombinase polymerase amplification (direct-RPA) microdevice for multiplex and real-time identification of food poisoning bacteria.

    PubMed

    Choi, Goro; Jung, Jae Hwan; Park, Byung Hyun; Oh, Seung Jun; Seo, Ji Hyun; Choi, Jong Seob; Kim, Do Hyun; Seo, Tae Seok

    2016-06-21

    In this study, we developed a centrifugal direct recombinase polymerase amplification (direct-RPA) microdevice for multiplex and real-time identification of food poisoning bacteria contaminated milk samples. The microdevice was designed to contain identical triplicate functional units and each unit has four reaction chambers, thereby making it possible to perform twelve direct-RPA reactions simultaneously. The integrated microdevice consisted of two layers: RPA reagents were injected in the top layer, while spiked milk samples with food poisoning bacteria were loaded into sample reservoirs in the bottom layer. For multiplex bacterial detection, the target gene-specific primers and probes were dried in each reaction chamber. The introduced samples and reagents could be equally aliquoted and dispensed into each reaction chamber by centrifugal force, and then the multiplex direct-RPA reaction was executed. The target genes of bacteria spiked in milk could be amplified at 39 °C without a DNA extraction step by using the direct-RPA cocktails, which were a combination of a direct PCR buffer and RPA enzymes. As the target gene amplification proceeded, the increased fluorescence signals coming from the reaction chambers were recorded in real-time at an interval of 2 min. The entire process, including the sample distribution, the direct-RPA reaction, and the real-time analysis, was accomplished with a custom-made portable genetic analyzer and a miniaturized optical detector. Monoplex, duplex, and triplex food poisoning bacteria (Salmonella enterica, Escherichia coli O157:H7, and Vibrio parahaemolyticus) detection was successfully performed with a detection sensitivity of 4 cells per 3.2 μL of milk samples within 30 min. By implementing the direct-PRA on the miniaturized centrifugal microsystem, the on-site food poisoning bacteria analysis would be feasible with high speed, sensitivity, and multiplicity. PMID:27216297

  6. Molecular identification of Mycobacterium avium subsp. silvaticum by duplex high-resolution melt analysis and subspecies-specific real-time PCR.

    PubMed

    Rónai, Zsuzsanna; Csivincsik, Ágnes; Dán, Ádám

    2015-05-01

    Accurate identification of mycobacterial species and subspecies is essential to evaluate their significance and to perform epidemiological studies. The subspecies of Mycobacterium avium have different attributes but coincide in their zoonotic potential. Our knowledge about M. avium subsp. silvaticum is limited, since its identification is uncertain. Mycobacterium avium subsp. avium and M. avium subsp. silvaticum can be discriminated from each other based only on phenotypic characteristics, as they have almost identical genome sequences. Here we describe the development of a diagnostic method which enables the molecular identification of M. avium subsp. silvaticum and discrimination from M. avium subsp. avium based on genomic differences in a duplex high-resolution melt and M. avium subsp. silvaticum-specific mismatch real-time PCR. The developed assay was tested on reference strains and 199 field isolates, which were analyzed by phenotypic methods previously. This assay not only identified all 63 M. avium subsp. silvaticum and 138 M. avium subsp. avium strains correctly but also enabled the detection of mixed M. avium subsp. avium-M. avium subsp. silvaticum cultures. This is the first time that such a large panel of strains has been analyzed, and we also report the first isolation of M. avium subsp. silvaticum from red fox, red deer, wild boar, cattle, and badger. This assay is reliable, rapid, simple, inexpensive, and robust. It eliminates the long-existing problem of ambiguous phenotypic identification and opens up the possibility for detailed and comprehensive strain studies.

  7. A real-time structural parametric identification system based on fiber optic sensing and neural network algorithms

    NASA Astrophysics Data System (ADS)

    Wu, Zhishen; Xu, Bin

    2003-07-01

    A structural parametric identification strategy based on neural networks algorithms using dynamic macro-strain measurements in time domain from a long-gage strain sensor by fiber optic sensing technique such as Fiber Bragg Grating (FBG) sensor is developed. An array of long-gage sensors is bounded on the structure to measure reliably and accurately macro-strains. By the proposed methodology, the structural parameter of stiffness can be identified. A beam model with known mass distribution is considered as an object structure. Without any eigenvalue analysis or optimization computation, the structural parameter of stiffness can be identified. First an emulator neural network is presented to identify the beam structure in current state. Free vibration macro-strain responses of the beam structure are used to train the emulator neural network. The trained emulator neural network can be used to forecast the free vibration macro-strain response of the beam structure with enough precision and decide the difference between the free vibration macro-strain responses of other assumed structure with different structural parameters and those of the original beam structure. The root mean square (RMS) error vector is presented to evaluate the difference. Subsequently, corresponding to each assumed structure with different structural parameters, the RMS error vector can be calculated. By using the training data set composed of the structural parameters and RMS error vector, a parametric evaluation neural network is trained. A beam structure is considered as an existing structure, based on the trained parametric evaluation neural network, the stiffness of the beam structure can be forecast. It is shown that the parametric identification strategy using macro-strain measurement from long-gage sensors has the potential of being a practical tool for a health monitoring methodology applied to civil engineering structures.

  8. A Simultaneous Analytical Method for Duplex Identification of Porcine and Horse in the Meat Products by EvaGreen based Real-time PCR.

    PubMed

    Sakalar, Ergün; Ergün, Seyma Özçirak; Akar, Emine

    2015-01-01

    A duplex real-time polymerase chain reaction (PCR) based assay for the detection of porcine and horse meat in sausages was designed by using EvaGreen fluorescent dye. Primers were selected from mitochondrial 12S rRNA and 16S rRNA genes which are powerful regions for identification of horse and porcine meat. DNA from reference samples and industrial products was successfully extracted using the GIDAGEN® Multi-Fast DNA Isolation Kit. Genomes were identified based on their specific melting peaks (Mp) which are 82.5℃ and 78℃ for horse and porcine, respectively. The assay used in this study allowed the detection of as little as 0.0001% level of horse meat and 0.001% level of porcine meat in the experimental admixtures. These findings indicate that EvaGreen based duplex real-time PCR is a potentially sensitive, reliable, rapid and accurate assay for the detection of meat species adulterated with porcine and horse meats. PMID:26761852

  9. A Simultaneous Analytical Method for Duplex Identification of Porcine and Horse in the Meat Products by EvaGreen based Real-time PCR.

    PubMed

    Sakalar, Ergün; Ergün, Seyma Özçirak; Akar, Emine

    2015-01-01

    A duplex real-time polymerase chain reaction (PCR) based assay for the detection of porcine and horse meat in sausages was designed by using EvaGreen fluorescent dye. Primers were selected from mitochondrial 12S rRNA and 16S rRNA genes which are powerful regions for identification of horse and porcine meat. DNA from reference samples and industrial products was successfully extracted using the GIDAGEN® Multi-Fast DNA Isolation Kit. Genomes were identified based on their specific melting peaks (Mp) which are 82.5℃ and 78℃ for horse and porcine, respectively. The assay used in this study allowed the detection of as little as 0.0001% level of horse meat and 0.001% level of porcine meat in the experimental admixtures. These findings indicate that EvaGreen based duplex real-time PCR is a potentially sensitive, reliable, rapid and accurate assay for the detection of meat species adulterated with porcine and horse meats.

  10. Rapid detection and identification of Wuchereria bancrofti, Brugia malayi, B. pahangi, and Dirofilaria immitis in mosquito vectors and blood samples by high resolution melting real-time PCR.

    PubMed

    Thanchomnang, Tongjit; Intapan, Pewpan M; Tantrawatpan, Chairat; Lulitanond, Viraphong; Chungpivat, Sudchit; Taweethavonsawat, Piyanan; Kaewkong, Worasak; Sanpool, Oranuch; Janwan, Penchom; Choochote, Wej; Maleewong, Wanchai

    2013-12-01

    A simple, rapid, and high-throughput method for detection and identification of Wuchereria bancrofti, Brugia malayi, Brugia pahangi, and Dirofilaria immitis in mosquito vectors and blood samples was developed using a real-time PCR combined with high-resolution melting (HRM) analysis. Amplicons of the 4 filarial species were generated from 5S rRNA and spliced leader sequences by the real-time PCR and their melting temperatures were determined by the HRM method. Melting of amplicons from W. bancrofti, B. malayi, D. immitis, and B. pahangi peaked at 81.5±0.2℃, 79.0±0.3℃, 76.8±0.1℃, and 79.9±0.1℃, respectively. This assay is relatively cheap since it does not require synthesis of hybridization probes. Its sensitivity and specificity were 100%. It is a rapid and technically simple approach, and an important tool for population surveys as well as molecular xenomonitoring of parasites in vectors. PMID:24516268

  11. Novel multiplex real-time PCR diagnostic assay for identification and differentiation of Mycobacterium tuberculosis, Mycobacterium canettii, and Mycobacterium tuberculosis complex strains.

    PubMed

    Reddington, Kate; O'Grady, Justin; Dorai-Raj, Siobhan; Maher, Majella; van Soolingen, Dick; Barry, Thomas

    2011-02-01

    Tuberculosis (TB) in humans is caused by members of the Mycobacterium tuberculosis complex (MTC). Rapid detection of the MTC is necessary for the timely initiation of antibiotic treatment, while differentiation between members of the complex may be important to guide the appropriate antibiotic treatment and provide epidemiological information. In this study, a multiplex real-time PCR diagnostics assay using novel molecular targets was designed to identify the MTC while simultaneously differentiating between M. tuberculosis and M. canettii. The lepA gene was targeted for the detection of members of the MTC, the wbbl1 gene was used for the differentiation of M. tuberculosis and M. canettii from the remainder of the complex, and a unique region of the M. canettii genome, a possible novel region of difference (RD), was targeted for the specific identification of M. canettii. The multiplex real-time PCR assay was tested using 125 bacterial strains (64 MTC isolates, 44 nontuberculosis mycobacteria [NTM], and 17 other bacteria). The assay was determined to be 100% specific for the mycobacteria tested. Limits of detection of 2.2, 2.17, and 0.73 cell equivalents were determined for M. tuberculosis/M. canettii, the MTC, and M. canettii, respectively, using probit regression analysis. Further validation of this diagnostics assay, using clinical samples, should demonstrate its potential for the rapid, accurate, and sensitive diagnosis of TB caused by M. tuberculosis, M. canettii, and the other members of the MTC.

  12. Detection, quantitation and identification of enteroviruses from surface waters and sponge tissue from the Florida Keys using real-time RT-PCR

    USGS Publications Warehouse

    Donaldson, K.A.; Griffin, Dale W.; Paul, J.H.

    2002-01-01

    A method was developed for the quantitative detection of pathogenic human enteroviruses from surface waters in the Florida Keys using Taqman (R) one-step Reverse transcription (RT)-PCR with the Model 7700 ABI Prism (R) Sequence Detection System. Viruses were directly extracted from unconcentrated grab samples of seawater, from seawater concentrated by vortex flow filtration using a 100kD filter and from sponge tissue. Total RNA was extracted from the samples, purified and concentrated using spin-column chromatography. A 192-196 base pair portion of the 5??? untranscribed region was amplified from these extracts. Enterovirus concentrations were estimated using real-time RT-PCR technology. Nine of 15 sample sites or 60% were positive for the presence of pathogenic human enteroviruses. Considering only near-shore sites, 69% were positive with viral concentrations ranging from 9.3viruses/ml to 83viruses/g of sponge tissue (uncorrected for extraction efficiency). Certain amplicons were selected for cloning and sequencing for identification. Three strains of waterborne enteroviruses were identified as Coxsackievirus A9, Coxsackievirus A16, and Poliovirus Sabin type 1. Time and cost efficiency of this one-step real-time RT-PCR methodology makes this an ideal technique to detect, quantitate and identify pathogenic enteroviruses in recreational waters. Copyright ?? 2002 Elsevier Science Ltd.

  13. A Simultaneous Analytical Method for Duplex Identification of Porcine and Horse in the Meat Products by EvaGreen based Real-time PCR

    PubMed Central

    2015-01-01

    A duplex real-time polymerase chain reaction (PCR) based assay for the detection of porcine and horse meat in sausages was designed by using EvaGreen fluorescent dye. Primers were selected from mitochondrial 12S rRNA and 16S rRNA genes which are powerful regions for identification of horse and porcine meat. DNA from reference samples and industrial products was successfully extracted using the GIDAGEN® Multi-Fast DNA Isolation Kit. Genomes were identified based on their specific melting peaks (Mp) which are 82.5℃ and 78℃ for horse and porcine, respectively. The assay used in this study allowed the detection of as little as 0.0001% level of horse meat and 0.001% level of porcine meat in the experimental admixtures. These findings indicate that EvaGreen based duplex real-time PCR is a potentially sensitive, reliable, rapid and accurate assay for the detection of meat species adulterated with porcine and horse meats. PMID:26761852

  14. Real-time PCR detection and quantification of elephantid DNA: species identification for highly processed samples associated with the ivory trade.

    PubMed

    Wozney, Kristyne Michelle; Wilson, Paul J

    2012-06-10

    The ivory industry is the single most serious threat to global elephant populations. A highly sensitive, species-specific real-time PCR assay has been developed to detect and quantify African elephant (Loxodonta africana), Asian elephant (Elephas maximus) and Woolly Mammoth (Mammuthus primigenius) mitochondrial DNA from highly processed samples involved in the international ivory trade. This assay is especially useful for highly processed samples where there are no distinguishing morphological features to identify the species of origin. Using species-specific Taqman(®) probes targeting a region of the mitochondrial cytochrome b gene, we developed an assay that can be used to positively identify samples containing elephant or Woolly mammoth DNA faster and more cost-effectively than traditional sequencing methods. Furthermore, this assay provides a diagnostic result based on probe hybridization that eliminates ambiguities associated with traditional DNA sequence protocols involving low template DNA. The real-time method is highly sensitive, producing accurate and reproducible results in samples with as few as 100 copies of template DNA. This protocol can be applied to the enforcement of the Convention on the International Trade of Endangered Species (CITES), when positive identification of species from illegally traded products is required by conservation officers in wildlife forensic cases.

  15. Measurement-device-independent quantum key distribution.

    PubMed

    Lo, Hoi-Kwong; Curty, Marcos; Qi, Bing

    2012-03-30

    How to remove detector side channel attacks has been a notoriously hard problem in quantum cryptography. Here, we propose a simple solution to this problem--measurement-device-independent quantum key distribution (QKD). It not only removes all detector side channels, but also doubles the secure distance with conventional lasers. Our proposal can be implemented with standard optical components with low detection efficiency and highly lossy channels. In contrast to the previous solution of full device independent QKD, the realization of our idea does not require detectors of near unity detection efficiency in combination with a qubit amplifier (based on teleportation) or a quantum nondemolition measurement of the number of photons in a pulse. Furthermore, its key generation rate is many orders of magnitude higher than that based on full device independent QKD. The results show that long-distance quantum cryptography over say 200 km will remain secure even with seriously flawed detectors.

  16. Measurement-device-independent quantum key distribution.

    PubMed

    Lo, Hoi-Kwong; Curty, Marcos; Qi, Bing

    2012-03-30

    How to remove detector side channel attacks has been a notoriously hard problem in quantum cryptography. Here, we propose a simple solution to this problem--measurement-device-independent quantum key distribution (QKD). It not only removes all detector side channels, but also doubles the secure distance with conventional lasers. Our proposal can be implemented with standard optical components with low detection efficiency and highly lossy channels. In contrast to the previous solution of full device independent QKD, the realization of our idea does not require detectors of near unity detection efficiency in combination with a qubit amplifier (based on teleportation) or a quantum nondemolition measurement of the number of photons in a pulse. Furthermore, its key generation rate is many orders of magnitude higher than that based on full device independent QKD. The results show that long-distance quantum cryptography over say 200 km will remain secure even with seriously flawed detectors. PMID:22540686

  17. Real-time PCR and sequencing assays for rapid detection and identification of avian schistosomes in environmental samples.

    PubMed

    Jothikumar, Narayanan; Mull, Bonnie J; Brant, Sara V; Loker, Eric S; Collinson, Jeremy; Secor, W Evan; Hill, Vincent R

    2015-06-15

    Cercarial dermatitis, also known as swimmer's itch, is an allergenic skin reaction followed by intense itching caused by schistosome cercariae penetrating human skin. Cercarial dermatitis outbreaks occur globally and are frequently associated with freshwater lakes and are occasionally associated with marine or estuarine waters where birds reside year-round or where migratory birds reside. In this study, a broadly reactive TaqMan assay targeting 18S rRNA gene (ribosomal DNA [rDNA]) sequences that was based on a genetically diverse panel of schistosome isolates representing 13 genera and 20 species (the 18S rDNA TaqMan assay) was developed. A PCR assay was also developed to amplify a 28S rDNA region for subsequent sequencing to identify schistosomes. When applied to surface water samples seeded with Schistosoma mansoni cercariae, the 18S rDNA TaqMan assay enabled detection at a level of 5 S. mansoni cercariae in 100 liters of lake water. The 18S rDNA TaqMan and 28S rDNA PCR sequencing assays were also applied to 100-liter water samples collected from lakes in Nebraska and Wisconsin where there were reported dermatitis outbreaks. Avian schistosome DNA was detected in 11 of 34 lake water samples using the TaqMan assay. Further 28S rDNA sequence analysis of positive samples confirmed the presence of avian schistosome DNA and provided a preliminary identification of the avian schistosomes in 10 of the 11 samples. These data indicate that the broadly schistosome-reactive TaqMan assay can be effective for rapid screening of large-volume water samples for detection of avian schistosomes, thereby facilitating timely response actions to mitigate or prevent dermatitis outbreaks. Additionally, samples positive by the 18S rDNA TaqMan assay can be further assayed using the 28S rDNA sequencing assay to both confirm the presence of schistosomes and contribute to their identification.

  18. Real-Time PCR and Sequencing Assays for Rapid Detection and Identification of Avian Schistosomes in Environmental Samples

    PubMed Central

    Mull, Bonnie J.; Brant, Sara V.; Loker, Eric S.; Collinson, Jeremy; Secor, W. Evan; Hill, Vincent R.

    2015-01-01

    Cercarial dermatitis, also known as swimmer's itch, is an allergenic skin reaction followed by intense itching caused by schistosome cercariae penetrating human skin. Cercarial dermatitis outbreaks occur globally and are frequently associated with freshwater lakes and are occasionally associated with marine or estuarine waters where birds reside year-round or where migratory birds reside. In this study, a broadly reactive TaqMan assay targeting 18S rRNA gene (ribosomal DNA [rDNA]) sequences that was based on a genetically diverse panel of schistosome isolates representing 13 genera and 20 species (the 18S rDNA TaqMan assay) was developed. A PCR assay was also developed to amplify a 28S rDNA region for subsequent sequencing to identify schistosomes. When applied to surface water samples seeded with Schistosoma mansoni cercariae, the 18S rDNA TaqMan assay enabled detection at a level of 5 S. mansoni cercariae in 100 liters of lake water. The 18S rDNA TaqMan and 28S rDNA PCR sequencing assays were also applied to 100-liter water samples collected from lakes in Nebraska and Wisconsin where there were reported dermatitis outbreaks. Avian schistosome DNA was detected in 11 of 34 lake water samples using the TaqMan assay. Further 28S rDNA sequence analysis of positive samples confirmed the presence of avian schistosome DNA and provided a preliminary identification of the avian schistosomes in 10 of the 11 samples. These data indicate that the broadly schistosome-reactive TaqMan assay can be effective for rapid screening of large-volume water samples for detection of avian schistosomes, thereby facilitating timely response actions to mitigate or prevent dermatitis outbreaks. Additionally, samples positive by the 18S rDNA TaqMan assay can be further assayed using the 28S rDNA sequencing assay to both confirm the presence of schistosomes and contribute to their identification. PMID:25862226

  19. A HRM Real-Time PCR Assay for Rapid and Specific Identification of the Emerging Pest Spotted-Wing Drosophila (Drosophila suzukii)

    PubMed Central

    Dhami, Manpreet K.; Kumarasinghe, Lalith

    2014-01-01

    Spotted wing drosophila (Drosophila suzukii) is an emerging pest that began spreading in 2008 and its distribution now includes 13 countries across two continents. Countries where it is established have reported significant economic losses of fresh produce, such as cherries due to this species of fly. At larval stages, it is impossible to identify due to its striking similarities with other cosmopolitan and harmless drosophilids. Molecular methods allow identification but the current technique of DNA barcoding is time consuming. We developed and validated a rapid, highly sensitive and specific assay based on real-time PCR and high resolution melt (HRM) analysis using EvaGreen DNA intercalating dye chemistry. Performance characteristics of this qualitative assay, validation and applicability in a New Zealand quarantine framework are discussed. Application of this robust and independently validated assay across the spectrum of key food production and border protection industries will allow us to reduce the further spread of this damaging species worldwide. PMID:24927410

  20. Identification and validation of reference genes for accurate normalization of real-time quantitative PCR data in kiwifruit.

    PubMed

    Ferradás, Yolanda; Rey, Laura; Martínez, Óscar; Rey, Manuel; González, Ma Victoria

    2016-05-01

    Identification and validation of reference genes are required for the normalization of qPCR data. We studied the expression stability produced by eight primer pairs amplifying four common genes used as references for normalization. Samples representing different tissues, organs and developmental stages in kiwifruit (Actinidia chinensis var. deliciosa (A. Chev.) A. Chev.) were used. A total of 117 kiwifruit samples were divided into five sample sets (mature leaves, axillary buds, stigmatic arms, fruit flesh and seeds). All samples were also analysed as a single set. The expression stability of the candidate primer pairs was tested using three algorithms (geNorm, NormFinder and BestKeeper). The minimum number of reference genes necessary for normalization was also determined. A unique primer pair was selected for amplifying the 18S rRNA gene. The primer pair selected for amplifying the ACTIN gene was different depending on the sample set. 18S 2 and ACT 2 were the candidate primer pairs selected for normalization in the three sample sets (mature leaves, fruit flesh and stigmatic arms). 18S 2 and ACT 3 were the primer pairs selected for normalization in axillary buds. No primer pair could be selected for use as the reference for the seed sample set. The analysis of all samples in a single set did not produce the selection of any stably expressing primer pair. Considering data previously reported in the literature, we validated the selected primer pairs amplifying the FLOWERING LOCUS T gene for use in the normalization of gene expression in kiwifruit.

  1. Identification and validation of reference genes for accurate normalization of real-time quantitative PCR data in kiwifruit.

    PubMed

    Ferradás, Yolanda; Rey, Laura; Martínez, Óscar; Rey, Manuel; González, Ma Victoria

    2016-05-01

    Identification and validation of reference genes are required for the normalization of qPCR data. We studied the expression stability produced by eight primer pairs amplifying four common genes used as references for normalization. Samples representing different tissues, organs and developmental stages in kiwifruit (Actinidia chinensis var. deliciosa (A. Chev.) A. Chev.) were used. A total of 117 kiwifruit samples were divided into five sample sets (mature leaves, axillary buds, stigmatic arms, fruit flesh and seeds). All samples were also analysed as a single set. The expression stability of the candidate primer pairs was tested using three algorithms (geNorm, NormFinder and BestKeeper). The minimum number of reference genes necessary for normalization was also determined. A unique primer pair was selected for amplifying the 18S rRNA gene. The primer pair selected for amplifying the ACTIN gene was different depending on the sample set. 18S 2 and ACT 2 were the candidate primer pairs selected for normalization in the three sample sets (mature leaves, fruit flesh and stigmatic arms). 18S 2 and ACT 3 were the primer pairs selected for normalization in axillary buds. No primer pair could be selected for use as the reference for the seed sample set. The analysis of all samples in a single set did not produce the selection of any stably expressing primer pair. Considering data previously reported in the literature, we validated the selected primer pairs amplifying the FLOWERING LOCUS T gene for use in the normalization of gene expression in kiwifruit. PMID:26897117

  2. Multicentric Evaluation of a New Real-Time PCR Assay for Quantification of Cryptosporidium spp. and Identification of Cryptosporidium parvum and Cryptosporidium hominis

    PubMed Central

    Chapey, E.; Dutoit, E.; Guyot, K.; Hasseine, L.; Jeddi, F.; Menotti, J.; Paraud, C.; Pomares, C.; Rabodonirina, M.; Rieux, A.; Derouin, F.

    2013-01-01

    Cryptosporidium is a protozoan parasite responsible for gastroenteritis, especially in immunocompromised patients. Laboratory diagnosis of cryptosporidiosis relies on microscopy, antigen detection, and nucleic acid detection and analysis. Among the numerous molecular targets available, the 18S rRNA gene displays the best sensitivity and sequence variations between species and can be used for molecular typing assays. This paper presents a new real-time PCR assay for the detection and quantification of all Cryptosporidium species associated with the identification of Cryptosporidium hominis and Cryptosporidium parvum. The sensitivity and specificity of this new PCR assay were assessed on a multicentric basis, using well-characterized Cryptosporidium-positive and -negative human stool samples, and the efficiencies of nine extraction methods were comparatively assessed using Cryptosporidium-seeded stool samples and phosphate-buffered saline samples. A comparison of extraction yields showed that the most efficient extraction method was the Boom technique in association with mechanical grinding, and column extraction showed higher binding capacity than extraction methods based on magnetic silica. Our PCR assay was able to quantify at least 300 oocysts per gram of stool. Satisfactory reproducibility between laboratories was observed. The two main species causing human disease, Cryptosporidium hominis and Cryptosporidium parvum, were identified using a duplex real-time PCR assay with specific TaqMan minor-groove-binding ligand (MGB) probes for the same amplicon. To conclude, this one-step quantitative PCR is well suited to the routine diagnosis of cryptosporidiosis since practical conditions, including DNA extraction, quantification using well-defined standards, and identification of the two main species infecting humans, have been positively assessed. PMID:23720792

  3. Real-Time Quantitative Broad-Range PCR Assay for Detection of the 16S rRNA Gene Followed by Sequencing for Species Identification

    PubMed Central

    Zucol, Franziska; Ammann, Roland A.; Berger, Christoph; Aebi, Christoph; Altwegg, Martin; Niggli, Felix K.; Nadal, David

    2006-01-01

    Here we determined the analytical sensitivities of broad-range real-time PCR-based assays employing one of three different genomic DNA extraction protocols in combination with one of three different primer pairs targeting the 16S rRNA gene to detect a panel of 22 bacterial species. DNA extraction protocol III, using lysozyme, lysostaphin, and proteinase K, followed by PCR with the primer pair Bak11W/Bak2, giving amplicons of 796 bp in length, showed the best overall sensitivity, detecting DNA of 82% of the strains investigated at concentrations of ≤102 CFU in water per reaction. DNA extraction protocols I and II, using less enzyme treatment, combined with other primer pairs giving shorter amplicons of 466 bp and 342 or 346 bp, respectively, were slightly more sensitive for the detection of gram-negative but less sensitive for the detection of gram-positive bacteria. The obstacle of detecting background DNA in blood samples spiked with bacteria was circumvented by introducing a broad-range hybridization probe, and this preserved the minimal detection limits observed in samples devoid of blood. Finally, sequencing of the amplicons generated using the primer pair Bak11W/Bak2 allowed species identification of the detected bacterial DNA. Thus, broad-spectrum PCR targeting the 16S rRNA gene in the quantitative real-time format can achieve an analytical sensitivity of 1 to 10 CFU per reaction in water, avoid detection of background DNA with the introduction of a broad-range probe, and generate amplicons that allow species identification of the detected bacterial DNA by sequencing. These prerequisites are important for its application to blood-containing patient samples. PMID:16891488

  4. Portable, real-time alloy identification of metallic wear debris from machinery lubrication systems: laser-induced breakdown spectroscopy versus x-ray fluorescence

    NASA Astrophysics Data System (ADS)

    Suresh, Pooja

    2014-05-01

    Alloy identification of oil-borne wear debris captured on chip detectors, filters and magnetic plugs allows the machinery maintainer to assess the health of the engine or gearbox and identify specific component damage. Today, such identification can be achieved in real time using portable, at-line laser-induced breakdown spectroscopy (LIBS) and Xray fluorescence (XRF) instruments. Both techniques can be utilized in various industries including aviation, marine, railways, heavy diesel and other industrial machinery with, however, some substantial differences in application and instrument performance. In this work, the performances of a LIBS and an XRF instrument are compared based on measurements of a wide range of typical aerospace alloys including steels, titanium, aluminum and nickel alloys. Measurement results were analyzed with a staged correlation technique specifically developed for the purposes of this study - identifying the particle alloy composition using a pre-recorded library of spectral signatures. The analysis is performed in two stages: first, the base element of the alloy is determined by correlation with the stored elemental spectra and then, the alloy is identified by matching the particle's spectral signature using parametric correlation against the stored spectra of all alloys that have the same base element. The correlation analysis has achieved highly repeatable discrimination between alloys of similar composition. Portable LIBS demonstrates higher detection accuracy and better identification of alloys comprising lighter elements as compared to that of the portable XRF system, and reveals a significant reduction in the analysis time over XRF.

  5. SRIdent: A novel pipeline for real-time identification of species from high-throughput sequencing reads in Metagenomics and clinical diagnostic assays.

    PubMed

    Karimi, Ramin; Hajdu, Andras

    2015-01-01

    New advances in rapid sequencing of large amounts of DNA have brought a great potential for the study of complex communities of microorganisms. One of the challenging problems is rapid identification of species from sequenced reads. Delays in the identification of pathogens are a barrier to the early diagnosis and proper treatment of infectious diseases. In this paper we proposed SRIdent (Short Read Identifier), an effective pipeline for real-time identification of species from high-throughput sequencing reads in Metagenomics and clinical diagnostic assays. This pipeline is based on generating k-mers from the short reads and searching the existence of DNA signatures in the Reads k-mers, by using Apache Hive data-warehousing. RkmerG (Read k-mers Generator) is a software program presented in this paper, for producing k-mers of the short reads, in order to use in the pipeline. The purpose of this study is to identify the species in a sample, directly from the reads without assembling and alignment.

  6. Real-time radiography

    SciTech Connect

    Bossi, R.H.; Oien, C.T.

    1981-02-26

    Real-time radiography is used for imaging both dynamic events and static objects. Fluorescent screens play an important role in converting radiation to light, which is then observed directly or intensified and detected. The radiographic parameters for real-time radiography are similar to conventional film radiography with special emphasis on statistics and magnification. Direct-viewing fluoroscopy uses the human eye as a detector of fluorescent screen light or the light from an intensifier. Remote-viewing systems replace the human observer with a television camera. The remote-viewing systems have many advantages over the direct-viewing conditions such as safety, image enhancement, and the capability to produce permanent records. This report reviews real-time imaging system parameters and components.

  7. Evaluation of a novel real-time PCR test based on the ssrA gene for the identification of group B streptococci in vaginal swabs

    PubMed Central

    2009-01-01

    Background Despite the implementation of prevention guidelines, early-onset group B streptococci (GBS) disease remains a cause of neonatal morbidity and mortality worldwide. Strategies to identify women who are at risk of transmitting GBS to their infant and the administration of intrapartum antibiotics have greatly reduced the incidence of neonatal GBS disease. However, there is a requirement for a rapid diagnostic test for GBS that can be carried out in a labour ward setting especially for women whose GBS colonisation status is unknown at the time of delivery. We report the design and evaluation of a real-time PCR test (RiboSEQ GBS test) for the identification of GBS in vaginal swabs from pregnant women. Methods The qualitative real-time PCR RiboSEQ GBS test was designed based on the bacterial ssrA gene and incorporates a competitive internal standard control. The analytical sensitivity of the test was established using crude lysate extracted from serial dilutions of overnight GBS culture using the IDI Lysis kit. Specificity studies were performed using DNA prepared from a panel of GBS strains, related streptococci and other species found in the genital tract environment. The RiboSEQ GBS test was evaluated on 159 vaginal swabs from pregnant women and compared with the GeneOhm™ StrepB Assay and culture for the identification of GBS. Results The RiboSEQ GBS test is specific and has an analytical sensitivity of 1-10 cell equivalents. The RiboSEQ GBS test was 96.4% sensitive and 95.8% specific compared to "gold standard" culture for the identification of GBS in vaginal swabs from pregnant women. In this study, the RiboSEQ GBS test performed slightly better than the commercial BD GeneOhm™ StrepB Assay which gave a sensitivity of 94.6% and a specificity of 89.6% compared to culture. Conclusion The RiboSEQ GBS test is a valuable method for the rapid, sensitive and specific detection of GBS in pregnant women. This study also validates the ssrA gene as a suitable and

  8. Direct identification and discernment of Mycobacterium avium and Mycobacterium intracellulare using a real-time RNA isothermal amplification and detection method.

    PubMed

    Cui, Zhenling; Li, Yuanyuan; Cheng, Song; Yang, Hua; Lu, Junmei; Zhu, Honglei; Hu, Zhongyi

    2015-12-01

    The purpose of this work was to establish a real-time simultaneous amplification and testing method for identification and discernment of Mycobacterium avium and Mycobacterium intracellulare (SAT-MAC assay) and to evaluate the efficiency with which this method can detect isolated strains and clinical sputum specimens. The specific 16S rRNA sequences of M. avium and M. intracellulare were used as targets to design RNA probes and a reverse transcription primer containing T7 promoter. RNA isothermal amplification and real-time fluorescence detection were performed at 42 °C. SAT-MAC assay, culture tests on Lowenstein-Jensen (L-J) culture medium and PCR-sequencing were used to test the clinical isolated strains and sputum specimens. The limit of detection (LOD) of M. avium and M. intracellulare by SAT-MAC was found to be 30 CFU/mL and 20 CFU/mL. SAT-MAC showed high specificity in 21 species of mycobacteria standard strains and 5 species of non-mycobacteria bacteria. Using PCR-sequencing as the reference method, both rates of SAT-MAC assay for identifying M. avium and M. intracellulare from clinical isolates were 100% (259/259). Consistent with the results of L-J culture combined PCR-sequencing, the coincidence rate of SAT-MAC assay in clinical sputum specimens was 100% (369/369) for M. avium and 99.19% (366/369) for Mycobacterium intracellular. The SAT-MAC assay can identify and distinguish M. avium and M. intracellulare rapidly and accurately. It may be suitable for use in clinical microbiology laboratories.

  9. Development of a real-time RT-PCR assay for the simultaneous identification, quantitation and differentiation of avian metapneumovirus subtypes A and B.

    PubMed

    Cecchinato, Mattia; Lupini, Caterina; Munoz Pogoreltseva, Olga Svetlana; Listorti, Valeria; Mondin, Alessandra; Drigo, Michele; Catelli, Elena

    2013-01-01

    In recent years, special attention has been paid to real-time polymerase chain reaction (PCR) for avian metapneumovirus (AMPV) diagnosis, due to its numerous advantages over classical PCR. A new multiplex quantitative real-time reverse transcription-PCR (qRT-PCR) with molecular beacon probe assay, designed to target the SH gene, was developed. The test was evaluated in terms of specificity, sensitivity and repeatability, and compared with conventional RT nested-PCR based on the G gene. All of the AMPV subtype A and B strains tested were amplified and specifically detected while no amplification occurred with other non-target bird respiratory pathogens. The detection limit of the assay was 10(-0.41) median infectious dose/ml and 10(1.15) median infectious dose/ml when the AMPV-B strain IT/Ty/B/Vr240/87 and the AMPV-A strain IT/Ty/A/259-01/03 were used, respectively, as templates. In all cases, the amplification efficiency was approximately 2 and the error values were <0.2. Standard curves, generated either using the serial dilution of an RNA suspension or RNA extracted from the serial dilution of titrated viral suspensions as templates, exhibited good linearity (R (2)>0.9375) between crossing point values and virus quantities, making the assay herein designed reliable for quantification. When the newly developed qRT-PCR was compared with a conventional RT nested-PCR, it showed greater sensitivity with RNA extracted from both positive controls and from experimentally infected birds. This assay can be effectively used for the detection, identification, differentiation and quantitation of AMPV subtype A or subtype B to assist in disease diagnosis and to carry out rapid surveillance with high levels of sensitivity and specificity.

  10. Development and testing of real-time PCR assays for determining fecal loading and source identification (cattle, human, etc.) in surface water and groundwater

    NASA Astrophysics Data System (ADS)

    McKay, L. D.; Layton, A.; Gentry, R.

    2004-12-01

    A multi-disciplinary group of researchers at the University of Tennessee is developing and testing a series of microbial assay methods based on real-time PCR to detect fecal bacterial concentrations and host sources in water samples. Real-time PCR is an enumeration technique based on the unique and conserved nucleic acid sequences present in all organisms. The first research task was development of an assay (AllBac) to detect total amount of Bacteroides, which represents up to 30 percent of fecal mass. Subsequent assays were developed to detect Bacteroides from cattle (BoBac) and humans (HuBac) using 16sRNA genes based on DNA sequences in the national GenBank, as well as sequences from local fecal samples. The assays potentially have significant advantages over conventional bacterial source tracking methods because: 1. unlike traditional enumeration methods, they do not require bacterial cultivation; 2. there are no known non-fecal sources of Bacteroides; 3. the assays are quantitative with results for total concentration and for each species expressed in mg/l; and 4. they show little regional variation within host species, meaning that they do not require development of extensive local gene libraries. The AllBac and BoBac assays have been used in a study of fecal contamination in a small rural watershed (Stock Creek) near Knoxville, TN, and have proven useful in identification of areas where cattle represent a significant fecal input and in development of BMPs. It is expected that these types of assays (and future assays for birds, hogs, etc.) could have broad applications in monitoring fecal impacts from Animal Feeding Operations, as well as from wildlife and human sources.

  11. Real-time sonography

    SciTech Connect

    Fleischey, A.C.; James, A.E. Jr.

    1984-01-01

    This textbook acquaints the reader with normal and pathologic anatomy as depicted on dynamic or real-time scanning. Chapters are organized by specialty, such as abdominal, urologic, or pediatric. The text is illustrated with still-frame images and line drawings. The drawings show important areas of interest and provide graphic notation as to where and in what orientation the scan was obtained.

  12. Real-time trace detection and identification of chemical warfare agent simulants using recent advances in proton transfer reaction time-of-flight mass spectrometry.

    PubMed

    Petersson, Fredrik; Sulzer, Philipp; Mayhew, Chris A; Watts, Peter; Jordan, Alfons; Märk, Lukas; Märk, Tilmann D

    2009-12-01

    This work demonstrates for the first time the potential of using recent developments in proton transfer reaction mass spectrometry for the rapid detection and identification of chemical warfare agents (CWAs) in real-time. A high-resolution (m/Deltam up to 8000) and high-sensitivity (approximately 50 cps/ppbv) proton transfer reaction time-of-flight mass spectrometer (PTR-TOF 8000 from Ionicon Analytik GmBH) has been successfully used to detect a number of CWA simulants at room temperature; namely dimethyl methylphosphonate, diethyl methylphosphonate, diisopropyl methylphosphonate, dipropylene glycol monomethyl ether and 2-chloroethyl ethyl sulfide. Importantly, we demonstrate in this paper the potential to identify CWAs with a high level of confidence in complex chemical environments, where multiple threat agents and interferents could also be present in trace amounts, thereby reducing the risk of false positives. Instantaneous detection and identification of trace quantities of chemical threats using proton transfer reaction mass spectrometry could form the basis for a timely warning system capability with greater precision and accuracy than is currently provided by existing analytical technologies.

  13. Real-Time Identification of Smoldering and Flaming Combustion Phases in Forest Using a Wireless Sensor Network-Based Multi-Sensor System and Artificial Neural Network

    PubMed Central

    Yan, Xiaofei; Cheng, Hong; Zhao, Yandong; Yu, Wenhua; Huang, Huan; Zheng, Xiaoliang

    2016-01-01

    Diverse sensing techniques have been developed and combined with machine learning method for forest fire detection, but none of them referred to identifying smoldering and flaming combustion phases. This study attempts to real-time identify different combustion phases using a developed wireless sensor network (WSN)-based multi-sensor system and artificial neural network (ANN). Sensors (CO, CO2, smoke, air temperature and relative humidity) were integrated into one node of WSN. An experiment was conducted using burning materials from residual of forest to test responses of each node under no, smoldering-dominated and flaming-dominated combustion conditions. The results showed that the five sensors have reasonable responses to artificial forest fire. To reduce cost of the nodes, smoke, CO2 and temperature sensors were chiefly selected through correlation analysis. For achieving higher identification rate, an ANN model was built and trained with inputs of four sensor groups: smoke; smoke and CO2; smoke and temperature; smoke, CO2 and temperature. The model test results showed that multi-sensor input yielded higher predicting accuracy (≥82.5%) than single-sensor input (50.9%–92.5%). Based on these, it is possible to reduce the cost with a relatively high fire identification rate and potential application of the system can be tested in future under real forest condition. PMID:27527175

  14. Development and validation of a multiplex real-time PCR method to simultaneously detect 47 targets for the identification of genetically modified organisms.

    PubMed

    Cottenet, Geoffrey; Blancpain, Carine; Sonnard, Véronique; Chuah, Poh Fong

    2013-08-01

    Considering the increase of the total cultivated land area dedicated to genetically modified organisms (GMO), the consumers' perception toward GMO and the need to comply with various local GMO legislations, efficient and accurate analytical methods are needed for their detection and identification. Considered as the gold standard for GMO analysis, the real-time polymerase chain reaction (RTi-PCR) technology was optimised to produce a high-throughput GMO screening method. Based on simultaneous 24 multiplex RTi-PCR running on a ready-to-use 384-well plate, this new procedure allows the detection and identification of 47 targets on seven samples in duplicate. To comply with GMO analytical quality requirements, a negative and a positive control were analysed in parallel. In addition, an internal positive control was also included in each reaction well for the detection of potential PCR inhibition. Tested on non-GM materials, on different GM events and on proficiency test samples, the method offered high specificity and sensitivity with an absolute limit of detection between 1 and 16 copies depending on the target. Easy to use, fast and cost efficient, this multiplex approach fits the purpose of GMO testing laboratories.

  15. Real-Time Identification of Smoldering and Flaming Combustion Phases in Forest Using a Wireless Sensor Network-Based Multi-Sensor System and Artificial Neural Network.

    PubMed

    Yan, Xiaofei; Cheng, Hong; Zhao, Yandong; Yu, Wenhua; Huang, Huan; Zheng, Xiaoliang

    2016-01-01

    Diverse sensing techniques have been developed and combined with machine learning method for forest fire detection, but none of them referred to identifying smoldering and flaming combustion phases. This study attempts to real-time identify different combustion phases using a developed wireless sensor network (WSN)-based multi-sensor system and artificial neural network (ANN). Sensors (CO, CO₂, smoke, air temperature and relative humidity) were integrated into one node of WSN. An experiment was conducted using burning materials from residual of forest to test responses of each node under no, smoldering-dominated and flaming-dominated combustion conditions. The results showed that the five sensors have reasonable responses to artificial forest fire. To reduce cost of the nodes, smoke, CO₂ and temperature sensors were chiefly selected through correlation analysis. For achieving higher identification rate, an ANN model was built and trained with inputs of four sensor groups: smoke; smoke and CO₂; smoke and temperature; smoke, CO₂ and temperature. The model test results showed that multi-sensor input yielded higher predicting accuracy (≥82.5%) than single-sensor input (50.9%-92.5%). Based on these, it is possible to reduce the cost with a relatively high fire identification rate and potential application of the system can be tested in future under real forest condition. PMID:27527175

  16. DNA barcoding, species-specific PCR and real-time PCR techniques for the identification of six Tribolium pests of stored products

    PubMed Central

    Zhang, Tao; Wang, Yi-Jiao; Guo, Wei; Luo, Dan; Wu, Yi; Kučerová, Zuzana; Stejskal, Václav; Opit, George; Cao, Yang; Li, Fu-Jun; Li, Zhi-Hong

    2016-01-01

    Flour beetles of the genus Tribolium Macleay (Coleoptera: Tenebrionidae) are important stored product pests in China and worldwide. They are often found or are intercepted in grain depots, flour mills, and entry-exit ports, etc. Traditionally, Tribolium species are identified according to the morphological characteristics of the adult. However, it is almost impossible to rapidly identify adult fragments and non-adult stages based on external morphological characteristics. Molecular techniques for the rapid and accurate identification of Tribolium species are required, particularly for pest monitoring and the quarantine of stored products pests. Here, we establish DNA barcoding, species-specific PCR, and real-time PCR techniques for the identification of six stored-product pest Tribolium species including T. castaneum, T. confusum, T. destructor, T. madens, T. freemani and T. brevicornis. We detected the mitochondrial DNA cytochrome oxidase subunit I (COI) barcodes for Tribolium from 18 geographic populations and 101 individuals, built a Tribolium DNA barcode library, and designed species-specific primers and TaqMan probes for the above six Tribolium species. The three techniques were applied to identify Tribolium collected from stored samples and samples captured from quarantine ports. The results demonstrated that three techniques were all able to identify the six species of Tribolium both rapidly and accurately. PMID:27352804

  17. Direct analysis in real time - high resolution mass spectrometry (DART-HRMS): a high throughput strategy for identification and quantification of anabolic steroid esters.

    PubMed

    Doué, Mickael; Dervilly-Pinel, Gaud; Pouponneau, Karinne; Monteau, Fabrice; Le Bizec, Bruno

    2015-07-01

    High throughput screening is essential for doping, forensic, and food safety laboratories. While hyphenated chromatography-mass spectrometry (MS) remains the approach of choice, recent ambient MS techniques, such as direct analysis in real time (DART), offer more rapid and more versatile strategies and thus gain in popularity. In this study, the potential of DART hyphenated with Orbitrap-MS for fast identification and quantification of 21 anabolic steroid esters has been evaluated. Direct analysis in high resolution scan mode allowed steroid esters screening by accurate mass measurement (Resolution = 60 000 and mass error < 3 ppm). Steroid esters identification was further supported by collision-induced dissociation (CID) experiments through the generation of two additional ions. Moreover, the use of labelled internal standards allowed quantitative data to be recovered based on isotopic dilution approach. Linearity (R(2)  > 0.99), dynamic range (from 1 to 1000 ng mL(-1) ), bias (<10%), sensitivity (1 ng mL(-1) ), repeatability and reproducibility (RSD < 20%) were evaluated as similar to those obtained with hyphenated chromatography-mass spectrometry techniques. This innovative high throughput approach was successfully applied for the characterization of oily commercial preparations, and thus fits the needs of the competent authorities in the fight against forbidden or counterfeited substances.

  18. Device-Independent Certification of Entangled Measurements

    NASA Astrophysics Data System (ADS)

    Rabelo, Rafael; Ho, Melvyn; Cavalcanti, Daniel; Brunner, Nicolas; Scarani, Valerio

    2011-07-01

    We present a device-independent protocol to test if a given black-box measurement device is entangled, that is, has entangled eigenstates. Our scheme involves three parties and is inspired by entanglement swapping; the test uses the Clauser-Horne-Shimony-Holt Bell inequality, checked between each pair of parties. In the case where all particles are qubits, we characterize quantitatively the deviation of the measurement device from a perfect Bell-state measurement.

  19. Pragmatic Approach to Device-Independent Color

    NASA Technical Reports Server (NTRS)

    Brandt, R. D.; Capraro, K. S.

    1995-01-01

    JPL has been producing images of planetary bodies for over 30 years. The results of an effort to implement device-independent color on three types of devices are described. The goal is to produce near the same eye-brain response when the observer views the image produced by each device under the correct lighting conditions. The procedure used to calibrate and obtain each device profile is described.

  20. Design of Multiplexed Detection Assays for Identification of Avian Influenza A Virus Subtypes Pathogenic to Humans by SmartCycler Real-Time Reverse Transcription-PCR ▿

    PubMed Central

    Wang, Wei; Ren, Peijun; Mardi, Sek; Hou, Lili; Tsai, Cheguo; Chan, Kwok Hung; Cheng, Peter; Sheng, Jun; Buchy, Philippe; Sun, Bing; Toyoda, Tetsuya; Lim, Wilina; Peiris, J. S. Malik; Zhou, Paul; Deubel, Vincent

    2009-01-01

    Influenza A virus (IAV) epidemics are the result of human-to-human or poultry-to-human transmission. Tracking seasonal outbreaks of IAV and other avian influenza virus (AIV) subtypes that can infect humans, aquatic and migratory birds, poultry, and pigs is essential for epidemiological surveillance and outbreak alerts. In this study, we performed four real-time reverse transcription-PCR (rRT-PCR) assays for identification of the IAV M and hemagglutinin (HA) genes from six known AIVs infecting pigs, birds, and humans. IAV M1 gene-positive samples tested by single-step rRT-PCR and a fluorogenic Sybr green I detection system were further processed for H5 subtype identification by using two-primer-set multiplex and Sybr green I rRT-PCR assays. H5 subtype-negative samples were then tested with either a TaqMan assay for subtypes H1 and H3 or a TaqMan assay for subtypes H2, H7, and H9 and a beacon multiplex rRT-PCR identification assay. The four-tube strategy was able to detect 10 RNA copies of the HA genes of subtypes H1, H2, H3, H5, and H7 and 100 RNA copies of the HA gene of subtype H9. At least six H5 clades of H5N1 viruses isolated in Southeast Asia and China were detected by that test. Using rRT-PCR assays for the M1 and HA genes in 202 nasopharyngeal swab specimens from children with acute respiratory infections, we identified a total of 39 samples positive for the IAV M1 gene and subtypes H1 and H3. When performed with a portable SmartCycler instrument, the assays offer an efficient, flexible, and reliable platform for investigations of IAV and AIV in remote hospitals and in the field. PMID:18971359

  1. design of multiplexed detection assays for identification of avian influenza a virus subtypes pathogenic to humans by SmartCycler real-time reverse transcription-PCR.

    PubMed

    Wang, Wei; Ren, Peijun; Mardi, Sek; Hou, Lili; Tsai, Cheguo; Chan, Kwok Hung; Cheng, Peter; Sheng, Jun; Buchy, Philippe; Sun, Bing; Toyoda, Tetsuya; Lim, Wilina; Peiris, J S Malik; Zhou, Paul; Deubel, Vincent

    2009-01-01

    Influenza A virus (IAV) epidemics are the result of human-to-human or poultry-to-human transmission. Tracking seasonal outbreaks of IAV and other avian influenza virus (AIV) subtypes that can infect humans, aquatic and migratory birds, poultry, and pigs is essential for epidemiological surveillance and outbreak alerts. In this study, we performed four real-time reverse transcription-PCR (rRT-PCR) assays for identification of the IAV M and hemagglutinin (HA) genes from six known AIVs infecting pigs, birds, and humans. IAV M1 gene-positive samples tested by single-step rRT-PCR and a fluorogenic Sybr green I detection system were further processed for H5 subtype identification by using two-primer-set multiplex and Sybr green I rRT-PCR assays. H5 subtype-negative samples were then tested with either a TaqMan assay for subtypes H1 and H3 or a TaqMan assay for subtypes H2, H7, and H9 and a beacon multiplex rRT-PCR identification assay. The four-tube strategy was able to detect 10 RNA copies of the HA genes of subtypes H1, H2, H3, H5, and H7 and 100 RNA copies of the HA gene of subtype H9. At least six H5 clades of H5N1 viruses isolated in Southeast Asia and China were detected by that test. Using rRT-PCR assays for the M1 and HA genes in 202 nasopharyngeal swab specimens from children with acute respiratory infections, we identified a total of 39 samples positive for the IAV M1 gene and subtypes H1 and H3. When performed with a portable SmartCycler instrument, the assays offer an efficient, flexible, and reliable platform for investigations of IAV and AIV in remote hospitals and in the field.

  2. Real-Time PCR

    NASA Astrophysics Data System (ADS)

    Evrard, A.; Boulle, N.; Lutfalla, G. S.

    Over the past few years there has been a considerable development of DNA amplification by polymerase chain reaction (PCR), and real-time PCR has now superseded conventional PCR techniques in many areas, e.g., the quantification of nucleic acids and genotyping. This new approach is based on the detection and quantification of a fluorescent signal proportional to the amount of amplicons generated by PCR. Real-time detection is achieved by coupling a thermocycler with a fluorimeter. This chapter discusses the general principles of quantitative real-time PCR, the different steps involved in implementing the technique, and some examples of applications in medicine. The polymerase chain reaction (PCR) provides a way of obtaining a large number of copies of a double-stranded DNA fragment of known sequence. This DNA amplification technique, developed in 1985 by K. Mullis (Cetus Corporation), saw a spectacular development over the space of a few years, revolutionising the methods used up to then in molecular biology. Indeed, PCR has many applications, such as the detection of small amounts of DNA, cloning, and quantitative analysis (assaying), each of which will be discussed further below.

  3. Real-time polymerase chain reaction method for detection of toxigenic Clostridium difficile from stools and presumptive identification of NAP1 clone.

    PubMed

    Jayaratne, Padman A; Monkman, Lori; Broukhanski, George; Pillai, Dillan R; Lee, Christine

    2013-02-01

    This study describes the development of a cost-effective, multiplex real-time polymerase chain reaction (RTPCR) method for detection of toxigenic Clostridium difficile from stools and presumptive identification of the NAP-1 strain. The diagnostic value of the new method is for the detection of toxigenic C. difficile which has the following performance characteristics: 99.8% specificity, 95.1% sensitivity, 97.5% positive predictive value, and 99.5% negative predictive value. Examination of 24 specimens presumptively identified as NAP1 strain by RTPCR with Pulsed-field gel electrophoresis performed on C. difficile isolated from those specimens showed 100% agreement. This RTPCR showed equivalent test performance characteristics as the 2 commercially available assays which were evaluated. The estimated cost per test is CAD$9.50 and which is significantly less than the commercial assays. The average turnaround time from setup to detection is 3.5 h. The RTPCR method described here is a cost-effective and highly sensitive test which can be implemented in a clinical laboratory to assist clinicians in establishing the diagnosis of C. difficile infection and indirectly determine the presence of the hypervirulent epidemic binary toxin (BI)/NAP 1 strain for prompt infection control interventions. PMID:23182075

  4. Real-time PCR Tests in Dutch Exotic Mosquito Surveys; Implementation of Aedes aegypti and Aedes albopictus Identification Tests, and the Development of Tests for the Identification of Aedes atropalpus and Aedes japonicus japonicus (Diptera: Culicidae).

    PubMed

    van de Vossenberg, B T L H; Ibáñez-Justicia, A; Metz-Verschure, E; van Veen, E J; Bruil-Dieters, M L; Scholte, E J

    2015-05-01

    Since 2009, The Netherlands Food and Consumer Product Safety Authority carries out surveys focusing on, amongst others, the presence of invasive mosquito species (IMS). Special attention is given to exotic container-breeding Aedes species Aedes aegypti (L.), Aedes albopictus (Skuse), Aedes atropalpus (Coquillett), and Aedes japonicus japonicus (Theobald). This study describes the implementation of real-time PCR tests described by Hill et al. (2008) for the identification of Ae. aegypti and Ae. albopictus, and the development of two novel real-time PCR tests for the identification of Ae. atropalpus and Ae. j. japonicus. Initial test showed that optimization of elements of the Ae. aegypti and Ae. albopictus tests was needed. Method validation tests were performed to determine if the implemented and newly developed tests are fit for routine diagnostics. Performance criteria of analytical sensitivity, analytical specificity, selectivity, repeatability, and reproducibility were determined. In addition, experiments were performed to determine the influence of environmental conditions on the usability of DNA extracted from mosquito specimens trapped in BG-Sentinel traps. The real-time PCR tests were demonstrated to be sensitive, specific, repeatable, reproducible, and are less prone to false negative results compared to partial cytochrome c oxidase I gene sequencing owing to the DNA fragmentation caused by environmental influences. PMID:26334807

  5. Real-time PCR Tests in Dutch Exotic Mosquito Surveys; Implementation of Aedes aegypti and Aedes albopictus Identification Tests, and the Development of Tests for the Identification of Aedes atropalpus and Aedes japonicus japonicus (Diptera: Culicidae).

    PubMed

    van de Vossenberg, B T L H; Ibáñez-Justicia, A; Metz-Verschure, E; van Veen, E J; Bruil-Dieters, M L; Scholte, E J

    2015-05-01

    Since 2009, The Netherlands Food and Consumer Product Safety Authority carries out surveys focusing on, amongst others, the presence of invasive mosquito species (IMS). Special attention is given to exotic container-breeding Aedes species Aedes aegypti (L.), Aedes albopictus (Skuse), Aedes atropalpus (Coquillett), and Aedes japonicus japonicus (Theobald). This study describes the implementation of real-time PCR tests described by Hill et al. (2008) for the identification of Ae. aegypti and Ae. albopictus, and the development of two novel real-time PCR tests for the identification of Ae. atropalpus and Ae. j. japonicus. Initial test showed that optimization of elements of the Ae. aegypti and Ae. albopictus tests was needed. Method validation tests were performed to determine if the implemented and newly developed tests are fit for routine diagnostics. Performance criteria of analytical sensitivity, analytical specificity, selectivity, repeatability, and reproducibility were determined. In addition, experiments were performed to determine the influence of environmental conditions on the usability of DNA extracted from mosquito specimens trapped in BG-Sentinel traps. The real-time PCR tests were demonstrated to be sensitive, specific, repeatable, reproducible, and are less prone to false negative results compared to partial cytochrome c oxidase I gene sequencing owing to the DNA fragmentation caused by environmental influences.

  6. Development and validation of a rotor-gene real-time PCR assay for detection, identification, and quantification of Chlamydia trachomatis in a single reaction.

    PubMed

    Jalal, Hamid; Stephen, Hannah; Curran, Martin D; Burton, Janet; Bradley, Michelle; Carne, Christopher

    2006-01-01

    A multitarget real-time PCR (MRT-PCR) for detection of Chlamydia trachomatis DNA was developed and validated. There were three targets for amplification in a single reaction: the cryptic plasmid (CP), the major outer membrane protein (MOMP) gene, and an internal control. The assay had the following characteristics: (i) detection and confirmation of the presence of C. trachomatis DNA in a single reaction, (ii) detection of all genovars of C. trachomatis without any cross-reactivity with pathogenic bacteria or commensal organisms of the oropharynx and genital tract, (iii) a 95% probability of detection with three copies of MOMP and one copy of CP per reaction mixture, (iv) identification of the inhibition of amplification, (v) a quantitative dynamic range of 25 to 250,000 genome copies per reaction mixture, (vi) high intra- and interassay reproducibilities, and (vii) correct identification of all samples in the validation panel. There were 146 COBAS Amplicor PCR (Amplicor PCR)-positive samples and 122 Amplicor PCR-negative samples in the panel. MRT-PCR detected CP DNA alone in 6 (4%) Amplicor PCR-positive samples and both CP and MOMP DNAs in 140 (96%) of 146 Amplicor PCR-positive samples. The quantity of MOMP DNA in 95 (68%) of 140 samples was within the dynamic range of the assay. The median C. trachomatis load in these samples was 321 genome copies per reaction mixture (range, 26 to 40,137 genome copies per reaction mixture). Due to the inclusion of two different C. trachomatis-specific targets, the assay confirmed 259 (97%) of 268 results in a single reaction. This assay could be used in the qualitative format for the routine detection of C. trachomatis and in the quantitative format for study of the pathogenesis of C. trachomatis-associated diseases. The assay demonstrated the potential to eliminate the need for confirmatory testing in almost all samples, thus reducing the turnaround time and the workload.

  7. Real time Faraday spectrometer

    DOEpatents

    Smith, Jr., Tommy E.; Struve, Kenneth W.; Colella, Nicholas J.

    1991-01-01

    This invention uses a dipole magnet to bend the path of a charged particle beam. As the deflected particles exit the magnet, they are spatially dispersed in the bend-plane of the magnet according to their respective momenta and pass to a plurality of chambers having Faraday probes positioned therein. Both the current and energy distribution of the particles is then determined by the non-intersecting Faraday probes located along the chambers. The Faraday probes are magnetically isolated from each other by thin metal walls of the chambers, effectively providing real time current-versus-energy particle measurements.

  8. Real time SAR processing

    NASA Technical Reports Server (NTRS)

    Premkumar, A. B.; Purviance, J. E.

    1990-01-01

    A simplified model for the SAR imaging problem is presented. The model is based on the geometry of the SAR system. Using this model an expression for the entire phase history of the received SAR signal is formulated. From the phase history, it is shown that the range and the azimuth coordinates for a point target image can be obtained by processing the phase information during the intrapulse and interpulse periods respectively. An architecture for a VLSI implementation for the SAR signal processor is presented which generates images in real time. The architecture uses a small number of chips, a new correlation processor, and an efficient azimuth correlation process.

  9. Real-Time Revolution?

    PubMed

    Berlin, Joey

    2016-03-01

    Austin Regional Clinic (ARC) physicians and officials know patient feedback is important, but getting patients to provide it can be a challenge. A pilot program of a new, real-time feedback system provided ARC patients a high-tech convenience previous attempts lacked and produced participation numbers dwarfing those past efforts. ARC's initial results with the system, in which patients answer five to seven questions on a computer tablet and can leave free-text comments, were so successful the clinic is already planning to expand it to all of its locations by the end of June.

  10. Experimental measurement-device-independent entanglement detection.

    PubMed

    Nawareg, Mohamed; Muhammad, Sadiq; Amselem, Elias; Bourennane, Mohamed

    2015-01-01

    Entanglement is one of the most puzzling features of quantum theory and of great importance for the new field of quantum information. The determination whether a given state is entangled or not is one of the most challenging open problems of the field. Here we report on the experimental demonstration of measurement-device-independent (MDI) entanglement detection using witness method for general two qubits photon polarization systems. In the MDI settings, there is no requirement to assume perfect implementations or neither to trust the measurement devices. This experimental demonstration can be generalized for the investigation of properties of quantum systems and for the realization of cryptography and communication protocols. PMID:25649664

  11. Fully device-independent quantum key distribution.

    PubMed

    Vazirani, Umesh; Vidick, Thomas

    2014-10-01

    Quantum cryptography promises levels of security that are impossible to replicate in a classical world. Can this security be guaranteed even when the quantum devices on which the protocol relies are untrusted? This central question dates back to the early 1990s when the challenge of achieving device-independent quantum key distribution was first formulated. We answer this challenge by rigorously proving the device-independent security of a slight variant of Ekert's original entanglement-based protocol against the most general (coherent) attacks. The resulting protocol is robust: While assuming only that the devices can be modeled by the laws of quantum mechanics and are spatially isolated from each other and from any adversary's laboratory, it achieves a linear key rate and tolerates a constant noise rate in the devices. In particular, the devices may have quantum memory and share arbitrary quantum correlations with the eavesdropper. The proof of security is based on a new quantitative understanding of the monogamous nature of quantum correlations in the context of a multiparty protocol.

  12. Fully device-independent quantum key distribution.

    PubMed

    Vazirani, Umesh; Vidick, Thomas

    2014-10-01

    Quantum cryptography promises levels of security that are impossible to replicate in a classical world. Can this security be guaranteed even when the quantum devices on which the protocol relies are untrusted? This central question dates back to the early 1990s when the challenge of achieving device-independent quantum key distribution was first formulated. We answer this challenge by rigorously proving the device-independent security of a slight variant of Ekert's original entanglement-based protocol against the most general (coherent) attacks. The resulting protocol is robust: While assuming only that the devices can be modeled by the laws of quantum mechanics and are spatially isolated from each other and from any adversary's laboratory, it achieves a linear key rate and tolerates a constant noise rate in the devices. In particular, the devices may have quantum memory and share arbitrary quantum correlations with the eavesdropper. The proof of security is based on a new quantitative understanding of the monogamous nature of quantum correlations in the context of a multiparty protocol. PMID:25325625

  13. Measurement-device-independent quantum digital signatures

    NASA Astrophysics Data System (ADS)

    Puthoor, Ittoop Vergheese; Amiri, Ryan; Wallden, Petros; Curty, Marcos; Andersson, Erika

    2016-08-01

    Digital signatures play an important role in software distribution, modern communication, and financial transactions, where it is important to detect forgery and tampering. Signatures are a cryptographic technique for validating the authenticity and integrity of messages, software, or digital documents. The security of currently used classical schemes relies on computational assumptions. Quantum digital signatures (QDS), on the other hand, provide information-theoretic security based on the laws of quantum physics. Recent work on QDS Amiri et al., Phys. Rev. A 93, 032325 (2016);, 10.1103/PhysRevA.93.032325 Yin, Fu, and Zeng-Bing, Phys. Rev. A 93, 032316 (2016), 10.1103/PhysRevA.93.032316 shows that such schemes do not require trusted quantum channels and are unconditionally secure against general coherent attacks. However, in practical QDS, just as in quantum key distribution (QKD), the detectors can be subjected to side-channel attacks, which can make the actual implementations insecure. Motivated by the idea of measurement-device-independent quantum key distribution (MDI-QKD), we present a measurement-device-independent QDS (MDI-QDS) scheme, which is secure against all detector side-channel attacks. Based on the rapid development of practical MDI-QKD, our MDI-QDS protocol could also be experimentally implemented, since it requires a similar experimental setup.

  14. Identification and Validation of Reference Genes for Quantification of Target Gene Expression with Quantitative Real-time PCR for Tall Fescue under Four Abiotic Stresses

    PubMed Central

    Hu, Baoyun; Tan, Zhiqun; Huang, Bingru

    2015-01-01

    Tall fescue (Festuca arundinacea Schreb.) is widely utilized as a major forage and turfgrass species in the temperate regions of the world and is a valuable plant material for studying molecular mechanisms of grass stress tolerance due to its superior drought and heat tolerance among cool-season species. Selection of suitable reference genes for quantification of target gene expression is important for the discovery of molecular mechanisms underlying improved growth traits and stress tolerance. The stability of nine potential reference genes (ACT, TUB, EF1a, GAPDH, SAND, CACS, F-box, PEPKR1 and TIP41) was evaluated using four programs, GeNorm, NormFinder, BestKeeper, and RefFinder. The combinations of SAND and TUB or TIP41 and TUB were most stably expressed in salt-treated roots or leaves. The combinations of GAPDH with TIP41 or TUB were stable in roots and leaves under drought stress. TIP41 and PEPKR1 exhibited stable expression in cold-treated roots, and the combination of F-box, TIP41 and TUB was also stable in cold-treated leaves. CACS and TUB were the two most stable reference genes in heat-stressed roots. TIP41 combined with TUB and ACT was stably expressed in heat-stressed leaves. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) assays of the target gene FaWRKY1 using the identified most stable reference genes confirmed the reliability of selected reference genes. The selection of suitable reference genes in tall fescue will allow for more accurate identification of stress-tolerance genes and molecular mechanisms conferring stress tolerance in this stress-tolerant species. PMID:25786207

  15. Identification and validation of reference genes for quantification of target gene expression with quantitative real-time PCR for tall fescue under four abiotic stresses.

    PubMed

    Yang, Zhimin; Chen, Yu; Hu, Baoyun; Tan, Zhiqun; Huang, Bingru

    2015-01-01

    Tall fescue (Festuca arundinacea Schreb.) is widely utilized as a major forage and turfgrass species in the temperate regions of the world and is a valuable plant material for studying molecular mechanisms of grass stress tolerance due to its superior drought and heat tolerance among cool-season species. Selection of suitable reference genes for quantification of target gene expression is important for the discovery of molecular mechanisms underlying improved growth traits and stress tolerance. The stability of nine potential reference genes (ACT, TUB, EF1a, GAPDH, SAND, CACS, F-box, PEPKR1 and TIP41) was evaluated using four programs, GeNorm, NormFinder, BestKeeper, and RefFinder. The combinations of SAND and TUB or TIP41 and TUB were most stably expressed in salt-treated roots or leaves. The combinations of GAPDH with TIP41 or TUB were stable in roots and leaves under drought stress. TIP41 and PEPKR1 exhibited stable expression in cold-treated roots, and the combination of F-box, TIP41 and TUB was also stable in cold-treated leaves. CACS and TUB were the two most stable reference genes in heat-stressed roots. TIP41 combined with TUB and ACT was stably expressed in heat-stressed leaves. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) assays of the target gene FaWRKY1 using the identified most stable reference genes confirmed the reliability of selected reference genes. The selection of suitable reference genes in tall fescue will allow for more accurate identification of stress-tolerance genes and molecular mechanisms conferring stress tolerance in this stress-tolerant species.

  16. Computerized patient identification for the EMBRACA clinical trial using real-time data from the PRAEGNANT network for metastatic breast cancer patients.

    PubMed

    Hein, Alexander; Gass, Paul; Walter, Christina Barbara; Taran, Florin-Andrei; Hartkopf, Andreas; Overkamp, Friedrich; Kolberg, Hans-Christian; Hadji, Peyman; Tesch, Hans; Ettl, Johannes; Wuerstlein, Rachel; Lounsbury, Debra; Lux, Michael P; Lüftner, Diana; Wallwiener, Markus; Müller, Volkmar; Belleville, Erik; Janni, Wolfgang; Fehm, Tanja N; Wallwiener, Diethelm; Ganslandt, Thomas; Ruebner, Matthias; Beckmann, Matthias W; Schneeweiss, Andreas; Fasching, Peter A; Brucker, Sara Y

    2016-07-01

    As breast cancer is a diverse disease, clinical trials are becoming increasingly diversified and are consequently being conducted in very small subgroups of patients, making study recruitment increasingly difficult. The aim of this study was to assess the use of data from a remote data entry system that serves a large national registry for metastatic breast cancer. The PRAEGNANT network is a real-time registry with an integrated biomaterials bank that was designed as a scientific study and as a means of identifying patients who are eligible for clinical trials, based on clinical and molecular information. Here, we report on the automated use of the clinical data documented to identify patients for a clinical trial (EMBRACA) for patients with metastatic breast cancer. The patients' charts were assessed by two independent physicians involved in the clinical trial and also by a computer program that tested patients for eligibility using a structured query language script. In all, 326 patients from two study sites in the PRAEGNANT network were included in the analysis. Using expert assessment, 120 of the 326 patients (37 %) appeared to be eligible for inclusion in the EMBRACA study; with the computer algorithm assessment, a total of 129 appeared to be eligible. The sensitivity of the computer algorithm was 0.87 and its specificity was 0.88. Using computer-based identification of patients for clinical trials appears feasible. With the instrument's high specificity, its application in a large cohort of patients appears to be feasible, and the workload for reassessing the patients is limited.

  17. Real time automated inspection

    DOEpatents

    Fant, K.M.; Fundakowski, R.A.; Levitt, T.S.; Overland, J.E.; Suresh, B.R.; Ulrich, F.W.

    1985-05-21

    A method and apparatus are described relating to the real time automatic detection and classification of characteristic type surface imperfections occurring on the surfaces of material of interest such as moving hot metal slabs produced by a continuous steel caster. A data camera transversely scans continuous lines of such a surface to sense light intensities of scanned pixels and generates corresponding voltage values. The voltage values are converted to corresponding digital values to form a digital image of the surface which is subsequently processed to form an edge-enhanced image having scan lines characterized by intervals corresponding to the edges of the image. The edge-enhanced image is thresholded to segment out the edges and objects formed by the edges by interval matching and bin tracking. Features of the objects are derived and such features are utilized to classify the objects into characteristic type surface imperfections. 43 figs.

  18. Real time automated inspection

    DOEpatents

    Fant, Karl M.; Fundakowski, Richard A.; Levitt, Tod S.; Overland, John E.; Suresh, Bindinganavle R.; Ulrich, Franz W.

    1985-01-01

    A method and apparatus relating to the real time automatic detection and classification of characteristic type surface imperfections occurring on the surfaces of material of interest such as moving hot metal slabs produced by a continuous steel caster. A data camera transversely scans continuous lines of such a surface to sense light intensities of scanned pixels and generates corresponding voltage values. The voltage values are converted to corresponding digital values to form a digital image of the surface which is subsequently processed to form an edge-enhanced image having scan lines characterized by intervals corresponding to the edges of the image. The edge-enhanced image is thresholded to segment out the edges and objects formed by the edges are segmented out by interval matching and bin tracking. Features of the objects are derived and such features are utilized to classify the objects into characteristic type surface imperfections.

  19. Detector-device-independent quantum key distribution

    SciTech Connect

    Lim, Charles Ci Wen; Korzh, Boris; Martin, Anthony; Bussières, Félix; Thew, Rob; Zbinden, Hugo

    2014-12-01

    Recently, a quantum key distribution (QKD) scheme based on entanglement swapping, called measurement-device-independent QKD (mdiQKD), was proposed to bypass all measurement side-channel attacks. While mdiQKD is conceptually elegant and offers a supreme level of security, the experimental complexity is challenging for practical systems. For instance, it requires interference between two widely separated independent single-photon sources, and the secret key rates are dependent on detecting two photons—one from each source. Here, we demonstrate a proof-of-principle experiment of a QKD scheme that removes the need for a two-photon system and instead uses the idea of a two-qubit single-photon to significantly simplify the implementation and improve the efficiency of mdiQKD in several aspects.

  20. Measurement-device-independent quantum cryptography

    SciTech Connect

    Xu, Feihu; Curty, Marcos; Qi, Bing; Lo, Hoi-Kwong

    2014-12-18

    In theory, quantum key distribution (QKD) provides information-theoretic security based on the laws of physics. Owing to the imperfections of real-life implementations, however, there is a big gap between the theory and practice of QKD, which has been recently exploited by several quantum hacking activities. To fill this gap, a novel approach, called measurement-device-independent QKD (mdiQKD), has been proposed. In addition, it can remove all side-channels from the measurement unit, arguably the most vulnerable part in QKD systems, thus offering a clear avenue toward secure QKD realisations. In this study, we review the latest developments in the framework of mdiQKD, together with its assumptions, strengths, and weaknesses.

  1. Measurement-device-independent quantum cryptography

    DOE PAGESBeta

    Xu, Feihu; Curty, Marcos; Qi, Bing; Lo, Hoi-Kwong

    2014-12-18

    In theory, quantum key distribution (QKD) provides information-theoretic security based on the laws of physics. Owing to the imperfections of real-life implementations, however, there is a big gap between the theory and practice of QKD, which has been recently exploited by several quantum hacking activities. To fill this gap, a novel approach, called measurement-device-independent QKD (mdiQKD), has been proposed. In addition, it can remove all side-channels from the measurement unit, arguably the most vulnerable part in QKD systems, thus offering a clear avenue toward secure QKD realisations. In this study, we review the latest developments in the framework of mdiQKD,more » together with its assumptions, strengths, and weaknesses.« less

  2. Identification of Common Bacterial Pathogens Causing Meningitis in Culture-Negative Cerebrospinal Fluid Samples Using Real-Time Polymerase Chain Reaction.

    PubMed

    Khater, Walaa Shawky; Elabd, Safia Hamed

    2016-01-01

    Background. Meningitis is a serious communicable disease with high morbidity and mortality rates. It is an endemic disease in Egypt caused mainly by Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae. In some settings, bacterial meningitis is documented depending mainly on positive cerebrospinal fluid (CSF) culture results or CSF positive latex agglutination test, missing the important role of prior antimicrobial intake which can yield negative culture and latex agglutination test results. This study aimed to utilize molecular technology in order to diagnose bacterial meningitis in culture-negative CSF samples. Materials and Methods. Forty culture-negative CSF samples from suspected cases of bacterial meningitis were examined by real-time polymerase chain reaction (real-time PCR) for the presence of lytA, bexA, and ctrA genes specific for Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, respectively. Results. Positive real-time PCR results for Streptococcus pneumoniae were detected in 36 (90%) of culture-negative CSF samples while no positive results for Haemophilus influenzae or Neisseria meningitidis were detected. Four (10%) samples were negative by real-time PCR for all tested organisms. Conclusion. The use of molecular techniques as real-time PCR can provide a valuable addition to the proportion of diagnosed cases of bacterial meningitis especially in settings with high rates of culture-negative results. PMID:27563310

  3. Identification of Common Bacterial Pathogens Causing Meningitis in Culture-Negative Cerebrospinal Fluid Samples Using Real-Time Polymerase Chain Reaction

    PubMed Central

    2016-01-01

    Background. Meningitis is a serious communicable disease with high morbidity and mortality rates. It is an endemic disease in Egypt caused mainly by Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae. In some settings, bacterial meningitis is documented depending mainly on positive cerebrospinal fluid (CSF) culture results or CSF positive latex agglutination test, missing the important role of prior antimicrobial intake which can yield negative culture and latex agglutination test results. This study aimed to utilize molecular technology in order to diagnose bacterial meningitis in culture-negative CSF samples. Materials and Methods. Forty culture-negative CSF samples from suspected cases of bacterial meningitis were examined by real-time polymerase chain reaction (real-time PCR) for the presence of lytA, bexA, and ctrA genes specific for Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, respectively. Results. Positive real-time PCR results for Streptococcus pneumoniae were detected in 36 (90%) of culture-negative CSF samples while no positive results for Haemophilus influenzae or Neisseria meningitidis were detected. Four (10%) samples were negative by real-time PCR for all tested organisms. Conclusion. The use of molecular techniques as real-time PCR can provide a valuable addition to the proportion of diagnosed cases of bacterial meningitis especially in settings with high rates of culture-negative results. PMID:27563310

  4. Real time polarimetric dehazing.

    PubMed

    Mudge, Jason; Virgen, Miguel

    2013-03-20

    Remote sensing is a rich topic due to its utility in gathering detailed accurate information from locations that are not economically feasible traveling destinations or are physically inaccessible. However, poor visibility over long path lengths is problematic for a variety of reasons. Haze induced by light scatter is one cause for poor visibility and is the focus of this article. Image haze comes about as a result of light scattering off particles and into the imaging path causing a haziness to appear on the image. Image processing using polarimetric information of light scatter can be used to mitigate image haze. An imaging polarimeter which provides the Stokes values in real time combined with a "dehazing" algorithm can automate image haze removal for instant applications. Example uses are to improve visual display providing on-the-spot detection or imbedding in an active control loop to improve viewing and tracking while on a moving platform. In addition, removing haze in this manner allows the trade space for a system operational waveband to be opened up to bands which are object matched and not necessarily restricted by scatter effects. PMID:23518739

  5. Identification and validation of quantitative real-time reverse transcription PCR reference genes for gene expression analysis in teak (Tectona grandis L.f.)

    PubMed Central

    2014-01-01

    Background Teak (Tectona grandis L.f.) is currently the preferred choice of the timber trade for fabrication of woody products due to its extraordinary qualities and is widely grown around the world. Gene expression studies are essential to explore wood formation of vascular plants, and quantitative real-time reverse transcription PCR (qRT-PCR) is a sensitive technique employed for quantifying gene expression levels. One or more appropriate reference genes are crucial to accurately compare mRNA transcripts through different tissues/organs and experimental conditions. Despite being the focus of some genetic studies, a lack of molecular information has hindered genetic exploration of teak. To date, qRT-PCR reference genes have not been identified and validated for teak. Results Identification and cloning of nine commonly used qRT-PCR reference genes from teak, including ribosomal protein 60s (rp60s), clathrin adaptor complexes medium subunit family (Cac), actin (Act), histone 3 (His3), sand family (Sand), β-Tubulin (Β-Tub), ubiquitin (Ubq), elongation factor 1-α (Ef-1α), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Expression profiles of these genes were evaluated by qRT-PCR in six tissue and organ samples (leaf, flower, seedling, root, stem and branch secondary xylem) of teak. Appropriate gene cloning and sequencing, primer specificity and amplification efficiency was verified for each gene. Their stability as reference genes was validated by NormFinder, BestKeeper, geNorm and Delta Ct programs. Results obtained from all programs showed that TgUbq and TgEf-1α are the most stable genes to use as qRT-PCR reference genes and TgAct is the most unstable gene in teak. The relative expression of the teak cinnamyl alcohol dehydrogenase (TgCAD) gene in lignified tissues at different ages was assessed by qRT-PCR, using TgUbq and TgEf-1α as internal controls. These analyses exposed a consistent expression pattern with both reference genes. Conclusion This study

  6. Identification and evaluation of reliable reference genes for quantitative real-time PCR analysis in tea plant (Camellia sinensis (L.) O. Kuntze)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantitative real-time polymerase chain reaction (qRT-PCR) is a commonly used technique for measuring gene expression levels due to its simplicity, specificity, and sensitivity. Reliable reference selection for the accurate quantification of gene expression under various experimental conditions is a...

  7. Usefulness of three-channel multiplex real-time PCR and melting curve analysis for simultaneous detection and identification of the Mycobacterium tuberculosis complex and nontuberculous mycobacteria.

    PubMed

    Hong, Yun Ji; Chung, Young Hoon; Kim, Taek Soo; Song, Sang Hoon; Park, Kyoung Un; Yim, Jae Joon; Song, Junghan; Lee, Jae Ho; Kim, Eui Chong

    2011-11-01

    We attempted to determine the benefits of three-channel multiplex real-time PCR and melting curve analysis not only in detecting and distinguishing between nontuberculous mycobacteria (NTM) and the Mycobacterium tuberculosis complex but also in identifying NTM to the species level.

  8. Quality of bulk tank milk samples from Danish dairy herds based on real-time polymerase chain reaction identification of mastitis pathogens.

    PubMed

    Katholm, J; Bennedsgaard, T W; Koskinen, M T; Rattenborg, E

    2012-10-01

    Results of a commercial real-time PCR analysis for 11 mastitis pathogens from bulk tank milk (BTM) samples from all 4,258 Danish dairy herds in November 2009 to January 2010 were compared with somatic cell count (SCC) and total bacteria count (TBC) estimates in BTM. For Streptococcus agalactiae, Streptococcus dysgalactiae, and Streptococcus uberis, a low real-time PCR cycle threshold (Ct) value (corresponding to high bacterial DNA quantity) was correlated with higher SCC and higher TBC. For Staphylococcus aureus, low Ct values were correlated only with higher SCC. For the environmental mastitis pathogens Klebsiella spp., Enterococcus spp., and Escherichia coli, low Ct values had a correlation with higher TBC. Staphylococcus spp. were found in the BTM from all herds, Strep. uberis in 95%, Staph. aureus in 91%, and Strep. dysgalactiae in 86%, whereas E. coli, Klebsiella, and Strep. agalactiae were found in 61, 13, and 7% of the herds. It is concluded that the real-time PCR used provides results that are related to the milk quality in the herds. Real-time PCR can be used in the same way as culture for monitoring BTM samples, and is especially useful for bacteria with low prevalence (e.g., Strep. agalactiae). PMID:22921631

  9. Completely device-independent quantum key distribution

    NASA Astrophysics Data System (ADS)

    Aguilar, Edgar A.; Ramanathan, Ravishankar; Kofler, Johannes; Pawłowski, Marcin

    2016-08-01

    Quantum key distribution (QKD) is a provably secure way for two distant parties to establish a common secret key, which then can be used in a classical cryptographic scheme. Using quantum entanglement, one can reduce the necessary assumptions that the parties have to make about their devices, giving rise to device-independent QKD (DIQKD). However, in all existing protocols to date the parties need to have an initial (at least partially) random seed as a resource. In this work, we show that this requirement can be dropped. Using recent advances in the fields of randomness amplification and randomness expansion, we demonstrate that it is sufficient for the message the parties want to communicate to be (partially) unknown to the adversaries—an assumption without which any type of cryptography would be pointless to begin with. One party can use her secret message to locally generate a secret sequence of bits, which can then be openly used by herself and the other party in a DIQKD protocol. Hence our work reduces the requirements needed to perform secure DIQKD and establish safe communication.

  10. Analysis of real-time vibration data

    USGS Publications Warehouse

    Safak, E.

    2005-01-01

    In recent years, a few structures have been instrumented to provide continuous vibration data in real time, recording not only large-amplitude motions generated by extreme loads, but also small-amplitude motions generated by ambient loads. The main objective in continuous recording is to track any changes in structural characteristics, and to detect damage after an extreme event, such as an earthquake or explosion. The Fourier-based spectral analysis methods have been the primary tool to analyze vibration data from structures. In general, such methods do not work well for real-time data, because real-time data are mainly composed of ambient vibrations with very low amplitudes and signal-to-noise ratios. The long duration, linearity, and the stationarity of ambient data, however, allow us to utilize statistical signal processing tools, which can compensate for the adverse effects of low amplitudes and high noise. The analysis of real-time data requires tools and techniques that can be applied in real-time; i.e., data are processed and analyzed while being acquired. This paper presents some of the basic tools and techniques for processing and analyzing real-time vibration data. The topics discussed include utilization of running time windows, tracking mean and mean-square values, filtering, system identification, and damage detection.

  11. Identification and quantification of genetically modified Moonshade carnation lines using conventional and TaqMan real-time polymerase chain reaction methods.

    PubMed

    Li, Peng; Jia, Junwei; Bai, Lan; Pan, Aihu; Tang, Xueming

    2013-07-01

    Genetically modified carnation (Dianthus caryophyllus L.) Moonshade was approved for planting and commercialization in several countries from 2004. Developing methods for analyzing Moonshade is necessary for implementing genetically modified organism labeling regulations. In this study, the 5'-transgene integration sequence was isolated using thermal asymmetric interlaced (TAIL)-PCR. Based upon the 5'-transgene integration sequence, conventional and TaqMan real-time PCR assays were established. The relative limit of detection for the conventional PCR assay was 0.05 % for Moonshade using 100 ng total carnation genomic DNA, corresponding to approximately 79 copies of the carnation haploid genome, and the limits of detection and quantification of the TaqMan real-time PCR assay were estimated to be 51 and 254 copies of haploid carnation genomic DNA, respectively. These results are useful for identifying and quantifying Moonshade and its derivatives.

  12. A multiplex real-time PCR assay for identification of Pneumocystis jirovecii, Histoplasma capsulatum, and Cryptococcus neoformans/Cryptococcus gattii in samples from AIDS patients with opportunistic pneumonia.

    PubMed

    Gago, Sara; Esteban, Cristina; Valero, Clara; Zaragoza, Oscar; Puig de la Bellacasa, Jorge; Buitrago, María José

    2014-04-01

    A molecular diagnostic technique based on real-time PCR was developed for the simultaneous detection of three of the most frequent causative agents of fungal opportunistic pneumonia in AIDS patients: Pneumocystis jirovecii, Histoplasma capsulatum, and Cryptococcus neoformans/Cryptococcus gattii. This technique was tested in cultured strains and in clinical samples from HIV-positive patients. The methodology used involved species-specific molecular beacon probes targeted to the internal transcribed spacer regions of the rDNA. An internal control was also included in each assay. The multiplex real-time PCR assay was tested in 24 clinical strains and 43 clinical samples from AIDS patients with proven fungal infection. The technique developed showed high reproducibility (r(2) of >0.98) and specificity (100%). For H. capsulatum and Cryptococcus spp., the detection limits of the method were 20 and 2 fg of genomic DNA/20 μl reaction mixture, respectively, while for P. jirovecii the detection limit was 2.92 log10 copies/20 μl reaction mixture. The sensitivity in vitro was 100% for clinical strains and 90.7% for clinical samples. The assay was positive for 92.5% of the patients. For one of the patients with proven histoplasmosis, P. jirovecii was also detected in a bronchoalveolar lavage sample. No PCR inhibition was detected. This multiplex real-time PCR technique is fast, sensitive, and specific and may have clinical applications.

  13. Real-Time Benchmark Suite

    1992-01-17

    This software provides a portable benchmark suite for real time kernels. It tests the performance of many of the system calls, as well as the interrupt response time and task response time to interrupts. These numbers provide a baseline for comparing various real-time kernels and hardware platforms.

  14. Application of the real-time PCR method for genotypic identification of β-lactam resistance in isolates from invasive pneumococcal diseases.

    PubMed

    Chiba, Naoko; Morozumi, Miyuki; Ubukata, Kimiko

    2012-04-01

    We sought to identify genotypic resistance classes by real-time PCR in 300 Streptococcus pneumoniae isolates from invasive pneumococcal diseases. Primers and molecular beacon probes were designed for the lytA gene, 3 pbp genes, and the mefA/ermB genes. Targeted sequences of pbp1a, pbp2x, and pbp2b genes in susceptible strain R6 corresponded to those of penicillin G-nonsusceptible strains, including sites within or adjacent to conserved amino acid motifs. If amplification did not occur, the corresponding penicillin-binding protein (PBP) was considered to possess amino acid substitution(s) affecting minimal inhibitory concentrations (MICs) of β-lactam antibiotics. Real-time PCR required 90 min or less. Strains were assigned to six genotypic classes: Genotypic penicillin-susceptible S. pneumoniae (gPSSP) with 3 normal genes (22.3%); genotypic penicillin-intermediate S. pneumoniae (gPISP) (pbp2x) with an abnormal pbp2x gene (25.3%); gPISP (pbp2b) with an abnormal pbp2b gene (7.3%); gPISP (pbp1a+2x) with abnormal pbp1a+2x genes (11.3%); gPISP (pbp2x+2b) with abnormal pbp2x+2b genes (4.7%); or genotypic penicillin-resistant S. pneumoniae (gPRSP) with 3 abnormal PBP genes (29.0%). Sensitivity and specificity of real-time PCR compared with those of conventional PCR were high, 73.7-100% and 97.7-100%, respectively. As for relationships between genotype and β-lactam MICs, 90% of MICs for every resistance class were distributed within three serial dilutions for almost all antibiotics. MICs of each β-lactam antibiotic were estimated with high probability from genotypic patterns. In conclusion, determination of genotypic classes of S. pneumoniae using rapid real-time PCR is useful in selecting effective therapeutic agents for patients with pneumococcal infection.

  15. Use of tissue culture techniques for producing virus-free plant in garlic and their identification through real-time PCR.

    PubMed

    Taşkın, Hatıra; Baktemur, Gökhan; Kurul, Mehmet; Büyükalaca, Saadet

    2013-01-01

    This study was performed for comparison of meristem culture technique with shoot tip culture technique for obtaining virus-free plant, comparison of micropropagation success of two different nutrient media, and determination of effectiveness of real-time PCR assay for the detection of viruses. Two different garlic species (Allium sativum and Allium tuncelianum) and two different nutrient media were used in this experiment. Results showed that Medium 2 was more successful compared to Medium 1 for both A. tuncelianum and A. sativum (Kastamonu garlic clone). In vitro plants obtained via meristem and shoot tip cultures were tested for determination of onion yellow dwarf virus (OYDV) and leek yellow stripe virus (LYSV) through real-time PCR assay. In garlic plants propagated via meristem culture, we could not detect any virus. OYDV and LYSV viruses were detected in plants obtained via shoot tip culture. OYDV virus was observed in amount of 80% and 73% of tested plants for A. tuncelianum and A. sativum, respectively. LYSV virus was found in amount of 67% of tested plants of A. tuncelianum and in amount of 87% of tested plants of A. sativum in this study. PMID:23935432

  16. Real-time feedback for improving compliance to hand sanitization among healthcare workers in an open layout ICU using radiofrequency identification.

    PubMed

    Radhakrishna, Kedar; Waghmare, Abijeet; Ekstrand, Maria; Raj, Tony; Selvam, Sumithra; Sreerama, Sai Madhukar; Sampath, Sriram

    2015-06-01

    The aim of this study is to increase hand sanitizer usage among healthcare workers by developing and implementing a low-cost intervention using RFID and wireless mesh networks to provide real-time alarms for increasing hand hygiene compliance during opportune moments in an open layout Intensive Care Unit (ICU). A wireless, RFID based system was developed and implemented in the ICU. The ICU beds were divded into an intervention arm (n = 10) and a control arm (n = 14). Passive RFID tags were issued to the doctors, nurses and support staff of the ICU. Long range RFID readers were positioned strategically. Sensors were placed beneath the hand sanitizers to record sanitizer usage. The system would alert the HCWs by flashing a light if an opportune moment for hand sanitization was detected. A significant increase in hand sanitizer use was noted in the intervention arm. Usage was highest during the early part of the workday and decreased as the day progressed. Hand wash events per person hour was highest among the ancilliary staff followed by the doctors and nurses. Real-time feedback has potential to increase hand hygiene compliance among HCWs. The system demonstrates the possibility of automating compliance monitoring in an ICU with an open layout. PMID:25957165

  17. REAL-TIME FEEDBACK FOR IMPROVING COMPLIANCE TO HAND SANITIZATION AMONG HEALTHCARE WORKERS IN AN OPEN LAYOUT ICU USING RADIOFREQUENCY IDENTIFICATION

    PubMed Central

    Waghmare, Abijeet; Ekstrand, Maria; Raj, Tony; Selvam, Sumithra; Sreerama, Sai Madhukar; Sampath, Sriram

    2015-01-01

    Objective To increase hand sanitizer usage among healthcare workers by developing and implementing a low-cost intervention using RFID and wireless mesh networks to provide real-time alarms for increasing hand hygiene compliance during opportune moments in an open layout Intensive Care Unit (ICU). Method A wireless, RFID based system was developed and deployed in the ICU. The ICU beds were divded into an intervention arm (n=10) and a control arm (n=14). Passive RFID tags were issued to the doctors, nurses and support staff of the ICU. Long range RFID readers were positioned strategically. Sensors were placed beneath the hand sanitizers to record sanitizer usage. The system would alert the HCWs by flashing a light if an opportune moment for hand sanitization was detected. Results A significant increase in hand sanitizer use was noted in the intervention arm. Usage was highest during the early part of the workday and decreased as the day progressed. Hand wash events per person hour was highest among the ancilliary staff followed by the doctors and nurses. Conclusion Real-time feedback has potential to increase hand hygiene compliance among HCWs. The system demonstrates the possibility of automating compliance monitoring in an ICU with an open layout. PMID:25957165

  18. Real-time feedback for improving compliance to hand sanitization among healthcare workers in an open layout ICU using radiofrequency identification.

    PubMed

    Radhakrishna, Kedar; Waghmare, Abijeet; Ekstrand, Maria; Raj, Tony; Selvam, Sumithra; Sreerama, Sai Madhukar; Sampath, Sriram

    2015-06-01

    The aim of this study is to increase hand sanitizer usage among healthcare workers by developing and implementing a low-cost intervention using RFID and wireless mesh networks to provide real-time alarms for increasing hand hygiene compliance during opportune moments in an open layout Intensive Care Unit (ICU). A wireless, RFID based system was developed and implemented in the ICU. The ICU beds were divded into an intervention arm (n = 10) and a control arm (n = 14). Passive RFID tags were issued to the doctors, nurses and support staff of the ICU. Long range RFID readers were positioned strategically. Sensors were placed beneath the hand sanitizers to record sanitizer usage. The system would alert the HCWs by flashing a light if an opportune moment for hand sanitization was detected. A significant increase in hand sanitizer use was noted in the intervention arm. Usage was highest during the early part of the workday and decreased as the day progressed. Hand wash events per person hour was highest among the ancilliary staff followed by the doctors and nurses. Real-time feedback has potential to increase hand hygiene compliance among HCWs. The system demonstrates the possibility of automating compliance monitoring in an ICU with an open layout.

  19. Rapid differentiation and identification of potential severe strains of Citrus tristeza virus by real-time reverse transcription-polymerase chain reaction assays.

    PubMed

    Yokomi, R K; Saponari, M; Sieburth, P J

    2010-04-01

    A multiplex Taqman-based real-time reverse transcription (RT) polymerase chain reaction (PCR) assay was developed to identify potential severe strains of Citrus tristeza virus (CTV) and separate genotypes that react with the monoclonal antibody MCA13. Three strain-specific probes were developed using intergene sequences between the major and minor coat protein genes (CPi) in a multiplex reaction. Probe CPi-VT3 was designed for VT and T3 genotypes; probe CPi-T36 for T36 genotypes; and probe CPi-T36-NS to identify isolates in an outgroup clade of T36-like genotypes mild in California. Total nucleic acids extracted by chromatography on silica particles, sodium dodecyl sulfate-potassium acetate, and CTV virion immunocapture all yielded high quality templates for real-time PCR detection of CTV. These assays successfully differentiated CTV isolates from California, Florida, and a large panel of CTV isolates from an international collection maintained in Beltsville, MD. The utility of the assay was validated using field isolates collected in California and Florida. PMID:20205535

  20. Rapid, high-throughput, multiplex, real-time PCR for identification of mutations in the cyp51A gene of Aspergillus fumigatus that confer resistance to itraconazole.

    PubMed

    Balashov, Sergey V; Gardiner, Rebecca; Park, Steven; Perlin, David S

    2005-01-01

    Aspergillus fumigatus is an important cause of life-threatening invasive fungal disease in patients with compromised immune systems. Resistance to itraconazole in A. fumigatus is closely linked to amino acid substitutions in Cyp51A that replace Gly54. In an effort to develop a new class of molecular diagnostic assay that can rapidly assess drug resistance, a multiplexed assay was established. This assay uses molecular beacons corresponding to the wild-type cyp51A gene and seven mutant alleles encoding either Arg54, Lys54, Val54, Trp54, or Glu54. Molecular beacon structure design and real-time PCR conditions were optimized to increase the assay specificity. The multiplex assay was applied to the analysis of chromosomal DNA samples from a collection of 48 A. fumigatus clinical and laboratory-derived isolates, most with reduced susceptibility to itraconazole. The cyp51A allelic identities for codon 54 were established for all of the strains tested, and mutations altering Gly54 in 23 strains were revealed. These mutations included G(54)W (n = 1), G(54)E (n = 12), G(54)K (n = 3), G(54)R (n = 3), and G(54)V (n = 4). Molecular beacon assay results were confirmed by DNA sequencing. Multiplex real-time PCR with molecular beacons is a powerful technique for allele differentiation and analysis of resistance mutations that is dynamic and suitable for rapid high-throughput assessment of drug resistance.

  1. Real-time Identification and Control of Satellite Signal Impairments Solution and Application of the Stratonovich Equation Part 1. Theoretical Development

    NASA Technical Reports Server (NTRS)

    Manning, Robert M.

    2016-01-01

    As satellite communications systems become both more complex and reliant with respect to their operating environment, it has become imperative to be able to identify, during real-time operation, the onset of one or more impairments to the quality of overall communications system integrity. One of the most important aspects to monitor of a satellite link operating within the Earth's atmosphere is the signal fading due to the occurrence of rain and/or phase scintillations. This, of course, must be done in the presence of the associated measurement uncertainty or potentially faulty measurement equipment such as in the Advanced Communication Technology Satellite (ACTS) experiment. In the present work, an approach originally suggested in 1991, and apparently still considered iconoclastic, will be significantly developed and applied to the satellite communications link on which the deleterious composite signal fade is the result of one or many component fade mechanisms. Through the measurement (with the attendant uncertainty or 'error' in the measurement) of such a composite fading satellite signal, it is desired to extract the level of each of the individual fading mechanisms so they can be appropriately mitigated before they impact the overall performance of the communications network. Rather than employing simple-minded deterministic filtering to the real-time fading, the present approach is built around all the models and/or descriptions used to describe the individual fade components, including their dynamic evolution. The latter is usually given by a first-order Langevin equation. This circumstance allows the description of the associated temporal transition probability densities of each of the component processes. By using this description, along with the real-time measurements of the composite fade (along with the measurement errors), one can obtain statistical estimates of the levels of each of the component fading mechanisms as well as their predicted values

  2. Combined real-time PCR and rpoB gene pyrosequencing for rapid identification of Mycobacterium tuberculosis and determination of rifampin resistance directly in clinical specimens.

    PubMed

    Halse, Tanya A; Edwards, Justine; Cunningham, Phyllis L; Wolfgang, William J; Dumas, Nellie B; Escuyer, Vincent E; Musser, Kimberlee A

    2010-04-01

    Our laboratory has developed a rapid, sensitive, and specific molecular approach for detection in clinical specimens, within 48 h of receipt, of both Mycobacterium tuberculosis complex (MTBC) DNA and mutations within the 81-bp core region of the rpoB gene that are associated with rifampin (RIF) resistance. This approach, which combines an initial real-time PCR with internal inhibition assessment and a pyrosequencing assay, was validated for direct use with clinical specimens. To assess the suitability of real-time PCR for use with respiratory, nonrespiratory, acid-fast bacillus (AFB)-positive and AFB-negative specimens, we evaluated specimens received in our laboratory between 11 October 2007 and 30 June 2009. With culture used as the "gold standard," the sensitivity, specificity, and positive and negative predictive values were determined for 1,316 specimens to be as follows: for respiratory specimens, 94.7%, 99.9%, 99.6%, and 98.6%, respectively; for nonrespiratory specimens, 88.5%, 100.0%, 100.0%, and 96.9%, respectively; for AFB-positive specimens, 99.6%, 100.0%, 100.0%, and 97.7%, respectively; and for AFB-negative specimens, 75.4%, 99.9%, 98.0%, and 98.4%, respectively. PCR inhibition was determined to be minimal in this assay, occurring in 0.2% of tests. The rpoB gene pyrosequencing assay was evaluated in a similar prospective study, in which 148 clinical specimens positive for MTBC DNA by real-time PCR were tested. The final results revealed that the results of direct testing of clinical specimens by the pyrosequencing assay were 98.6% concordant with the results of conventional testing for susceptibility to RIF in liquid culture and that our assay displayed adequate sensitivity for 96.6% of the clinical specimens tested. Used together, these assays provide reliable results that aid with the initial management of patients with suspected tuberculosis prior to the availability of the results for cultured material, and they also provide the ability to predict

  3. Rapid identification of Bordetella pertussis pertactin gene variants using LightCycler real-time polymerase chain reaction combined with melting curve analysis and gel electrophoresis.

    PubMed Central

    Mäkinen, J.; Viljanen, M. K.; Mertsola, J.; Arvilommi, H.; He, Q.

    2001-01-01

    Recently, eight allelic variants of the pertactin gene (prn1-8) have been characterized in Bordetella pertussis strains isolated in Europe and the United States. It has been suggested that the divergence of the pertactin types of clinical isolates from those of the B. pertussis vaccine strains is a result of vaccine-driven evolution. Sequencing of the prn, which is relatively time-consuming, has so far been the only method for the differentiation of prn types. We have developed a rapid real-time polymerase chain reaction assay suitable for large-scale screening of the prn type of the circulating strains. This method correctly identified the prn type of all tested 41 clinical isolates and two Finnish vaccine strains. The method is simple and reliable and provides an alternative for sequencing in pertussis research. PMID:11747721

  4. Real-time PCR for the detection and quantification of geodermatophilaceae from stone samples and identification of new members of the genus blastococcus.

    PubMed

    Salazar, Oscar; Valverde, Aranzazu; Genilloud, Olga

    2006-01-01

    Real-time PCR (RT-PCR) technology was used for the specific detection and quantification of members of the family Geodermatophilaceae in stone samples. Differences in the nucleotide sequences of the 16S rRNA gene region were used to design a pair of family-specific primers that were used to detect and quantify by RT-PCR DNA from members of this family in stone samples from different geographical origins in Spain. These primers were applied later to identify by PCR-specific amplification new members of the family Geodermatophilaceae isolated from the same stone samples. The diversity and taxonomic position of the wild-type strains identified from ribosomal sequence analysis suggest the presence of a new lineage within the genus Blastococcus.

  5. Identification of Endogenous HLA-A2–Restricted Reactivity Against Shared Melanoma Antigens in Patients Using the Quantitative Real-Time Polymerase Chain Reaction

    PubMed Central

    Thurber, Stacy E.; Khong, Hung T.; Kammula, Udai S.; Rosenberg, Steven A.

    2008-01-01

    Summary This study was conducted to determine whether reactivity to melanoma cells of pretreatment peripheral blood mononuclear cells (PBMCs) from patients with metastatic melanoma correlated with subsequent response to treatment with interleukin-2 (IL-2). The sensitivity of the quantitative real-time polymerase chain reaction (PCR) assay was optimized, including the total number of cells used (3 × 106 in 1 mL), the responder-to-stimulator cell ratio (5:1), the optimal time to incubate PBMCs with tumor (2 h), the appropriate tumor stimulators (melanoma cell lines differing only in the expression of histocompatibility leukocyte antigen [HLA-A2]), the duration of recovery in the culture of PBMCs after cryopreservation (18–24 h), and the medium used (Iscove, 10% human AB serum). Using this optimized assay to detect HLA-A2–restricted antitumor reactivity in the pretreatment PBMCs from patients with melanoma, positive reactive responses were detected in 7 of 28 patients with an objective clinical response to IL-2 therapy compared with 6 of 21 positive reactive responses in nonresponding patients. None of 12 healthy donors were positive in this study. Thus, there was no significant difference in the reactivity of pretreatment PBMCs when responders were compared with nonresponders, although the melanoma patients had an increased incidence of response compared with healthy donors (p = 0.05). The PBMCs from 11 of the 13 melanoma patients with pretreatment HLA-A2–restricted antimelanoma reactivity were tested against a panel of transfectants expressing known shared melanoma antigens. Anti–MART-1 reactivity was detected in the pretreatment PBMCs of three patients. It thus appears that some melanoma patients are immunologically primed to antigens expressed on the tumor surface, although the HLA-A2–restricted antimelanoma activity detected in this real-time PCR assay was not predictive of patients’ responses to IL-2 therapy. PMID:11924911

  6. Real time gamma-ray signature identifier

    DOEpatents

    Rowland, Mark; Gosnell, Tom B.; Ham, Cheryl; Perkins, Dwight; Wong, James

    2012-05-15

    A real time gamma-ray signature/source identification method and system using principal components analysis (PCA) for transforming and substantially reducing one or more comprehensive spectral libraries of nuclear materials types and configurations into a corresponding concise representation/signature(s) representing and indexing each individual predetermined spectrum in principal component (PC) space, wherein an unknown gamma-ray signature may be compared against the representative signature to find a match or at least characterize the unknown signature from among all the entries in the library with a single regression or simple projection into the PC space, so as to substantially reduce processing time and computing resources and enable real-time characterization and/or identification.

  7. Real-time software receiver

    NASA Technical Reports Server (NTRS)

    Ledvina, Brent M. (Inventor); Psiaki, Mark L. (Inventor); Powell, Steven P. (Inventor); Kintner, Jr., Paul M. (Inventor)

    2007-01-01

    A real-time software receiver that executes on a general purpose processor. The software receiver includes data acquisition and correlator modules that perform, in place of hardware correlation, baseband mixing and PRN code correlation using bit-wise parallelism.

  8. Real-time software receiver

    NASA Technical Reports Server (NTRS)

    Ledvina, Brent M. (Inventor); Psiaki, Mark L. (Inventor); Powell, Steven P. (Inventor); Kintner, Jr., Paul M. (Inventor)

    2006-01-01

    A real-time software receiver that executes on a general purpose processor. The software receiver includes data acquisition and correlator modules that perform, in place of hardware correlation, baseband mixing and PRN code correlation using bit-wise parallelism.

  9. Real-time vision systems

    SciTech Connect

    Johnson, R.; Hernandez, J.E.; Lu, Shin-yee

    1994-11-15

    Many industrial and defence applications require an ability to make instantaneous decisions based on sensor input of a time varying process. Such systems are referred to as `real-time systems` because they process and act on data as it occurs in time. When a vision sensor is used in a real-time system, the processing demands can be quite substantial, with typical data rates of 10-20 million samples per second. A real-time Machine Vision Laboratory (MVL) was established in FY94 to extend our years of experience in developing computer vision algorithms to include the development and implementation of real-time vision systems. The laboratory is equipped with a variety of hardware components, including Datacube image acquisition and processing boards, a Sun workstation, and several different types of CCD cameras, including monochrome and color area cameras and analog and digital line-scan cameras. The equipment is reconfigurable for prototyping different applications. This facility has been used to support several programs at LLNL, including O Division`s Peacemaker and Deadeye Projects as well as the CRADA with the U.S. Textile Industry, CAFE (Computer Aided Fabric Inspection). To date, we have successfully demonstrated several real-time applications: bullet tracking, stereo tracking and ranging, and web inspection. This work has been documented in the ongoing development of a real-time software library.

  10. Application of qualitative and quantitative real-time PCR, direct sequencing, and terminal restriction fragment length polymorphism analysis for detection and identification of polymicrobial 16S rRNA genes in ascites.

    PubMed

    Krohn, Sandra; Böhm, Stephan; Engelmann, Cornelius; Hartmann, Jan; Brodzinski, Annika; Chatzinotas, Antonis; Zeller, Katharina; Prywerek, Delia; Fetzer, Ingo; Berg, Thomas

    2014-05-01

    Qualitative and quantitative 16S rRNA gene-based real-time PCR and direct sequencing were applied for rapid detection and identification of bacterial DNA (bactDNA) in 356 ascites samples. bactDNA was detected in 35% of samples, with a mean of 3.24 log copies ml(-1). Direct sequencing of PCR products revealed 62% mixed chromatograms predominantly belonging to Gram-positive bacteria. Terminal restriction fragment length polymorphism (T-RFLP) results of a sample subset confirmed sequence data showing polymicrobial DNA contents in 67% of bactDNA-positive ascites samples.

  11. Multiplex Real-Time PCR Assay Using TaqMan Probes for the Identification of Trypanosoma cruzi DTUs in Biological and Clinical Samples

    PubMed Central

    Cura, Carolina I.; Duffy, Tomas; Lucero, Raúl H.; Bisio, Margarita; Péneau, Julie; Jimenez-Coello, Matilde; Calabuig, Eva; Gimenez, María J.; Valencia Ayala, Edward; Kjos, Sonia A.; Santalla, José; Mahaney, Susan M.; Cayo, Nelly M.; Nagel, Claudia; Barcán, Laura; Málaga Machaca, Edith S.; Acosta Viana, Karla Y.; Brutus, Laurent; Ocampo, Susana B.; Aznar, Christine; Cuba Cuba, Cesar A.; Gürtler, Ricardo E.; Ramsey, Janine M.; Ribeiro, Isabela; VandeBerg, John L.; Yadon, Zaida E.; Osuna, Antonio; Schijman, Alejandro G.

    2015-01-01

    Background Trypanosoma cruzi has been classified into six Discrete Typing Units (DTUs), designated as TcI–TcVI. In order to effectively use this standardized nomenclature, a reproducible genotyping strategy is imperative. Several typing schemes have been developed with variable levels of complexity, selectivity and analytical sensitivity. Most of them can be only applied to cultured stocks. In this context, we aimed to develop a multiplex Real-Time PCR method to identify the six T. cruzi DTUs using TaqMan probes (MTq-PCR). Methods/Principal Findings The MTq-PCR has been evaluated in 39 cultured stocks and 307 biological samples from vectors, reservoirs and patients from different geographical regions and transmission cycles in comparison with a multi-locus conventional PCR algorithm. The MTq-PCR was inclusive for laboratory stocks and natural isolates and sensitive for direct typing of different biological samples from vectors, reservoirs and patients with acute, congenital infection or Chagas reactivation. The first round SL-IR MTq-PCR detected 1 fg DNA/reaction tube of TcI, TcII and TcIII and 1 pg DNA/reaction tube of TcIV, TcV and TcVI reference strains. The MTq-PCR was able to characterize DTUs in 83% of triatomine and 96% of reservoir samples that had been typed by conventional PCR methods. Regarding clinical samples, 100% of those derived from acute infected patients, 62.5% from congenitally infected children and 50% from patients with clinical reactivation could be genotyped. Sensitivity for direct typing of blood samples from chronic Chagas disease patients (32.8% from asymptomatic and 22.2% from symptomatic patients) and mixed infections was lower than that of the conventional PCR algorithm. Conclusions/Significance Typing is resolved after a single or a second round of Real-Time PCR, depending on the DTU. This format reduces carryover contamination and is amenable to quantification, automation and kit production. PMID:25993316

  12. OPAD-EDIFIS Real-Time Processing

    NASA Technical Reports Server (NTRS)

    Katsinis, Constantine

    1997-01-01

    The Optical Plume Anomaly Detection (OPAD) detects engine hardware degradation of flight vehicles through identification and quantification of elemental species found in the plume by analyzing the plume emission spectra in a real-time mode. Real-time performance of OPAD relies on extensive software which must report metal amounts in the plume faster than once every 0.5 sec. OPAD software previously written by NASA scientists performed most necessary functions at speeds which were far below what is needed for real-time operation. The research presented in this report improved the execution speed of the software by optimizing the code without changing the algorithms and converting it into a parallelized form which is executed in a shared-memory multiprocessor system. The resulting code was subjected to extensive timing analysis. The report also provides suggestions for further performance improvement by (1) identifying areas of algorithm optimization, (2) recommending commercially available multiprocessor architectures and operating systems to support real-time execution and (3) presenting an initial study of fault-tolerance requirements.

  13. Identification and Evaluation of Suitable Reference Genes for Gene Expression Studies in the Whitefly Bemisia tabaci (Asia I) by Reverse Transcription Quantitative Real-Time PCR

    PubMed Central

    Collins, Carl; Patel, Mitulkumar V.; Colvin, John; Bailey, David; Seal, Susan

    2014-01-01

    This study presents a reliable method for performing reverse transcription quantitative real-time PCR (RT-qPCR) to measure gene expression in the whitefly Bemisia tabaci (Asia I) (Gennadius) (Hemiptera: Aleyrodidae), utilising suitable reference genes for data normalisation. We identified orthologs of commonly used reference genes (actin (ACT), cyclophilin 1 (CYP1), elongation factor 1α (EF1A), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), ribosomal protein L13a (RPL13A), and α-tubulin (TUB1A)), measured the levels of their transcripts by RT-qPCR during development and in response to thermal stress, and evaluated their suitability as endogenous controls using geNorm, BestKeeper, and NormFinder programs. Overall, TUB1A, RPL13A, and CYP1 were the most stable reference genes during B. tabaci development, and TUB1A, GAPDH, and RPL13A were the most stable reference genes in the context of thermal stress. An analysis of the effects of reference gene choice on the transcript profile of a developmentally-regulated gene encoding vitellogenin demonstrated the importance of selecting the correct endogenous controls for RT-qPCR studies. We propose the use of TUB1A, RPL13A, and CYP1 as endogenous controls for transcript profiling studies of B. tabaci development, whereas the combination of TUB1A, GAPDH, and RPL13A should be employed for studies into thermal stress. The data presented here will assist future transcript profiling studies in whiteflies. PMID:25373210

  14. Identification of the major capsid protein of erythrocytic necrosis virus (ENV) and development of quantitative real-time PCR assays for quantification of ENV DNA

    USGS Publications Warehouse

    Purcell, Maureen K.; Pearman-Gillman, Schuyler; Thompson, Rachel L.; Gregg, Jacob L.; Hart, Lucas M.; Winton, James R.; Emmenegger, Eveline J.; Hershberger, Paul K.

    2016-01-01

    Viral erythrocytic necrosis (VEN) is a disease of marine and anadromous fish that is caused by the erythrocytic necrosis virus (ENV), which was recently identified as a novel member of family Iridoviridae by next-generation sequencing. Phylogenetic analysis of the ENV DNA polymerase grouped ENV with other erythrocytic iridoviruses from snakes and lizards. In the present study, we identified the gene encoding the ENV major capsid protein (MCP) and developed a quantitative real-time PCR (qPCR) assay targeting this gene. Phylogenetic analysis of the MCP gene sequence supported the conclusion that ENV does not group with any of the currently described iridovirus genera. Because there is no information regarding genetic variation of the MCP gene across the reported host and geographic range for ENV, we also developed a second qPCR assay for a more conserved ATPase-like gene region. The MCP and ATPase qPCR assays demonstrated good analytical and diagnostic sensitivity and specificity based on samples from laboratory challenges of Pacific herring Clupea pallasii. The qPCR assays had similar diagnostic sensitivity and specificity as light microscopy of stained blood smears for the presence of intraerythrocytic inclusion bodies. However, the qPCR assays may detect viral DNA early in infection prior to the formation of inclusion bodies. Both qPCR assays appear suitable for viral surveillance or as a confirmatory test for ENV in Pacific herring from the Salish Sea.

  15. Identification of the major capsid protein of erythrocytic necrosis virus (ENV) and development of quantitative real-time PCR assays for quantification of ENV DNA.

    PubMed

    Purcell, Maureen K; Pearman-Gillman, Schuyler; Thompson, Rachel L; Gregg, Jacob L; Hart, Lucas M; Winton, James R; Emmenegger, Eveline J; Hershberger, Paul K

    2016-07-01

    Viral erythrocytic necrosis (VEN) is a disease of marine and anadromous fish that is caused by the erythrocytic necrosis virus (ENV), which was recently identified as a novel member of family Iridoviridae by next-generation sequencing. Phylogenetic analysis of the ENV DNA polymerase grouped ENV with other erythrocytic iridoviruses from snakes and lizards. In the present study, we identified the gene encoding the ENV major capsid protein (MCP) and developed a quantitative real-time PCR (qPCR) assay targeting this gene. Phylogenetic analysis of the MCP gene sequence supported the conclusion that ENV does not group with any of the currently described iridovirus genera. Because there is no information regarding genetic variation of the MCP gene across the reported host and geographic range for ENV, we also developed a second qPCR assay for a more conserved ATPase-like gene region. The MCP and ATPase qPCR assays demonstrated good analytical and diagnostic sensitivity and specificity based on samples from laboratory challenges of Pacific herring Clupea pallasii The qPCR assays had similar diagnostic sensitivity and specificity as light microscopy of stained blood smears for the presence of intraerythrocytic inclusion bodies. However, the qPCR assays may detect viral DNA early in infection prior to the formation of inclusion bodies. Both qPCR assays appear suitable for viral surveillance or as a confirmatory test for ENV in Pacific herring from the Salish Sea. PMID:27154315

  16. Identification of sexually dimorphic gene expression in brain tissue of the fish Leporinus macrocephalus through mRNA differential display and real time PCR analyses.

    PubMed

    Alves-Costa, Fernanda A; Wasko, A P

    2010-03-01

    Differentially expressed genes in males and females of vertebrate species generally have been investigated in gonads and, to a lesser extent, in other tissues. Therefore, we attempted to identify sexually dimorphic gene expression in the brains of adult males and females of Leporinus macrocephalus, a gonochoristic fish species that presents a ZZ/ZW sex determination system, throughout a comparative analysis using differential display reverse transcriptase-PCR and real-time PCR. Four cDNA fragments were characterized, representing candidate genes with differential expression between the samples. Two of these fragments presented no significant identity with previously reported gene sequences. The other two fragments, isolated from male specimens, were associated to the gene that codes for the protein APBA2 (amyloid beta (A4) precursor protein-binding, family A, member 2) and to the Rab 37 gene, a member of the Ras oncogene family. The overexpression of these genes has been associated to a greater production of the beta-amyloid protein which, in turns, is the major factor that leads to Alzheimer's disease, and to the development of brain-tumors, respectively. Quantitative RT-PCR analyses revealed a higher Apba2 gene expression in males, thus validating the previous data on differential display. L. macrocephalus may represent an interesting animal model to the understanding of the function of several vertebrate genes, including those involved in neurodegenerative and cancer diseases.

  17. Sequential real-time PCR assays applied to identification of genomic signatures in formalin-fixed paraffin-embedded tissues: a case report about brucella-induced osteomyelitis.

    PubMed

    Zhang, Binxue; Wear, Douglas J; Stojadinovic, Alexander; Izadjoo, Mina

    2013-01-01

    Brucellosis is a zoonotic infection transmitted from animals to human by ingestion of infected food products, direct contact with an infected animal, or inhalation of aerosols. Brucella infection-induced osteomyelitis may present only with nonspecific clinical and radiographic findings, mild elevations in serum inflammatory markers, as well as nonspecific histological changes. We studied a case of an Iraqi war veteran with multifocal vertebral body and left iliac bone lesions on radio nucleotide scans and magnetic resonance imaging, clinically suspected osteomyelitis possibly because of Brucella. Although histomorphological findings were nonspecific, consisting of chronic inflammatory cell infiltrate and reactive fibrosis, tissue gram and silver impregnation stains of bone biopsies were informative, revealing gram-negative coccobacilli consistent in size with Brucella species. Total nucleic acids were extracted from formalin-fixed paraffin-embedded tissues and amplified by sequential real-time polymerase chain reaction, targeting genes coding (1) outer membrane protein (omp-31) of Brucella species and (2) insertion sequence (IS711) of Brucella abortus (b-abt). Polymerase chain reaction results confirmed B. abortus as the causative pathogens for presumed diagnosis of Brucella osteomyelitis. PMID:23356125

  18. Identification of CD70 as a diagnostic biomarker for clear cell renal cell carcinoma by gene expression profiling, real-time RT-PCR and immunohistochemistry.

    PubMed

    Diegmann, Julia; Junker, Kerstin; Gerstmayer, Bernhard; Bosio, Andreas; Hindermann, Winfried; Rosenhahn, Julia; von Eggeling, Ferdinand

    2005-08-01

    The underlying molecular mechanisms of renal cell carcinoma (RCC) are poorly understood and more reliable markers for early diagnosis are needed. Hence, alternative strategies for biomarker discovery with appropriate validation technologies have to be performed. To elucidate genesis and progression of RCC we used high parallel chip based gene expression profiling comparing normal and tumour tissues. We compared corresponding control and tumour tissue samples from 10 patients with clear cell RCC. We isolated RNA from histologically well characterised tissue sections and performed reverse transcription, labelling and linear RNA amplification. Samples were hybridised on microarrays containing 642 human cDNAs. Of the 352 differentially expressed genes found, CD70 and FRA2 were selected for further evaluation by real-time RT-PCR. The analysis all showed a high potential to discriminate between normal and tumour tissue. Moreover, increased CD70 mRNA expression in tumour cells could be correlated to its expression at the protein level. Immunohistochemistry (IHC) showed very strong expression of CD70 in all tumour samples but no expression in adjacent normal kidney tissue. With our combined approach we were able to identify CD70 as a new marker for RCC, which may be useful in the future for improved immunohistochemical diagnosis. PMID:16043348

  19. Real-time identification of bacteria and Candida species in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

    PubMed

    Ferroni, Agnès; Suarez, Stéphanie; Beretti, Jean-Luc; Dauphin, Brunhilde; Bille, Emmanuelle; Meyer, Julie; Bougnoux, Marie-Elisabeth; Alanio, Alexandre; Berche, Patrick; Nassif, Xavier

    2010-05-01

    Delays in the identification of microorganisms are a barrier to the establishment of adequate empirical antibiotic therapy of bacteremia. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) allows the identification of microorganisms directly from colonies within minutes. In this study, we have adapted and tested this technology for use with blood culture broths, thus allowing identification in less than 30 min once the blood culture is detected as positive. Our method is based on the selective recovery of bacteria by adding a detergent that solubilizes blood cells but not microbial membranes. Microorganisms are then extracted by centrifugation and analyzed by MALDI-TOF-MS. This strategy was first tested by inoculating various bacterial and fungal species into negative blood culture bottles. We then tested positive patient blood or fluid samples grown in blood culture bottles, and the results obtained by MALDI-TOF-MS were compared with those obtained using conventional strategies. Three hundred twelve spiked bottles and 434 positive cultures from patients were analyzed. Among monomicrobial fluids, MALDI-TOF-MS allowed a reliable identification at the species, group, and genus/family level in 91%, 5%, and 2% of cases, respectively, in 20 min. In only 2% of these samples, MALDI-TOF MS did not yield any result. When blood cultures were multibacterial, identification was improved by using specific databases based on the Gram staining results. MALDI-TOF-MS is currently the fastest technique to accurately identify microorganisms grown in positive blood culture broths.

  20. Identification of normalization factors for quantitative real-time RT-PCR analysis of gene expression in Pacific abalone Haliotis discus hannai

    NASA Astrophysics Data System (ADS)

    Qiu, Reng; Sun, Boguang; Fang, Shasha; Sun, Li; Liu, Xiao

    2013-03-01

    Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is widely used in studies of gene expression. In most of these studies, housekeeping genes are used as internal references without validation. To identify appropriate reference genes for qRT-PCR in Pacific abalone Haliotis discus hannai, we examined the transcription stability of six housekeeping genes in abalone tissues in the presence and absence of bacterial infection. For this purpose, abalone were infected with the bacterial pathogen Vibrio anguillarum for 12 h and 48 h. The mRNA levels of the housekeeping genes in five tissues (digestive glands, foot muscle, gill, hemocyte, and mantle) were determined by qRT-PCR. The PCR data was subsequently analyzed with the geNorm and NormFinder algorithms. The results show that in the absence of bacterial infection, elongation factor-1-alpha and beta-actin were the most stably expressed genes in all tissues, and thus are suitable as cross-tissue type normalization factors. However, we did not identify any universal reference genes post infection because the most stable genes varied between tissue types. Furthermore, for most tissues, the optimal reference genes identified by both algorithms at 12 h and 48 h post-infection differed. These results indicate that bacterial infection induced significant changes in the expression of abalone housekeeping genes in a manner that is dependent on tissue type and duration of infection. As a result, different normalization factors must be used for different tissues at different infection points.

  1. Identification and validation of reference genes for Populus euphratica gene expression analysis during abiotic stresses by quantitative real-time PCR.

    PubMed

    Wang, Hou-Ling; Chen, Jinhuan; Tian, Qianqian; Wang, Shu; Xia, Xinli; Yin, Weilun

    2014-11-01

    Populus euphratica is the only arboreal species that is established in the world's largest shifting-sand desert in China and is well-adapted to the extreme desert environment, so it is widely considered a model system for researching into abiotic stress resistance of woody plants. However, few P. euphratica reference genes (RGs) have been identified for quantitative real-time polymerase chain reaction (qRT-PCR) until now. Validation of suitable RGs is essential for gene expression normalization research. In this study, we screened 16 endogenous candidate RGs in P. euphratica leaves in six abiotic stress treatments, including abscisic acid (ABA), cold, dehydration, drought, short-duration salt (SS) and long-duration salt (LS) treatments, each with 6 treatment gradients. After calculation of PCR efficiencies, three different software tools, NormFinder, geNorm and BestKeeper, were employed to analyze the qRT-PCR data systematically, and the outputs were merged by means of a non-weighted unsupervised rank aggregation method. The genes selected as optimal for gene expression analysis of the six treatments were RPL17 (ribosomal protein L17) in ABA, EF1α (elongation factor-1 alpha) in cold, HIS (histone superfamily protein H3) in dehydration, GIIα in drought and SS, and TUB (tubulin) in LS. The expression of 60S (the 60S ribosomal protein) varied the least during all treatments. To illustrate the suitability of these RGs, the relative quantifications of three stress-inducible genes, PePYL1, PeSCOF-1 and PeSCL7 were investigated with different RGs. The results, calculated using qBasePlus software, showed that compared with the least-appropriate RGs, the expression profiles normalized by the recommended RGs were closer to expectations. Our study provided an important RG application guideline for P. euphratica gene expression characterization. PMID:24720378

  2. Light-scattering sensor for real-time identification of Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae colonies on solid agar plate.

    PubMed

    Huff, Karleigh; Aroonnual, Amornrat; Littlejohn, Amy E Fleishman; Rajwa, Bartek; Bae, Euiwon; Banada, Padmapriya P; Patsekin, Valery; Hirleman, E Daniel; Robinson, J Paul; Richards, Gary P; Bhunia, Arun K

    2012-09-01

    The three most common pathogenic species of Vibrio, Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus, are of major concerns due to increased incidence of water- and seafood-related outbreaks and illness worldwide. Current methods are lengthy and require biochemical and molecular confirmation. A novel label-free forward light-scattering sensor was developed to detect and identify colonies of these three pathogens in real time in the presence of other vibrios in food or water samples. Vibrio colonies grown on agar plates were illuminated by a 635 nm laser beam and scatter-image signatures were acquired using a CCD (charge-coupled device) camera in an automated BARDOT (BActerial Rapid Detection using Optical light-scattering Technology) system. Although a limited number of Vibrio species was tested, each produced a unique light-scattering signature that is consistent from colony to colony. Subsequently a pattern recognition system analysing the collected light-scatter information provided classification in 1-2 min with an accuracy of 99%. The light-scattering signatures were unaffected by subjecting the bacteria to physiological stressors: osmotic imbalance, acid, heat and recovery from a viable but non-culturable state. Furthermore, employing a standard sample enrichment in alkaline peptone water for 6 h followed by plating on selective thiosulphate citrate bile salts sucrose agar at 30°C for ∼ 12 h, the light-scattering sensor successfully detected V. cholerae, V. parahaemolyticus and V. vulnificus present in oyster or water samples in 18 h even in the presence of other vibrios or other bacteria, indicating the suitability of the sensor as a powerful screening tool for pathogens on agar plates.

  3. Real-Time Detection and Identification of Chlamydophila Species in Veterinary Specimens by Using SYBR Green-Based PCR Assays ▿

    PubMed Central

    Nordentoft, Steen; Kabell, Susanne; Pedersen, Karl

    2011-01-01

    Infections caused by members of the Chlamydiaceae family have long been underestimated due to the requirement of special laboratory facilities for the detection of this group of intracellular pathogens. Furthermore, new studies of this group of intracellular pathogens have revealed that host specificity of different species is not as clear as recently believed. As most members of the genus Chlamydophila have shown to be transmissible from animals to humans, sensitive and fast detection methods are required. In this study, SYBR green-based real-time assays were developed that detect all members of Chlamydiaceae and differentiate the most prevalent veterinary Chlamydophila species: Cp. psittaci, Cp. abortus, Cp. felis, and Cp. caviae. By adding bovine serum albumin to the master mixes, target DNA could be detected directly in crude lysates of enzymatically digested conjunctival or pharyngeal swabs or tissue specimens from heart, liver, and spleen without further purification. The assays were evaluated on veterinary specimens where all samples were screened using a family-specific PCR, and positive samples were further tested using species-specific PCRs. Cp. psittaci was detected in 47 birds, Cp. felis was found in 10 cats, Cp. caviae was found in one guinea pig, and Cp. abortus was detected in one sheep. The screening assay appeared more sensitive than traditional microscopical examination of stained tissue smears. By combining a fast, robust, and cost-effective method for sample preparation with a highly sensitive family-specific PCR, we were able to screen for Chlamydiaceae in veterinary specimens and confirm the species in positive samples with additional PCR assays. PMID:21764961

  4. Development and Validation of LNA-Based Quantitative Real-Time PCR Assays for Detection and Identification of the Root-Knot Nematode Meloidogyne enterolobii in Complex DNA Backgrounds.

    PubMed

    Kiewnick, Sebastian; Frey, Jürg E; Braun-Kiewnick, Andrea

    2015-09-01

    Meloidogyne enterolobii is a quarantine root-knot nematode posing a major threat to agricultural production systems worldwide. It attacks many host plants, including important agricultural crops, ornamentals, and trees. M. enterolobii is a highly virulent and pathogenic root-knot nematode species, able to reproduce on plants resistant to other Meloidogyne spp. Significant crop damage has been reported in Asia, South America, Africa, the United States, France, and greenhouses in Switzerland. To identify potential introduction pathways and ensure appropriate phytosanitary measures and management strategies, accurate detection and identification tools are needed. Therefore, two real-time quantitative polymerase chain reaction (PCR) assays based on the second intergenic spacer region of the ribosomal DNA cistron and the cytochrome oxidase c subunit I (COI) gene using locked nucleic acid probes were developed and validated for fast and reliable detection and identification of M. enterolobii. Analytical specificity was confirmed with 16 M. enterolobii populations, 16 populations of eight closely related Meloidogyne spp., and four species from other nematode genera. Optimizing and testing the assays on two real-time PCR platforms revealed an analytical sensitivity of one juvenile in a background of 1,000 nematodes and the intended limit of detection of one juvenile per 100 ml of soil. Both assays performed equally well, with the COI-based assay showing a slightly better performance concerning detection of M. enterolobii target DNA in complex DNA backgrounds.

  5. Real-Time Moire Holography

    NASA Astrophysics Data System (ADS)

    Soares, O. D. D.; Lage, A. I. V. S.

    1986-08-01

    Interferometric techniques including hologrametry, both classical and electronic, present high sensitivity making difficult its practical use in real-time. The introduction of the differencial concept as moire evaluation techniques permits to use with advantage an arbitrary reference pattern within the correlation range. The carrier spatial spectrum can be directly the interferogram fringe pattern instead of the original interference pattern of wavelength dimensional scale. A moire techniques is in itself an optical processing method reducing evaluation time which is advantageous when real-time response is desired from hybrid metrological systems. The moire evaluation is performed via a dynamical digital memory that executes arithmetic operations on two frames temporally in sequence, at TV rate. These characteristics of the moire evaluation techniques can be implemented on a real-time holographic (or speckle based) hybrid system with great practical advantage for dynamical studies.

  6. Real-Time Identification of Bacteria and Candida Species in Positive Blood Culture Broths by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry▿

    PubMed Central

    Ferroni, Agnès; Suarez, Stéphanie; Beretti, Jean-Luc; Dauphin, Brunhilde; Bille, Emmanuelle; Meyer, Julie; Bougnoux, Marie-Elisabeth; Alanio, Alexandre; Berche, Patrick; Nassif, Xavier

    2010-01-01

    Delays in the identification of microorganisms are a barrier to the establishment of adequate empirical antibiotic therapy of bacteremia. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) allows the identification of microorganisms directly from colonies within minutes. In this study, we have adapted and tested this technology for use with blood culture broths, thus allowing identification in less than 30 min once the blood culture is detected as positive. Our method is based on the selective recovery of bacteria by adding a detergent that solubilizes blood cells but not microbial membranes. Microorganisms are then extracted by centrifugation and analyzed by MALDI-TOF-MS. This strategy was first tested by inoculating various bacterial and fungal species into negative blood culture bottles. We then tested positive patient blood or fluid samples grown in blood culture bottles, and the results obtained by MALDI-TOF-MS were compared with those obtained using conventional strategies. Three hundred twelve spiked bottles and 434 positive cultures from patients were analyzed. Among monomicrobial fluids, MALDI-TOF-MS allowed a reliable identification at the species, group, and genus/family level in 91%, 5%, and 2% of cases, respectively, in 20 min. In only 2% of these samples, MALDI-TOF MS did not yield any result. When blood cultures were multibacterial, identification was improved by using specific databases based on the Gram staining results. MALDI-TOF-MS is currently the fastest technique to accurately identify microorganisms grown in positive blood culture broths. PMID:20237092

  7. Identification of tuna species in commercial cans by minor groove binder probe real-time polymerase chain reaction analysis of mitochondrial DNA sequences.

    PubMed

    Terio, Valentina; Di Pinto, Pietro; Decaro, Nicola; Parisi, Antonio; Desario, Costantina; Martella, Vito; Buonavoglia, Canio; Tantillo, Marilia Giuseppina

    2010-12-01

    Three different minor groove binder (MGB) probe assays have been developed for rapid and accurate identification of the species commonly used for production of canned tuna, i.e. yellowfin (Thunnus albacares), bluefin (Thunnus thynnus) and albacore (Thunnus alalunga) tunas. The assays targeting the mitochondrial cytochrome b gene were able to discriminate efficiently between the three species contained in fresh or canned tunas and did not react with other Scombroidei that were tested. A correct species prediction was obtained even from artificial mixtures prepared with different amounts of the reference tuna species and subjected to the sterilisation treatment. Testing of 27 commercial canned tunas by PCR-RFLP, MGB probe assays and sequence analysis showed a concordance of 100% between the last two techniques, whereas by using PCR-RFLP several samples were uncharacterised or mischaracterised. These results make the established MGB probe assays an attractive tool for direct and rapid species identification in canned tuna. PMID:20691254

  8. A real-time data acquisition and control of gradient coil noise for fMRI identification of hearing disorder in children with history of ear infection

    PubMed Central

    Lee, Jaeseung; Holte, James

    2013-01-01

    Early ear infection and trauma, from birth to age 12 are known to have a significant effect on sensory and cognitive development. This effect can be demonstrated through the fMRI study of children who have a history of ear infection compared to a control group. A second research question is the extent to which brain plasticity at an early age can reduce the impact of infection on hearing and cognitive development. Functional Magnetic Resonance Imaging (fMRI) provides a mapping of brain activity in cognitive and sensory regions by recording the oxygenation state of the local cerebral blood flow. The gradient coils of fMRI scanners generate intense acoustic noise (GCN) - to which the subject is in close proximity - in the range of 90 to 140 db SPL during the imaging process. Clearly this noise will impress its signature on low level brain response patterns. An Active Noise Canceller (ANC) system can suppress the effect of GCN on the subject’s perception of a phonetic stimulus at the phoneme, word or phrase level. Due to a superimposition of the frequency and time domain components of the test signal and GCN for MR test, the ANC filtering system performs its function in real time - we must capture the brain’s response to the test signal AFTER the noise has been removed. This goal is achieved through the application of field programmable gate array (FPGA) technology of NI LabVIEW. The presentation (in the noisy fMRI environment) of test words and phrases to hearing impaired children can identify sources of distortion to their perceptual processes associated with GCN. Once this distortion has been identified, learning strategies may be introduced to replace the hearing function distorted by early infection as well as the short term effect of GCN. The study of speech cognition without the confounding effect of GCN and with the varying level of GCN for a repeated test signal at later age can be allowed to a measure of recovery through brain plasticity. PMID:23482910

  9. Identification of Suitable Reference Genes for Gene Expression Normalization in the Quantitative Real-Time PCR Analysis of Sweet Osmanthus (Osmanthus fragrans Lour.)

    PubMed Central

    Wang, Yiguang; Bao, Zhiyi; Zhao, Hongbo

    2015-01-01

    Quantitative real-time PCR (RT-qPCR), a sensitive technique for quantifying gene expression, depends on the stability of the reference gene(s) used for data normalization. Several studies examining the selection of reference genes have been performed in ornamental plants but none in sweet osmanthus (Osmanthus fragrans Lour.). Based on transcriptomic sequencing data from O. fragrans buds at four developmental stages, six reference genes (OfACT, OfEF1α, OfIDH, OfRAN1, OfTUB, and OfUBC2) with stable expression (0.5 to 2 fold change in expression levels between any two developmental stages), as well as the commonly used reference gene Of18S, were selected as candidates for gene expression normalization in the RT-qPCR analysis of O. fragrans. For the normalization of RT-qPCR with two dyes, SYBR Green and EvaGreen, the expressional stability of seven candidate reference genes in 43 O. fragrans samples was analyzed using geNorm, NormFinder and BestKeeper. For RT-qPCR using SYBR Green, OfRAN1 and OfUBC2 were the optimal reference genes for all samples and different cultivars, OfACT and OfEF1α were suitable for different floral developmental stages, and OfACT was the optimal reference gene for different temperature treatments. The geometric mean values of the optimal reference gene pairs for the normalization of RT-qPCR are recommended to be used for all samples, different cultivars and different floral developmental stages in O. fragrans. For RT-qPCR using EvaGreen, OfUBC2 was the optimal reference gene for all samples and different cultivars, and OfACT was the optimal reference gene for different floral developmental stages and different temperature treatments. As the worst reference gene, Of18S should not be used as a reference gene in O. fragrans in the future. Our results provide a reference gene application guideline for O. fragrans gene expression characterization using RT-qPCR. PMID:26302211

  10. Comparison of quantitative real time PCR with Sequencing and ribosomal RNA-FISH for the identification of fungi in Formalin fixed, paraffin-embedded tissue specimens

    PubMed Central

    2011-01-01

    Background Identification of the causative agents of invasive fungal infections (IFI) is critical for guiding antifungal therapy. Cultures remain negative in a substantial number of IFI cases. Accordingly, species identification from formalin fixed, paraffin embedded (FFPE) tissue specimens by molecular methods such as fluorescence in situ hybridisation (FISH) and PCR provides an appealing approach to improve management of patients. Methods We designed FISH probes targeting the 28S rRNA of Aspergillus and Candida and evaluated them with type strains. Fluorescence microscopy (FM), using FISH probes and quantitative broad-range fungal PCR targeting the rRNA gene were applied to FFPE tissue specimens from patients with proven IFI in order to explore benefits and limitations of each approach. Results PCR followed by sequencing identified a broad spectrum of pathogenic fungi in 28 of 40 evaluable samples (70%). Hybridisation of FISH probes to fungal rRNA was documented in 19 of 40 tissue samples (47.5%), including 3 PCR negative samples with low fungal burden. The use of FISH was highly sensitive in invasive yeast infections, but less sensitive for moulds. In samples with hyphal elements, the evaluation of hybridisation was impaired due to autofluorescence of hyphae and necrotic tissue background. Conclusions While PCR appears to be more sensitive in identifying the causative agents of IFI, some PCR negative and FISH positive samples suggest that FISH has some potential in the rapid identification of fungi from FFPE tissue samples. PMID:21791040

  11. Real Time Sonic Boom Display

    NASA Technical Reports Server (NTRS)

    Haering, Ed

    2014-01-01

    This presentation will provide general information about sonic boom mitigation technology to the public in order to supply information to potential partners and licensees. The technology is a combination of flight data, atmospheric data and terrain information implemented into a control room real time display for flight planning. This research is currently being performed and as such, any results and conclusions are ongoing.

  12. Identification and Quantification of a Toxigenic and Non-Toxigenic Aspergillus flavus Strain in Contaminated Maize Using Quantitative Real-Time PCR.

    PubMed

    Mylroie, J Erik; Ozkan, Seval; Shivaji, Renuka; Windham, Gary L; Alpe, Michael N; Williams, W Paul

    2016-01-01

    Aflatoxins, which are produced by Aspergillus flavus, are toxic to humans, livestock, and pets. The value of maize (Zea mays) grain is markedly reduced when contaminated with aflatoxin. Plant resistance and biological control using non-toxin producing strains are considered effective strategies for reducing aflatoxin accumulation in maize grain. Distinguishing between the toxin and non-toxin producing strains is important in determining the effectiveness of bio-control strategies and understanding inter-strain interactions. Using polymorphisms found in the fungal rRNA intergenic spacer region (IGS) between a toxigenic strain of A. flavus (NRRL 3357) and the non-toxigenic strain used in the biological control agent Afla-Guard(®) (NRRL 21882), we developed a set of primers that allows for the identification and quantification of the two strains using quantitative PCR. This primer set has been used to screen maize grain that was inoculated with the two strains individually and co-inoculated with both strains, and it has been shown to be effective in both the identification and quantification of both strains. Screening of co-inoculated ears from multiple resistant and susceptible genotypic crosses revealed no significant differences in fungal biomass accumulation of either strain in the field tests from 2010 and 2011 when compared across the means of all genotypes. Only one genotype/year combination showed significant differences in strain accumulation. Aflatoxin accumulation analysis showed that, as expected, genotypes inoculated with the toxigenic strain accumulated more aflatoxin than when co-inoculated with both strains or inoculated with only the non-toxigenic strain. Furthermore, accumulation of toxigenic fungal mass was significantly correlated with aflatoxin accumulation while non-toxigenic fungal accumulation was not. This primer set will allow researchers to better determine how the two fungal strains compete on the maize ear and investigate the interaction

  13. Identification and Quantification of a Toxigenic and Non-Toxigenic Aspergillus flavus Strain in Contaminated Maize Using Quantitative Real-Time PCR

    PubMed Central

    Mylroie, J. Erik; Ozkan, Seval; Shivaji, Renuka; Windham, Gary L.; Alpe, Michael N.; Williams, W. Paul

    2016-01-01

    Aflatoxins, which are produced by Aspergillus flavus, are toxic to humans, livestock, and pets. The value of maize (Zea mays) grain is markedly reduced when contaminated with aflatoxin. Plant resistance and biological control using non-toxin producing strains are considered effective strategies for reducing aflatoxin accumulation in maize grain. Distinguishing between the toxin and non-toxin producing strains is important in determining the effectiveness of bio-control strategies and understanding inter-strain interactions. Using polymorphisms found in the fungal rRNA intergenic spacer region (IGS) between a toxigenic strain of A. flavus (NRRL 3357) and the non-toxigenic strain used in the biological control agent Afla-Guard® (NRRL 21882), we developed a set of primers that allows for the identification and quantification of the two strains using quantitative PCR. This primer set has been used to screen maize grain that was inoculated with the two strains individually and co-inoculated with both strains, and it has been shown to be effective in both the identification and quantification of both strains. Screening of co-inoculated ears from multiple resistant and susceptible genotypic crosses revealed no significant differences in fungal biomass accumulation of either strain in the field tests from 2010 and 2011 when compared across the means of all genotypes. Only one genotype/year combination showed significant differences in strain accumulation. Aflatoxin accumulation analysis showed that, as expected, genotypes inoculated with the toxigenic strain accumulated more aflatoxin than when co-inoculated with both strains or inoculated with only the non-toxigenic strain. Furthermore, accumulation of toxigenic fungal mass was significantly correlated with aflatoxin accumulation while non-toxigenic fungal accumulation was not. This primer set will allow researchers to better determine how the two fungal strains compete on the maize ear and investigate the interaction

  14. Real time psychrometric data collection

    SciTech Connect

    McDaniel, K.H.

    1996-12-31

    Eight Mine Weather Stations (MWS) installed at the Waste Isolation Pilot Plant (WIPP) to monitor the underground ventilation system are helping to simulate real-time ventilation scenarios. Seasonal weather extremes can result in variations of Natural Ventilation Pressure (NVP) which can significantly effect the ventilation system. The eight MWS(s) (which previously collected and stored temperature, barometric pressure and relative humidity data for subsequent NVP calculations) were upgraded to provide continuous real-time data to the site wide Central monitoring System. This data can now be utilized by the ventilation engineer to create realtime ventilation simulations and trends which assist in the prediction and mitigation of NVP and psychrometric related events.

  15. Real-time tritium imaging

    SciTech Connect

    Malinowski, M.E.

    1981-09-15

    A real-time image of a tritium-containing titanium film has been made by detecting the secondary electrons produced by tritium ..beta.. decay with a simple two-element electrostatic lens and microchannel plate image intensifier. The obtained image indicates that a resolution of better than 100 ..mu..m is currently obtainable and suggests that image magnification to enhance resolution should be possible.

  16. Evaluation of RNA extraction methods and identification of putative reference genes for real-time quantitative polymerase chain reaction expression studies on olive (Olea europaea L.) fruits.

    PubMed

    Nonis, Alberto; Vezzaro, Alice; Ruperti, Benedetto

    2012-07-11

    Genome wide transcriptomic surveys together with targeted molecular studies are uncovering an ever increasing number of differentially expressed genes in relation to agriculturally relevant processes in olive (Olea europaea L). These data need to be supported by quantitative approaches enabling the precise estimation of transcript abundance. qPCR being the most widely adopted technique for mRNA quantification, preliminary work needs to be done to set up robust methods for extraction of fully functional RNA and for the identification of the best reference genes to obtain reliable quantification of transcripts. In this work, we have assessed different methods for their suitability for RNA extraction from olive fruits and leaves and we have evaluated thirteen potential candidate reference genes on 21 RNA samples belonging to fruit developmental/ripening series and to leaves subjected to wounding. By using two different algorithms, GAPDH2 and PP2A1 were identified as the best reference genes for olive fruit development and ripening, and their effectiveness for normalization of expression of two ripening marker genes was demonstrated.

  17. [Real time 3D echocardiography

    NASA Technical Reports Server (NTRS)

    Bauer, F.; Shiota, T.; Thomas, J. D.

    2001-01-01

    Three-dimensional representation of the heart is an old concern. Usually, 3D reconstruction of the cardiac mass is made by successive acquisition of 2D sections, the spatial localisation and orientation of which require complex guiding systems. More recently, the concept of volumetric acquisition has been introduced. A matricial emitter-receiver probe complex with parallel data processing provides instantaneous of a pyramidal 64 degrees x 64 degrees volume. The image is restituted in real time and is composed of 3 planes (planes B and C) which can be displaced in all spatial directions at any time during acquisition. The flexibility of this system of acquisition allows volume and mass measurement with greater accuracy and reproducibility, limiting inter-observer variability. Free navigation of the planes of investigation allows reconstruction for qualitative and quantitative analysis of valvular heart disease and other pathologies. Although real time 3D echocardiography is ready for clinical usage, some improvements are still necessary to improve its conviviality. Then real time 3D echocardiography could be the essential tool for understanding, diagnosis and management of patients.

  18. [Real time 3D echocardiography].

    PubMed

    Bauer, F; Shiota, T; Thomas, J D

    2001-07-01

    Three-dimensional representation of the heart is an old concern. Usually, 3D reconstruction of the cardiac mass is made by successive acquisition of 2D sections, the spatial localisation and orientation of which require complex guiding systems. More recently, the concept of volumetric acquisition has been introduced. A matricial emitter-receiver probe complex with parallel data processing provides instantaneous of a pyramidal 64 degrees x 64 degrees volume. The image is restituted in real time and is composed of 3 planes (planes B and C) which can be displaced in all spatial directions at any time during acquisition. The flexibility of this system of acquisition allows volume and mass measurement with greater accuracy and reproducibility, limiting inter-observer variability. Free navigation of the planes of investigation allows reconstruction for qualitative and quantitative analysis of valvular heart disease and other pathologies. Although real time 3D echocardiography is ready for clinical usage, some improvements are still necessary to improve its conviviality. Then real time 3D echocardiography could be the essential tool for understanding, diagnosis and management of patients. PMID:11494630

  19. Real-time exploitation system

    NASA Astrophysics Data System (ADS)

    Riedel, Richard D.

    1998-11-01

    The proliferation and technology advances of digital sensors for reconnaissance imaging require a commensurate increase in the productivity of ground-based exploitation system to process the increased volume of remotely-sensed data. Systems to support this level of production, themselves, must have significantly reduced development and life-cycle costs from previously installed systems. For cost, growth, and integration advantages, reconnaissance exploitation systems should be designed to maximize Commercial-Off-The-Shelf (COTS) hardware and software. As an example, the Real-Time Exploitation System is a state-of-the-art system for photo interpretation and exploitation of real-time digital reconnaissance imagery. Using COTS hardware, the system is able to receive imagery at rates greater than 80 Mpixels/sec; perform detailed interpretation, exploitation and report generation, and; disseminate reports to intelligence users over secure networks. New technologies have been applied in workflow management, database management, and user interfaces to provide the image analyst with superior analysis tools and access to other intelligence data sources. Photogrammetric functions are also provided for monoscopic and stereoscopic imagery. These functions provide greater geographic accuracy than is achievable in most reconnaissance exploitation systems. The Real-Time Exploitation System significantly reduces timelines for the analysis and report generation process, and significantly increases the quality and accuracy of reports.

  20. Performance of device-independent quantum key distribution

    NASA Astrophysics Data System (ADS)

    Cao, Zhu; Zhao, Qi; Ma, Xiongfeng

    2016-07-01

    Quantum key distribution provides information-theoretically-secure communication. In practice, device imperfections may jeopardise the system security. Device-independent quantum key distribution solves this problem by providing secure keys even when the quantum devices are untrusted and uncharacterized. Following a recent security proof of the device-independent quantum key distribution, we improve the key rate by tightening the parameter choice in the security proof. In practice where the system is lossy, we further improve the key rate by taking into account the loss position information. From our numerical simulation, our method can outperform existing results. Meanwhile, we outline clear experimental requirements for implementing device-independent quantum key distribution. The maximal tolerable error rate is 1.6%, the minimal required transmittance is 97.3%, and the minimal required visibility is 96.8 % .

  1. The First Results of Testing Methods and Algorithms for Automatic Real Time Identification of Waveforms Introduction from Local Earthquakes in Increased Level of Man-induced Noises for the Purposes of Ultra-short-term Warning about an Occurred Earthquake

    NASA Astrophysics Data System (ADS)

    Gravirov, V. V.; Kislov, K. V.

    2009-12-01

    The chief hazard posed by earthquakes consists in their suddenness. The number of earthquakes annually recorded is in excess of 100,000; of these, over 1000 are strong ones. Great human losses usually occur because no devices exist for advance warning of earthquakes. It is therefore high time that mobile information automatic systems should be developed for analysis of seismic information at high levels of manmade noise. The systems should be operated in real time with the minimum possible computational delays and be able to make fast decisions. The chief statement of the project is that sufficiently complete information about an earthquake can be obtained in real time by examining its first onset as recorded by a single seismic sensor or a local seismic array. The essential difference from the existing systems consists in the following: analysis of local seismic data at high levels of manmade noise (that is, when the noise level may be above the seismic signal level), as well as self-contained operation. The algorithms developed during the execution of the project will be capable to be used with success for individual personal protection kits and for warning the population in earthquake-prone areas over the world. The system being developed for this project uses P and S waves as well. The difference in the velocities of these seismic waves permits a technique to be developed for identifying a damaging earthquake. Real time analysis of first onsets yields the time that remains before surface waves arrive and the damage potential of these waves. Estimates show that, when the difference between the earthquake epicenter and the monitored site is of order 200 km, the time difference between the arrivals of P waves and surface waves will be about 30 seconds, which is quite sufficient to evacuate people from potentially hazardous space, insertion of moderators at nuclear power stations, pipeline interlocking, transportation stoppage, warnings issued to rescue services

  2. Real-time flutter analysis

    NASA Technical Reports Server (NTRS)

    Walker, R.; Gupta, N.

    1984-01-01

    The important algorithm issues necessary to achieve a real time flutter monitoring system; namely, the guidelines for choosing appropriate model forms, reduction of the parameter convergence transient, handling multiple modes, the effect of over parameterization, and estimate accuracy predictions, both online and for experiment design are addressed. An approach for efficiently computing continuous-time flutter parameter Cramer-Rao estimate error bounds were developed. This enables a convincing comparison of theoretical and simulation results, as well as offline studies in preparation for a flight test. Theoretical predictions, simulation and flight test results from the NASA Drones for Aerodynamic and Structural Test (DAST) Program are compared.

  3. Real-time streamflow conditions

    USGS Publications Warehouse

    Graczyk, David J.; Gebert, Warren A.

    1996-01-01

    Would you like to know streamflow conditions before you go fishing in Wisconsin or in more distant locations? Real-time streamflow data throughout Wisconsin and the United States are available on the Internet from the U.S. Geological Survey. You can see if the stream you are interested in fishing is high due to recent rain or low because of an extended dry spell. Flow conditions at more than 100 stream-gaging stations located throughout Wisconsin can be viewed by accessing the Wisconsin District Home Page at: http://wwwdwimdn.er.usgs.gov

  4. Real time infrared aerosol analyzer

    DOEpatents

    Johnson, Stanley A.; Reedy, Gerald T.; Kumar, Romesh

    1990-01-01

    Apparatus for analyzing aerosols in essentially real time includes a virtual impactor which separates coarse particles from fine and ultrafine particles in an aerosol sample. The coarse and ultrafine particles are captured in PTFE filters, and the fine particles impact onto an internal light reflection element. The composition and quantity of the particles on the PTFE filter and on the internal reflection element are measured by alternately passing infrared light through the filter and the internal light reflection element, and analyzing the light through infrared spectrophotometry to identify the particles in the sample.

  5. Device-independent bit commitment based on the CHSH inequality

    NASA Astrophysics Data System (ADS)

    Aharon, N.; Massar, S.; Pironio, S.; Silman, J.

    2016-02-01

    Bit commitment and coin flipping occupy a unique place in the device-independent landscape, as the only device-independent protocols thus far suggested for these tasks are reliant on tripartite GHZ correlations. Indeed, we know of no other bipartite tasks, which admit a device-independent formulation, but which are not known to be implementable using only bipartite nonlocality. Another interesting feature of these protocols is that the pseudo-telepathic nature of GHZ correlations—in contrast to the generally statistical character of nonlocal correlations, such as those arising in the violation of the CHSH inequality—is essential to their formulation and analysis. In this work, we present a device-independent bit commitment protocol based on CHSH testing, which achieves the same security as the optimal GHZ-based protocol, albeit at the price of fixing the time at which Alice reveals her commitment. The protocol is analyzed in the most general settings, where the devices are used repeatedly and may have long-term quantum memory. We also recast the protocol in a post-quantum setting where both honest and dishonest parties are restricted only by the impossibility of signaling, and find that overall the supra-quantum structure allows for greater security.

  6. Memory Attacks on Device-Independent Quantum Cryptography

    NASA Astrophysics Data System (ADS)

    Barrett, Jonathan; Colbeck, Roger; Kent, Adrian

    2013-01-01

    Device-independent quantum cryptographic schemes aim to guarantee security to users based only on the output statistics of any components used, and without the need to verify their internal functionality. Since this would protect users against untrustworthy or incompetent manufacturers, sabotage, or device degradation, this idea has excited much interest, and many device-independent schemes have been proposed. Here we identify a critical weakness of device-independent protocols that rely on public communication between secure laboratories. Untrusted devices may record their inputs and outputs and reveal information about them via publicly discussed outputs during later runs. Reusing devices thus compromises the security of a protocol and risks leaking secret data. Possible defenses include securely destroying or isolating used devices. However, these are costly and often impractical. We propose other more practical partial defenses as well as a new protocol structure for device-independent quantum key distribution that aims to achieve composable security in the case of two parties using a small number of devices to repeatedly share keys with each other (and no other party).

  7. Memory attacks on device-independent quantum cryptography.

    PubMed

    Barrett, Jonathan; Colbeck, Roger; Kent, Adrian

    2013-01-01

    Device-independent quantum cryptographic schemes aim to guarantee security to users based only on the output statistics of any components used, and without the need to verify their internal functionality. Since this would protect users against untrustworthy or incompetent manufacturers, sabotage, or device degradation, this idea has excited much interest, and many device-independent schemes have been proposed. Here we identify a critical weakness of device-independent protocols that rely on public communication between secure laboratories. Untrusted devices may record their inputs and outputs and reveal information about them via publicly discussed outputs during later runs. Reusing devices thus compromises the security of a protocol and risks leaking secret data. Possible defenses include securely destroying or isolating used devices. However, these are costly and often impractical. We propose other more practical partial defenses as well as a new protocol structure for device-independent quantum key distribution that aims to achieve composable security in the case of two parties using a small number of devices to repeatedly share keys with each other (and no other party). PMID:23383767

  8. Memory attacks on device-independent quantum cryptography.

    PubMed

    Barrett, Jonathan; Colbeck, Roger; Kent, Adrian

    2013-01-01

    Device-independent quantum cryptographic schemes aim to guarantee security to users based only on the output statistics of any components used, and without the need to verify their internal functionality. Since this would protect users against untrustworthy or incompetent manufacturers, sabotage, or device degradation, this idea has excited much interest, and many device-independent schemes have been proposed. Here we identify a critical weakness of device-independent protocols that rely on public communication between secure laboratories. Untrusted devices may record their inputs and outputs and reveal information about them via publicly discussed outputs during later runs. Reusing devices thus compromises the security of a protocol and risks leaking secret data. Possible defenses include securely destroying or isolating used devices. However, these are costly and often impractical. We propose other more practical partial defenses as well as a new protocol structure for device-independent quantum key distribution that aims to achieve composable security in the case of two parties using a small number of devices to repeatedly share keys with each other (and no other party).

  9. Real-time analysis keratometer

    NASA Technical Reports Server (NTRS)

    Adachi, Iwao P. (Inventor); Adachi, Yoshifumi (Inventor); Frazer, Robert E. (Inventor)

    1987-01-01

    A computer assisted keratometer in which a fiducial line pattern reticle illuminated by CW or pulsed laser light is projected on a corneal surface through lenses, a prismoidal beamsplitter quarterwave plate, and objective optics. The reticle surface is curved as a conjugate of an ideal corneal curvature. The fiducial image reflected from the cornea undergoes a polarization shift through the quarterwave plate and beamsplitter whereby the projected and reflected beams are separated and directed orthogonally. The reflected beam fiducial pattern forms a moire pattern with a replica of the first recticle. This moire pattern contains transverse aberration due to differences in curvature between the cornea and the ideal corneal curvature. The moire pattern is analyzed in real time by computer which displays either the CW moire pattern or a pulsed mode analysis of the transverse aberration of the cornea under observation, in real time. With the eye focused on a plurality of fixation points in succession, a survey of the entire corneal topography is made and a contour map or three dimensional plot of the cornea can be made as a computer readout in addition to corneal radius and refractive power analysis.

  10. Real time analysis under EDS

    NASA Astrophysics Data System (ADS)

    Schneberk, D.

    1985-07-01

    The analysis component of the Enrichment Diagnostic System (EDS) developed for the Atomic Vapor Laser Isotope Separation Program (AVLIS) at Lawrence Livermore National Laboratory (LLNL) is described. Four different types of analysis are performed on data acquired through EDS: (1) absorption spectroscopy on laser-generated spectral lines, (2) mass spectrometer analysis, (3) general purpose waveform analysis, and (4) separation performance calculations. The information produced from this data includes: measures of particle density and velocity, partial pressures of residual gases, and overall measures of isotope enrichment. The analysis component supports a variety of real-time modeling tasks, a means for broadcasting data to other nodes, and a great degree of flexibility for tailoring computations to the exact needs of the process. A particular data base structure and program flow is common to all types of analysis. Key elements of the analysis component are: (1) a fast access data base which can configure all types of analysis, (2) a selected set of analysis routines, (3) a general purpose data manipulation and graphics package for the results of real time analysis.

  11. Real-time face tracking

    NASA Astrophysics Data System (ADS)

    Liang, Yufeng; Wilder, Joseph

    1998-10-01

    A real-time face tracker is presented in this paper. The system has achieved 15 frames/second tracking using a Pentium 200 PC with a Datacube MaxPCI image processing board and a Panasonic RGB color camera. It tracks human faces in the camera's field of view while people move freely. A stochastic model to characterize the skin color distribution of human skin is used to segment the face and other skin areas from the background. Median filtering is then used to clean up the background noise. Geometric constraints are applied to the segmented image to extract the face from the background. To reduce computation and achieve real-time tracking, 1D projections (horizontal and vertical) of the image are analyzed instead of the 2D image. Run-length- encoding and frequency domain analysis algorithms are used to separate faces from other skin-like blobs. The system is robust to illumination intensity variations and different skin colors. It can be applied to many human-computer interaction applications such as sound locating, lip- reading, gaze tracking and face recognition.

  12. Development of a new pentaplex real-time PCR assay for the identification of poly-microbial specimens containing Staphylococcus aureus and other staphylococci, with simultaneous detection of staphylococcal virulence and methicillin resistance markers.

    PubMed

    Okolie, Charles E; Wooldridge, Karl G; Turner, David P; Cockayne, Alan; James, Richard

    2015-06-01

    Staphylococcus aureus strains harbouring genes encoding virulence and antibiotic resistance are of public health importance. In clinical samples, pathogenic S. aureus is often mixed with putatively less pathogenic coagulase-negative staphylococci (CoNS), both of which can harbour mecA, the gene encoding staphylococcal methicillin-resistance. There have been previous attempts at distinguishing MRSA from MRCoNS, most of which were based on the detection of one of the pathognomonic markers of S. aureus, such as coa, nuc or spa. That approach might suffice for discrete colonies and mono-microbial samples; it is inadequate for identification of clinical specimens containing mixtures of S. aureus and CoNS. In the present study, a real-time pentaplex PCR assay has been developed which simultaneously detects markers for bacteria (16S rRNA), coagulase-negative staphylococcus (cns), S. aureus (spa), Panton-Valentine leukocidin (pvl) and methicillin resistance (mecA). Staphylococcal and non-staphylococcal bacterial strains (n = 283) were used to validate the new assay. The applicability of this test to clinical samples was evaluated using spiked blood cultures (n = 43) containing S. aureus and CoNS in mono-microbial and poly-microbial models, which showed that the 5 markers were all detected as expected. Cycling completes within 1 h, delivering 100% specificity, NPV and PPV with a detection limit of 1.0 × 10(1) to 3.0 × 10(1) colony forming units (CFU)/ml, suggesting direct applicability in routine diagnostic microbiology. This is the most multiplexed real-time PCR-based PVL-MRSA assay and the first detection of a unique marker for CoNS without recourse to the conventional elimination approach. There was no evidence that this new assay produced invalid/indeterminate test results.

  13. Screening and identification of compounds with antiviral activity against hepatitis B virus using a safe compound library and novel real-time immune-absorbance PCR-based high throughput system.

    PubMed

    Lamontagne, Jason; Mills, Courtney; Mao, Richeng; Goddard, Cally; Cai, Dawei; Guo, Haitao; Cuconati, Andy; Block, Timothy; Lu, Xuanyong

    2013-04-01

    There are now seven nucleoside/tide analogues, along with interferon-α, that are approved by the FDA for the management of chronic hepatitis B virus (HBV) infection, a disease affecting hundreds of millions of people worldwide. These medications, however, are limited in usefulness, and significant side effects and the emergence of viral escape mutants make the development of novel and updated therapeutics a pressing need in the treatment of HBV. With this in mind, a library containing 2000 compounds already known to be safe in both humans and mice with known mechanisms of action in mammalian cells were tested for the possibility of either antiviral activity against HBV or selective toxicity in HBV producing cell lines. A modified real-time immune-absorbance-polymerase chain reaction (IA-PCR) assay was developed for this screen, utilizing cells that produce and secrete intact HBV virions. In this procedure, viral particles are first captured by an anti-HBs antibody immobilized on a plate. The viral load is subsequently assessed by real-time PCR directly on captured particles. Using this assay, eight compounds were shown to consistently reduce the amount of secreted HBV viral particles in the culture medium under conditions that had no detectable impact on cell viability. Two compounds, proparacaine and chlorophyllide, were shown to reduce HBV levels 4- to 6-fold with an IC₅₀ of 1 and 1.5 μM, respectively, and were selected for further study. The identification of these compounds as promising antiviral drug candidates against HBV, despite a lack of previous recognition of HBV antiviral activity, supports the validity and utility of testing known compounds for "off-pathogen target" activity against HBV, and also validates this IA-PCR assay as an important tool for the detection of anti-viral activity against enveloped viruses.

  14. A mitochondrial species identification assay for Australian blacktip sharks (Carcharhinus tilstoni, C. limbatus and C. amblyrhynchoides) using real-time PCR and high-resolution melt analysis.

    PubMed

    Morgan, Jess A T; Welch, David J; Harry, Alistair V; Street, Raewyn; Broderick, Damien; Ovenden, Jennifer R

    2011-09-01

    Tropical Australian shark fisheries target two morphologically indistinguishable blacktip sharks, the Australian blacktip (Carcharhinus tilstoni) and the common blacktip (C. limbatus). Their relative contributions to northern and eastern Australian coastal fisheries are unclear because of species identification difficulties. The two species differ in their number of precaudal vertebrae, which is difficult and time consuming to obtain in the field. But, the two species can be distinguished genetically with diagnostic mutations in their mitochondrial DNA ND4 gene. A third closely related sister species, the graceful shark C. amblyrhynchoides, can also be distinguished by species-specific mutations in this gene. DNA sequencing is an effective diagnostic tool, but is relatively expensive and time consuming. In contrast, real-time high-resolution melt (HRM) PCR assays are rapid and relatively inexpensive. These assays amplify regions of DNA with species-specific genetic mutations that result in PCR products with unique melt profiles. A real-time HRM PCR species-diagnostic assay (RT-HRM-PCR) has been developed based on the mtDNA ND4 gene for rapid typing of C. tilstoni, C. limbatus and C. amblyrhynchoides. The assay was developed using ND4 sequences from 66 C. tilstoni, 33. C. limbatus and five C. amblyrhynchoides collected from Indonesia and Australian states and territories; Western Australia, the Northern Territory, Queensland and New South Wales. The assay was shown to be 100% accurate on 160 unknown blacktip shark tissue samples by full mtDNA ND4 sequencing. PMID:21565127

  15. Development of a Real-Time PCR for a Sensitive One-Step Coprodiagnosis Allowing both the Identification of Carnivore Feces and the Detection of Toxocara spp. and Echinococcus multilocularis

    PubMed Central

    Umhang, Gérald; Poulle, Marie-Lazarine; Millon, Laurence

    2016-01-01

    Studying the environmental occurrence of parasites of concern for humans and animals based on coprosamples is an expanding field of work in epidemiology and the ecology of health. Detecting and quantifying Toxocara spp. and Echinococcus multilocularis, two predominant zoonotic helminths circulating in European carnivores, in feces may help to better target measures for prevention. A rapid, sensitive, and one-step quantitative PCR (qPCR) allowing detection of E. multilocularis and Toxocara spp. was developed in the present study, combined with a host fecal test based on the identification of three carnivores (red fox, dog, and cat) involved in the life cycles of these parasites. A total of 68 coprosamples were collected from identified specimens from Vulpes vulpes, Canis lupus familiaris, Canis lupus, Felis silvestris catus, Meles meles, Martes foina, and Martes martes. With DNA coprosamples, real-time PCR was performed in duplex with a qPCR inhibitor control specifically designed for this study. All the coprosample host identifications were confirmed by qPCR combined with sequencing, and parasites were detected and confirmed (E. multilocularis in red foxes and Toxocara cati in cats; 16% of samples presented inhibition). By combining parasite detection and quantification, the host fecal test, and a new qPCR inhibitor control, we created a technique with a high sensitivity that may considerably improve environmental studies of pathogens. PMID:26969697

  16. Development of a Real-Time PCR for a Sensitive One-Step Coprodiagnosis Allowing both the Identification of Carnivore Feces and the Detection of Toxocara spp. and Echinococcus multilocularis.

    PubMed

    Knapp, Jenny; Umhang, Gérald; Poulle, Marie-Lazarine; Millon, Laurence

    2016-05-15

    Studying the environmental occurrence of parasites of concern for humans and animals based on coprosamples is an expanding field of work in epidemiology and the ecology of health. Detecting and quantifying Toxocara spp. and Echinococcus multilocularis, two predominant zoonotic helminths circulating in European carnivores, in feces may help to better target measures for prevention. A rapid, sensitive, and one-step quantitative PCR (qPCR) allowing detection of E. multilocularis and Toxocara spp. was developed in the present study, combined with a host fecal test based on the identification of three carnivores (red fox, dog, and cat) involved in the life cycles of these parasites. A total of 68 coprosamples were collected from identified specimens from Vulpes vulpes, Canis lupus familiaris, Canis lupus, Felis silvestris catus, Meles meles, Martes foina, and Martes martes With DNA coprosamples, real-time PCR was performed in duplex with a qPCR inhibitor control specifically designed for this study. All the coprosample host identifications were confirmed by qPCR combined with sequencing, and parasites were detected and confirmed (E. multilocularis in red foxes and Toxocara cati in cats; 16% of samples presented inhibition). By combining parasite detection and quantification, the host fecal test, and a new qPCR inhibitor control, we created a technique with a high sensitivity that may considerably improve environmental studies of pathogens. PMID:26969697

  17. Autonomous Real Time Requirements Tracing

    NASA Technical Reports Server (NTRS)

    Plattsmier, George; Stetson, Howard

    2014-01-01

    One of the more challenging aspects of software development is the ability to verify and validate the functional software requirements dictated by the Software Requirements Specification (SRS) and the Software Detail Design (SDD). Insuring the software has achieved the intended requirements is the responsibility of the Software Quality team and the Software Test team. The utilization of Timeliner-TLX(sup TM) Auto- Procedures for relocating ground operations positions to ISS automated on-board operations has begun the transition that would be required for manned deep space missions with minimal crew requirements. This transition also moves the auto-procedures from the procedure realm into the flight software arena and as such the operational requirements and testing will be more structured and rigorous. The autoprocedures would be required to meet NASA software standards as specified in the Software Safety Standard (NASASTD- 8719), the Software Engineering Requirements (NPR 7150), the Software Assurance Standard (NASA-STD-8739) and also the Human Rating Requirements (NPR-8705). The Autonomous Fluid Transfer System (AFTS) test-bed utilizes the Timeliner-TLX(sup TM) Language for development of autonomous command and control software. The Timeliner-TLX(sup TM) system has the unique feature of providing the current line of the statement in execution during real-time execution of the software. The feature of execution line number internal reporting unlocks the capability of monitoring the execution autonomously by use of a companion Timeliner-TLX(sup TM) sequence as the line number reporting is embedded inside the Timeliner-TLX(sup TM) execution engine. This negates I/O processing of this type data as the line number status of executing sequences is built-in as a function reference. This paper will outline the design and capabilities of the AFTS Autonomous Requirements Tracker, which traces and logs SRS requirements as they are being met during real-time execution of the

  18. Autonomous Real Time Requirements Tracing

    NASA Technical Reports Server (NTRS)

    Plattsmier, George I.; Stetson, Howard K.

    2014-01-01

    One of the more challenging aspects of software development is the ability to verify and validate the functional software requirements dictated by the Software Requirements Specification (SRS) and the Software Detail Design (SDD). Insuring the software has achieved the intended requirements is the responsibility of the Software Quality team and the Software Test team. The utilization of Timeliner-TLX(sup TM) Auto-Procedures for relocating ground operations positions to ISS automated on-board operations has begun the transition that would be required for manned deep space missions with minimal crew requirements. This transition also moves the auto-procedures from the procedure realm into the flight software arena and as such the operational requirements and testing will be more structured and rigorous. The autoprocedures would be required to meet NASA software standards as specified in the Software Safety Standard (NASASTD- 8719), the Software Engineering Requirements (NPR 7150), the Software Assurance Standard (NASA-STD-8739) and also the Human Rating Requirements (NPR-8705). The Autonomous Fluid Transfer System (AFTS) test-bed utilizes the Timeliner-TLX(sup TM) Language for development of autonomous command and control software. The Timeliner- TLX(sup TM) system has the unique feature of providing the current line of the statement in execution during real-time execution of the software. The feature of execution line number internal reporting unlocks the capability of monitoring the execution autonomously by use of a companion Timeliner-TLX(sup TM) sequence as the line number reporting is embedded inside the Timeliner-TLX(sup TM) execution engine. This negates I/O processing of this type data as the line number status of executing sequences is built-in as a function reference. This paper will outline the design and capabilities of the AFTS Autonomous Requirements Tracker, which traces and logs SRS requirements as they are being met during real-time execution of the

  19. Real-time flood forecasting

    USGS Publications Warehouse

    Lai, C.; Tsay, T.-K.; Chien, C.-H.; Wu, I.-L.

    2009-01-01

    Researchers at the Hydroinformatic Research and Development Team (HIRDT) of the National Taiwan University undertook a project to create a real time flood forecasting model, with an aim to predict the current in the Tamsui River Basin. The model was designed based on deterministic approach with mathematic modeling of complex phenomenon, and specific parameter values operated to produce a discrete result. The project also devised a rainfall-stage model that relates the rate of rainfall upland directly to the change of the state of river, and is further related to another typhoon-rainfall model. The geographic information system (GIS) data, based on precise contour model of the terrain, estimate the regions that were perilous to flooding. The HIRDT, in response to the project's progress, also devoted their application of a deterministic model to unsteady flow of thermodynamics to help predict river authorities issue timely warnings and take other emergency measures.

  20. Real Time Simulation of Power Grid Disruptions

    SciTech Connect

    Chinthavali, Supriya; Dimitrovski, Aleksandar D; Fernandez, Steven J; Groer, Christopher S; Nutaro, James J; Olama, Mohammed M; Omitaomu, Olufemi A; Shankar, Mallikarjun; Spafford, Kyle L; Vacaliuc, Bogdan

    2012-11-01

    DOE-OE and DOE-SC workshops (Reference 1-3) identified the key power grid problem that requires insight addressable by the next generation of exascale computing is coupling of real-time data streams (1-2 TB per hour) as the streams are ingested to dynamic models. These models would then identify predicted disruptions in time (2-4 seconds) to trigger the smart grid s self healing functions. This project attempted to establish the feasibility of this approach and defined the scientific issues, and demonstrated example solutions to important smart grid simulation problems. These objectives were accomplished by 1) using the existing frequency recorders on the national grid to establish a representative and scalable real-time data stream; 2) invoking ORNL signature identification algorithms; 3) modeling dynamically a representative region of the Eastern interconnect using an institutional cluster, measuring the scalability and computational benchmarks for a national capability; and 4) constructing a prototype simulation for the system s concept of smart grid deployment. The delivered ORNL enduring capability included: 1) data processing and simulation metrics to design a national capability justifying exascale applications; 2) Software and intellectual property built around the example solutions; 3) demonstrated dynamic models to design few second self-healing.

  1. Measurement-device-independent entanglement-based quantum key distribution

    NASA Astrophysics Data System (ADS)

    Yang, Xiuqing; Wei, Kejin; Ma, Haiqiang; Sun, Shihai; Liu, Hongwei; Yin, Zhenqiang; Li, Zuohan; Lian, Shibin; Du, Yungang; Wu, Lingan

    2016-05-01

    We present a quantum key distribution protocol in a model in which the legitimate users gather statistics as in the measurement-device-independent entanglement witness to certify the sources and the measurement devices. We show that the task of measurement-device-independent quantum communication can be accomplished based on monogamy of entanglement, and it is fairly loss tolerate including source and detector flaws. We derive a tight bound for collective attacks on the Holevo information between the authorized parties and the eavesdropper. Then with this bound, the final secret key rate with the source flaws can be obtained. The results show that long-distance quantum cryptography over 144 km can be made secure using only standard threshold detectors.

  2. Implementation of a measurement-device-independent entanglement witness.

    PubMed

    Xu, Ping; Yuan, Xiao; Chen, Luo-Kan; Lu, He; Yao, Xing-Can; Ma, Xiongfeng; Chen, Yu-Ao; Pan, Jian-Wei

    2014-04-11

    Entanglement, the essential resource in quantum information processing, should be witnessed in many tasks such as quantum computing and quantum communication. The conventional entanglement witness method, relying on an idealized implementation of measurements, could wrongly conclude a separable state to be entangled due to imperfect detections. Inspired by the idea of a time-shift attack, we construct an attack on the conventional entanglement witness process and demonstrate that a separable state can be falsely identified to be entangled. To close such detection loopholes, based on a recently proposed measurement-device-independent entanglement witness method, we design and experimentally demonstrate a measurement-device-independent entanglement witness for a variety of two-qubit states. By the new scheme, we show that an entanglement witness can be realized without detection loopholes.

  3. Adaptive prefetching for device-independent file I/O

    NASA Astrophysics Data System (ADS)

    Revel, Dan; McNamee, Dylan; Steere, David C.; Walpole, Jonathan

    1997-12-01

    Device independent I/O has been a holy grail to operating system designers since the early days of UNIX. Unfortunately, existing operating systems fall short of this goal for multimedia applications. Techniques such as caching and sequential read-ahead can help mask I/O latency in some cases, but in others they increase latency and add substantial jitter. Multimedia applications, such as video players, are sensitive to vagaries in performance since I/O latency and jitter affect the quality of presentation. Our solution uses adaptive prefetching to reduce both latency and jitter. Applications submit file access plans to the prefetcher, which then generates I/O requests to the operating system and manages the buffer cache to isolate the application from variations in device performance. Our experiments show device independence can be achieved: an MPEG video player sees the same latency when reading from a local disk or an NFS server. Moreover, our approach reduces jitter substantially.

  4. Efficient measurement-device-independent detection of multipartite entanglement structure

    NASA Astrophysics Data System (ADS)

    Zhao, Qi; Yuan, Xiao; Ma, Xiongfeng

    2016-07-01

    Witnessing entanglement is crucial in quantum information processing. With properly preparing ancillary states, it has been shown previously that genuine entanglement can be witnessed without trusting measurement devices. In this work we generalize the scenario and show that generic multipartite entanglement structures, including entanglement of subsystems and entanglement depth, can be witnessed via measurement-device-independent means. As the original measurement-device-independent entanglement witness scheme exploits only one out of four Bell measurement outcomes for each party, a direct generalization to multipartite quantum states will inevitably cause inefficiency in entanglement detection after taking account of statistical fluctuations. To resolve this problem, we also present a way to utilize all the measurement outcomes. The scheme is efficient for multipartite entanglement detection and can be realized with state-of-the-art technologies.

  5. Device-independent security of quantum cryptography against collective attacks.

    PubMed

    Acín, Antonio; Brunner, Nicolas; Gisin, Nicolas; Massar, Serge; Pironio, Stefano; Scarani, Valerio

    2007-06-01

    We present the optimal collective attack on a quantum key distribution protocol in the "device-independent" security scenario, where no assumptions are made about the way the quantum key distribution devices work or on what quantum system they operate. Our main result is a tight bound on the Holevo information between one of the authorized parties and the eavesdropper, as a function of the amount of violation of a Bell-type inequality.

  6. Real-time scene generator

    NASA Astrophysics Data System (ADS)

    Lord, Eric; Shand, David J.; Cantle, Allan J.

    1996-05-01

    This paper describes the techniques which have been developed for an infra-red (IR) target, countermeasure and background image generation system working in real time for HWIL and Trial Proving applications. Operation is in the 3 to 5 and 8 to 14 micron bands. The system may be used to drive a scene projector (otherwise known as a thermal picture synthesizer) or for direct injection into equipment under test. The provision of realistic IR target and countermeasure trajectories and signatures, within representative backgrounds, enables the full performance envelope of a missile system to be evaluated. It also enables an operational weapon system to be proven in a trials environment without compromising safety. The most significant technique developed has been that of line by line synthesis. This minimizes the processing delays to the equivalent of 1.5 frames from input of target and sightline positions to the completion of an output image scan. Using this technique a scene generator has been produced for full closed loop HWIL performance analysis for the development of an air to air missile system. Performance of the synthesis system is as follows: 256 * 256 pixels per frame; 350 target polygons per frame; 100 Hz frame rate; and Gouraud shading, simple reflections, variable geometry targets and atmospheric scaling. A system using a similar technique has also bee used for direct insertion into the video path of a ground to air weapon system in live firing trials. This has provided realistic targets without degrading the closed loop performance. Delay of the modified video signal has been kept to less than 5 lines. The technique has been developed using a combination of 4 high speed Intel i860 RISC processors in parallel with the 4000 series XILINX field programmable gate arrays (FPGA). Start and end conditions for each line of target pixels are prepared and ordered in the I860. The merging with background pixels and output shading and scaling is then carried out in

  7. Real time cardiac radionuclide imaging

    SciTech Connect

    Jarkewicz, G.G.

    1986-04-29

    A data acquisition system is described for use in radionuclide cardiac imaging of a patient having been administered a myocardium specific radionuclide, comprising: (a) means for monitoring the electrical activity of the heart; (b) first temporary storage means for accumulating respective pages of data corresponding to nuclear events during each cardiac cycle; (c) means, responsive to the means for monitoring, for determining the time duration of each successive cardiac cycle; (d) means for comparing each determined duration of a cardiac cycle with a preselected time duration range; (e) second temporary storage means; and (f) means for conditionally transferring pages of data from the first temporary storage means to the second temporary storage means if the measured duration associated with each page has predetermined correspondence with the preselected duration range, whereby pages of data having the predetermined correspondence may be collated into a quasi-real time study, while pages of data having different correspondence with the preselected time duration range are discarded from the study.

  8. Mobile real time radiography system

    SciTech Connect

    Vigil, J.; Taggart, D.; Betts, S.

    1997-11-01

    A 450-keV Mobile Real Time Radiography (RTR) System was delivered to Los Alamos National Laboratory (LANL) in January 1996. It was purchased to inspect containers of radioactive waste produced at (LANL). Since its delivery it has been used to radiograph more than 600 drums of radioactive waste at various LANL sites. It has the capability of inspecting waste containers of various sizes from <1-gal. buckets up to standard waste boxes (SWB, dimensions 54.5 in. x 71 in. x 37 in.). It has three independent x-ray acquisition formats. The primary system used is a 12- in. image intensifier, the second is a 36-in. linear diode array (LDA) and the last is an open system. It is fully self contained with on board generator, HVAC, and a fire suppression system. It is on a 53-ft long x 8-ft. wide x 14-ft. high trailer that can be moved over any highway requiring only an easily obtainable overweight permit because it weights {approximately}38 tons. It was built to conform to industry standards for a cabinet system which does not require an exclusion zone. The fact that this unit is mobile has allowed us to operate where the waste is stored, rather than having to move the waste to a fixed facility.

  9. Students Collecting Real time Data

    NASA Astrophysics Data System (ADS)

    Miller, P.

    2006-05-01

    Students Collecting Real-Time Data The Hawaiian Islands Humpback Whale National Marine Sanctuary has created opportunities for middle and high school students to become Student Researchers and to be involved in real-time marine data collection. It is important that we expose students to different fields of science and encourage them to enter scientific fields of study. The Humpback Whale Sanctuary has an education visitor center in Kihei, Maui. Located right on the beach, the site has become a living classroom facility. There is a traditional Hawaiian fishpond fronting the property. The fishpond wall is being restored, using traditional methods. The site has the incredible opportunity of incorporating Hawaiian cultural practices with scientific studies. The Sanctuary offers opportunities for students to get involved in monitoring and data collection studies. Invasive Seaweed Study: Students are collecting data on invasive seaweed for the University of Hawaii. They pull a large net through the shallow waters. Seaweed is sorted, identified and weighed. The invasive seaweeds are removed. The data is recorded and sent to UH. Remote controlled monitoring boats: The sanctuary has 6 boogie board sized remote controlled boats used to monitor reefs. Boats have a camera with lights on the underside. The boats have water quality monitoring devices and GPS units. The video from the underwater camera is transmitted via a wireless transmission. Students are able to monitor the fish, limu and invertebrate populations on the reef and collect water quality data via television monitors or computers. The boat can also pull a small plankton tow net. Data is being compiled into data bases. Artificial Reef Modules: The Sanctuary has a scientific permit from the state to build and deploy artificial reef modules. High school students are designing and building modules. These are deployed out in the Fishpond fronting the Sanctuary site and students are monitoring them on a weekly basis

  10. Real-Time Data Display

    NASA Technical Reports Server (NTRS)

    Pedings, Marc

    2007-01-01

    RT-Display is a MATLAB-based data acquisition environment designed to use a variety of commercial off-the-shelf (COTS) hardware to digitize analog signals to a standard data format usable by other post-acquisition data analysis tools. This software presents the acquired data in real time using a variety of signal-processing algorithms. The acquired data is stored in a standard Operator Interactive Signal Processing Software (OISPS) data-formatted file. RT-Display is primarily configured to use the Agilent VXI (or equivalent) data acquisition boards used in such systems as MIDDAS (Multi-channel Integrated Dynamic Data Acquisition System). The software is generalized and deployable in almost any testing environment, without limitations or proprietary configuration for a specific test program or project. With the Agilent hardware configured and in place, users can start the program and, in one step, immediately begin digitizing multiple channels of data. Once the acquisition is completed, data is converted into a common binary format that also can be translated to specific formats used by external analysis software, such as OISPS and PC-Signal (product of AI Signal Research Inc.). RT-Display at the time of this reporting was certified on Agilent hardware capable of acquisition up to 196,608 samples per second. Data signals are presented to the user on-screen simultaneously for 16 channels. Each channel can be viewed individually, with a maximum capability of 160 signal channels (depending on hardware configuration). Current signal presentations include: time data, fast Fourier transforms (FFT), and power spectral density plots (PSD). Additional processing algorithms can be easily incorporated into this environment.

  11. Long-distance measurement-device-independent multiparty quantum communication.

    PubMed

    Fu, Yao; Yin, Hua-Lei; Chen, Teng-Yun; Chen, Zeng-Bing

    2015-03-01

    The Greenberger-Horne-Zeilinger (GHZ) entanglement, originally introduced to uncover the extreme violation of local realism against quantum mechanics, is an important resource for multiparty quantum communication tasks. But the low intensity and fragility of the GHZ entanglement source in current conditions have made the practical applications of these multiparty tasks an experimental challenge. Here we propose a feasible scheme for practically distributing the postselected GHZ entanglement over a distance of more than 100 km for experimentally accessible parameter regimes. Combining the decoy-state and measurement-device-independent protocols for quantum key distribution, we anticipate that our proposal suggests an important avenue for practical multiparty quantum communication.

  12. Toward Real Time Neural Net Flight Controllers

    NASA Technical Reports Server (NTRS)

    Jorgensen, C. C.; Mah, R. W.; Ross, J.; Lu, Henry, Jr. (Technical Monitor)

    1994-01-01

    NASA Ames Research Center has an ongoing program in neural network control technology targeted toward real time flight demonstrations using a modified F-15 which permits direct inner loop control of actuators, rapid switching between alternative control designs, and substitutable processors. An important part of this program is the ACTIVE flight project which is examining the feasibility of using neural networks in the design, control, and system identification of new aircraft prototypes. This paper discusses two research applications initiated with this objective in mind: utilization of neural networks for wind tunnel aircraft model identification and rapid learning algorithms for on line reconfiguration and control. The first application involves the identification of aerodynamic flight characteristics from analysis of wind tunnel test data. This identification is important in the early stages of aircraft design because complete specification of control architecture's may not be possible even though concept models at varying scales are available for aerodynamic wind tunnel testing. Testing of this type is often a long and expensive process involving measurement of aircraft lift, drag, and moment of inertia at varying angles of attack and control surface configurations. This information in turn can be used in the design of the flight control systems by applying the derived lookup tables to generate piece wise linearized controllers. Thus, reduced costs in tunnel test times and the rapid transfer of wind tunnel insights into prototype controllers becomes an important factor in more efficient generation and testing of new flight systems. NASA Ames Research Center is successfully applying modular neural networks as one way of anticipating small scale aircraft model performances prior to testing, thus reducing the number of in tunnel test hours and potentially, the number of intermediate scaled models required for estimation of surface flow effects.

  13. Real-Time "Garbage Collection" for List Processing

    NASA Technical Reports Server (NTRS)

    Shuler, Robert L., Jr.

    1987-01-01

    Two proposed algorithmic techniques for list processing enable immediate identification of computer memory cells having become inactive through disconnection from active cells, together with addition of these inactive cells to pool of reusable cells. These two "garbage collection" techniques reduce memory requirements of list processors or increase their speed or both. With both techniques, processing continuity maintained, enabling real-time processing.

  14. Research in Distributed Real-Time Systems

    NASA Technical Reports Server (NTRS)

    Mukkamala, R.

    1997-01-01

    This document summarizes the progress we have made on our study of issues concerning the schedulability of real-time systems. Our study has produced several results in the scalability issues of distributed real-time systems. In particular, we have used our techniques to resolve schedulability issues in distributed systems with end-to-end requirements. During the next year (1997-98), we propose to extend the current work to address the modeling and workload characterization issues in distributed real-time systems. In particular, we propose to investigate the effect of different workload models and component models on the design and the subsequent performance of distributed real-time systems.

  15. Experimental measurement-device-independent quantum key distribution.

    PubMed

    Liu, Yang; Chen, Teng-Yun; Wang, Liu-Jun; Liang, Hao; Shentu, Guo-Liang; Wang, Jian; Cui, Ke; Yin, Hua-Lei; Liu, Nai-Le; Li, Li; Ma, Xiongfeng; Pelc, Jason S; Fejer, M M; Peng, Cheng-Zhi; Zhang, Qiang; Pan, Jian-Wei

    2013-09-27

    Quantum key distribution is proven to offer unconditional security in communication between two remote users with ideal source and detection. Unfortunately, ideal devices never exist in practice and device imperfections have become the targets of various attacks. By developing up-conversion single-photon detectors with high efficiency and low noise, we faithfully demonstrate the measurement-device-independent quantum-key-distribution protocol, which is immune to all hacking strategies on detection. Meanwhile, we employ the decoy-state method to defend attacks on a nonideal source. By assuming a trusted source scenario, our practical system, which generates more than a 25 kbit secure key over a 50 km fiber link, serves as a stepping stone in the quest for unconditionally secure communications with realistic devices. PMID:24116758

  16. Experimental Measurement-Device-Independent Quantum Key Distribution

    NASA Astrophysics Data System (ADS)

    Liu, Yang; Chen, Teng-Yun; Wang, Liu-Jun; Liang, Hao; Shentu, Guo-Liang; Wang, Jian; Cui, Ke; Yin, Hua-Lei; Liu, Nai-Le; Li, Li; Ma, Xiongfeng; Pelc, Jason S.; Fejer, M. M.; Peng, Cheng-Zhi; Zhang, Qiang; Pan, Jian-Wei

    2013-09-01

    Quantum key distribution is proven to offer unconditional security in communication between two remote users with ideal source and detection. Unfortunately, ideal devices never exist in practice and device imperfections have become the targets of various attacks. By developing up-conversion single-photon detectors with high efficiency and low noise, we faithfully demonstrate the measurement-device-independent quantum-key-distribution protocol, which is immune to all hacking strategies on detection. Meanwhile, we employ the decoy-state method to defend attacks on a nonideal source. By assuming a trusted source scenario, our practical system, which generates more than a 25 kbit secure key over a 50 km fiber link, serves as a stepping stone in the quest for unconditionally secure communications with realistic devices.

  17. Memory-assisted measurement-device-independent quantum key distribution

    NASA Astrophysics Data System (ADS)

    Panayi, Christiana; Razavi, Mohsen; Ma, Xiongfeng; Lütkenhaus, Norbert

    2014-04-01

    A protocol with the potential of beating the existing distance records for conventional quantum key distribution (QKD) systems is proposed. It borrows ideas from quantum repeaters by using memories in the middle of the link, and that of measurement-device-independent QKD, which only requires optical source equipment at the user's end. For certain memories with short access times, our scheme allows a higher repetition rate than that of quantum repeaters with single-mode memories, thereby requiring lower coherence times. By accounting for various sources of nonideality, such as memory decoherence, dark counts, misalignment errors, and background noise, as well as timing issues with memories, we develop a mathematical framework within which we can compare QKD systems with and without memories. In particular, we show that with the state-of-the-art technology for quantum memories, it is potentially possible to devise memory-assisted QKD systems that, at certain distances of practical interest, outperform current QKD implementations.

  18. Device-independent parallel self-testing of two singlets

    NASA Astrophysics Data System (ADS)

    Wu, Xingyao; Bancal, Jean-Daniel; McKague, Matthew; Scarani, Valerio

    2016-06-01

    Device-independent self-testing offers the possibility of certifying the quantum state and measurements, up to local isometries, using only the statistics observed by querying uncharacterized local devices. In this paper we study parallel self-testing of two maximally entangled pairs of qubits; in particular, the local tensor product structure is not assumed but derived. We prove two criteria that achieve the desired result: a double use of the Clauser-Horne-Shimony-Holt inequality and the 3 ×3 magic square game. This demonstrate that the magic square game can only be perfectly won by measuring a two-singlet state. The tolerance to noise is well within reach of state-of-the-art experiments.

  19. Resource-Efficient Measurement-Device-Independent Entanglement Witness

    DOE PAGESBeta

    Verbanis, E.; Martin, A.; Rosset, D.; Lim, C. C. W.; Thew, R. T.; Zbinden, H.

    2016-05-09

    Imperfections in experimental measurement schemes can lead to falsely identifying, or over estimating, entanglement in a quantum system. A recent solution to this is to define schemes that are robust to measurement imperfections—measurement-device-independent entanglement witness (MDI-EW). This approach can be adapted to witness all entangled qubit states for a wide range of physical systems and does not depend on detection efficiencies or classical communication between devices. In this paper, we extend the theory to remove the necessity of prior knowledge about the two-qubit states to be witnessed. Moreover, we tested this model via a novel experimental implementation for MDI-EW thatmore » significantly reduces the experimental complexity. Finally, by applying it to a bipartite Werner state, we demonstrate the robustness of this approach against noise by witnessing entanglement down to an entangled state fraction close to 0.4.« less

  20. Real time programming environment for Windows

    SciTech Connect

    LaBelle, D.R.

    1998-04-01

    This document provides a description of the Real Time Programming Environment (RTProE). RTProE tools allow a programmer to create soft real time projects under general, multi-purpose operating systems. The basic features necessary for real time applications are provided by RTProE, leaving the programmer free to concentrate efforts on his specific project. The current version supports Microsoft Windows{trademark} 95 and NT. The tasks of real time synchronization and communication with other programs are handled by RTProE. RTProE includes a generic method for connecting a graphical user interface (GUI) to allow real time control and interaction with the programmer`s product. Topics covered in this paper include real time performance issues, portability, details of shared memory management, code scheduling, application control, Operating System specific concerns and the use of Computer Aided Software Engineering (CASE) tools. The development of RTProE is an important step in the expansion of the real time programming community. The financial costs associated with using the system are minimal. All source code for RTProE has been made publicly available. Any person with access to a personal computer, Windows 95 or NT, and C or FORTRAN compilers can quickly enter the world of real time modeling and simulation.

  1. Novel real-time PCR assays using TaqMan minor groove binder probes for identification of fecal carriage of Streptococcus bovis/Streptococcus equinus complex from rectal swab specimens.

    PubMed

    Lopes, Paulo Guilherme Markus; Cantarelli, Vlademir Vicente; Agnes, Grasiela; Costabeber, Ane Micheli; d'Azevedo, Pedro Alves

    2014-03-01

    Real-time PCR based on the recN and gyrB genes was developed to detect four Streptococcus bovis/Streptococcus equinus complex (SBEC) subspecies from rectal swab specimens. The overall prevalence was 35.2%: Streptococcus gallolyticus subsp. gallolyticus (11.1%), S. gallolyticus subsp. pasteurianus (13%), Streptococcus infantarius subsp. coli (20.4%), and S. infantarius subsp. infantarius (11.1%). To conclude, these real-time PCR assays provide a reliable molecular method to detect SBEC pathogenic subspecies from rectal swab specimens.

  2. Waste collection multi objective model with real time traceability data.

    PubMed

    Faccio, Maurizio; Persona, Alessandro; Zanin, Giorgia

    2011-12-01

    Waste collection is a highly visible municipal service that involves large expenditures and difficult operational problems, plus it is expensive to operate in terms of investment costs (i.e. vehicles fleet), operational costs (i.e. fuel, maintenances) and environmental costs (i.e. emissions, noise and traffic congestions). Modern traceability devices, like volumetric sensors, identification RFID (Radio Frequency Identification) systems, GPRS (General Packet Radio Service) and GPS (Global Positioning System) technology, permit to obtain data in real time, which is fundamental to implement an efficient and innovative waste collection routing model. The basic idea is that knowing the real time data of each vehicle and the real time replenishment level at each bin makes it possible to decide, in function of the waste generation pattern, what bin should be emptied and what should not, optimizing different aspects like the total covered distance, the necessary number of vehicles and the environmental impact. This paper describes a framework about the traceability technology available in the optimization of solid waste collection, and introduces an innovative vehicle routing model integrated with the real time traceability data, starting the application in an Italian city of about 100,000 inhabitants. The model is tested and validated using simulation and an economical feasibility study is reported at the end of the paper.

  3. Research of real-time communication software

    NASA Astrophysics Data System (ADS)

    Li, Maotang; Guo, Jingbo; Liu, Yuzhong; Li, Jiahong

    2003-11-01

    Real-time communication has been playing an increasingly important role in our work, life and ocean monitor. With the rapid progress of computer and communication technique as well as the miniaturization of communication system, it is needed to develop the adaptable and reliable real-time communication software in the ocean monitor system. This paper involves the real-time communication software research based on the point-to-point satellite intercommunication system. The object-oriented design method is adopted, which can transmit and receive video data and audio data as well as engineering data by satellite channel. In the real-time communication software, some software modules are developed, which can realize the point-to-point satellite intercommunication in the ocean monitor system. There are three advantages for the real-time communication software. One is that the real-time communication software increases the reliability of the point-to-point satellite intercommunication system working. Second is that some optional parameters are intercalated, which greatly increases the flexibility of the system working. Third is that some hardware is substituted by the real-time communication software, which not only decrease the expense of the system and promotes the miniaturization of communication system, but also aggrandizes the agility of the system.

  4. The ALMA Real Time Control System

    NASA Astrophysics Data System (ADS)

    Kern, Jeffrey S.; Juerges, Thomas A.; Marson, Ralph G.

    2009-01-01

    The Atacama Large Millimeter Array (ALMA) is a revolutionary millimeter and submillimeter array being developed on the Atacama plateau of northern Chile. An international partnership lead by NRAO, ESO, and NAOJ this powerful and flexible telescope will provide unprecedented observations of this relatively unexplored frequency range. The control subsystem for the Atacama Large Millimeter Array must coordinate the monitor and control of at least sixty six antennas (in four different styles), two correlators, and all of the ancillary equipment (samplers, local oscillators, front ends, etc.). This equipment will be spread over tens of kilometers and operated remotely. Operation of the array requires a robust, scalable, and maintainable real time control system. The real time control system is responsible for monitoring and control of any devices where there are fixed deadlines. Examples in the ALMA context are antenna pointing and fringe tracking. Traditionally the real time portion of a large software system is an intricate and error prone portion of the software. As a result the real time portion is very expensive in terms of effort expended both during construction and during maintenance phases of a project. The ALMA real time control system uses a Linux based real time operating system to interact with the hardware and the CORBA based ALMA Common Software to communicate in the distributed computing environment. Mixing the requirements of real time computing and the non-deterministic CORBA middleware has produced an interesting design. We discuss the architecture, design, and implementation of the ALMA real time control system. Highlight some lessons learned along the way, and justify our assertion that this should be the last large scale real time control system in radio astronomy.

  5. Real time sensor for therapeutic radiation delivery

    DOEpatents

    Bliss, Mary; Craig, Richard A.; Reeder, Paul L.

    1998-01-01

    The invention is a real time sensor for therapeutic radiation. A probe is placed in or near the patient that senses in real time the dose at the location of the probe. The strength of the dose is determined by either an insertion or an exit probe. The location is determined by a series of vertical and horizontal sensing elements that gives the operator a real time read out dose location relative to placement of the patient. The increased accuracy prevents serious tissue damage to the patient by preventing overdose or delivery of a dose to a wrong location within the body.

  6. Real time sensor for therapeutic radiation delivery

    DOEpatents

    Bliss, M.; Craig, R.A.; Reeder, P.L.

    1998-01-06

    The invention is a real time sensor for therapeutic radiation. A probe is placed in or near the patient that senses in real time the dose at the location of the probe. The strength of the dose is determined by either an insertion or an exit probe. The location is determined by a series of vertical and horizontal sensing elements that gives the operator a real time read out dose location relative to placement of the patient. The increased accuracy prevents serious tissue damage to the patient by preventing overdose or delivery of a dose to a wrong location within the body. 14 figs.

  7. Real-time monitoring of landslides

    USGS Publications Warehouse

    Reid, Mark E.; LaHusen, Richard G.; Baum, Rex L.; Kean, Jason W.; Schulz, William H.; Highland, Lynn M.

    2012-01-01

    Landslides cause fatalities and property damage throughout the Nation. To reduce the impact from hazardous landslides, the U.S. Geological Survey develops and uses real-time and near-real-time landslide monitoring systems. Monitoring can detect when hillslopes are primed for sliding and can provide early indications of rapid, catastrophic movement. Continuous information from up-to-the-minute or real-time monitoring provides prompt notification of landslide activity, advances our understanding of landslide behavior, and enables more effective engineering and planning efforts.

  8. Real-time medical applications and telecommunications.

    PubMed

    Stravs, M

    1999-01-01

    Telecommunications play an important role in telemedicine. Many forms of telecommunication services based on different telecommunication technologies are developed for various needs. The paper deals with complex real-time applications which demand high telecommunication requirements. At the beginning, medical applications are categorised and real-time applications qualified as multimedia applications. Requirements for multimedia elements are listed separately. Later on, short introduction of related telecommunication protocols is given. Real-time medical applications can show their ability in case of guaranteed quality of services delivered by telecommunication network as it is explained in the end.

  9. Security of Semi-Device-Independent Random Number Expansion Protocols

    PubMed Central

    Li, Dan-Dan; Wen, Qiao-Yan; Wang, Yu-Kun; Zhou, Yu-Qian; Gao, Fei

    2015-01-01

    Semi-device-independent random number expansion (SDI-RNE) protocols require some truly random numbers to generate fresh ones, with making no assumptions on the internal working of quantum devices except for the dimension of the Hilbert space. The generated randomness is certified by non-classical correlation in the prepare-and-measure test. Until now, the analytical relations between the amount of the generated randomness and the degree of non-classical correlation, which are crucial for evaluating the security of SDI-RNE protocols, are not clear under both the ideal condition and the practical one. In the paper, first, we give the analytical relation between the above two factors under the ideal condition. As well, we derive the analytical relation under the practical conditions, where devices’ behavior is not independent and identical in each round and there exists deviation in estimating the non-classical behavior of devices. Furthermore, we choose a different randomness extractor (i.e., two-universal random function) and give the security proof. PMID:26503335

  10. Security of Semi-Device-Independent Random Number Expansion Protocols.

    PubMed

    Li, Dan-Dan; Wen, Qiao-Yan; Wang, Yu-Kun; Zhou, Yu-Qian; Gao, Fei

    2015-01-01

    Semi-device-independent random number expansion (SDI-RNE) protocols require some truly random numbers to generate fresh ones, with making no assumptions on the internal working of quantum devices except for the dimension of the Hilbert space. The generated randomness is certified by non-classical correlation in the prepare-and-measure test. Until now, the analytical relations between the amount of the generated randomness and the degree of non-classical correlation, which are crucial for evaluating the security of SDI-RNE protocols, are not clear under both the ideal condition and the practical one. In the paper, first, we give the analytical relation between the above two factors under the ideal condition. As well, we derive the analytical relation under the practical conditions, where devices' behavior is not independent and identical in each round and there exists deviation in estimating the non-classical behavior of devices. Furthermore, we choose a different randomness extractor (i.e., two-universal random function) and give the security proof.

  11. High-rate measurement-device-independent quantum cryptography

    NASA Astrophysics Data System (ADS)

    Pirandola, Stefano; Ottaviani, Carlo; Spedalieri, Gaetana; Weedbrook, Christian; Braunstein, Samuel L.; Lloyd, Seth; Gehring, Tobias; Jacobsen, Christian S.; Andersen, Ulrik L.

    2015-06-01

    Quantum cryptography achieves a formidable task—the remote distribution of secret keys by exploiting the fundamental laws of physics. Quantum cryptography is now headed towards solving the practical problem of constructing scalable and secure quantum networks. A significant step in this direction has been the introduction of measurement-device independence, where the secret key between two parties is established by the measurement of an untrusted relay. Unfortunately, although qubit-implemented protocols can reach long distances, their key rates are typically very low, unsuitable for the demands of a metropolitan network. Here we show, theoretically and experimentally, that a solution can come from the use of continuous-variable systems. We design a coherent-state network protocol able to achieve remarkably high key rates at metropolitan distances, in fact three orders of magnitude higher than those currently achieved. Our protocol could be employed to build high-rate quantum networks where devices securely connect to nearby access points or proxy servers.

  12. Real-time smart fluorescence sensor platform

    NASA Astrophysics Data System (ADS)

    Dickens, Jason E.; Vaughn, Mike S.; Taylor, Mervin; Ponstingl, Mike

    2011-06-01

    A novel compact LED array based light induced fluorescence (LIF) sensor has been developed for real-time in-line monitoring of intrinsic fluorophores in the solid and liquid state. The sensor is essential for on-the-spot, routine, and cost effective real-time analysis. The sensor is designed to provide real-time emission response along with various smart sensing parameters to ensure real-time measurement quality that is required for regulated GMP process monitoring applications. This work describes a LIF sensor tailored for solid-phase fluorometry. Fundamental figures of merit, excitation overexposure and smart sensing features required for modern process monitoring and control are discussed within the context of pharmaceutical solid-phase manufacturing and similar applications.

  13. The LAA real-time benchmarks

    SciTech Connect

    Block, R.K.; Krischer, W.; Lone, S.

    1989-04-01

    In the context of the LAA detector development program a subgroup Real Time Data Processing has tackled the problem of intelligent triggering. The main goal of this group is to show how fast digital devices, implemented as custom-made or commercial processors, can execute some basic algorithms, and how they can be embedded in the data flow between detector readout components and fully programmable commercial processors, which are expected to be the final data processing filter in real time.

  14. Real-time scheduling using minimum search

    NASA Technical Reports Server (NTRS)

    Tadepalli, Prasad; Joshi, Varad

    1992-01-01

    In this paper we consider a simple model of real-time scheduling. We present a real-time scheduling system called RTS which is based on Korf's Minimin algorithm. Experimental results show that the schedule quality initially improves with the amount of look-ahead search and tapers off quickly. So it sppears that reasonably good schedules can be produced with a relatively shallow search.

  15. Processing PCM Data in Real Time

    NASA Technical Reports Server (NTRS)

    Wissink, T. L.

    1982-01-01

    Novel hardware configuration makes it possible for Space Shuttle launch processing system to monitor pulse-code-modulated data in real time. Using two microprogramable "option planes," incoming PCM data are monitored for changes at rate of one frame of data (80 16-bit words) every 10 milliseconds. Real-time PCM processor utilizes CPU in mini-computer and CPU's in two option planes.

  16. Interferometer real time control development for SIM

    NASA Astrophysics Data System (ADS)

    Bell, Charles E.

    2003-02-01

    Real Time Control (RTC) for the Space Interferometry Mission will build on the real time core interferometer control technology under development at JPL since the mid 1990s, with heritage from the ground based MKII and Palomar Testbed Interferometer projects developed in the late '80s and early '90s. The core software and electronics technology for SIM interferometer real time control is successfully operating on several SIM technology demonstration testbeds, including the Real-time Interferometer Control System Testbed, System Testbed-3, and the Microarcsecond Metrology testbed. This paper provides an overview of the architecture, design, integration, and test of the SIM flight interferometer real time control to meet challenging flight system requirements for the high processor throughput, low-latency interconnect, and precise synchronization to support microarcsecond-level astrometric measurements for greater than five years at 1 AU in Earth-trailing orbit. The electronics and software architecture of the interferometer real time control core and its adaptation to a flight design concept are described. Control loops for pointing and pathlength control within each of four flight interferometers and for coordination of control and data across interferometers are illustrated. The nature of onboard data processing to fit average downlink rates while retaining post-processed astrometric measurement precision and accuracy is also addressed. Interferometer flight software will be developed using a software simulation environment incorporating models of the metrology and starlight sensors and actuators to close the real time control loops. RTC flight software and instrument flight electronics will in turn be integrated utilizing the same simulation architecture for metrology and starlight component models to close real time control loops and verify RTC functionality and performance prior to delivery to flight interferometer system integration at Lockheed Martin

  17. Development and validation of a TaqMan real-time PCR assay for the identification and quantification of roe deer (Capreolus capreolus) in food to detect food adulteration.

    PubMed

    Druml, Barbara; Mayer, Walter; Cichna-Markl, Margit; Hochegger, Rupert

    2015-07-01

    In order to protect the consumer from meat adulteration it is necessary to identify and quantify the meat content in foodstuffs. Game meat is particularly susceptible for fraudulent labeling since it is more valuable than meat from domestic animals. The paper presents a TaqMan real-time PCR assay for the quantitative determination of roe deer in meat products. The assay developed does not show cross-reactivity with 23 animal and 43 plant species tested and is therefore specific for roe deer. The amplification efficiency determined by analyzing serially diluted roe deer DNA extracts was found to be 93.9%. For quantifying the roe deer content in % (w/w), a reference system based on the myostatin gene was used. The quantification strategy was validated by determining the roe deer content in model meat mixtures and a model sausage. In addition, the real-time PCR assay was applied to the analysis of commercially available meat products.

  18. Performance and application of real-time hyperspectral imaging

    NASA Astrophysics Data System (ADS)

    Dombrowski, Mark S.; Willson, Paul D.; LaBaw, Clayton C.

    1998-10-01

    Hyperspectral imaging is the latest advent in imaging technology, providing the potential to extract information about the objects in a scene that is unavailable to panchromatic imagers. This increased utility, however, comes at the cost of tremendously increased data. The ultimate utility of hyperspectral imagery is in the information that can be gleaned from the spectral dimension, rather than in the hyperspectral imagery itself. To have the broadest range of applications, extraction of this information must occur in real-time. Attempting to produce and exploit complete cubes of hyperspectral imagery at video rates, however, present unique problems for both the imager and the processor, since data rates are scaled by the number of spectral planes in the cube. MIDIS, the Multi-band Identification and Discrimination Imaging Spectroradiometer, allows both real-time here are the major design innovations associated with producing high-speed, high-sensitivity hyperspectral imagers operating in the SWIR and LWIR, and of the electronics capable of handling data rates up to 160 megapixels per second, continuously. Discussion of real-time algorithms capable of exploiting the spectral dimension of the imagery is also included. Beyond design and performance issues associated with producing and processing hyperspectral imagery at such high speeds, this paper also discusses applications of real-time hyperspectral imaging technology. Example imagery includes such problems as detecting counterfeit money, inspecting surfaces, and countering CCD.

  19. Rendering energy-conservative scenes in real time

    NASA Astrophysics Data System (ADS)

    Olson, Eric M.; Garbo, Dennis L.; Crow, Dennis R.; Coker, Charles F.

    1997-07-01

    Real-time infrared (IR) scene generation from HardWare-in- the-Loop (HWIL) testing of IR seeker systems is a complex problem due to the required frame rates and image fidelity. High frame rates are required for current generation seeker systems to perform designation, discrimination, identification, tracking, and aimpoint selection tasks. Computational requirements for IR signature phenomenology and sensor effects have been difficult to perform in real- time to support HWIL testing. Commercial scene generation hardware is rapidly improving and is becoming a viable solution for HWIL testing activities being conducted at the Kinetic Kill Vehicle Hardware-in-the-Loop Simulator facility at Eglin AFB, Florida. This paper presents computational techniques performed to overcome IR scene rendering errors incurred with commercially available hardware and software for real-time scene generation in support of HWIL testing. These techniques provide an acceptable solution to real-time IR scene generation that strikes a balance between physical accuracy and image framing rates. The results of these techniques are investigated as they pertain to rendering accuracy and speed for target objects which begin as a point source during acquisition and develop into an extended source representation during aimpoint selection.

  20. REAL TIME SYSTEM OPERATIONS 2006-2007

    SciTech Connect

    Eto, Joseph H.; Parashar, Manu; Lewis, Nancy Jo

    2008-08-15

    The Real Time System Operations (RTSO) 2006-2007 project focused on two parallel technical tasks: (1) Real-Time Applications of Phasors for Monitoring, Alarming and Control; and (2) Real-Time Voltage Security Assessment (RTVSA) Prototype Tool. The overall goal of the phasor applications project was to accelerate adoption and foster greater use of new, more accurate, time-synchronized phasor measurements by conducting research and prototyping applications on California ISO's phasor platform - Real-Time Dynamics Monitoring System (RTDMS) -- that provide previously unavailable information on the dynamic stability of the grid. Feasibility assessment studies were conducted on potential application of this technology for small-signal stability monitoring, validating/improving existing stability nomograms, conducting frequency response analysis, and obtaining real-time sensitivity information on key metrics to assess grid stress. Based on study findings, prototype applications for real-time visualization and alarming, small-signal stability monitoring, measurement based sensitivity analysis and frequency response assessment were developed, factory- and field-tested at the California ISO and at BPA. The goal of the RTVSA project was to provide California ISO with a prototype voltage security assessment tool that runs in real time within California ISO?s new reliability and congestion management system. CERTS conducted a technical assessment of appropriate algorithms, developed a prototype incorporating state-of-art algorithms (such as the continuation power flow, direct method, boundary orbiting method, and hyperplanes) into a framework most suitable for an operations environment. Based on study findings, a functional specification was prepared, which the California ISO has since used to procure a production-quality tool that is now a part of a suite of advanced computational tools that is used by California ISO for reliability and congestion management.

  1. Characterization of real-time computers

    NASA Technical Reports Server (NTRS)

    Shin, K. G.; Krishna, C. M.

    1984-01-01

    A real-time system consists of a computer controller and controlled processes. Despite the synergistic relationship between these two components, they have been traditionally designed and analyzed independently of and separately from each other; namely, computer controllers by computer scientists/engineers and controlled processes by control scientists. As a remedy for this problem, in this report real-time computers are characterized by performance measures based on computer controller response time that are: (1) congruent to the real-time applications, (2) able to offer an objective comparison of rival computer systems, and (3) experimentally measurable/determinable. These measures, unlike others, provide the real-time computer controller with a natural link to controlled processes. In order to demonstrate their utility and power, these measures are first determined for example controlled processes on the basis of control performance functionals. They are then used for two important real-time multiprocessor design applications - the number-power tradeoff and fault-masking and synchronization.

  2. Visualization of Real-Time Data

    NASA Technical Reports Server (NTRS)

    Stansifer, Ryan; Engrand, Peter

    1996-01-01

    In this project we explored various approaches to presenting real-time data from the numerous systems monitored on the space shuttle to computer users. We examined the approach that several projects at the Kennedy Space Center (KSC) used to accomplish this. We undertook to build a prototype system to demonstrate that the Internet and the Java programming language could be used to present the real-time data conveniently. Several Java programs were developed that presented real-time data in different forms including one form that emulated the display screens of the PC GOAL system which is familiar to many at KSC. Also, we developed several communications programs to supply the data continuously. Furthermore, a framework was created using the World Wide Web (WWW) to organize the collection and presentation of the real-time data. We believe our demonstration project shows the great flexibility of the approach. We had no particular use of the data in mind, instead we wanted the most general and the least complex framework possible. People who wish to view data need only know how to use a WWW browser and the address (the URL). People wanting to build WWW documents containing real-time data need only know the values of a few parameters, they do not need to program in Java or any other language. These are stunning advantages over more monolithic systems.

  3. Real-time enhanced vision system

    NASA Astrophysics Data System (ADS)

    Hines, Glenn D.; Rahman, Zia-ur; Jobson, Daniel J.; Woodell, Glenn A.; Harrah, Steven D.

    2005-05-01

    Flying in poor visibility conditions, such as rain, snow, fog or haze, is inherently dangerous. However these conditions can occur at nearly any location, so inevitably pilots must successfully navigate through them. At NASA Langley Research Center (LaRC), under support of the Aviation Safety and Security Program Office and the Systems Engineering Directorate, we are developing an Enhanced Vision System (EVS) that combines image enhancement and synthetic vision elements to assist pilots flying through adverse weather conditions. This system uses a combination of forward-looking infrared and visible sensors for data acquisition. A core function of the system is to enhance and fuse the sensor data in order to increase the information content and quality of the captured imagery. These operations must be performed in real-time for the pilot to use while flying. For image enhancement, we are using the LaRC patented Retinex algorithm since it performs exceptionally well for improving low-contrast range imagery typically seen during poor visibility poor visibility conditions. In general, real-time operation of the Retinex requires specialized hardware. To date, we have successfully implemented a single-sensor real-time version of the Retinex on several different Digital Signal Processor (DSP) platforms. In this paper we give an overview of the EVS and its performance requirements for real-time enhancement and fusion and we discuss our current real-time Retinex implementations on DSPs.

  4. Real-time Enhanced Vision System

    NASA Technical Reports Server (NTRS)

    Hines, Glenn D.; Rahman, Zia-Ur; Jobson, Daniel J.; Woodell, Glenn A.; Harrah, Steven D.

    2005-01-01

    Flying in poor visibility conditions, such as rain, snow, fog or haze, is inherently dangerous. However these conditions can occur at nearly any location, so inevitably pilots must successfully navigate through them. At NASA Langley Research Center (LaRC), under support of the Aviation Safety and Security Program Office and the Systems Engineering Directorate, we are developing an Enhanced Vision System (EVS) that combines image enhancement and synthetic vision elements to assist pilots flying through adverse weather conditions. This system uses a combination of forward-looking infrared and visible sensors for data acquisition. A core function of the system is to enhance and fuse the sensor data in order to increase the information content and quality of the captured imagery. These operations must be performed in real-time for the pilot to use while flying. For image enhancement, we are using the LaRC patented Retinex algorithm since it performs exceptionally well for improving low-contrast range imagery typically seen during poor visibility conditions. In general, real-time operation of the Retinex requires specialized hardware. To date, we have successfully implemented a single-sensor real-time version of the Retinex on several different Digital Signal Processor (DSP) platforms. In this paper we give an overview of the EVS and its performance requirements for real-time enhancement and fusion and we discuss our current real-time Retinex implementations on DSPs.

  5. Really computing nonperturbative real time correlation functions

    NASA Astrophysics Data System (ADS)

    Bödeker, Dietrich; McLerran, Larry; Smilga, Andrei

    1995-10-01

    It has been argued by Grigoriev and Rubakov that one can simulate real time processes involving baryon number nonconservation at high temperature using real time evolution of classical equations, and summing over initial conditions with a classical thermal weight. It is known that such a naive algorithm is plagued by ultraviolet divergences. In quantum theory the divergences are regularized, but the corresponding graphs involve the contributions from the hard momentum region and also the new scale ~gT comes into play. We propose a modified algorithm which involves solving the classical equations of motion for the effective hard thermal loop Hamiltonian with an ultraviolet cutoff μ>>gT and integrating over initial conditions with a proper thermal weight. Such an algorithm should provide a determination of the infrared behavior of the real time correlation function T determining the baryon violation rate. Hopefully, the results obtained in this modified algorithm will be cutoff independent.

  6. Continuous, real time microwave plasma element sensor

    DOEpatents

    Woskov, P.P.; Smatlak, D.L.; Cohn, D.R.; Wittle, J.K.; Titus, C.H.; Surma, J.E.

    1995-12-26

    Microwave-induced plasma is described for continuous, real time trace element monitoring under harsh and variable conditions. The sensor includes a source of high power microwave energy and a shorted waveguide made of a microwave conductive, refractory material communicating with the source of the microwave energy to generate a plasma. The high power waveguide is constructed to be robust in a hot, hostile environment. It includes an aperture for the passage of gases to be analyzed and a spectrometer is connected to receive light from the plasma. Provision is made for real time in situ calibration. The spectrometer disperses the light, which is then analyzed by a computer. The sensor is capable of making continuous, real time quantitative measurements of desired elements, such as the heavy metals lead and mercury. 3 figs.

  7. Continuous, real time microwave plasma element sensor

    DOEpatents

    Woskov, Paul P.; Smatlak, Donna L.; Cohn, Daniel R.; Wittle, J. Kenneth; Titus, Charles H.; Surma, Jeffrey E.

    1995-01-01

    Microwave-induced plasma for continuous, real time trace element monitoring under harsh and variable conditions. The sensor includes a source of high power microwave energy and a shorted waveguide made of a microwave conductive, refractory material communicating with the source of the microwave energy to generate a plasma. The high power waveguide is constructed to be robust in a hot, hostile environment. It includes an aperture for the passage of gases to be analyzed and a spectrometer is connected to receive light from the plasma. Provision is made for real time in situ calibration. The spectrometer disperses the light, which is then analyzed by a computer. The sensor is capable of making continuous, real time quantitative measurements of desired elements, such as the heavy metals lead and mercury.

  8. Real-time, high frequency QRS electrocardiograph

    NASA Technical Reports Server (NTRS)

    Schlegel, Todd T. (Inventor); DePalma, Jude L. (Inventor); Moradi, Saeed (Inventor)

    2006-01-01

    Real time cardiac electrical data are received from a patient, manipulated to determine various useful aspects of the ECG signal, and displayed in real time in a useful form on a computer screen or monitor. The monitor displays the high frequency data from the QRS complex in units of microvolts, juxtaposed with a display of conventional ECG data in units of millivolts or microvolts. The high frequency data are analyzed for their root mean square (RMS) voltage values and the discrete RMS values and related parameters are displayed in real time. The high frequency data from the QRS complex are analyzed with imbedded algorithms to determine the presence or absence of reduced amplitude zones, referred to herein as RAZs. RAZs are displayed as go, no-go signals on the computer monitor. The RMS and related values of the high frequency components are displayed as time varying signals, and the presence or absence of RAZs may be similarly displayed over time.

  9. Durham adaptive optics real-time controller.

    PubMed

    Basden, Alastair; Geng, Deli; Myers, Richard; Younger, Eddy

    2010-11-10

    The Durham adaptive optics (AO) real-time controller was initially a proof of concept design for a generic AO control system. It has since been developed into a modern and powerful central-processing-unit-based real-time control system, capable of using hardware acceleration (including field programmable gate arrays and graphical processing units), based primarily around commercial off-the-shelf hardware. It is powerful enough to be used as the real-time controller for all currently planned 8 m class telescope AO systems. Here we give details of this controller and the concepts behind it, and report on performance, including latency and jitter, which is less than 10 μs for small AO systems.

  10. Real-time DNA microarray analysis

    PubMed Central

    Hassibi, Arjang; Vikalo, Haris; Riechmann, José Luis; Hassibi, Babak

    2009-01-01

    We present a quantification method for affinity-based DNA microarrays which is based on the real-time measurements of hybridization kinetics. This method, i.e. real-time DNA microarrays, enhances the detection dynamic range of conventional systems by being impervious to probe saturation in the capturing spots, washing artifacts, microarray spot-to-spot variations, and other signal amplitude-affecting non-idealities. We demonstrate in both theory and practice that the time-constant of target capturing in microarrays, similar to all affinity-based biosensors, is inversely proportional to the concentration of the target analyte, which we subsequently use as the fundamental parameter to estimate the concentration of the analytes. Furthermore, to empirically validate the capabilities of this method in practical applications, we present a FRET-based assay which enables the real-time detection in gene expression DNA microarrays. PMID:19723688

  11. Real-time DNA microarray analysis.

    PubMed

    Hassibi, Arjang; Vikalo, Haris; Riechmann, José Luis; Hassibi, Babak

    2009-11-01

    We present a quantification method for affinity-based DNA microarrays which is based on the real-time measurements of hybridization kinetics. This method, i.e. real-time DNA microarrays, enhances the detection dynamic range of conventional systems by being impervious to probe saturation in the capturing spots, washing artifacts, microarray spot-to-spot variations, and other signal amplitude-affecting non-idealities. We demonstrate in both theory and practice that the time-constant of target capturing in microarrays, similar to all affinity-based biosensors, is inversely proportional to the concentration of the target analyte, which we subsequently use as the fundamental parameter to estimate the concentration of the analytes. Furthermore, to empirically validate the capabilities of this method in practical applications, we present a FRET-based assay which enables the real-time detection in gene expression DNA microarrays. PMID:19723688

  12. Real-Time Visualization of Tissue Ischemia

    NASA Technical Reports Server (NTRS)

    Bearman, Gregory H. (Inventor); Chrien, Thomas D. (Inventor); Eastwood, Michael L. (Inventor)

    2000-01-01

    A real-time display of tissue ischemia which comprises three CCD video cameras, each with a narrow bandwidth filter at the correct wavelength is discussed. The cameras simultaneously view an area of tissue suspected of having ischemic areas through beamsplitters. The output from each camera is adjusted to give the correct signal intensity for combining with, the others into an image for display. If necessary a digital signal processor (DSP) can implement algorithms for image enhancement prior to display. Current DSP engines are fast enough to give real-time display. Measurement at three, wavelengths, combined into a real-time Red-Green-Blue (RGB) video display with a digital signal processing (DSP) board to implement image algorithms, provides direct visualization of ischemic areas.

  13. The real-time Neutron Monitor database

    NASA Astrophysics Data System (ADS)

    Klein, K.-L.; Steigies, C.; Nmdb Team

    2009-04-01

    In January 2007 the Real time database for high-resolution neutron monitor measurements (NMDB) project, which is supported by the 7th framework program of the European Commission, commenced. One year after the project start we have several neutron monitor stations that are sending their data in real-time to a publicly available prototype database in a common format. We have developed applications that make use of the real-time cosmic ray measurements for example for space weather applications and dose calculations at airplane altitudes. We are also in the process of establishing a public outreach site and a training site with material for university students and researchers and engineers who want to get familiar with cosmic rays and neutron monitor measurements. An overview of the project status as well as instructions on how to use the available data will be given. Possible future developments will be briefly discussed.

  14. Real-time inspection by submarine images

    NASA Astrophysics Data System (ADS)

    Tascini, Guido; Zingaretti, Primo; Conte, Giuseppe

    1996-10-01

    A real-time application of computer vision concerning tracking and inspection of a submarine pipeline is described. The objective is to develop automatic procedures for supporting human operators in the real-time analysis of images acquired by means of cameras mounted on underwater remotely operated vehicles (ROV) Implementation of such procedures gives rise to a human-machine system for underwater pipeline inspection that can automatically detect and signal the presence of the pipe, of its structural or accessory elements, and of dangerous or alien objects in its neighborhood. The possibility of modifying the image acquisition rate in the simulations performed on video- recorded images is used to prove that the system performs all necessary processing with an acceptable robustness working in real-time up to a speed of about 2.5 kn, widely greater than that the actual ROVs and the security features allow.

  15. Quantitative Real-Time PCR: Recent Advances.

    PubMed

    Singh, Charanjeet; Roy-Chowdhuri, Sinchita

    2016-01-01

    Quantitative real-time polymerase chain reaction is a technique for simultaneous amplification and product quantification of a target DNA as the process takes place in real time in a "closed-tube" system. Although this technique can provide an absolute quantification of the initial template copy number, quantification relative to a control sample or second sequence is typically adequate. The quantification process employs melting curve analysis and/or fluorescent detection systems and can provide amplification and genotyping in a relatively short time. Here we describe the properties and uses of various fluorescent detection systems used for quantification. PMID:26843055

  16. Imaging of living cells in real time

    NASA Astrophysics Data System (ADS)

    Tychinsky, Vladimir P.; Koufal, Georgy E.; Perevedentseva, Elena V.; Vyshenskaia, Tatiana V.; Nikandrov, Serguei L.

    1996-12-01

    Parameters of intrinsic cell motility is one of the cell activity characteristics which can be measured in real-time. For evaluation of certain organelles velocity we propose to use high sensitivity of computer-aided phase microscope airyscan to local phase changes connected with refractive index. This method is based on periodical scanning of cell profile in direction perpendicular to organelles movement. Analysis of the obtained 2-dimensional time-coordinate matrix allows us to define organelle velocity in quasi-real time and areas of cell activity. The experiments with onion cells confirm the method applicability for cell activity investigation.

  17. Software Package For Real-Time Graphics

    NASA Technical Reports Server (NTRS)

    Malone, Jacqueline C.; Moore, Archie L.

    1991-01-01

    Software package for master graphics interactive console (MAGIC) at Western Aeronautical Test Range (WATR) of NASA Ames Research Center provides general-purpose graphical display system for real-time and post-real-time analysis of data. Written in C language and intended for use on workstation of interactive raster imaging system (IRIS) equipped with level-V Unix operating system. Enables flight researchers to create their own displays on basis of individual requirements. Applicable to monitoring of complicated processes in chemical industry.

  18. Real-Time, Interactive Sonic Boom Display

    NASA Technical Reports Server (NTRS)

    Haering, Jr., Edward A. (Inventor); Plotkin, Kenneth J. (Inventor)

    2012-01-01

    The present invention is an improved real-time, interactive sonic boom display for aircraft. By using physical properties obtained via various sensors and databases, the invention determines, in real-time, sonic boom impacts locations and intensities for aircraft traveling at supersonic speeds. The information is provided to a pilot via a display that lists a selectable set of maneuvers available to the pilot to mitigate sonic boom issues. Upon selection of a maneuver, the information as to the result of the maneuver is displayed and the pilot may proceed with making the maneuver, or provide new data to the system in order to calculate a different maneuver.

  19. Real-Time Occupancy Change Analyzer

    2005-03-30

    The Real-Time Occupancy Change Analyzer (ROCA) produces an occupancy grid map of an environment around the robot, scans the environment to generate a current obstacle map relative to a current robot position, and converts the current obstacle map to a current occupancy grid map. Changes in the occupancy grid can be reported in real time to support a number of tracking capabilities. The benefit of ROCA is that rather than only providing a vector tomore » the detected change, it provides the actual x,y position of the change.« less

  20. Axial Tomography from Digitized Real Time Radiography

    DOE R&D Accomplishments Database

    Zolnay, A. S.; McDonald, W. M.; Doupont, P. A.; McKinney, R. L.; Lee, M. M.

    1985-01-18

    Axial tomography from digitized real time radiographs provides a useful tool for industrial radiography and tomography. The components of this system are: x-ray source, image intensifier, video camera, video line extractor and digitizer, data storage and reconstruction computers. With this system it is possible to view a two dimensional x-ray image in real time at each angle of rotation and select the tomography plane of interest by choosing which video line to digitize. The digitization of a video line requires less than a second making data acquisition relatively short. Further improvements on this system are planned and initial results are reported.

  1. Automated real-time software development

    NASA Technical Reports Server (NTRS)

    Jones, Denise R.; Walker, Carrie K.; Turkovich, John J.

    1993-01-01

    A Computer-Aided Software Engineering (CASE) system has been developed at the Charles Stark Draper Laboratory (CSDL) under the direction of the NASA Langley Research Center. The CSDL CASE tool provides an automated method of generating source code and hard copy documentation from functional application engineering specifications. The goal is to significantly reduce the cost of developing and maintaining real-time scientific and engineering software while increasing system reliability. This paper describes CSDL CASE and discusses demonstrations that used the tool to automatically generate real-time application code.

  2. Real-time evaporimeter/hygrometer

    NASA Astrophysics Data System (ADS)

    Knopp, Jerome; Smiglewski, Leonard T.

    1998-07-01

    Laboratory measurements of microscopic level changes in a water tank were shown to have good correlation with the evaporation rate predicted using Dalton's Law. Submicron level changes in the tank were measured in real-time using an interferometer interfaced to a PC. The methodology developed offers a way to build an instrument that can be used as a standard for an evaporimeter or a hygrometer. The real-time measurement capability provides a tool for determining refined dynamic correlations of evaporation with fast changes in meteorological variables such as wind and solar radiation.

  3. Quantitative Real-Time PCR: Recent Advances.

    PubMed

    Singh, Charanjeet; Roy-Chowdhuri, Sinchita

    2016-01-01

    Quantitative real-time polymerase chain reaction is a technique for simultaneous amplification and product quantification of a target DNA as the process takes place in real time in a "closed-tube" system. Although this technique can provide an absolute quantification of the initial template copy number, quantification relative to a control sample or second sequence is typically adequate. The quantification process employs melting curve analysis and/or fluorescent detection systems and can provide amplification and genotyping in a relatively short time. Here we describe the properties and uses of various fluorescent detection systems used for quantification.

  4. Machine vision for real time orbital operations

    NASA Technical Reports Server (NTRS)

    Vinz, Frank L.

    1988-01-01

    Machine vision for automation and robotic operation of Space Station era systems has the potential for increasing the efficiency of orbital servicing, repair, assembly and docking tasks. A machine vision research project is described in which a TV camera is used for inputing visual data to a computer so that image processing may be achieved for real time control of these orbital operations. A technique has resulted from this research which reduces computer memory requirements and greatly increases typical computational speed such that it has the potential for development into a real time orbital machine vision system. This technique is called AI BOSS (Analysis of Images by Box Scan and Syntax).

  5. Direct Quantitative Detection and Identification of Lactococcal Bacteriophages from Milk and Whey by Real-Time PCR: Application for the Detection of Lactococcal Bacteriophages in Goat's Raw Milk Whey in France.

    PubMed

    Ly-Chatain, Mai Huong; Durand, Loïc; Rigobello, Véronique; Vera, Annabelle; Demarigny, Yann

    2011-01-01

    The presence of Lactococcus bacteriophages in milk can partly or completely inhibit milk fermentation. To prevent the problems associated with the bacteriophages, the real-time PCR was developed in this study for direct detection from whey and milk of three main groups of Lactococcus bacteriophages, c2, 936, and P335. The optimization of DNA extraction protocol from complex matrices such as whey and milk was optimized allowed the amplification of PCR without any matrix and nontarget contaminant interference. The real-time PCR program was specific and with the detection limit of 10(2) PFU/mL. The curve slopes were -3.49, -3.69, and -3.45 with the amplification efficiency estimated at 94%, 94%, and 98% and the correlation coefficient (R(2)) of 0.999, 0.999, and 0.998 for c2, 936 and P335 group, respectively. This method was then used to detect the bacteriophages in whey and goat's raw milk coming from three farms located in the Rhône-Alpes region (France).

  6. Real-time detection of optical transients with RAPTOR

    SciTech Connect

    Borozdin, K. N.; Brumby, Steven P.; Galassi, M. C.; McGowan, K. E.; Starr, D. L.; Vestrand, W. T.; White, R. R.; Wozniak, P. R.; Wren, J.

    2002-01-01

    Fast variability of optical objects is an interesting though poorly explored subject in modern astronomy. Real-time data processing and identification of transient, celestial events in the images is very important, for such study as it allows rapid follow-up with more sensitive instruments, We discuss an approach which we have chosen for the RAPTOR project which is a pioneering close-loop system combining real-time transient detection with rapid follow-up. Our data processing pipeline is able to identify and localize an optical transient within seconds after the observation. We describe the challenges we met, solutions we found and some results obtained in our search for fast optical transients. The software pipeline we have developed for RAPTOR can easily be applied to the data from other experiments.

  7. Real-Time GNSS Positioning Along Canada's Active Coastal Margin

    NASA Astrophysics Data System (ADS)

    Henton, J. A.; Dragert, H.; Lu, Y.

    2014-12-01

    High-rate, low-latency Global Navigation Satellite System (GNSS) data are being refined for real-time applications to monitor and report motions related to large earthquakes in coastal British Columbia. Given the tectonic setting of Canada's west coast, specific goals for real-time regional geodetic monitoring are: (1) the collection of GNSS data with adequate station density to identify the deformation field for regional earthquakes with M>7.3; (2) the robust, continuous real-time analyses of GNSS data with a precision of 1-2 cm and a latency of less than 10s; and (3) the display of results with attending automated alarms and estimations of earthquake parameters. Megathrust earthquakes (M>8) are the primary targets for immediate identification, since the tsunamis they generate will strike the coast within 15 to 20 min. However, large (6.0real-time precise point positioning streams for regional sites received from the Canadian Geodetic Survey (CGS), the Jet Propulsion Laboratory (JPL), and the Plate Boundary Observatory (PBO). The comparison of these various real-time solutions allows a realistic evaluation of day-to-day software performance especially when faced with adverse conditions such as data gaps or poor satellite geometry. Forward models for scenario earthquakes in this region are used to "fingerprint" the coseismic displacements expected from various offshore events which allows an evaluation of the effectiveness of the current regional coverage. The present distribution and density of real-time sites is largely sufficient for aiding the timely estimation of size, location

  8. NASADIG - NASA DEVICE INDEPENDENT GRAPHICS LIBRARY (AMDAHL VERSION)

    NASA Technical Reports Server (NTRS)

    Rogers, J. E.

    1994-01-01

    The NASA Device Independent Graphics Library, NASADIG, can be used with many computer-based engineering and management applications. The library gives the user the opportunity to translate data into effective graphic displays for presentation. The software offers many features which allow the user flexibility in creating graphics. These include two-dimensional plots, subplot projections in 3D-space, surface contour line plots, and surface contour color-shaded plots. Routines for three-dimensional plotting, wireframe surface plots, surface plots with hidden line removal, and surface contour line plots are provided. Other features include polar and spherical coordinate plotting, world map plotting utilizing either cylindrical equidistant or Lambert equal area projection, plot translation, plot rotation, plot blowup, splines and polynomial interpolation, area blanking control, multiple log/linear axes, legends and text control, curve thickness control, and multiple text fonts (18 regular, 4 bold). NASADIG contains several groups of subroutines. Included are subroutines for plot area and axis definition; text set-up and display; area blanking; line style set-up, interpolation, and plotting; color shading and pattern control; legend, text block, and character control; device initialization; mixed alphabets setting; and other useful functions. The usefulness of many routines is dependent on the prior definition of basic parameters. The program's control structure uses a serial-level construct with each routine restricted for activation at some prescribed level(s) of problem definition. NASADIG provides the following output device drivers: Selanar 100XL, VECTOR Move/Draw ASCII and PostScript files, Tektronix 40xx, 41xx, and 4510 Rasterizer, DEC VT-240 (4014 mode), IBM AT/PC compatible with SmartTerm 240 emulator, HP Lasergrafix Film Recorder, QMS 800/1200, DEC LN03+ Laserprinters, and HP LaserJet (Series III). NASADIG is written in FORTRAN and is available for several

  9. NASADIG - NASA DEVICE INDEPENDENT GRAPHICS LIBRARY (CRAY VERSION)

    NASA Technical Reports Server (NTRS)

    Rogers, J. E.

    1994-01-01

    The NASA Device Independent Graphics Library, NASADIG, can be used with many computer-based engineering and management applications. The library gives the user the opportunity to translate data into effective graphic displays for presentation. The software offers many features which allow the user flexibility in creating graphics. These include two-dimensional plots, subplot projections in 3D-space, surface contour line plots, and surface contour color-shaded plots. Routines for three-dimensional plotting, wireframe surface plots, surface plots with hidden line removal, and surface contour line plots are provided. Other features include polar and spherical coordinate plotting, world map plotting utilizing either cylindrical equidistant or Lambert equal area projection, plot translation, plot rotation, plot blowup, splines and polynomial interpolation, area blanking control, multiple log/linear axes, legends and text control, curve thickness control, and multiple text fonts (18 regular, 4 bold). NASADIG contains several groups of subroutines. Included are subroutines for plot area and axis definition; text set-up and display; area blanking; line style set-up, interpolation, and plotting; color shading and pattern control; legend, text block, and character control; device initialization; mixed alphabets setting; and other useful functions. The usefulness of many routines is dependent on the prior definition of basic parameters. The program's control structure uses a serial-level construct with each routine restricted for activation at some prescribed level(s) of problem definition. NASADIG provides the following output device drivers: Selanar 100XL, VECTOR Move/Draw ASCII and PostScript files, Tektronix 40xx, 41xx, and 4510 Rasterizer, DEC VT-240 (4014 mode), IBM AT/PC compatible with SmartTerm 240 emulator, HP Lasergrafix Film Recorder, QMS 800/1200, DEC LN03+ Laserprinters, and HP LaserJet (Series III). NASADIG is written in FORTRAN and is available for several

  10. NASADIG - NASA DEVICE INDEPENDENT GRAPHICS LIBRARY (UNIX VERSION)

    NASA Technical Reports Server (NTRS)

    Rogers, J. E.

    1994-01-01

    The NASA Device Independent Graphics Library, NASADIG, can be used with many computer-based engineering and management applications. The library gives the user the opportunity to translate data into effective graphic displays for presentation. The software offers many features which allow the user flexibility in creating graphics. These include two-dimensional plots, subplot projections in 3D-space, surface contour line plots, and surface contour color-shaded plots. Routines for three-dimensional plotting, wireframe surface plots, surface plots with hidden line removal, and surface contour line plots are provided. Other features include polar and spherical coordinate plotting, world map plotting utilizing either cylindrical equidistant or Lambert equal area projection, plot translation, plot rotation, plot blowup, splines and polynomial interpolation, area blanking control, multiple log/linear axes, legends and text control, curve thickness control, and multiple text fonts (18 regular, 4 bold). NASADIG contains several groups of subroutines. Included are subroutines for plot area and axis definition; text set-up and display; area blanking; line style set-up, interpolation, and plotting; color shading and pattern control; legend, text block, and character control; device initialization; mixed alphabets setting; and other useful functions. The usefulness of many routines is dependent on the prior definition of basic parameters. The program's control structure uses a serial-level construct with each routine restricted for activation at some prescribed level(s) of problem definition. NASADIG provides the following output device drivers: Selanar 100XL, VECTOR Move/Draw ASCII and PostScript files, Tektronix 40xx, 41xx, and 4510 Rasterizer, DEC VT-240 (4014 mode), IBM AT/PC compatible with SmartTerm 240 emulator, HP Lasergrafix Film Recorder, QMS 800/1200, DEC LN03+ Laserprinters, and HP LaserJet (Series III). NASADIG is written in FORTRAN and is available for several

  11. NASADIG - NASA DEVICE INDEPENDENT GRAPHICS LIBRARY (VAX VMS VERSION)

    NASA Technical Reports Server (NTRS)

    Rogers, J. E.

    1994-01-01

    The NASA Device Independent Graphics Library, NASADIG, can be used with many computer-based engineering and management applications. The library gives the user the opportunity to translate data into effective graphic displays for presentation. The software offers many features which allow the user flexibility in creating graphics. These include two-dimensional plots, subplot projections in 3D-space, surface contour line plots, and surface contour color-shaded plots. Routines for three-dimensional plotting, wireframe surface plots, surface plots with hidden line removal, and surface contour line plots are provided. Other features include polar and spherical coordinate plotting, world map plotting utilizing either cylindrical equidistant or Lambert equal area projection, plot translation, plot rotation, plot blowup, splines and polynomial interpolation, area blanking control, multiple log/linear axes, legends and text control, curve thickness control, and multiple text fonts (18 regular, 4 bold). NASADIG contains several groups of subroutines. Included are subroutines for plot area and axis definition; text set-up and display; area blanking; line style set-up, interpolation, and plotting; color shading and pattern control; legend, text block, and character control; device initialization; mixed alphabets setting; and other useful functions. The usefulness of many routines is dependent on the prior definition of basic parameters. The program's control structure uses a serial-level construct with each routine restricted for activation at some prescribed level(s) of problem definition. NASADIG provides the following output device drivers: Selanar 100XL, VECTOR Move/Draw ASCII and PostScript files, Tektronix 40xx, 41xx, and 4510 Rasterizer, DEC VT-240 (4014 mode), IBM AT/PC compatible with SmartTerm 240 emulator, HP Lasergrafix Film Recorder, QMS 800/1200, DEC LN03+ Laserprinters, and HP LaserJet (Series III). NASADIG is written in FORTRAN and is available for several

  12. Real-Time Blackboards For Sensor Fusions

    NASA Astrophysics Data System (ADS)

    Johnson, Donald H.; Shaw, Scott W.; Reynolds, Steven; Himayat, Nageen

    1989-09-01

    Multi-sensor fusion, at the most basic level, can be cast into a concise, elegant model. Reality demands, however, that this model be modified and augmented. These modifications often result in software systems that are confusing in function and difficult to debug. This problem can be ameliorated by adopting an object-oriented, data-flow programming style. For real-time applications, this approach simplifies data communications and storage management. The concept of object-oriented, data-flow programming is conveniently embodied in the black-board style of software architecture. Blackboard systems allow diverse programs access to a central data base. When the blackboard is described as an object, it can be distributed over multiple processors for real-time applications. Choosing the appropriate parallel architecture is the subject of ongoing research. A prototype blackboard has been constructed to fuse optical image regions and Doppler radar events. The system maintains tracks of simulated targets in real time. The results of this simulation have been used to direct further research on real-time blackboard systems.

  13. Real-time cleaning performance feedback

    SciTech Connect

    Meltzer, M.

    1994-12-01

    Monitoring contamination levels on parts during cleaning operations will provide feedback that can be useful in reducing waste generation and air emissions caused by over- or under-cleaning. Such real-time process controls can help eliminate pollution in a wide variety of industries, including aerospace, electronics, and metal finishing.

  14. REAL TIME CONTROL OF URBAN DRAINAGE NETWORKS

    EPA Science Inventory

    Real-time control (RTC) is a custom-designed, computer-assisted management technology for a specific sewerage network to meet the operational objectives of its collection/conveyance system. RTC can operate in several modes, including a mode that is activated during a wet weather ...

  15. Real Time Grid Reliability Management 2005

    SciTech Connect

    Eto, Joe; Eto, Joe; Lesieutre, Bernard; Lewis, Nancy Jo; Parashar, Manu

    2008-07-07

    The increased need to manage California?s electricity grid in real time is a result of the ongoing transition from a system operated by vertically-integrated utilities serving native loads to one operated by an independent system operator supporting competitive energy markets. During this transition period, the traditional approach to reliability management -- construction of new transmission lines -- has not been pursued due to unresolved issues related to the financing and recovery of transmission project costs. In the absence of investments in new transmission infrastructure, the best strategy for managing reliability is to equip system operators with better real-time information about actual operating margins so that they can better understand and manage the risk of operating closer to the edge. A companion strategy is to address known deficiencies in offline modeling tools that are needed to ground the use of improved real-time tools. This project: (1) developed and conducted first-ever demonstrations of two prototype real-time software tools for voltage security assessment and phasor monitoring; and (2) prepared a scoping study on improving load and generator response models. Additional funding through two separate subsequent work authorizations has already been provided to build upon the work initiated in this project.

  16. The Power of Real-Time PCR

    ERIC Educational Resources Information Center

    Valasek, Mark A.; Repa, Joyce J.

    2005-01-01

    In recent years, real-time polymerase chain reaction (PCR) has emerged as a robust and widely used methodology for biological investigation because it can detect and quantify very small amounts of specific nucleic acid sequences. As a research tool, a major application of this technology is the rapid and accurate assessment of changes in gene…

  17. Real Time Estimation Of Object Spectrocolorimettic Features

    NASA Astrophysics Data System (ADS)

    Petrov, Peter V.; Lukarsky, Christo D.; Christov, Victor V.; Grancharov, Parashkev A.; Arshinkova, Iren I.

    1989-03-01

    The results obtained in the development of a laboratory prototype of intelligent spectrometric system with real time digital signal processing are shown in this paper. The system is acombination of visible range spectrophotometer and focussing holographic grid with photodiode linear structure, i.e.the sensor, real time digital signal processing controller and display processor for gray level visualization, together with PC/XT controlLing computer. The twodimesional adaptive differential pulse code modulator with simultaneous correction of sensor dark current introduced into the real time controller allows the registration of measurments with resolution of 10 bit/el and real time data compression 2.5 times. During computation of colorimetric estimations or wideband photo-metric compression the possibilities for express analysis increase together with the enhancement of the signal-to-noise ratio. The system control and the visualization of spectral and colorimetric features in the data flux is made with personal computer together with display processor with resolution 512x512x8 and interactive software. It may be used for ground-based and onboard complexes.

  18. Feedback as Real-Time Constructions

    ERIC Educational Resources Information Center

    Keiding, Tina Bering; Qvortrup, Ane

    2014-01-01

    This article offers a re-description of feedback and the significance of time in feedback constructions based on systems theory. It describes feedback as internal, real-time constructions in a learning system. From this perspective, feedback is neither immediate nor delayed, but occurs in the very moment it takes place. This article argues for a…

  19. Real-time PCR detection chemistry.

    PubMed

    Navarro, E; Serrano-Heras, G; Castaño, M J; Solera, J

    2015-01-15

    Real-time PCR is the method of choice in many laboratories for diagnostic and food applications. This technology merges the polymerase chain reaction chemistry with the use of fluorescent reporter molecules in order to monitor the production of amplification products during each cycle of the PCR reaction. Thus, the combination of excellent sensitivity and specificity, reproducible data, low contamination risk and reduced hand-on time, which make it a post-PCR analysis unnecessary, has made real-time PCR technology an appealing alternative to conventional PCR. The present paper attempts to provide a rigorous overview of fluorescent-based methods for nucleic acid analysis in real-time PCR described in the literature so far. Herein, different real-time PCR chemistries have been classified into two main groups; the first group comprises double-stranded DNA intercalating molecules, such as SYBR Green I and EvaGreen, whereas the second includes fluorophore-labeled oligonucleotides. The latter, in turn, has been divided into three subgroups according to the type of fluorescent molecules used in the PCR reaction: (i) primer-probes (Scorpions, Amplifluor, LUX, Cyclicons, Angler); (ii) probes; hydrolysis (TaqMan, MGB-TaqMan, Snake assay) and hybridization (Hybprobe or FRET, Molecular Beacons, HyBeacon, MGB-Pleiades, MGB-Eclipse, ResonSense, Yin-Yang or displacing); and (iii) analogues of nucleic acids (PNA, LNA, ZNA, non-natural bases: Plexor primer, Tiny-Molecular Beacon). In addition, structures, mechanisms of action, advantages and applications of such real-time PCR probes and analogues are depicted in this review.

  20. Two alternative multiplex PCRs for the identification of the seven species of anglerfish (Lophius spp.) using an end-point or a melting curve analysis real-time protocol.

    PubMed

    Castigliego, Lorenzo; Armani, Andrea; Tinacci, Lara; Gianfaldoni, Daniela; Guidi, Alessandra

    2015-01-01

    Anglerfish (Lophius spp.) is consumed worldwide and is an important economic resource though its seven species are often fraudulently interchanged due to their different commercial value, especially when sold in the form of fillets or pieces. Molecular analysis is the only possible mean to verify traceability and counteract fraud. We developed two multiplex PCRs, one end-point and one real-time with melting curve post-amplification analysis, which can even be run with the simplest two-channel thermocyclers. The two methods were tested on seventy-five reference samples. Their specificity was checked in twenty more species of those most commonly available on the market and in other species of the Lophiidae family. Both methods, the choice of which depends on the equipment and budget of the lab, provide a rapid and easy-to-read response, improving both the simplicity and cost-effectiveness of existing methods for identifying Lophius species. PMID:25053020

  1. Two alternative multiplex PCRs for the identification of the seven species of anglerfish (Lophius spp.) using an end-point or a melting curve analysis real-time protocol.

    PubMed

    Castigliego, Lorenzo; Armani, Andrea; Tinacci, Lara; Gianfaldoni, Daniela; Guidi, Alessandra

    2015-01-01

    Anglerfish (Lophius spp.) is consumed worldwide and is an important economic resource though its seven species are often fraudulently interchanged due to their different commercial value, especially when sold in the form of fillets or pieces. Molecular analysis is the only possible mean to verify traceability and counteract fraud. We developed two multiplex PCRs, one end-point and one real-time with melting curve post-amplification analysis, which can even be run with the simplest two-channel thermocyclers. The two methods were tested on seventy-five reference samples. Their specificity was checked in twenty more species of those most commonly available on the market and in other species of the Lophiidae family. Both methods, the choice of which depends on the equipment and budget of the lab, provide a rapid and easy-to-read response, improving both the simplicity and cost-effectiveness of existing methods for identifying Lophius species.

  2. Identification and real-time expression analysis of selected Toxoplasma gondii in-vivo induced antigens recognized by IgG and IgM in sera of acute toxoplasmosis patients

    PubMed Central

    2013-01-01

    Background Toxoplasma gondii is an obligate intracellular zoonotic parasite of the phylum Apicomplexa which infects a wide range of warm-blooded animals, including humans. In this study in-vivo induced antigens of this parasite was investigated using in-vivo induced antigen technology (IVIAT) and pooled sera from patients with serological evidence of acute infection. Methods The pooled sera was first pre-absorbed against three different preparations of antigens from in-vitro-grown cells of each T. gondii and E. coli XL1-Blue MRF’, subsequently it was used to screen T. gondii cDNA phage expression library. Positive clones from each group were subjected to quantitative real-time PCR expression analysis on mRNA of in-vivo and in-vitro grown parasites. Results A total of 29 reactive clones from each IgM and IgG immunoscreenings were found to have high homology to T. gondii genes. Quantitative real-time PCR expression analysis showed that 20 IgM-detected genes and 11 IgG-detected genes were up-regulated in-vivo relative to their expression levels in-vitro. These included genes encoding micronemes, sterol-regulatory element binding protein site, SRS34A, MIC2-associated protein M2AP, nucleoredoxin, protein phosphatase 2C and several hypothetical proteins. A hypothetical protein (GenBank accession no. 7899266) detected by IgG had the highest in-vivo over in-vitro fold change of 499.86; while another up-regulated hypothetical protein (GenBank accession no. 7898829) recognized by IgM showed high sensitivity (90%) and moderate specificity (70%) in detecting T. gondii antibodies when tested with 20 individual serum samples. Conclusion The highly up-regulated genes and the corresponding proteins, in particular the hypothetical proteins, may be useful in further studies on understanding the disease pathogenesis and as potential vaccine candidates. PMID:23800344

  3. ALMA Correlator Real-Time Data Processor

    NASA Astrophysics Data System (ADS)

    Pisano, J.; Amestica, R.; Perez, J.

    2005-10-01

    The design of a real-time Linux application utilizing Real-Time Application Interface (RTAI) to process real-time data from the radio astronomy correlator for the Atacama Large Millimeter Array (ALMA) is described. The correlator is a custom-built digital signal processor which computes the cross-correlation function of two digitized signal streams. ALMA will have 64 antennas with 2080 signal streams each with a sample rate of 4 giga-samples per second. The correlator's aggregate data output will be 1 gigabyte per second. The software is defined by hard deadlines with high input and processing data rates, while requiring interfaces to non real-time external computers. The designed computer system - the Correlator Data Processor or CDP, consists of a cluster of 17 SMP computers, 16 of which are compute nodes plus a master controller node all running real-time Linux kernels. Each compute node uses an RTAI kernel module to interface to a 32-bit parallel interface which accepts raw data at 64 megabytes per second in 1 megabyte chunks every 16 milliseconds. These data are transferred to tasks running on multiple CPUs in hard real-time using RTAI's LXRT facility to perform quantization corrections, data windowing, FFTs, and phase corrections for a processing rate of approximately 1 GFLOPS. Highly accurate timing signals are distributed to all seventeen computer nodes in order to synchronize them to other time-dependent devices in the observatory array. RTAI kernel tasks interface to the timing signals providing sub-millisecond timing resolution. The CDP interfaces, via the master node, to other computer systems on an external intra-net for command and control, data storage, and further data (image) processing. The master node accesses these external systems utilizing ALMA Common Software (ACS), a CORBA-based client-server software infrastructure providing logging, monitoring, data delivery, and intra-computer function invocation. The software is being developed in tandem

  4. Real-Time Seismology in Portugal

    NASA Astrophysics Data System (ADS)

    Custodio, S.; Marreiros, C.; Carvalho, S.; Vales, D.; Lima, V.; Carrilho, F.

    2012-12-01

    Portugal is located next to the plate boundary between Eurasia (Iberia) and Africa (Nubia). The country has been repeatedly affected by some of the largest earthquakes, both onshore and offshore, in the historical European record, including the largest historical European earthquake, the great Lisbon earthquake of 1755 (~M8.5). The Portuguese territory has suffered directly the consequences of strong ground shaking (collapse of buildings, etc) and also some of the most destructive consequences of earthquakes (e.g. tsunamis, fires, etc). However, the rate of tectonic deformation in the Portuguese territory is low (the Eurasian-African plates converge at a rate of ~ 5 mm/yr), which results in long recurrence intervals between earthquakes. This low to moderate rate of seismic activity has two major negative effects: 1) it is difficult to study the regional seismo-tectonics with traditional passive methods; 2) the population is little aware of earthquake risk and unprepared to react in case of disaster. In this scenario, real-time seismology is key to monitoring earthquake crisis in real-time, providing early warnings about potentially destructive events, and assisting in the channeling of recovery efforts in case of disaster. In this paper we will present the real-time algorithms implemented at Instituto de Meteorologia (IM), the institution responsible for seismic monitoring in Portugal. In particular, we will focus on the following aspects: 1) Data collection and real-time transmission to the headquarters. Broadband seismological stations are owned and operated by five different institutions. The last years have witnessed an effort for integration, and presently most data arrives at IM lab in real-time. 2) Earthquake location and local magnitude determination. Data is automatically analyzed in order to obtain a first earthquake hypocenter and ML. While this process is mostly automatic, it still requires the revision by an operator, who is available 24h. 3

  5. Real-time imaging of quantum entanglement.

    PubMed

    Fickler, Robert; Krenn, Mario; Lapkiewicz, Radek; Ramelow, Sven; Zeilinger, Anton

    2013-01-01

    Quantum Entanglement is widely regarded as one of the most prominent features of quantum mechanics and quantum information science. Although, photonic entanglement is routinely studied in many experiments nowadays, its signature has been out of the grasp for real-time imaging. Here we show that modern technology, namely triggered intensified charge coupled device (ICCD) cameras are fast and sensitive enough to image in real-time the effect of the measurement of one photon on its entangled partner. To quantitatively verify the non-classicality of the measurements we determine the detected photon number and error margin from the registered intensity image within a certain region. Additionally, the use of the ICCD camera allows us to demonstrate the high flexibility of the setup in creating any desired spatial-mode entanglement, which suggests as well that visual imaging in quantum optics not only provides a better intuitive understanding of entanglement but will improve applications of quantum science.

  6. Real Time Radiation Exposure And Health Risks

    NASA Technical Reports Server (NTRS)

    Hu, Shaowen; Barzilla, Janet E.; Semones, Edward J.

    2015-01-01

    Radiation from solar particle events (SPEs) poses a serious threat to future manned missions outside of low Earth orbit (LEO). Accurate characterization of the radiation environment in the inner heliosphere and timely monitoring the health risks to crew are essential steps to ensure the safety of future Mars missions. In this project we plan to develop an approach that can use the particle data from multiple satellites and perform near real-time simulations of radiation exposure and health risks for various exposure scenarios. Time-course profiles of dose rates will be calculated with HZETRN and PDOSE from the energy spectrum and compositions of the particles archived from satellites, and will be validated from recent radiation exposure measurements in space. Real-time estimation of radiation risks will be investigated using ARRBOD. This cross discipline integrated approach can improve risk mitigation by providing critical information for risk assessment and medical guidance to crew during SPEs.

  7. Real Time Radiation Monitoring Using Nanotechnology

    NASA Technical Reports Server (NTRS)

    Li, Jing (Inventor); Wilkins, Richard T. (Inventor); Hanratty, James J. (Inventor); Lu, Yijiang (Inventor)

    2016-01-01

    System and method for monitoring receipt and estimating flux value, in real time, of incident radiation, using two or more nanostructures (NSs) and associated terminals to provide closed electrical paths and to measure one or more electrical property change values .DELTA.EPV, associated with irradiated NSs, during a sequence of irradiation time intervals. Effects of irradiation, without healing and with healing, of the NSs, are separately modeled for first order and second order healing. Change values.DELTA.EPV are related to flux, to cumulative dose received by NSs, and to radiation and healing effectivity parameters and/or.mu., associated with the NS material and to the flux. Flux and/or dose are estimated in real time, based on EPV change values, using measured .DELTA.EPV values. Threshold dose for specified changes of biological origin (usually undesired) can be estimated. Effects of time-dependent radiation flux are analyzed in pre-healing and healing regimes.

  8. Real time radiography of Titan 4 booster

    NASA Astrophysics Data System (ADS)

    Lachapell, M.; Turner, D.; Dolan, K.; Perkins, D.; Costerus, B.

    1993-04-01

    Lawrence Livermore National Laboratory successfully completed a real-time radiography of the Titan 4 booster motor in February 1993. The success of this project depended on the quick response to Air Force criteria and securing a multi-disciplinary team addressing the numerous technical challenges. The team's challenges included the following: large area imager design and fabrication problems; vibrating mitigation obstacles; sound mitigation dilemmas; high levels of fail safe confidence; and operating a fragile, transportable x-ray linear accelerator. The data was viewed in real-time and stored utilizing standard video hardware. The data from the test is presently being analyzed. The multi-disciplinary team was presented with many serious technical challenges that needed to be addressed expeditiously. The purpose of this paper is to examine some of the technical issues and how they were executed.

  9. Real time animation of space plasma phenomena

    NASA Technical Reports Server (NTRS)

    Jordan, K. F.; Greenstadt, E. W.

    1987-01-01

    In pursuit of real time animation of computer simulated space plasma phenomena, the code was rewritten for the Massively Parallel Processor (MPP). The program creates a dynamic representation of the global bowshock which is based on actual spacecraft data and designed for three dimensional graphic output. This output consists of time slice sequences which make up the frames of the animation. With the MPP, 16384, 512 or 4 frames can be calculated simultaneously depending upon which characteristic is being computed. The run time was greatly reduced which promotes the rapid sequence of images and makes real time animation a foreseeable goal. The addition of more complex phenomenology in the constructed computer images is now possible and work proceeds to generate these images.

  10. Real-Time Gauge/Gravity Duality

    SciTech Connect

    Skenderis, Kostas; Rees, Balt C. van

    2008-08-22

    We present a general prescription for the holographic computation of real-time n-point functions in nontrivial states. In quantum field theory such real-time computations involve a choice of a time contour in the complex time plane. The holographic prescription amounts to 'filling in' this contour with bulk solutions: real segments of the contour are filled in with Lorentzian solutions while imaginary segments are filled in with Riemannian solutions and appropriate matching conditions are imposed at the corners of the contour. We illustrate the general discussion by computing the 2-point function of a scalar operator using this prescription and by showing that this leads to an unambiguous answer with the correct i{epsilon} insertions.

  11. Visualizations for Real-time Pricing Demonstration

    SciTech Connect

    Marinovici, Maria C.; Hammerstrom, Janelle L.; Widergren, Steven E.; Dayley, Greg K.

    2014-10-13

    In this paper, the visualization tools created for monitoring the operations of a real-time pricing demonstration system that runs at a distribution feeder level are presented. The information these tools provide gives insights into demand behavior from automated price responsive devices, distribution feeder characteristics, impact of weather on system’s development, and other significant dynamics. Given the large number of devices that bid into a feeder-level real-time electricity market, new techniques are explored to summarize the present state of the system and contrast that with previous trends as well as future projections. To better understand the system behavior and correctly inform decision-making procedures, effective visualization of the data is imperative.

  12. AMON: Transition to real-time operations

    NASA Astrophysics Data System (ADS)

    Cowen, D. F.; Keivani, A.; Tešić, G.

    2016-04-01

    The Astrophysical Multimessenger Observatory Network (AMON) will link the world's leading high-energy neutrino, cosmic-ray, gamma-ray and gravitational wave observatories by performing real-time coincidence searches for multimessenger sources from observatories' subthreshold data streams. The resulting coincidences will be distributed to interested parties in the form of electronic alerts for real-time follow-up observation. We will present the science case, design elements, current and projected partner observatories, status of the AMON project, and an initial AMON-enabled analysis. The prototype of the AMON server has been online since August 2014 and processing archival data. Currently, we are deploying new high-uptime servers and will be ready to start issuing alerts as early as winter 2015/16.

  13. System Equivalent for Real Time Digital Simulator

    NASA Astrophysics Data System (ADS)

    Lin, Xi

    2011-07-01

    The purpose of this research is to develop a method of making system equivalents for the Real Time Digital Simulator (RTDS), which should enhance its capability of simulating large power systems. The proposed equivalent combines a Frequency Dependent Network Equivalent (FDNE) for the high frequency electromagnetic transients and a Transient Stability Analysis (TSA) type simulation block for the electromechanical transients. The frequency dependent characteristic for FDNE is obtained by curve-fitting frequency domain admittance characteristics using the Vector Fitting method. An approach for approximating the frequency dependent characteristic of large power networks from readily available typical power-flow data is also introduced. A new scheme of incorporating TSA solution in RTDS is proposed. This report shows how the TSA algorithm can be adapted to a real time platform. The validity of this method is confirmed with examples, including the study of a multi in-feed HVDC system based network.

  14. "Fast" Is Not "Real-Time": Designing Effective Real-Time AI Systems

    NASA Astrophysics Data System (ADS)

    O'Reilly, Cindy A.; Cromarty, Andrew S.

    1985-04-01

    Realistic practical problem domains (such as robotics, process control, and certain kinds of signal processing) stand to benefit greatly from the application of artificial intelligence techniques. These problem domains are of special interest because they are typified by complex dynamic environments in which the ability to select and initiate a proper response to environmental events in real time is a strict prerequisite to effective environmental interaction. Artificial intelligence systems developed to date have been sheltered from this real-time requirement, however, largely by virtue of their use of simplified problem domains or problem representations. The plethora of colloquial and (in general) mutually inconsistent interpretations of the term "real-time" employed by workers in each of these domains further exacerbates the difficul-ties in effectively applying state-of-the-art problem solving tech-niques to time-critical problems. Indeed, the intellectual waters are by now sufficiently muddied that the pursuit of a rigorous treatment of intelligent real-time performance mandates the redevelopment of proper problem perspective on what "real-time" means, starting from first principles. We present a simple but nonetheless formal definition of real-time performance. We then undertake an analysis of both conventional techniques and AI technology with respect to their ability to meet substantive real-time performance criteria. This analysis provides a basis for specification of problem-independent design requirements for systems that would claim real-time performance. Finally, we discuss the application of these design principles to a pragmatic problem in real-time signal understanding.

  15. CRTF Real-Time Aperture Flux system

    SciTech Connect

    Davis, D.B.

    1980-01-01

    The Real-Time Aperture Flux system (TRAF) is a test measurement system designed to determine the input power/unit area (flux density) during solar experiments conducted at the Central Receiver Test Facility, Sandia National Laboratories, Albuquerque, New Mexico. The RTAF is capable of using both thermal sensors and photon sensors to determine the flux densities in the RTAF measuring plane. These data are manipulated in various ways to derive input power and flux density distribution to solar experiments.

  16. Thermal imaging with real time picture presentation.

    PubMed

    Borg, S B

    1968-09-01

    The accomplishment of thermal imaging with real-time picture presentation represents a significant advance in nondestructive testing. Described here is the AGA Thermovision, capable of producing such imaging. Operating principles, basic features, and recording techniques are reviewed, and a survey is made of the range of applications. Examples include electrical power distribution elements, a turbine blade, and a missile model in a wind tunnel.

  17. Real-Time Clinical Monitoring of Biomolecules

    NASA Astrophysics Data System (ADS)

    Rogers, Michelle L.; Boutelle, Martyn G.

    2013-06-01

    Continuous monitoring of clinical biomarkers offers the exciting possibility of new therapies that use biomarker levels to guide treatment in real time. This review explores recent progress toward this goal. We initially consider measurements in body fluids by a range of analytical methods. We then discuss direct tissue measurements performed by implanted sensors; sampling techniques, including microdialysis and ultrafiltration; and noninvasive methods. A future directions section considers analytical methods at the cusp of clinical use.

  18. Real-Time X-Ray Inspection

    NASA Technical Reports Server (NTRS)

    Bulthuis, Ronald V.

    1988-01-01

    X-ray imaging instrument adapted to continuous scanning. Modern version of fluoroscope enables rapid x-ray inspection of parts. Developed for detection of buckling in insulated ducts. Uses radiation from radioactive gadolinium or thallium source. Instrument weighs only 6 1/2 lb. Quickly scanned by hand along duct surface, providing real-time image. Based on Lixiscope, developed at Goddard Space Flight Center.

  19. Real-time interactive treatment planning.

    PubMed

    Otto, Karl

    2014-09-01

    The goal of this work is to develop an interactive treatment planning platform that permits real-time manipulation of dose distributions including DVHs and other dose metrics. The hypothesis underlying the approach proposed here is that the process of evaluating potential dose distribution options and deciding on the best clinical trade-offs may be separated from the derivation of the actual delivery parameters used for the patient's treatment. For this purpose a novel algorithm for deriving an Achievable Dose Estimate (ADE) was developed. The ADE algorithm is computationally efficient so as to update dose distributions in effectively real-time while accurately incorporating the limits of what can be achieved in practice. The resulting system is a software environment for interactive real-time manipulation of dose that permits the clinician to rapidly develop a fully customized 3D dose distribution. Graphical navigation of dose distributions is achieved by a sophisticated method of identifying contributing fluence elements, modifying those elements and re-computing the entire dose distribution. 3D dose distributions are calculated in ~2-20 ms. Including graphics processing overhead, clinicians may visually interact with the dose distribution (e.g. 'drag' a DVH) and display updates of the dose distribution at a rate of more than 20 times per second. Preliminary testing on various sites shows that interactive planning may be completed in ~1-5 min, depending on the complexity of the case (number of targets and OARs). Final DVHs are derived through a separate plan optimization step using a conventional VMAT planning system and were shown to be achievable within 2% and 4% in high and low dose regions respectively. With real-time interactive planning trade-offs between Target(s) and OARs may be evaluated efficiently providing a better understanding of the dosimetric options available to each patient in static or adaptive RT.

  20. Software Analyzes Complex Systems in Real Time

    NASA Technical Reports Server (NTRS)

    2008-01-01

    Expert system software programs, also known as knowledge-based systems, are computer programs that emulate the knowledge and analytical skills of one or more human experts, related to a specific subject. SHINE (Spacecraft Health Inference Engine) is one such program, a software inference engine (expert system) designed by NASA for the purpose of monitoring, analyzing, and diagnosing both real-time and non-real-time systems. It was developed to meet many of the Agency s demanding and rigorous artificial intelligence goals for current and future needs. NASA developed the sophisticated and reusable software based on the experience and requirements of its Jet Propulsion Laboratory s (JPL) Artificial Intelligence Research Group in developing expert systems for space flight operations specifically, the diagnosis of spacecraft health. It was designed to be efficient enough to operate in demanding real time and in limited hardware environments, and to be utilized by non-expert systems applications written in conventional programming languages. The technology is currently used in several ongoing NASA applications, including the Mars Exploration Rovers and the Spacecraft Health Automatic Reasoning Pilot (SHARP) program for the diagnosis of telecommunication anomalies during the Neptune Voyager Encounter. It is also finding applications outside of the Space Agency.

  1. Real-time monitoring system for microfluidics

    NASA Astrophysics Data System (ADS)

    Sapuppo, F.; Cantelli, G.; Fortuna, L.; Arena, P.; Bucolo, M.

    2007-05-01

    A new non-invasive real-time system for the monitoring and control of microfluidodynamic phenomena is proposed. The general purpose design of such system is suitable for in vitro and in vivo experimental setup and therefore for microfluidic application in the biomedical field such as lab-on-chip and for research studies in the field of microcirculation. The system consists of an ad hoc optical setup for image magnification providing images suitable for image acquisition and processing. The optic system was designed and developed using discrete opto-mechanic components mounted on a breadboard in order to provide an optic path accessible at any point where the information needs to be acquired. The optic sensing, acquisition, and processing were performed using an integrated vision system based on the Cellular Nonlinear Networks (CNNs) analogic technology called Focal Plane Processor (FPP, Eye-RIS, Anafocus) and inserted in the optic path. Ad hoc algorithms were implemented for the real-time analysis and extraction of fluido-dynamic parameters in micro-channels. They were tested on images recorded during in vivo microcirculation experiments on hamsters and then they were applied on images optically acquired and processed in real-time during in vitro experiments on a continuous microfluidic device (serpentine mixer, ThinXXS) with a two-phase fluid.

  2. Turning movement estimation in real time

    SciTech Connect

    Martin, P.T.

    1997-08-01

    Fast processors offer exciting opportunities for real-time traffic monitoring. Conventional transportation planning models that assume stable and predictable travel patterns do not lend themselves to on-line traffic forecasting. This paper describes how a new traffic flow inference model has the potential to determine comprehensive flow information in real time. Its philosophical basis is borrowed from the field of operational research, where it has been used for optimizing water and electricity flows. This paper shows how road traffic turning movement flows can be estimated from link detected flows at small recurrent intervals, in real time. The paper details the formulation of the problem, outlines the structure of the data set that provides the detector data for the model input and observed turning flows for the model evaluation. The theoretical principles that define the model are described briefly. Turning movement flow estimates, at 5-min intervals, from two independent surveys are presented and analyzed. The results show an overall mean coefficient of determination (r{sup 2}) of 79--82% between observed and modeled turning movement flows.

  3. Steering a mobile robot in real time

    NASA Astrophysics Data System (ADS)

    Chuah, Mei C.; Fennema, Claude L., Jr.

    1994-10-01

    Using computer vision for mobile robot navigation has been of interest since the 1960s. This interest is evident in even the earliest robot projects: at SRI International (`Shakey') and at the Stanford University (`Stanford Cart'). These pioneering projects provided a foundation for late work but fell far short of providing real time solutions. Since the mid 1980s, the ARPA sponsored ALV and UGV projects have established a need for real time navigation. To achieve the necessary speed, some researchers have focused on building faster hardware; others have turned to the use of new computational architectures, such as neural nets. The work described in this paper uses another approach that has become known as `perceptual servoing.' Previously reported results show that perceptual servoing is both fast and accurate when used to steer vehicles equipped with precise odometers. When the instrumentation on the vehicle does not give precise measurements of distance traveled, as could be the case for a vehicle traveling on ice or mud, new techniques are required to accommodate the reduced ability to make accurate predictions about motion and control. This paper presents a method that computes estimates of distance traveled using landmarks and path information. The new method continues to perform in real time using modest computational facilities, and results demonstrate the effects of the new implementation on steering accuracy.

  4. Real-time optical image processing techniques

    NASA Technical Reports Server (NTRS)

    Liu, Hua-Kuang

    1988-01-01

    Nonlinear real-time optical processing on spatial pulse frequency modulation has been pursued through the analysis, design, and fabrication of pulse frequency modulated halftone screens and the modification of micro-channel spatial light modulators (MSLMs). Micro-channel spatial light modulators are modified via the Fabry-Perot method to achieve the high gamma operation required for non-linear operation. Real-time nonlinear processing was performed using the halftone screen and MSLM. The experiments showed the effectiveness of the thresholding and also showed the needs of higher SBP for image processing. The Hughes LCLV has been characterized and found to yield high gamma (about 1.7) when operated in low frequency and low bias mode. Cascading of two LCLVs should also provide enough gamma for nonlinear processing. In this case, the SBP of the LCLV is sufficient but the uniformity of the LCLV needs improvement. These include image correlation, computer generation of holograms, pseudo-color image encoding for image enhancement, and associative-retrieval in neural processing. The discovery of the only known optical method for dynamic range compression of an input image in real-time by using GaAs photorefractive crystals is reported. Finally, a new architecture for non-linear multiple sensory, neural processing has been suggested.

  5. Identification of novel genes that co-cluster with estrogen receptor alpha in breast tumor biopsy specimens, using a large-scale real-time reverse transcription-PCR approach.

    PubMed

    Tozlu, S; Girault, I; Vacher, S; Vendrell, J; Andrieu, C; Spyratos, F; Cohen, P; Lidereau, R; Bieche, I

    2006-12-01

    The estrogen receptor alpha (ERalpha) plays a critical role in the pathogenesis and clinical behavior of breast cancer. To obtain further insights into the molecular basis of estrogen-dependent forms of this malignancy, we used real-time quantitative reverse transcription (RT)-PCR to compare the mRNA expression of 560 selected genes in ERalpha-positive and ERalpha-negative breast tumors. Fifty-one (9.1%) of the 560 genes were significantly upregulated in ERalpha-positive breast tumors compared with ERalpha-negative breast tumors. In addition to well-known ERalpha-induced genes (PGR, TFF1/PS2, BCL2, ERBB4, CCND1, etc.) and genes recently identified by cDNA microarray-based approaches (GATA3, TFF3, MYB, STC2, HPN/HEPSIN, FOXA1, XBP1, SLC39A6/LIV-1, etc.), an appreciable number of novel genes were identified, many of, which were weakly expressed. This validates the use of large-scale real-time RT-PCR as a method complementary to cDNA microarrays for molecular tumor profiling. Most of the new genes identified here encoded secreted proteins (SEMA3B and CLU), growth factors (BDNF, FGF2 and EGF), growth factor receptors (IL6ST, PTPRT, RET, VEGFR1 and FGFR2) or metabolic enzymes (CYP2B6, CA12, ACADSB, NAT1, LRBA, SLC7A2 and SULT2B1). Importantly, we also identified a large number of genes encoding proteins with either pro-apoptotic (PUMA, NOXA and TATP73) or anti-apoptotic properties (BCL2, DNTP73 and TRAILR3). Surprisingly, only a small proportion of the 51 genes identified in breast tumor biopsy specimens were confirmed to be ERalpha-regulated and/or E2-regulated in vitro (cultured cell lines). Therefore, this study identified a limited number of genes and signaling pathways, which better delineate the role of ERalpha in breast cancer. Some of the genes identified here could be useful for diagnosis or for predicting endocrine responsiveness, and could form the basis for novel therapeutic strategies.

  6. Development of hydrolysis probe-based real-time PCR for identification of virulent gene targets of Burkholderia pseudomallei and B. mallei--a retrospective study on archival cases of service members with melioidosis and glanders.

    PubMed

    Zhang, Binxue; Wear, Douglas J; Kim, H S; Weina, Peter; Stojadinovic, Alexander; Izadjoo, Mina

    2012-02-01

    Burkholderia pseudomallei and B. mallei are two highly pathogenic bacteria responsible for melioidosis and glanders, respectively. Our laboratory developed hydrolysis probe-based real-time polymerase chain reaction assays targeting type three secretion system (TTS) and transposase family protein (TFP) of B. pseudomallei and B. malli, respectively. The assays were validated for target specificity, amplification sensitivity, and reproducibility. A bacterial DNA panel, composed of B. pseudomallei (13 strains), B. mallei (11 strains), Burkholderia species close neighbors (5 strains), and other bacterial species (17 strains), was prepared for specificity testing. Reference DNAs from B. pseudomallei and B. mallei bacterial cultures were used as controls for amplification, limit of detection, and reproducibility testing. The two TaqMan assays, Bp-TTS 1 and Bm-TFP, were optimized and applied in a retrospective study of archived cases from the Armed Forces Institute of Pathology. We tested 10 formalin-fixed paraffin-embedded blocks originally from autopsy specimens of patients who died of melioidosis or glanders during or after overseas tours in 1960s. Polymerase chain reaction results confirmed that DNA samples from formalin-fixed paraffin-embedded blocks of eight patients with melioidosis were positive for Bp-TTS 1 target and two patients with glanders were positive for Bm-TFP target.

  7. Real-time safety risk assessment based on a real-time location system for hydropower construction sites.

    PubMed

    Jiang, Hanchen; Lin, Peng; Fan, Qixiang; Qiang, Maoshan

    2014-01-01

    The concern for workers' safety in construction industry is reflected in many studies focusing on static safety risk identification and assessment. However, studies on real-time safety risk assessment aimed at reducing uncertainty and supporting quick response are rare. A method for real-time safety risk assessment (RTSRA) to implement a dynamic evaluation of worker safety states on construction site has been proposed in this paper. The method provides construction managers who are in charge of safety with more abundant information to reduce the uncertainty of the site. A quantitative calculation formula, integrating the influence of static and dynamic hazards and that of safety supervisors, is established to link the safety risk of workers with the locations of on-site assets. By employing the hidden Markov model (HMM), the RTSRA provides a mechanism for processing location data provided by the real-time location system (RTLS) and analyzing the probability distributions of different states in terms of false positives and negatives. Simulation analysis demonstrated the logic of the proposed method and how it works. Application case shows that the proposed RTSRA is both feasible and effective in managing construction project safety concerns.

  8. Real-Time Safety Risk Assessment Based on a Real-Time Location System for Hydropower Construction Sites

    PubMed Central

    Fan, Qixiang; Qiang, Maoshan

    2014-01-01

    The concern for workers' safety in construction industry is reflected in many studies focusing on static safety risk identification and assessment. However, studies on real-time safety risk assessment aimed at reducing uncertainty and supporting quick response are rare. A method for real-time safety risk assessment (RTSRA) to implement a dynamic evaluation of worker safety states on construction site has been proposed in this paper. The method provides construction managers who are in charge of safety with more abundant information to reduce the uncertainty of the site. A quantitative calculation formula, integrating the influence of static and dynamic hazards and that of safety supervisors, is established to link the safety risk of workers with the locations of on-site assets. By employing the hidden Markov model (HMM), the RTSRA provides a mechanism for processing location data provided by the real-time location system (RTLS) and analyzing the probability distributions of different states in terms of false positives and negatives. Simulation analysis demonstrated the logic of the proposed method and how it works. Application case shows that the proposed RTSRA is both feasible and effective in managing construction project safety concerns. PMID:25114958

  9. Bell nonlocality: a resource for device-independent quantum information protocols

    NASA Astrophysics Data System (ADS)

    Acin, Antonio

    2015-05-01

    Bell nonlocality is not only one of the most fundamental properties of quantum physics, but has also recently acquired the status of an information resource for device-independent quantum information protocols. In the device-independent approach, protocols are designed so that their performance is independent of the internal working of the devices used in the implementation. We discuss all these ideas and argue that device-independent protocols are especially relevant or cryptographic applications, as they are insensitive to hacking attacks exploiting imperfections on the modelling of the devices.

  10. Device-independent two-party cryptography secure against sequential attacks

    NASA Astrophysics Data System (ADS)

    Kaniewski, Jędrzej; Wehner, Stephanie

    2016-05-01

    The goal of two-party cryptography is to enable two parties, Alice and Bob, to solve common tasks without the need for mutual trust. Examples of such tasks are private access to a database, and secure identification. Quantum communication enables security for all of these problems in the noisy-storage model by sending more signals than the adversary can store in a certain time frame. Here, we initiate the study of device-independent (DI) protocols for two-party cryptography in the noisy-storage model. Specifically, we present a relatively easy to implement protocol for a cryptographic building block known as weak string erasure and prove its security even if the devices used in the protocol are prepared by the dishonest party. DI two-party cryptography is made challenging by the fact that Alice and Bob do not trust each other, which requires new techniques to establish security. We fully analyse the case of memoryless devices (for which sequential attacks are optimal) and the case of sequential attacks for arbitrary devices. The key ingredient of the proof, which might be of independent interest, is an explicit (and tight) relation between the violation of the Clauser-Horne-Shimony-Holt inequality observed by Alice and Bob and uncertainty generated by Alice against Bob who is forced to measure his system before finding out Alice’s setting (guessing with postmeasurement information). In particular, we show that security is possible for arbitrarily small violation.

  11. Acting to gain information: Real-time reasoning meets real-time perception

    NASA Technical Reports Server (NTRS)

    Rosenschein, Stan

    1994-01-01

    Recent advances in intelligent reactive systems suggest new approaches to the problem of deriving task-relevant information from perceptual systems in real time. The author will describe work in progress aimed at coupling intelligent control mechanisms to real-time perception systems, with special emphasis on frame rate visual measurement systems. A model for integrated reasoning and perception will be discussed, and recent progress in applying these ideas to problems of sensor utilization for efficient recognition and tracking will be described.

  12. Exploring Earthquakes in Real-Time

    NASA Astrophysics Data System (ADS)

    Bravo, T. K.; Kafka, A. L.; Coleman, B.; Taber, J. J.

    2013-12-01

    Earthquakes capture the attention of students and inspire them to explore the Earth. Adding the ability to view and explore recordings of significant and newsworthy earthquakes in real-time makes the subject even more compelling. To address this opportunity, the Incorporated Research Institutions for Seismology (IRIS), in collaboration with Moravian College, developed ';jAmaSeis', a cross-platform application that enables students to access real-time earthquake waveform data. Students can watch as the seismic waves are recorded on their computer, and can be among the first to analyze the data from an earthquake. jAmaSeis facilitates student centered investigations of seismological concepts using either a low-cost educational seismograph or streamed data from other educational seismographs or from any seismic station that sends data to the IRIS Data Management System. After an earthquake, students can analyze the seismograms to determine characteristics of earthquakes such as time of occurrence, distance from the epicenter to the station, magnitude, and location. The software has been designed to provide graphical clues to guide students in the analysis and assist in their interpretations. Since jAmaSeis can simultaneously record up to three stations from anywhere on the planet, there are numerous opportunities for student driven investigations. For example, students can explore differences in the seismograms from different distances from an earthquake and compare waveforms from different azimuthal directions. Students can simultaneously monitor seismicity at a tectonic plate boundary and in the middle of the plate regardless of their school location. This can help students discover for themselves the ideas underlying seismic wave propagation, regional earthquake hazards, magnitude-frequency relationships, and the details of plate tectonics. The real-time nature of the data keeps the investigations dynamic, and offers students countless opportunities to explore.

  13. Prototype COBRA near-real-time processor

    NASA Astrophysics Data System (ADS)

    Earp, Samuel L.; Marshall, J. W.; Anthony, E. R.

    1996-05-01

    The U.S. Marine Corps COBRA countermine surveillance program has developed, as a risk- reduction alternative, a near real-time processor for the output of the COBRA multispectral camera. This processor has been tested using approximately 13.5 hours of video data from the COBRA DT-0 developmental test, representing approximately 243,000 frames of multispectral data. The results have been very encouraging--the system is robust and the minefield detection performance has met the goals of the COBRA program. The MITRE COBRA prototype processor is built from commercial-off-the-shelf VME bus technology. Video capture is provided by a Transtech TDM 435 capture/display VME card. Control is performed on a GMSV64 Super Sparc card that resides in two VME slots. The compute engine consists of two Pentek 4270 Quad TMS320C40 digital signal processing boards. There are two additional 6U VME boards to provide fast SCSI IO. The system is capable of capturing, digitizing and processing the COBRA data stream at between one-eighth and one-half real-time, depending on processing options. The nominal compute power of the system is 2.2 GOPS, 450 MFLOPS. The system is easily upgradeable due to the open architecture--one proposed upgrade will be to increase the number of available TMS320C40 processors to sixteen, providing real-time performance without compromising the current investment in software and hardware. The software for the system is primarily written in C, with hand-optimized assembler code for portions of the compute kernel. The algorithm that is implemented is based on the MITRE minefield detection algorithm detailed at AeroSense '95. The system development required a registration algorithm--this was the only algorithm development that was performed, the rest of the algorithms coming from previous MITRE effort on the COBRA program. Lessons learned from the development and upgrade/test plans will be presented.

  14. Real-time structured light depth extraction

    NASA Astrophysics Data System (ADS)

    Keller, Kurtis; Ackerman, Jeremy D.

    2000-03-01

    Gathering depth data using structured light has been a procedure for many different environments and uses. Many of these system are utilized instead of laser line scanning because of their quickness. However, to utilize depth extraction for some applications, in our case laparoscopic surgery, the depth extraction must be in real time. We have developed an apparatus that speeds up the raw image display and grabbing in structured light depth extraction from 30 frames per second to 60 and 180 frames per second. This results in an updated depth and texture map of about 15 times per second versus about 3. This increased update rate allows for real time depth extraction for use in augmented medical/surgical applications. Our miniature, fist-sized projector utilizes an internal ferro-reflective LCD display that is illuminated with cold light from a flex light pipe. The miniature projector, attachable to a laparoscope, displays inverted pairs of structured light into the body where these images are then viewed by a high-speed camera set slightly off axis from the projector that grabs images synchronously. The images from the camera are ported to a graphics-processing card where six frames are worked on simultaneously to extract depth and create mapped textures from these images. This information is then sent to the host computer with 3D coordinate information of the projector/camera and the associated textures. The surgeon is then able to view body images in real time from different locations without physically moving the laparoscope imager/projector, thereby, reducing the trauma of moving laparoscopes in the patient.

  15. Real-time failure control (SAFD)

    NASA Technical Reports Server (NTRS)

    Panossian, Hagop V.; Kemp, Victoria R.; Eckerling, Sherry J.

    1990-01-01

    The Real Time Failure Control program involves development of a failure detection algorithm, referred as System for Failure and Anomaly Detection (SAFD), for the Space Shuttle Main Engine (SSME). This failure detection approach is signal-based and it entails monitoring SSME measurement signals based on predetermined and computed mean values and standard deviations. Twenty four engine measurements are included in the algorithm and provisions are made to add more parameters if needed. Six major sections of research are presented: (1) SAFD algorithm development; (2) SAFD simulations; (3) Digital Transient Model failure simulation; (4) closed-loop simulation; (5) SAFD current limitations; and (6) enhancements planned for.

  16. Open Source Real Time Operating Systems Overview

    SciTech Connect

    Straumann, Till

    2001-12-11

    Modern control systems applications are often built on top of a real time operating system (RTOS) which provides the necessary hardware abstraction as well as scheduling, networking and other services. Several open source RTOS solutions are publicly available, which is very attractive, both from an economic (no licensing fees) as well as from a technical (control over the source code) point of view. This contribution gives an overview of the RTLinux and RTEMS systems (architecture, development environment, API etc.). Both systems feature most popular CPUs, several APIs (including Posix), networking, portability and optional commercial support. Some performance figures are presented, focusing on interrupt latency and context switching delay.

  17. Systems Analyze Water Quality in Real Time

    NASA Technical Reports Server (NTRS)

    2010-01-01

    A water analyzer developed under Small Business Innovation Research (SBIR) contracts with Kennedy Space Center now monitors treatment processes at water and wastewater facilities around the world. Originally designed to provide real-time detection of nutrient levels in hydroponic solutions for growing plants in space, the ChemScan analyzer, produced by ASA Analytics Inc., of Waukesha, Wisconsin, utilizes spectrometry and chemometric algorithms to automatically analyze multiple parameters in the water treatment process with little need for maintenance, calibration, or operator intervention. The company has experienced a compound annual growth rate of 40 percent over its 15-year history as a direct result of the technology's success.

  18. Real-time teleteaching in medical physics.

    PubMed

    Woo, M; Ng, Kh

    2008-01-01

    Medical physics is a relatively small professional community, usually with a scarcity of expertise that could greatly benefit students entering the field. However, the reach of the profession can span great geographical distances, making the training of students a difficult task. In addition to the requirement of training new students, the evolving field of medical physics, with its many emerging advanced techniques and technologies, could benefit greatly from ongoing continuing education as well as consultation with experts.Many continuing education courses and workshops are constantly being offered, including many web-based study courses and virtual libraries. However, one mode of education and communication that has not been widely used is the real-time interactive process. Video-based conferencing systems do exist, but these usually require a substantial amount of effort and cost to set up.The authors have been working on promoting the ever-expanding capability of the Internet to facilitate the education of medical physics to students entering the field. A pilot project has been carried out for six years and reported previously. The project is a collaboration between the Department of Medical Physics at the Toronto Odette Cancer Centre in Canada and the Department of Biomedical Imaging at the University of Malaya in Malaysia. Since 2001, medical physics graduate students at the University of Malaya have been taught by lecturers from Toronto every year, using the Internet as the main tool of communication.The pilot study explored the different methods that can be used to provide real-time interactive remote education, and delivered traditional classroom lectures as well as hands-on workshops.Another similar project was started in 2007 to offer real-time teaching to a class of medical physics students at Wuhan University in Hubei, China. There are new challenges as well as new opportunities associated with this project. By building an inventory of tools and

  19. General purpose computers in real time

    SciTech Connect

    Biel, J.R.

    1989-09-18

    I see three main trends in the use of general purpose computers in real time. The first is more processing power. The second is the use of higher speed interconnects between computers (allowing more data to be delivered to the processors). The third is the use of larger programs running in the computers. Although there is still work that needs to be done, I believe that all indications are that the online need for general purpose computers should be available for the SCC and LHC machines. 2 figs.

  20. Real-Time Reed-Solomon Decoder

    NASA Technical Reports Server (NTRS)

    Maki, Gary K.; Cameron, Kelly B.; Owsley, Patrick A.

    1994-01-01

    Generic Reed-Solomon decoder fast enough to correct errors in real time in practical applications designed to be implemented in fewer and smaller very-large-scale integrated, VLSI, circuit chips. Configured to operate in pipelined manner. One outstanding aspect of decoder design is that Euclid multiplier and divider modules contain Galoisfield multipliers configured as combinational-logic cells. Operates at speeds greater than older multipliers. Cellular configuration highly regular and requires little interconnection area, making it ideal for implementation in extraordinarily dense VLSI circuitry. Flight electronics single chip version of this technology implemented and available.

  1. Object detection in real-time

    NASA Astrophysics Data System (ADS)

    Solder, Ulrich; Graefe, Volker

    1991-03-01

    An algorithm working on monocular gray-scale image sequences for object detection combined with a road tracker is presented. This algorithm appropriate for the real-time demands of an autonomous car driving with speeds over 40 km/h may be used for triggering obstacle avoidance maneuvers such as coming to a safe stop automatically in front of an obstacle or following another car. Moving and static objects have been detected in real-world experiments on various types of roads even under unfavorable weather conditions. . Morgenthaler and

  2. [Development of real-time CT fluoroscopy].

    PubMed

    Katada, K; Anno, H; Takeshita, G; Ogura, Y; Koga, S; Ida, Y; Nonomura, K; Kanno, T; Ohashi, A; Sata, S

    1994-10-25

    A new CT system that permits real-time monitoring of CT images was developed. Phantom and volunteer studies revealed that the images were displayed at a rate of six per second with a delay time of 0.83 second with clinically sufficient resolution (256 x 256) using the newly developed fast image processor and partial-reconstruction algorithm. The clinical trial of stereotactic aspiration of intracerebral hematoma was successful. The initial trial with CT fluoroscopy revealed potential usefulness of the system in biopsy and other CT-guided interventions. PMID:9261196

  3. Near real time data processing system

    NASA Astrophysics Data System (ADS)

    Mousessian, Ardvas; Vuu, Christina

    2008-08-01

    Raytheon recently developed and implemented a Near Real Time (NRT) data processing subsystem for Earth Observing System (EOS) Microwave Limb Sounder (MLS3) instrument on NASA Aura spacecraft. The NRT can be viewed as a customized Science Information Processing System (SIPS) where the measurements and information provided by the instrument are expeditiously processed, packaged, and delivered. The purpose of the MLS NRT is to process Level 0 data up through Level 2, and distribute standard data products to the customer within 3-5 hours of the first set of data arrival.

  4. Real time analysis of voiced sounds

    NASA Technical Reports Server (NTRS)

    Hong, J. P. (Inventor)

    1976-01-01

    A power spectrum analysis of the harmonic content of a voiced sound signal is conducted in real time by phase-lock-loop tracking of the fundamental frequency, (f sub 0) of the signal and successive harmonics (h sub 1 through h sub n) of the fundamental frequency. The analysis also includes measuring the quadrature power and phase of each frequency tracked, differentiating the power measurements of the harmonics in adjacent pairs, and analyzing successive differentials to determine peak power points in the power spectrum for display or use in analysis of voiced sound, such as for voice recognition.

  5. Real-Time Optical Monitoring of GRBs

    NASA Astrophysics Data System (ADS)

    Hudec, René; Křížek, Miroslav

    2006-05-01

    Even the fastest alert robotic follow-up telescope is unable to cover the times just after (within first 10 seconds) and before GRB triggers. This time domain is accessible by optical monitors only. We report on analyses of GRB positions on images taken by optical photographic monitors (now operated remotely) within the European meteor network EN. This system is able to provide real-time and pre-burst optical data for GRBs with limiting magnitudes up to 12 in the best cases. The image database is searchable by special software for coincidences with GRBs and the particular images are then scanned and evaluated by computer.

  6. Real-time virtual room acoustic simulation

    NASA Astrophysics Data System (ADS)

    Carneal, James P.; Johnson, Jan; Johnson, Troge; Johnson, Marty

    2003-10-01

    A realistic virtual room acoustic simulation has been implemented on a PC-based computer in near real-time. Room acoustics are calculated by the image source method using realistic absorption coefficients for a variety of realistic surfaces and programmed in MATLAB. The resulting impulse response filters are then applied in near real-time using fast convolution DSP techniques using data being read from a CD-ROM. The system was implemented in a virtual acoustic room facility. Optimizations have been performed to retain the realistic virtual room effect while minimizing computations through limited psycho-acoustic testing. In general, realistic anechoic to reverberant virtual rooms have been re-created with six 8192 coefficient filters. To provide realistic simulations, special care must be taken to accurately reproduce the low frequency acoustics. Since the virtual room acoustic facility was not totally anechoic (as are most anechoic chambers), inverse filters were applied to compensate for over-amplified acoustics at frequencies below 350 Hz.

  7. Real-time applications of neural nets

    SciTech Connect

    Spencer, J.E.

    1989-05-01

    Producing, accelerating and colliding very high power, low emittance beams for long periods is a formidable problem in real-time control. As energy has grown exponentially in time so has the complexity of the machines and their control systems. Similar growth rates have occurred in many areas, e.g., improved integrated circuits have been paid for with comparable increases in complexity. However, in this case, reliability, capability and cost have improved due to reduced size, high production and increased integration which allow various kinds of feedback. In contrast, most large complex systems (LCS) are perceived to lack such possibilities because only one copy is made. Neural nets, as a metaphor for LCS, suggest ways to circumvent such limitations. It is argued that they are logically equivalent to multi-loop feedback/forward control of faulty systems. While complimentary to AI, they mesh nicely with characteristics desired for real-time systems. Such issues are considered, examples given and possibilities discussed. 21 refs., 6 figs.

  8. Residential Real-time Price Response Simulation

    SciTech Connect

    Widergren, Steven E.; Subbarao, Krishnappa; Chassin, David P.; Fuller, Jason C.; Pratt, Robert G.

    2011-10-10

    The electric industry is gaining experience with innovative price responsive demand pilots and limited roll-outs to customers. One of these pilots is investigating real-time pricing signals to engage end-use systems and local distributed generation and storage in a distributed optimization process. Attractive aspects about the approach include strong scalability characteristics, simplified interfaces between automation devices, and the adaptability to integrate a wide variety of devices and systems. Experience in this nascent field is revealing a rich array of for engineering decisions and the application of complexity theory. To test the decisions, computer simulations are used to reveal insights about design, demand elasticity, and the limits of response (including consumer fatigue). Agent-based approaches lend themselves well in the simulation to modeling the participation and interaction of each piece of equipment on a distribution feeder. This paper discusses rate design and simulation experiences at the distribution feeder level where consumers and their HVAC systems and water heaters on a feeder receive real-time pricing signals.

  9. Real-time adaptive video image enhancement

    NASA Astrophysics Data System (ADS)

    Garside, John R.; Harrison, Chris G.

    1999-07-01

    As part of a continuing collaboration between the University of Manchester and British Aerospace, a signal processing array has been constructed to demonstrate that it is feasible to compensate a video signal for the degradation caused by atmospheric haze in real-time. Previously reported work has shown good agreement between a simple physical model of light scattering by atmospheric haze and the observed loss of contrast. This model predicts a characteristic relationship between contrast loss in the image and the range from the camera to the scene. For an airborne camera, the slant-range to a point on the ground may be estimated from the airplane's pose, as reported by the inertial navigation system, and the contrast may be obtained from the camera's output. Fusing data from these two streams provides a means of estimating model parameters such as the visibility and the overall illumination of the scene. This knowledge allows the same model to be applied in reverse, thus restoring the contrast lost to atmospheric haze. An efficient approximation of range is vital for a real-time implementation of the method. Preliminary results show that an adaptive approach to fitting the model's parameters, exploiting the temporal correlation between video frames, leads to a robust implementation with a significantly accelerated throughput.

  10. Real-Time Flight Envelope Monitoring System

    NASA Technical Reports Server (NTRS)

    Kerho, Michael; Bragg, Michael B.; Ansell, Phillip J.

    2012-01-01

    The objective of this effort was to show that real-time aircraft control-surface hinge-moment information could be used to provide a robust and reliable prediction of vehicle performance and control authority degradation. For a given airfoil section with a control surface -- be it a wing with an aileron, rudder, or elevator -- the control-surface hinge moment is sensitive to the aerodynamic characteristics of the section. As a result, changes in the aerodynamics of the section due to angle-of-attack or environmental effects such as icing, heavy rain, surface contaminants, bird strikes, or battle damage will affect the control surface hinge moment. These changes include both the magnitude of the hinge moment and its sign in a time-averaged sense, and the variation of the hinge moment with time. The current program attempts to take the real-time hinge moment information from the aircraft control surfaces and develop a system to predict aircraft envelope boundaries across a range of conditions, alerting the flight crew to reductions in aircraft controllability and flight boundaries.

  11. Neutron monitor database in real time

    NASA Astrophysics Data System (ADS)

    Kozlov, Valery; Kudela, Karel; Starodubtsev, Sergei; Turpanov, Alexey; Usoskin, Ilya; Yanke, Victor

    2003-09-01

    A first distributed Real Time Cosmic Ray Database using measurements of several neutron monitors is presented. The aim of the project is to develop a unified database with data from different neutron monitors collected together, in unified format and to provide a user with several commonly used data access methods. The database contains original cosmic ray as well as all housekeeping and technical data necessary for scientific data analysis. Currently the database includes Lomnicky Stit, Moscow, Oulu, Tixie Bay, Yakutsk stations and it is opened for other neutron monitors. The main database server is located in IKFIA SB RAS (Yakutsk) but there will be several mirrors of the database. The datbase and all its mirrors are updated on the nearly real-time (1 hour) basis. The data access software includes WWW-interface, Perl scipts and C library, which may be linked to a user program. Most of frequently used functions are implemented to make it operable to users without SQL language knowledge. A draft of the data representation standard is suggested, based on common practice of neutron monitor community. The database engine is freely distributed open-sourced PostgreSQL server coupled with a set of replication tools developed at Bioengineering division of the IRCCS E. Medea, Italy.

  12. Near-real-time Jason-1 Images

    NASA Astrophysics Data System (ADS)

    Rigor, E. M.; Bingham, A.; Case, K.

    2002-12-01

    The Jason-1 satellite mission provides sea surface height measurements in near-real-time (NRT). These operational data can be used for a variety of scientific and commercial applications, including marine meteorology, ship routing, and climate prediction. The Physical Oceanography Distributed Active Archive Center (PO.DAAC), NASA's primary data center for archiving and distributing oceanographic data, is supporting the JASON-1 mission by capturing NRT data from Jason Ground System (JGS) and distributing the data to operational users. In addition, PO.DAAC will be processing the data to create value-added NRT browse images, which will be made available, along with their associated binary data, through the Near-Real-Time Image Distribution Server (NEREIDS). Two NRT data products will be processed by JGS and captured by PO.DAAC: Operational Sensor Data Records (OSDRs) and Interim Geophysical Data Records (IGDRs). OSDRs have a latency of three hours from data collection and an orbit accuracy of 30 cm; IGDRs are available seventy-two hours after collection and have an accuracy of 2.5 cm. After capturing these data, PO.DAAC will automatically create significant wave height, wind speed, and water vapor content browse images from the OSDR data. Additional parameters will be provided from the IGDR data product, such as the sea surface height anomaly, among others. In this poster, we describe the functionality of NEREIDS and demonstrate the usefulness of operational altimetric data for scientific applications.

  13. Real-time design with peer tasks

    NASA Technical Reports Server (NTRS)

    Goforth, Andre; Howes, Norman R.; Wood, Jonathan D.; Barnes, Michael J.

    1995-01-01

    We introduce a real-time design methodology for large scale, distributed, parallel architecture, real-time systems (LDPARTS), as an alternative to those methods using rate or dead-line monotonic analysis. In our method the fundamental units of prioritization, work items, are domain specific objects with timing requirements (deadlines) found in user's specification. A work item consists of a collection of tasks of equal priority. Current scheduling theories are applied with artifact deadlines introduced by the designer whereas our method schedules work items to meet user's specification deadlines (sometimes called end-to-end deadlines). Our method supports these scheduling properties. Work item scheduling is based on domain specific importance instead of task level urgency and still meets as many user specification deadlines as can be met by scheduling tasks with respect to urgency. Second, the minimum (closest) on-line deadline that can be guaranteed for a work item of highest importance, scheduled at run time, is approximately the inverse of the throughput, measured in work items per second. Third, throughput is not degraded during overload and instead of resorting to task shedding during overload, the designer can specify which work items to shed. We prove these properties in a mathematical model.

  14. 3D MR imaging in real time

    NASA Astrophysics Data System (ADS)

    Guttman, Michael A.; McVeigh, Elliot R.

    2001-05-01

    A system has been developed to produce live 3D volume renderings from an MR scanner. Whereas real-time 2D MR imaging has been demonstrated by several groups, 3D volumes are currently rendered off-line to gain greater understanding of anatomical structures. For example, surgical planning is sometimes performed by viewing 2D images or 3D renderings from previously acquired image data. A disadvantage of this approach is misregistration which could occur if the anatomy changes due to normal muscle contractions or surgical manipulation. The ability to produce volume renderings in real-time and present them in the magnet room could eliminate this problem, and enable or benefit other types of interventional procedures. The system uses the data stream generated by a fast 2D multi- slice pulse sequence to update a volume rendering immediately after a new slice is available. We demonstrate some basic types of user interaction with the rendering during imaging at a rate of up to 20 frames per second.

  15. Real-Time and Near Real-Time Data for Space Weather Applications and Services

    NASA Astrophysics Data System (ADS)

    Singer, H. J.; Balch, C. C.; Biesecker, D. A.; Matsuo, T.; Onsager, T. G.

    2015-12-01

    Space weather can be defined as conditions in the vicinity of Earth and in the interplanetary environment that are caused primarily by solar processes and influenced by conditions on Earth and its atmosphere. Examples of space weather are the conditions that result from geomagnetic storms, solar particle events, and bursts of intense solar flare radiation. These conditions can have impacts on modern-day technologies such as GPS or electric power grids and on human activities such as astronauts living on the International Space Station or explorers traveling to the moon or Mars. While the ultimate space weather goal is accurate prediction of future space weather conditions, for many applications and services, we rely on real-time and near-real time observations and model results for the specification of current conditions. In this presentation, we will describe the space weather system and the need for real-time and near-real time data that drive the system, characterize conditions in the space environment, and are used by models for assimilation and validation. Currently available data will be assessed and a vision for future needs will be given. The challenges for establishing real-time data requirements, as well as acquiring, processing, and disseminating the data will be described, including national and international collaborations. In addition to describing how the data are used for official government products, we will also give examples of how these data are used by both the public and private sector for new applications that serve the public.

  16. Real-time PCR validation of visually identified snapper Chrysophrys auratus (Sparidae) eggs.

    PubMed

    Dias, P J; Wakefield, C B; Fairclough, D V; Jackson, G; Travers, M J; Snow, M

    2016-02-01

    In this study, a total of 212 eggs were visually identified as snapper Chrysophrys auratus. Real-time PCR confirmed visual identification in 69% of cases but corroboration varied widely among plankton samples. The use of molecular tools to support visual identification prior to adopting daily egg production stock assessment methods should be considered.

  17. Diagnostic Molecular Mycobacteriology in Regions With Low Tuberculosis Endemicity: Combining Real-time PCR Assays for Detection of Multiple Mycobacterial Pathogens With Line Probe Assays for Identification of Resistance Mutations.

    PubMed

    Deggim-Messmer, Vanessa; Bloemberg, Guido V; Ritter, Claudia; Voit, Antje; Hömke, Rico; Keller, Peter M; Böttger, Erik C

    2016-07-01

    Molecular assays have not yet been able to replace time-consuming culture-based methods in clinical mycobacteriology. Using 6875 clinical samples and a study period of 35months we evaluated the use of PCR-based assays to establish a diagnostic workflow with a fast time-to-result of 1-2days, for 1. detection of Mycobacterium tuberculosis complex (MTB), 2. detection and identification of nontuberculous mycobacteria (NTM), and 3. identification of drug susceptible MTB. MTB molecular-based detection and culture gave concordant results for 97.7% of the specimens. NTM PCR-based detection and culture gave concordant results for 97.0% of the specimens. Defining specimens on the basis of combined laboratory data as true positives or negatives with discrepant results resolved by clinical chart reviews, we calculated sensitivity, specificity, PPV and NPV for PCR-based MTB detection as 84.7%, 100%, 100%, and 98.7%; the corresponding values for culture-based MTB detection were 86.3%, 100%, 100%, and 98.8%. PCR-based detection of NTM had a sensitivity of 84.7% compared to 78.0% of that of culture-based NTM detection. Molecular drug susceptibility testing (DST) by line-probe assay was found to predict phenotypic DST results in MTB with excellent accuracy. Our findings suggest a diagnostic algorithm to largely replace lengthy culture-based techniques by rapid molecular-based methods.

  18. Real-time, face recognition technology

    SciTech Connect

    Brady, S.

    1995-11-01

    The Institute for Scientific Computing Research (ISCR) at Lawrence Livermore National Laboratory recently developed the real-time, face recognition technology KEN. KEN uses novel imaging devices such as silicon retinas developed at Caltech or off-the-shelf CCD cameras to acquire images of a face and to compare them to a database of known faces in a robust fashion. The KEN-Online project makes that recognition technology accessible through the World Wide Web (WWW), an internet service that has recently seen explosive growth. A WWW client can submit face images, add them to the database of known faces and submit other pictures that the system tries to recognize. KEN-Online serves to evaluate the recognition technology and grow a large face database. KEN-Online includes the use of public domain tools such as mSQL for its name-database and perl scripts to assist the uploading of images.

  19. Wi-Fi real time location systems

    NASA Astrophysics Data System (ADS)

    Doll, Benjamin A.

    This thesis objective was to determine the viability of utilizing an untrained Wi-Fi. real time location system as a GPS alternative for indoor environments. Background. research showed that GPS is rarely able to penetrate buildings to provide reliable. location data. The benefit of having location information in a facility and how they might. be used for disaster or emergency relief personnel and their resources motivated this. research. A building was selected with a well-deployed Wi-Fi infrastructure and its. untrained location feature was used to determine the distance between the specified. test points and the system identified location. It was found that the average distance. from the test point throughout the facility was 14.3 feet 80% of the time. This fell within. the defined viable range and supported that an untrained Wi-Fi RTLS system could be a. viable solution for GPS's lack of availability indoors.

  20. Real time software tools and methodologies

    NASA Technical Reports Server (NTRS)

    Christofferson, M. J.

    1981-01-01

    Real time systems are characterized by high speed processing and throughput as well as asynchronous event processing requirements. These requirements give rise to particular implementations of parallel or pipeline multitasking structures, of intertask or interprocess communications mechanisms, and finally of message (buffer) routing or switching mechanisms. These mechanisms or structures, along with the data structue, describe the essential character of the system. These common structural elements and mechanisms are identified, their implementation in the form of routines, tasks or macros - in other words, tools are formalized. The tools developed support or make available the following: reentrant task creation, generalized message routing techniques, generalized task structures/task families, standardized intertask communications mechanisms, and pipeline and parallel processing architectures in a multitasking environment. Tools development raise some interesting prospects in the areas of software instrumentation and software portability. These issues are discussed following the description of the tools themselves.

  1. Near real-time traffic routing

    NASA Technical Reports Server (NTRS)

    Yang, Chaowei (Inventor); Cao, Ying (Inventor); Xie, Jibo (Inventor); Zhou, Bin (Inventor)

    2012-01-01

    A near real-time physical transportation network routing system comprising: a traffic simulation computing grid and a dynamic traffic routing service computing grid. The traffic simulator produces traffic network travel time predictions for a physical transportation network using a traffic simulation model and common input data. The physical transportation network is divided into a multiple sections. Each section has a primary zone and a buffer zone. The traffic simulation computing grid includes multiple of traffic simulation computing nodes. The common input data includes static network characteristics, an origin-destination data table, dynamic traffic information data and historical traffic data. The dynamic traffic routing service computing grid includes multiple dynamic traffic routing computing nodes and generates traffic route(s) using the traffic network travel time predictions.

  2. Real time speech formant analyzer and display

    DOEpatents

    Holland, G.E.; Struve, W.S.; Homer, J.F.

    1987-02-03

    A speech analyzer for interpretation of sound includes a sound input which converts the sound into a signal representing the sound. The signal is passed through a plurality of frequency pass filters to derive a plurality of frequency formants. These formants are converted to voltage signals by frequency-to-voltage converters and then are prepared for visual display in continuous real time. Parameters from the inputted sound are also derived and displayed. The display may then be interpreted by the user. The preferred embodiment includes a microprocessor which is interfaced with a television set for displaying of the sound formants. The microprocessor software enables the sound analyzer to present a variety of display modes for interpretive and therapeutic used by the user. 19 figs.

  3. Real time speech formant analyzer and display

    DOEpatents

    Holland, George E.; Struve, Walter S.; Homer, John F.

    1987-01-01

    A speech analyzer for interpretation of sound includes a sound input which converts the sound into a signal representing the sound. The signal is passed through a plurality of frequency pass filters to derive a plurality of frequency formants. These formants are converted to voltage signals by frequency-to-voltage converters and then are prepared for visual display in continuous real time. Parameters from the inputted sound are also derived and displayed. The display may then be interpreted by the user. The preferred embodiment includes a microprocessor which is interfaced with a television set for displaying of the sound formants. The microprocessor software enables the sound analyzer to present a variety of display modes for interpretive and therapeutic used by the user.

  4. In-line real time air monitor

    DOEpatents

    Wise, M.B.; Thompson, C.V.

    1998-07-14

    An in-line gas monitor capable of accurate gas composition analysis in a continuous real time manner even under strong applied vacuum conditions operates by mixing an air sample with helium forming a sample gas in two complementary sample loops embedded in a manifold which includes two pairs of 3-way solenoid valves. The sample gas is then analyzed in an ion trap mass spectrometer on a continuous basis. Two valve drivers actuate the two pairs of 3-way valves in a reciprocating fashion, so that there is always flow through the in-line gas monitor via one or the other of the sample loops. The duty cycle for the two pairs of 3-way valves is varied by tuning the two valve drivers to a duty cycle typically between 0.2 to 0.7 seconds. 3 figs.

  5. In-line real time air monitor

    DOEpatents

    Wise, Marcus B.; Thompson, Cyril V.

    1998-01-01

    An in-line gas monitor capable of accurate gas composition analysis in a continuous real time manner even under strong applied vacuum conditions operates by mixing an air sample with helium forming a sample gas in two complementary sample loops embedded in a manifold which includes two pairs of 3-way solenoid valves. The sample gas is then analyzed in an ion trap mass spectrometer on a continuous basis. Two valve drivers actuate the two pairs of 3-way valves in a reciprocating fashion, so that there is always flow through the in-line gas monitor via one or the other of the sample loops. The duty cycle for the two pairs of 3-way valves is varied by tuning the two valve drivers to a duty cycle typically between 0.2 to 0.7 seconds.

  6. Filming protein fibrillogenesis in real time

    NASA Astrophysics Data System (ADS)

    Bella, Angelo; Shaw, Michael; Ray, Santanu; Ryadnov, Maxim G.

    2014-12-01

    Protein fibrillogenesis is a universal tool of nano-to-micro scale construction supporting different forms of biological function. Its exploitable potential in nanoscience and technology is substantial, but the direct observation of homogeneous fibre growth able to underpin a kinetic-based rationale for building customized nanostructures in situ is lacking. Here we introduce a kinetic model of de novo protein fibrillogenesis which we imaged at the nanoscale and in real time, filmed. The model helped to reveal that, in contrast to heterogeneous amyloid assemblies, homogeneous protein recruitment is principally characterized by uniform rates of cooperative growth at both ends of growing fibers, bi-directional growth, with lateral growth arrested at a post-seeding stage. The model provides a foundation for in situ engineering of sequence-prescribed fibrous architectures.

  7. PCs stir reliability, real-time concerns

    SciTech Connect

    Strothman, J.

    1994-11-01

    While pre-Christmas price wars regularly boost personal computer sales this time of year, price cuts alone won`t cause process control systems designers to open their wallets and buy PCs. User studies and user feedback to process control equipment suppliers show several other issues continue to rank higher than price including: (1) Hardware and software reliability; (2) easy-to-use user interfaces; (3) ability to do multitasking; (4) need for real-time updates. These and several other non-price issues - including open versus proprietary systems, slower scan rates from PCs compared to programmable controllers, and assurances that the PC will work in an industrial environment - scored high in a study authored earlier this year by Jesse Yoder, owner of Idea Network, Clinton, NJ. The report, titled {open_quotes}The World Market for Process Control Equipment,{close_quotes} was written for FIND/SVP, a New York City market research firm.

  8. A Flexible Real-Time Architecture

    SciTech Connect

    WICKSTROM,GREGORY L.

    2000-08-17

    Assuring hard real-time characteristics of I/O associated with embedded software is often a difficult task. Input-Output related statements are often intermixed with the computational code, resulting in I/O timing that is dependent on the execution path and computational load. One way to mitigate this problem is through the use of interrupts. However, the non-determinism that is introduced by interrupt driven I/O may be so difficult to analyze that it is prohibited in some high consequence systems. This paper describes a balanced hardware/software solution to obtain consistent interrupt-free I/O timing, and results in software that is much more amenable to analysis.

  9. Terrestrial Real-Time Volcano Monitoring

    NASA Astrophysics Data System (ADS)

    Franke, M.

    2013-12-01

    As volcano monitoring involves more and different sensors from seismic to GPS receivers, from video and thermal cameras to multi-parameter probes measuring temperature, ph values and humidity in the ground and the air, it becomes important to design real-time networks that integrate and leverage the multitude of available parameters. In order to do so some simple principles need to be observed: a) a common time base for all measurements, b) a packetized general data communication protocol for acquisition and distribution, c) an open and well documented interface to the data permitting standard and emerging innovative processing, and d) an intuitive visualization platform for scientists and civil defense personnel. Although mentioned as simple principles, the list above does not necessarily lead to obvious solutions or integrated systems, which is, however, required to take advantage of the available data. Only once the different data streams are put into context to each other in terms of time and location can a broader view be obtained and additional information extracted. The presentation is a summary of currently available technologies and how they can achieve the goal of an integrated real-time volcano monitoring system. A common time base are standard for seismic and GPS networks. In different projects we extended this to video feeds and time-lapse photography. Other probes have been integrated with vault interface enclosures (VIE) as used in the Transportable Array (TA) of the USArray. The VIE can accommodate the sensors employed in volcano monitoring. The TA has shown that Antelope is a versatile and robust middleware. It provides the required packetized general communication protocol that is independent from the actual physical communication link leaving the network design to adopt appropriate and possible hybrid solutions. This applies for the data acquisition and the data/information dissemination providing both a much needed collaboration platform, as

  10. Real-time slicing of data space

    SciTech Connect

    Crawfis, R.A.

    1996-07-01

    Real-time rendering of iso-contour surfaces is problematic for large complex data sets. In this paper, an algorithm is presented that allows very rapid representation of an interval set surrounding a iso-contour surface. The algorithm draws upon three main ideas. A fast indexing scheme is used to select only those data points near the contour surface. Hardware assisted splatting is then employed on these data points to produce a volume rendering of the interval set. Finally, by shifting a small window through the indexing scheme or data space, animated volumes are produced showing the changing contour values. In addition to allowing fast selection and rendering of the data, the indexing scheme allows a much compressed representation of the data by eliminating ``noise`` data points.

  11. REAL TIME DATA FOR REMEDIATION ACTIVITIES [11505

    SciTech Connect

    BROCK CT

    2011-01-13

    Health physicists from the CH2M HILL Plateau Remediation Company collaborated with Berkeley Nucleonics Corporation to modify the SAM 940 isotope identifier instrument to be used for nuclear waste remediation. These modifications coupled with existing capabilities of the SAM 940 have proven to be invaluable during remediation activities, reducing disposal costs by allowing swift remediation of targeted areas that have been identified as having isotopes of concern (IOC), and eliminating multiple visits to sites by declaring an excavation site clear of IOCs before demobilizing from the site. These advantages are enabled by accumulating spectral data for specific isotopes that is nearly 100 percent free of false positives, which are filtered out in 'real time.'

  12. Real-time snapshot hyperspectral imaging endoscope.

    PubMed

    Kester, Robert T; Bedard, Noah; Gao, Liang; Tkaczyk, Tomasz S

    2011-05-01

    Hyperspectral imaging has tremendous potential to detect important molecular biomarkers of early cancer based on their unique spectral signatures. Several drawbacks have limited its use for in vivo screening applications: most notably the poor temporal and spatial resolution, high expense, and low optical throughput of existing hyperspectral imagers. We present the development of a new real-time hyperspectral endoscope (called the image mapping spectroscopy endoscope) based on an image mapping technique capable of addressing these challenges. The parallel high throughput nature of this technique enables the device to operate at frame rates of 5.2 frames per second while collecting a (x, y, λ) datacube of 350 × 350 × 48. We have successfully imaged tissue in vivo, resolving a vasculature pattern of the lower lip while simultaneously detecting oxy-hemoglobin. PMID:21639573

  13. Identifying financial crises in real time

    NASA Astrophysics Data System (ADS)

    da Fonseca, Eder Lucio; Ferreira, Fernando F.; Muruganandam, Paulsamy; Cerdeira, Hilda A.

    2013-03-01

    Following the thermodynamic formulation of a multifractal measure that was shown to enable the detection of large fluctuations at an early stage, here we propose a new index which permits us to distinguish events like financial crises in real time. We calculate the partition function from which we can obtain thermodynamic quantities analogous to the free energy and specific heat. The index is defined as the normalized energy variation and it can be used to study the behavior of stochastic time series, such as financial market daily data. Famous financial market crashes-Black Thursday (1929), Black Monday (1987) and the subprime crisis (2008)-are identified with clear and robust results. The method is also applied to the market fluctuations of 2011. From these results it appears as if the apparent crisis of 2011 is of a different nature to the other three. We also show that the analysis has forecasting capabilities.

  14. Real Time Correction of Aircraft Flight Fonfiguration

    NASA Technical Reports Server (NTRS)

    Schipper, John F. (Inventor)

    2009-01-01

    Method and system for monitoring and analyzing, in real time, variation with time of an aircraft flight parameter. A time-dependent recovery band, defined by first and second recovery band boundaries that are spaced apart at at least one time point, is constructed for a selected flight parameter and for a selected time recovery time interval length .DELTA.t(FP;rec). A flight parameter, having a value FP(t=t.sub.p) at a time t=t.sub.p, is likely to be able to recover to a reference flight parameter value FP(t';ref), lying in a band of reference flight parameter values FP(t';ref;CB), within a time interval given by t.sub.p.ltoreq.t'.ltoreq.t.sub.p.DELTA.t(FP;rec), if (or only if) the flight parameter value lies between the first and second recovery band boundary traces.

  15. Real-time forecasts of dengue epidemics

    NASA Astrophysics Data System (ADS)

    Yamana, T. K.; Shaman, J. L.

    2015-12-01

    Dengue is a mosquito-borne viral disease prevalent in the tropics and subtropics, with an estimated 2.5 billion people at risk of transmission. In many areas with endemic dengue, disease transmission is seasonal but prone to high inter-annual variability with occasional severe epidemics. Predicting and preparing for periods of higher than average transmission is a significant public health challenge. Here we present a model of dengue transmission and a framework for optimizing model simulations with real-time observational data of dengue cases and environmental variables in order to generate ensemble-based forecasts of the timing and severity of disease outbreaks. The model-inference system is validated using synthetic data and dengue outbreak records. Retrospective forecasts are generated for a number of locations and the accuracy of these forecasts is quantified.

  16. Cerebral Autoregulation Real-Time Monitoring

    PubMed Central

    Tsalach, Adi; Ratner, Eliahu; Lokshin, Stas; Silman, Zmira; Breskin, Ilan; Budin, Nahum; Kamar, Moshe

    2016-01-01

    Cerebral autoregulation is a mechanism which maintains constant cerebral blood flow (CBF) despite changes in mean arterial pressure (MAP). Assessing whether this mechanism is intact or impaired and determining its boundaries is important in many clinical settings, where primary or secondary injuries to the brain may occur. Herein we describe the development of a new ultrasound tagged near infra red light monitor which tracks CBF trends, in parallel, it continuously measures blood pressure and correlates them to produce a real time autoregulation index. Its performance is validated in both in-vitro experiment and a pre-clinical case study. Results suggest that using such a tool, autoregulation boundaries as well as its impairment or functioning can be identified and assessed. It may therefore assist in individualized MAP management to ensure adequate organ perfusion and reduce the risk of postoperative complications, and might play an important role in patient care. PMID:27571474

  17. Intraoperative, real-time, functional MRI.

    PubMed

    Gering, D T; Weber, D M

    1998-01-01

    Functional MRI (fMRI) methods have been demonstrated to noninvasively identify motor-sensory, visual, and other areas of eloquent cortex for guiding surgical intervention. Typically, fMRI data are acquired preoperatively during a conventional surgical planning MRI examination. Unlike direct cortical stimulation at the time of surgery, however, preoperative fMRI methods do not account for the potential movement of tissues (relative to the time of functional imaging) that may occur in the surgical suite as a direct result of the intervention. Recently, an MRI device has been demonstrated for use in the surgical suite that has the potential to reduce the extent of cortical exposure required for the intervention. However, the invasive requirements of cortical mapping may supersede the invasive requirements of the surgical intervention itself. Consequently, we demonstrate here a modification to the intraoperative MRI device that facilitates a noninvasive, real-time, functional MR examination in the surgical suite.

  18. Near Real-Time Solar Image Reconstruction

    NASA Astrophysics Data System (ADS)

    Yang, G.; Denker, C.; Wang, H.

    2001-05-01

    We use a Linux Beowulf cluster to build a system for near real-time solar image reconstruction with the goal to obtain diffraction limited solar images at a cadence of one minute. This gives us immediate access to high-level data products and enables direct visualization of dynamic processes on the Sun. Space weather warnings and flare forecasting will benefit from this project. The image processing algorithms are based on the speckle masking method combined with frame selection. The parallel programs use explicit message passing via Parallel Virtual Machine (PVM). The preliminary results are very promising. Now, we can construct a 256 by 256 pixel image out of 50 short-exposure images within one minute on a Beowulf cluster with four 500~MHz CPUs. In addition, we want to explore the possibility of applying parallel computing on Beowulf clusters to other complex data reduction and analysis problems that we encounter, e.g., in multi-dimensional spectro-polarimetry.

  19. Near real-time stereo vision system

    NASA Technical Reports Server (NTRS)

    Anderson, Charles H. (Inventor); Matthies, Larry H. (Inventor)

    1993-01-01

    The apparatus for a near real-time stereo vision system for use with a robotic vehicle is described. The system is comprised of two cameras mounted on three-axis rotation platforms, image-processing boards, a CPU, and specialized stereo vision algorithms. Bandpass-filtered image pyramids are computed, stereo matching is performed by least-squares correlation, and confidence ranges are estimated by means of Bayes' theorem. In particular, Laplacian image pyramids are built and disparity maps are produced from the 60 x 64 level of the pyramids at rates of up to 2 seconds per image pair. The first autonomous cross-country robotic traverses (of up to 100 meters) have been achieved using the stereo vision system of the present invention with all computing done onboard the vehicle. The overall approach disclosed herein provides a unifying paradigm for practical domain-independent stereo ranging.

  20. Near real-time stereo vision system

    NASA Astrophysics Data System (ADS)

    Matthies, Larry H.; Anderson, Charles H.

    1991-12-01

    The apparatus for a near real-time stereo vision system for use with a robotic vehicle is described. The system is comprised of two cameras mounted on three-axis rotation platforms, image-processing boards, a CPU, and specialized stereo vision algorithms. Bandpass-filtered image pyramids are computed, stereo matching is performed by least-squares correlation, and confidence ranges are estimated by means of Bayes' theorem. In particular, Laplacian image pyramids are built and disparity maps are produced from the 60 x 64 level of the pyramids at rates of up to 2 seconds per image pair. The first autonomous cross-country robotic traverses (of up to 100 meters) have been achieved using the stereo vision system of the present invention with all computing done onboard the vehicle. The overall approach disclosed herein provides a unifying paradigm for practical domain-independent stereo ranging.

  1. Real time visualization of quantum walk

    SciTech Connect

    Miyazaki, Akihide; Hamada, Shinji; Sekino, Hideo

    2014-02-20

    Time evolution of quantum particles like electrons is described by time-dependent Schrödinger equation (TDSE). The TDSE is regarded as the diffusion equation of electrons with imaginary diffusion coefficients. And the TDSE is solved by quantum walk (QW) which is regarded as a quantum version of a classical random walk. The diffusion equation is solved in discretized space/time as in the case of classical random walk with additional unitary transformation of internal degree of freedom typical for quantum particles. We call the QW for solution of the TDSE a Schrödinger walk (SW). For observation of one quantum particle evolution under a given potential in atto-second scale, we attempt a successive computation and visualization of the SW. Using Pure Data programming, we observe the correct behavior of a probability distribution under the given potential in real time for observers of atto-second scale.

  2. Real-time value-driven diagnosis

    NASA Technical Reports Server (NTRS)

    Dambrosio, Bruce

    1995-01-01

    Diagnosis is often thought of as an isolated task in theoretical reasoning (reasoning with the goal of updating our beliefs about the world). We present a decision-theoretic interpretation of diagnosis as a task in practical reasoning (reasoning with the goal of acting in the world), and sketch components of our approach to this task. These components include an abstract problem description, a decision-theoretic model of the basic task, a set of inference methods suitable for evaluating the decision representation in real-time, and a control architecture to provide the needed continuing coordination between the agent and its environment. A principal contribution of this work is the representation and inference methods we have developed, which extend previously available probabilistic inference methods and narrow, somewhat, the gap between probabilistic and logical models of diagnosis.

  3. Real-time visualization of joint cavitation.

    PubMed

    Kawchuk, Gregory N; Fryer, Jerome; Jaremko, Jacob L; Zeng, Hongbo; Rowe, Lindsay; Thompson, Richard

    2015-01-01

    Cracking sounds emitted from human synovial joints have been attributed historically to the sudden collapse of a cavitation bubble formed as articular surfaces are separated. Unfortunately, bubble collapse as the source of joint cracking is inconsistent with many physical phenomena that define the joint cracking phenomenon. Here we present direct evidence from real-time magnetic resonance imaging that the mechanism of joint cracking is related to cavity formation rather than bubble collapse. In this study, ten metacarpophalangeal joints were studied by inserting the finger of interest into a flexible tube tightened around a length of cable used to provide long-axis traction. Before and after traction, static 3D T1-weighted magnetic resonance images were acquired. During traction, rapid cine magnetic resonance images were obtained from the joint midline at a rate of 3.2 frames per second until the cracking event occurred. As traction forces increased, real-time cine magnetic resonance imaging demonstrated rapid cavity inception at the time of joint separation and sound production after which the resulting cavity remained visible. Our results offer direct experimental evidence that joint cracking is associated with cavity inception rather than collapse of a pre-existing bubble. These observations are consistent with tribonucleation, a known process where opposing surfaces resist separation until a critical point where they then separate rapidly creating sustained gas cavities. Observed previously in vitro, this is the first in-vivo macroscopic demonstration of tribonucleation and as such, provides a new theoretical framework to investigate health outcomes associated with joint cracking.

  4. Real-Time Visualization of Joint Cavitation

    PubMed Central

    Rowe, Lindsay

    2015-01-01

    Cracking sounds emitted from human synovial joints have been attributed historically to the sudden collapse of a cavitation bubble formed as articular surfaces are separated. Unfortunately, bubble collapse as the source of joint cracking is inconsistent with many physical phenomena that define the joint cracking phenomenon. Here we present direct evidence from real-time magnetic resonance imaging that the mechanism of joint cracking is related to cavity formation rather than bubble collapse. In this study, ten metacarpophalangeal joints were studied by inserting the finger of interest into a flexible tube tightened around a length of cable used to provide long-axis traction. Before and after traction, static 3D T1-weighted magnetic resonance images were acquired. During traction, rapid cine magnetic resonance images were obtained from the joint midline at a rate of 3.2 frames per second until the cracking event occurred. As traction forces increased, real-time cine magnetic resonance imaging demonstrated rapid cavity inception at the time of joint separation and sound production after which the resulting cavity remained visible. Our results offer direct experimental evidence that joint cracking is associated with cavity inception rather than collapse of a pre-existing bubble. These observations are consistent with tribonucleation, a known process where opposing surfaces resist separation until a critical point where they then separate rapidly creating sustained gas cavities. Observed previously in vitro, this is the first in-vivo macroscopic demonstration of tribonucleation and as such, provides a new theoretical framework to investigate health outcomes associated with joint cracking. PMID:25875374

  5. A real-time pulsed photon dosimeter

    NASA Astrophysics Data System (ADS)

    Brown, David; Olsher, Richard H.; Eisen, Yosef; Rodriguez, Joseph F.

    1996-02-01

    Radiation sources producing short pulses of photon radiation are now widespread. Such sources include electron and proton linear accelerators, betatrons, synchrotrons, and field-emission impulse generators. It is often desirable to measure leakage and skyshine radiation from such sources in real time, on a single-pulse basis as low as 8.7 nGy (1 μR) per pulse. This paper describes the design and performance of a prototype, real-time, pulsed photon dosimeter (PPD) capable of single-pulse dose measurements over the range from 3.5 nGy to 3.5 μGy (0.4 to 400 μR). The PPD may also be operated in a multiple-pulse mode that integrates the dose from a train of radiation pulses over a 3-s period. A pulse repetition rate of up to 300 Hz is accommodated. The design is eminently suitable for packaging as a lightweight, portable, survey meter. The PPD uses a CdWO 4 scintillator optically coupled to a photodiode to generate a charge at the diode output. A pulse amplifier converts the charge to a voltage pulse. A digitizer circuit generates a burst of logic pulses whose number is proportional to the peak value of the voltage pulse. The digitizer output is recorded by a pulse counter and suitably displayed. A prototype PPD was built for testing and evaluation purposes. The performance of the PPD was evaluated with a variety of pulsed photon sources. The dynamic range, energy response, and response to multiple pulses were characterized. The experimental data confirm the viability of the PPD for pulsed photon dosimetry.

  6. Towards real time speckle controlled retinal photocoagulation

    NASA Astrophysics Data System (ADS)

    Bliedtner, Katharina; Seifert, Eric; Stockmann, Leoni; Effe, Lisa; Brinkmann, Ralf

    2016-03-01

    Photocoagulation is a laser treatment widely used for the therapy of several retinal diseases. Intra- and inter-individual variations of the ocular transmission, light scattering and the retinal absorption makes it impossible to achieve a uniform effective exposure and hence a uniform damage throughout the therapy. A real-time monitoring and control of the induced damage is highly requested. Here, an approach to realize a real time optical feedback using dynamic speckle analysis is presented. A 532 nm continuous wave Nd:YAG laser is used for coagulation. During coagulation, speckle dynamics are monitored by a coherent object illumination using a 633nm HeNe laser and analyzed by a CMOS camera with a frame rate up to 1 kHz. It is obvious that a control system needs to determine whether the desired damage is achieved to shut down the system in a fraction of the exposure time. Here we use a fast and simple adaption of the generalized difference algorithm to analyze the speckle movements. This algorithm runs on a FPGA and is able to calculate a feedback value which is correlated to the thermal and coagulation induced tissue motion and thus the achieved damage. For different spot sizes (50-200 μm) and different exposure times (50-500 ms) the algorithm shows the ability to discriminate between different categories of retinal pigment epithelial damage ex-vivo in enucleated porcine eyes. Furthermore in-vivo experiments in rabbits show the ability of the system to determine tissue changes in living tissue during coagulation.

  7. A real-time groundwater management model using data assimilation

    NASA Astrophysics Data System (ADS)

    Cheng, Wei-Chen; Putti, Mario; Kendall, Donald R.; Yeh, William W.-G.

    2011-06-01

    This study develops a groundwater management model for real-time operation of an aquifer system. A groundwater flow model is allied with a nudging data assimilation algorithm that reduces the forecast error, minimizes the risk of system failure, and improves management strategies. The nudging algorithm treats the unknown private pumping as an additional sink term in the groundwater flow equation and provides a consistently physical interpretation for the identification of pumping rates. The system response due to pumping and injection is represented by a response matrix that is generated by the influence coefficient method. The response matrix (with a much smaller dimension) is used as a reduced model and is embedded directly in the management model as a part of the constraint set. Additionally, the influence coefficient method is utilized to include the nudging effect in the reduced model. The management model optimizes the monthly operation for 12 months into the future and determines the optimal strategy using the information provided by nudging. The management model is updated at the beginning of each month when new head observations and pumping data become available. We also discuss the utility, accuracy, and efficiency of the proposed management model for real-time operation.

  8. Authentication of Atlantic cod (Gadus morhua) using real time PCR.

    PubMed

    Herrero, Beatriz; Madriñán, María; Vieites, Juan M; Espiñeira, Montserrat

    2010-04-28

    This work describes the development of a real-time polymerase chain reaction (RT-PCR) system for the detection and identification of Atlantic cod (Gadus morhua). Among the advantages of this technique, it is worth highlighting that this is reliable in terms of specificity and sensitivity. The TaqMan real-time PCR is the simplest, fastest testing process and has the highest potential for automation, therefore representing the currently most suitable method for screening, allowing the detection of fraudulent or unintentional mislabeling of this species. The method can be applied to all kinds of products, fresh, frozen, and processed products, including those undergoing intensive processes of transformation. The developed methodology using specific primer-probe set was validated and further applied to 40 commercial samples labeled as cod in order to determinate if the species used for their manufacturing corresponded to G. morhua, detecting 20% that were incorrectly labeled. A C(t) value of about 19 was obtained when G. morhua was present. In samples with a species mixture, all samples that had a fluorescence signal were positive (C(t) < 30) for the presence of G. morhua by conventional end-point RT-PCR, and the estimated limit of detection for these type of samples was of 20 pg of DNA. The methodology herein developed is useful to check the fulfilment of labeling regulations for seafood products and verify the correct traceability in commercial trade and for fisheries control.

  9. Graph-based real-time fault diagnostics

    NASA Technical Reports Server (NTRS)

    Padalkar, S.; Karsai, G.; Sztipanovits, J.

    1988-01-01

    A real-time fault detection and diagnosis capability is absolutely crucial in the design of large-scale space systems. Some of the existing AI-based fault diagnostic techniques like expert systems and qualitative modelling are frequently ill-suited for this purpose. Expert systems are often inadequately structured, difficult to validate and suffer from knowledge acquisition bottlenecks. Qualitative modelling techniques sometimes generate a large number of failure source alternatives, thus hampering speedy diagnosis. In this paper we present a graph-based technique which is well suited for real-time fault diagnosis, structured knowledge representation and acquisition and testing and validation. A Hierarchical Fault Model of the system to be diagnosed is developed. At each level of hierarchy, there exist fault propagation digraphs denoting causal relations between failure modes of subsystems. The edges of such a digraph are weighted with fault propagation time intervals. Efficient and restartable graph algorithms are used for on-line speedy identification of failure source components.

  10. A tool for modeling concurrent real-time computation

    NASA Technical Reports Server (NTRS)

    Sharma, D. D.; Huang, Shie-Rei; Bhatt, Rahul; Sridharan, N. S.

    1990-01-01

    Real-time computation is a significant area of research in general, and in AI in particular. The complexity of practical real-time problems demands use of knowledge-based problem solving techniques while satisfying real-time performance constraints. Since the demands of a complex real-time problem cannot be predicted (owing to the dynamic nature of the environment) powerful dynamic resource control techniques are needed to monitor and control the performance. A real-time computation model for a real-time tool, an implementation of the QP-Net simulator on a Symbolics machine, and an implementation on a Butterfly multiprocessor machine are briefly described.

  11. Approaching near real-time biosensing: microfluidic microsphere based biosensor for real-time analyte detection.

    PubMed

    Cohen, Noa; Sabhachandani, Pooja; Golberg, Alexander; Konry, Tania

    2015-04-15

    In this study we describe a simple lab-on-a-chip (LOC) biosensor approach utilizing well mixed microfluidic device and a microsphere-based assay capable of performing near real-time diagnostics of clinically relevant analytes such cytokines and antibodies. We were able to overcome the adsorption kinetics reaction rate-limiting mechanism, which is diffusion-controlled in standard immunoassays, by introducing the microsphere-based assay into well-mixed yet simple microfluidic device with turbulent flow profiles in the reaction regions. The integrated microsphere-based LOC device performs dynamic detection of the analyte in minimal amount of biological specimen by continuously sampling micro-liter volumes of sample per minute to detect dynamic changes in target analyte concentration. Furthermore we developed a mathematical model for the well-mixed reaction to describe the near real time detection mechanism observed in the developed LOC method. To demonstrate the specificity and sensitivity of the developed real time monitoring LOC approach, we applied the device for clinically relevant analytes: Tumor Necrosis Factor (TNF)-α cytokine and its clinically used inhibitor, anti-TNF-α antibody. Based on the reported results herein, the developed LOC device provides continuous sensitive and specific near real-time monitoring method for analytes such as cytokines and antibodies, reduces reagent volumes by nearly three orders of magnitude as well as eliminates the washing steps required by standard immunoassays.

  12. The multispectral advanced volumetric real-time imaging compositor for real-time distributed scene generation

    NASA Astrophysics Data System (ADS)

    Morris, Joseph W.; Ballard, Gary H.; Bunfield, Dennis H.; Peddycoart, Thomas E.; Trimble, Darian E.

    2011-06-01

    AMRDEC has developed the Multi-spectral Advanced Volumetric Real-time Imaging Compositor (MAVRIC) prototype for distributed real-time hardware-in-the-loop (HWIL) scene generation. MAVRIC is a dynamic object-based energy conserved scene compositor that can seamlessly convolve distributed scene elements into temporally aligned physicsbased scenes for enhancing existing AMRDEC scene generation codes. The volumetric compositing process accepts input independent of depth order. This real-time compositor framework is built around AMRDEC's ContinuumCore API which provides the common messaging interface leveraging the Neutral Messaging Language (NML) for local, shared memory, reflective memory, network, and remote direct memory access (RDMA) communications and the Joint Signature Image Generator (JSIG) that provides energy conserved scene component interface at each render node. This structure allows for a highly scalable real-time environment capable of rendering individual objects at high fidelity while being considerate of real-time hardware-in-the-loop concerns, such as latency. As such, this system can be scaled to handle highly complex detailed scenes such as urban environments. This architecture provides the basis for common scene generation as it provides disparate scene elements to be calculated by various phenomenology codes and integrated seamlessly into a unified composited environment. This advanced capability is the gateway to higher fidelity scene generation such as ray-tracing. The high speed interconnects using PCI Express and InfiniBand were examined to support distributed scene generation whereby the scene graph, associated phenomenology, and the scene elements can be dynamically distributed across multiple high performance computing assets to maximize system performance.

  13. Clinical experience with real-time ultrasound

    NASA Astrophysics Data System (ADS)

    Chimiak, William J.; Wolfman, Neil T.; Covitz, Wesley

    1995-05-01

    After testing the extended multimedia interface (EMMI) product which is an asynchronous transmission mode (ATM) user to network interface (UNI) of AT&T at the Society for Computer Applications in Radiology conference in Winston-Salem, the Department of Radiology together with AT&T are implementing a tele-ultrasound system to combine real- time ultrasound with the static imaging features of more traditional digital ultrasound systems. Our current ultrasound system archives digital images to an optical disk system. Static images are sent using our digital radiology systems. This could be transferring images from one digital imaging and communications (DICOM)-compliant machine to another, or the current image transfer methodologies. The prototype of a live ultrasound system using the EMMI demonstrated the feasibility of doing live ultrasound. We now are developing the scenarios using a mix of the two methodologies. Utilizing EMMI technology, radiologists at the BGSM review at a workstation both static images and real-time scanning done by a technologist on patients at a remote site in order to render on-line primary diagnosis. Our goal is to test the feasibility of operating an ultrasound laboratory at a remote site utilizing a trained technologist without the necessity of having a full-time radiologist at that site. Initial plans are for a radiologist to review an initial set of static images on a patient taken by the technologist. If further scanning is required, the EMMI is used to transmit real-time imaging and audio using the audio input of a standard microphone system and the National Television Standards Committee (NTSC) output of the ultrasound equipment from the remote site to the radiologist in the department review station. The EMMI digitally encodes this data and places it in an ATM format. This ATM data stream goes to the GCNS2000 and then to the other EMMI where the ATM data stream is decoded into the live studies and voice communication which are then

  14. Real Time Earthquake Information System in Japan

    NASA Astrophysics Data System (ADS)

    Doi, K.; Kato, T.

    2003-12-01

    An early earthquake notification system in Japan had been developed by the Japan Meteorological Agency (JMA) as a governmental organization responsible for issuing earthquake information and tsunami forecasts. The system was primarily developed for prompt provision of a tsunami forecast to the public with locating an earthquake and estimating its magnitude as quickly as possible. Years after, a system for a prompt provision of seismic intensity information as indices of degrees of disasters caused by strong ground motion was also developed so that concerned governmental organizations can decide whether it was necessary for them to launch emergency response or not. At present, JMA issues the following kinds of information successively when a large earthquake occurs. 1) Prompt report of occurrence of a large earthquake and major seismic intensities caused by the earthquake in about two minutes after the earthquake occurrence. 2) Tsunami forecast in around three minutes. 3) Information on expected arrival times and maximum heights of tsunami waves in around five minutes. 4) Information on a hypocenter and a magnitude of the earthquake, the seismic intensity at each observation station, the times of high tides in addition to the expected tsunami arrival times in 5-7 minutes. To issue information above, JMA has established; - An advanced nationwide seismic network with about 180 stations for seismic wave observation and about 3,400 stations for instrumental seismic intensity observation including about 2,800 seismic intensity stations maintained by local governments, - Data telemetry networks via landlines and partly via a satellite communication link, - Real-time data processing techniques, for example, the automatic calculation of earthquake location and magnitude, the database driven method for quantitative tsunami estimation, and - Dissemination networks, via computer-to-computer communications and facsimile through dedicated telephone lines. JMA operationally

  15. CRANS - CONFIGURABLE REAL-TIME ANALYSIS SYSTEM

    NASA Technical Reports Server (NTRS)

    Mccluney, K.

    1994-01-01

    In a real-time environment, the results of changes or failures in a complex, interconnected system need evaluation quickly. Tabulations showing the effects of changes and/or failures of a given item in the system are generally only useful for a single input, and only with regard to that item. Subsequent changes become harder to evaluate as combinations of failures produce a cascade effect. When confronted by multiple indicated failures in the system, it becomes necessary to determine a single cause. In this case, failure tables are not very helpful. CRANS, the Configurable Real-time ANalysis System, can interpret a logic tree, constructed by the user, describing a complex system and determine the effects of changes and failures in it. Items in the tree are related to each other by Boolean operators. The user is then able to change the state of these items (ON/OFF FAILED/UNFAILED). The program then evaluates the logic tree based on these changes and determines any resultant changes to other items in the tree. CRANS can also search for a common cause for multiple item failures, and allow the user to explore the logic tree from within the program. A "help" mode and a reference check provide the user with a means of exploring an item's underlying logic from within the program. A commonality check determines single point failures for an item or group of items. Output is in the form of a user-defined matrix or matrices of colored boxes, each box representing an item or set of items from the logic tree. Input is via mouse selection of the matrix boxes, using the mouse buttons to toggle the state of the item. CRANS is written in C-language and requires the MIT X Window System, Version 11 Revision 4 or Revision 5. It requires 78K of RAM for execution and a three button mouse. It has been successfully implemented on Sun4 workstations running SunOS, HP9000 workstations running HP-UX, and DECstations running ULTRIX. No executable is provided on the distribution medium; however

  16. Real-time reconfigurable subthreshold CMOS perceptron.

    PubMed

    Aunet, S; Oelmann, B; Norseng, P A; Berg, Y

    2008-04-01

    In this paper, a new, real-time reconfigurable perceptron circuit element is presented. A six-transistor version used as a threshold gate, having a fan-in of three, producing adequate outputs for threshold of T =1, 2 and 3 is demonstrated by chip measurements. Subthreshold operation for supply voltages in the range of 100-350 mV is shown. The circuit performs competitively with a standard static complimentary metal-oxide-semiconductor (CMOS) implementation when maximum speed and energy delay product are taken into account, when used in a ring oscillator. Functionality per transistor is, to our knowledge, the highest reported for a variety of comparable circuits not based on floating gate techniques. Statistical simulations predict probabilities for making working circuits under mismatch and process variations. The simulations, in 120-nm CMOS, also support discussions regarding lower limits to supply voltage and redundancy. A brief discussion on how the circuit may be exploited as a basic building block for future defect tolerant mixed signal circuits, as well as neural networks, exploiting redundancy, is included.

  17. Real-Time Principal-Component Analysis

    NASA Technical Reports Server (NTRS)

    Duong, Vu; Duong, Tuan

    2005-01-01

    A recently written computer program implements dominant-element-based gradient descent and dynamic initial learning rate (DOGEDYN), which was described in Method of Real-Time Principal-Component Analysis (NPO-40034) NASA Tech Briefs, Vol. 29, No. 1 (January 2005), page 59. To recapitulate: DOGEDYN is a method of sequential principal-component analysis (PCA) suitable for such applications as data compression and extraction of features from sets of data. In DOGEDYN, input data are represented as a sequence of vectors acquired at sampling times. The learning algorithm in DOGEDYN involves sequential extraction of principal vectors by means of a gradient descent in which only the dominant element is used at each iteration. Each iteration includes updating of elements of a weight matrix by amounts proportional to a dynamic initial learning rate chosen to increase the rate of convergence by compensating for the energy lost through the previous extraction of principal components. In comparison with a prior method of gradient-descent-based sequential PCA, DOGEDYN involves less computation and offers a greater rate of learning convergence. The sequential DOGEDYN computations require less memory than would parallel computations for the same purpose. The DOGEDYN software can be executed on a personal computer.

  18. Real-Time 3D Visualization

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Butler Hine, former director of the Intelligent Mechanism Group (IMG) at Ames Research Center, and five others partnered to start Fourth Planet, Inc., a visualization company that specializes in the intuitive visual representation of dynamic, real-time data over the Internet and Intranet. Over a five-year period, the then NASA researchers performed ten robotic field missions in harsh climes to mimic the end- to-end operations of automated vehicles trekking across another world under control from Earth. The core software technology for these missions was the Virtual Environment Vehicle Interface (VEVI). Fourth Planet has released VEVI4, the fourth generation of the VEVI software, and NetVision. VEVI4 is a cutting-edge computer graphics simulation and remote control applications tool. The NetVision package allows large companies to view and analyze in virtual 3D space such things as the health or performance of their computer network or locate a trouble spot on an electric power grid. Other products are forthcoming. Fourth Planet is currently part of the NASA/Ames Technology Commercialization Center, a business incubator for start-up companies.

  19. Correction of deformed images in real time

    NASA Astrophysics Data System (ADS)

    Van der Jeught, Sam; Buytaert, Jan A. N.; Dirckx, Joris J. J.

    2011-09-01

    Optical lens systems generally contain non-linear distortion artifacts that impose important limitations on the direct interpretation of the images. Image processing can be used to correct for these artifacts, but due to the calculation-intensive nature of the required distortion correction process, this is usually performed offline. This is not an option in image-based applications that operate interactively, however, where the real-time display of distortion corrected images can be vital. To this end, we propose a new technique to correct for arbitrary geometric lens distortion that uses the parallel processing power of a commercial graphics processing unit (GPU). By offloading the distortion correction process to the GPU, we can relieve the central processing unit (CPU) of doing this computationally very demanding task. We successfully implemented the full distortion correction algorithm on the GPU, thereby achieving a display rate of over 30 frames/sec for fully processed images of size 1024 × 768 pixels without the need for any additional digital image processing hardware.

  20. Real time radiation measurements in space

    NASA Astrophysics Data System (ADS)

    Thomson, I.; Mackay, G.

    Radiation composed of energetic electrons, protons, photons, and galactic cosmic rays will be experienced by all space missions and may have effects on radiation sensitive electronic components and biological specimens. Radiation issues of interest to microgravity and biological experiments are discussed and the design of a new direct reading electronic radiation monitoring system is described. The proposed system consists of a radiation sensitive metal oxide semiconductor field effect transistor (MOSFET) specially designed to respond to ionizing radiation. On exposure to radiation, a permanent charge is stored in the MOSFET's insulating oxide, altering the device's electrical characteristics in a manner directly proportional to the dose exposed. A simple circuit reads the MOSFET's cumulative dose, making it possible to obtain real-time measurements and store the data or transfer the data to an earth station. Tests have shown that the MOSFET dosimeter shows a linear response up to at least 30,000 centiGray at a resolution of 0.1 centiGray. The MOSFET dosimetry system will be installed on the European Space Agency's ARTEP satellite scheduled for launch in November 1991.

  1. Extrasolar Giant Impacts in Real Time

    NASA Astrophysics Data System (ADS)

    Rieke, George; Meng, Huan; Su, Kate

    2013-10-01

    Spitzer observations in the previous cycles have revealed 3.6 and 4.5 um variability and periodicity in extreme debris disks on timescales of weeks or even shorter. Such disks typically have warm temperatures and strong crystalline silicate emission, indicative of very fine dust particles in the terrestrial planet zone and below the blowout sizes of the stars. Many of the disks are around solar-like stars in the age range of 30 - 100+ Myr, the expected time for the final buildup of terrestrial planets through massive collisions. These young extrasolar systems are probably going through this phase with series of violent collisions, or possible analogs of the Moon-forming impact, providing rare opportunities to investigate terrestrial planet formation and collision in real time, and put our own Solar System in context. Here we propose to continue the monitoring of three such systems with daily sampling cadence. The observations will provide insight into the physical and dynamical processes of the planet-forming disks.

  2. Optimizing near real time accountability for reprocessing.

    SciTech Connect

    Cipiti, Benjamin B.

    2010-06-01

    Near Real Time Accountability (NRTA) of actinides at high precision in reprocessing plants has been a long sought-after goal in the safeguards community. Achieving this goal is hampered by the difficulty of making precision measurements in the reprocessing environment, equipment cost, and impact to plant operations. Thus the design of future reprocessing plants requires an optimization of different approaches. The Separations and Safeguards Performance Model, developed at Sandia National Laboratories, was used to evaluate a number of NRTA strategies in a UREX+ reprocessing plant. Strategies examined include the incorporation of additional actinide measurements of internal plant vessels, more use of process monitoring data, and the option of periodic draining of inventory to key tanks. Preliminary results show that the addition of measurement technologies can increase the overall measurement uncertainty due to additional error propagation, so care must be taken when designing an advanced system. Initial results also show that relying on a combination of different NRTA techniques will likely be the best option. The model provides a platform for integrating all the data. The modeling results for the different NRTA options under various material loss conditions will be presented.

  3. High sensitivity real-time NVR monitor

    NASA Technical Reports Server (NTRS)

    Bowers, William D. (Inventor); Chuan, Raymond L. (Inventor)

    1997-01-01

    A real time non-volatile residue (NVR) monitor, which utilizes surface acoustic wave (SAW) resonators to detect molecular contamination in a given environment. The SAW resonators operate at a resonant frequency of approximately 200 MHz-2,000 MHz which enables the NVR monitor to detect molecular contamination on the order of 10.sup.-11 g-cm.sup.-2 to 10.sup.-13 g-cm.sup.2. The NVR monitor utilizes active temperature control of (SAW) resonators to achieve a stable resonant frequency. The temperature control system of the NVR monitor is able to directly heat and cool the SAW resonators utilizing a thermoelectric element to maintain the resonators at a present temperature independent of the environmental conditions. In order to enable the direct heating and cooling of the SAW resonators, the SAW resonators are operatively mounted to a heat sink. In one embodiment, the heat sink is located in between the SAW resonators and an electronic circuit board which contains at least a portion of the SAW control electronics. The electrical leads of the SAW resonators are connected through the heat sink to the circuit board via an electronic path which prevents inaccurate frequency measurement.

  4. Real-time scheduling of software tasks

    SciTech Connect

    Hoff, L.T.

    1995-12-01

    When designing real-time systems, it is often desirable to schedule execution of software tasks based on the occurrence of events. The events may be clock ticks, interrupts from a hardware device, or software signals from other software tasks. If the nature of the events, is well understood, this scheduling is normally a static part of the system design. If the nature of the events is not completely understood, or is expected to change over time, it may be necessary to provide a mechanism for adjusting the scheduling of the software tasks. RHIC front-end computers (FECs) provide such a mechanism. The goals in designing this mechanism were to be as independent as possible of the underlying operating system, to allow for future expansion of the mechanism to handle new types of events, and to allow easy configuration. Some considerations which steered the design were programming paradigm (object oriented vs. procedural), programming language, and whether events are merely interesting moments in time, or whether they intrinsically have data associated with them. The design also needed to address performance and robustness tradeoffs involving shared task contexts, task priorities, and use of interrupt service routine (ISR) contexts vs. task contexts. This paper will explore these considerations and tradeoffs.

  5. Real-time video watermarking technique

    NASA Astrophysics Data System (ADS)

    Lee, Han H.; Chae, Jong J.; Choi, Jong U.

    2002-04-01

    Most previous video watermarking algorithms cannot be supported by real-time processing. Our algorithm proposed the specific embedding method in the spatial domain directly rather than the frequency domain. Also the algorithm supports the robustness from the video attacking skills. In the paper, for example, watermark is inserted immediately into the output frame of Digital Video (DV) camcorder. We select the Y component from the DV signal, and then the watermark information is inserted in all of the Y frames. The watermarked video frames put in the video MPEG encoder. We consider embedding information to the high quality video streams, such as a DVD, HDTV. Our experimental results show the high quality of the video even if compressed. Therefore, the robustness from compression is tested by MPEG-2 of 6Mbits/sec of 720x480 frame size and the invisibility is proved by measurement of PSNR. The results also show the robustness from several video editing methods, such as a cut-and-splice and cut-insert-splice, and video conversions, letterboxing, pan & span, and wide screen of media.

  6. Real-time optoacoustic monitoring of stroke

    NASA Astrophysics Data System (ADS)

    Kneipp, Moritz; Turner, Jake; Hambauer, Sebastian; Krieg, Sandro M.; Lehmberg, Jens; Lindauer, Ute; Razansky, Daniel

    2014-03-01

    Characterizing disease progression and identifying possible therapeutic interventions in stroke is greatly aided by the use of longitudinal function imaging studies. In this study, we investigate the applicability of real-time multispectral optoacoustic tomography (MSOT) as a tool for non-invasive monitoring of the progression of stroke in the whole brain. The middle cerebral artery occlusion (MCAO) method was used to induce stroke. Mice were imaged under isoflurane anesthesia preoperatively and at several time points during and after the 60-minute occlusion. The animals were sacrificed after 24 hours and their excised brains frozen at -80°C for sectioning. The cryosection were stained using H&E staining to identify the ischemic lesion. Major vessels are readily identifiable in the whole mouse head in the in vivo optoacoustic scans. During ischemia, a reduction in cerebral blood volume is detectable in the cortex. Post ischemia, spectral unmixing of the optoacoustic signals shows an asymmetry of the deoxygenated hemoglobin in the hemisphere affected by MCAO. This hypoxic area was mainly located around the boundary of the ischemic lesion and was therefore identified as the ischemic penumbra. Non-invasive functional MSOT imaging is able to visualize the hypoxic penumbra in brains affected by stroke. Stopping the spread of the infarct area and revitalizing the penumbra is central in stroke research, this new imaging technique may therefore prove to be a valuable tool in the monitoring and developing new treatments.

  7. Recommendations for Real-Time Speech MRI

    PubMed Central

    Lingala, Sajan Goud; Sutton, Brad P.; Miquel, Marc E.; Nayak, Krishna S.

    2016-01-01

    Real-time magnetic resonance imaging (RT-MRI) is being increasingly used for speech and vocal production research studies. Several imaging protocols have emerged based on advances in RT-MRI acquisition, reconstruction, and audio-processing methods. This review summarizes the state-of-the-art, discusses technical considerations, and provides specific guidance for new groups entering this field. We provide recommendations for performing RT-MRI of the upper airway. This is a consensus statement stemming from the ISMRM-endorsed Speech MRI summit held in Los Angeles, February 2014. A major unmet need identified at the summit was the need for consensus on protocols that can be easily adapted by researchers equipped with conventional MRI systems. To this end, we provide a discussion of tradeoffs in RT-MRI in terms of acquisition requirements, a priori assumptions, artifacts, computational load, and performance for different speech tasks. We provide four recommended protocols and identify appropriate acquisition and reconstruction tools. We list pointers to open-source software that facilitate implementation. We conclude by discussing current open challenges in the methodological aspects of RT-MRI of speech. PMID:26174802

  8. Real-time information management environment (RIME)

    NASA Astrophysics Data System (ADS)

    DeCleene, Brian T.; Griffin, Sean; Matchett, Garry; Niejadlik, Richard

    2000-08-01

    Whereas data mining and exploitation improve the quality and quantity of information available to the user, there remains a mission requirement to assist the end-user in managing the access to this information and ensuring that the appropriate information is delivered to the right user in time to make decisions and take action. This paper discusses TASC's federated architecture to next- generation information management, contrasts the approach against emerging technologies, and quantifies the performance gains. This architecture and implementation, known as Real-time Information Management Environment (RIME), is based on two key concepts: information utility and content-based channelization. The introduction of utility allows users to express the importance and delivery requirements of their information needs in the context of their mission. Rather than competing for resources on a first-come/first-served basis, the infrastructure employs these utility functions to dynamically react to unanticipated loading by optimizing the delivered information utility. Furthermore, commander's resource policies shape these functions to ensure that resources are allocated according to military doctrine. Using information about the desired content, channelization identifies opportunities to aggregate users onto shared channels reducing redundant transmissions. Hence, channelization increases the information throughput of the system and balances sender/receiver processing load.

  9. Real time visual servoing using controlled illumination

    NASA Astrophysics Data System (ADS)

    Urban, J. P.; Motyl, G.; Gallice, J.

    1994-02-01

    A real-time visual servoing approach is applied to robotics tasks consisting of the positioning of the end effector with respect to a priori known polyhedral objects. The vision apparatus is consituted by a compact CCD camera rigidly coupled with two laser stripes mounted on the wrist of a robot manipulator. The objective is to servo the robot and effector at a constant position and orientation with respect to a known object in three- dimensional space in the field of view of the sensory system. The approach is expressed in terms of sensor-based control applied to visual servoing. In the case of camera-light stripe coupling, the elementary visual signals used for visual servoing are the points of discontinuity in the light stripes. The feasibility of the approach is demonstrated in a factory automation task consisting of the positioning of the end-effector tool over a vehicle battery. Both simulation and experimentation results are presented, proving the robustness and stability of the algorithm.

  10. Real-time, portable genome sequencing for Ebola surveillance.

    PubMed

    Quick, Joshua; Loman, Nicholas J; Duraffour, Sophie; Simpson, Jared T; Severi, Ettore; Cowley, Lauren; Bore, Joseph Akoi; Koundouno, Raymond; Dudas, Gytis; Mikhail, Amy; Ouédraogo, Nobila; Afrough, Babak; Bah, Amadou; Baum, Jonathan H J; Becker-Ziaja, Beate; Boettcher, Jan Peter; Cabeza-Cabrerizo, Mar; Camino-Sánchez, Álvaro; Carter, Lisa L; Doerrbecker, Juliane; Enkirch, Theresa; García-Dorival, Isabel; Hetzelt, Nicole; Hinzmann, Julia; Holm, Tobias; Kafetzopoulou, Liana Eleni; Koropogui, Michel; Kosgey, Abigael; Kuisma, Eeva; Logue, Christopher H; Mazzarelli, Antonio; Meisel, Sarah; Mertens, Marc; Michel, Janine; Ngabo, Didier; Nitzsche, Katja; Pallasch, Elisa; Patrono, Livia Victoria; Portmann, Jasmine; Repits, Johanna Gabriella; Rickett, Natasha Y; Sachse, Andreas; Singethan, Katrin; Vitoriano, Inês; Yemanaberhan, Rahel L; Zekeng, Elsa G; Racine, Trina; Bello, Alexander; Sall, Amadou Alpha; Faye, Ousmane; Faye, Oumar; Magassouba, N'Faly; Williams, Cecelia V; Amburgey, Victoria; Winona, Linda; Davis, Emily; Gerlach, Jon; Washington, Frank; Monteil, Vanessa; Jourdain, Marine; Bererd, Marion; Camara, Alimou; Somlare, Hermann; Camara, Abdoulaye; Gerard, Marianne; Bado, Guillaume; Baillet, Bernard; Delaune, Déborah; Nebie, Koumpingnin Yacouba; Diarra, Abdoulaye; Savane, Yacouba; Pallawo, Raymond Bernard; Gutierrez, Giovanna Jaramillo; Milhano, Natacha; Roger, Isabelle; Williams, Christopher J; Yattara, Facinet; Lewandowski, Kuiama; Taylor, James; Rachwal, Phillip; Turner, Daniel J; Pollakis, Georgios; Hiscox, Julian A; Matthews, David A; O'Shea, Matthew K; Johnston, Andrew McD; Wilson, Duncan; Hutley, Emma; Smit, Erasmus; Di Caro, Antonino; Wölfel, Roman; Stoecker, Kilian; Fleischmann, Erna; Gabriel, Martin; Weller, Simon A; Koivogui, Lamine; Diallo, Boubacar; Keïta, Sakoba; Rambaut, Andrew; Formenty, Pierre; Günther, Stephan; Carroll, Miles W

    2016-02-11

    The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is desirable to characterize the infectious agent and determine its evolutionary rate. Genome sequencing also allows the identification of signatures of host adaptation, identification and monitoring of diagnostic targets, and characterization of responses to vaccines and treatments. The Ebola virus (EBOV) genome substitution rate in the Makona strain has been estimated at between 0.87 × 10(-3) and 1.42 × 10(-3) mutations per site per year. This is equivalent to 16-27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions. Genomic surveillance during the epidemic has been sporadic owing to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities. To address this problem, here we devise a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. We present sequence data and analysis of 142 EBOV samples collected during the period March to October 2015. We were able to generate results less than 24 h after receiving an Ebola-positive sample, with the sequencing process taking as little as 15-60 min. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks. PMID:26840485

  11. Real Time Data Management for Estimating Probabilities of Incidents and Near Misses

    NASA Astrophysics Data System (ADS)

    Stanitsas, P. D.; Stephanedes, Y. J.

    2011-08-01

    Advances in real-time data collection, data storage and computational systems have led to development of algorithms for transport administrators and engineers that improve traffic safety and reduce cost of road operations. Despite these advances, problems in effectively integrating real-time data acquisition, processing, modelling and road-use strategies at complex intersections and motorways remain. These are related to increasing system performance in identification, analysis, detection and prediction of traffic state in real time. This research develops dynamic models to estimate the probability of road incidents, such as crashes and conflicts, and incident-prone conditions based on real-time data. The models support integration of anticipatory information and fee-based road use strategies in traveller information and management. Development includes macroscopic/microscopic probabilistic models, neural networks, and vector autoregressions tested via machine vision at EU and US sites.

  12. Real-time nucleic acid sequence-based amplification in nanoliter volumes.

    PubMed

    Gulliksen, Anja; Solli, Lars; Karlsen, Frank; Rogne, Henrik; Hovig, Eivind; Nordstrøm, Trine; Sirevåg, Reidun

    2004-01-01

    Real-time nucleic acid sequence-based amplification (NASBA) is an isothermal method specifically designed for amplification of RNA. Fluorescent molecular beacon probes enable real-time monitoring of the amplification process. Successful identification, utilizing the real-time NASBA technology, was performed on a microchip with oligonucleotides at a concentration of 1.0 and 0.1 microM, in 10- and 50-nL reaction chambers, respectively. The microchip was developed in a silicon-glass structure. An instrument providing thermal control and an optical detection system was built for amplification readout. Experimental results demonstrate distinct amplification processes. Miniaturized real-time NASBA in microchips makes high-throughput diagnostics of bacteria, viruses, and cancer markers possible, at reduced cost and without contamination.

  13. Ames Lab 101: Real-Time 3D Imaging

    ScienceCinema

    Zhang, Song

    2016-07-12

    Ames Laboratory scientist Song Zhang explains his real-time 3-D imaging technology. The technique can be used to create high-resolution, real-time, precise, 3-D images for use in healthcare, security, and entertainment applications.

  14. Ames Lab 101: Real-Time 3D Imaging

    SciTech Connect

    Zhang, Song

    2010-01-01

    Ames Laboratory scientist Song Zhang explains his real-time 3-D imaging technology. The technique can be used to create high-resolution, real-time, precise, 3-D images for use in healthcare, security, and entertainment applications.

  15. Semi-device-independent security of one-way quantum key distribution

    SciTech Connect

    Pawlowski, Marcin; Brunner, Nicolas

    2011-07-15

    By testing nonlocality, the security of entanglement-based quantum key distribution (QKD) can be enhanced to being ''device-independent.'' Here we ask whether such a strong form of security could also be established for one-way (prepare and measure) QKD. While fully device-independent security is impossible, we show that security can be guaranteed against individual attacks in a semi-device-independent scenario. In the latter, the devices used by the trusted parties are noncharacterized, but the dimensionality of the quantum systems used in the protocol is assumed to be bounded. Our security proof relies on the analogies between one-way QKD, dimension witnesses, and random-access codes.

  16. The enhanced measurement-device-independent quantum key distribution with two-intensity decoy states

    NASA Astrophysics Data System (ADS)

    Zhu, Jian-Rong; Zhu, Feng; Zhou, Xing-Yu; Wang, Qin

    2016-09-01

    We put forward a new scheme for implementing the measurement-device-independent quantum key distribution (QKD) with weak coherent source, while using only two different intensities. In the new scheme, we insert a beam splitter and a local detector at both Alice's and Bob's side, and then all the triggering and non-triggering signals could be employed to process parameter estimations, resulting in very precise estimations for the two-single-photon contributions. Besides, we compare its behavior with two other often used methods, i.e., the conventional standard three-intensity decoy-state measurement-device-independent QKD and the passive measurement-device-independent QKD. Through numerical simulations, we demonstrate that our new approach can exhibit outstanding characteristics not only in the secure transmission distance, but also in the final key generation rate.

  17. Comment on "Device-independent entanglement-based Bennett 1992 protocol"

    NASA Astrophysics Data System (ADS)

    Tan, Yong-gang; Cai, Qing-yu

    2016-06-01

    Recently, Lucamarini et al. proposed the device-independent entanglement-based Bennett 1992 protocol [Phys. Rev. A 86, 032325 (2012), 10.1103/PhysRevA.86.032325]. By exploiting the results in device-independent quantum key distribution with the Clauser-Horne-Shimony-Holt inequality, they claimed the security of their protocol. We will show, however, the way of encoding and the process for the latent eavesdropper to obtain the illegal information are different in these two protocols. Thus the security of their protocol cannot rely on Bell's theorem only.

  18. Real-time support for high performance aircraft operation

    NASA Technical Reports Server (NTRS)

    Vidal, Jacques J.

    1989-01-01

    The feasibility of real-time processing schemes using artificial neural networks (ANNs) is investigated. A rationale for digital neural nets is presented and a general processor architecture for control applications is illustrated. Research results on ANN structures for real-time applications are given. Research results on ANN algorithms for real-time control are also shown.

  19. Apparatus Characterizes Transient Voltages in Real Time

    NASA Technical Reports Server (NTRS)

    Medelius, Pedro

    2005-01-01

    is received, a volatile memory is filled with data for a total time of 200 ms. After the data are transferred to nonvolatile memory, the recorder rearms itself within 400 ms to enable recording of subsequent transients. Unfortunately, the recorded data must be retrieved through a serial communication link. Depending on the amount of data recorded, the memory can be filled before retrieval is completed. Although large amounts of data are recorded and retrieved, only a small part of the information (the selected parameters) is usually required. The present transient-voltage recorder provides the required information, without incurring the overhead associated with the recording, storage, and retrieval of complete transient-waveform data. In operation, this apparatus processes transient voltage waveforms in real time to extract and record the selected parameters. An analog-to-digital converter that operates at a speed of as much as 100 mega-samples per second is used to sample a transient waveform. A real-time comparator and peak detector are implemented by use of fast field-programmable gate arrays.

  20. Public Science with Real-Time Experiments

    NASA Astrophysics Data System (ADS)

    Lenardic, A.

    2013-12-01

    One of the best ways for professional scientists to engage in public outreach is to get outside of the university and/or lab walls and go out into the public. That is, go to public spaces to do some science experiments with the public - this includes students of all ages that constitute that public. Technological advance in portable measurement gear now allow one to do real, or near real, time experiments in outdoor, public spaces. We have been running a meta-experiment of this sort, aimed at the public display of science, for about a year now in Houston TX at the Lee and Joe Jamail Skatepark. The project goes under the title of Sk8Lab Houston and has introduced students of all ages to the power of scientific experimentation. We bring a portable science pack with us to the park. The pack has a range of wireless measurement gear that allow experiments to be done on the spot. Some of the experiments are designed by us but many are designed on by whoever suggests them to us that day. Over time the Sk8Lab scientists have built up a level of "trust" with the people who frequent the park (no one feels like we are gonna grade them at the park and they know that the learning is not on some regimented clock). This has broken down some learning walls and allowed for a more informal mode of exploration and a more genuine mode of experimentation (as compared to what often happens in class labs when students feel like they are just being forced to reproduce some known result). We will describe some of the test case experiments we have run and also discuss some of the trials, tribulations, and happy successes (many unplanned) along the way.

  1. Real-Time Feature Tracking Using Homography

    NASA Technical Reports Server (NTRS)

    Clouse, Daniel S.; Cheng, Yang; Ansar, Adnan I.; Trotz, David C.; Padgett, Curtis W.

    2010-01-01

    This software finds feature point correspondences in sequences of images. It is designed for feature matching in aerial imagery. Feature matching is a fundamental step in a number of important image processing operations: calibrating the cameras in a camera array, stabilizing images in aerial movies, geo-registration of images, and generating high-fidelity surface maps from aerial movies. The method uses a Shi-Tomasi corner detector and normalized cross-correlation. This process is likely to result in the production of some mismatches. The feature set is cleaned up using the assumption that there is a large planar patch visible in both images. At high altitude, this assumption is often reasonable. A mathematical transformation, called an homography, is developed that allows us to predict the position in image 2 of any point on the plane in image 1. Any feature pair that is inconsistent with the homography is thrown out. The output of the process is a set of feature pairs, and the homography. The algorithms in this innovation are well known, but the new implementation improves the process in several ways. It runs in real-time at 2 Hz on 64-megapixel imagery. The new Shi-Tomasi corner detector tries to produce the requested number of features by automatically adjusting the minimum distance between found features. The homography-finding code now uses an implementation of the RANSAC algorithm that adjusts the number of iterations automatically to achieve a pre-set probability of missing a set of inliers. The new interface allows the caller to pass in a set of predetermined points in one of the images. This allows the ability to track the same set of points through multiple frames.

  2. Real time monitoring of electroless nickel plating

    NASA Astrophysics Data System (ADS)

    Rains, Aaron E.; Kline, Ronald A.

    2013-01-01

    This work deals with the design and manufacturing of the heat and chemical resistant transducer case required for on-line immersion testing, experimental design, data acquisition and signal processing. Results are presented for several depositions with an accuracy of two ten-thousandths of an inch in coating thickness obtained. Monitoring the deposition rate of Electroless Nickel (EN) plating in-situ will provide measurement of the accurate dimensions of the component being plated, in real time. EN is used as for corrosion and wear protection for automotive an - Electroless Nickel (EN) plating is commonly used for corrosion and wear protection for automotive and aerospace components. It plates evenly and symmetrically, theoretically allowing the part to be plated to its final dimension. Currently the standard approach to monitoring the thickness of the deposited nickel is to remove the component from the plating bath and physically measure the part. This can lead to plating problems such as pitting, non-adhesion of the deposit and contamination of the plating solution. The goal of this research effort is to demonstrate that plating thickness can be rapidly and accurately measured using ultrasonic testing. Here a special housing is designed to allow immersion of the ultrasonic transducers directly into the plating bath. An FFT based signal processing algorithm was developed to resolve closely spaced echoes for precise thickness determination. The technique in this research effort was found to be capable of measuring plating thicknesses to within 0.0002 inches. It is expected that this approach will lead to cost savings in many EN plating operations.

  3. A real-time prediction of UTC

    NASA Technical Reports Server (NTRS)

    Thomas, Claudine; Allan, David W.

    1994-01-01

    The reference time scale for all scientific and technologic applications on the Earth, the Universal Coordinated Time (UTC), must be as stable, reliable, and accurate as possible. With this in view the BIPM and before it the BIH, have always calculated and then disseminated UTC with a delay of about 80 days. There are three fundamental reasons for doing this: (1) It takes some weeks for data, gathered from some 200 clocks spread world-wide, to be collected and for errors to be eliminated; (2) changes in clock rates can only be measured with high precision well after the fact; and (3) the measurement noise originating in time links, in particular using Loran-C, is smoothed out only when averaging over an extended period. Until mid-1992, the ultimate stability of UTC was reached at averaging times of about 100 days and corresponded to an Allan deviation sigma(sub y)(tau) of about 1,5x10(exp -14) then compared to the best primary clock in the world, the PTB CS2. For several years now, a predicted UTC has been computed by the USNO through an extrapolation of the values as published in deferred time by the BIPM. This is made available through the USNO Series 4, through the USNO Automated Data Service, and through GPS signals. Due to the instability of UTC, the poor predictability of the available clocks, and the intentional SA degradation of GPS signals, the real-time access to this extrapolated UTC has represented the true deferred-time UTC only to within several hundreds of nanoseconds.

  4. Real time PV manufacturing diagnostic system

    SciTech Connect

    Kochergin, Vladimir; Crawford, Michael A.

    2015-09-01

    The main obstacle Photovoltaic (PV) industry is facing at present is the higher cost of PV energy compared to that of fossil energy. While solar cell efficiencies continue to make incremental gains these improvements are so far insufficient to drive PV costs down to match that of fossil energy. Improved in-line diagnostics however, has the potential to significantly increase the productivity and reduce cost by improving the yield of the process. On this Phase I/Phase II SBIR project MicroXact developed and demonstrated at CIGS pilot manufacturing line a high-throughput in-line PV manufacturing diagnostic system, which was verified to provide fast and accurate data on the spatial uniformity of thickness, an composition of the thin films comprising the solar cell as the solar cell is processed reel-to-reel. In Phase II project MicroXact developed a stand-alone system prototype and demonstrated the following technical characteristics: 1) ability of real time defect/composition inconsistency detection over 60cm wide web at web speeds up to 3m/minute; 2) Better than 1mm spatial resolution on 60cm wide web; 3) an average better than 20nm spectral resolution resulting in more than sufficient sensitivity to composition imperfections (copper-rich and copper-poor regions were detected). The system was verified to be high vacuum compatible. Phase II results completely validated both technical and economic feasibility of the proposed concept. MicroXact’s solution is an enabling technique for in-line PV manufacturing diagnostics to increase the productivity of PV manufacturing lines and reduce the cost of solar energy, thus reducing the US dependency on foreign oil while simultaneously reducing emission of greenhouse gasses.

  5. Practical Real-Time Imaging Stereo Matcher

    NASA Astrophysics Data System (ADS)

    Nishihara, H. K.

    1984-10-01

    A binocular-stereo-matching algorithm for making rapid visual range measurements in noisy images is described. This technique is developed for application to problems in robotics where noise tolerance, reliability, and speed are predominant issues. A high speed pipelined convolver for preprocessing images and an unstructured light technique for improving signal quality are introduced to help enhance performance to meet the demands of this task domain. These optimizations, however, are not sufficient. A closer examination of the problems encountered suggests that broader interpretations of both the objective of binocular stereo and of the zero-crossing theory of Marr and Poggio [Proc. R. Soc. Lond. B 204, 301 (1979)] are required. In this paper, we restrict ourselves to the problem of making a single primitive surface measurement for example, to determine whether or not a specified volume of space is occupied, to measure the range to a surface at an indicated image location, or to determine the elevation gradient at that position. In this framework we make a subtle but important shift from the explicit use of zero-crossing contours (in bandpass-filtered images) as the elements matched between left and right images, to the use of the signs between zero crossings. With this change, we obtain a simpler algorithm with a reduced sensitivity to noise and a more predictable behavior. The practical real-time imaging stereo matcher (PRISM) system incorporates this algorithm with the unstructured light technique and a high speed digital convolver. It has been used successfully by others as a sensor in a path-planning system and a bin-picking system.

  6. Satellite clock corrections estimation to accomplish real time ppp: experiments for brazilian real time network

    NASA Astrophysics Data System (ADS)

    Marques, Haroldo; Monico, João; Aquino, Marcio; Melo, Weyller

    2014-05-01

    The real time PPP method requires the availability of real time precise orbits and satellites clocks corrections. Currently, it is possible to apply the solutions of clocks and orbits available by BKG within the context of IGS Pilot project or by using the operational predicted IGU ephemeris. The accuracy of the satellite position available in the IGU is enough for several applications requiring good quality. However, the satellites clocks corrections do not provide enough accuracy (3 ns ~ 0.9 m) to accomplish real time PPP with the same level of accuracy. Therefore, for real time PPP application it is necessary to further research and develop appropriated methodologies for estimating the satellite clock corrections in real time with better accuracy. Currently, it is possible to apply the real time solutions of clocks and orbits available by Federal Agency for Cartography and Geodesy (BKG) within the context of IGS Pilot project. The BKG corrections are disseminated by a new proposed format of the RTCM 3.x and can be applied in the broadcasted orbits and clocks. Some investigations have been proposed for the estimation of the satellite clock corrections using GNSS code and phase observable at the double difference level between satellites and epochs (MERVAT, DOUSA, 2007). Another possibility consists of applying a Kalman Filter in the PPP network mode (HAUSCHILD, 2010) and it is also possible the integration of both methods, using network PPP and observables at double difference level in specific time intervals (ZHANG; LI; GUO, 2010). For this work the methodology adopted consists in the estimation of the satellite clock corrections based on the data adjustment in the PPP mode, but for a network of GNSS stations. The clock solution can be solved by using two types of observables: code smoothed by carrier phase or undifferenced code together with carrier phase. In the former, we estimate receiver clock error; satellite clock correction and troposphere, considering

  7. Instrumentation development for real time brainwave monitoring.

    SciTech Connect

    Anderson, Lawrence Frederick; Clough, Benjamin W.

    2005-12-01

    The human brain functions through a chemically-induced biological process which operates in a manner similar to electrical systems. The signal resulting from this biochemical process can actually be monitored and read using tools and having patterns similar to those found in electrical and electronics engineering. The primary signature of this electrical activity is the ''brain wave'', which looks remarkably similar to the output of many electrical systems. Likewise, the device currently used in medical arenas to read brain electrical activity is the electroencephalogram (EEG) which is synonymous with a multi-channel oscilloscope reading. Brain wave readings and recordings for medical purposes are traditionally taken in clinical settings such as hospitals, laboratories or diagnostic clinics. The signal is captured via externally applied scalp electrodes using semi-viscous gel to reduce impedance. The signal will be in the 10 to 100 microvolt range. In other instances, where surgeons are attempting to isolate particular types of minute brain signals, the electrodes may actually be temporarily implanted in the brain during a preliminary procedure. The current configurations of equipment required for EEGs involve large recording instruments, many electrodes, wires, and large amounts of hard disk space devoted to storing large files of brain wave data which are then eventually analyzed for patterns of concern. Advances in sensors, signal processing, data storage and microelectronics over the last decade would seem to have paved the way for the realization of devices capable of ''real time'' external monitoring, and possible assessment, of brain activity. A myriad of applications for such a capability are likewise presenting themselves, including the ability to assess brain functioning, level of functioning and malfunctioning. Our plan is to develop the sensors, signal processing, and portable instrumentation package which could capture, analyze, and communicate

  8. Real Time Wide Area Radiation Surveillance System

    NASA Astrophysics Data System (ADS)

    Biafore, M.

    2012-04-01

    We present the REWARD project, financed within the FP7 programme, theme SEC-2011.1.5-1 (Development of detection capabilities of difficult to detect radioactive sources and nuclear materials - Capability Project). Within this project, we propose a novel mobile system for real time, wide area radiation surveillance. The system is based on the integration of new miniaturized solid-state radiation sensors: a CdZnTe detector for gamma radiation and a high efficiency neutron detector based on novel silicon technologies. The sensing unit will include a wireless communication interface to send the data remotely to a monitoring base station which also uses a GPS system to calculate the position of the tag. The system will also incorporate middleware and high level software to provide web-service interfaces for the exchange of information, and that will offer top level functionalities as management of users, mobile tags and environment data and alarms, database storage and management and a web-based graphical user interface. Effort will be spent to ensure that the software is modular and re-usable across as many architectural levels as possible. Finally, an expert system will continuously analyze the information from the radiation sensor and correlate it with historical data from the tag location in order to generate an alarm when an abnormal situation is detected. The system will be useful for many different scenarios, including such lost radioactive sources and radioactive contamination. It will be possible to deploy in emergency units and in general in any type of mobile or static equipment. The sensing units will be highly portable thanks to their low size and low energy consumption. The complete system will be scalable in terms of complexity and cost and will offer very high precision on both the measurement and the location of the radiation. The modularity and flexibility of the system will allow for a realistic introduction to the market. Authorities may start with a

  9. Real-time Forensic Disaster Analysis

    NASA Astrophysics Data System (ADS)

    Wenzel, F.; Daniell, J.; Khazai, B.; Mühr, B.; Kunz-Plapp, T.; Markus, M.; Vervaeck, A.

    2012-04-01

    The Center for Disaster Management and Risk Reduction Technology (CEDIM, www.cedim.de) - an interdisciplinary research center founded by the German Research Centre for Geoscience (GFZ) and Karlsruhe Institute of Technology (KIT) - has embarked on a new style of disaster research known as Forensic Disaster Analysis. The notion has been coined by the Integrated Research on Disaster Risk initiative (IRDR, www.irdrinternational.org) launched by ICSU in 2010. It has been defined as an approach to studying natural disasters that aims at uncovering the root causes of disasters through in-depth investigations that go beyond the reconnaissance reports and case studies typically conducted after disasters. In adopting this comprehensive understanding of disasters CEDIM adds a real-time component to the assessment and evaluation process. By comprehensive we mean that most if not all relevant aspects of disasters are considered and jointly analysed. This includes the impact (human, economy, and infrastructure), comparisons with recent historic events, social vulnerability, reconstruction and long-term impacts on livelihood issues. The forensic disaster analysis research mode is thus best characterized as "event-based research" through systematic investigation of critical issues arising after a disaster across various inter-related areas. The forensic approach requires (a) availability of global data bases regarding previous earthquake losses, socio-economic parameters, building stock information, etc.; (b) leveraging platforms such as the EERI clearing house, relief-web, and the many sources of local and international sources where information is organized; and (c) rapid access to critical information (e.g., crowd sourcing techniques) to improve our understanding of the complex dynamics of disasters. The main scientific questions being addressed are: What are critical factors that control loss of life, of infrastructure, and for economy? What are the critical interactions

  10. Natural Framework for Device-Independent Quantification of Quantum Steerability, Measurement Incompatibility, and Self-Testing

    NASA Astrophysics Data System (ADS)

    Chen, Shin-Liang; Budroni, Costantino; Liang, Yeong-Cherng; Chen, Yueh-Nan

    2016-06-01

    We introduce the concept of assemblage moment matrices, i.e., a collection of matrices of expectation values, each associated with a conditional quantum state obtained in a steering experiment. We demonstrate how it can be used for quantum states and measurements characterization in a device-independent manner, i.e., without invoking any assumption about the measurement or the preparation device. Specifically, we show how the method can be used to lower bound the steerability of an underlying quantum state directly from the observed correlation between measurement outcomes. Combining such device-independent quantifications with earlier results established by Piani and Watrous [Phys. Rev. Lett. 114, 060404 (2015)], our approach immediately provides a device-independent lower bound on the generalized robustness of entanglement, as well as the usefulness of the underlying quantum state for a type of subchannel discrimination problem. In addition, by proving a quantitative relationship between steering robustness and the recently introduced incompatibility robustness, our approach also allows for a device-independent quantification of the incompatibility between various measurements performed in a Bell-type experiment. Explicit examples where such bounds provide a kind of self-testing of the performed measurements are provided.

  11. Device Independent Layout and Style Editing Using Multi-Level Style Sheets

    NASA Astrophysics Data System (ADS)

    Dees, Walter

    This paper describes a layout and styling framework that is based on the multi-level style sheets approach. It shows some of the techniques that can be used to add layout and style information to a UI in a device-independent manner, and how to reuse the layout and style information to create user interfaces for different devices

  12. A Real-Time Groundwater Management Model Using Data Assimilation

    NASA Astrophysics Data System (ADS)

    Cheng, W.; Putti, M.; Kendall, D.; Yeh, W. W.

    2009-12-01

    This study develops a groundwater management model for real time operation of an aquifer system. A groundwater flow model is allied with a nudging data assimilation algorithm that reduces the forecast error, minimizes the risk of system failure, and improves management strategies. The nudging algorithm treats the unknown private pumping as an additional sink term in the groundwater flow equations and provides a consistently physical interpretation for pumping rates identification. The response of the groundwater simulation model due to pumping/injection is represented by a response matrix which is generated by the influence coefficient method. The response matrix with a much smaller dimension (referred to as the reduced simulation model) is directly embedded in the management model as a part of the constraint set. Additionally, the influence coefficient method is utilized to include the nudging effect as additional terms in the reduced simulation model. The management model optimizes monthly operational policy for 12 months into the future with given initial condition and system constraints. We apply the developed management model to the Aquifer Storage and Recovery (ASR) project of the Las Posas Groundwater Basin in southern California. We consider both the injection and pumping scenarios. In the case studies, six unknown pumping rates from private wells are estimated using measured heads from four observation wells. The management model determines the optimal operational strategies using the information provided by nudging and is updated at the beginning of each month when new head observations become available. We also discuss the utility, accuracy, and efficiency of the proposed management model for real time operation.

  13. Real-time, portable genome sequencing for Ebola surveillance

    PubMed Central

    Bore, Joseph Akoi; Koundouno, Raymond; Dudas, Gytis; Mikhail, Amy; Ouédraogo, Nobila; Afrough, Babak; Bah, Amadou; Baum, Jonathan HJ; Becker-Ziaja, Beate; Boettcher, Jan-Peter; Cabeza-Cabrerizo, Mar; Camino-Sanchez, Alvaro; Carter, Lisa L.; Doerrbecker, Juiliane; Enkirch, Theresa; Dorival, Isabel Graciela García; Hetzelt, Nicole; Hinzmann, Julia; Holm, Tobias; Kafetzopoulou, Liana Eleni; Koropogui, Michel; Kosgey, Abigail; Kuisma, Eeva; Logue, Christopher H; Mazzarelli, Antonio; Meisel, Sarah; Mertens, Marc; Michel, Janine; Ngabo, Didier; Nitzsche, Katja; Pallash, Elisa; Patrono, Livia Victoria; Portmann, Jasmine; Repits, Johanna Gabriella; Rickett, Natasha Yasmin; Sachse, Andrea; Singethan, Katrin; Vitoriano, Inês; Yemanaberhan, Rahel L; Zekeng, Elsa G; Trina, Racine; Bello, Alexander; Sall, Amadou Alpha; Faye, Ousmane; Faye, Oumar; Magassouba, N’Faly; Williams, Cecelia V.; Amburgey, Victoria; Winona, Linda; Davis, Emily; Gerlach, Jon; Washington, Franck; Monteil, Vanessa; Jourdain, Marine; Bererd, Marion; Camara, Alimou; Somlare, Hermann; Camara, Abdoulaye; Gerard, Marianne; Bado, Guillaume; Baillet, Bernard; Delaune, Déborah; Nebie, Koumpingnin Yacouba; Diarra, Abdoulaye; Savane, Yacouba; Pallawo, Raymond Bernard; Gutierrez, Giovanna Jaramillo; Milhano, Natacha; Roger, Isabelle; Williams, Christopher J; Yattara, Facinet; Lewandowski, Kuiama; Taylor, Jamie; Rachwal, Philip; Turner, Daniel; Pollakis, Georgios; Hiscox, Julian A.; Matthews, David A.; O’Shea, Matthew K.; Johnston, Andrew McD; Wilson, Duncan; Hutley, Emma; Smit, Erasmus; Di Caro, Antonino; Woelfel, Roman; Stoecker, Kilian; Fleischmann, Erna; Gabriel, Martin; Weller, Simon A.; Koivogui, Lamine; Diallo, Boubacar; Keita, Sakoba; Rambaut, Andrew; Formenty, Pierre; Gunther, Stephan; Carroll, Miles W.

    2016-01-01

    The Ebola virus disease (EVD) epidemic in West Africa is the largest on record, responsible for >28,599 cases and >11,299 deaths 1. Genome sequencing in viral outbreaks is desirable in order to characterize the infectious agent to determine its evolutionary rate, signatures of host adaptation, identification and monitoring of diagnostic targets and responses to vaccines and treatments. The Ebola virus genome (EBOV) substitution rate in the Makona strain has been estimated at between 0.87 × 10−3 to 1.42 × 10−3 mutations per site per year. This is equivalent to 16 to 27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic 2-7. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought-after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions 8. Genomic surveillance during the epidemic has been sporadic due to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities 9. In order to address this problem, we devised a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. Here we present sequence data and analysis of 142 Ebola virus (EBOV) samples collected during the period March to October 2015. We were able to generate results in less than 24 hours after receiving an Ebola positive sample, with the sequencing process taking as little as 15-60 minutes. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks. PMID:26840485

  14. A Real-Time Screening Alert Improves Patient Recruitment Efficiency

    PubMed Central

    Weng, Chunhua; Batres, Candido; Borda, Tomas; Weiskopf, Nicole G.; Wilcox, Adam B.; Bigger, J Thomas; Davidson, Karina W.

    2011-01-01

    The scarcity of cost-effective patient identification methods represents a significant barrier to clinical research. Research recruitment alerts have been designed to facilitate physician referrals but limited support is available to clinical researchers. We conducted a retrospective data analysis to evaluate the efficacy of a real-time patient identification alert delivered to clinical research coordinators recruiting for a clinical prospective cohort study. Data from log analysis and informal interviews with coordinators were triangulated. Over a 12-month period, 11,295 were screened electronically, 1,449 were interviewed, and 282 were enrolled. The enrollment rates for the alert and two other conventional methods were 4.65%, 2.01%, and 1.34% respectively. A taxonomy of eligibility status was proposed to precisely categorize research patients. Practical ineligibility factors were identified and their correlation with age and gender were analyzed. We conclude that the automatic prescreening alert improves screening efficiency and is an effective aid to clinical research coordinators. PMID:22195213

  15. Real-time application of the Rat Grimace Scale as a welfare refinement in laboratory rats

    PubMed Central

    Leung, Vivian; Zhang, Emily; Pang, Daniel SJ

    2016-01-01

    Rodent grimace scales have been recently validated for pain assessment, allowing evaluation of facial expressions associated with pain. The standard scoring method is retrospective, limiting its application beyond pain research. This study aimed to assess if real-time application of the Rat Grimace Scale (RGS) could reliably and accurately assess pain in rats when compared to the standard method. Thirty-two male and female Sprague-Dawley rats were block randomized into three treatment groups: buprenorphine (0.03 mg/kg, subcutaneously), multimodal analgesia (buprenorphine [0.03 mg/kg] and meloxicam [2 mg/kg], subcutaneously), or saline, followed by intra-plantar carrageenan. Real-time observations (interval and point) were compared to the standard RGS method using concurrent video-recordings. Real-time interval observations reflected the results from the standard RGS method by successfully discriminating between analgesia and saline treatments. Real-time point observations showed poor discrimination between treatments. Real-time observations showed minimal bias (<0.1) and acceptable limits of agreement. These results indicate that applying the RGS in real-time through an interval scoring method is feasible and effective, allowing refinement of laboratory rat welfare through rapid identification of pain and early intervention. PMID:27530823

  16. Development of a cyber-physical experimental platform for real-time dynamic model updating

    NASA Astrophysics Data System (ADS)

    Song, Wei; Dyke, Shirley

    2013-05-01

    Model updating procedures are traditionally performed off-line. With the significant recent advances in embedded systems and the related real-time computing capabilities, online or real-time, model updating can be performed to inform decision making and controller actions. The applications for real-time model updating are mainly in the areas of (i) condition diagnosis and prognosis of engineering systems; and (ii) control systems that benefit from accurate modeling of the system plant. Herein, the development of a cyber-physical real-time model updating experimental platform, including real-time computing environment, model updating algorithm, hardware architecture and testbed, is described. Results from two challenging experimental implementations are presented to illustrate the performance of this cyber-physical platform in achieving the goal of updating nonlinear systems in real-time. The experiments consider typical nonlinear engineering systems that exhibit hysteresis. Among the available algorithms capable of identification of such complex nonlinearities, the unscented Kalman filter (UKF) is selected for these experiments as an effective method to update nonlinear dynamic system models under realistic conditions. The implementation of the platform is discussed for successful completion of these experiments, including required timing constraints and overall evaluation of the system.

  17. Real-time application of the Rat Grimace Scale as a welfare refinement in laboratory rats.

    PubMed

    Leung, Vivian; Zhang, Emily; Pang, Daniel Sj

    2016-01-01

    Rodent grimace scales have been recently validated for pain assessment, allowing evaluation of facial expressions associated with pain. The standard scoring method is retrospective, limiting its application beyond pain research. This study aimed to assess if real-time application of the Rat Grimace Scale (RGS) could reliably and accurately assess pain in rats when compared to the standard method. Thirty-two male and female Sprague-Dawley rats were block randomized into three treatment groups: buprenorphine (0.03 mg/kg, subcutaneously), multimodal analgesia (buprenorphine [0.03 mg/kg] and meloxicam [2 mg/kg], subcutaneously), or saline, followed by intra-plantar carrageenan. Real-time observations (interval and point) were compared to the standard RGS method using concurrent video-recordings. Real-time interval observations reflected the results from the standard RGS method by successfully discriminating between analgesia and saline treatments. Real-time point observations showed poor discrimination between treatments. Real-time observations showed minimal bias (<0.1) and acceptable limits of agreement. These results indicate that applying the RGS in real-time through an interval scoring method is feasible and effective, allowing refinement of laboratory rat welfare through rapid identification of pain and early intervention. PMID:27530823

  18. Fecal Source Identification with Real-Time Quantitative PCR

    EPA Science Inventory

    Waterborne diseases that originate from fecal pollution remain a significant public health issue. Current fecal indicator technologies recommended by the U.S. Environmental Protection Agency for water quality testing do not discriminate between different animal sources of fecal ...

  19. DEVELOPMENT OF A REAL-TIME FLUORESCENCE RESONANCE ENERGY TRANSFER (FRET) PCR TO DETECT ARCOBACTER SPECIES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A real-time PCR targeting the gyrase A subunit gene outside the quinolone resistance-determining region has been developed to detect Arcobacter species. The species identification was made by probe hybridization and melting curve analysis, using the Fluorescence Resonance Energy Transfer technology...

  20. DEVELOPMENT OF A REAL-TIME FLUORESCENCE RESONANCE ENERGY TRANSFER PCR TO DETECT ARCOBACTER SPECIES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A real-time PCR targeting the gyrase A subunit gene outside the quinolone resistance-determining region has been developed to detect Arcobacter species. The species identification was made by probe hybridization and melting curve analysis, using Fluorescence Resonance Energy Transfer technology. D...

  1. Identifying Haemophilus haemolyticus and Haemophilus influenzae by SYBR Green real-time PCR.

    PubMed

    Latham, Roger; Zhang, Bowen; Tristram, Stephen

    2015-05-01

    SYBR Green real time PCR assays for protein D (hpd), fuculose kinase (fucK) and [Cu, Zn]-superoxide dismutase (sodC) were designed for use in an algorithm for the identification of Haemophilus influenzae and H. haemolyticus. When tested on 127 H. influenzae and 60 H. haemolyticus all isolates were identified correctly. PMID:25753676

  2. Interlaboratory Comparison of Real-time PCR Protocols for Quantification of General Fecal Indicator Bacteria

    EPA Science Inventory

    The application of quantitative real-time PCR (qPCR) technologies for the rapid identification of fecal bacteria in environmental waters is being considered for use as a national water quality metric in the United States. The transition from research tool to a standardized proto...

  3. Real time UAV autonomy through offline calculations

    NASA Astrophysics Data System (ADS)

    Jung, Sunghun

    . Once one or several targets are detected, UAVs near the target are manipulated to approach to the target. If the number of detected targets is more than one, UAVs are evenly grouped to track targets. After a specific period of time, UAVs hand off and continue their original tasks. Thirdly, Emergency algorithm is generated to avoid losses of UAVs when UAVs have system failures. If one UAV is out of fuel or control during the mission, the Emergency algorithm brings the malfunctioning UAV to the point of departure and let the rest UAVs to continue an aerial reconnaissance. An UAV which finishes its task the earliest will continue to search a region which the failed UAV is supposed to search. In addition, Emergency algorithm prevents UAVs colliding into each other by using emergency altitude. Overall, the framework developed here facilitates the solution of several mission planning problems. The robustness built into our discretization of space and time permits feedback corrections on real-time to vehicle trajectories. The library of off-line solutions proposed and developed here minimizes computational overhead during operations.

  4. Real Time Flux Control in PM Motors

    SciTech Connect

    Otaduy, P.J.

    2005-09-27

    Significant research at the Oak Ridge National Laboratory (ORNL) Power Electronics and Electric Machinery Research Center (PEEMRC) is being conducted to develop ways to increase (1) torque, (2) speed range, and (3) efficiency of traction electric motors for hybrid electric vehicles (HEV) within existing current and voltage bounds. Current is limited by the inverter semiconductor devices' capability and voltage is limited by the stator wire insulation's ability to withstand the maximum back-electromotive force (emf), which occurs at the upper end of the speed range. One research track has been to explore ways to control the path and magnitude of magnetic flux while the motor is operating. The phrase, real time flux control (RTFC), refers to this mode of operation in which system parameters are changed while the motor is operating to improve its performance and speed range. RTFC has potential to meet an increased torque demand by introducing additional flux through the main air gap from an external source. It can augment the speed range by diverting flux away from the main air gap to reduce back-emf at high speeds. Conventional RTFC technology is known as vector control [1]. Vector control decomposes the stator current into two components; one that produces torque and a second that opposes (weakens) the magnetic field generated by the rotor, thereby requiring more overall stator current and reducing the efficiency. Efficiency can be improved by selecting a RTFC method that reduces the back-emf without increasing the average current. This favors methods that use pulse currents or very low currents to achieve field weakening. Foremost in ORNL's effort to develop flux control is the work of J. S. Hsu. Early research [2,3] introduced direct control of air-gap flux in permanent magnet (PM) machines and demonstrated it with a flux-controlled generator. The configuration eliminates the problem of demagnetization because it diverts all the flux from the magnets instead of

  5. Real-Time Wireless Data Acquisition System

    NASA Technical Reports Server (NTRS)

    Valencia, Emilio J.; Perotti, Jose; Lucena, Angel; Mata, Carlos

    2007-01-01

    Current and future aerospace requirements demand the creation of a new breed of sensing devices, with emphasis on reduced weight, power consumption, and physical size. This new generation of sensors must possess a high degree of intelligence to provide critical data efficiently and in real-time. Intelligence will include self-calibration, self-health assessment, and pre-processing of raw data at the sensor level. Most of these features are already incorporated in the Wireless Sensors Network (SensorNet(TradeMark)), developed by the Instrumentation Group at Kennedy Space Center (KSC). A system based on the SensorNet(TradeMark) architecture consists of data collection point(s) called Central Stations (CS) and intelligent sensors called Remote Stations (RS) where one or more CSs can be accommodated depending on the specific application. The CS's major function is to establish communications with the Remote Stations and to poll each RS for data and health information. The CS also collects, stores and distributes these data to the appropriate systems requiring the information. The system has the ability to perform point-to-point, multi-point and relay mode communications with an autonomous self-diagnosis of each communications link. Upon detection of a communication failure, the system automatically reconfigures to establish new communication paths. These communication paths are automatically and autonomously selected as the best paths by the system based on the existing operating environment. The data acquisition system currently under development at KSC consists of the SensorNet(TradeMark) wireless sensors as the remote stations and the central station called the Radio Frequency Health Node (RFHN). The RFF1N is the central station which remotely communicates with the SensorNet(TradeMark) sensors to control them and to receive data. The system's salient feature is the ability to provide deterministic sensor data with accurate time stamps for both time critical and non

  6. Real-time forensic DNA analysis at a crime scene using a portable microchip analyzer.

    PubMed

    Liu, Peng; Yeung, Stephanie H I; Crenshaw, Karin A; Crouse, Cecelia A; Scherer, James R; Mathies, Richard A

    2008-09-01

    An integrated lab-on-a-chip system has been developed and successfully utilized for real-time forensic short tandem repeat (STR) analysis. The microdevice comprises a 160-nL polymerase chain reaction reactor with an on-chip heater and a temperature sensor for thermal cycling, microvalves for fluidic manipulation, a co-injector for sizing standard injection, and a 7-cm-long separation channel for capillary electrophoretic analysis. A 9-plex autosomal STR typing system consisting of amelogenin and eight combined DNA index system (CODIS) core STR loci has been constructed and optimized for this real-time human identification study. Reproducible STR profiles of control DNA samples are obtained in 2h and 30min with real-time STR analyses were carried out at a mock crime scene prepared by the Palm Beach County Sheriff's Office (PBSO). Blood stain sample collection, DNA extraction, and STR analyses on the portable microsystem were conducted in the field, and a successful "mock" CODIS hit was generated on the suspect's sample within 6h. This demonstration of on-site STR analysis establishes the feasibility of real-time DNA typing to identify the contributor of probative biological evidence at a crime scene and for real-time human identification.

  7. Easy and hard testbeds for real-time search algorithms

    SciTech Connect

    Koenig, S.; Simmons, R.G.

    1996-12-31

    Although researchers have studied which factors influence the behavior of traditional search algorithms, currently not much is known about how domain properties influence the performance of real-time search algorithms. In this paper we demonstrate, both theoretically and experimentally, that Eulerian state spaces (a super set of undirected state spaces) are very easy for some existing real-time search algorithms to solve: even real-time search algorithms that can be intractable, in general, are efficient for Eulerian state spaces. Because traditional real-time search testbeds (such as the eight puzzle and gridworlds) are Eulerian, they cannot be used to distinguish between efficient and inefficient real-time search algorithms. It follows that one has to use non-Eulerian domains to demonstrate the general superiority of a given algorithm. To this end, we present two classes of hard-to-search state spaces and demonstrate the performance of various real-time search algorithms on them.

  8. PERTS: A Prototyping Environment for Real-Time Systems

    NASA Technical Reports Server (NTRS)

    Liu, Jane W. S.; Lin, Kwei-Jay; Liu, C. L.

    1993-01-01

    PERTS is a prototyping environment for real-time systems. It is being built incrementally and will contain basic building blocks of operating systems for time-critical applications, tools, and performance models for the analysis, evaluation and measurement of real-time systems and a simulation/emulation environment. It is designed to support the use and evaluation of new design approaches, experimentations with alternative system building blocks, and the analysis and performance profiling of prototype real-time systems.

  9. Real-time and postprocessing holographic effects in dichromated pullulan.

    PubMed

    Savić, Svetlana; Pantelić, Dejan; Jakovijević, Dragica

    2002-08-01

    Experimental results concerning both real-time and postprocessing (after-development) behavior of a novel photosensitive material, dichromate-sensitized pullulan (DCP), are investigated. The exposure mechanism and possibilities for controlling holographic grating properties are discussed. We have shown that it is possible to maximize the diffraction efficiency of interference gratings after development by controlling diffraction efficiency in real time. Stronger real-time effects of DCP compared with those of dichromated gelatin are achieved. PMID:12153075

  10. Methods for real-time speech processing on Unix

    SciTech Connect

    Romberger, A.

    1982-01-01

    The author discusses computer programming done at the University of California, Berkeley, in support of research work in the area of speech analysis and synthesis. The purpose of this programming is to set up a system for doing real-time speech sampling using the Unix operating system. Two alternative approaches to real time work on Unix are discussed. The first approach is to do the real-time input/output on a secondary (satellite) machine that is not running Unix. The second approach is to do the real-time input/output on the main machine with the aid of special hardware.

  11. Investigation of a Real-time Processing System for the NASA Multifrequency Microwave Radiometer

    NASA Technical Reports Server (NTRS)

    1976-01-01

    A study was conducted to investigate the data reduction and processing requirements for the multifrequency microwave radiometer system (MFMR). The objectives were to develop and evaluate algorithms and processing techniques which might provide for dedicated real time or near real time data processing and to develop a configuration design and processor recommendation to accomplish the data reduction. An analysis of the required data reduction and calibration equations was included along with the identification of sources of error which may be present in the (MFMR) data. The definition and evaluation of the significance of effects introduced by aircraft perturbation was given.

  12. A new device-independent dimension witness and its experimental implementation

    NASA Astrophysics Data System (ADS)

    Cai, Yu; Bancal, Jean-Daniel; Romero, Jacquiline; Scarani, Valerio

    2016-07-01

    A dimension witness is a criterion that sets a lower bound on the dimension needed to reproduce the observed data. Three types of dimension witnesses can be found in the literature: device-dependent ones, in which the bound is obtained assuming some knowledge on the state and the measurements; device-independent prepare-and-measure ones, that can be applied to any system including classical ones; and device-independent Bell-based ones, that certify the minimal dimension of some entangled systems. Here we consider the Collins-Gisin-Linden-Massar-Popescu Bell-type inequality for four outcomes. We show that a sufficiently high violation of this inequality witnesses d≥slant 4 and present a proof-of-principle experimental observation of such a violation. This presents a first experimental violation of the third type of dimension witness beyond qutrits.

  13. Handheld Real-Time Volumetric Imaging of The Spine: Technology Development

    PubMed Central

    Tiouririne, Mohamed; Nguyen, Sarah; Hossack, John A.; Owen, Kevin; Mauldin, F. William

    2014-01-01

    Technical difficulties, poor image quality and reliance on pattern identifications represent some of the drawbacks of two-dimensional ultrasound imaging of spinal bone anatomy. To overcome these limitations, we sought to develop real-time volumetric imaging of the spine using a portable handheld device. The device measured 19.2 cm x 9.2 cm x 9.0 cm and imaged at 5 MHz center frequency. 2D imaging under conventional ultrasound and volumetric (3D) imaging in real time was achieved and verified by inspection using a custom spine phantom. Further device performance was assessed and revealed a 75-minute battery life and average frame rate of 17.7 Hz in volumetric imaging mode. Our results suggest that real-time volumetric imaging of the spine is a feasible technique for more intuitive visualization of the spine. These results may have important ramifications for a large array of neuraxial procedures. PMID:24446802

  14. The NASA Smart Probe Project for real-time multiple microsensor tissue recognition

    NASA Technical Reports Server (NTRS)

    Andrews, Russell J.; Mah, Robert W.

    2003-01-01

    BACKGROUND: Remote surgery requires automated sensors, effectors and sensor-effector communication. The NASA Smart Probe Project has focused on the sensor aspect. METHODS: The NASA Smart Probe uses neural networks and data from multiple microsensors for a unique tissue signature in real time. Animal and human trials use several probe configurations: (1) 8-microsensor probe (2.5 mm in diameter) for rodent studies (normal and subcutaneous mammary tumor tissues), and (2) 21-gauge needle probe with 3 spectroscopic fibers and an impedance microelectrode for breast cancer diagnosis in humans. Multisensor data are collected in real time (update 100 times/s) using PCs. RESULTS: Human data (collected by NASA licensee BioLuminate) from 15 women undergoing breast biopsy distinguished normal tissue from both benign tumors and breast carcinoma. Tumor margins and necrosis are rapidly detected. CONCLUSION: Real-time tissue identification is achievable. Potential applications, including probes incorporating nanoelectrode arrays, are presented. Copyright 2003 S. Karger AG, Basel.

  15. Implementing cascade approach in real-time video stream processing

    NASA Astrophysics Data System (ADS)

    Ermakov, Dmitry M.; Chernushich, Andrey P.

    2005-10-01

    A lot of nowadays machine vision tasks imply real-time video stream processing at rates of order of (25 frames / sec) x (640 x 480 pixels / frame) x (24 bit / pixel) = 184 Megabit / sec and higher. As reasonable estimations show, a very limited number of operations (even quite primitive) is allowed to be applied to each pixel of every video frame being processed in order to realize the processing rate required. Hence implementing algorithms widely exploiting formal methods (e.g. sorts of iterative approaches, transformations in multidimensional feature space etc) over the whole video stream becomes unaffordable. A potential (and practically working) overcome is introducing a cascade approach. From architectural viewpoint cascade processing consists of several predefined stages. Video frame passes through them from the zero stage (original frame) to the final stage (processing results). Some stages can be skipped, and the whole processing can be canceled at any stage. Passing through two sequential stages can be viewed as applying some operation to the information left to be processed. The keystone of cascade approach is designing an optimal sequence in which the simplest operations precede the more complex ones, so that the processing mechanism becomes essentially non-uniform and non-linear in terms of processing rates: the great amount of useless data is discriminated on the initial quick stages while the further analysis exploits smart algorithms over comparatively low data flux. The presentation demonstrates a practical example of cascade approach for the task of airplanes' tail identification numbers recognition.

  16. Real-time beyond the horizon vessel detection

    NASA Astrophysics Data System (ADS)

    Roarty, Hugh J.; Smith, Michael; Glenn, Scott M.; Barrick, Donald E.

    2013-05-01

    The marine transportation system (MTS) is a vital component of the United States Economy. Waterborne cargo accounts for more than $742 billion of the nation's economy and creates employment for 13 million citizens. A disruption in this system would have far reaching consequences to the security of the country. The US National High Frequency radar network, which comprises 130 radar stations around the country, became operational in May 2009. It provides hourly measurements of surface currents to the US Coast Guard for search and rescue (SAR). This system has the capability of being a dual use system providing information for environmental monitoring as well as vessel position information for maritime security. Real time vessel detection has been implemented at two of the radar stations outside New York Harbor. Several experiments were conducted to see the amount vessel traffic that the radar could capture. The radars were able to detect a majority of the vessels that are reporting via the Automatic Identification System (AIS) as well as 30 percent of mid to large size vessels that are not reporting via AIS. The radars were able to detect vessels out to 60 km from the coast. The addition of a vessel detection capability to the National HF radar network will provide valuable information to maritime security sector. This dual use capability will fill a gap in the current surveillance of US coastal waters. It will also provide longer-range situational awareness necessary to detect and track smaller size vessels in the large vessel clutter.

  17. Real-time Fluorescence Image-Guided Oncologic Surgery

    PubMed Central

    Mondal, Suman B.; Gao, Shengkui; Zhu, Nan; Liang, Rongguang; Gruev, Viktor; Achilefu, Samuel

    2014-01-01

    Medical imaging plays a critical role in cancer diagnosis and planning. Many of these patients rely on surgical intervention for curative outcomes. This requires a careful identification of the primary and microscopic tumors, and the complete removal of cancer. Although there have been efforts to adapt traditional imaging modalities for intraoperative image guidance, they suffer from several constraints such as large hardware footprint, high operation cost, and disruption of the surgical workflow. Because of the ease of image acquisition, relatively low cost devices and intuitive operation, optical imaging methods have received tremendous interests for use in real-time image-guided surgery. To improve imaging depth under low interference by tissue autofluorescence, many of these applications utilize light in the near-infra red (NIR) wavelengths, which is invisible to human eyes. With the availability of a wide selection of tumor-avid contrast agents, advancements in imaging sensors, electronic and optical designs, surgeons are able to combine different attributes of NIR optical imaging techniques to improve treatment outcomes. The emergence of diverse commercial and experimental image guidance systems, which are in various stages of clinical translation, attests to the potential high impact of intraoperative optical imaging methods to improve speed of oncologic surgery with high accuracy and minimal margin positivity. PMID:25287689

  18. Real time gesture based control: A prototype development

    NASA Astrophysics Data System (ADS)

    Bhargava, Deepshikha; Solanki, L.; Rai, Satish Kumar

    2016-03-01

    The computer industry is getting advanced. In a short span of years, industry is growing high with advanced techniques. Robots have been replacing humans, increasing the efficiency, accessibility and accuracy of the system and creating man-machine interaction. Robotic industry is developing many new trends. However, they still need to be controlled by humans itself. This paper presents an approach to control a motor like a robot with hand gestures not by old ways like buttons or physical devices. Controlling robots with hand gestures is very popular now-a-days. Currently, at this level, gesture features are applied for detecting and tracking the hand in real time. A principal component analysis algorithm is being used for identification of a hand gesture by using open CV image processing library. Contours, convex-hull, and convexity defects are the gesture features. PCA is a statistical approach used for reducing the number of variables in hand recognition. While extracting the most relevant information (feature) contained in the images (hand). After detecting and recognizing hand a servo motor is being controlled, which uses hand gesture as an input device (like mouse and keyboard), and reduces human efforts.

  19. 76 FR 42536 - Real-Time System Management Information Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-19

    ... System Management Information Program on November 8, 2010, at 75 FR 68418. The final rule document also... Federal Highway Administration 23 CFR Part 511 RIN 2125-AF19 Real-Time System Management Information... available and share traffic and travel conditions information via real-time information programs as...

  20. REAL-TIME ENVIRONMENTAL MONITORING: APPLICATIONS FOR HOMELAND SECURITY

    EPA Science Inventory

    Real-time monitoring technology developed as part of the EMPACT program has a variety of potential applications. These tools can measure a variety of potential contaminants in the air, water, in buildings, or in the soil. Real-time monitoring technology allows these detection sys...