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. 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

  3. Genus identification of toxic plant by real-time PCR.

    PubMed

    Matsuyama, Shuji; Nishi, Katsuji

    2011-03-01

    Some plants have toxicities that are dangerous for humans. In the case of poisoning by toxic plants, a rapid and easy screening test is required for accurate medical treatment or forensic investigation. In this study, we designed specific primer pairs for identification of toxic plants, such as subgenus Aconitum, genus Ricinus, genus Illicium, and genus Scopolia, by internal transcribed spacer sequences of nuclear ribosomal DNA. Allied species of target plants, foods, and human DNA were not detected, but each primer pair provided a specific PCR product from the target plant using real-time PCR. This method can detect the subgenus Aconitum, genus Ricinus, and genus Scopolia with template DNA of 10 pg, respectively, and genus Illicium with 1 pg. Furthermore, each primer pair provided the exact PCR product from digested target plants in artificial gastric fluid. When a trace unknown plant sample in forensic investigation is collected from stomach contents, this PCR assay may be useful for screening toxic plants. PMID:20623131

  4. Real-time speaker identification for video conferencing

    NASA Astrophysics Data System (ADS)

    Saravi, S.; Zafar, I.; Edirisinghe, E. A.; Kalawsky, R. S.

    2010-05-01

    Automatic speaker identification in a videoconferencing environment will allow conference attendees to focus their attention on the conference rather than having to be engaged manually in identifying which channel is active and who may be the speaker within that channel. In this work we present a real-time, audio-coupled video based approach to address this problem, but focus more on the video analysis side. The system is driven by the need for detecting a talking human via the use of computer vision algorithms. The initial stage consists of a face detector which is subsequently followed by a lip-localization algorithm that segments the lip region. A novel approach for lip movement detection based on image registration and using the Coherent Point Drift (CPD) algorithm is proposed. Coherent Point Drift (CPD) is a technique for rigid and non-rigid registration of point sets. We provide experimental results to analyse the performance of the algorithm when used in monitoring real life videoconferencing data.

  5. An architecture for device independent interfacing

    SciTech Connect

    Pace, D.M.

    1990-01-01

    Achieving device independence for software applications is required for all but a small number of critical real time applications. Device independence is achieved by establishing protocols and building protocol interpreters for the specific devices. Data structures containing pointers to functions provide a flexible architecture for implementing protocol translation. 3 refs., 5 figs.

  6. Real time identification of large space structures. Ph.D. Thesis - MIT

    NASA Technical Reports Server (NTRS)

    Voss, Janice E.

    1987-01-01

    Identification of frequencies, damping ratios, and mode shapes of large space structures (LSSs) are examined in real time. Real time processing allows for quick updates of model processing after a reconfiguration of structural failure. Recursive lattice least squares (RLLS) was selected as the baseline algorithm for the identification. Simulation results on a one dimensional LSS demonstrated that it provides good estimates, was not ill-conditioned in the presence of under-excited modes, allowed activity by a supervisory control system which prevented damage to the LSS or excessive drift, and was capable of real-time processing for typical LSS models. A suboptimal version of RLLS, which is equivalent to simulated parallel processing, was derived. A NASTRAN model of the dual keel U.S. space station was used to demonstrate the input/identification algorithm package in a more realistic simulation. Because the first eight flexible modes were very close together, the identification was much more difficult than in the simple examples. Even so, the model was accurately identified in real time.

  7. Identification and Quantification of Pathogenic Rhizoctonia solani and R. oryzae Using Real-time PCR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rhizoctonia solani and R. oryzae are the principal causal agents of Rhizoctonia root rot in dryland cereal production systems of the Pacific Northwest. To facilitate the identification and quantification of these pathogens in agricultural samples, we developed SYBR Green I-based real-time quantitati...

  8. Rapid and Accurate Identification of Coagulase-Negative Staphylococci by Real-Time PCR

    PubMed Central

    Edwards, K. J.; Kaufmann, M. E.; Saunders, N. A.

    2001-01-01

    Biprobe identification assays based on real-time PCR were designed for 15 species of coagulase-negative staphylococci (CNS). Three sets of primers and four biprobes were designed from two variable regions of the 16S rRNA gene. An identification scheme was developed based on the pattern of melting peaks observed with the four biprobes that had been tested on 24 type strains. This scheme was then tested on 100 previously identified clinical isolates and 42 blindly tested isolates. For 125 of the 142 clinical isolates there was a perfect correlation between the biprobe identification and the result of the ID 32 Staph phenotypic tests and PCR. For 12 of the other isolates a 300-bp portion of the 16S rRNA gene was sequenced to determine identity. The remaining five isolates could not be fully identified. LightCycler real-time PCR allowed rapid and accurate identification of the important CNS implicated in infection. PMID:11526126

  9. 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. PMID:19199849

  10. 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. PMID:26987970

  11. 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.

  12. A tool for real-time acoustic species identification of delphinid whistles.

    PubMed

    Oswald, Julie N; Rankin, Shannon; Barlow, Jay; Lammers, Marc O

    2007-07-01

    The ability to identify delphinid vocalizations to species in real-time would be an asset during shipboard surveys. An automated system, Real-time Odontocete Call Classification Algorithm (ROCCA), is being developed to allow real-time acoustic species identification in the field. This Matlab-based tool automatically extracts ten variables (beginning, end, minimum and maximum frequencies, duration, slope of the beginning and end sweep, number of inflection points, number of steps, and presence/absence of harmonics) from whistles selected from a real-time scrolling spectrograph (ISHMAEL). It uses classification and regression tree analysis (CART) and discriminant function analysis (DFA) to identify whistles to species. Schools are classified based on running tallies of individual whistle classifications. Overall, 46% of schools were correctly classified for seven species and one genus (Tursiops truncatus, Stenella attenuata, S. longirostris, S. coeruleoalba, Steno bredanensis, Delphinus species, Pseudorca crassidens, and Globicephala macrorhynchus), with correct classification as high as 80% for some species. If classification success can be increased, this tool will provide a method for identifying schools that are difficult to approach and observe, will allow species distribution data to be collected when visual efforts are compromised, and will reduce the time necessary for post-cruise data analysis. PMID:17614515

  13. 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

  14. 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

  15. 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.

  16. Real-Time Near-Infrared Fluorescence-Guided Identification of the Ureters using Methylene Blue

    PubMed Central

    Matsui, Aya; Tanaka, Eiichi; Choi, Hak Soo; Kianzad, Vida; Gioux, Sylvain; Lomnes, Stephen J.; Frangioni, John V.

    2009-01-01

    Background The aim of this study was to determine whether the invisible near-infrared (NIR) fluorescence properties of methylene blue (MB), a dye already FDA-approved for other indications, could be exploited for real-time, intraoperative identification of the ureters. Methods The optical properties of MB were quantified in vitro. Open surgery and laparoscopic NIR fluorescence imaging systems were employed. Yorkshire pigs were injected intravenously with: 0.1 mg/kg MB (n = 8), 10 mg furosemide followed by 0.1 mg/kg MB (n = 6), or 0.5 mg/kg MB (n = 6). The contrast-to-background ratio (CBR) of the kidney and ureters, and MB concentration in urine, were quantified. Results Peak MB absorbance, emission, and intensity in urine occurred at 668 nm, 688 nm, and 20 μM, respectively. After intravenous injection, doses as low as 0.1 mg/kg MB provided prolonged imaging of the ureters, and a dose of 0.5 mg/kg provided statistically significant improvement of CBR. Pre-injection of furosemide increased urine volume but did not improve CBR. Laparoscopic identification of the ureter using MB NIR fluorescence was demonstrated. Conclusions Ureteral imaging using MB NIR fluorescence provides sensitive, real-time, intraoperative identification of the ureters during open and laparoscopic surgeries. PMID:20117811

  17. 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.

  18. 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

  19. 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.

  20. Identification of pork in meat products using real-time loop-mediated isothermal amplification

    PubMed Central

    Yang, Lixia; Fu, Shujun; Peng, Xinkai; Li, Le; Song, Taoping; Li, Lin

    2014-01-01

    In this study, a one-step, real-time, loop-mediated isothermal amplification (RealAmp) assay was developed, for the highly specific detection of pork DNA. For the assay, the mtDNA of cytochrome b (cytb) gene was amplified at 63 °C using SYBR Green I for 45 min with a Real-Time Polymerase Chain Reaction (PCR) System that measured the fluorescent signal at one-minute intervals. As little as 1 pg of template DNA could be detected, without any cross-reactivity with non-target species. Meat mixtures, heat-treated at 100 °C for 15 min, prepared by mixing pork meat with beef at different ratios (0.01%–10%) were tested, and the RealAmp assays allowed the detection of as little as 0.01% pork in the meat mixtures. Thus, this work showed that RealAmp could be used for specific identification and sensitive quantification of meat species, even for heat-treated meat products. PMID:26019573

  1. Identification of the IMF sector structure in near-real time by ground magnetic data

    NASA Astrophysics Data System (ADS)

    Janzhura, A. S.; Troshichev, O. A.

    2011-08-01

    A method is proposed to determine in near-real time the interplanetary magnetic field (IMF) sector structure (SS) effect on geomagnetic data from polar cap stations. To separate the SS effect, whose polarity is invariant within an interval from some days to 2 weeks, from the disturbed solar wind effects with periodicity from minutes to hours, the daily median values of geomagnetic H (or D) component are estimated. Then the median values for 9 days preceding the current day are subjected to 3-days running averages and the interpolation procedure is applied to these smoothed averages. Comparisons of the sector structure reconstructed from the ground magnetic data with the actual variations of the GSM IMF By component measured onboard the ACE spacecraft in the summer months of 1990 and 2001 demonstrate their good agreement with coefficient of correlation R=0.96-0.97 for the H-component and R=0.93-0.95 for the D-component. The proposed simple method makes possible identification of the SS effect in the same near real-time regime as the derivation of the quiet daily curve and as level of reference for the polar cap magnetic disturbances in the calculation of the polar cap magnetic activity PC index.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. Evaluation of an updated real-time RT-PCR test for the identification of the H7 subtype

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rapid detection of avian influenza (AI) virus and identification of the H5 and H7 subtypes is critical for wild bird monitoring programs. A real-time RT-PCR test for identification of the H7 subtype in North America was first reported in 2002. With the recent surveillance in wild birds it was disc...

  9. Dynamic fuel cell stack model for real-time simulation based on system identification

    NASA Astrophysics Data System (ADS)

    Meiler, M.; Schmid, O.; Schudy, M.; Hofer, E. P.

    The authors have been developing an empirical mathematical model to predict the dynamic behaviour of a polymer electrolyte membrane fuel cell (PEMFC) stack. Today there is a great number of models, describing steady-state behaviour of fuel cells by estimating the equilibrium voltage for a certain set of operating parameters, but models capable of predicting the transient process between two steady-state points are rare. However, in automotive applications round about 80% of operating situations are dynamic. To improve the reliability of fuel cell systems by model-based control for real-time simulation dynamic fuel cell stack model is needed. Physical motivated models, described by differential equations, usually are complex and need a lot of computing time. To meet the real-time capability the focus is set on empirical models. Fuel cells are highly nonlinear systems, so often used auto-regressive (AR), output-error (OE) or Box-Jenkins (BJ) models do not accomplish satisfying accuracy. Best results are achieved by splitting the behaviour into a nonlinear static and a linear dynamic subsystem, a so-called Uryson-Model. For system identification and model validation load steps with different amplitudes are applied to the fuel cell stack at various operation points and the voltage response is recorded. The presented model is implemented in MATLAB environment and has a computing time of less than 1 ms per step on a standard desktop computer with a 2.8 MHz CPU and 504 MB RAM. Lab tests are carried out at DaimlerChrysler R&D Centre with DaimlerChrysler PEMFC hardware and a good agreement is found between model simulations and lab tests.

  10. 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.

  11. 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. PMID:26092191

  12. 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. PMID:26772407

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. Identification of Reference Genes for Real-Time Quantitative PCR Experiments in the Liverwort Marchantia polymorpha

    PubMed Central

    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

  18. 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

  19. 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

  20. 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...

  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. [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

  4. Coupling Modified Constitutive Relation Error, Model Reduction and Kalman Filtering Algorithms for Real-Time Parameters Identification

    NASA Astrophysics Data System (ADS)

    Marchand, Basile; Chamoin, Ludovic; Rey, Christian

    2015-11-01

    In this work we propose a new identification strategy based on the coupling between a probabilistic data assimilation method and a deterministic inverse problem approach using the modified Constitutive Relation Error energy functional. The idea is thus to offer efficient identification despite of highly corrupted data for time-dependent systems. In order to perform real-time identification, the modified Constitutive Relation Error is here associated to a model reduction method based on Proper Generalized Decomposition. The proposed strategy is applied to two thermal problems with identification of time-dependent boundary conditions, or material parameters.

  5. Real-Time PCR System for Detection of Orthopoxviruses and Simultaneous Identification of Smallpox Virus

    PubMed Central

    Olson, Victoria A.; Laue, Thomas; Laker, Miriam T.; Babkin, Igor V.; Drosten, Christian; Shchelkunov, Sergei N.; Niedrig, Matthias; Damon, Inger K.; Meyer, Hermann

    2004-01-01

    A screening assay for real-time LightCycler (Roche Applied Science, Mannheim, Germany) PCR identification of smallpox virus DNA was developed and compiled in a kit system under good manufacturing practice conditions with standardized reagents. In search of a sequence region unique to smallpox virus, the nucleotide sequence of the 14-kDa fusion protein gene of each of 14 variola virus isolates of the Russian World Health Organization smallpox virus repository was determined and compared to published sequences. PCR primers were designed to detect all Eurasian-African species of the genus Orthopoxvirus. A single nucleotide mismatch resulting in a unique amino acid substitution in smallpox virus was used to design a hybridization probe pair with a specific sensor probe that allows reliable differentiation of smallpox virus from other orthopoxviruses by melting-curve analysis. The applicability was demonstrated by successful amplification of 120 strains belonging to the orthopoxvirus species variola, vaccinia, camelpox, mousepox, cowpox, and monkeypox virus. The melting temperatures (Tms) determined for 46 strains of variola virus (Tms, 55.9 to 57.8°C) differed significantly (P = 0.005) from those obtained for 11 strains of vaccinia virus (Tms, 61.7 to 62.7°C), 15 strains of monkeypox virus (Tms, 61.9 to 62.2°C), 40 strains of cowpox virus (Tms, 61.3 to 63.7°C), 8 strains of mousepox virus (Tm, 61.9°C), and 8 strains of camelpox virus (Tms, 64.0 to 65.0°C). As most of the smallpox virus samples were derived from infected cell cultures and tissues, smallpox virus DNA could be detected in a background of human DNA. By applying probit regression analysis, the analytical sensitivity was determined to be 4 copies of smallpox virus target DNA per sample. The DNAs of several human herpesviruses as well as poxviruses other than orthopoxviruses were not detected by this method. The assay proved to be a reliable technique for the detection of orthopoxviruses, with the

  6. 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

  7. 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

    2016-01-01

    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. PMID:27457073

  8. 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.

  9. 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.

  10. 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...

  11. 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...

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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. PMID:26549195

  17. 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.

  18. 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

  19. A Real-Time Cell Analyzing Assay for Identification of Novel Antiviral Compounds against Chikungunya Virus.

    PubMed

    Zandi, Keivan

    2016-01-01

    Screening of viral inhibitors through induction of cytopathic effects (CPE) by conventional method has been applied for various viruses including Chikungunya virus (CHIKV), a significant arbovirus. However, it does not provide the information about cytopathic effect from the beginning and throughout the course of virus replication. Conventionally, most of the approaches are constructed on laborious end-point assays which are not capable for detecting minute and rapid changes in cellular morphology. Therefore, we developed a label-free and dynamical method for monitoring the cellular features that comprises cell attachment, proliferation, and viral cytopathogenicity, known as the xCELLigence real-time cell analysis (RTCA). In this chapter, we provide a RTCA protocol for quantitative analysis of CHIKV replication using an infected Vero cell line treated with ribavirin as an in vitro model. PMID:27233278

  20. 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.

  1. Real-time PCR identification of lake whitefish Coregonus clupeaformis in the Laurentian Great Lakes.

    PubMed

    Overdyk, L M; Braid, H E; Naaum, A M; Crawford, S S; Hanner, R H

    2016-04-01

    The purpose of this study was to develop a real-time PCR assay to specifically identify lake whitefish Coregonus clupeaformis in larval fish assemblages based on a 122 bp amplicon from the mitochondrial genome. The efficiency of the reaction, as calculated from the standard curve, was 90·77% with the standard curve having an r(2) value of 0·998. Specificity of the assay provided single melt peak in a melt-curve analysis and amplification of only the target species. The assay successfully identified target DNA in as low as 0·1% proportion of a DNA mixture. This assay was designed on the portable Smart Cycler II platform and can be used in both field and laboratory settings to successfully identify C. clupeaformis. PMID:26932125

  2. Rapid and Accurate Identification by Real-Time PCR of Biotoxin-Producing Dinoflagellates from the Family Gymnodiniaceae

    PubMed Central

    Smith, Kirsty F.; de Salas, Miguel; Adamson, Janet; Rhodes, Lesley L.

    2014-01-01

    The identification of toxin-producing dinoflagellates for monitoring programmes and bio-compound discovery requires considerable taxonomic expertise. It can also be difficult to morphologically differentiate toxic and non-toxic species or strains. Various molecular methods have been used for dinoflagellate identification and detection, and this study describes the development of eight real-time polymerase chain reaction (PCR) assays targeting the large subunit ribosomal RNA (LSU rRNA) gene of species from the genera Gymnodinium, Karenia, Karlodinium, and Takayama. Assays proved to be highly specific and sensitive, and the assay for G. catenatum was further developed for quantification in response to a bloom in Manukau Harbour, New Zealand. The assay estimated cell densities from environmental samples as low as 0.07 cells per PCR reaction, which equated to three cells per litre. This assay not only enabled conclusive species identification but also detected the presence of cells below the limit of detection for light microscopy. This study demonstrates the usefulness of real-time PCR as a sensitive and rapid molecular technique for the detection and quantification of micro-algae from environmental samples. PMID:24608972

  3. [Real time PCR hybridization for the rapid and specific identification of Francisella tularensis].

    PubMed

    Bielawska-Drózd, Agata; Niemcewicz, Marcin; Gaweł, Jerzy; Bartoszcze, Michał; Graniak, Grzegorz; Joniec, Justyna; Kołodziej, Marcin

    2010-01-01

    Tularemia is highly infectious and fatal zoonotic disease caused by Gram negative bacteria Francisella tularensis. The necessity to undergo medical treatment in early phase of illness in humans and possibility of making use of bacterial aerosol by terrorists in an attack create an urgent need to implement a rapid and effective method which enables to identify the agent. In our study two primers FopA F/R and hybridization probes FopA S1/S2 designed from fopA gene sequence, were tested for their potential applicability to identify F. tularensis. In this research 50 strains of F. tularensis were used and the test gave positive results. Reaction specificity was confirmed by using of non-Francisella tularensis bacterial species. The results obtained in the real-time PCR reaction with primers Tul4 F/R and hybridization probes Tul4 S1/S2, designed from tul4 gene, were comparable to the results from previous experiment with fopA - primers set. Investigation of fopA and tul4 primers and hybridization probes properties revealed characteristic Tm (melting temperature) value of the products--61 degrees C and 60 degrees C, respectively. Detection sensitivity was remarkably higher when fopA primers set was used 1 fg/microl, and for tul4 primers set, minimal detectable concentration is 10 fg/microl. PMID:21473100

  4. Identification of complex scattered signals with a fast real-time hybrid electro-optical correlator

    NASA Astrophysics Data System (ADS)

    Majumdar, Arun K.; Sandomirsky, Sergey

    1997-10-01

    The goal of this work was to develop a fast optical correlator for automatic real-time target recognition. The tremendous importance of optical correlators for military and civilian applications was recognized recently and approved by a US conference committee of senators nd representatives. This publication presents the experimental results of detecting and identifying complex scattered signals by using an innovative, hybrid electro-optical correlator. Our technique is based on achieving optical correlation by utilizing state-of-the-art devices: time delay integration, charge coupled devices, liquid crystal displays, and electronically controllable light sources. Results of the experiment with our optical correlator, performed with simulated sonar signals with a center frequency of 100 kHz and duration of 8 to 512 pulses, show the possibility of recognizing a Doppler shift of 20 Hz. This Doppler shift corresponds to a target velocity of 20.7 m/sec. Simulation results indicate that we can achieve significant correlation for a noisy signal by using appropriate signal length. Our experiments demonstrate that we can perform approximately 1010 multiply accumulate operations per second with the high parallel optical corrector, compared to approximately 106 multiply accumulate operations per second using a Pentium 133 MHz personal computer. This new optical correlation scheme can provide solutions for overcoming the inherent shortcomings attributable to the low dynamic range of CCD, and the problem of compatibility caused by different pixel patterns between LCD and CCD by making use of high-quality optics and modern means of achieving uniform illumination.

  5. Rapid Identification and Enumeration of Saccharomyces cerevisiae Cells in Wine by Real-Time PCR

    PubMed Central

    Martorell, P.; Querol, A.; Fernández-Espinar, M. T.

    2005-01-01

    Despite the beneficial role of Saccharomyces cerevisiae in the food industry for food and beverage production, it is able to cause spoilage in wines. We have developed a real-time PCR method to directly detect and quantify this yeast species in wine samples to provide winemakers with a rapid and sensitive method to detect and prevent wine spoilage. Specific primers were designed for S. cerevisiae using the sequence information obtained from a cloned random amplified polymorphic DNA band that differentiated S. cerevisiae from its sibling species Saccharomyces bayanus, Saccharomyces pastorianus, and Saccharomyces paradoxus. The specificity of the primers was demonstrated for typical wine spoilage yeast species. The method was useful for estimating the level of S. cerevisiae directly in sweet wines and red wines without preenrichment when yeast is present in concentrations as low as 3.8 and 5 CFU per ml. This detection limit is in the same order as that obtained from glucose-peptone-yeast growth medium (GPY). Moreover, it was possible to quantify S. cerevisiae in artificially contaminated samples accurately. Limits for accurate quantification in wine were established, from 3.8 × 105 to 3.8 CFU/ml in sweet wine and from 5 × 106 to 50 CFU/ml in red wine. PMID:16269715

  6. 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.

  7. Direct identification of mycobacteria from liquid media using a triplex real-time PCR coupled with pyrosequencing method.

    PubMed

    Kim, Jeong-Uk; Cha, Choong-Hwan; Park, Seon-Hee

    2015-12-01

    Culture in enriched broth, as well as on a solid medium, is recommended for primary isolation of mycobacteria. With the introduction of liquid mycobacterial culture methods, a substantial workload regarding the identification of culture-recovered mycobacterial species, particularly Mycobacterium tuberculosis complex (MTC), has been imposed on our laboratory. We thus developed a triplex, real-time PCR coupled with pyrosequencing assay that can directly identify mycobacterial species from liquid media, which can reduce the workload. In this assay, real-time PCR simultaneously detects MTC and Mycobacterium xenopi, and amplifies the region of 16S rRNA gene containing hypervariable region A for pyrosequencing analysis; subsequent, pyrosequencing identifies many other nontuberculous mycobacteria. The assay was evaluated using 333 DNA samples directly prepared from liquid media, including 24 reference strains and 309 clinical isolates. Three hundred and twenty-eight (98.5%) of the 333 samples were correctly identified. The remaining five were determined as indeterminate. In conclusion, this coupled assay would be an alternative method for rapid identification of mycobacteria directly from liquid media in a clinical laboratory with a high workload in regions where tuberculosis is endemic. PMID:26471200

  8. CATSI EDM: a new sensor for the real-time passive stand-off detection and identification of chemicals

    NASA Astrophysics Data System (ADS)

    Thériault, Jean-Marc; Lacasse, Paul; Lavoie, Hugo; Bouffard, François; Montembeault, Yan; Farley, Vincent; Belhumeur, Louis; Lagueux, Philippe

    2010-04-01

    DRDC Valcartier recently completed the development of the CATSI EDM (Compact Atmospheric Sounding Interferometer Engineering Development Model) for the Canadian Forces (CF). It is a militarized sensor designed to meet the needs of the CF in the development of area surveillance capabilities for the detection and identification of chemical Warfare Agents (CWA) and toxic industrial chemicals (TIC). CATSI EDM is a passive infrared double-beam Fourier spectrometer system designed for real-time stand-off detection and identification of chemical vapours at distances up to 5 km. It is based on the successful passive differential detection technology. This technique known as optical subtraction, results in a target gas spectrum which is almost free of background, thus making possible detection of weak infrared emission in strong background emission. This paper summarizes the system requirements, achievements, hardware and software characteristics and test results.

  9. Real-time ligation chain reaction for DNA quantification and identification on the FO-SPR.

    PubMed

    Knez, Karel; Spasic, Dragana; Delport, Filip; Lammertyn, Jeroen

    2015-05-15

    Different assays have been developed in the past years to meet point-of-care diagnostic tests requirements for fast and sensitive quantification and identification of targets. In this paper, we developed the ligation chain reaction (LCR) assay on the Fiber Optic Surface Plasmon Resonance (FO-SPR) platform, which enabled simultaneous quantification and cycle-to-cycle identification of DNA during amplification. The newly developed assay incorporated FO-SPR DNA melting assay, previously developed by our group. This required establishment of several assay parameters, including buffer ionic strength and thermal ramping speed as these parameters both influence the ligation enzyme performance and the hybridization yield of the gold nanoparticles (Au NPs) on the FO-SPR sensor. Quantification and identification of DNA targets was achieved over a wide concentration range with a calibration curve spanning 7 orders of magnitude and LOD of 13.75 fM. Moreover, the FO-SPR LCR assay could discriminate single nucleotide polymorphism (SNPs) without any post reaction analysis, featuring thus all the essential requirements of POC tests. PMID:25212376

  10. Development of a multiplex real-time PCR assay for identification of members of the Anopheles gambiae species complex.

    PubMed

    Bass, Chris; Williamson, Martin S; Field, Linda M

    2008-07-01

    Two high-throughput assays for the identification of members of the Anopheles gambiae sensu lato species complex have recently been reported. These methods, are based on TaqMan single nucleotide polymorphism (SNP) genotyping that enables rapid scoring of mosquito DNA samples in real-time PCR reactions. Unfortunately, both assays are restricted in the number of species that they can identify and a combination of the two assays may be required to identify all possible species in certain regions. To overcome this limitation, and thereby further increase throughput while reducing costs, we have developed a new multiplex real-time PCR assay for identifying members of the An. gambiae complex. The new method uses three probes labelled with fluorophores with distinct emission and excitation spectra, allowing simultaneous detection of the two main malaria vectors from the non-vector sibling species, and can be used on single mosquito legs from silica-dried specimens. A genotyping trial of over 450 specimens collected from 13 countries in sub-Saharan Africa showed the multiplex assay to be highly specific and sensitive and it compared well against the two previously reported TaqMan assays and standard allele-specific PCR. PMID:18490000

  11. 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

  12. 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

  13. Quantitative Real-Time PCR Assays for Detection of Human Adenoviruses and Identification of Serotypes 40 and 41

    PubMed Central

    Jothikumar, Narayanan; Cromeans, Theresa L.; Hill, Vincent R.; Lu, Xiaoyan; Sobsey, Mark D.; Erdman, Dean D.

    2005-01-01

    A quantitative real-time TaqMan PCR assay for detection of human adenoviruses (HAdV) was developed using broadly reactive consensus primers and a TaqMan probe targeting a conserved region of the hexon gene. The TaqMan assay correctly identified 56 representative adenovirus prototype strains and field isolates from all six adenovirus species (A to F). Based on infectious units, the TaqMan assay was able to detect as few as 0.4 and 0.004 infectious units of adenovirus serotype 2 (AdV2) and AdV41, respectively, with results obtained in less than 90 min. Using genomic equivalents, the broadly reactive TaqMan assay was able to detect 5 copies of AdV40 (which had zero mismatches with the PCR primers and probe), 8 copies of AdV41, and 350 copies of AdV3 (which had the most mismatches [seven] of any adenovirus serotype tested). For specific detection and identification of F species serotypes AdV40 and AdV41, a second real-time PCR assay was developed using fluorescence resonance energy transfer (FRET) probes that target the adenovirus fiber gene. The FRET-based assay had a detection limit of 3 to 5 copies of AdV40 and AdV41 standard DNA and was able to distinguish between AdV40 and AdV41 based on melting curve analysis. Both the TaqMan and FRET PCR assays were quantitative over a wide range of virus titers. Application of these assays for detection of adenoviruses and type-specific identification of AdV40 and AdV41 will be useful for identifying these viruses in environmental and clinical samples. PMID:15933012

  14. 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. PMID:26237339

  15. Laser-induced breakdown spectroscopy: a tool for real-time, in vitro and in vivo identification of carious teeth

    PubMed Central

    Samek, Ota; Telle, Helmut H; Beddows, David CS

    2001-01-01

    Background Laser Induced Breakdown Spectroscopy (LIBS) can be used to measure trace element concentrations in solids, liquids and gases, with spatial resolution and absolute quantifaction being feasible, down to parts-per-million concentration levels. Some applications of LIBS do not necessarily require exact, quantitative measurements. These include applications in dentistry, which are of a more "identify-and-sort" nature – e.g. identification of teeth affected by caries. Methods A one-fibre light delivery / collection assembly for LIBS analysis was used, which in principle lends itself for routine in vitro / in vivo applications in a dental practice. A number of evaluation algorithms for LIBS data can be used to assess the similarity of a spectrum, measured at specific sample locations, with a training set of reference spectra. Here, the description has been restricted to one pattern recognition algorithm, namely the so-called Mahalanobis Distance method. Results The plasma created when the laser pulse ablates the sample (in vitro / in vivo), was spectrally analysed. We demonstrated that, using the Mahalanobis Distance pattern recognition algorithm, we could unambiguously determine the identity of an "unknown" tooth sample in real time. Based on single spectra obtained from the sample, the transition from caries-affected to healthy tooth material could be distinguished, with high spatial resolution. Conclusions The combination of LIBS and pattern recognition algorithms provides a potentially useful tool for dentists for fast material identification problems, such as for example the precise control of the laser drilling / cleaning process. PMID:11801201

  16. 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. PMID:22841800

  17. 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

  18. 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

  19. Identification of WA-type three-line hybrid rice with real-time polymerase chain reaction (PCR) method.

    PubMed

    Cheng, Y; Gao, B D; Chen, H Y; Mao, J J; Cao, A X; Zhu, J G; Zhu, S F

    2012-02-01

    A real-time fluorescent PCR (RTF-PCR) was developed to detect and quantify wild abortive (WA)-type three-line hybrid rice (Oryza sativa L.). The mitochondrial R₂₋₆₃₀ WA gene was reported to be closely related to male sterility in plants, and developed as a molecular maker to identify the cytoplasmic male sterility system of hybrid rice. First, we got the DNA sequence of R₂₋₆₃₀ WA gene in 17 rice species with traditional PCR. Then, a pair of specific primers (P₃, P₄) and TaqMan fluorescence probe (P₃₋₁₄) were designed based on the R₂₋₆₃₀ DNA sequence. The following RTF-PCR was performed on the 17 rice species finally. The results indicate that the probes used here are specific for three-line hybrid rice F₁ and male sterile lines. We can even identify a single hybrid seed using the probes, which confirmed that the probes can be applied to the identification and quantification of the WA-type three-line hybrid rice. In addition, the RFT-PCR system can be optimized when the annealing temperature is 60 °C and the Mg²⁺ concentration is 3.5 mmol/L. PMID:22161239

  20. 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. PMID:23764217

  1. 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

  2. Real-Time Operating System/360

    NASA Technical Reports Server (NTRS)

    Hoffman, R. L.; Kopp, R. S.; Mueller, H. H.; Pollan, W. D.; Van Sant, B. W.; Weiler, P. W.

    1969-01-01

    RTOS has a cost savings advantage for real-time applications, such as those with random inputs requiring a flexible data routing facility, display systems simplified by a device independent interface language, and complex applications needing added storage protection and data queuing.

  3. Real-time intraoperative full-range complex FD-OCT guided cerebral blood vessel identification and brain tumor resection in neurosurgery

    NASA Astrophysics Data System (ADS)

    Zhang, Kang; Huang, Yong; Pradilla, Gustavo; Tyler, Betty; Kang, Jin U.

    2011-03-01

    This work utilized an ultra-high-speed full-range complex-conjugate-free optical coherence tomography (FD-OCT) system to perform real-time intraoperative imaging to guide two common neurosurgical procedures: the cerebral blood vessel identification and the brain tumor resection. The cerebral blood vessel identification experiment is conducted ex vivo on human cadaver specimen. Specific cerebral arteries and veins in different positions of the specimen are visualized and the spatial relations between adjacent vessels are indentified through real-time 3D visualization. The brain tumor resection experiment is conducted in vivo on 9L gliomas established in rat brains. The normal brain-tumor margin can be clearly identified in depth of the tissue from sagittal, coronal and axial slices of the intraoperatively acquired 3D data set. The real-time full-range FD-OCT guided in vivo rat flank tumor resection is also conducted.

  4. Real-Time Intraoperative Near-Infrared Fluorescence Identification of the Extrahepatic Bile Ducts using Clinically-Available Contrast Agents

    PubMed Central

    Matsui, Aya; Tanaka, Eiichi; Choi, Hak Soo; Winer, Joshua H.; Kianzad, Vida; Gioux, Sylvain; Laurence, Rita G.; Frangioni, John V.

    2009-01-01

    Background Iatrogenic bile duct injuries are serious complications with patient morbidity. We hypothesized that the invisible near-infrared (NIR) fluorescence properties of methylene blue (MB) and indocyanine green (ICG) could be exploited for real-time, intraoperative imaging of the extrahepatic bile ducts during open and laparoscopic surgeries. Methods 2.0 mg/kg of MB and 0.05 mg/kg of ICG were intravenously injected into 35-kg female Yorkshire pigs and the extrahepatic bile ducts imaged over time using either the FLARE™ image-guided surgery system (open surgery) or a custom NIR fluorescence laparoscopy system. Surgical anatomy was confirmed using x-ray cholangiography. Contrast-to-background ratio (CBR), contrast-to-liver ratio (CLR), and chemical concentrations in the cystic duct (CD) and common bile duct (CBD) were measured, and the performance of each agent quantified. Results Using NIR fluorescence of MB, the CD and CBD could be identified with good sensitivity (CBR and CLR ≥ 4), during both open and laparoscopic surgeries, from 10 to 120 min post-injection. Functional impairment of the ducts, including constriction and injury were immediately identifiable. Using NIR fluorescence of ICG, extrahepatic bile ducts did not become visible until 90 min post-injection due to strong residual liver retention, however, between 90 to 240 min, ICG provided exquisitely high sensitivity for both CD and CBD, with CBR ≥ 8 and CLR ≥ 4. Conclusions We demonstrate that two clinically available NIR fluorophores, MB fluorescing at 700 nm and ICG fluorescing at 800 nm, provide sensitive, prolonged identification of the extrahepatic bile ducts and assessment of their functional status. PMID:20117813

  5. Rapid identification of Brucella isolates to the species level by real time PCR based single nucleotide polymorphism (SNP) analysis

    PubMed Central

    Gopaul, Krishna K; Koylass, Mark S; Smith, Catherine J; Whatmore, Adrian M

    2008-01-01

    Background Brucellosis, caused by members of the genus Brucella, remains one of the world's major zoonotic diseases. Six species have classically been recognised within the family Brucella largely based on a combination of classical microbiology and host specificity, although more recently additional isolations of novel Brucella have been reported from various marine mammals and voles. Classical identification to species level is based on a biotyping approach that is lengthy, requires extensive and hazardous culturing and can be difficult to interpret. Here we describe a simple and rapid approach to identification of Brucella isolates to the species level based on real-time PCR analysis of species-specific single nucleotide polymorphisms (SNPs) that were identified following a robust and extensive phylogenetic analysis of the genus. Results Seven pairs of short sequence Minor Groove Binding (MGB) probes were designed corresponding to SNPs shown to possess an allele specific for each of the six classical Brucella spp and the marine mammal Brucella. Assays were optimised to identical reaction parameters in order to give a multiple outcome assay that can differentiate all the classical species and Brucella isolated from marine mammals. The scope of the assay was confirmed by testing of over 300 isolates of Brucella, all of which typed as predicted when compared to other phenotypic and genotypic approaches. The assay is sensitive being capable of detecting and differentiating down to 15 genome equivalents. We further describe the design and testing of assays based on three additional SNPs located within the 16S rRNA gene that ensure positive discrimination of Brucella from close phylogenetic relatives on the same platform. Conclusion The multiple-outcome assay described represents a new tool for the rapid, simple and unambiguous characterisation of Brucella to the species level. Furthermore, being based on a robust phylogenetic framework, the assay provides a platform

  6. 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

  7. 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...

  8. 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

  9. 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

  10. Simple distortion-invariant optical identification tag based on encrypted binary-phase computer-generated hologram for real-time vehicle identification and verification

    NASA Astrophysics Data System (ADS)

    Kim, Cheol-Su

    2010-11-01

    A simple distortion-invariant optical identification (ID) tag is presented for real-time vehicle identification and verification. The proposed scheme is composed of image encryption, ID tag creation, image decryption, and optical correlation for verification. To create the ID tag, a binary-phase computer-generated hologram (BPCGH) of a symbol image representing a vehicle is created using a simulated annealing algorithm. The BPCGH is then encrypted using an XOR operation and enlargement transformed into polar coordinates. The resulting ID tag is then attached to the vehicle. As the BPCGH consists of only binary phase values, it is robust to external distortions. To identify and verify the vehicle, several reverse processes are required, such as capturing the ID tag with a camera, extracting the ID tag from the captured image, transformation of the ID tag into rectangular coordinates, decryption, an inverse Fourier transform, and correlation. Computer simulation and experimental results confirm that the proposed optical ID tag is secure and robust to such distortions as scaling, rotation, cropping (scratches), and random noise. The ID tag can also be easily implemented, as it consists of only binary phase components.

  11. 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

  12. 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

  13. 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

  14. Rapid identification of Aedes albopictus, Aedes scutellaris, and Aedes aegypti life stages using real-time polymerase chain reaction assays.

    PubMed

    Hill, Lydia A; Davis, Joseph B; Hapgood, George; Whelan, Peter I; Smith, Greg A; Ritchie, Scott A; Cooper, R D; van den Hurk, Andrew F

    2008-12-01

    In 2005, a widespread infestation of Aedes albopictus was discovered in the Torres Strait, the region between northern Australia and New Guinea. To contain this species, an eradication program was implemented in 2006. However, the progress of this program is impeded by the difficulty of morphologically separating Ae. albopictus larvae from the endemic species Aedes scutellaris. In this study, three real-time TaqMan polymerase chain reaction assays that target the ribosomal internal transcribed spacer 1 region were developed to rapidly identify Aedes aegypti, Ae. albopictus, and Ae. scutellaris from northern Australia. Individual eggs, larvae, pupae, and adults, as well as the species composition of mixed pools were accurately identified. The assay method was validated using 703 field-collected specimens from the Torres Strait. PMID:19052295

  15. Identification and Acute Targeting of Gaps in Atrial Ablation Lesion Sets using a Real Time MRI System

    PubMed Central

    Ranjan, Ravi; Kholmovski, Eugene G.; Blauer, Joshua; Vijayakumar, Sathya; Volland, Nelly A.; Salama, Mohamed E.; Parker, Dennis L.; MacLeod, Rob; Marrouche, Nassir F.

    2013-01-01

    Background Radiofrequency ablation is routinely used to treat cardiac arrhythmias, but gaps remain in ablation lesion sets, as there is no direct visualization of ablation related changes. In this study we describe using a real time MRI (RT-MRI) system to acutely identify and target gaps leading to a complete and transmural ablation in the atrium. Methods and Results A swine model was used for these studies (n=12). Ablation lesions with a gap were created in the atrium using fluoroscopy and an electro-anatomical system in the first group (n=5). The animal was then moved to a 3 Tesla MRI system where high-resolution late gadolinium enhancement (LGE) MRI was used to identify the gap. Using a RT-MRI catheter navigation and visualization system the gap area was ablated in the MR scanner. In a second group (n=7) ablation lesions with varying gaps in between were created under RT-MRI guidance and gap lengths determined using LGE MR images were correlated with gap length measured from gross pathology. Gaps up to 1.0 mm were identified using gross pathology and 1.4 mm using LGE MRI. Using a RT-MRI system with active catheter navigation gaps can be targeted acutely, leading to lesion sets with no gaps. The correlation coefficient (R2) between gap length identified using MRI and gross pathology was 0.95. Conclusions Real time MRI system can be used to identify and acutely target gaps in atrial ablation lesion sets. Acute targeting of gaps in ablation lesion sets can potentially lead to significant improvement in clinical outcomes. PMID:23071143

  16. A real-time TaqMan polymerase chain reaction for the identification of Culex vectors of West Nile and Saint Louis encephalitis viruses in North America.

    PubMed

    Sanogo, Yibayiri O; Kim, Chang-Hyun; Lampman, Richard; Novak, Robert J

    2007-07-01

    In North America, West Nile and St. Louis encephalitis viruses have been detected in a wide range of vector species, but the majority of isolations continue to be from pools of mixed mosquitoes in the Culex subgenus Culex. Unfortunately, the morphologic identification of these important disease vectors is often difficult, particularly in regions of sympatry. We developed a sensitive real-time TaqMan polymerase chain reaction assay that allows reliable identification of Culex mosquitoes including Culex pipiens pipiens, Cx. p. quinquefasciatus, Cx. restuans, Cx. salinarius, Cx. nigripalpus, and Cx. tarsalis. Primers and fluorogenic probes specific to each species were designed based on sequences of the acetylcholinesterase gene (Ace2). Both immature and adult mosquitoes were successfully identified as individuals and as mixed species pools. This identification technique provides the basis for a rapid, sensitive, and high-throughput method for expounding the species-specific contribution of vectors to various phases of arbovirus transmission. PMID:17620631

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

    PubMed Central

    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

  18. 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

  19. 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. PMID:27105774

  20. Development of PrimeTime-Real-Time PCR for Species Identification of Soybean Cyst Nematode (Heterodera glycines Ichinohe, 1952) in North Carolina.

    PubMed

    Ye, Weimin

    2012-09-01

    Soybean cyst nematode (SCN) is an obligate, sedentary parasite that is a major pathogen of soybean and accounts for an estimated 1 billion dollars in production losses annually in the United States of America. This paper describes the development of a real-time PCR method for rapid, sensitive, species-specific and accurate identification of SCN alone or on mixed populations with other nematodes in North Carolina. The 83-bp DNA fragment of PrimeTime-real-time PCR was designed based on a 477-bp-SCN-SCAR marker previously proved to be SCN-specific. A total of 44 populations including cyst forming nematodes (Heterodera glycines, H. fici, H. schachtii, H. trifolii, Cactodera weissi, Globodera tabacum, Meloidodera floridensis and other unidentified cyst nematodes) and non-cyst forming nematodes (Ditylenchus dipsaci, Meloidogyne incognita and Xiphinema chambersi) were tested in this study, all SCN populations are tested positive and non-SCN populations negative. This assay for the detection and identification has been successfully applied for testing a single SCN cyst, a 2(nd)-stage-SCN juvenile, a single SCN egg, up to ten SCN cysts, a 10-fold dilution of a single 2(nd)-stage-SCN juvenile and 20-fold dilution of one SCN cyst. The assay is not SCN-race specific. It gave an accurate positive result when SCN is mixed with other cyst species. Also, nematode universal primers/probes for real-time PCR amplification as a nematode endogenous control to detect the presence of 18S ribosomal RNA (rRNA) gene were employed in this assay, so that a SCN-negative sample can be tested to exclude false negative. This method will be very useful for a broad range of research programs as well as the regulatory response and management of SCN in North Carolina and other region of the southeastern U.S.A. PMID:23481469

  1. A Comparative Study of Real-Time Aircraft Parameter Identification Schemes Applied to NASA F/A-18 HARV Flight Data

    NASA Astrophysics Data System (ADS)

    Song, Yongkyu; Napolitano, Marcello

    In this paper, two recently introduced parameter identification (PID) methods are applied to the real-time estimation of aerodynamic coefficients from the flight data of the NASA F/A-18 HARV aircraft. The study specifically addresses the computational effort for each PID technique, which can be a decisive factor for on-line real-time application purposes. The results are also compared with off-line parameter identification results obtained through the well-known Maximum Likelihood method as well as wind tunnel data. Following a coding for the two on-line methods organized to minimize the computations, the required on-line computational effort associated with the frequency domain PID method is shown to be lower than that with the time domain PID method by almost one order of magnitude. The overall results show that two on-line PID methods exhibit consistent performance. The frequency domain-based method seems to provide estimates closer to the Maximum Likelihood and wind tunnel results for both longitudinal and lateral/directional dynamics.

  2. A novel real-time PCR assay for the specific identification and quantification of Weissella viridescens in blood sausages.

    PubMed

    Gómez-Rojo, Erica M; Romero-Santacreu, L; Jaime, I; Rovira, J

    2015-12-23

    Weissella viridescens has been identified as one of the lactic acid bacteria (LAB) responsible for the spoilage of "morcilla de Burgos". In order to identify and quantify this bacterium in "morcilla de Burgos", a new specific PCR procedure has been developed. The primers and Taqman probe were designed on the basis of a sequence from the gene recN. To confirm the specificity of the primers, 77 strains from the genera Carnobacterium, Enterococcus, Lactobacillus, Leuconostoc, Pediococcus, Streptococcus, Vagococcus and Weissella were tested by conventional PCR. The specificity of the primers and the correct functioning of the probe was confirmed by performing real-time PCR (qPCR) with 21 W. viridescens strains and 27 strains from other LAB genera. The levels of detection and quantification for the qPCR procedure proposed herein were determined for a pure culture of W. viridescens CECT 283(T) and for "morcilla de Burgos" artificially inoculated with this species. The primers were specific for W. viridescens, with only one product of 91 bp being observed for this species. Similarly, the qPCR reactions were found to be specific, amplifying at a mean CT of 15.0±0.4 only for W. viridescens strains. The limit of detection (LOD) and quantification (LOQ) for this procedure was established in 0.082 pg for genomic DNA from W. viridescens. With regard to the artificially inoculated "morcilla", the limit of quantification was established in 80 CFU/reaction and the limit of detection in 8 CFU/reaction. Consequently, the qPCR developed herein can be considered to be a good, fast, simple and accurate tool for the specific detection and quantification of W. viridescens in meat samples. PMID:26318409

  3. 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

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

    PubMed

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

    2003-10-01

    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

  5. In Vivo Protein Interaction Network Identified with a Novel Real-Time Cross-Linked Peptide Identification Strategy

    PubMed Central

    Weisbrod, Chad R.; Chavez, Juan D.; Eng, Jimmy K.; Yang, Li; Zheng, Chunxiang; Bruce, James E.

    2013-01-01

    Protein interaction topologies are critical determinants of biological function. Large-scale or proteome-wide measurements of protein interaction topologies in cells currently pose an unmet challenge that could dramatically improve understanding of complex biological systems. A primary impediment includes direct protein topology and interaction measurements from living systems since interactions that lack biological significance may be introduced during cell lysis. Furthermore, many biologically relevant protein interactions will likely not survive the lysis/sample preparation and may only be measured with in vivo methods. As a step toward meeting this challenge, a new mass spectrometry method called Real-time Analysis for Cross-linked peptide Technology (ReACT) has been developed that enables assignment of cross-linked peptides “on-the-fly”. Using ReACT, 708 unique cross-linked (<5% FDR) peptide pairs were identified from cross-linked E. coli cells. These data allow assembly of the first protein interaction network that also contains topological features of every interaction, as it existed in cells during cross-linker application. Of the identified interprotein cross-linked peptide pairs, 40% are derived from known interactions and provide new topological data that can help visualize how these interactions exist in cells. Other identified cross-linked peptide pairs are from proteins known to be involved within the same complex, but yield newly discovered direct physical interactors. ReACT enables the first view of these interactions inside cells, and the results acquired with this method suggest cross-linking can play a major role in future efforts to map the interactome in cells. PMID:23413883

  6. Multiplex real-time PCR for detection, identification and quantification of 'Candidatus Liberibacter solanacearum' in potato plants with zebra chip.

    PubMed

    Li, Wenbin; Abad, Jorge A; French-Monar, Ronald D; Rascoe, John; Wen, Aimin; Gudmestad, Neil C; Secor, Gary A; Lee, Ing-Ming; Duan, Yongping; Levy, Laurene

    2009-07-01

    The new Liberibacter species, 'Candidatus Liberibacter solanacearum' (Lso) recently associated with potato/tomato psyllid-transmitted diseases in tomato and capsicum in New Zealand, was found to be consistently associated with a newly emerging potato zebra chip (ZC) disease in Texas and other southwestern states in the USA. A species-specific primer LsoF was developed for both quantitative real-time PCR (qPCR) and conventional PCR (cPCR) to detect and quantify Lso in infected samples. In multiplex qPCR, a plant cytochrome oxidase (COX)-based probe-primer set was used as a positive internal control for host plants, which could be used to reliably access the DNA extraction quality and to normalize qPCR data for accurate quantification of the bacterial populations in environment samples. Neither the qPCR nor the cPCR using the primer and/or probe sets with LsoF reacted with other Liberibacter species infecting citrus or other potato pathogens. The low detection limit of the multiplex qPCR was about 20 copies of the target 16S rDNA templates per reaction for field samples. Lso was readily detected and quantified in various tissues of ZC-affected potato plants collected from fields in Texas. A thorough but uneven colonization of Lso was revealed in various tissues of potato plants. The highest Lso populations were about 3x10(8) genomes/g tissue in the root, which were 3-order higher than those in the above-ground tissues of potato plants. The Lso bacterial populations were normally distributed across the ZC-affected potato plants collected from fields in Texas, with 60% of ZC-affected potato plants harboring an average Lso population from 10(5) to 10(6) genomes/g tissue, 4% of plants hosting above 10(7) Lso genomes/g tissue, and 8% of plants holding below 10(3) Lso genomes/g tissue. The rapid, sensitive, specific and reliable multiplex qPCR showed its potential to become a powerful tool for early detection and quantification of the new Liberibacter species associated

  7. 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

  8. 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.

  9. 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

  10. Development and validation of real-time PCR tests for the identification of four Spodoptera species: Spodoptera eridania, Spodoptera frugiperda, Spodoptera littoralis, and Spodoptera litura (Lepidoptera: Noctuidae).

    PubMed

    Van de Vossenberg, B T L H; Van der Straten, M J

    2014-08-01

    The genus Spodoptera comprises 31 species, 4 of which are listed as quarantine pests for the European Union: Spodoptera eridania (Cramer), Spodoptera frugiperda (Smith), Spodoptera littoralis (Boisduval), and Spodoptera litura (F.). In international trade, the earlier life stages (eggs and larvae) are being intercepted at point of inspection most frequently, challenging the possibilities of morphological identification. To realize a rapid and reliable identification for all stages, we developed and validated four simplex real-time polymerase chain reaction identification tests based on the mitochondrial cytochrome b gene using dual-labeled hydrolysis probes. Method validation on dilutions of extracted DNA of the target organisms showed that low levels of template (up to 0.2-100 pg) can reliably be identified. No cross-reactivity was observed with 14 nontarget Spodoptera and 5 non-Spodoptera species in the specific Spodoptera tests. The tests showed to be repeatable, reproducible (both 100%), and robust. The new Spodoptera tests have proven to be suitable tools for routine identification of all life stages of S. eridania, S. frugiperda, S. littoralis, and S. litura. PMID:25195458

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. Novel Multiplex Real-Time PCR Diagnostic Assay for Identification and Differentiation of Mycobacterium tuberculosis, Mycobacterium canettii, and Mycobacterium tuberculosis Complex Strains▿†

    PubMed Central

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

    2011-01-01

    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. PMID:21123525

  16. 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

  17. 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 Central

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

    2013-01-01

    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

  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. PMID:26897117

  1. 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.

  2. Quantitative real-time PCR for detection and identification of Candidatus Liberibacter species associated with citrus huanglongbing.

    PubMed

    Li, Wenbin; Hartung, John S; Levy, Laurene

    2006-07-01

    :13,000 (w/w) and 1:1000 (c/c: target copy/target copy) in DNA extracts obtained by a standard CTAB method. Our rapid, sensitive and specific TaqMan PCR assay for the detection, identification and quantification of Ca. Liberibacter species has been successfully used in the confirmation of HLB caused by Las in Florida, and will be very useful for a broad range of research programs as well as the regulatory response and management of HLB disease. PMID:16414133

  3. 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

  4. Device-independent tests of entropy.

    PubMed

    Chaves, Rafael; Brask, Jonatan Bohr; Brunner, Nicolas

    2015-09-11

    We show that the entropy of a message can be tested in a device-independent way. Specifically, we consider a prepare-and-measure scenario with classical or quantum communication, and develop two different methods for placing lower bounds on the communication entropy, given observable data. The first method is based on the framework of causal inference networks. The second technique, based on convex optimization, shows that quantum communication provides an advantage over classical communication, in the sense of requiring a lower entropy to reproduce given data. These ideas may serve as a basis for novel applications in device-independent quantum information processing. PMID:26406813

  5. 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.

  6. 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

  7. 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.

  8. 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. PMID:19902419

  9. 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

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

    PubMed

    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

  11. 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. PMID:25262809

  12. A multiplex, internally controlled real-time PCR assay for detection of toxigenic Clostridium difficile and identification of hypervirulent strain 027/ST-1.

    PubMed

    Hoegh, A M; Nielsen, J B; Lester, A; Friis-Møller, A; Schønning, K

    2012-06-01

    The purpose of this study was to validate a multiplex real-time PCR assay capable of detecting toxigenic Clostridium difficile and simultaneously identifying C. difficile ribotype 027/ST-1 by targeting the toxin genes tcdA, tcdB and cdtA in one reaction and in a separate reaction identifying the Δ117 deletion in tcdC associated with ribotype 027/ST-1. PCR was done prospectively on 704 samples routinely submitted to our department and results were compared to results of toxigenic culture. Sequencing of tcdC, multi locus sequence typing (MLST) and PCR ribotyping were done on cultured isolates to confirm the correct identification of the Δ117 deletion in tcdC and C. difficile ribotype 027/ST-1, respectively. The PCR assay displayed a sensitivity, specificity, PPV and NPV of 99.0%, 97.4%, 87.4% and 99.8%, respectively, compared to toxigenic culture on 665 samples evaluable both by PCR and culture. Sequencing of tcdC, ribotyping and MLST of cultured isolates validated the genotyping assay and confirmed the ability of the assay to correctly identify C. difficile ribotype 027/ST-1 in our current epidemiological setting. We describe the use of a combination of two separate PCR assays for sensitive and specific detection of toxigenic C. difficile and presumptive identification of C. difficile 027/ST-1. PMID:21938539

  13. 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. PMID:23831826

  14. 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

  15. 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

  16. Real-Time Simulation

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Coryphaeus Software, founded in 1989 by former NASA electronic engineer Steve Lakowske, creates real-time 3D software. Designer's Workbench, the company flagship product, is a modeling and simulation tool for the development of both static and dynamic 3D databases. Other products soon followed. Activation, specifically designed for game developers, allows developers to play and test the 3D games before they commit to a target platform. Game publishers can shorten development time and prove the "playability" of the title, maximizing their chances of introducing a smash hit. Another product, EasyT, lets users create massive, realistic representation of Earth terrains that can be viewed and traversed in real time. Finally, EasyScene software control the actions among interactive objects within a virtual world. Coryphaeus products are used on Silican Graphics workstation and supercomputers to simulate real-world performance in synthetic environments. Customers include aerospace, aviation, architectural and engineering firms, game developers, and the entertainment industry.

  17. 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

  18. 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.

  19. Development of a novel DNA extraction method for identification and quantification of Mycobacterium avium subsp. paratuberculosis from tissue samples by real-time PCR.

    PubMed

    Park, Kun Taek; Allen, Andrew J; Davis, William C

    2014-04-01

    Mycobacterium avium subsp. paratuberculosis (Map) is the causative agent of Johne's disease in ruminants and possibly associated with human Crohn's disease. One impediment in furthering our understanding of this potential association has been the lack of an accurate method for detection of Map in affected tissues. Real time polymerase chain reaction (RT-PCR) methods have been reported to have different sensitivities in detection of Map. This is in part attributable to the difficulties of extracting Map DNA and removing PCR inhibitors from the clinical specimens. The maximum efficiency of RT-PCR can only be achieved by using high quality DNA samples. In this study, we present a novel pre-treatment method which significantly increases Map DNA recovery and decreases PCR inhibitors (p<0.05). When the pre-treatment method was combined with the DNeasy Blood and Tissue kit (Qiagen), PCR inhibition was not detected in any of three different RT-PCR methods tested in this study. The results obtained with the IS900 probe showed an excellent Kappa value (0.849) and a high correlation coefficient r (0.940) compared to the results of culture method. When used to examine unknown field samples (n=15), more positive tissues were identified with DNA extracts prepared with pre-treatment method than without (5 vs 3). This improved Map DNA extraction method from tissue samples will make RT-PCR a more powerful tool for a wide range of applications for Map identification and quantification. PMID:24534783

  20. 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

  1. Optimising the diagnostic strategy for onychomycosis from sample collection to FUNGAL identification evaluation of a diagnostic kit for real-time PCR.

    PubMed

    Petinataud, Dimitri; Berger, Sibel; Ferdynus, Cyril; Debourgogne, Anne; Contet-Audonneau, Nelly; Machouart, Marie

    2016-05-01

    Onychomycosis is a common nail disorder mainly due to dermatophytes for which the conventional diagnosis requires direct microscopic observation and culture of a biological sample. Nevertheless, antifungal treatments are commonly prescribed without a mycological examination having been performed, partly because of the slow growth of dermatophytes. Therefore, molecular biology has been applied to this pathology, to support a quick and accurate distinction between onychomycosis and other nail damage. Commercial kits are now available from several companies for improving traditional microbiological diagnosis. In this paper, we present the first evaluation of the real-time PCR kit marketed by Bio Evolution for the diagnosis of dermatophytosis. Secondly, we compare the efficacy of the kit on optimal and non-optimal samples. This study was conducted on 180 nails samples, processed by conventional methods and retrospectively analysed using this kit. According to our results, this molecular kit has shown high specificity and sensitivity in detecting dermatophytes, regardless of sample quality. On the other hand, and as expected, optimal samples allowed the identification of a higher number of dermatophytes by conventional mycological diagnosis, compared to non-optimal samples. Finally, we have suggested several strategies for the practical use of such a kit in a medical laboratory for quick pathogen detection. PMID:26806228

  2. Device-independent quantum key distribution

    NASA Astrophysics Data System (ADS)

    Hänggi, Esther

    2010-12-01

    In this thesis, we study two approaches to achieve device-independent quantum key distribution: in the first approach, the adversary can distribute any system to the honest parties that cannot be used to communicate between the three of them, i.e., it must be non-signalling. In the second approach, we limit the adversary to strategies which can be implemented using quantum physics. For both approaches, we show how device-independent quantum key distribution can be achieved when imposing an additional condition. In the non-signalling case this additional requirement is that communication is impossible between all pairwise subsystems of the honest parties, while, in the quantum case, we demand that measurements on different subsystems must commute. We give a generic security proof for device-independent quantum key distribution in these cases and apply it to an existing quantum key distribution protocol, thus proving its security even in this setting. We also show that, without any additional such restriction there always exists a successful joint attack by a non-signalling adversary.

  3. 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.

  4. 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

  5. Experimental Measurement-Device-Independent Entanglement Detection

    PubMed Central

    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

  6. 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

  7. 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. PMID:27283834

  8. Real-time RT-PCR for detection, identification and absolute quantification of viral haemorrhagic septicaemia virus using different types of standards.

    PubMed

    Lopez-Vazquez, C; Bandín, I; Dopazo, C P

    2015-05-21

    In the present study, 2 systems of real-time RT-PCR-one based on SYBR Green and the other on TaqMan-were designed to detect strains from any genotype of viral haemorrhagic septicaemia virus (VHSV), with high sensitivity and repeatability/reproducibility. In addition, the method was optimized for quantitative purposes (qRT-PCR), and standard curves with different types of reference templates were constructed and compared. Specificity was tested against 26 isolates from 4 genotypes. The sensitivity of the procedures was first tested against cell culture isolation, obtaining a limit of detection (LD) of 100 TCID50 ml-1 (100-fold below the LD using cell culture), at a threshold cycle value (Ct) of 36. Sensitivity was also evaluated using RNA from crude (LD = 1 fg; 160 genome copies) and purified virus (100 ag; 16 copies), plasmid DNA (2 copies) and RNA transcript (15 copies). No differences between both chemistries were observed in sensitivity and dynamic range. To evaluate repeatability and reproducibility, all experiments were performed in triplicate and on 3 different days, by workers with different levels of experience, obtaining Ct values with coefficients of variation always <5. This fact, together with the high efficiency and R2 values of the standard curves, encouraged us to analyse the reliability of the method for viral quantification. The results not only demonstrated that the procedure can be used for detection, identification and quantification of this virus, but also demonstrated a clear correlation between the regression lines obtained with different standards, which will help scientists to compare sensitivity results between different studies. PMID:25993885

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. [DNA extraction and identification of Trichophyton rubrum by real-time polymerase chain reaction from direct nail scraping specimens of patients with onycomycosis].

    PubMed

    Berk, Elife; Kuştimur, Semra; Kalkancı, Ayşe; Oztaş, O Murat

    2011-01-01

    Trichophyton rubrum is the most frequently encountered dermatophyte species causing onichomycosis. The routine diagnosis of dermatophytes depends on the direct microscopic examination (DME) and culture methods, however due to the phenotypic identification problems related to those agents, the molecular methods come into question. The aim of this study was to evaluate the diagnostic performance of real-time polymerase chain reaction (RT-PCR) for the identification of T.rubrum by comparing to DME and culture methods, from nail samples of patients with the complaints of onychomycosis. A total of 90 patients of whom 58 were male who were admitted to the dermatology outpatients clinics of our hospital with the complaints of color/shape changes in the nails and thickening of the nail, were included in the study, together with the 20 healthy volunteer subjects as controls. The nail scraping samples obtained from the patients and controls were examined with direct microscopy using 15% potassium hydroxide, dimethyl sulphoxide and chlorazole black mixture and cultivated onto Sabouraud dextrose agar with and without cycloheximide. For DNA isolation, after the disruption of nail samples with a steel tool, phenol-chloroform-isoamyl alcohol purification method were used. The amplification and demonstration of the T.rubrum DNA have been performed by using specific primers and probes following TaqMan protocol of RT-PCR (LightCycler-Roche, USA) method. Seventy-two of the patients yielded positive and 18 yielded negative results with DME. Growth of molds was detected in the cultures of 20 (27.8%) of the 72 DME positive patients and all of the isolates were identified as T.rubrum. No fungal growth was seen in the samples of 18 patients who were DME negative. In DME positive group, 67 (93%) patients were found to be positive in RT-PCR, while 8 (44.4%) patients were RT-PCR positive in DME negative group. All of the culture positive samples (n= 20) were also found positive in RT

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. Rapid Differentiation and Identification of Potential Severe Strains of Citrus tristeza Virus by Real-Time Reverse Transcription Polymerase Chain Reaction Assays

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A multiplex Taqman®-based real-time reverse transcription (RT) polymerase chain reaction (PCR) assay was developed to detect all strains of Citrus tristeza virus (CTV) and to identify potentially severe strains of the virus. A CTV TaqMan probe (CTV-CY5) based on the coat protein (CP) gene sequences...

  1. 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...

  2. 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

  3. 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.

  4. 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.

  5. Measurement-device-independent quantum coin tossing

    NASA Astrophysics Data System (ADS)

    Zhao, Liangyuan; Yin, Zhenqiang; Wang, Shuang; Chen, Wei; Chen, Hua; Guo, Guangcan; Han, Zhengfu

    2015-12-01

    Quantum coin tossing (QCT) is an important primitive of quantum cryptography and has received continuous interest. However, in practical QCT, Bob's detectors can be subjected to detector-side channel attacks launched by dishonest Alice, which will possibly make the protocol completely insecure. Here, we report a simple strategy of a detector-blinding attack based on a recent experiment. To remove all the detector side channels, we present a solution of measurement-device-independent QCT (MDI-QCT). This method is similar to the idea of MDI quantum key distribution (QKD). MDI-QCT is loss tolerant with single-photon sources and has the same bias as the original loss-tolerant QCT under a coherent attack. Moreover, it provides the potential advantage of doubling the secure distance for some special cases. Finally, MDI-QCT can also be modified to fit the weak coherent-state sources. Thus, based on the rapid development of practical MDI-QKD, our proposal can be implemented easily.

  6. Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data

    PubMed Central

    2010-01-01

    Background Normalizing through reference genes, or housekeeping genes, can make more accurate and reliable results from reverse transcription real-time quantitative polymerase chain reaction (qPCR). Recent studies have shown that no single housekeeping gene is universal for all experiments. Thus, suitable reference genes should be the first step of any qPCR analysis. Only a few studies on the identification of housekeeping gene have been carried on plants. Therefore qPCR studies on important crops such as cotton has been hampered by the lack of suitable reference genes. Results By the use of two distinct algorithms, implemented by geNorm and NormFinder, we have assessed the gene expression of nine candidate reference genes in cotton: GhACT4, GhEF1α5, GhFBX6, GhPP2A1, GhMZA, GhPTB, GhGAPC2, GhβTUB3 and GhUBQ14. The candidate reference genes were evaluated in 23 experimental samples consisting of six distinct plant organs, eight stages of flower development, four stages of fruit development and in flower verticils. The expression of GhPP2A1 and GhUBQ14 genes were the most stable across all samples and also when distinct plants organs are examined. GhACT4 and GhUBQ14 present more stable expression during flower development, GhACT4 and GhFBX6 in the floral verticils and GhMZA and GhPTB during fruit development. Our analysis provided the most suitable combination of reference genes for each experimental set tested as internal control for reliable qPCR data normalization. In addition, to illustrate the use of cotton reference genes we checked the expression of two cotton MADS-box genes in distinct plant and floral organs and also during flower development. Conclusion We have tested the expression stabilities of nine candidate genes in a set of 23 tissue samples from cotton plants divided into five different experimental sets. As a result of this evaluation, we recommend the use of GhUBQ14 and GhPP2A1 housekeeping genes as superior references for normalization of gene

  7. Development of a single-tube duplex EvaGreen real-time PCR for the detection and identification of EHV-1 and EHV-4.

    PubMed

    Hu, Zhe; Zhu, Chao; Chang, Hao; Guo, Wei; Liu, Diqiu; Xiang, Wenhua; Wang, Xiaojun

    2014-05-01

    The objective of this study was to develop a novel EvaGreen (EG) based real-time PCR technique for the simultaneous detection of Equine herpesvirus 1 (EHV-1) and Equine herpesvirus 4 (EHV-4) genomes from equine nasal swabs. Viral genomes were identified based on their specific melting temperatures (T m), which are 88.0 and 84.4 °C for EHV-1 and EHV-4, respectively. The detection limitation of this method was 50 copies/μl or 0.15 pg/μl for EHV-1 and 5 copies/μl or 2.5 fg/μl for EHV-4. This assay was 50-1,000 times more sensitive than the SYBR Green (SG)-based assay using the same primer pairs and as sensitive as the TaqMan-MGB probe-based assay. The validity of the real-time PCR assays was confirmed by testing 13 clinical samples. When all results of the EG, SG, and TaqMan probe-based singleplex and duplex real-time PCRs were considered together, a total of 84.6 % (11/13) horses and donkeys were positive for at least one virus. EHV-1 and EHV-4 coexisted in 81.8 % (9/11) horses. Overall, we report that the EvaGreen duplex real-time PCR is an economical and alternative diagnostic method for the rapid differentiation of EHV-1 and EHV-4 in nasal swabs. PMID:24615388

  8. 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 Central

    Gago, Sara; Esteban, Cristina; Valero, Clara; Zaragoza, Óscar; Puig de la Bellacasa, Jorge

    2014-01-01

    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 (r2 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. PMID:24478409

  9. Successful intraoperative identification of an anomalous origin of the left coronary artery from the pulmonary artery using real time three-dimensional transesophageal echocardiography.

    PubMed

    Jin, Yao Dong; Hsiung, Ming C; Tsai, Shen Kou; Chang, Chung-Yi; Wei, Jeng; Ou, Ching-huei; Chang, Yi Cheng; Lee, Kuo Chen; Sue, Sung-How

    2011-08-01

    Anomalous origin of the left coronary artery (LCA) from the pulmonary artery (ALCAPA) is a rare congenital defect that presents only infrequently in adults. An adult diagnosed with ALCAPA, heart failure, and mitral regurgitation underwent surgical ligation of the anomalous origin of the LCA from the pulmonary artery (PA) and coronary artery bypass grafting (CABG). The anomalous origin in the PA and proximal segment of the left anterior descending artery (LAD) was successfully delineated via real time, three-dimensional transesophageal echocardiography during surgery. This modality allows for fast assessment and novel views of complex cardiac abnormalities and can aid in perioperative monitoring.  PMID:21564280

  10. Real-Time Benchmark Suite

    Energy Science and Technology Software Center (ESTSC)

    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.

  11. 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

  12. 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

  13. 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. PMID:15634974

  14. 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

  15. 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

  16. Real-Time PCR for the Detection and Quantification of Geodermatophilaceae from Stone Samples and Identification of New Members of the Genus Blastococcus†

    PubMed Central

    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. PMID:16391063

  17. 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. PMID:16391063

  18. 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

  19. Identification of Human Adenovirus in Respiratory Samples with Luminex Respiratory Virus Panel Fast V2 Assay and Real-Time Polymerase Chain Reaction.

    PubMed

    Esposito, Susanna; Scala, Alessia; Bianchini, Sonia; Zampiero, Alberto; Fossali, Emilio; Principi, Nicola

    2016-01-01

    In order to compare the last version of the Respiratory Virus Panel (RVP) Fast assay for human Adenovirus (hAdv) detection with a specific real-time polymerase chain reaction (qPCR), which is considered the gold standard for hAdv detection, nasopharyngeal samples collected from 309 children (age range, four months to eight years) with respiratory tract infection were tested using the RVP Fast v2 assay (Luminex Molecular Diagnostics, Inc., Toronto, ON, Canada) and a specific TaqMan qPCR to identify hAdv DNA. The RVP Fast v2 assay detected 30/61 (49.2%) hAdv infections that had been identified by real-time qPCR, demonstrating a significantly lower detection rate (p < 0.001). The sensitivity of the RVP Fast v2 assay in comparison to qPCR was lower in younger children (42.9% vs. 57.7%; Cohen's kappa coefficient, 0.53); in samples with co-infections (40.0% vs. 56.7%; Cohen's kappa coefficient, 0.52); and in samples with hAdv type C (45.9% vs. 57.1%; Cohen's kappa coefficient, 0.60). Samples with lower viral loads were associated with a significantly lower sensitivity of the RVP Fast v2 assay (35.1% vs. 68.2%, p = 0.01; Cohen's kappa coefficients, 0.49). The RVP Fast v2 assay has important limitations for the detection of hAdv and cannot be used to evaluate whether hAdvs are the main etiologic agent responsible for an outbreak or when epidemiological studies are performed. PMID:26927078

  20. Identification of Helicobacter pylori and the cagA genotype in gastric biopsies using highly sensitive real-time PCR as a new diagnostic tool.

    PubMed

    Yamazaki, Shiho; Kato, Shunji; Matsukura, Norio; Ohtani, Masahiro; Ito, Yoshiyuki; Suto, Hiroyuki; Yamazaki, Yukinao; Yamakawa, Akiyo; Tokudome, Shinkan; Higashi, Hideaki; Hatakeyama, Masanori; Azuma, Takeshi

    2005-06-01

    The CagA protein is one of the virulence factors of Helicobacter pylori, and two major subtypes of CagA have been observed, the Western and East Asian type. CagA is injected from the bacteria into gastric epithelial cells, undergoes tyrosine phosphorylation, and binds to Src homology 2 domain-containing protein-tyrosine phosphatase SHP-2. The East Asian type CagA binds to SHP-2 more strongly than the Western type CagA. Here, we tried to distinguish the CagA type by highly sensitive real-time PCR with the objective of establishing a system to detect H. pylori and CagA subtypes from gastric biopsies. We designed primers and probe sets for Western or East Asian-cagA at Western-specific or East Asian-specific sequence regions, respectively, and H. pylori 16S rRNA. We could detect the H. pylori 16S rRNA gene, Western and East Asian-cagA gene from DNA of gastric biopsies. The sensitivity and specificity for H. pylori infection was 100% in this system. In Thai patients, 87.8% (36/41) were cagA-positive; 26.8% (11/41) were Western-cagA positive and 53.7% (22/41) were East Asian-cagA positive, while 7.3% (3/41) reacted with both types of cagA. These results suggest that this real-time PCR system provides a highly sensitive assessment of CagA type as a new diagnostic tool for the pathogenicity of H. pylori infection. PMID:15907447

  1. 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.

  2. 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.

  3. Real-time refinery optimization

    SciTech Connect

    Kennedy, J.P.

    1989-05-01

    This article discusses refinery operation with specific consideration of the topics of: gasoline; control projects; catalytic reforming control; hydrocracker control packages; blending optimization; real-time data acquisition; and other plant automation packages.

  4. 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.

  5. Real Time Data System (RTDS)

    NASA Technical Reports Server (NTRS)

    Muratore, John F.

    1991-01-01

    Lessons learned from operational real time expert systems are examined. The basic system architecture is discussed. An expert system is any software that performs tasks to a standard that would normally require a human expert. An expert system implies knowledge contained in data rather than code. And an expert system implies the use of heuristics as well as algorithms. The 15 top lessons learned by the operation of a real time data system are presented.

  6. 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.

  7. 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

  8. Assessing direct analysis in real-time-mass spectrometry (DART-MS) for the rapid identification of additives in food packaging.

    PubMed

    Ackerman, L K; Noonan, G O; Begley, T H

    2009-12-01

    The ambient ionization technique direct analysis in real time (DART) was characterized and evaluated for the screening of food packaging for the presence of packaging additives using a benchtop mass spectrometer (MS). Approximate optimum conditions were determined for 13 common food-packaging additives, including plasticizers, anti-oxidants, colorants, grease-proofers, and ultraviolet light stabilizers. Method sensitivity and linearity were evaluated using solutions and characterized polymer samples. Additionally, the response of a model additive (di-ethyl-hexyl-phthalate) was examined across a range of sample positions, DART, and MS conditions (temperature, voltage and helium flow). Under optimal conditions, molecular ion (M+H+) was the major ion for most additives. Additive responses were highly sensitive to sample and DART source orientation, as well as to DART flow rates, temperatures, and MS inlet voltages, respectively. DART-MS response was neither consistently linear nor quantitative in this setting, and sensitivity varied by additive. All additives studied were rapidly identified in multiple food-packaging materials by DART-MS/MS, suggesting this technique can be used to screen food packaging rapidly. However, method sensitivity and quantitation requires further study and improvement. PMID:19753496

  9. Identification of eusynstyelamide B as a potent cell cycle inhibitor following the generation and screening of an ascidian-derived extract library using a real time cell analyzer.

    PubMed

    Liberio, Michelle S; Sadowski, Martin C; Nelson, Colleen C; Davis, Rohan A

    2014-10-01

    Ascidians are marine invertebrates that have been a source of numerous cytotoxic compounds. Of the first six marine-derived drugs that made anticancer clinical trials, three originated from ascidian specimens. In order to identify new anti-neoplastic compounds, an ascidian extract library (143 samples) was generated and screened in MDA-MB-231 breast cancer cells using a real-time cell analyzer (RTCA). This resulted in 143 time-dependent cell response profiles (TCRP), which are read-outs of changes to the growth rate, morphology, and adhesive characteristics of the cell culture. Twenty-one extracts affected the TCRP of MDA-MB-231 cells and were further investigated regarding toxicity and specificity, as well as their effects on cell morphology and cell cycle. The results of these studies were used to prioritize extracts for bioassay-guided fractionation, which led to the isolation of the previously identified marine natural product, eusynstyelamide B (1). This bis-indole alkaloid was shown to display an IC50 of 5 µM in MDA-MB-231 cells. Moreover, 1 caused a strong cell cycle arrest in G2/M and induced apoptosis after 72 h treatment, making this molecule an attractive candidate for further mechanism of action studies. PMID:25329705

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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. PMID:25775103

  15. The use of laser microdissection in the identification of suitable reference genes for normalization of quantitative real-time PCR in human FFPE epithelial ovarian tissue samples.

    PubMed

    Cai, Jing; Li, Tao; Huang, Bangxing; Cheng, Henghui; Ding, Hui; Dong, Weihong; Xiao, Man; Liu, Ling; Wang, Zehua

    2014-01-01

    Quantitative real-time PCR (qPCR) is a powerful and reproducible method of gene expression analysis in which expression levels are quantified by normalization against reference genes. Therefore, to investigate the potential biomarkers and therapeutic targets for epithelial ovarian cancer by qPCR, it is critical to identify stable reference genes. In this study, twelve housekeeping genes (ACTB, GAPDH, 18S rRNA, GUSB, PPIA, PBGD, PUM1, TBP, HRPT1, RPLP0, RPL13A, and B2M) were analyzed in 50 ovarian samples from normal, benign, borderline, and malignant tissues. For reliable results, laser microdissection (LMD), an effective technique used to prepare homogeneous starting material, was utilized to precisely excise target tissues or cells. One-way analysis of variance (ANOVA) and nonparametric (Kruskal-Wallis) tests were used to compare the expression differences. NormFinder and geNorm software were employed to further validate the suitability and stability of the candidate genes. Results showed that epithelial cells occupied a small percentage of the normal ovary indeed. The expression of ACTB, PPIA, RPL13A, RPLP0, and TBP were stable independent of the disease progression. In addition, NormFinder and geNorm identified the most stable combination (ACTB, PPIA, RPLP0, and TBP) and the relatively unstable reference gene GAPDH from the twelve commonly used housekeeping genes. Our results highlight the use of homogeneous ovarian tissues and multiple-reference normalization strategy, e.g. the combination of ACTB, PPIA, RPLP0, and TBP, for qPCR in epithelial ovarian tissues, whereas GAPDH, the most commonly used reference gene, is not recommended, especially as a single reference gene. PMID:24776823

  16. 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.

  17. Identification of Valid Housekeeping Genes for Real-Time Quantitative PCR Analysis of Collapsed Lung Tissues of Neonatal Somatic Cell Nuclear Transfer-Derived Cattle.

    PubMed

    Liu, Yan; Zhang, Yunhai; Jiang, Qiuling; Rao, Man; Sheng, Zheya; Zhang, Yu; Du, Weihua; Hao, Haisheng; Zhao, Xueming; Xu, Zhe; Liu, Jianning; Zhu, Huabin

    2015-10-01

    Cloned calves produced by somatic cell nuclear transfer frequently suffer alveolar collapse as newborns. To study the underlying pathophysiological mechanisms responsible for this phenomenon, the expression profiles of numerous genes involved in lung development need to be investigated. Quantitative real-time PCR is commonly adopted in gene expression analysis. However, selection of an appropriate reference gene for normalization is critical for obtaining reliable and accurate results. Seven housekeeping genes-β-glucuronidase (GUSB), phosphoglycerate kinase 1 (PGK1), β-2-microglobolin (B2M), peptidylprolyl isomerase A (PPIA), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), TATA-box binding protein (TBP), and 5.8S ribosomal RNA (5.8S rRNA)-were selected and evaluated as candidates. Their gene expression levels in the collapsed lungs of deceased neonate cloned calves and normal lung derived from normal calves were assessed. The ranking of gene expression stability was estimated by the geNorm, NormFinder, and BestKeeper programs. 5.8S rRNA and PPIA were determined to be the most stable reference genes by geNorm and BestKeeper, whereas the combination of GAPDH and TBP was suggested as reference genes by NormFinder. Taking these results into account, we conclude that 5.8S rRNA and PPIA could be the most reliable reference genes for studying the genes involved in alveolar collapse. Moreover, 5.8S rRNA could be represented as a uniform reference gene in similar cases. PMID:26393896

  18. Quantitative identification of fecal water pollution sources by TaqMan real-time PCR assays using Bacteroidales 16S rRNA genetic markers.

    PubMed

    Lee, Dae-Young; Weir, Susan C; Lee, Hung; Trevors, Jack T

    2010-12-01

    PCR-based analysis of Bacteroidales 16S rRNA genes has emerged as a promising tool to identify sources of fecal water pollution. In this study, three TaqMan real-time PCR assays (BacGeneral, BacHuman, and BacBovine) were developed and evaluated for their ability to quantitatively detect general (total), human-specific, and bovine-specific Bacteroidales 16S rRNA genetic markers. The detection sensitivity was determined to be 6.5 copies of 16S rRNA gene for the BacGeneral and BacHuman assays and 10 copies for the BacBovine assay. The assays were capable of detecting approximately one to two cells per PCR. When tested with 70 fecal samples from various sources (human, cattle, pig, deer, dog, cat, goose, gull, horse, and raccoon), the three assays positively identified the target markers in all samples without any false-negative results. The BacHuman and BacBovine assays exhibited false-positive reactions with non-target samples in a few cases. However, the level of the false-positive reactions was about 50 times smaller than that of the true-positive ones, and therefore, these cross-reactions were unlikely to cause misidentifications of the fecal pollution sources. Microbial source-tracking capability was tested at two freshwater streams of which water quality was influenced by human and cattle feces, respectively. The assays accurately detected the presence of the corresponding host-specific markers upon fecal pollution and the persistence of the markers in downstream areas. The assays are expected to reliably determine human and bovine fecal pollution sources in environmental water samples. PMID:20871990

  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 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

  20. 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

  1. 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

  2. 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

    Lee, Jaeseung; Holte, James; Ritenour, E Russell

    2013-02-01

    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

  3. 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

  4. Real-time criteria based on spectral dynamics of medium response for the detection and identification of substance using THz signal

    NASA Astrophysics Data System (ADS)

    Trofimov, Vyacheslav A.; Varentsova, Svetlana A.

    2014-10-01

    We propose effective criteria based on the analysis of spectral dynamics of medium response for the detection and identification of dangerous substances at using pulsed THz signal containing a few cycles and fixed absolute phase. These criteria are integral criteria in time. We show the applicability of these criteria for distinguishing the drugs and for drugs detection in the mixture with neutral substances and explosives in transmission mode. We also apply these criteria for the detection of PWM C4 explosive with complicated shape of the surface in reflection mode.

  5. 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.

  6. Real Time Data System (RTDS)

    NASA Technical Reports Server (NTRS)

    Heindel, Troy A.

    1991-01-01

    Information is given in viewgraph form on the Real Time Data System (RTDS). Topics covered include applications to the Space Station Freedom, the Space Shuttle flight controllers, the Mission Control Center workstations, and the Remote Manipulator Systems (RMS). Also covered are the technology gap, pacing factors, and lessons learned during research.

  7. 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

  8. Molecular Identification and Real-time Quantitative PCR (qPCR) for Rapid Detection of Thelohanellus kitauei, a Myxozoan Parasite Causing Intestinal Giant Cystic Disease in the Israel Carp

    PubMed Central

    Seo, Jung Soo; Jeon, Eun Ji; Kim, Moo Sang; Woo, Sung Ho; Kim, Jin Do; Jung, Sung Hee; Park, Myoung Ae; Jee, Bo Young; Kim, Jin Woo; Kim, Yi-Cheong

    2012-01-01

    Intestinal giant-cystic disease (IGCD) of the Israel carp (Cyprinus carpio nudus) has been recognized as one of the most serious diseases afflicting inland farmed fish in the Republic of Korea, and Thelohanellus kitauei has been identified as the causative agent of the disease. Until now, studies concerning IGCD caused by T. kitauei in the Israel carp have been limited to morphological and histopathological examinations. However, these types of diagnostic examinations are relatively time-consuming, and the infection frequently cannot be detected in its early stages. In this study, we cloned the full-length 18S rRNA gene of T. kitauei isolated from diseased Israel carps, and carried out molecular identification by comparing the sequence with those of other myxosporeans. Moreover, conventional PCR and real-time quantitative PCR (qPCR) using oligonucleotide primers for the amplification of 18S rRNA gene fragment were established for further use as methods for rapid diagnosis of IGCD. Our results demonstrated that both the conventional PCR and real-time quantitative PCR systems applied herein are effective for rapid detection of T. kitauei spores in fish tissues and environmental water. PMID:22711920

  9. Towards falls prevention: a wearable wireless and battery-less sensing and automatic identification tag for real time monitoring of human movements.

    PubMed

    Ranasinghe, Damith C; Shinmoto Torres, Roberto L; Sample, Alanson P; Smith, Joshua R; Hill, Keith; Visvanathan, Renuka

    2012-01-01

    Falls related injuries among elderly patients in hospitals or residents in residential care facilities is a significant problem that causes emotional and physical trauma to those involved while presenting a rising healthcare expense in countries such as Australia where the population is ageing. Novel approaches using low cost and privacy preserving sensor enabled Radio Frequency Identification (RFID) technology may have the potential to provide a low cost and effective technological intervention to prevent falls in hospitals. We outline the details of a wearable sensor enabled RFID tag that is battery free, low cost, lightweight, maintenance free and can be worn continuously for automatic and unsupervised remote monitoring of activities of frail patients at acute hospitals or residents in residential care. The technological developments outlined in the paper forms part of an overall technological intervention developed to reduce falls at acute hospitals or in residential care facilities. This paper outlines the details of the technology, underlying algorithms and the results (where an accuracy of 94-100% was achieved) of a successful pilot trial. PMID:23367394

  10. The Raptor Real-Time Processing Architecture

    NASA Astrophysics Data System (ADS)

    Galassi, M.; Starr, D.; Wozniak, P.; Brozdin, K.

    The primary goal of Raptor is ambitious: to identify interesting optical transients from very wide field of view telescopes in real time, and then to quickly point the higher resolution Raptor ``fovea'' cameras and spectrometer to the location of the optical transient. The most interesting of Raptor's many applications is the real-time search for orphan optical counterparts of Gamma Ray Bursts. The sequence of steps (data acquisition, basic calibration, source extraction, astrometry, relative photometry, the smarts of transient identification and elimination of false positives, telescope pointing feedback, etc.) is implemented with a ``component'' approach. All basic elements of the pipeline functionality have been written from scratch or adapted (as in the case of SExtractor for source extraction) to form a consistent modern API operating on memory resident images and source lists. The result is a pipeline which meets our real-time requirements and which can easily operate as a monolithic or distributed processing system. Finally, the Raptor architecture is entirely based on free software (sometimes referred to as ``open source'' software). In this paper we also discuss the interplay between various free software technologies in this type of astronomical problem.

  11. Raptor -- Mining the Sky in Real Time

    NASA Astrophysics Data System (ADS)

    Galassi, M.; Borozdin, K.; Casperson, D.; McGowan, K.; Starr, D.; White, R.; Wozniak, P.; Wren, J.

    2004-06-01

    The primary goal of Raptor is ambitious: to identify interesting optical transients from very wide field of view telescopes in real time, and then to quickly point the higher resolution Raptor ``fovea'' cameras and spectrometer to the location of the optical transient. The most interesting of Raptor's many applications is the real-time search for orphan optical counterparts of Gamma Ray Bursts. The sequence of steps (data acquisition, basic calibration, source extraction, astrometry, relative photometry, the smarts of transient identification and elimination of false positives, telescope pointing feedback...) is implemented with a ``component'' aproach. All basic elements of the pipeline functionality have been written from scratch or adapted (as in the case of SExtractor for source extraction) to form a consistent modern API operating on memory resident images and source lists. The result is a pipeline which meets our real-time requirements and which can easily operate as a monolithic or distributed processing system. Finally: the Raptor architecture is entirely based on free software (sometimes referred to as "open source" software). In this paper we also discuss the interplay between various free software technologies in this type of astronomical problem.

  12. Development of novel real-time TaqMan(®) PCR assays for the species and sex identification of otter (Lutra lutra) and their application to noninvasive genetic monitoring.

    PubMed

    O'Neill, David; Turner, Peter D; O'Meara, Denise B; Chadwick, Elizabeth A; Coffey, Lee; O'Reilly, Catherine

    2013-09-01

    Developing strategies to maintain biodiversity requires baseline information on the current status of each individual species. The development of genetic techniques and their application to noninvasively collected samples have the potential to yield information on the structure of elusive animal populations and so are important tools in conservation management. Using DNA isolated from faecal samples can be challenging owing to low quantity and quality. This study, however, presents the development of novel real-time polymerase chain reaction assays using fluorescently labelled TaqMan(®) MGB probes enabling species and sex identification of Eurasian otter (Lutra lutra) spraints (faeces). These assays can also be used in determining an optimum microsatellite panel and can be employed as cost-saving screening tools for downstream genetic testing including microsatellite genotyping and haplotype analysis. The techniques are shown to work efficiently with L. lutra DNA isolated from tissue, hair, spraint, blood and anal jelly samples. PMID:23870402

  13. Real Time Identification of Drug-Induced Liver Injury (DILI) through Daily Screening of ALT Results: A Prospective Pilot Cohort Study

    PubMed Central

    M'Kada, Helmi; Perazzo, Hugo; Munteanu, Mona; Ngo, Yen; Ramanujam, Nittia; Fautrel, Bruno; Imbert-Bismut, Françoise; Ratziu, Vlad; Schuppe-Koistinen, Ina; Leblond, Véronique; Delattre, Jean Yves; Samson, Yves; Caen, Olivier Lyon; Bricaire, François; Khayat, David; Pierrot-Deseilligny, Charles; Herson, Serge; Amoura, Zahir; Tilleul, Patrick; Deckmyn, Olivier; Coriat, Pierre; Delpech, Vincent Nicolas; Boulogne, Philippe; Bonnefont-Rousselot, Dominique; Poynard, Thierry

    2012-01-01

    Objective Identification of drug-induced liver disease (DILI) is difficult, even among hospitalized patients. The aim of this pilot study was to assess the impact of a specific strategy for DILI screening. Design We prospectively compared the number of acute DILI cases identified in one week of a proactive strategy based on centralized elevated ALT values to those identified with a standard of care strategy for 24-week period based on referral cases to the hepatology unit. In the centralized strategy, a designated study biochemist identified patients with ALT greater than 3 times the upper limit of normal values (ULN) and notified the designated hepatologists, who then went to the patients' wards, analyzed the charts, and if necessary, interviewed the identified patients. During these two periods, patients with possible DILI were included after signing an informed consent in an ongoing European diagnostic study (SAFE-T consortium). Results During the 24-week period of the standard strategy, 12 (0.04%) patients out of a total of 28,145 were identified as having possible DILI, and 11 of these accepted to be included in the protocol. During the one-week proactive period, 7 patients out of a total of 1407 inpatients (0.498%) [odds ratio vs. standard = 12.1 (95% CI, 3.9–32.3); P<0.0001] were identified with possible DILI, and 5 were included in the protocol. Conclusion A simple strategy based on the daily analysis of cases with ALT >3 ULN by designated biochemists and hepatologists identified 12 times more acute cases of drug-induced liver disease than the standard strategy. This pilot cohort is registered on the number AP-HP P110201/1/08-03-2011 and AFSSAPS B110346-70. PMID:22905129

  14. 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.

  15. Real Time Data System (RTDS)

    NASA Technical Reports Server (NTRS)

    Heindel, Troy A.

    1991-01-01

    Information is given in viewgraph form on the Real Time Data System (RTDS). The goals are to increase the quality of flight decision making, reduce and enhance flight controller training time, and serve as a near-operations technology test-bed. Information is given on the growth of RTDS; flight control disciplines; RTDS technology deployment in 1987-1989 and 1990-91; a functionality comparison of mainframes and workstations; and technology transfer activities.

  16. Real-time ultrasound elastography

    NASA Astrophysics Data System (ADS)

    Bae, Unmin; Kim, Yongmin

    2007-03-01

    Ultrasound elastography can provide tissue stiffness information that is complementary to the anatomy and blood flow information offered by conventional ultrasound machines, but it is computationally challenging due to many time-consuming modules and a large amount of data. To facilitate real-time implementations of ultrasound elastography, we have developed new methods that can significantly reduce the computational burden of common processing components in ultrasound elastography, such as the crosscorrelation analysis and spatial filtering applied to displacement and strain estimates. Using the new correlation-based search algorithm, the computational requirement of correlation-based search does not increase with the correlation window size. For typical parameters used in ultrasound elastography, the computation in correlation-based search can be reduced by a factor of more than 30. Median filtering is often performed to suppress the spike-like noise that results from correlation-based search. For fast median filtering, we have developed a method that efficiently finds a new median value utilizing the sort result of the previous pixel. With careful mapping of the new algorithms on digital signal processors, our work has led to development of a clinical ultrasound machine supporting real-time elastography. Our methods can help real-time implementations of various applications including ultrasound elastography, which could lead to increased use of ultrasound elastography in the clinic.

  17. [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

  18. [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.

  19. 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

  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. 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.

  2. 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

  3. 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.

  4. 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. PMID:25790897

  5. 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

  6. 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.

  7. 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.

  8. 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).

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. Real-time PCR in microfluidic devices

    NASA Astrophysics Data System (ADS)

    Becker, Holger; Hlawatsch, Nadine; Klemm, Richard; Moche, Christian; Hansen-Hagge, Thomas; Gärtner, Claudia

    2014-03-01

    A central method in a standard biochemical laboratory is represented by the polymerase chain reaction (PCR), therefore many attempts have been performed so far to implement this technique in lab-on-a-chip (LOC) devices. PCR is an ideal candidate for miniaturization because of a reduction of assay time and decreased costs for expensive bio-chemicals. In case of the "classical" PCR, detection is done by identification of DNA fragments electrophoretically separated in agarose gels. This method is meanwhile frequently replaced by the so-called Real-Time-PCR because here the exponential increase of amplificates can be observed directly by measurement of DNA interacting fluorescent dyes. Two main methods for on-chip PCRs are available: traditional "batch" PCR in chambers on a chip using thermal cycling, requiring about 30 minutes for a typical PCR protocol and continuous-flow PCR, where the liquid is guided over stationary temperature zones. In the latter case, the PCR protocol can be as fast as 5 minutes. In the presented work, a proof of concept is demonstrated for a real-time-detection of PCR products in microfluidic systems.

  16. Data modeling augmentation of JPEG for real-time streaming video

    NASA Astrophysics Data System (ADS)

    Jaenisch, Holger M.; Handley, James W.

    2005-05-01

    This paper explores sub-sampling in conjunction with JPEG compression algorithms. Rather than directly compressing large high-resolution images, we propose decimation to thumbnails followed by compression. This enables Redundant Array of Independent Disks (RAID) compression and facilitates real-time streaming video with small bandwidth requirements. Image reconstruction occurs on demand at the receiver to any resolution required using Data Modeling based fractal interpolation. The receive side first uncompresses JPEG and then fractal interpolates to any required resolution. This device independent resolution capability is useful for real-time sharing of image data across virtual networks where each node has a different innate resolution capability. The same image is constructed to whatever limitations exist at each individual node, keeping image data device independent and image resolution scalable up or down as hardware/bandwidth limitations and options evolve.

  17. 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.

  18. 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.

  19. Device-independent quantum cryptography for continuous variables

    NASA Astrophysics Data System (ADS)

    Marshall, Kevin; Weedbrook, Christian

    2014-10-01

    We present a device-independent quantum cryptography protocol for continuous variables. Our scheme is based on the Gottesman-Kitaev-Preskill encoding scheme whereby a qubit is embedded in the infinite-dimensional space of a quantum harmonic oscillator. The application of discrete-variable device-independent quantum key distribution to this encoding enables a continuous-variable analog. Since the security of this protocol is based on discrete variables we inherit by default security against collective attacks and, under certain memoryless assumptions, coherent attacks. We find that our protocol is valid over the same distances as its discrete-variable counterpart, except that we are able to take advantage of high efficiency commercially available detectors where, for the most part, only homodyne detection is required. This offers the prospect of closing the loopholes associated with Bell inequalities.

  20. PGPLOT: Device-independent Graphics Package for Simple Scientific Graphs

    NASA Astrophysics Data System (ADS)

    Pearson, Tim

    2011-03-01

    The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time. The PGPLOT library consists of two major parts: a device-independent part and a set of device-dependent "device handler" subroutines for output on various terminals, image displays, dot-matrix printers, laser printers, and pen plotters. Common file formats supported include PostScript and GIF. PGPLOT itself is written mostly in standard Fortran-77, with a few non-standard, system-dependent subroutines. PGPLOT subroutines can be called directly from a Fortran-77 or Fortran-90 program. A C binding library (cpgplot) and header file (cpgplot.h) are provided that allow PGPLOT to be called from a C or C++ program; the binding library handles conversion between C and Fortran argument-passing conventions.

  1. MISR Level 1 Near Real Time Products

    Atmospheric Science Data Center

    2014-09-15

    Level 1 Near Real Time The MISR Near Real Time Level 1 data products consist of radiance measurements organized in 10-50 minute ... (off-nadir) cameras. The remaining channels are sampled at 1.1 km. ...

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. Real-time PCR for Strongyloides stercoralis-associated meningitis.

    PubMed

    Nadir, Eyal; Grossman, Tamar; Ciobotaro, Pnina; Attali, Malka; Barkan, Daniel; Bardenstein, Rita; Zimhony, Oren

    2016-03-01

    Four immunocompromised patients, immigrants from Ethiopia, presented with diverse clinical manifestations of meningitis associated with Strongyloides stercoralis dissemination as determined by identification of intestinal larvae. The cerebrospinal fluid of 3 patients was tested by a validated (for stool) real-time PCR for S. stercoralis and was found positive, establishing this association. PMID:26704620

  7. 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.

  8. Continuous-variable measurement-device-independent multipartite quantum communication

    NASA Astrophysics Data System (ADS)

    Wu, Yadong; Zhou, Jian; Gong, Xinbao; Guo, Ying; Zhang, Zhi-Ming; He, Guangqiang

    2016-02-01

    A continuous-variable measurement-device-independent multiparty quantum communication protocol is investigated in this paper. Utilizing the distributed continuous-variable Greenberger-Horne-Zeilinger state, this protocol can implement both quantum cryptographic conference and quantum secret sharing. We analyze the security of the protocol against both the entangling cloner attack and the coherent attack. The entangling cloner attack is a practical individual attack, and the coherent attack is the optimal attack Eve can implement. Simulation results show that the coherent attack can greatly reduce the secret key rate. Different kinds of entangled attacks are compared and we finally discuss the optimal coherent attacks.

  9. Semi device independence of the BB84 protocol

    NASA Astrophysics Data System (ADS)

    Woodhead, Erik

    2016-05-01

    The BB84 quantum key distribution protocol is semi device independent in the sense that it can be shown to be secure if just one of the users’ devices is restricted to a qubit Hilbert space. Here, we derive an analytic lower bound on the asymptotic secret key rate for the entanglement-based version of BB84 assuming only that one of the users performs unknown qubit POVMs. The result holds against the class of collective attacks and reduces to the well known Shor–Preskill key rate for correlations corresponding to the ideal BB84 correlations mixed with any amount of random noise.

  10. The optimization of measurement device independent quantum key distribution

    NASA Astrophysics Data System (ADS)

    Gao, Feng; Ma, Hai-Qiang; Jiao, Rong-Zhen

    2016-04-01

    Measurement device independent quantum key distribution (MDI-QKD) is a promising method for realistic quantum communication which could remove all the side-channel attacks from the imperfections of the devices. Here in this study, we theoretically analyzed the performance of the MDI-QKD system. The asymptotic case rate with the increment of the transmission distance at different polarization misalignment, background count rate and intensity is calculated respectively. The result may provide important parameters for practical application of quantum communications.