Real-time logo detection and tracking in video
George, M.; Kehtarnavaz, N.; Rahman, M.; Carlsohn, M.
2010-05-01
This paper presents a real-time implementation of a logo detection and tracking algorithm in video. The motivation of this work stems from applications on smart phones that require the detection of logos in real-time. For example, one application involves detecting company logos so that customers can easily get special offers in real-time. This algorithm uses a hybrid approach by initially running the Scale Invariant Feature Transform (SIFT) algorithm on the first frame in order to obtain the logo location and then by using an online calibration of color within the SIFT detected area in order to detect and track the logo in subsequent frames in a time efficient manner. The results obtained indicate that this hybrid approach allows robust logo detection and tracking to be achieved in real-time.
Real-Time Pore Pressure Detection: Indicators and Improved Methods
Directory of Open Access Journals (Sweden)
Jincai Zhang
2017-01-01
Full Text Available High uncertainties may exist in the predrill pore pressure prediction in new prospects and deepwater subsalt wells; therefore, real-time pore pressure detection is highly needed to reduce drilling risks. The methods for pore pressure detection (the resistivity, sonic, and corrected d-exponent methods are improved using the depth-dependent normal compaction equations to adapt to the requirements of the real-time monitoring. A new method is proposed to calculate pore pressure from the connection gas or elevated background gas, which can be used for real-time pore pressure detection. The pore pressure detection using the logging-while-drilling, measurement-while-drilling, and mud logging data is also implemented and evaluated. Abnormal pore pressure indicators from the well logs, mud logs, and wellbore instability events are identified and analyzed to interpret abnormal pore pressures for guiding real-time drilling decisions. The principles for identifying abnormal pressure indicators are proposed to improve real-time pore pressure monitoring.
Real time freeway incident detection.
2014-04-01
The US Department of Transportation (US-DOT) estimates that over half of all congestion : events are caused by highway incidents rather than by rush-hour traffic in big cities. Real-time : incident detection on freeways is an important part of any mo...
Real-time change detection in data streams with FPGAs
International Nuclear Information System (INIS)
Vega, J.; Dormido-Canto, S.; Cruz, T.; Ruiz, M.; Barrera, E.; Castro, R.; Murari, A.; Ochando, M.
2014-01-01
Highlights: • Automatic recognition of changes in data streams of multidimensional signals. • Detection algorithm based on testing exchangeability on-line. • Real-time and off-line applicability. • Real-time implementation in FPGAs. - Abstract: The automatic recognition of changes in data streams is useful in both real-time and off-line data analyses. This article shows several effective change-detecting algorithms (based on martingales) and describes their real-time applicability in the data acquisition systems through the use of Field Programmable Gate Arrays (FPGA). The automatic event recognition system is absolutely general and it does not depend on either the particular event to detect or the specific data representation (waveforms, images or multidimensional signals). The developed approach provides good results for change detection in both the temporal evolution of profiles and the two-dimensional spatial distribution of volume emission intensity. The average computation time in the FPGA is 210 μs per profile
Real-time door detection for indoor autonomous vehicle
He, Zhihao; Zhu, Ming
2017-07-01
Indoor Autonomous Vehicle(IAV) is used in many indoor scenes. Such as hotels and hospitals. Door detection is a key issue to guide the IAV into rooms. In this paper, we consider door detection in the use of indoor navigation of IAV. Since real-time properties are important for real-world IAV, the detection algorithm must be fast enough. Most monocular-camera based door detection model need a perfect detection of the four line segments of the door or the four corners. But in many situations, line segments could be extended or cut off. And there could be many false detected corners. And few of them can distinguish doors from door-like objects with door-like shape effectively. We proposed a 2-D vision model of the door that is made up of line segments. The number of parts detected is used to determine the possibility of a door. Our algorithm is tested on a database of doors.1 The robustness and real-time are verified. The precision is 89.4%. Average time consumed for processing a 640x320 figure is 44.73ms.
A comparison of moving object detection methods for real-time moving object detection
Roshan, Aditya; Zhang, Yun
2014-06-01
Moving object detection has a wide variety of applications from traffic monitoring, site monitoring, automatic theft identification, face detection to military surveillance. Many methods have been developed across the globe for moving object detection, but it is very difficult to find one which can work globally in all situations and with different types of videos. The purpose of this paper is to evaluate existing moving object detection methods which can be implemented in software on a desktop or laptop, for real time object detection. There are several moving object detection methods noted in the literature, but few of them are suitable for real time moving object detection. Most of the methods which provide for real time movement are further limited by the number of objects and the scene complexity. This paper evaluates the four most commonly used moving object detection methods as background subtraction technique, Gaussian mixture model, wavelet based and optical flow based methods. The work is based on evaluation of these four moving object detection methods using two (2) different sets of cameras and two (2) different scenes. The moving object detection methods have been implemented using MatLab and results are compared based on completeness of detected objects, noise, light change sensitivity, processing time etc. After comparison, it is observed that optical flow based method took least processing time and successfully detected boundary of moving objects which also implies that it can be implemented for real-time moving object detection.
Cohen, Noa; Sabhachandani, Pooja; Golberg, Alexander; Konry, Tania
2015-04-15
In this study we describe a simple lab-on-a-chip (LOC) biosensor approach utilizing well mixed microfluidic device and a microsphere-based assay capable of performing near real-time diagnostics of clinically relevant analytes such cytokines and antibodies. We were able to overcome the adsorption kinetics reaction rate-limiting mechanism, which is diffusion-controlled in standard immunoassays, by introducing the microsphere-based assay into well-mixed yet simple microfluidic device with turbulent flow profiles in the reaction regions. The integrated microsphere-based LOC device performs dynamic detection of the analyte in minimal amount of biological specimen by continuously sampling micro-liter volumes of sample per minute to detect dynamic changes in target analyte concentration. Furthermore we developed a mathematical model for the well-mixed reaction to describe the near real time detection mechanism observed in the developed LOC method. To demonstrate the specificity and sensitivity of the developed real time monitoring LOC approach, we applied the device for clinically relevant analytes: Tumor Necrosis Factor (TNF)-α cytokine and its clinically used inhibitor, anti-TNF-α antibody. Based on the reported results herein, the developed LOC device provides continuous sensitive and specific near real-time monitoring method for analytes such as cytokines and antibodies, reduces reagent volumes by nearly three orders of magnitude as well as eliminates the washing steps required by standard immunoassays. Copyright © 2014 Elsevier B.V. All rights reserved.
Muraosa, Yasunori; Toyotome, Takahito; Yahiro, Maki; Watanabe, Akira; Shikanai-Yasuda, Maria Aparecida; Kamei, Katsuhiko
2016-05-01
We developed new cycling probe-based real-time PCR and nested real-time PCR assays for the detection of Histoplasma capsulatum that were designed to detect the gene encoding N-acetylated α-linked acidic dipeptidase (NAALADase), which we previously identified as an H. capsulatum antigen reacting with sera from patients with histoplasmosis. Both assays specifically detected the DNAs of all H. capsulatum strains but not those of other fungi or human DNA. The limited of detection (LOD) of the real-time PCR assay was 10 DNA copies when using 10-fold serial dilutions of the standard plasmid DNA and 50 DNA copies when using human serum spiked with standard plasmid DNA. The nested real-time PCR improved the LOD to 5 DNA copies when using human serum spiked with standard plasmid DNA, which represents a 10-fold higher than that observed with the real-time PCR assay. To assess the ability of the two assays to diagnose histoplasmosis, we analyzed a small number of clinical specimens collected from five patients with histoplasmosis, such as sera (n = 4), formalin-fixed paraffin-embedded (FFPE) tissue (n = 4), and bronchoalveolar lavage fluid (BALF) (n = 1). Although clinical sensitivity of the real-time PCR assay was insufficiently sensitive (33%), the nested real-time PCR assay increased the clinical sensitivity (77%), suggesting it has a potential to be a useful method for detecting H. capsulatum DNA in clinical specimens. © The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Real-Time PCR for Universal Phytoplasma Detection and Quantification
DEFF Research Database (Denmark)
Christensen, Nynne Meyn; Nyskjold, Henriette; Nicolaisen, Mogens
2013-01-01
Currently, the most efficient detection and precise quantification of phytoplasmas is by real-time PCR. Compared to nested PCR, this method is less sensitive to contamination and is less work intensive. Therefore, a universal real-time PCR method will be valuable in screening programs and in other...
Real-Time EEG-Based Happiness Detection System
Directory of Open Access Journals (Sweden)
Noppadon Jatupaiboon
2013-01-01
Full Text Available We propose to use real-time EEG signal to classify happy and unhappy emotions elicited by pictures and classical music. We use PSD as a feature and SVM as a classifier. The average accuracies of subject-dependent model and subject-independent model are approximately 75.62% and 65.12%, respectively. Considering each pair of channels, temporal pair of channels (T7 and T8 gives a better result than the other area. Considering different frequency bands, high-frequency bands (Beta and Gamma give a better result than low-frequency bands. Considering different time durations for emotion elicitation, that result from 30 seconds does not have significant difference compared with the result from 60 seconds. From all of these results, we implement real-time EEG-based happiness detection system using only one pair of channels. Furthermore, we develop games based on the happiness detection system to help user recognize and control the happiness.
Real-time Detection of Antihydrogen Annihilations and Applications to Spectroscopy
Directory of Open Access Journals (Sweden)
Stracka Simone
2014-04-01
Full Text Available A detection scheme based on real-time measurement of antihydrogen annihilations during radiation injection is presented, which allows an efficient use of the trapped atoms for laser and microwave spectroscopy. The application of real-time detection of H¯$\\bar H$ annihilations to microwave spectroscopy, which yielded the first evidence of microwave induced spin-flip transitions in trapped antihydrogen [1], is reported.
Microcontroller-based real-time QRS detection.
Sun, Y; Suppappola, S; Wrublewski, T A
1992-01-01
The authors describe the design of a system for real-time detection of QRS complexes in the electrocardiogram based on a single-chip microcontroller (Motorola 68HC811). A systematic analysis of the instrumentation requirements for QRS detection and of the various design techniques is also given. Detection algorithms using different nonlinear transforms for the enhancement of QRS complexes are evaluated by using the ECG database of the American Heart Association. The results show that the nonlinear transform involving multiplication of three adjacent, sign-consistent differences in the time domain gives a good performance and a quick response. When implemented with an appropriate sampling rate, this algorithm is also capable of rejecting pacemaker spikes. The eight-bit single-chip microcontroller provides sufficient throughput and shows a satisfactory performance. Implementation of multiple detection algorithms in the same system improves flexibility and reliability. The low chip count in the design also favors maintainability and cost-effectiveness.
Real-time detection of musical onsets with linear prediction and sinusoidal modeling
Glover, John; Lazzarini, Victor; Timoney, Joseph
2011-12-01
Real-time musical note onset detection plays a vital role in many audio analysis processes, such as score following, beat detection and various sound synthesis by analysis methods. This article provides a review of some of the most commonly used techniques for real-time onset detection. We suggest ways to improve these techniques by incorporating linear prediction as well as presenting a novel algorithm for real-time onset detection using sinusoidal modelling. We provide comprehensive results for both the detection accuracy and the computational performance of all of the described techniques, evaluated using Modal, our new open source library for musical onset detection, which comes with a free database of samples with hand-labelled note onsets.
FPGA-Based Real-Time Motion Detection for Automated Video Surveillance Systems
Directory of Open Access Journals (Sweden)
Sanjay Singh
2016-03-01
Full Text Available Design of automated video surveillance systems is one of the exigent missions in computer vision community because of their ability to automatically select frames of interest in incoming video streams based on motion detection. This research paper focuses on the real-time hardware implementation of a motion detection algorithm for such vision based automated surveillance systems. A dedicated VLSI architecture has been proposed and designed for clustering-based motion detection scheme. The working prototype of a complete standalone automated video surveillance system, including input camera interface, designed motion detection VLSI architecture, and output display interface, with real-time relevant motion detection capabilities, has been implemented on Xilinx ML510 (Virtex-5 FX130T FPGA platform. The prototyped system robustly detects the relevant motion in real-time in live PAL (720 × 576 resolution video streams directly coming from the camera.
Real-time thermal neutron radiographic detection systems
International Nuclear Information System (INIS)
Berger, H.; Bracher, D.A.
1976-01-01
Systems for real-time detection of thermal neutron images are reviewed. Characteristics of one system are presented; the data include contrast, resolution and speed of response over the thermal neutron intensity range 2.5 10 3 n/cm 2 -sec to 10 7 n/cm 2 -sec
Study on APD real time compensation methods of laser Detection system
International Nuclear Information System (INIS)
Feng Ying; Zhang He; Zhang Xiangjin; Liu Kun
2011-01-01
their operating principles. The constant false alarm rate compensation can't detect the pulse signal which comes randomly. Therefore real-time performance can't be realized. The noise compensation can meet the request of real-time performance. If it is used in the environment where background light is intense or changes acutely, there is a better effect. The temperature compensation can also achieve the real-time performance request. If it is used in the environment where temperature changes acutely, there is also a better effect. Aim at such problems, this paper presents that different APD real-time compensations should be adopt to adapt to different environments. The exiting temperature compensation adjusts output voltage by using variable resistance to regulate input voltage. Its structure is complex; the real-time performance is worse. In order to remedy these defects, a real-time temperature compensation which is based on switch on-off time of switching power supply is designed. Its feasibility and operating stability are confirmed by plate making and experiment. At last, the comparison experiments between the real-time noise compensation and the real-time temperature compensation is carried out in the environments where temperature is almost invariant and background light acutely changes from5lux to150lux . The result shows that the operating effect of the real-time noise compensation is better here, the noise minifies to a sixth of original noise. The comparison experiments between the real-time noise compensation and the real-time temperature compensation is carried out in darkroom where background light is 5lux and temperature almost rapidly changes from -20 deg. C to 80 deg. C. The result shows that the operating effect of the real-time temperature compensation is better here, the noise minifies to a seventh of original noise. Moreover, these methods can be applied to other type detection systems of weak photoelectric signal; they have high actual application
Study on APD real time compensation methods of laser Detection system
Energy Technology Data Exchange (ETDEWEB)
Feng Ying; Zhang He; Zhang Xiangjin; Liu Kun, E-mail: fy_caimi@163.com [ZNDY of Ministerial Key Laboratory, Nanjing University of Science and Technology, Nanjing 210094 (China)
2011-02-01
by analyzing their operating principles. The constant false alarm rate compensation can't detect the pulse signal which comes randomly. Therefore real-time performance can't be realized. The noise compensation can meet the request of real-time performance. If it is used in the environment where background light is intense or changes acutely, there is a better effect. The temperature compensation can also achieve the real-time performance request. If it is used in the environment where temperature changes acutely, there is also a better effect. Aim at such problems, this paper presents that different APD real-time compensations should be adopt to adapt to different environments. The exiting temperature compensation adjusts output voltage by using variable resistance to regulate input voltage. Its structure is complex; the real-time performance is worse. In order to remedy these defects, a real-time temperature compensation which is based on switch on-off time of switching power supply is designed. Its feasibility and operating stability are confirmed by plate making and experiment. At last, the comparison experiments between the real-time noise compensation and the real-time temperature compensation is carried out in the environments where temperature is almost invariant and background light acutely changes from5lux to150lux . The result shows that the operating effect of the real-time noise compensation is better here, the noise minifies to a sixth of original noise. The comparison experiments between the real-time noise compensation and the real-time temperature compensation is carried out in darkroom where background light is 5lux and temperature almost rapidly changes from -20 deg. C to 80 deg. C. The result shows that the operating effect of the real-time temperature compensation is better here, the noise minifies to a seventh of original noise. Moreover, these methods can be applied to other type detection systems of weak photoelectric signal; they
Study on APD real time compensation methods of laser Detection system
Ying, Feng; He, Zhang; Xiangjin, Zhang; Kun, Liu
2011-02-01
their operating principles. The constant false alarm rate compensation can't detect the pulse signal which comes randomly. Therefore real-time performance can't be realized. The noise compensation can meet the request of real-time performance. If it is used in the environment where background light is intense or changes acutely, there is a better effect. The temperature compensation can also achieve the real-time performance request. If it is used in the environment where temperature changes acutely, there is also a better effect. Aim at such problems, this paper presents that different APD real-time compensations should be adopt to adapt to different environments. The exiting temperature compensation adjusts output voltage by using variable resistance to regulate input voltage. Its structure is complex; the real-time performance is worse. In order to remedy these defects, a real-time temperature compensation which is based on switch on-off time of switching power supply is designed. Its feasibility and operating stability are confirmed by plate making and experiment. At last, the comparison experiments between the real-time noise compensation and the real-time temperature compensation is carried out in the environments where temperature is almost invariant and background light acutely changes from5lux to150lux . The result shows that the operating effect of the real-time noise compensation is better here, the noise minifies to a sixth of original noise. The comparison experiments between the real-time noise compensation and the real-time temperature compensation is carried out in darkroom where background light is 5lux and temperature almost rapidly changes from -20°C to 80°C. The result shows that the operating effect of the real-time temperature compensation is better here, the noise minifies to a seventh of original noise. Moreover, these methods can be applied to other type detection systems of weak photoelectric signal; they have high actual application value.
Anomaly detection in real-time gross payment data
Triepels, Ron; Daniels, Hennie; Heijmans, R.; Camp, Olivier; Filipe, Joaquim
2017-01-01
We discuss how an autoencoder can detect system-level anomalies in a real-time gross settlement system by reconstructing a set of liquidity vectors. A liquidity vector is an aggregated representation of the underlying payment network of a settlement system for a particular time interval.
Video-based real-time on-street parking occupancy detection system
Bulan, Orhan; Loce, Robert P.; Wu, Wencheng; Wang, YaoRong; Bernal, Edgar A.; Fan, Zhigang
2013-10-01
Urban parking management is receiving significant attention due to its potential to reduce traffic congestion, fuel consumption, and emissions. Real-time parking occupancy detection is a critical component of on-street parking management systems, where occupancy information is relayed to drivers via smart phone apps, radio, Internet, on-road signs, or global positioning system auxiliary signals. Video-based parking occupancy detection systems can provide a cost-effective solution to the sensing task while providing additional functionality for traffic law enforcement and surveillance. We present a video-based on-street parking occupancy detection system that can operate in real time. Our system accounts for the inherent challenges that exist in on-street parking settings, including illumination changes, rain, shadows, occlusions, and camera motion. Our method utilizes several components from video processing and computer vision for motion detection, background subtraction, and vehicle detection. We also present three traffic law enforcement applications: parking angle violation detection, parking boundary violation detection, and exclusion zone violation detection, which can be integrated into the parking occupancy cameras as a value-added option. Our experimental results show that the proposed parking occupancy detection method performs in real-time at 5 frames/s and achieves better than 90% detection accuracy across several days of videos captured in a busy street block under various weather conditions such as sunny, cloudy, and rainy, among others.
Real-time implementation of logo detection on open source BeagleBoard
George, M.; Kehtarnavaz, N.; Estevez, L.
2011-03-01
This paper presents the real-time implementation of our previously developed logo detection and tracking algorithm on the open source BeagleBoard mobile platform. This platform has an OMAP processor that incorporates an ARM Cortex processor. The algorithm combines Scale Invariant Feature Transform (SIFT) with k-means clustering, online color calibration and moment invariants to robustly detect and track logos in video. Various optimization steps that are carried out to allow the real-time execution of the algorithm on BeagleBoard are discussed. The results obtained are compared to the PC real-time implementation results.
Real-time pedestrian detection with the videos of car camera
Directory of Open Access Journals (Sweden)
Yunling Zhang
2015-12-01
Full Text Available Pedestrians in the vehicle path are in danger of being hit, thus causing severe injury to pedestrians and vehicle occupants. Therefore, real-time pedestrian detection with the video of vehicle-mounted camera is of great significance to vehicle–pedestrian collision warning and traffic safety of self-driving car. In this article, a real-time scheme was proposed based on integral channel features and graphics processing unit. The proposed method does not need to resize the input image. Moreover, the computationally expensive convolution of the detectors and the input image was converted into the dot product of two larger matrixes, which can be computed effectively using a graphics processing unit. The experiments showed that the proposed method could be employed to detect pedestrians in the video of car camera at 20+ frames per second with acceptable error rates. Thus, it can be applied in real-time detection tasks with the videos of car camera.
Frame based Motion Detection for real-time Surveillance
Brajesh Patel; Neelam Patel
2012-01-01
In this paper a series of algorithm has been formed to track the feature of motion detection under surveillance system. In the proposed work a pixel variant plays a vital role in detection of moving object of a particular clip. If there is a little bit motion in a frame then it is detected very easily by calculating pixel variance. This algorithm detects the zero variation only when there is no motion in a real-time video sequence. It is simple and easier for motion detection in the fames of ...
Real-time change detection for countering improvised explosive devices
Wouw, van de D.W.J.M.; Rens, van K.; Lint, van R.H.; Jaspers, Egbert; With, de P.H.N.; Loce, R.P.; Saber, E.
2014-01-01
We explore an automatic real-time change detection system to assist military personnel during transport and surveillance, by detection changes in the environment with respect to a previous operation. Such changes may indicate the presence of Improvised Explosive Devices (IEDs), which can then be
Real time avalanche detection for high risk areas.
2014-12-01
Avalanches routinely occur on State Highway 21 (SH21) between Lowman and Stanley, Idaho each winter. The avalanches pose : a threat to the safety of maintenance workers and the traveling public. A real-time avalanche detection system will allow the :...
Near Real Time Ship Detection Experiments
Brusch, S.; Lehner, S.; Schwarz, E.; Fritz, T.
2010-04-01
A new Near Real Time (NRT) ship detection processor SAINT (SAR AIS Integrated Toolbox) was developed in the framework of the ESA project MARISS. Data are received at DLRs ground segment DLR-BN (Neustrelitz, Germany). Results of the ship detection are available on ftp server within 30 min after the acquisition started. The detectability of ships on Synthetic Aperture Radar (SAR) ERS-2, ENVISAT ASAR and TerraSAR-X (TS-X) images is validated by coastal (live) AIS and space AIS. The monitoring areas chosen for surveillance are the North-, Baltic Sea, and Cape Town. The detectability in respect to environmental parameters like wind field, sea state, currents and changing coastlines due to tidal effects is investigated. In the South Atlantic a tracking experiment of the German research vessel Polarstern has been performed. Issues of piracy in particular in respect to ships hijacked at the Somali coast are discussed. Some examples using high resolution images from TerraSAR-X are given.
Real-time biscuit tile image segmentation method based on edge detection.
Matić, Tomislav; Aleksi, Ivan; Hocenski, Željko; Kraus, Dieter
2018-05-01
In this paper we propose a novel real-time Biscuit Tile Segmentation (BTS) method for images from ceramic tile production line. BTS method is based on signal change detection and contour tracing with a main goal of separating tile pixels from background in images captured on the production line. Usually, human operators are visually inspecting and classifying produced ceramic tiles. Computer vision and image processing techniques can automate visual inspection process if they fulfill real-time requirements. Important step in this process is a real-time tile pixels segmentation. BTS method is implemented for parallel execution on a GPU device to satisfy the real-time constraints of tile production line. BTS method outperforms 2D threshold-based methods, 1D edge detection methods and contour-based methods. Proposed BTS method is in use in the biscuit tile production line. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.
Wide area surveillance real-time motion detection systems
2014-01-01
The book describes a system for visual surveillance using intelligent cameras. The camera uses robust techniques for detecting and tracking moving objects. The real time capture of the objects is then stored int he database. The tracking data stored in the database is analysed to study the camera view, detect and track objects, and study object behavior. These set of models provide a robust framework for coordinating the tracking of objects between overlapping and non-overlapping cameras, and recording the activity of objects detected by the system.
Real-time sensor failure detection by dynamic modelling of a PWR plant
International Nuclear Information System (INIS)
Turkcan, E.; Ciftcioglu, O.
1992-06-01
Signal validation and sensor failure detection is an important problem in real-time nuclear power plant (NPP) surveillance. Although conventional sensor redundancy, in a way, is a solution, identification of faulty sensor is necessary for further preventive actions to be taken. A comprehensive solution for the system so that any sensory reading is verified by its model based estimated counterpart, in real-time. Such a realization is accomplished by means of dynamic system's states estimation methodology using Kalman filter modelling technique. The method is investigated by means of real-time data of the steam generator of Borssele nuclear power plant and the method has proved to be satisfactory for real-time sensor failure detection as well as model validation verification. (author). 5 refs.; 6 figs.; 1 tab
Real-time Multiple Abnormality Detection in Video Data
DEFF Research Database (Denmark)
Have, Simon Hartmann; Ren, Huamin; Moeslund, Thomas B.
2013-01-01
Automatic abnormality detection in video sequences has recently gained an increasing attention within the research community. Although progress has been seen, there are still some limitations in current research. While most systems are designed at detecting specific abnormality, others which...... are capable of detecting more than two types of abnormalities rely on heavy computation. Therefore, we provide a framework for detecting abnormalities in video surveillance by using multiple features and cascade classifiers, yet achieve above real-time processing speed. Experimental results on two datasets...... show that the proposed framework can reliably detect abnormalities in the video sequence, outperforming the current state-of-the-art methods....
Real-Time Detection of a Virus Using Detection Dogs
Directory of Open Access Journals (Sweden)
Craig eAngle
2016-01-01
Full Text Available Viral infections are ubiquitous in humans, animals, and plants. Real-time methods to identify viral infections are limited and do not exist for use in harsh or resource-constrained environments. Previous research identified that tissues produce unique volatile organic compounds (VOC and demonstrated that VOC concentrations change during pathologic states including infection, neoplasia, or metabolic disease. Patterns of VOC expression may be pathogen-specific and may be associated with an odor that could be used for disease detection.We investigated the ability of two trained dogs to detect cell cultures infected with bovine viral diarrhea virus (BVDV and to discriminate BVDV-infected cell cultures from uninfected cell cultures and from cell cultures infected with bovine herpes virus 1 (BHV 1 and bovine parainfluenza virus 3 (BPIV 3. Dogs were trained to recognize cell cultures infected with two different biotypes of BVDV propagated in MDBK cells using one of three culture media. For detection trials, one target and seven distractors were presented on a scent wheel by a dog handler unaware of the location of targets and distractors.Detection of BVDV- infected cell cultures by Dog 1 had a diagnostic sensitivity of 0.850 (95% CI: 0.701 - 0.942, which was lower than Dog 2 (0.967, 95% CI: 0.837 - 0.994. Both dogs exhibited very high diagnostic specificity (0.981, 95% CI: 0.960 - 0.993 and (0.993, 95% CI: 0.975 - 0.999, respectively.These findings demonstrate that trained dogs can differentiate between cultured cells infected with BVDV, BHV1, and BPIV3 and are a realistic real-time mobile pathogen sensing technology for viral pathogens. The ability to discriminate between target and distractor samples plausibly results from expression of unique VOC patterns virus-infected and uninfected cells.
Real-Time Detection of a Virus Using Detection Dogs.
Angle, T Craig; Passler, Thomas; Waggoner, Paul L; Fischer, Terrence D; Rogers, Bart; Galik, Patricia K; Maxwell, Herris S
2015-01-01
Viral infections are ubiquitous in humans, animals, and plants. Real-time methods to identify viral infections are limited and do not exist for use in harsh or resource-constrained environments. Previous research identified that tissues produce unique volatile organic compounds (VOC) and demonstrated that VOC concentrations change during pathologic states, including infection, neoplasia, or metabolic disease. Patterns of VOC expression may be pathogen specific and may be associated with an odor that could be used for disease detection. We investigated the ability of two trained dogs to detect cell cultures infected with bovine viral diarrhea virus (BVDV) and to discriminate BVDV-infected cell cultures from uninfected cell cultures and from cell cultures infected with bovine herpes virus 1 (BHV 1) and bovine parainfluenza virus 3 (BPIV 3). Dogs were trained to recognize cell cultures infected with two different biotypes of BVDV propagated in Madin-Darby bovine kidney cells using one of three culture media. For detection trials, one target and seven distractors were presented on a scent wheel by a dog handler unaware of the location of targets and distractors. Detection of BVDV-infected cell cultures by Dog 1 had a diagnostic sensitivity of 0.850 (95% CI: 0.701-0.942), which was lower than Dog 2 (0.967, 95% CI: 0.837-0.994). Both dogs exhibited very high diagnostic specificity (0.981, 95% CI: 0.960-0.993) and (0.993, 95% CI: 0.975-0.999), respectively. These findings demonstrate that trained dogs can differentiate between cultured cells infected with BVDV, BHV1, and BPIV3 and are a realistic real-time mobile pathogen sensing technology for viral pathogens. The ability to discriminate between target and distractor samples plausibly results from expression of unique VOC patterns in virus-infected and -uninfected cells.
Real-Time Analytics for the Healthcare Industry: Arrhythmia Detection.
Agneeswaran, Vijay Srinivas; Mukherjee, Joydeb; Gupta, Ashutosh; Tonpay, Pranay; Tiwari, Jayati; Agarwal, Nitin
2013-09-01
It is time for the healthcare industry to move from the era of "analyzing our health history" to the age of "managing the future of our health." In this article, we illustrate the importance of real-time analytics across the healthcare industry by providing a generic mechanism to reengineer traditional analytics expressed in the R programming language into Storm-based real-time analytics code. This is a powerful abstraction, since most data scientists use R to write the analytics and are not clear on how to make the data work in real-time and on high-velocity data. Our paper focuses on the applications necessary to a healthcare analytics scenario, specifically focusing on the importance of electrocardiogram (ECG) monitoring. A physician can use our framework to compare ECG reports by categorization and consequently detect Arrhythmia. The framework can read the ECG signals and uses a machine learning-based categorizer that runs within a Storm environment to compare different ECG signals. The paper also presents some performance studies of the framework to illustrate the throughput and accuracy trade-off in real-time analytics.
Choi, Yeonim; Jeon, Bo-Young; Shim, Tae Sun; Jin, Hyunwoo; Cho, Sang-Nae; Lee, Hyeyoung
2014-12-01
Rapid, accurate detection of Mycobacterium tuberculosis is crucial in the diagnosis of tuberculosis (TB), but conventional diagnostic methods have limited sensitivity and specificity or are time consuming. A new highly sensitive nucleic acid amplification test, combined nested and real-time polymerase chain reaction (PCR) in a single tube (one-tube nested real-time PCR), was developed for detecting M. tuberculosis, which takes advantage of two PCR techniques, i.e., nested PCR and real-time PCR. One-tube nested real-time PCR was designed to have two sequential reactions with two sets of primers and dual probes for the insertion sequence (IS) 6110 sequence of M. tuberculosis in a single closed tube. The minimum limits of detection of IS6110 real-time PCR and IS6110 one-tube nested real-time PCR were 100 fg/μL and 1 fg/μL of M. tuberculosis DNA, respectively. AdvanSure TB/non-tuberculous mycobacteria (NTM) real-time PCR, IS6110 real-time PCR, and two-tube nested real-time PCR showed 100% sensitivity and 100% specificity for clinical M. tuberculosis isolates and NTM isolates. In comparison, the sensitivities of AdvanSure TB/NTM real-time PCR, single IS6110 real-time PCR, and one-tube nested real-time PCR were 91% (152/167), 94.6% (158/167), and 100% (167/167) for sputum specimens, respectively. In conclusion, IS6110 one-tube nested real-time PCR is useful for detecting M. tuberculosis due to its high sensitivity and simple manipulation. Copyright © 2014 Elsevier Inc. All rights reserved.
A Real-Time PCR Detection of Genus Salmonella in Meat and Milk Samples
Directory of Open Access Journals (Sweden)
Jaroslav Pochop
2013-05-01
Full Text Available The aim of this study was follow the contamination of ready to eat milk and meat products with Salmonella spp. by using the Step One real-time PCR. Classical microbiological methods for detection of food-borne bacteria involve the use of pre-enrichment and/or specific enrichment, followed by the isolation of the bacteria in solid media and a final confirmation by biochemical and/or serological tests. We used the PrepSEQ Rapid Spin Sample Preparation Kit for isolation of DNA and SensiFAST SYBR Hi-ROX Kit for the real-time PCR performance. In the investigated samples without incubation we could detect strain of Salmonella sp. in five out of twenty three samples (swabs. This Step One real-time PCR assay is extremely useful for any laboratory in possession of a real-time PCR. It is a fast, reproducible, simple, specific and sensitive way to detect nucleic acids, which could be used in clinical diagnostic tests in the future. Our results indicated that the Step One real-time PCR assay developed in this study could sensitively detect Salmonella spp. in ready to eat food.
Real-time PCR for detection of Theileria equi and Babesia caballi ...
African Journals Online (AJOL)
Real-time PCR for detection of Theileria equi and Babesia caballi parasites in ticks. ... This study aimed to develop a real-time PCR screening test for Babesia caballi and Theileria equi in ticks. Adult D. reticulatus were ... This test is suitable for application in epidemiological surveillance of equine babesiosis and theileriosis.
Real-time DSP implementation for MRF-based video motion detection.
Dumontier, C; Luthon, F; Charras, J P
1999-01-01
This paper describes the real time implementation of a simple and robust motion detection algorithm based on Markov random field (MRF) modeling, MRF-based algorithms often require a significant amount of computations. The intrinsic parallel property of MRF modeling has led most of implementations toward parallel machines and neural networks, but none of these approaches offers an efficient solution for real-world (i.e., industrial) applications. Here, an alternative implementation for the problem at hand is presented yielding a complete, efficient and autonomous real-time system for motion detection. This system is based on a hybrid architecture, associating pipeline modules with one asynchronous module to perform the whole process, from video acquisition to moving object masks visualization. A board prototype is presented and a processing rate of 15 images/s is achieved, showing the validity of the approach.
Real-time progressive hyperspectral image processing endmember finding and anomaly detection
Chang, Chein-I
2016-01-01
The book covers the most crucial parts of real-time hyperspectral image processing: causality and real-time capability. Recently, two new concepts of real time hyperspectral image processing, Progressive Hyperspectral Imaging (PHSI) and Recursive Hyperspectral Imaging (RHSI). Both of these can be used to design algorithms and also form an integral part of real time hyperpsectral image processing. This book focuses on progressive nature in algorithms on their real-time and causal processing implementation in two major applications, endmember finding and anomaly detection, both of which are fundamental tasks in hyperspectral imaging but generally not encountered in multispectral imaging. This book is written to particularly address PHSI in real time processing, while a book, Recursive Hyperspectral Sample and Band Processing: Algorithm Architecture and Implementation (Springer 2016) can be considered as its companion book. Includes preliminary background which is essential to those who work in hyperspectral ima...
A Real-time License Plate Detection System for Parking Access
Directory of Open Access Journals (Sweden)
Roenadi Koesdijarto
2010-08-01
Full Text Available The automatic and real-time license plate detection system can be used as an access control entry of vehicles into the parking area. The problem is how to recognize the vehicles that will go into the parking lot and how to recognize various types of license plates in various light conditions quickly and accurately. In this research, the prototype was developed with a detection system to recognize the vehicles that will enter the parking area, and a license plate recognition system. In the license plate recognition system, the Fourier transform and Hidden Markov model method have proposed to detect location of license plate and as characters segmentation to recognize Indonesia license plates. The research results have shown that the developed prototype system has successfully recognized all Indonesia license plates in several of light condition and camera position. The percentage of plate recognition in the real-time experiment is 84.38%, and the average execution time for all recognition process is 5.834 second.
Real-Time Rotational Activity Detection in Atrial Fibrillation
Ríos-Muñoz, Gonzalo R.; Arenal, Ángel; Artés-Rodríguez, Antonio
2018-01-01
Rotational activations, or spiral waves, are one of the proposed mechanisms for atrial fibrillation (AF) maintenance. We present a system for assessing the presence of rotational activity from intracardiac electrograms (EGMs). Our system is able to operate in real-time with multi-electrode catheters of different topologies in contact with the atrial wall, and it is based on new local activation time (LAT) estimation and rotational activity detection methods. The EGM LAT estimation method is based on the identification of the highest sustained negative slope of unipolar signals. The method is implemented as a linear filter whose output is interpolated on a regular grid to match any catheter topology. Its operation is illustrated on selected signals and compared to the classical Hilbert-Transform-based phase analysis. After the estimation of the LAT on the regular grid, the detection of rotational activity in the atrium is done by a novel method based on the optical flow of the wavefront dynamics, and a rotation pattern match. The methods have been validated using in silico and real AF signals. PMID:29593566
Real-time Face Detection using Skin Color Model
Institute of Scientific and Technical Information of China (English)
LU Yao-xin; LIU Zhi-Qiang; ZHU Xiang-hua
2004-01-01
This paper presents a new face detection approach to real-time applications, which is based on the skin color model and the morphological filtering. First the non-skin color pixels of the input image are removed based on the skin color model in the YCrCb chrominance space, from which we extract candidate human face regions. Then a mathematical morphological filter is used to remove noisy regions and fill the holes in the candidate skin color regions. We adopt the similarity between the human face features and the candidate face regions to locate the face regions in the original image. We have implemented the algorithm in our smart media system. The experiment results show that this system is effective in real-time applications.
Lin, Shuo; Wang, Wei; Ju, Xiao-Jie; Xie, Rui; Liu, Zhuang; Yu, Hai-Rong; Zhang, Chuan; Chu, Liang-Yin
2016-02-23
Real-time online detection of trace threat analytes is critical for global sustainability, whereas the key challenge is how to efficiently convert and amplify analyte signals into simple readouts. Here we report an ultrasensitive microfluidic platform incorporated with smart microgel for real-time online detection of trace threat analytes. The microgel can swell responding to specific stimulus in flowing solution, resulting in efficient conversion of the stimulus signal into significantly amplified signal of flow-rate change; thus highly sensitive, fast, and selective detection can be achieved. We demonstrate this by incorporating ion-recognizable microgel for detecting trace Pb(2+), and connecting our platform with pipelines of tap water and wastewater for real-time online Pb(2+) detection to achieve timely pollution warning and terminating. This work provides a generalizable platform for incorporating myriad stimuli-responsive microgels to achieve ever-better performance for real-time online detection of various trace threat molecules, and may expand the scope of applications of detection techniques.
Performances of the New Real Time Tsunami Detection Algorithm applied to tide gauges data
Chierici, F.; Embriaco, D.; Morucci, S.
2017-12-01
Real-time tsunami detection algorithms play a key role in any Tsunami Early Warning System. We have developed a new algorithm for tsunami detection (TDA) based on the real-time tide removal and real-time band-pass filtering of seabed pressure time series acquired by Bottom Pressure Recorders. The TDA algorithm greatly increases the tsunami detection probability, shortens the detection delay and enhances detection reliability with respect to the most widely used tsunami detection algorithm, while containing the computational cost. The algorithm is designed to be used also in autonomous early warning systems with a set of input parameters and procedures which can be reconfigured in real time. We have also developed a methodology based on Monte Carlo simulations to test the tsunami detection algorithms. The algorithm performance is estimated by defining and evaluating statistical parameters, namely the detection probability, the detection delay, which are functions of the tsunami amplitude and wavelength, and the occurring rate of false alarms. In this work we present the performance of the TDA algorithm applied to tide gauge data. We have adapted the new tsunami detection algorithm and the Monte Carlo test methodology to tide gauges. Sea level data acquired by coastal tide gauges in different locations and environmental conditions have been used in order to consider real working scenarios in the test. We also present an application of the algorithm to the tsunami event generated by Tohoku earthquake on March 11th 2011, using data recorded by several tide gauges scattered all over the Pacific area.
Real-time petroleum spill detection system
International Nuclear Information System (INIS)
Dakin, D.T.
2001-01-01
A real-time autonomous oil and fuel spill detection system has been developed to rapidly detect of a wide range of petroleum products floating on, or suspended in water. The system consists of an array of spill detection buoys distributed within the area to be monitored. The buoys are composed of a float and a multispectral fluorometer, which looks up through the top 5 cm of water to detect floating and suspended petroleum products. The buoys communicate to a base station computer that controls the sampling of the buoys and analyses the data from each buoy to determine if a spill has occurred. If statistically significant background petroleum levels are detected, the system raises an oil spill alarm. The system is useful because early detection of a marine oil spill allows for faster containment, thereby minimizing the contaminated area and reducing cleanup costs. This paper also provided test results for biofouling, various petroleum product detection, water turbidity and wave tolerance. The technology has been successfully demonstrated. The UV light source keeps the optic window free from biofouling, and the electronics are fully submerged so there is no risk that the unit could ignite the vapours of a potential oil spill. The system can also tolerate moderately turbid waters and can therefore be used in many rivers, harbours, water intakes and sumps. The system can detect petroleum products with an average thickness of less than 3 micrometers floating on the water surface. 3 refs., 15 figs
DIRADTM - a system for real time detection and identification of radioactive objects
International Nuclear Information System (INIS)
Guillot, L.; Reboli, A.
2009-01-01
The authors present the DIRAD system (DIRAD stands for Detection and Identification of Radionuclides), an automatic system for real time identification of a radioactive anomaly and its interpretation in terms of risk level. It can be adapted to different contexts: pedestrian control, parcel or luggage control, road traffic control, and so on. In case of risk detection, an alert is transmitted in real time to a supervision station along with the whole set of spectral data
Memory Efficient VLSI Implementation of Real-Time Motion Detection System Using FPGA Platform
Directory of Open Access Journals (Sweden)
Sanjay Singh
2017-06-01
Full Text Available Motion detection is the heart of a potentially complex automated video surveillance system, intended to be used as a standalone system. Therefore, in addition to being accurate and robust, a successful motion detection technique must also be economical in the use of computational resources on selected FPGA development platform. This is because many other complex algorithms of an automated video surveillance system also run on the same platform. Keeping this key requirement as main focus, a memory efficient VLSI architecture for real-time motion detection and its implementation on FPGA platform is presented in this paper. This is accomplished by proposing a new memory efficient motion detection scheme and designing its VLSI architecture. The complete real-time motion detection system using the proposed memory efficient architecture along with proper input/output interfaces is implemented on Xilinx ML510 (Virtex-5 FX130T FPGA development platform and is capable of operating at 154.55 MHz clock frequency. Memory requirement of the proposed architecture is reduced by 41% compared to the standard clustering based motion detection architecture. The new memory efficient system robustly and automatically detects motion in real-world scenarios (both for the static backgrounds and the pseudo-stationary backgrounds in real-time for standard PAL (720 × 576 size color video.
Aircraft Fault Detection Using Real-Time Frequency Response Estimation
Grauer, Jared A.
2016-01-01
A real-time method for estimating time-varying aircraft frequency responses from input and output measurements was demonstrated. The Bat-4 subscale airplane was used with NASA Langley Research Center's AirSTAR unmanned aerial flight test facility to conduct flight tests and collect data for dynamic modeling. Orthogonal phase-optimized multisine inputs, summed with pilot stick and pedal inputs, were used to excite the responses. The aircraft was tested in its normal configuration and with emulated failures, which included a stuck left ruddervator and an increased command path latency. No prior knowledge of a dynamic model was used or available for the estimation. The longitudinal short period dynamics were investigated in this work. Time-varying frequency responses and stability margins were tracked well using a 20 second sliding window of data, as compared to a post-flight analysis using output error parameter estimation and a low-order equivalent system model. This method could be used in a real-time fault detection system, or for other applications of dynamic modeling such as real-time verification of stability margins during envelope expansion tests.
Automated real-time detection of tonic-clonic seizures using a wearable EMG device
DEFF Research Database (Denmark)
Beniczky, Sándor; Conradsen, Isa; Henning, Oliver
2018-01-01
OBJECTIVE: To determine the accuracy of automated detection of generalized tonic-clonic seizures (GTCS) using a wearable surface EMG device. METHODS: We prospectively tested the technical performance and diagnostic accuracy of real-time seizure detection using a wearable surface EMG device....... The seizure detection algorithm and the cutoff values were prespecified. A total of 71 patients, referred to long-term video-EEG monitoring, on suspicion of GTCS, were recruited in 3 centers. Seizure detection was real-time and fully automated. The reference standard was the evaluation of video-EEG recordings...
Detecting changes in real-time data: a user's guide to optimal detection.
Johnson, P; Moriarty, J; Peskir, G
2017-08-13
The real-time detection of changes in a noisily observed signal is an important problem in applied science and engineering. The study of parametric optimal detection theory began in the 1930s, motivated by applications in production and defence. Today this theory, which aims to minimize a given measure of detection delay under accuracy constraints, finds applications in domains including radar, sonar, seismic activity, global positioning, psychological testing, quality control, communications and power systems engineering. This paper reviews developments in optimal detection theory and sequential analysis, including sequential hypothesis testing and change-point detection, in both Bayesian and classical (non-Bayesian) settings. For clarity of exposition, we work in discrete time and provide a brief discussion of the continuous time setting, including recent developments using stochastic calculus. Different measures of detection delay are presented, together with the corresponding optimal solutions. We emphasize the important role of the signal-to-noise ratio and discuss both the underlying assumptions and some typical applications for each formulation.This article is part of the themed issue 'Energy management: flexibility, risk and optimization'. © 2017 The Author(s).
Aggregated channels network for real-time pedestrian detection
Ghorban, Farzin; Marín, Javier; Su, Yu; Colombo, Alessandro; Kummert, Anton
2018-04-01
Convolutional neural networks (CNNs) have demonstrated their superiority in numerous computer vision tasks, yet their computational cost results prohibitive for many real-time applications such as pedestrian detection which is usually performed on low-consumption hardware. In order to alleviate this drawback, most strategies focus on using a two-stage cascade approach. Essentially, in the first stage a fast method generates a significant but reduced amount of high quality proposals that later, in the second stage, are evaluated by the CNN. In this work, we propose a novel detection pipeline that further benefits from the two-stage cascade strategy. More concretely, the enriched and subsequently compressed features used in the first stage are reused as the CNN input. As a consequence, a simpler network architecture, adapted for such small input sizes, allows to achieve real-time performance and obtain results close to the state-of-the-art while running significantly faster without the use of GPU. In particular, considering that the proposed pipeline runs in frame rate, the achieved performance is highly competitive. We furthermore demonstrate that the proposed pipeline on itself can serve as an effective proposal generator.
Real-time detection with AdaBoost-svm combination in various face orientation
Fhonna, R. P.; Nasution, M. K. M.; Tulus
2018-03-01
Most of the research has used algorithm AdaBoost-SVM for face detection. However, to our knowledge so far there is no research has been facing detection on real-time data with various orientations using the combination of AdaBoost and Support Vector Machine (SVM). Characteristics of complex and diverse face variations and real-time data in various orientations, and with a very complex application will slow down the performance of the face detection system this becomes a challenge in this research. Face orientation performed on the detection system, that is 900, 450, 00, -450, and -900. This combination method is expected to be an effective and efficient solution in various face orientations. The results showed that the highest average detection rate is on the face detection oriented 00 and the lowest detection rate is in the face orientation 900.
Design of Wearable Breathing Sound Monitoring System for Real-Time Wheeze Detection
Directory of Open Access Journals (Sweden)
Shih-Hong Li
2017-01-01
Full Text Available In the clinic, the wheezing sound is usually considered as an indicator symptom to reflect the degree of airway obstruction. The auscultation approach is the most common way to diagnose wheezing sounds, but it subjectively depends on the experience of the physician. Several previous studies attempted to extract the features of breathing sounds to detect wheezing sounds automatically. However, there is still a lack of suitable monitoring systems for real-time wheeze detection in daily life. In this study, a wearable and wireless breathing sound monitoring system for real-time wheeze detection was proposed. Moreover, a breathing sounds analysis algorithm was designed to continuously extract and analyze the features of breathing sounds to provide the objectively quantitative information of breathing sounds to professional physicians. Here, normalized spectral integration (NSI was also designed and applied in wheeze detection. The proposed algorithm required only short-term data of breathing sounds and lower computational complexity to perform real-time wheeze detection, and is suitable to be implemented in a commercial portable device, which contains relatively low computing power and memory. From the experimental results, the proposed system could provide good performance on wheeze detection exactly and might be a useful assisting tool for analysis of breathing sounds in clinical diagnosis.
TractorEYE: Vision-based Real-time Detection for Autonomous Vehicles in Agriculture
DEFF Research Database (Denmark)
Christiansen, Peter
) using a smaller memory footprint and 7.3-times faster processing. Low memory footprint and fast processing makes DeepAnomaly suitable for real-time applications running on an embedded GPU. FieldSAFE is a multi-modal dataset for detection of static and moving obstacles in agriculture. The dataset...... (four for rgb camera, one for thermal camera and one for a Multi-beam lidar) and fuse detection information in a common format using either 3D positions or Inverse Sensor Models. A GPU powered computational platform is able to run detection algorithms online. For the rgb camera, a deep learning...... algorithm is proposed DeepAnomaly to perform real-time anomaly detection of distant, heavy occluded and unknown obstacles in agriculture. DeepAnomaly is - compared to a state-of-the-art object detector Faster R-CNN - for an agricultural use-case able to detect humans better and at longer ranges (45-90m...
Real-time billboard trademark detection and recognition in sports video
Bu, Jiang; Lao, Song-Yan; Bai, Liang
2013-03-01
Nowadays, different applications like automatic video indexing, keyword based video search and TV commercials can be developed by detecting and recognizing the billboard trademark. We propose a hierarchical solution for real-time billboard trademark recognition in various sports video, billboard frames are detected in the first level, fuzzy decision tree with easily-computing features are employed to accelerate the process, while in the second level, color and regional SIFT features are combined for the first time to describe the appearance of trademarks, and the shared nearest neighbor (SNN) clustering with x2 distance is utilized instead of traditional K-means clustering to construct the SIFT vocabulary, at last, Latent Semantic Analysis (LSA) based SIFT vocabulary matching is performed on the template trademark and the candidate regions in billboard frame. The preliminary experiments demonstrate the effectiveness of the hierarchical solution, and real time constraints are also met by our solution.
REAL-TIME PCR DETECTION OF LISTERIA MONOCYTOGENES IN FOOD SAMPLES OF ANIMAL ORIGIN
Directory of Open Access Journals (Sweden)
Jaroslav Pochop
2013-02-01
Full Text Available The aim of this study was to follow the contamination of food with Listeria monocytogenes by using Step One real time polymerase chain reaction (PCR. We used the PrepSEQ Rapid Spin Sample Preparation Kit for isolation of DNA and SensiFAST SYBR Hi-ROX Kit for the real-time PCR performance. In 24 samples of food of animal origin without incubation were detected strains of Listeria monocytogenes in 15 samples (swabs. Nine samples were negative. Our results indicated that the real-time PCR assay developed in this study could sensitively detect Listeria monocytogenes in food of animal origin without incubation. This could prevent infection caused by Listeria monocytogenes, and also could benefit food manufacturing companies by extending their product’s shelf-life as well as saving the cost of warehousing their food products while awaiting pathogen testing results. The rapid real-time PCR-based method performed very well compared to the conventional method. It is a fast, simple, specific and sensitive way to detect nucleic acids, which could be used in clinical diagnostic tests in the future.
Near real-time shadow detection and removal in aerial motion imagery application
Silva, Guilherme F.; Carneiro, Grace B.; Doth, Ricardo; Amaral, Leonardo A.; Azevedo, Dario F. G. de
2018-06-01
This work presents a method to automatically detect and remove shadows in urban aerial images and its application in an aerospace remote monitoring system requiring near real-time processing. Our detection method generates shadow masks and is accelerated by GPU programming. To obtain the shadow masks, we converted images from RGB to CIELCh model, calculated a modified Specthem ratio, and applied multilevel thresholding. Morphological operations were used to reduce shadow mask noise. The shadow masks are used in the process of removing shadows from the original images using the illumination ratio of the shadow/non-shadow regions. We obtained shadow detection accuracy of around 93% and shadow removal results comparable to the state-of-the-art while maintaining execution time under real-time constraints.
Ubiquitous health monitoring and real-time cardiac arrhythmias detection: a case study.
Li, Jian; Zhou, Haiying; Zuo, Decheng; Hou, Kun-Mean; De Vaulx, Christophe
2014-01-01
As the symptoms and signs of heart diseases that cause sudden cardiac death, cardiac arrhythmia has attracted great attention. Due to limitations in time and space, traditional approaches to cardiac arrhythmias detection fail to provide a real-time continuous monitoring and testing service applicable in different environmental conditions. Integrated with the latest technologies in ECG (electrocardiograph) analysis and medical care, the pervasive computing technology makes possible the ubiquitous cardiac care services, and thus brings about new technical challenges, especially in the formation of cardiac care architecture and realization of the real-time automatic ECG detection algorithm dedicated to care devices. In this paper, a ubiquitous cardiac care prototype system is presented with its architecture framework well elaborated. This prototype system has been tested and evaluated in all the clinical-/home-/outdoor-care modes with a satisfactory performance in providing real-time continuous cardiac arrhythmias monitoring service unlimitedly adaptable in time and space.
Shape based kinetic outlier detection in real-time PCR
Directory of Open Access Journals (Sweden)
D'Atri Mario
2010-04-01
Full Text Available Abstract Background Real-time PCR has recently become the technique of choice for absolute and relative nucleic acid quantification. The gold standard quantification method in real-time PCR assumes that the compared samples have similar PCR efficiency. However, many factors present in biological samples affect PCR kinetic, confounding quantification analysis. In this work we propose a new strategy to detect outlier samples, called SOD. Results Richards function was fitted on fluorescence readings to parameterize the amplification curves. There was not a significant correlation between calculated amplification parameters (plateau, slope and y-coordinate of the inflection point and the Log of input DNA demonstrating that this approach can be used to achieve a "fingerprint" for each amplification curve. To identify the outlier runs, the calculated parameters of each unknown sample were compared to those of the standard samples. When a significant underestimation of starting DNA molecules was found, due to the presence of biological inhibitors such as tannic acid, IgG or quercitin, SOD efficiently marked these amplification profiles as outliers. SOD was subsequently compared with KOD, the current approach based on PCR efficiency estimation. The data obtained showed that SOD was more sensitive than KOD, whereas SOD and KOD were equally specific. Conclusion Our results demonstrated, for the first time, that outlier detection can be based on amplification shape instead of PCR efficiency. SOD represents an improvement in real-time PCR analysis because it decreases the variance of data thus increasing the reliability of quantification.
Chen, Jieshi; Schafer, Benjamin Carrion; Ho, Ivan Wang-Hei
2016-01-01
With the growing demand of real-time traffic monitoring nowadays, software-based image processing can hardly meet the real-time data processing requirement due to the serial data processing nature. In this paper, the implementation of a hardware-based feature detection and networking system prototype for real-time traffic monitoring as well as data transmission is presented. The hardware architecture of the proposed system is mainly composed of three parts: data collection, feature detection,...
Matsuoka, Takayuki; Shigemura, Katsumi; Yamamichi, Fukashi; Fujisawa, Masato; Kawabata, Masato; Shirakawa, Toshiro
2012-06-27
The objective of this study is to investigate and compare the sensitivity in conventional PCR, quantitative real time PCR, nested PCR and western blots for detection of prostate cancer tumor markers using prostate cancer (PCa) cells. We performed conventional PCR, quantitative real time PCR, nested PCR, and western blots using 5 kinds of PCa cells. Prostate specific antigen (PSA), prostate specific membrane antigen (PSMA), and androgen receptor (AR) were compared for their detection sensitivity by real time PCR and nested PCR. In real time PCR, there was a significant correlation between cell number and the RNA concentration obtained (R(2)=0.9944) for PSA, PSMA, and AR. We found it possible to detect these markers from a single LNCaP cell in both real time and nested PCR. By comparison, nested PCR reached a linear curve in fewer PCR cycles than real time PCR, suggesting that nested PCR may offer PCR results more quickly than real time PCR. In conclusion, nested PCR may offer tumor maker detection in PCa cells more quickly (with fewer PCR cycles) with the same high sensitivity as real time PCR. Further study is necessary to establish and evaluate the best tool for PCa tumor marker detection.
Real-Time RT-PCR for the Detection of Lyssavirus Species
Directory of Open Access Journals (Sweden)
A. Deubelbeiss
2014-01-01
Full Text Available The causative agents of rabies are single-stranded, negative-sense RNA viruses in the genus Lyssavirus of Rhabdoviridae, consisting of twelve classified and three as yet unclassified species including classical rabies virus (RABV. Highly neurotropic RABV causes rapidly progressive encephalomyelitis with nearly invariable fatal outcome. Rapid and reliable diagnosis of rabies is highly relevant for public and veterinary health. Due to growing variety of the genus Lyssavirus observed, the development of suitable molecular assays for diagnosis and differentiation is challenging. This work focused on the establishment of a suitable real-time RT-PCR technique for rabies diagnosis as a complement to fluorescent antibody test and rabies tissue culture infection test as gold standard for diagnosis and confirmation. The real-time RT-PCR was adapted with the goal to detect the whole spectrum of lyssavirus species, for nine of which synthesized DNA fragments were used. For the detection of species, seven probes were developed. Serial dilutions of the rabies virus strain CVS-11 showed a 100-fold higher sensitivity of real-time PCR compared to heminested RT-PCR. Using a panel of thirty-one lyssaviruses representing four species, the suitability of the protocol could be shown. Phylogenetic analysis of the sequences obtained by heminested PCR allowed correct classification of all viruses used.
Real-time driver fatigue detection based on face alignment
Tao, Huanhuan; Zhang, Guiying; Zhao, Yong; Zhou, Yi
2017-07-01
The performance and robustness of fatigue detection largely decrease if the driver with glasses. To address this issue, this paper proposes a practical driver fatigue detection method based on face alignment at 3000 FPS algorithm. Firstly, the eye regions of the driver are localized by exploiting 6 landmarks surrounding each eye. Secondly, the HOG features of the extracted eye regions are calculated and put into SVM classifier to recognize the eye state. Finally, the value of PERCLOS is calculated to determine whether the driver is drowsy or not. An alarm will be generated if the eye is closed for a specified period of time. The accuracy and real-time on testing videos with different drivers demonstrate that the proposed algorithm is robust and obtain better accuracy for driver fatigue detection compared with some previous method.
Abdeljaber, Osama; Avci, Onur; Kiranyaz, Serkan; Gabbouj, Moncef; Inman, Daniel J.
2017-02-01
Structural health monitoring (SHM) and vibration-based structural damage detection have been a continuous interest for civil, mechanical and aerospace engineers over the decades. Early and meticulous damage detection has always been one of the principal objectives of SHM applications. The performance of a classical damage detection system predominantly depends on the choice of the features and the classifier. While the fixed and hand-crafted features may either be a sub-optimal choice for a particular structure or fail to achieve the same level of performance on another structure, they usually require a large computation power which may hinder their usage for real-time structural damage detection. This paper presents a novel, fast and accurate structural damage detection system using 1D Convolutional Neural Networks (CNNs) that has an inherent adaptive design to fuse both feature extraction and classification blocks into a single and compact learning body. The proposed method performs vibration-based damage detection and localization of the damage in real-time. The advantage of this approach is its ability to extract optimal damage-sensitive features automatically from the raw acceleration signals. Large-scale experiments conducted on a grandstand simulator revealed an outstanding performance and verified the computational efficiency of the proposed real-time damage detection method.
Automated Detection of Short Optical Transients of Astrophysical Origin in Real Time
Directory of Open Access Journals (Sweden)
Marcin Sokołowski
2010-01-01
Full Text Available The detection of short optical transients of astrophysical origin in real time is an important task for existing robotic telescopes. The faster a new optical transient is detected, the earlier follow-up observations can be started. The sooner the object is identified, the more data can be collected before the source fades away, particularly in the most interesting early period of the transient. In this the real-time pipeline designed for identification of optical flashes with the “Pi of the Sky” project will be presented in detail together with solutions used by other experiments.
Development of real-time PCR for detection and quantitation of Streptococcus parauberis.
Nguyen, T L; Lim, Y J; Kim, D-H; Austin, B
2016-01-01
Streptococcus parauberis is an increasing threat to aquaculture of olive flounder, Paralichthys olivaceus Temminck & Schlegel, in South Korea. We developed a real-time polymerase chain reaction (PCR) method using the TaqMan probe assay to detect and quantify S. parauberis by targeting the gyrB gene sequences, which are effective for molecular analysis of the genus Streptococcus. Our real-time PCR assay is capable of detecting 10 fg of genomic DNA per reaction. The intra- and interassay coefficient of variation (CV) values ranged from 0.42-1.95%, demonstrating that the assay has good reproducibility. There was not any cross-reactivity to Streptococcus iniae or to other streptococcal/lactococcal fish pathogens, such as S. agalactiae and Lactococcus garvieae, indicating that the assay is highly specific to S. parauberis. The results of the real-time PCR assay corresponded well to those of conventional culture assays for S. parauberis from inoculated tissue homogenates (r = 0.957; P < 0.05). Hence, this sensitive and specific real-time PCR is a valuable tool for diagnostic quantitation of S. parauberis in clinical samples. © 2014 John Wiley & Sons Ltd.
A Metrics-Based Approach to Intrusion Detection System Evaluation for Distributed Real-Time Systems
2002-04-01
Based Approach to Intrusion Detection System Evaluation for Distributed Real - Time Systems Authors: G. A. Fink, B. L. Chappell, T. G. Turner, and...Distributed, Security. 1 Introduction Processing and cost requirements are driving future naval combat platforms to use distributed, real - time systems of...distributed, real - time systems . As these systems grow more complex, the timing requirements do not diminish; indeed, they may become more constrained
A one-step, real-time PCR assay for rapid detection of rhinovirus.
Do, Duc H; Laus, Stella; Leber, Amy; Marcon, Mario J; Jordan, Jeanne A; Martin, Judith M; Wadowsky, Robert M
2010-01-01
One-step, real-time PCR assays for rhinovirus have been developed for a limited number of PCR amplification platforms and chemistries, and some exhibit cross-reactivity with genetically similar enteroviruses. We developed a one-step, real-time PCR assay for rhinovirus by using a sequence detection system (Applied Biosystems; Foster City, CA). The primers were designed to amplify a 120-base target in the noncoding region of picornavirus RNA, and a TaqMan (Applied Biosystems) degenerate probe was designed for the specific detection of rhinovirus amplicons. The PCR assay had no cross-reactivity with a panel of 76 nontarget nucleic acids, which included RNAs from 43 enterovirus strains. Excellent lower limits of detection relative to viral culture were observed for the PCR assay by using 38 of 40 rhinovirus reference strains representing different serotypes, which could reproducibly detect rhinovirus serotype 2 in viral transport medium containing 10 to 10,000 TCID(50) (50% tissue culture infectious dose endpoint) units/ml of the virus. However, for rhinovirus serotypes 59 and 69, the PCR assay was less sensitive than culture. Testing of 48 clinical specimens from children with cold-like illnesses for rhinovirus by the PCR and culture assays yielded detection rates of 16.7% and 6.3%, respectively. For a batch of 10 specimens, the entire assay was completed in 4.5 hours. This real-time PCR assay enables detection of many rhinovirus serotypes with the Applied Biosystems reagent-instrument platform.
Incremental Activation Detection for Real-Time fMRI Series Using Robust Kalman Filter
Directory of Open Access Journals (Sweden)
Liang Li
2014-01-01
Full Text Available Real-time functional magnetic resonance imaging (rt-fMRI is a technique that enables us to observe human brain activations in real time. However, some unexpected noises that emerged in fMRI data collecting, such as acute swallowing, head moving and human manipulations, will cause much confusion and unrobustness for the activation analysis. In this paper, a new activation detection method for rt-fMRI data is proposed based on robust Kalman filter. The idea is to add a variation to the extended kalman filter to handle the additional sparse measurement noise and a sparse noise term to the measurement update step. Hence, the robust Kalman filter is designed to improve the robustness for the outliers and can be computed separately for each voxel. The algorithm can compute activation maps on each scan within a repetition time, which meets the requirement for real-time analysis. Experimental results show that this new algorithm can bring out high performance in robustness and in real-time activation detection.
Visual detectability of elastic contrast in real-time ultrasound images
Miller, Naomi R.; Bamber, Jeffery C.; Doyley, Marvin M.; Leach, Martin O.
1997-04-01
Elasticity imaging (EI) has recently been proposed as a technique for imaging the mechanical properties of soft tissue. However, dynamic features, known as compressibility and mobility, are already employed to distinguish between different tissue types in ultrasound breast examination. This method, which involves the subjective interpretation of tissue motion seen in real-time B-mode images during palpation, is hereafter referred to as differential motion imaging (DMI). The purpose of this study was to develop the methodology required to perform a series of perception experiments to measure elastic lesion detectability by means of DMI and to obtain preliminary results for elastic contrast thresholds for different lesion sizes. Simulated sequences of real-time B-scans of tissue moving in response to an applied force were generated. A two-alternative forced choice (2-AFC) experiment was conducted and the measured contrast thresholds were compared with published results for lesions detected by EI. Although the trained observer was found to be quite skilled at the task of differential motion perception, it would appear that lesion detectability is improved when motion information is detected by computer processing and converted to gray scale before presentation to the observer. In particular, for lesions containing fewer than eight speckle cells, a signal detection rate of 100% could not be achieved even when the elastic contrast was very high.
Real-time Multiresolution Crosswalk Detection with Walk Light Recognition for the Blind
Directory of Open Access Journals (Sweden)
ROMIC, K.
2018-02-01
Full Text Available Real-time image processing and object detection techniques have a great potential to be applied in digital assistive tools for the blind and visually impaired persons. In this paper, algorithm for crosswalk detection and walk light recognition is proposed with the main aim to help blind person when crossing the road. The proposed algorithm is optimized to work in real-time on portable devices using standard cameras. Images captured by camera are processed while person is moving and decision about detected crosswalk is provided as an output along with the information about walk light if one is present. Crosswalk detection method is based on multiresolution morphological image processing, while the walk light recognition is performed by proposed 6-stage algorithm. The main contributions of this paper are accurate crosswalk detection with small processing time due to multiresolution processing and the recognition of the walk lights covering only small amount of pixels in image. The experiment is conducted using images from video sequences captured in realistic situations on crossings. The results show 98.3% correct crosswalk detections and 89.5% correct walk lights recognition with average processing speed of about 16 frames per second.
A software framework for real-time multi-modal detection of microsleeps.
Knopp, Simon J; Bones, Philip J; Weddell, Stephen J; Jones, Richard D
2017-09-01
A software framework is described which was designed to process EEG, video of one eye, and head movement in real time, towards achieving early detection of microsleeps for prevention of fatal accidents, particularly in transport sectors. The framework is based around a pipeline structure with user-replaceable signal processing modules. This structure can encapsulate a wide variety of feature extraction and classification techniques and can be applied to detecting a variety of aspects of cognitive state. Users of the framework can implement signal processing plugins in C++ or Python. The framework also provides a graphical user interface and the ability to save and load data to and from arbitrary file formats. Two small studies are reported which demonstrate the capabilities of the framework in typical applications: monitoring eye closure and detecting simulated microsleeps. While specifically designed for microsleep detection/prediction, the software framework can be just as appropriately applied to (i) other measures of cognitive state and (ii) development of biomedical instruments for multi-modal real-time physiological monitoring and event detection in intensive care, anaesthesiology, cardiology, neurosurgery, etc. The software framework has been made freely available for researchers to use and modify under an open source licence.
Real-time detection and discrimination of visual perception using electrocorticographic signals
Kapeller, C.; Ogawa, H.; Schalk, G.; Kunii, N.; Coon, W. G.; Scharinger, J.; Guger, C.; Kamada, K.
2018-06-01
Objective. Several neuroimaging studies have demonstrated that the ventral temporal cortex contains specialized regions that process visual stimuli. This study investigated the spatial and temporal dynamics of electrocorticographic (ECoG) responses to different types and colors of visual stimulation that were presented to four human participants, and demonstrated a real-time decoder that detects and discriminates responses to untrained natural images. Approach. ECoG signals from the participants were recorded while they were shown colored and greyscale versions of seven types of visual stimuli (images of faces, objects, bodies, line drawings, digits, and kanji and hiragana characters), resulting in 14 classes for discrimination (experiment I). Additionally, a real-time system asynchronously classified ECoG responses to faces, kanji and black screens presented via a monitor (experiment II), or to natural scenes (i.e. the face of an experimenter, natural images of faces and kanji, and a mirror) (experiment III). Outcome measures in all experiments included the discrimination performance across types based on broadband γ activity. Main results. Experiment I demonstrated an offline classification accuracy of 72.9% when discriminating among the seven types (without color separation). Further discrimination of grey versus colored images reached an accuracy of 67.1%. Discriminating all colors and types (14 classes) yielded an accuracy of 52.1%. In experiment II and III, the real-time decoder correctly detected 73.7% responses to face, kanji and black computer stimuli and 74.8% responses to presented natural scenes. Significance. Seven different types and their color information (either grey or color) could be detected and discriminated using broadband γ activity. Discrimination performance maximized for combined spatial-temporal information. The discrimination of stimulus color information provided the first ECoG-based evidence for color-related population
On-Site Molecular Detection of Soil-Borne Phytopathogens Using a Portable Real-Time PCR System.
DeShields, Joseph B; Bomberger, Rachel A; Woodhall, James W; Wheeler, David L; Moroz, Natalia; Johnson, Dennis A; Tanaka, Kiwamu
2018-02-23
On-site diagnosis of plant diseases can be a useful tool for growers for timely decisions enabling the earlier implementation of disease management strategies that reduce the impact of the disease. Presently in many diagnostic laboratories, the polymerase chain reaction (PCR), particularly real-time PCR, is considered the most sensitive and accurate method for plant pathogen detection. However, laboratory-based PCRs typically require expensive laboratory equipment and skilled personnel. In this study, soil-borne pathogens of potato are used to demonstrate the potential for on-site molecular detection. This was achieved using a rapid and simple protocol comprising of magnetic bead-based nucleic acid extraction, portable real-time PCR (fluorogenic probe-based assay). The portable real-time PCR approach compared favorably with a laboratory-based system, detecting as few as 100 copies of DNA from Spongospora subterranea. The portable real-time PCR method developed here can serve as an alternative to laboratory-based approaches and a useful on-site tool for pathogen diagnosis.
Quantitative Real-time PCR detection of putrescine-producing Gram-negative bacteria
Directory of Open Access Journals (Sweden)
Kristýna Maršálková
2017-01-01
Full Text Available Biogenic amines are indispensable components of living cells; nevertheless these compounds could be toxic for human health in higher concentrations. Putrescine is supposed to be the major biogenic amine associated with microbial food spoilage. Development of reliable, fast and culture-independent molecular methods to detect bacteria producing biogenic amines deserves the attention, especially of the food industry in purpose to protect health. The objective of this study was to verify the newly designed primer sets for detection of two inducible genes adiA and speF together in Salmonella enterica and Escherichia coli genome by Real-time PCR. These forenamed genes encode enzymes in the metabolic pathway which leads to production of putrescine in Gram-negative bacteria. Moreover, relative expression of these genes was studied in E. coli CCM 3954 strain using Real-time PCR. In this study, sets of new primers for the detection two inducible genes (speF and adiA in Salmonella enterica and E. coli by Real-time PCR were designed and tested. Amplification efficiency of a Real-time PCR was calculated from the slope of the standard curves (adiA, speF, gapA. An efficiency in a range from 95 to 105 % for all tested reactions was achieved. The gene expression (R of adiA and speF genes in E. coli was varied depending on culture conditions. The highest gene expression of adiA and speF was observed at 6, 24 and 36 h (RadiA ~ 3, 5, 9; RspeF ~11, 10, 9; respectively after initiation of growth of this bacteria in nutrient broth medium enchired with amino acids. The results show that these primers could be used for relative quantification analysis of E. coli.
Han, Yang; Hou, Shao-Yang; Ji, Shang-Zhi; Cheng, Juan; Zhang, Meng-Yue; He, Li-Juan; Ye, Xiang-Zhong; Li, Yi-Min; Zhang, Yi-Xuan
2017-11-15
A novel method, real-time reverse transcription PCR (real-time RT-PCR) coupled with probe-melting curve analysis, has been established to detect two kinds of samples within one fluorescence channel. Besides a conventional TaqMan probe, this method employs another specially designed melting-probe with a 5' terminus modification which meets the same label with the same fluorescent group. By using an asymmetric PCR method, the melting-probe is able to detect an extra sample in the melting stage effectively while it almost has little influence on the amplification detection. Thus, this method allows the availability of united employment of both amplification stage and melting stage for detecting samples in one reaction. The further demonstration by simultaneous detection of human immunodeficiency virus (HIV) and hepatitis C virus (HCV) in one channel as a model system is presented in this essay. The sensitivity of detection by real-time RT-PCR coupled with probe-melting analysis was proved to be equal to that detected by conventional real-time RT-PCR. Because real-time RT-PCR coupled with probe-melting analysis can double the detection throughputs within one fluorescence channel, it is expected to be a good solution for the problem of low-throughput in current real-time PCR. Copyright © 2017 Elsevier Inc. All rights reserved.
FRB microstructure revealed by the real-time detection of FRB170827
Farah, W.; Flynn, C.; Bailes, M.; Jameson, A.; Bannister, K. W.; Barr, E. D.; Bateman, T.; Bhandari, S.; Caleb, M.; Campbell-Wilson, D.; Chang, S. -W.; Deller, A.; Green, A. J.; Hunstead, R.; Jankowski, F.
2018-01-01
We report a new Fast Radio Burst (FRB) discovered in real-time as part of the UTMOST project at the Molonglo Observatory Synthesis Radio Telescope (MOST). FRB170827 is the first detected with our low-latency ($< 24$ s), machine-learning-based FRB detection system. The FRB discovery was accompanied by the capture of voltage data at the native time and frequency resolution of the observing system, enabling coherent dedispersion and detailed off-line analysis, which have unveiled fine temporal a...
Detection of Campylobacter spp. in chicken fecal samples by real-time PCR
DEFF Research Database (Denmark)
Lund, Marianne; Nordentoft, Steen; Pedersen, Karl
2004-01-01
A real-time PCR assay for detecting thermophilic Campylobacter spp. directly in chicken feces has been developed. DNA was isolated from fecal material by using magnetic beads followed by PCR with a prealiquoted PCR mixture, which had been stored at -18degreesC. Campylobacter could be detected...
Wu, Qingzhong; Prager, Katherine C; Goldstein, Tracey; Alt, David P; Galloway, Renee L; Zuerner, Richard L; Lloyd-Smith, James O; Schwacke, Lori
2014-08-11
Several real-time PCR assays are currently used for detection of pathogenic Leptospira spp.; however, few methods have been described for the successful evaluation of clinical urine samples. This study reports a rapid assay for the detection of pathogenic Leptospira spp. in California sea lions Zalophus californianus using real-time PCR with primers and a probe targeting the lipL32 gene. The PCR assay had high analytic sensitivity-the limit of detection was 3 genome copies per PCR volume using L. interrogans serovar Pomona DNA and 100% analytic specificity; it detected all pathogenic leptospiral serovars tested and none of the non-pathogenic Leptospira species (L. biflexa and L. meyeri serovar Semaranga), the intermediate species L. inadai, or the non-Leptospira pathogens tested. Our assay had an amplification efficiency of 1.00. Comparisons between the real-time PCR assay and culture isolation for detection of pathogenic Leptospira spp. in urine and kidney tissue samples from California sea lions showed that samples were more often positive by real-time PCR than by culture methods. Inclusion of an internal amplification control in the real-time PCR assay showed no inhibitory effects in PCR negative samples. These studies indicated that our real-time PCR assay has high analytic sensitivity and specificity for the rapid detection of pathogenic Leptospira species in urine and kidney tissue samples.
Wang, Qinqin; Zhou, Yanbin; Li, Shaoli; Zhuo, Chao; Xu, Siqi; Huang, Lixia; Yang, Ling; Liao, Kang
2013-01-01
Background Detection of Acinetobacter baumannii has been relying primarily on bacterial culture that often fails to return useful results in time. Although DNA-based assays are more sensitive than bacterial culture in detecting the pathogen, the molecular results are often inconsistent and challenged by doubts on false positives, such as those due to system- and environment-derived contaminations. In addition, these molecular tools require expensive laboratory instruments. Therefore, establishing molecular tools for field use require simpler molecular platforms. The loop-mediated isothermal amplification method is relatively simple and can be improved for better use in a routine clinical bacteriology laboratory. A simple and portable device capable of performing both the amplification and detection (by fluorescence) of LAMP in the same platform has been developed in recent years. This method is referred to as real-time loop-mediated isothermal amplification. In this study, we attempted to utilize this method for rapid detection of A. baumannii. Methodology and Significant Findings Species-specific primers were designed to test the utility of this method. Clinical samples of A. baumannii were used to determine the sensitivity and specificity of this system compared to bacterial culture and a polymerase chain reaction method. All positive samples isolated from sputum were confirmed to be the species of Acinetobacter by 16S rRNA gene sequencing. The RealAmp method was found to be simpler and allowed real-time detection of DNA amplification, and could distinguish A. baumannii from Acinetobacter calcoaceticus and Acinetobacter genomic species 3. DNA was extracted by simple boiling method. Compared to bacterial culture, the sensitivity and specificity of RealAmp in detecting A. baumannii was 98.9% and 75.0%, respectively. Conclusion The RealAmp assay only requires a single unit, and the assay positivity can be verified by visual inspection. Therefore, this assay has
Real-time detection of transient cardiac ischemic episodes from ECG signals
International Nuclear Information System (INIS)
Dranca, L; Goñi, A; Illarramendi, A
2009-01-01
We propose a new algorithm to detect and classify transient cardiac ischemia episodes, designed with the goal of providing a real-time execution without penalizing the classifier accuracy much. The algorithm is based on a novel mixture of time-domain analysis and machine learning techniques, specifically bagging of decision trees, and it has been developed using a well-recognized and freely distributed database, namely the long-term ST database. The ST episode detection sensitivity/positive predictivity using the annotation protocol A for this database is 68.26%/74.91%. The sensitivity result increases until 93.97% for the most dangerous episodes in terms of duration and magnitude (annotated according to protocol C). The test of the algorithm over the freely distributed part of the European Society of Cardiology database has shown results of sensitivity and positive predictivity of 83.33% and 77.31%, respectively. Those results are close to the results obtained by related works that present approaches to detect ischemia episodes off-line, which is remarkable if we take into account that in our real-time approach, less information is available during the classification process
Real-time detection of TDP1 activity using a fluorophore-quencher coupled DNA-biosensor
DEFF Research Database (Denmark)
Jensen, Pia Wrensted; Falconi, Mattia; Kristoffersen, Emil Laust
2013-01-01
structure of the biosensor. The specific action of TDP1 removes the quencher, thereby enabling optical detection of the fluorophore. Since the enzymatic action of TDP1 is the only “signal amplification” the increase in fluorescence may easily be followed in real-time and allows quantitative analyses of TDP1......Real-time detection of enzyme activities may present the easiest and most reliable way of obtaining quantitative analyses in biological samples. We present a new DNA-biosensor capable of detecting the activity of the potential anticancer drug target tyrosyl-DNA phosphodiesterase 1 (TDP1) in a very...... simple, high throughput, and real-time format. The biosensor is specific for Tdp1 even in complex biological samples, such as human cell extracts, and may consequently find future use in fundamental studies as well as a cancer predictive tool allowing fast analyses of diagnostic cell samples...
Real-time DDoS attack detection for Cisco IOS using NetFlow
van der Steeg, Daniël; Hofstede, R.J.; Sperotto, Anna; Pras, Aiko
Flow-based DDoS attack detection is typically performed by analysis applications that are installed on or close to a flow collector. Although this approach allows for easy deployment, it makes detection far from real-time and susceptible to DDoS attacks for the following reasons. First, the fact
George, Daniel; Huerta, E. A.
2018-03-01
The recent Nobel-prize-winning detections of gravitational waves from merging black holes and the subsequent detection of the collision of two neutron stars in coincidence with electromagnetic observations have inaugurated a new era of multimessenger astrophysics. To enhance the scope of this emergent field of science, we pioneered the use of deep learning with convolutional neural networks, that take time-series inputs, for rapid detection and characterization of gravitational wave signals. This approach, Deep Filtering, was initially demonstrated using simulated LIGO noise. In this article, we present the extension of Deep Filtering using real data from LIGO, for both detection and parameter estimation of gravitational waves from binary black hole mergers using continuous data streams from multiple LIGO detectors. We demonstrate for the first time that machine learning can detect and estimate the true parameters of real events observed by LIGO. Our results show that Deep Filtering achieves similar sensitivities and lower errors compared to matched-filtering while being far more computationally efficient and more resilient to glitches, allowing real-time processing of weak time-series signals in non-stationary non-Gaussian noise with minimal resources, and also enables the detection of new classes of gravitational wave sources that may go unnoticed with existing detection algorithms. This unified framework for data analysis is ideally suited to enable coincident detection campaigns of gravitational waves and their multimessenger counterparts in real-time.
A Real-Time Plagiarism Detection Tool for Computer-Based Assessments
Jeske, Heimo J.; Lall, Manoj; Kogeda, Okuthe P.
2018-01-01
Aim/Purpose: The aim of this article is to develop a tool to detect plagiarism in real time amongst students being evaluated for learning in a computer-based assessment setting. Background: Cheating or copying all or part of source code of a program is a serious concern to academic institutions. Many academic institutions apply a combination of…
Simplified Pan-species Real-time PCR-based Detection of Plasmodium Spp. in Blood Smear.
Hassanpour, Gholamreza; Mirhendi, Hossein; Mohebali, Mehdi; Raeisi, Ahmad; Zeraati, Hojjat; Keshavarz, Hossein
2016-01-01
We aimed to quicken and simplify the detection of Plasmodium in blood samples by developing and testing a pan- Plasmodium real-time PCR for accurate screening of individuals suspected of malaria. A single primer/probe set for pan-species Plasmodium -specific real time PCR targeting a conserved region of the small subunit 18S ribosomal DNA was designed and evaluated for rapid diagnosis and screening of malaria infections using dried blood smears. FTA cards were used for rapid and simple DNA extraction. The primers and probes showed a positive response with the DNA extracted from bloods infected with P. falciparum and P. vivax but not with DNA extracted from various smears from uninfected blood samples. Seven positive cases positive by both microscopy and nested PCR were found among 280 blood samples taken from in South and Southeast Iran. Five samples were identified as positive for P. vivax and two as positive for P. falciparum . All positive samples were positive by real-time PCR. Furthermore, all 38-blood samples positive by microscopy were positive by real-time PCR. No microscopy-negative samples were positive by real-time PCR. By using a simple FTA card for DNA extraction and by application of the real-time PCR developed in this study, sensitivity similar to nested-PCR and microscopy was achieved. This format simplifies the detection of Plasmodium in large numbers of samples.
Directory of Open Access Journals (Sweden)
Whyte Paul
2008-09-01
Full Text Available Abstract Background A real-time multiplex PCR assay was developed for the detection of multiple Salmonella serotypes in chicken samples. Poultry-associated serotypes detected in the assay include Enteritidis, Gallinarum, Typhimurium, Kentucky and Dublin. The traditional cultural method according to EN ISO 6579:2002 for the detection of Salmonella in food was performed in parallel. The real-time PCR based method comprised a pre-enrichment step in Buffered Peptone Water (BPW overnight, followed by a shortened selective enrichment in Rappaport Vasilliadis Soya Broth (RVS for 6 hours and subsequent DNA extraction. Results The real-time multiplex PCR assay and traditional cultural method showed 100% inclusivity and 100% exclusivity on all strains tested. The real-time multiplex PCR assay was as sensitive as the traditional cultural method in detecting Salmonella in artificially contaminated chicken samples and correctly identified the serotype. Artificially contaminated chicken samples resulted in a detection limit of between 1 and 10 CFU per 25 g sample for both methods. A total of sixty-three naturally contaminated chicken samples were investigated by both methods and relative accuracy, relative sensitivity and relative specificity of the real-time PCR method were determined to be 89, 94 and 87%, respectively. Thirty cultures blind tested were correctly identified by the real-time multiplex PCR method. Conclusion Real-time PCR methodology can contribute to meet the need for rapid identification and detection methods in food testing laboratories.
Real-time DNA Amplification and Detection System Based on a CMOS Image Sensor.
Wang, Tiantian; Devadhasan, Jasmine Pramila; Lee, Do Young; Kim, Sanghyo
2016-01-01
In the present study, we developed a polypropylene well-integrated complementary metal oxide semiconductor (CMOS) platform to perform the loop mediated isothermal amplification (LAMP) technique for real-time DNA amplification and detection simultaneously. An amplification-coupled detection system directly measures the photon number changes based on the generation of magnesium pyrophosphate and color changes. The photon number decreases during the amplification process. The CMOS image sensor observes the photons and converts into digital units with the aid of an analog-to-digital converter (ADC). In addition, UV-spectral studies, optical color intensity detection, pH analysis, and electrophoresis detection were carried out to prove the efficiency of the CMOS sensor based the LAMP system. Moreover, Clostridium perfringens was utilized as proof-of-concept detection for the new system. We anticipate that this CMOS image sensor-based LAMP method will enable the creation of cost-effective, label-free, optical, real-time and portable molecular diagnostic devices.
Real time detecting system for turning force
Energy Technology Data Exchange (ETDEWEB)
Xiaobin, Yue [China Academy of Engineering Physics, Mianyang (China). Inst. of Machinery Manufacturing Technology
2001-07-01
How to get the real-time value of forces dropped on the tool in the course of processing by piezoelectric sensors is introduced. First, the analog signals of the cutting force were achieved by these sensors, amplified and transferred into digital signals by A/D transferring card. Then real-time software reads the information, put it into its own coordinate, drew the curve of forces, displayed it on the screen by the real time and saved it for the technicians to analyze the situation of the tool. So the cutting parameter can be optimized to improve surface quality of the pieces.
Majid, Farjana; Jahan, Munira; Lutful Moben, Ahmed; Tabassum, Shahina
2014-01-01
Both real-time-polymerase chain reaction (PCR) and hybrid capture 2 (HC2) assay can detect and quantify hepatitis B virus (HBV) DNA. However, real-time-PCR can detect a wide range of HBV DNA, while HC2 assay could not detect lower levels of viremia. The present study was designed to detect and quantify HBV DNA by real-time-PCR and HC2 assay and compare the quantitative data of these two assays. A cross-sectional study was conducted in between July 2010 and June 2011. A total of 66 serologically diagnosed chronic hepatitis B (CHB) patients were selected for the study. Real-time-PCR and HC2 assay was done to detect HBV DNA. Data were analyzed by statistical Package for the social sciences (SPSS). Among 66 serologically diagnosed chronic hepatitis B patients 40 (60.61%) patients had detectable and 26 (39.39%) had undetectable HBV DNA by HC2 assay. Concordant results were obtained for 40 (60.61%) out of these 66 patients by real-time-PCR and HC2 assay with mean viral load of 7.06 ± 1.13 log 10 copies/ml and 6.95 ± 1.08 log 10 copies/ml, respectively. In the remaining 26 patients, HBV DNA was detectable by real-time-PCR in 20 patients (mean HBV DNA level was 3.67 ± 0.72 log 10 copies/ml. However, HBV DNA could not be detectable in six cases by the both assays. The study showed strong correlation (r = 0.915) between real-time-PCR and HC2 assay for the detection and quantification of HBV DNA. HC2 assay may be used as an alternative to real-time-PCR for CHB patients. How to cite this article: Majid F, Jahan M, Moben AL, Tabassum S. Comparison of Hybrid Capture 2 Assay with Real-time-PCR for Detection and Quantitation of Hepatitis B Virus DNA. Euroasian J Hepato-Gastroenterol 2014;4(1):31-35.
Zhou, Hui; Ji, Ning; Samuel, Oluwarotimi Williams; Cao, Yafei; Zhao, Zheyi; Chen, Shixiong; Li, Guanglin
2016-10-01
Real-time detection of gait events can be applied as a reliable input to control drop foot correction devices and lower-limb prostheses. Among the different sensors used to acquire the signals associated with walking for gait event detection, the accelerometer is considered as a preferable sensor due to its convenience of use, small size, low cost, reliability, and low power consumption. Based on the acceleration signals, different algorithms have been proposed to detect toe off (TO) and heel strike (HS) gait events in previous studies. While these algorithms could achieve a relatively reasonable performance in gait event detection, they suffer from limitations such as poor real-time performance and are less reliable in the cases of up stair and down stair terrains. In this study, a new algorithm is proposed to detect the gait events on three walking terrains in real-time based on the analysis of acceleration jerk signals with a time-frequency method to obtain gait parameters, and then the determination of the peaks of jerk signals using peak heuristics. The performance of the newly proposed algorithm was evaluated with eight healthy subjects when they were walking on level ground, up stairs, and down stairs. Our experimental results showed that the mean F1 scores of the proposed algorithm were above 0.98 for HS event detection and 0.95 for TO event detection on the three terrains. This indicates that the current algorithm would be robust and accurate for gait event detection on different terrains. Findings from the current study suggest that the proposed method may be a preferable option in some applications such as drop foot correction devices and leg prostheses.
Real-time vehicle detection and tracking in video based on faster R-CNN
Zhang, Yongjie; Wang, Jian; Yang, Xin
2017-08-01
Vehicle detection and tracking is a significant part in auxiliary vehicle driving system. Using the traditional detection method based on image information has encountered enormous difficulties, especially in complex background. To solve this problem, a detection method based on deep learning, Faster R-CNN, which has very high detection accuracy and flexibility, is introduced. An algorithm of target tracking with the combination of Camshift and Kalman filter is proposed for vehicle tracking. The computation time of Faster R-CNN cannot achieve realtime detection. We use multi-thread technique to detect and track vehicle by parallel computation for real-time application.
Real-time PCR detection of aldoxime dehydratase genes in nitrile-degrading microorganisms.
Dooley-Cullinane, Tríona Marie; O'Reilly, Catherine; Coffey, Lee
2017-02-01
Aldoxime dehydratase catalyses the conversion of aldoximes to their corresponding nitriles. Utilization of the aldoxime-nitrile metabolising enzyme pathway can facilitate the move towards a greener chemistry. In this work, a real-time PCR assay was developed for the detection of aldoxime dehydratase genes in aldoxime/nitrile metabolising microorganisms which have been purified from environmental sources. A conventional PCR assay was also designed allowing gene confirmation via sequencing. Aldoxime dehydratase genes were identified in 30 microorganisms across 11 genera including some not previously shown to harbour the gene. The assay displayed a limit of detection of 1 pg/μL DNA or 7 CFU/reaction. This real-time PCR assay should prove valuable in the high-throughput screening of micro-organisms for novel aldoxime dehydratase genes towards pharmaceutical and industrial applications.
Real Time Vision System for Obstacle Detection and Localization on FPGA
Alhamwi , Ali; Vandeportaele , Bertrand; Piat , Jonathan
2015-01-01
International audience; Obstacle detection is a mandatory function for a robot navigating in an indoor environment especially when interaction with humans is done in a cluttered environment. Commonly used vision-based solutions like SLAM (Simultaneous Localization and Mapping) or optical flow tend to be computation intensive and require powerful computation resources to meet low speed real-time constraints. Solutions using LIDAR (Light Detection And Ranging) sensors are more robust but not co...
Zhang, Fang; Wang, Liu; Fan, Kai; Wu, Jian; Ying, Yibin
2014-05-01
An isothermal cross-priming amplification (CPA) assay for Agrobacterium tumefaciens nopaline synthase terminator (T-Nos) was established and investigated in this work. A set of six specific primers, recognizing eight distinct regions on the T-Nos sequence, was designed. The CPA assay was performed at a constant temperature, 63 °C, and detected by real-time fluorescence. The results indicated that real-time fluorescent CPA had high specificity, and the limit of detection was 1.06 × 10(3) copies of rice genomic DNA, which could be detected in 40 min. Comparison of real-time fluorescent CPA and conventional polymerase chain reaction (PCR) was also performed. Results revealed that real-time fluorescent CPA had a comparable sensitivity to conventional real-time PCR and had taken a shorter time. In addition, different contents of genetically modified (GM)-contaminated rice seed powder samples were detected for practical application. The result showed real-time fluorescent CPA could detect 0.5 % GM-contaminated samples at least, and the whole reaction could be finished in 35 min. Real-time fluorescent CPA is sensitive enough to monitor labeling systems and provides an attractive method for the detection of GMO.
Mackay, Ian M; Arden, Katherine E; Nitsche, Andreas
2002-03-15
The use of the polymerase chain reaction (PCR) in molecular diagnostics has increased to the point where it is now accepted as the gold standard for detecting nucleic acids from a number of origins and it has become an essential tool in the research laboratory. Real-time PCR has engendered wider acceptance of the PCR due to its improved rapidity, sensitivity, reproducibility and the reduced risk of carry-over contamination. There are currently five main chemistries used for the detection of PCR product during real-time PCR. These are the DNA binding fluorophores, the 5' endonuclease, adjacent linear and hairpin oligoprobes and the self-fluorescing amplicons, which are described in detail. We also discuss factors that have restricted the development of multiplex real-time PCR as well as the role of real-time PCR in quantitating nucleic acids. Both amplification hardware and the fluorogenic detection chemistries have evolved rapidly as the understanding of real-time PCR has developed and this review aims to update the scientist on the current state of the art. We describe the background, advantages and limitations of real-time PCR and we review the literature as it applies to virus detection in the routine and research laboratory in order to focus on one of the many areas in which the application of real-time PCR has provided significant methodological benefits and improved patient outcomes. However, the technology discussed has been applied to other areas of microbiology as well as studies of gene expression and genetic disease.
Simplified Pan-species Real-time PCR-based Detection of Plasmodium Spp. in Blood Smear
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Gholamreza HASSANPOUR
2016-12-01
Full Text Available Background: We aimed to quicken and simplify the detection of Plasmodium in blood samples by developing and testing a pan-Plasmodium real-time PCR for accurate screening of individuals suspected of malaria.Methods: A single primer/probe set for pan-species Plasmodium-specific real time PCR targeting a conserved region of the small subunit 18S ribosomal DNA was designed and evaluated for rapid diagnosis and screening of malaria infections using dried blood smears. FTA cards were used for rapid and simple DNA extraction.Results: The primers and probes showed a positive response with the DNA extracted from bloods infected with P. falciparum and P. vivax but not with DNA extracted from various smears from uninfected blood samples. Seven positive cases positive by both microscopy and nested PCR were found among 280 blood samples taken from in South and Southeast Iran. Five samples were identified as positive for P. vivax and two as positive for P. falciparum. All positive samples were positive by real-time PCR. Furthermore, all 38-blood samples positive by microscopy were positive by real-time PCR. No microscopy-negative samples were positive by real-time PCR.Conclusion: By using a simple FTA card for DNA extraction and by application of the real-time PCR developed in this study, sensitivity similar to nested-PCR and microscopy was achieved. This format simplifies the detection of Plasmodium in large numbers of samples.
Dynamic modelling and real-time leak detection for NGL pipelines
Energy Technology Data Exchange (ETDEWEB)
Young, B.R.; Svrcek, W.Y. [Calgary Univ., AB (Canada). Dept. of Chemical and Petroleum Engineering; Cooke, J.G.; Daye, R.E. [Rangeland Engineering Ltd., Calgary, AB (Canada)
2004-07-01
This paper presented newly developed steady-state and dynamic models commissioned for natural gas liquids (NGL) pipelines near Empress, Alberta. The work demonstrates a unique university-industry collaboration for solving the challenge of reliable pipeline leak detection. The flexible, custom real-time leak detection system was tested on the dynamic simulation. It was successfully used to replace a volume balance system for NGL pipelines at Empress in March 2003. A custom pipeline monitoring system was also developed to integrate with the existing pipeline supervisory control and data acquisition (SCADA) system. Simulation results enabled a change in the control scheme of the pipelines that resulted in less transient operation. The premise of the leak detection system is a rigorous thermodynamics and dynamic mass balance calculation based on real-time information from field flow, pressure and temperature sensors. The application of the system makes it possible to minimize or eliminate false or nuisance alarms, which is critical to the confidence of the monitoring system. The volumetric and mass imbalance formulae permit the system to cross check the calculation and then make important decisions regarding the sounding of alarms. The custom solution offers flexibility for use in a wide variety of conditions and applications. In addition, it is cost effective and locally supported. 8 refs., 4 tabs., 5 figs.
Matching-range-constrained real-time loop closure detection with CNNs features.
Bai, Dongdong; Wang, Chaoqun; Zhang, Bo; Yi, Xiaodong; Tang, Yuhua
2016-01-01
The loop closure detection (LCD) is an essential part of visual simultaneous localization and mapping systems (SLAM). LCD is capable of identifying and compensating the accumulation drift of localization algorithms to produce an consistent map if the loops are checked correctly. Deep convolutional neural networks (CNNs) have outperformed state-of-the-art solutions that use traditional hand-crafted features in many computer vision and pattern recognition applications. After the great success of CNNs, there has been much interest in applying CNNs features to robotic fields such as visual LCD. Some researchers focus on using a pre-trained CNNs model as a method of generating an image representation appropriate for visual loop closure detection in SLAM. However, there are many fundamental differences and challenges involved in character between simple computer vision applications and robotic applications. Firstly, the adjacent images in the dataset of loop closure detection might have more resemblance than the images that form the loop closure. Secondly, real-time performance is one of the most critical demands for robots. In this paper, we focus on making use of the feature generated by CNNs layers to implement LCD in real environment. In order to address the above challenges, we explicitly provide a value to limit the matching range of images to solve the first problem; meanwhile we get better results than state-of-the-art methods and improve the real-time performance using an efficient feature compression method.
Real-time people and vehicle detection from UAV imagery
Gaszczak, Anna; Breckon, Toby P.; Han, Jiwan
2011-01-01
A generic and robust approach for the real-time detection of people and vehicles from an Unmanned Aerial Vehicle (UAV) is an important goal within the framework of fully autonomous UAV deployment for aerial reconnaissance and surveillance. Here we present an approach for the automatic detection of vehicles based on using multiple trained cascaded Haar classifiers with secondary confirmation in thermal imagery. Additionally we present a related approach for people detection in thermal imagery based on a similar cascaded classification technique combining additional multivariate Gaussian shape matching. The results presented show the successful detection of vehicle and people under varying conditions in both isolated rural and cluttered urban environments with minimal false positive detection. Performance of the detector is optimized to reduce the overall false positive rate by aiming at the detection of each object of interest (vehicle/person) at least once in the environment (i.e. per search patter flight path) rather than every object in each image frame. Currently the detection rate for people is ~70% and cars ~80% although the overall episodic object detection rate for each flight pattern exceeds 90%.
Jefferies, Ryan; Morgan, Eric R; Helm, Jenny; Robinson, Matthew; Shaw, Susan E
2011-12-01
This study reports the development of a real-time PCR assay and an indirect ELISA to improve on current detection of canine Angiostrongylus vasorum infection. A highly specific fluorescent probe-based, real-time PCR assay was developed to target the A. vasorum second internal transcribed spacer region and detected DNA in EDTA blood, lung tissue, broncho-alveolar larvage fluid, endotracheal mucus, pharyngeal swabs and faecal samples. PCR was fast (∼1 h), highly efficient when using EDTA blood samples, consistently detected a single molecule of parasite DNA and did not amplify DNA from other parasitic nematodes or definitive host species. An indirect ELISA was also developed using the soluble protein fraction from adult A. vasorum worms. Some cross-reactive antigen recognition was observed when tested against sera from dogs infected with Crenosoma vulpis (n = 8), Toxocara canis (n = 5) and Dirofilaria immitis (n = 5). This was largely overcome by setting the cut-off for a positive result at an appropriately high level. Field evaluation of the real-time PCR and ELISA was conducted by testing sera and EDTA blood from dogs with suspected A. vasorum infection (n = 148) and compared with the Baermann's larval migration test in faeces. Thirty-one dogs were positive by at least one test. Of these, 20 (65%) were detected by the Baermann method, 18 (58%) by blood PCR, 24 (77%) by ELISA and 28 (90%) by blood PCR and ELISA together. Combined testing using real-time PCR and ELISA therefore improved the detection rate of A. vasorum infection and holds promise for improved clinical diagnosis and epidemiological investigation.
Iida, Takao; Mizuno, Yukie; Kaizaki, Yasuharu
2017-10-27
Mutations in RAS and BRAF are predictors of the efficacy of anti-epidermal growth factor receptor (EGFR) therapy in patients with metastatic colorectal cancer (mCRC). Therefore, simple, rapid, cost-effective methods to detect these mutations in the clinical setting are greatly needed. In the present study, we evaluated BNA Real-time PCR Mutation Detection Kit Extended RAS (BNA Real-time PCR), a real-time PCR method that uses bridged nucleic acid clamping technology to rapidly detect mutations in RAS exons 2-4 and BRAF exon 15. Genomic DNA was extracted from 54 formalin-fixed paraffin-embedded (FFPE) tissue samples obtained from mCRC patients. Among the 54 FFPE samples, BNA Real-time PCR detected 21 RAS mutations (38.9%) and 5 BRAF mutations (9.3%), and the reference assay (KRAS Mutation Detection Kit and MEBGEN™ RASKET KIT) detected 22 RAS mutations (40.7%). The concordance rate of detected RAS mutations between the BNA Real-time PCR assay and the reference assays was 98.2% (53/54). The BNA Real-time PCR assay proved to be a more simple, rapid, and cost-effective method for detecting KRAS and RAS mutations compared with existing assays. These findings suggest that BNA Real-time PCR is a valuable tool for predicting the efficacy of early anti-EGFR therapy in mCRC patients. Copyright © 2017 Elsevier B.V. All rights reserved.
Real-time object detection, tracking and occlusion reasoning
Divakaran, Ajay; Yu, Qian; Tamrakar, Amir; Sawhney, Harpreet Singh; Zhu, Jiejie; Javed, Omar; Liu, Jingen; Cheng, Hui; Eledath, Jayakrishnan
2018-02-27
A system for object detection and tracking includes technologies to, among other things, detect and track moving objects, such as pedestrians and/or vehicles, in a real-world environment, handle static and dynamic occlusions, and continue tracking moving objects across the fields of view of multiple different cameras.
Real time in situ detection of organic nitrates in atmospheric aerosols.
Rollins, Andrew W; Smith, Jared D; Wilson, Kevin R; Cohen, Ronald C
2010-07-15
A novel instrument is described that quantifies total particle-phase organic nitrates in real time with a detection limit of 0.11 microg m(-3) min(-1), 45 ppt min(-1) (-ONO(2)). Aerosol nitrates are separated from gas-phase nitrates with a short residence time activated carbon denuder. Detection of organic molecules containing -ONO(2) subunits is accomplished using thermal dissociation coupled to laser induced fluorescence detection of NO(2). This instrument is capable of high time resolution (seconds) measurements of particle-phase organic nitrates, without interference from inorganic nitrate. Here we use it to quantify organic nitrates in secondary organic aerosol generated from high-NO(x) photooxidation of limonene, alpha-pinene, Delta-3-carene, and tridecane. In these experiments the organic nitrate moiety is observed to be 6-15% of the total SOA mass.
Deep Learning for Real-Time Capable Object Detection and Localization on Mobile Platforms
Particke, F.; Kolbenschlag, R.; Hiller, M.; Patiño-Studencki, L.; Thielecke, J.
2017-10-01
Industry 4.0 is one of the most formative terms in current times. Subject of research are particularly smart and autonomous mobile platforms, which enormously lighten the workload and optimize production processes. In order to interact with humans, the platforms need an in-depth knowledge of the environment. Hence, it is required to detect a variety of static and non-static objects. Goal of this paper is to propose an accurate and real-time capable object detection and localization approach for the use on mobile platforms. A method is introduced to use the powerful detection capabilities of a neural network for the localization of objects. Therefore, detection information of a neural network is combined with depth information from a RGB-D camera, which is mounted on a mobile platform. As detection network, YOLO Version 2 (YOLOv2) is used on a mobile robot. In order to find the detected object in the depth image, the bounding boxes, predicted by YOLOv2, are mapped to the corresponding regions in the depth image. This provides a powerful and extremely fast approach for establishing a real-time-capable Object Locator. In the evaluation part, the localization approach turns out to be very accurate. Nevertheless, it is dependent on the detected object itself and some additional parameters, which are analysed in this paper.
Development and validation of a real-time PCR assay for the detection of anguillid herpesvirus 1.
van Beurden, S J; Voorbergen-Laarman, M A; Roozenburg, I; van Tellingen, J; Haenen, O L M; Engelsma, M Y
2016-01-01
Anguillid herpesvirus 1 (AngHV1) causes a haemorrhagic disease with increased mortality in wild and farmed European eel, Anguilla anguilla (L.) and Japanese eel Anguilla japonica, Temminck & Schlegel). Detection of AngHV1 is currently based on virus isolation in cell culture, antibody-based typing assays or conventional PCR. We developed, optimized and concisely validated a diagnostic TaqMan probe based real-time PCR assay for the detection of AngHV1. The primers and probe target AngHV1 open reading frame 57, encoding the capsid protease and scaffold protein. Compared to conventional PCR, the developed real-time PCR is faster, less labour-intensive and has a reduced risk of cross-contamination. The real-time PCR assay was shown to be analytically sensitive and specific and has a high repeatability, efficiency and r(2) -value. The diagnostic performance of the assay was determined by testing 10% w/v organ suspensions and virus cultures from wild and farmed European eels from the Netherlands by conventional and real-time PCR. The developed real-time PCR assay is a useful tool for the rapid and sensitive detection of AngHV1 in 10% w/v organ suspensions from wild and farmed European eels. © 2015 John Wiley & Sons Ltd.
Simulation of a Real-Time Brain Computer Interface for Detecting a Self-Paced Hitting Task.
Hammad, Sofyan H; Kamavuako, Ernest N; Farina, Dario; Jensen, Winnie
2016-12-01
An invasive brain-computer interface (BCI) is a promising neurorehabilitation device for severely disabled patients. Although some systems have been shown to work well in restricted laboratory settings, their utility must be tested in less controlled, real-time environments. Our objective was to investigate whether a specific motor task could be reliably detected from multiunit intracortical signals from freely moving animals in a simulated, real-time setting. Intracortical signals were first obtained from electrodes placed in the primary motor cortex of four rats that were trained to hit a retractable paddle (defined as a "Hit"). In the simulated real-time setting, the signal-to-noise-ratio was first increased by wavelet denoising. Action potentials were detected, and features were extracted (spike count, mean absolute values, entropy, and combination of these features) within pre-defined time windows (200 ms, 300 ms, and 400 ms) to classify the occurrence of a "Hit." We found higher detection accuracy of a "Hit" (73.1%, 73.4%, and 67.9% for the three window sizes, respectively) when the decision was made based on a combination of features rather than on a single feature. However, the duration of the window length was not statistically significant (p = 0.5). Our results showed the feasibility of detecting a motor task in real time in a less restricted environment compared to environments commonly applied within invasive BCI research, and they showed the feasibility of using information extracted from multiunit recordings, thereby avoiding the time-consuming and complex task of extracting and sorting single units. © 2016 International Neuromodulation Society.
Directory of Open Access Journals (Sweden)
Abdelfattah M. Selim
2014-12-01
Full Text Available Abortion among dairy cattle is one of the major causes of economic losses in the livestock industry. This study describes a 1-step multiplex real-time polymerase chain reaction (PCR to detect Brucella spp., Leptospira spp. and Campylobacter foetus, these are significant bacteria commonly implicated in bovine abortion. ß-actin was added to the same PCR reaction as an internal control to detect any extraction failure or PCR inhibition. The detection limit of multiplex real-time PCR using purified DNA from cultured organisms was set to 5 fg for Leptospira spp. and C. foetus and to 50 fg for Brucella spp. The multiplex real-time PCR did not produce any non-specific amplification when tested with different strains of the 3 pathogens. This multiplex real-time PCR provides a valuable tool for diagnosis, simultaneous and rapid detection for the 3 pathogens causing abortion in bovine.
Real-time Bacterial Detection by Single Cell Based Sensors UsingSynchrotron FTIR Spectromicroscopy
Energy Technology Data Exchange (ETDEWEB)
Veiseh, Mandana; Veiseh, Omid; Martin, Michael C.; Bertozzi,Carolyn; Zhang, Miqin
2005-08-10
Microarrays of single macrophage cell based sensors weredeveloped and demonstrated for real time bacterium detection bysynchrotron FTIR microscopy. The cells were patterned on gold-SiO2substrates via a surface engineering technique by which the goldelectrodes were immobilized with fibronectin to mediate cell adhesion andthe silicon oxide background were passivated with PEG to resist proteinadsorption and cell adhesion. Cellular morphology and IR spectra ofsingle, double, and triple cells on gold electrodes exposed tolipopolysaccharide (LPS) of different concentrations were compared toreveal the detection capabilities of these biosensors. The single-cellbased sensors were found to generate the most significant IR wave numbervariation and thus provide the highest detection sensitivity. Changes inmorphology and IR spectrum for single cells exposed to LPS were found tobe time- and concentration-dependent and correlated with each other verywell. FTIR spectra from single cell arrays of gold electrodes withsurface area of 25 mu-m2, 100 mu-m2, and 400 mu-m2 were acquired usingboth synchrotron and conventional FTIR spectromicroscopes to study thesensitivity of detection. The results indicated that the developedsingle-cell platform can be used with conventional FTIRspectromicroscopy. This technique provides real-time, label-free, andrapid bacterial detection, and may allow for statistic and highthroughput analyses, and portability.
Pochop, Jaroslav; Kačániová, Miroslava; Hleba, Lukáš; Lopasovský, L'ubomír; Bobková, Alica; Zeleňáková, Lucia; Stričík, Michal
2012-01-01
The aim of this study was to follow contamination of ready-to-eat food with Listeria monocytogenes by using the Step One real time polymerase chain reaction (PCR). We used the PrepSEQ Rapid Spin Sample Preparation Kit for isolation of DNA and MicroSEQ® Listeria monocytogenes Detection Kit for the real-time PCR performance. In 30 samples of ready-to-eat milk and meat products without incubation we detected strains of Listeria monocytogenes in five samples (swabs). Internal positive control (IPC) was positive in all samples. Our results indicated that the real-time PCR assay developed in this study could sensitively detect Listeria monocytogenes in ready-to-eat food without incubation.
Detection of Balamuthia mandrillaris DNA by real-time PCR targeting the RNase P gene
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Lewin Astrid
2008-12-01
Full Text Available Abstract Background The free-living amoeba Balamuthia mandrillaris may cause fatal encephalitis both in immunocompromised and in – apparently – immunocompetent humans and other mammalian species. Rapid, specific, sensitive, and reliable detection requiring little pathogen-specific expertise is an absolute prerequisite for a successful therapy and a welcome tool for both experimental and epidemiological research. Results A real-time polymerase chain reaction assay using TaqMan® probes (real-time PCR was established specifically targeting the RNase P gene of B. mandrillaris amoebae. The assay detected at least 2 (down to 0.5 genomes of B. mandrillaris grown in axenic culture. It did not react with DNA from closely related Acanthamoeba (3 species, nor with DNA from Toxoplasma gondii, Leishmania major, Pneumocystis murina, Mycobacterium bovis (BCG, human brain, various mouse organs, or from human and murine cell lines. The assay efficiently detected B. mandrillaris DNA in spiked cell cultures, spiked murine organ homogenates, B. mandrillaris-infected mice, and CNS tissue-DNA preparations from 2 patients with proven cerebral balamuthiasis. This novel primer set was successfully combined with a published set that targets the B. mandrillaris 18S rRNA gene in a duplex real-time PCR assay to ensure maximum specificity and as a precaution against false negative results. Conclusion A real-time PCR assay for B. mandrillaris amoebae is presented, that is highly specific, sensitive, and reliable and thus suited both for diagnosis and for research.
Real-time Alarm Monitoring System for Detecting Driver Fatigue in Wireless Areas
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Rongrong Fu
2017-04-01
Full Text Available The purpose of this paper was to develop a real-time alarm monitoring system that can detect the fatigue driving state through wireless communication. The drivers’ electroencephalogram (EEG signals were recorded from occipital electrodes. Seven EEG rhythms with different frequency bands as gamma, hbeta, beta, sigma, alpha, theta and delta waves were extracted. They were simultaneously assessed using relative operating characteristic (ROC curves and grey relational analysis to select one as the fatigue feature. The research results showed that the performance of theta wave was the best one. Therefore, theta wave was used as fatigue feature in the following alarm device. The real-time alarm monitoring system based on the result has been developed, once the threshold was settled by using the data of the first ten minutes driving period. The developed system can detect driver fatigue and give alarm to indicate the onset of fatigue automatically.
Versatile real-time interferometer phase-detection system using high-speed digital techniques
International Nuclear Information System (INIS)
Mendell, D.S.; Willett, G.W.
1977-01-01
This paper describes the basic design and philosophy of a versatile real-time interferometer phase-detection system to be used on the 2XIIB and TMX magnetic-fusion experiments at Lawrence Livermore Laboratory. This diagnostics system is a satellite to a host computer and uses high-speed emitter-coupled logic techniques to derive data on real-time phase relationships. The system's input signals can be derived from interferometer outputs over a wide range of reference frequencies. An LSI-11 microcomputer is the interface between the high-speed phase-detection logic, buffer memory, human interaction, and host computer. Phase data on a storage CRT is immediately displayed after each experimental fusion shot. An operator can interrogate this phase data more closely from an interactive control panel, and the host computer can be simultaneously examining the system's buffer memory or arming the system for the next shot
Improvement of a real-time RT-PCR assay for the detection of enterovirus RNA
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Bruynseels Peggy
2009-07-01
Full Text Available Abstract We describe an improvement of an earlier reported real-time RT-PCR assay for the detection of enterovirus RNA, based on the 5' exonuclease digestion of a dual-labeled fluorogenic probe by Taq DNA polymerase. A different extraction method, real-time RT-PCR instrument and primer set were evaluated. Our data show that the optimized assay yields a higher sensitivity and reproducibility and resulted in a significant reduced hands-on time per sample.
Gomer, Nathaniel R.; Tazik, Shawna; Gardner, Charles W.; Nelson, Matthew P.
2017-05-01
Hyperspectral imaging (HSI) is a valuable tool for the detection and analysis of targets located within complex backgrounds. HSI can detect threat materials on environmental surfaces, where the concentration of the target of interest is often very low and is typically found within complex scenery. Unfortunately, current generation HSI systems have size, weight, and power limitations that prohibit their use for field-portable and/or real-time applications. Current generation systems commonly provide an inefficient area search rate, require close proximity to the target for screening, and/or are not capable of making real-time measurements. ChemImage Sensor Systems (CISS) is developing a variety of real-time, wide-field hyperspectral imaging systems that utilize shortwave infrared (SWIR) absorption and Raman spectroscopy. SWIR HSI sensors provide wide-area imagery with at or near real time detection speeds. Raman HSI sensors are being developed to overcome two obstacles present in standard Raman detection systems: slow area search rate (due to small laser spot sizes) and lack of eye-safety. SWIR HSI sensors have been integrated into mobile, robot based platforms and handheld variants for the detection of explosives and chemical warfare agents (CWAs). In addition, the fusion of these two technologies into a single system has shown the feasibility of using both techniques concurrently to provide higher probability of detection and lower false alarm rates. This paper will provide background on Raman and SWIR HSI, discuss the applications for these techniques, and provide an overview of novel CISS HSI sensors focusing on sensor design and detection results.
Wang, Jianchang; Wang, Jinfeng; Li, Ruiwen; Liu, Libing; Yuan, Wanzhe
2017-08-15
Canine distemper, caused by Canine distemper virus (CDV), is a highly contagious and fatal systemic disease in free-living and captive carnivores worldwide. Recombinase polymerase amplification (RPA), as an isothermal gene amplification technique, has been explored for the molecular detection of diverse pathogens. A real-time reverse transcription RPA (RT-RPA) assay for the detection of canine distemper virus (CDV) using primers and exo probe targeting the CDV nucleocapsid protein gene was developed. A series of other viruses were tested by the RT-RPA.Thirty-two field samples were further tested by RT-RPA, and the resuts were compared with those obtained by the real-time RT-PCR. The RT-RPA assay was performed successfully at 40 °C, and the results were obtained within 3 min-12 min. The assay could detect CDV, but did not show cross-detection of canine parvovirus-2 (CPV-2), canine coronavirus (CCoV), canine parainfluenza virus (CPIV), pseudorabies virus (PRV) or Newcastle disease virus (NDV), demonstrating high specificity. The analytical sensitivity of RT-RPA was 31.8 copies in vitro transcribed CDV RNA, which is 10 times lower than the real-time RT-PCR. The assay performance was validated by testing 32 field samples and compared to real-time RT-PCR. The results indicated an excellent correlation between RT-RPA and a reference real-time RT-PCR method. Both assays provided the same results, and R 2 value of the positive results was 0.947. The results demonstrated that the RT-RPA assay offers an alternative tool for simple, rapid, and reliable detection of CDV both in the laboratory and point-of-care facility, especially in the resource-limited settings.
DEFF Research Database (Denmark)
Liu, Shuiping; Gu, Tianxun; Fu, Jiajia
2014-01-01
In this work, novel hybrid nanosphere vehicles were synthesized for nitric oxide (NO) donating and real-time detection. The hybrid nanosphere vehicles consist of cadmium selenide quantum dots (CdSe QDs) as NO fluorescent probes, and the modified hyperbranched polyether (mHP)-based diazeniumdiolates...... as NO donors, respectively. The nanospheres have spherical outline with dimension of ~ 127 nm. The data of systematic characterization demonstrated that the mHP-based hybrid nanosphere vehicles (QDs-mHP-NO) can release and real-time detect NO with the low limit of 25 nM, based on fluorescence quenching...
Sun, Lihui; Wang, Yongzhong; He, Yongqiang
2007-01-01
The detection for motive small target in infrared image sequence has become a hot topic nowadays. Background suppress algorithm based on minim gradient median filter and temporal recursion target detection algorithm are introduced. On the basis of contents previously mentioned, a four stages pipeline structure infrared small target detection process system, which aims at characters of algorithm complexity, large amounts of data to process, high frame frequency and exigent real-time character in this kind of application, is designed and implemented. The logical structure of the system was introduced and the function and signals flows are programmed. The system is composed of two FPGA chips and two DSP chips of TI. According to the function of each part, the system is divided into image preprocess stage, target detection stage, track relation stage and image output stage. The experiment of running algorithms on the system presented in this paper proved that the system could meet acquisition and process of 50Hz 240x320 digital image and the system could real time detect small target with a signal-noise ratio more than 3 reliably. The system achieves the characters of large amount of memory, high real-time processing, excellent extension and favorable interactive interface.
A Portable Array-Type Optical Fiber Sensing Instrument for Real-Time Gas Detection
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San-Shan Hung
2016-12-01
Full Text Available A novel optical fiber array-type of sensing instrument with temperature compensation for real-time detection was developed to measure oxygen, carbon dioxide, and ammonia simultaneously. The proposed instrument is multi-sensing array integrated with real-time measurement module for portable applications. The sensing optical fibers were etched and polished before coating to increase sensitivities. The ammonia and temperature sensors were each composed of a dye-coated single-mode fiber with constructing a fiber Bragg grating and a long-period filter grating for detecting light intensity. Both carbon dioxide and oxygen sensing structures use multimode fibers where 1-hydroxy-3,6,8-pyrene trisulfonic acid trisodium salt is coated for carbon dioxide sensing and Tris(2,2′-bipyridyl dichlororuthenium(II hexahydrate and Tris(bipyridineruthenium(II chloride are coated for oxygen sensing. Gas-induced fluorescent light intensity variation was applied to detect gas concentration. The portable gas sensing array was set up by integrating with photo-electronic measurement modules and a human-machine interface to detect gases in real time. The measured data have been processed using piecewise-linear method. The sensitivity of the oxygen sensor were 1.54%/V and 9.62%/V for concentrations less than 1.5% and for concentrations between 1.5% and 6%, respectively. The sensitivity of the carbon dioxide sensor were 8.33%/V and 9.62%/V for concentrations less than 2% and for concentrations between 2% and 5%, respectively. For the ammonia sensor, the sensitivity was 27.78%/V, while ammonia concentration was less than 2%.
A Portable Array-Type Optical Fiber Sensing Instrument for Real-Time Gas Detection.
Hung, San-Shan; Chang, Hsing-Cheng; Chang, I-Nan
2016-12-08
A novel optical fiber array-type of sensing instrument with temperature compensation for real-time detection was developed to measure oxygen, carbon dioxide, and ammonia simultaneously. The proposed instrument is multi-sensing array integrated with real-time measurement module for portable applications. The sensing optical fibers were etched and polished before coating to increase sensitivities. The ammonia and temperature sensors were each composed of a dye-coated single-mode fiber with constructing a fiber Bragg grating and a long-period filter grating for detecting light intensity. Both carbon dioxide and oxygen sensing structures use multimode fibers where 1-hydroxy-3,6,8-pyrene trisulfonic acid trisodium salt is coated for carbon dioxide sensing and Tris(2,2'-bipyridyl) dichlororuthenium(II) hexahydrate and Tris(bipyridine)ruthenium(II) chloride are coated for oxygen sensing. Gas-induced fluorescent light intensity variation was applied to detect gas concentration. The portable gas sensing array was set up by integrating with photo-electronic measurement modules and a human-machine interface to detect gases in real time. The measured data have been processed using piecewise-linear method. The sensitivity of the oxygen sensor were 1.54%/V and 9.62%/V for concentrations less than 1.5% and for concentrations between 1.5% and 6%, respectively. The sensitivity of the carbon dioxide sensor were 8.33%/V and 9.62%/V for concentrations less than 2% and for concentrations between 2% and 5%, respectively. For the ammonia sensor, the sensitivity was 27.78%/V, while ammonia concentration was less than 2%.
Sarcastic sentiment detection in tweets streamed in real time: a big data approach
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S.K. Bharti
2016-08-01
Full Text Available Sarcasm is a type of sentiment where people express their negative feelings using positive or intensified positive words in the text. While speaking, people often use heavy tonal stress and certain gestural clues like rolling of the eyes, hand movement, etc. to reveal sarcastic. In the textual data, these tonal and gestural clues are missing, making sarcasm detection very difficult for an average human. Due to these challenges, researchers show interest in sarcasm detection of social media text, especially in tweets. Rapid growth of tweets in volume and its analysis pose major challenges. In this paper, we proposed a Hadoop based framework that captures real time tweets and processes it with a set of algorithms which identifies sarcastic sentiment effectively. We observe that the elapse time for analyzing and processing under Hadoop based framework significantly outperforms the conventional methods and is more suited for real time streaming tweets.
Directory of Open Access Journals (Sweden)
Yuexia Wang
2015-09-01
Full Text Available Real-time polymerase chain reaction (PCR allows rapid detection of Salmonella in frozen dairy products, but it might cause a false positive detection result because it might amplify DNA from dead target cells as well. In this study, Salmonella-free frozen ice cream was initially inoculated with heat-killed Salmonella Typhimurium cells and stored at −18°C. Bacterial DNA extracted from the sample was amplified using TaqMan probe-based real-time PCR targeting the invA gene. Our results indicated that DNA from the dead cells remained stable in frozen ice cream for at least 20 days, and could produce fluorescence signal for real-time PCR as well. To overcome this limitation, propidium monoazide (PMA was combined with real-time PCR. PMA treatment can effectively prevent PCR amplification from heat-killed Salmonella cells in frozen ice cream. The PMA real-time PCR assay can selectively detect viable Salmonella at as low as 103 CFU/mL. Combining 18 hours of pre-enrichment with the assay allows for the detection of viable Salmonella at 100 CFU/mL and avoiding the false-positive result of dead cells. The PMA real-time PCR assay provides an alternative specifically for detection of viable Salmonella in ice cream. However, when the PMA real-time PCR assay was evaluated in ice cream subjected to frozen storage, it obviously underestimated the contamination situation of viable Salmonella, which might lead to a false negative result. According to this result, the use of enrichment prior to PMA real-time PCR analysis remains as the more appropriate approach.
Wang, Yuexia; Yang, Ming; Liu, Shuchun; Chen, Wanyi; Suo, Biao
2015-09-01
Real-time polymerase chain reaction (PCR) allows rapid detection of Salmonella in frozen dairy products, but it might cause a false positive detection result because it might amplify DNA from dead target cells as well. In this study, Salmonella-free frozen ice cream was initially inoculated with heat-killed Salmonella Typhimurium cells and stored at -18°C. Bacterial DNA extracted from the sample was amplified using TaqMan probe-based real-time PCR targeting the invA gene. Our results indicated that DNA from the dead cells remained stable in frozen ice cream for at least 20 days, and could produce fluorescence signal for real-time PCR as well. To overcome this limitation, propidium monoazide (PMA) was combined with real-time PCR. PMA treatment can effectively prevent PCR amplification from heat-killed Salmonella cells in frozen ice cream. The PMA real-time PCR assay can selectively detect viable Salmonella at as low as 10 3 CFU/mL. Combining 18 hours of pre-enrichment with the assay allows for the detection of viable Salmonella at 10 0 CFU/mL and avoiding the false-positive result of dead cells. The PMA real-time PCR assay provides an alternative specifically for detection of viable Salmonella in ice cream. However, when the PMA real-time PCR assay was evaluated in ice cream subjected to frozen storage, it obviously underestimated the contamination situation of viable Salmonella, which might lead to a false negative result. According to this result, the use of enrichment prior to PMA real-time PCR analysis remains as the more appropriate approach. Copyright © 2015. Published by Elsevier B.V.
Investigation Model for DDoS Attack Detection in Real-Time
Directory of Open Access Journals (Sweden)
Abdulghani Ali Ahmed
2015-02-01
Full Text Available Investigating traffic of distributed denial of services (DDoS attack requires extra overhead which mostly results in network performance degradation. This study proposes an investigation model for detecting DDoS attack in real-time without causing negative degradation against network performance. The model investigates network traffic in a scalable way to detect user violations on quality of service regulations. Traffic investigation is triggered only when the network is congested; at that exact moment, burst gateways actually generate a congestion notification to misbehaving users. The misbehaving users are thus further investigated by measuring their consumption ratios of bandwidth. By exceeding the service level agreement bandwidth ratio, user traffic is filtered as DDoS traffic. Simulation results demonstrate that the proposed model efficiently monitors intrusive traffic and precisely detects DDoS attack.
Single reaction, real time RT-PCR detection of all known avian and human metapneumoviruses.
Lemaitre, E; Allée, C; Vabret, A; Eterradossi, N; Brown, P A
2018-01-01
Current molecular methods for the detection of avian and human metapneumovirus (AMPV, HMPV) are specifically targeted towards each virus species or individual subgroups of these. Here a broad range SYBR Green I real time RT-PCR was developed which amplified a highly conserved fragment of sequence in the N open reading frame. This method was sufficiently efficient and specific in detecting all MPVs. Its validation according to the NF U47-600 norm for the four AMPV subgroups estimated low limits of detection between 1000 and 10copies/μL, similar with detection levels described previously for real time RT-PCRs targeting specific subgroups. RNA viruses present a challenge for the design of durable molecular diagnostic test due to the rate of change in their genome sequences which can vary substantially in different areas and over time. The fact that the regions of sequence for primer hybridization in the described method have remained sufficiently conserved since the AMPV and HMPV diverged, should give the best chance of continued detection of current subgroups and of potential unknown or future emerging MPV strains. Copyright © 2017 Elsevier B.V. All rights reserved.
International Nuclear Information System (INIS)
Bossi, R.H.; Oien, C.T.
1981-01-01
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
Qiao, Tiezhu; Li, Xinyu; Pang, Y.; Lü, Yuxiang; Wang, Feng; Jin, Baoquan
2017-01-01
Conveyor belt longitudinal tear is one of the most serious problems in coal mining. Existing systems cannot realise lossless and real-time detection for longitudinal tear of conveyor belt. Currently, visual detecting systems are proposed by many researchers and are becoming the future trend. A
Highly sensitive real-time PCR for specific detection and quantification of Coxiella burnetii
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Linke Sonja
2006-01-01
Full Text Available Abstract Background Coxiella burnetii, the bacterium causing Q fever, is an obligate intracellular biosafety level 3 agent. Detection and quantification of these bacteria with conventional methods is time consuming and dangerous. During the last years, several PCR based diagnostic assays were developed to detect C. burnetii DNA in cell cultures and clinical samples. We developed and evaluated TaqMan-based real-time PCR assays that targeted the singular icd (isocitrate dehydrogenase gene and the transposase of the IS1111a element present in multiple copies in the C. burnetii genome. Results To evaluate the precision of the icd and IS1111 real-time PCR assays, we performed different PCR runs with independent DNA dilutions of the C. burnetii Nine Mile RSA493 strain. The results showed very low variability, indicating efficient reproducibility of both assays. Using probit analysis, we determined that the minimal number of genome equivalents per reaction that could be detected with a 95% probability was 10 for the icd marker and 6.5 for the IS marker. Plasmid standards with cloned icd and IS1111 fragments were used to establish standard curves which were linear over a range from 10 to 107 starting plasmid copy numbers. We were able to quantify cell numbers of a diluted, heat-inactivated Coxiella isolate with a detection limit of 17 C. burnetii particles per reaction. Real-time PCR targeting both markers was performed with DNA of 75 different C. burnetii isolates originating from all over the world. Using this approach, the number of IS1111 elements in the genome of the Nine Mile strain was determined to be 23, close to 20, the number revealed by genome sequencing. In other isolates, the number of IS1111 elements varied widely (between seven and 110 and seemed to be very high in some isolates. Conclusion We validated TaqMan-based real-time PCR assays targeting the icd and IS1111 markers of C. burnetii. The assays were shown to be specific, highly
Directory of Open Access Journals (Sweden)
Saba Rezvanian
2016-04-01
Full Text Available Injuries associated with fall incidences continue to pose a significant burden to persons with Parkinson’s disease (PD both in terms of human suffering and economic loss. Freezing of gait (FOG, which is one of the symptoms of PD, is a common cause of falls in this population. Although a significant amount of work has been performed to characterize/detect FOG using both qualitative and quantitative methods, there remains paucity of data regarding real-time detection of FOG, such as the requirements for minimum sensor nodes, sensor placement locations, and appropriate sampling period and update time. Here, the continuous wavelet transform (CWT is employed to define an index for correctly identifying FOG. Since the CWT method uses both time and frequency components of a waveform in comparison to other methods utilizing only the frequency component, we hypothesized that using this method could lead to a significant improvement in the accuracy of FOG detection. We tested the proposed index on the data of 10 PD patients who experience FOG. Two hundred and thirty seven (237 FOG events were identified by the physiotherapists. The results show that the index could discriminate FOG in the anterior–posterior axis better than other two axes, and is robust to the update time variability. These results suggest that real time detection of FOG may be realized by using CWT of a single shank sensor with window size of 2 s and update time of 1 s (82.1% and 77.1% for the sensitivity and specificity, respectively. Although implicated, future studies should examine the utility of this method in real-time detection of FOG.
Qvarnstrom, Yvonne; Xayavong, Maniphet; da Silva, Ana Cristina Aramburu; Park, Sarah Y; Whelen, A Christian; Calimlim, Precilia S; Sciulli, Rebecca H; Honda, Stacey A A; Higa, Karen; Kitsutani, Paul; Chea, Nora; Heng, Seng; Johnson, Stuart; Graeff-Teixeira, Carlos; Fox, LeAnne M; da Silva, Alexandre J
2016-01-01
Angiostrongylus cantonensis is the most common infectious cause of eosinophilic meningitis. Timely diagnosis of these infections is difficult, partly because reliable laboratory diagnostic methods are unavailable. The aim of this study was to evaluate the usefulness of a real-time polymerase chain reaction (PCR) assay for the detection of A. cantonensis DNA in human cerebrospinal fluid (CSF) specimens. A total of 49 CSF specimens from 33 patients with eosinophilic meningitis were included: A. cantonensis DNA was detected in 32 CSF specimens, from 22 patients. Four patients had intermittently positive and negative real-time PCR results on subsequent samples, indicating that the level of A. cantonensis DNA present in CSF may fluctuate during the course of the illness. Immunodiagnosis and/or supplemental PCR testing supported the real-time PCR findings for 30 patients. On the basis of these observations, this real-time PCR assay can be useful to detect A. cantonensis in the CSF from patients with eosinophilic meningitis. © The American Society of Tropical Medicine and Hygiene.
Real-Life/Real-Time Elderly Fall Detection with a Triaxial Accelerometer.
Sucerquia, Angela; López, José David; Vargas-Bonilla, Jesús Francisco
2018-04-05
The consequences of a fall on an elderly person can be reduced if the accident is attended by medical personnel within the first hour. Independent elderly people often stay alone for long periods of time, being in more risk if they suffer a fall. The literature offers several approaches for detecting falls with embedded devices or smartphones using a triaxial accelerometer. Most of these approaches have not been tested with the target population or cannot be feasibly implemented in real-life conditions. In this work, we propose a fall detection methodology based on a non-linear classification feature and a Kalman filter with a periodicity detector to reduce the false positive rate. This methodology requires a sampling rate of only 25 Hz; it does not require large computations or memory and it is robust among devices. We tested our approach with the SisFall dataset achieving 99.4% of accuracy. We then validated it with a new round of simulated activities with young adults and an elderly person. Finally, we give the devices to three elderly persons for full-day validations. They continued with their normal life and the devices behaved as expected.
Real-time 3-dimensional contrast-enhanced ultrasound in detecting hemorrhage of blunt renal trauma.
Xu, Rui-Xue; Li, Ye-Kuo; Li, Ting; Wang, Sha-Sha; Yuan, Gui-Zhong; Zhou, Qun-Fang; Zheng, Hai-Rong; Yan, Fei
2013-10-01
The objective of this study is to evaluate the diagnostic value of real-time 3-dimensional contrast-enhanced ultrasound in the hemorrhage of blunt renal trauma. Eighteen healthy New Zealand white rabbits were randomly divided into 3 groups. Blunt renal trauma was performed on each group by using minitype striker. Ultrasonography, color Doppler flow imaging, and contrast-enhanced 2-dimensional and real-time 3-dimensional ultrasound were applied before and after the strike. The time to shock and blood pressure were subjected to statistical analysis. Then, a comparative study of ultrasound and pathology was carried out. All the struck kidneys were traumatic. In the ultrasonography, free fluid was found under the renal capsule. In the color Doppler flow imaging, active hemorrhage was not identified. In 2-dimensional contrast-enhanced ultrasound, active hemorrhage of the damaged kidney was characterized. Real-time 3-dimensional contrast-enhanced ultrasound showed a real-time and stereoscopic ongoing bleeding of the injured kidney. The wider the hemorrhage area in 4-dimensional contrast-enhanced ultrasound was, the faster the blood pressure decreased. Real-time 3-dimensional contrast-enhanced ultrasound is a promising noninvasive tool for stereoscopically and vividly detecting ongoing hemorrhage of blunt renal trauma in real time. © 2013.
MO-FG-202-07: Real-Time EPID-Based Detection Metric For VMAT Delivery Errors
International Nuclear Information System (INIS)
Passarge, M; Fix, M K; Manser, P; Stampanoni, M F M; Siebers, J V
2016-01-01
Purpose: To create and test an accurate EPID-frame-based VMAT QA metric to detect gross dose errors in real-time and to provide information about the source of error. Methods: A Swiss cheese model was created for an EPID-based real-time QA process. The system compares a treatmentplan- based reference set of EPID images with images acquired over each 2° gantry angle interval. The metric utilizes a sequence of independent consecutively executed error detection Methods: a masking technique that verifies infield radiation delivery and ensures no out-of-field radiation; output normalization checks at two different stages; global image alignment to quantify rotation, scaling and translation; standard gamma evaluation (3%, 3 mm) and pixel intensity deviation checks including and excluding high dose gradient regions. Tolerances for each test were determined. For algorithm testing, twelve different types of errors were selected to modify the original plan. Corresponding predictions for each test case were generated, which included measurement-based noise. Each test case was run multiple times (with different noise per run) to assess the ability to detect introduced errors. Results: Averaged over five test runs, 99.1% of all plan variations that resulted in patient dose errors were detected within 2° and 100% within 4° (∼1% of patient dose delivery). Including cases that led to slightly modified but clinically equivalent plans, 91.5% were detected by the system within 2°. Based on the type of method that detected the error, determination of error sources was achieved. Conclusion: An EPID-based during-treatment error detection system for VMAT deliveries was successfully designed and tested. The system utilizes a sequence of methods to identify and prevent gross treatment delivery errors. The system was inspected for robustness with realistic noise variations, demonstrating that it has the potential to detect a large majority of errors in real-time and indicate the error
MO-FG-202-07: Real-Time EPID-Based Detection Metric For VMAT Delivery Errors
Energy Technology Data Exchange (ETDEWEB)
Passarge, M; Fix, M K; Manser, P [Division of Medical Radiation Physics and Department of Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern (Switzerland); Stampanoni, M F M [Institute for Biomedical Engineering, ETH Zurich, and PSI, Villigen (Switzerland); Siebers, J V [Department of Radiation Oncology, University of Virginia, Charlottesville, VA (United States)
2016-06-15
Purpose: To create and test an accurate EPID-frame-based VMAT QA metric to detect gross dose errors in real-time and to provide information about the source of error. Methods: A Swiss cheese model was created for an EPID-based real-time QA process. The system compares a treatmentplan- based reference set of EPID images with images acquired over each 2° gantry angle interval. The metric utilizes a sequence of independent consecutively executed error detection Methods: a masking technique that verifies infield radiation delivery and ensures no out-of-field radiation; output normalization checks at two different stages; global image alignment to quantify rotation, scaling and translation; standard gamma evaluation (3%, 3 mm) and pixel intensity deviation checks including and excluding high dose gradient regions. Tolerances for each test were determined. For algorithm testing, twelve different types of errors were selected to modify the original plan. Corresponding predictions for each test case were generated, which included measurement-based noise. Each test case was run multiple times (with different noise per run) to assess the ability to detect introduced errors. Results: Averaged over five test runs, 99.1% of all plan variations that resulted in patient dose errors were detected within 2° and 100% within 4° (∼1% of patient dose delivery). Including cases that led to slightly modified but clinically equivalent plans, 91.5% were detected by the system within 2°. Based on the type of method that detected the error, determination of error sources was achieved. Conclusion: An EPID-based during-treatment error detection system for VMAT deliveries was successfully designed and tested. The system utilizes a sequence of methods to identify and prevent gross treatment delivery errors. The system was inspected for robustness with realistic noise variations, demonstrating that it has the potential to detect a large majority of errors in real-time and indicate the error
Giri, Sidhartha; Rajan, Anand K; Kumar, Nirmal; Dhanapal, Pavithra; Venkatesan, Jayalakshmi; Iturriza-Gomara, Miren; Taniuchi, Mami; John, Jacob; Abraham, Asha Mary; Kang, Gagandeep
2017-08-01
Although, culture is considered the gold standard for poliovirus detection from stool samples, real-time PCR has emerged as a faster and more sensitive alternative. Detection of poliovirus from the stool of recently vaccinated children by culture, single and multiplex real-time PCR was compared. Of the 80 samples tested, 55 (68.75%) were positive by culture compared to 61 (76.25%) and 60 (75%) samples by the single and one step multiplex real-time PCR assays respectively. Real-time PCR (singleplex and multiplex) is more sensitive than culture for poliovirus detection in stool, although the difference was not statistically significant. © 2017 Wiley Periodicals, Inc.
Energy Technology Data Exchange (ETDEWEB)
Ertürk, Gizem [Department of Biotechnology, Lund University, Lund (Sweden); Department of Biology, Hacettepe University, Ankara (Turkey); Hedström, Martin [Department of Biotechnology, Lund University, Lund (Sweden); CapSenze HB, Medicon Village, SE-223 63 Lund (Sweden); Tümer, M. Aşkın [Department of Biology, Hacettepe University, Ankara (Turkey); Denizli, Adil [Department of Chemistry, Hacettepe University, Ankara (Turkey); Mattiasson, Bo, E-mail: Bo.Mattiasson@biotek.lu.se [Department of Biotechnology, Lund University, Lund (Sweden); CapSenze HB, Medicon Village, SE-223 63 Lund (Sweden)
2015-09-03
Prostate specific antigen (PSA) is a valuable biomarker for early detection of prostate cancer, the third most common cancer in men. Ultrasensitive detection of PSA is crucial to screen the prostate cancer in an early stage and to detect the recurrence of the disease after treatment. In this report, microcontact-PSA imprinted (PSA-MIP) capacitive biosensor chip was developed for real-time, highly sensitive and selective detection of PSA. PSA-MIP electrodes were prepared in the presence of methacrylic acid (MAA) as the functional monomer and ethylene glycol dimethacrylate (EGDMA) as the cross-linker via UV polymerization. Immobilized Anti-PSA antibodies on electrodes (Anti-PSA) for capacitance measurements were also prepared to compare the detection performances of both methods. The electrodes were characterized by atomic force microscopy (AFM), scanning electron microscopy (SEM) and cyclic voltammetry (CV) and real-time PSA detection was performed with standard PSA solutions in the concentration range of 10 fg mL{sup −1}–100 ng mL{sup −1}. The detection limits were found as 8.0 × 10{sup −5} ng mL{sup −1} (16 × 10{sup −17} M) and 6.0 × 10{sup −4} ng mL{sup −1} (12 × 10{sup −16} M) for PSA-MIP and Anti-PSA electrodes, respectively. Selectivity studies were performed against HSA and IgG and selectivity coefficients were calculated. PSA detection was also carried out from diluted human serum samples and finally, reproducibility of the electrodes was tested. The results are promising and show that when the sensitivity of the capacitive system is combined with the selectivity and reproducibility of the microcontact-imprinting procedure, the resulting system might be used successfully for real-time detection of various analytes even in very low concentrations. - Highlights: • Microcontact imprinting method was used for preparing the sensor chip for capacitive biosensing. • High sensitivity was obtained. • Good selectivity was
International Nuclear Information System (INIS)
Ertürk, Gizem; Hedström, Martin; Tümer, M. Aşkın; Denizli, Adil; Mattiasson, Bo
2015-01-01
Prostate specific antigen (PSA) is a valuable biomarker for early detection of prostate cancer, the third most common cancer in men. Ultrasensitive detection of PSA is crucial to screen the prostate cancer in an early stage and to detect the recurrence of the disease after treatment. In this report, microcontact-PSA imprinted (PSA-MIP) capacitive biosensor chip was developed for real-time, highly sensitive and selective detection of PSA. PSA-MIP electrodes were prepared in the presence of methacrylic acid (MAA) as the functional monomer and ethylene glycol dimethacrylate (EGDMA) as the cross-linker via UV polymerization. Immobilized Anti-PSA antibodies on electrodes (Anti-PSA) for capacitance measurements were also prepared to compare the detection performances of both methods. The electrodes were characterized by atomic force microscopy (AFM), scanning electron microscopy (SEM) and cyclic voltammetry (CV) and real-time PSA detection was performed with standard PSA solutions in the concentration range of 10 fg mL"−"1–100 ng mL"−"1. The detection limits were found as 8.0 × 10"−"5 ng mL"−"1 (16 × 10"−"1"7 M) and 6.0 × 10"−"4 ng mL"−"1 (12 × 10"−"1"6 M) for PSA-MIP and Anti-PSA electrodes, respectively. Selectivity studies were performed against HSA and IgG and selectivity coefficients were calculated. PSA detection was also carried out from diluted human serum samples and finally, reproducibility of the electrodes was tested. The results are promising and show that when the sensitivity of the capacitive system is combined with the selectivity and reproducibility of the microcontact-imprinting procedure, the resulting system might be used successfully for real-time detection of various analytes even in very low concentrations. - Highlights: • Microcontact imprinting method was used for preparing the sensor chip for capacitive biosensing. • High sensitivity was obtained. • Good selectivity was demonstrated. • Stability of
A novel time-domain signal processing algorithm for real time ventricular fibrillation detection
International Nuclear Information System (INIS)
Monte, G E; Scarone, N C; Liscovsky, P O; Rotter, P
2011-01-01
This paper presents an application of a novel algorithm for real time detection of ECG pathologies, especially ventricular fibrillation. It is based on segmentation and labeling process of an oversampled signal. After this treatment, analyzing sequence of segments, global signal behaviours are obtained in the same way like a human being does. The entire process can be seen as a morphological filtering after a smart data sampling. The algorithm does not require any ECG digital signal pre-processing, and the computational cost is low, so it can be embedded into the sensors for wearable and permanent applications. The proposed algorithms could be the input signal description to expert systems or to artificial intelligence software in order to detect other pathologies.
A novel time-domain signal processing algorithm for real time ventricular fibrillation detection
Monte, G. E.; Scarone, N. C.; Liscovsky, P. O.; Rotter S/N, P.
2011-12-01
This paper presents an application of a novel algorithm for real time detection of ECG pathologies, especially ventricular fibrillation. It is based on segmentation and labeling process of an oversampled signal. After this treatment, analyzing sequence of segments, global signal behaviours are obtained in the same way like a human being does. The entire process can be seen as a morphological filtering after a smart data sampling. The algorithm does not require any ECG digital signal pre-processing, and the computational cost is low, so it can be embedded into the sensors for wearable and permanent applications. The proposed algorithms could be the input signal description to expert systems or to artificial intelligence software in order to detect other pathologies.
A real time QRS detection using delay-coordinate mapping for the microcontroller implementation.
Lee, Jeong-Whan; Kim, Kyeong-Seop; Lee, Bongsoo; Lee, Byungchae; Lee, Myoung-Ho
2002-01-01
In this article, we propose a new algorithm using the characteristics of reconstructed phase portraits by delay-coordinate mapping utilizing lag rotundity for a real-time detection of QRS complexes in ECG signals. In reconstructing phase portrait the mapping parameters, time delay, and mapping dimension play important roles in shaping of portraits drawn in a new dimensional space. Experimentally, the optimal mapping time delay for detection of QRS complexes turned out to be 20 ms. To explore the meaning of this time delay and the proper mapping dimension, we applied a fill factor, mutual information, and autocorrelation function algorithm that were generally used to analyze the chaotic characteristics of sampled signals. From these results, we could find the fact that the performance of our proposed algorithms relied mainly on the geometrical property such as an area of the reconstructed phase portrait. For the real application, we applied our algorithm for designing a small cardiac event recorder. This system was to record patients' ECG and R-R intervals for 1 h to investigate HRV characteristics of the patients who had vasovagal syncope symptom and for the evaluation, we implemented our algorithm in C language and applied to MIT/BIH arrhythmia database of 48 subjects. Our proposed algorithm achieved a 99.58% detection rate of QRS complexes.
Simultaneous Detection of Ricin and Abrin DNA by Real-Time PCR (qPCR
Directory of Open Access Journals (Sweden)
Roman Wölfel
2012-08-01
Full Text Available Ricin and abrin are two of the most potent plant toxins known and may be easily obtained in high yield from the seeds using rather simple technology. As a result, both toxins are potent and available toxins for criminal or terrorist acts. However, as the production of highly purified ricin or abrin requires sophisticated equipment and knowledge, it may be more likely that crude extracts would be used by non-governmental perpetrators. Remaining plant-specific nucleic acids in these extracts allow the application of a real-time PCR (qPCR assay for the detection and identification of abrin or ricin genomic material. Therefore, we have developed a duplex real-time PCR assays for simultaneous detection of ricin and abrin DNA based on the OmniMix HS bead PCR reagent mixture. Novel primers and hybridization probes were designed for detection on a SmartCycler instrument by using 5′-nuclease technology. The assay was thoroughly optimized and validated in terms of analytical sensitivity. Evaluation of the assay sensitivity by probit analysis demonstrated a 95% probability of detection at 3 genomes per reaction for ricin DNA and 1.2 genomes per reaction for abrin DNA. The suitability of the assays was exemplified by detection of ricin and abrin contaminations in a food matrix.
Wang, Jianchang; Liu, Libing; Wang, Jinfeng; Pang, Xiaoyu; Yuan, Wanzhe
2018-02-15
The objective of this study was to develop a dual real-time recombinase polymerase amplification (RPA) assay using exo probes for the detection and differentiation of pseudorabies virus (PRV). Specific RPA primers and probes were designed for gB and gE genes of PRV within the conserved region of viral genome. The reaction process can be completed in 20 min at 39 °C. The dual real-time RPA assay performed in the single tube was capable of specific detecting and differentiating of the wild-type PRV and gE-deleted vaccine strains, without cross-reactions with other non-targeted pig viruses. The analytical sensitivity of the assay was 10 2 copies for gB and gE genes. The dual real-time RPA demonstrated a 100% diagnostic agreement with the real-time PCR on 4 PRV strains and 37 clinical samples. Through the linear regression analysis, the R 2 value of the real-time RPA and the real-time PCR for gB and gE was 0.983 and 0.992, respectively. The dual real-time RPA assay provides an alternative useful tool for rapid, simple, and reliable detection and differentiation of PRV, especially in remote and rural areas. Copyright © 2017 Elsevier Inc. All rights reserved.
Real time testing of intelligent relays for synchronous distributed generation islanding detection
Zhuang, Davy
As electric power systems continue to grow to meet ever-increasing energy demand, their security, reliability, and sustainability requirements also become more stringent. The deployment of distributed energy resources (DER), including generation and storage, in conventional passive distribution feeders, gives rise to integration problems involving protection and unintentional islanding. Distributed generators need to be islanded for safety reasons when disconnected or isolated from the main feeder as distributed generator islanding may create hazards to utility and third-party personnel, and possibly damage the distribution system infrastructure, including the distributed generators. This thesis compares several key performance indicators of a newly developed intelligent islanding detection relay, against islanding detection devices currently used by the industry. The intelligent relay employs multivariable analysis and data mining methods to arrive at decision trees that contain both the protection handles and the settings. A test methodology is developed to assess the performance of these intelligent relays on a real time simulation environment using a generic model based on a real-life distribution feeder. The methodology demonstrates the applicability and potential advantages of the intelligent relay, by running a large number of tests, reflecting a multitude of system operating conditions. The testing indicates that the intelligent relay often outperforms frequency, voltage and rate of change of frequency relays currently used for islanding detection, while respecting the islanding detection time constraints imposed by standing distributed generator interconnection guidelines.
Detection of Tomato black ring virus by real-time one-step RT-PCR.
Harper, Scott J; Delmiglio, Catia; Ward, Lisa I; Clover, Gerard R G
2011-01-01
A TaqMan-based real-time one-step RT-PCR assay was developed for the rapid detection of Tomato black ring virus (TBRV), a significant plant pathogen which infects a wide range of economically important crops. Primers and a probe were designed against existing genomic sequences to amplify a 72 bp fragment from RNA-2. The assay amplified all isolates of TBRV tested, but no amplification was observed from the RNA of other nepovirus species or healthy host plants. The detection limit of the assay was estimated to be around nine copies of the TBRV target region in total RNA. A comparison with conventional RT-PCR and ELISA, indicated that ELISA, the current standard test method, lacked specificity and reacted to all nepovirus species tested, while conventional RT-PCR was approximately ten-fold less sensitive than the real-time RT-PCR assay. Finally, the real-time RT-PCR assay was tested using five different RT-PCR reagent kits and was found to be robust and reliable, with no significant differences in sensitivity being found. The development of this rapid assay should aid in quarantine and post-border surveys for regulatory agencies. Copyright © 2010 Elsevier B.V. All rights reserved.
Li, Jia; Tian, Yonghong; Gao, Wen
2008-01-01
In recent years, the amount of streaming video has grown rapidly on the Web. Often, retrieving these streaming videos offers the challenge of indexing and analyzing the media in real time because the streams must be treated as effectively infinite in length, thus precluding offline processing. Generally speaking, captions are important semantic clues for video indexing and retrieval. However, existing caption detection methods often have difficulties to make real-time detection for streaming video, and few of them concern on the differentiation of captions from scene texts and scrolling texts. In general, these texts have different roles in streaming video retrieval. To overcome these difficulties, this paper proposes a novel approach which explores the inter-frame correlation analysis and wavelet-domain modeling for real-time caption detection in streaming video. In our approach, the inter-frame correlation information is used to distinguish caption texts from scene texts and scrolling texts. Moreover, wavelet-domain Generalized Gaussian Models (GGMs) are utilized to automatically remove non-text regions from each frame and only keep caption regions for further processing. Experiment results show that our approach is able to offer real-time caption detection with high recall and low false alarm rate, and also can effectively discern caption texts from the other texts even in low resolutions.
Real-time centre detection of an OLED structure
Pieters, R.S.; Jonker, P.P.; Nijmeijer, H.
2009-01-01
The research presented in this paper focuses on real-time image processing for visual servoing, i.e. the positioning of a x-y table by using a camera only instead of encoders. A camera image stream plus real-time image processing determines the position in the next iteration of the table controller.
Real-Time Center Detection of an OLED Structure
Pieters, R.S.; Jonker, P.P.; Nijmeijer, H.; Blanc-Talon, J.; Philips, W.; Popescu, D.; Scheunders, P.
2009-01-01
The research presented in this paper focuses on real-time image processing for visual servoing, i.e. the positioning of a x-y table by using a camera only instead of encoders. A camera image stream plus real-time image processing determines the position in the next iteration of the table controller.
European validation of Real-Time PCR method for detection of Salmonella spp. in pork meat.
Delibato, Elisabetta; Rodriguez-Lazaro, David; Gianfranceschi, Monica; De Cesare, Alessandra; Comin, Damiano; Gattuso, Antonietta; Hernandez, Marta; Sonnessa, Michele; Pasquali, Frédérique; Sreter-Lancz, Zuzsanna; Saiz-Abajo, María-José; Pérez-De-Juan, Javier; Butrón, Javier; Prukner-Radovcic, Estella; Horvatek Tomic, Danijela; Johannessen, Gro S; Jakočiūnė, Džiuginta; Olsen, John E; Chemaly, Marianne; Le Gall, Francoise; González-García, Patricia; Lettini, Antonia Anna; Lukac, Maja; Quesne, Segolénè; Zampieron, Claudia; De Santis, Paola; Lovari, Sarah; Bertasi, Barbara; Pavoni, Enrico; Proroga, Yolande T R; Capuano, Federico; Manfreda, Gerardo; De Medici, Dario
2014-08-01
The classical microbiological method for detection of Salmonella spp. requires more than five days for final confirmation, and consequently there is a need for an alternative methodology for detection of this pathogen particularly in those food categories with a short shelf-life. This study presents an international (at European level) ISO 16140-based validation study of a non-proprietary Real-Time PCR-based method that can generate final results the day following sample analysis. It is based on an ISO compatible enrichment coupled to an easy and inexpensive DNA extraction and a consolidated Real-Time PCR assay. Thirteen laboratories from seven European Countries participated to this trial, and pork meat was selected as food model. The limit of detection observed was down to 10 CFU per 25 g of sample, showing excellent concordance and accordance values between samples and laboratories (100%). In addition, excellent values were obtained for relative accuracy, specificity and sensitivity (100%) when the results obtained for the Real-Time PCR-based methods were compared to those of the ISO 6579:2002 standard method. The results of this international trial demonstrate that the evaluated Real-Time PCR-based method represents an excellent alternative to the ISO standard. In fact, it shows an equal and solid performance as well as it reduces dramatically the extent of the analytical process, and can be easily implemented routinely by the Competent Authorities and Food Industry laboratories. Copyright © 2014 Elsevier B.V. All rights reserved.
Gianfranceschi, Monica Virginia; Rodriguez-Lazaro, David; Hernandez, Marta; González-García, Patricia; Comin, Damiano; Gattuso, Antonietta; Delibato, Elisabetta; Sonnessa, Michele; Pasquali, Frederique; Prencipe, Vincenza; Sreter-Lancz, Zuzsanna; Saiz-Abajo, María-José; Pérez-De-Juan, Javier; Butrón, Javier; Kozačinski, Lidija; Tomic, Danijela Horvatek; Zdolec, Nevijo; Johannessen, Gro S; Jakočiūnė, Džiuginta; Olsen, John Elmerdahl; De Santis, Paola; Lovari, Sarah; Bertasi, Barbara; Pavoni, Enrico; Paiusco, Antonella; De Cesare, Alessandra; Manfreda, Gerardo; De Medici, Dario
2014-08-01
The classical microbiological method for detection of Listeria monocytogenes requires around 7 days for final confirmation, and due to perishable nature of RTE food products, there is a clear need for an alternative methodology for detection of this pathogen. This study presents an international (at European level) ISO 16140-based validation trial of a non-proprietary real-time PCR-based methodology that can generate final results in the following day of the analysis. This methodology is based on an ISO compatible enrichment coupled to a bacterial DNA extraction and a consolidated real-time PCR assay. Twelve laboratories from six European countries participated in this trial, and soft cheese was selected as food model since it can represent a difficult matrix for the bacterial DNA extraction and real-time PCR amplification. The limit of detection observed was down to 10 CFU per 25 of sample, showing excellent concordance and accordance values between samples and laboratories (>75%). In addition, excellent values were obtained for relative accuracy, specificity and sensitivity (82.75%, 96.70% and 97.62%, respectively) when the results obtained for the real-time PCR-based methods were compared to those of the ISO 11290-1 standard method. An interesting observation was that the L. monocytogenes detection by the real-time PCR method was less affected in the presence of Listeria innocua in the contaminated samples, proving therefore to be more reliable than the reference method. The results of this international trial demonstrate that the evaluated real-time PCR-based method represents an excellent alterative to the ISO standard since it shows a higher performance as well as reduce the extent of the analytical process, and can be easily implemented routinely by the competent authorities and food industry laboratories. Copyright © 2014 Elsevier B.V. All rights reserved.
Facial Expression Emotion Detection for Real-Time Embedded Systems
Directory of Open Access Journals (Sweden)
Saeed Turabzadeh
2018-01-01
Full Text Available Recently, real-time facial expression recognition has attracted more and more research. In this study, an automatic facial expression real-time system was built and tested. Firstly, the system and model were designed and tested on a MATLAB environment followed by a MATLAB Simulink environment that is capable of recognizing continuous facial expressions in real-time with a rate of 1 frame per second and that is implemented on a desktop PC. They have been evaluated in a public dataset, and the experimental results were promising. The dataset and labels used in this study were made from videos, which were recorded twice from five participants while watching a video. Secondly, in order to implement in real-time at a faster frame rate, the facial expression recognition system was built on the field-programmable gate array (FPGA. The camera sensor used in this work was a Digilent VmodCAM — stereo camera module. The model was built on the Atlys™ Spartan-6 FPGA development board. It can continuously perform emotional state recognition in real-time at a frame rate of 30. A graphical user interface was designed to display the participant’s video in real-time and two-dimensional predict labels of the emotion at the same time.
Energy Technology Data Exchange (ETDEWEB)
Liu, Shuiping; Gu, Tianxun; Fu, Jiajia [Key Laboratory of Eco-Textiles, Ministry of Education (Jiangnan University), Wuxi 214122 (China); College of Textile and Clothing, Jiangnan University, Wuxi 214122 (China); Li, Xiaoqiang, E-mail: leecaiwei@163.com [Key Laboratory of Eco-Textiles, Ministry of Education (Jiangnan University), Wuxi 214122 (China); College of Textile and Clothing, Jiangnan University, Wuxi 214122 (China); Technical University of Denmark, DTU Food, Søltofts plads, B227, 2800 Kgs. Lyngby (Denmark); Chronakis, Ioannis S. [Technical University of Denmark, DTU Food, Søltofts plads, B227, 2800 Kgs. Lyngby (Denmark); Ge, Mingqiao [Key Laboratory of Eco-Textiles, Ministry of Education (Jiangnan University), Wuxi 214122 (China); College of Textile and Clothing, Jiangnan University, Wuxi 214122 (China)
2014-12-01
In this work, novel hybrid nanosphere vehicles were synthesized for nitric oxide (NO) donating and real-time detection. The hybrid nanosphere vehicles consist of cadmium selenide quantum dots (CdSe QDs) as NO fluorescent probes, and the modified hyperbranched polyether (mHP)-based diazeniumdiolates as NO donors, respectively. The nanospheres have spherical outline with dimension of ∼ 127 nm. The data of systematic characterization demonstrated that the mHP-based hybrid nanosphere vehicles (QDs-mHP-NO) can release and real-time detect NO with the low limit of 25 nM, based on fluorescence quenching mechanism. The low cell-toxicity of QDs-mHP-NO nanospheres was verified by means of MTT assay on L929 cells viability. The QDs-mHP-NO nanospheres provide perspectives for designing a new class of biocompatible NO donating and imaging systems. - Highlights: • QDs-mHP-NO fluorescent probe was prepared. • The QDs-mHP-NO probe is capable of releasing NO. • The QDs-mHP-NO probe can quantitatively detecting the release of NO in real time. • The low cell-toxicity of QDs-mHP-NO nanospheres was verified.
Matsuoka, Takayuki; Shigemura, Katsumi; Yamamichi, Fukashi; Fujisawa, Masato; Kawabata, Masato; Shirakawa, Toshiro
2012-01-01
The objective of this study is to investigate and compare the sensitivity in conventional PCR, quantitative real time PCR, nested PCR and western blots for detection of prostate cancer tumor markers using prostate cancer (PCa) cells. We performed conventional PCR, quantitative real time PCR, nested PCR, and western blots using 5 kinds of PCa cells. Prostate specific antigen (PSA), prostate specific membrane antigen (PSMA), and androgen receptor (AR) were compared for their detection sensitivi...
Real time failure detection in unreinforced cementitious composites with triboluminescent sensor
International Nuclear Information System (INIS)
Olawale, David O.; Kliewer, Kaitlyn; Okoye, Annuli; Dickens, Tarik J.; Uddin, Mohammed J.; Okoli, Okenwa I.
2014-01-01
The in-situ triboluminescent optical fiber (ITOF) sensor has an integrated sensing and transmission component that converts the energy from damage events like impacts and crack propagation into optical signals that are indicative of the magnitude of damage in composite structures like concrete bridges. Utilizing the triboluminescence (TL) property of ZnS:Mn, the ITOF sensor has been successfully integrated into unreinforced cementitious composite beams to create multifunctional smart structures with in-situ failure detection capabilities. The fabricated beams were tested under flexural loading, and real time failure detection was made by monitoring the TL signals generated by the integrated ITOF sensor. Tested beam samples emitted distinctive TL signals at the instance of failure. In addition, we report herein a new and promising approach to damage characterization using TL emission profiles. Analysis of TL emission profiles indicates that the ITOF sensor responds to crack propagation through the beam even when not in contact with the crack. Scanning electron microscopy analysis indicated that fracto-triboluminescence was responsible for the TL signals observed at the instance of beam failure. -- Highlights: • Developed a new approach to triboluminescence (TL)-based sensing with ZnS:Mn. • Damage-induced excitation of ZnS:Mn enabled real time damage detection in composite. • Based on sensor position, correlation exists between TL signal and failure stress. • Introduced a new approach to damage characterization with TL profile analysis
Eischeid, Anne C; Kim, Bang-hyun; Kasko, Sasha M
2013-06-19
Food allergen detection methods must be able to specifically detect minute quantities of an allergenic food in a complex food matrix. One technique that can be used is real-time PCR. For the work described here, real-time PCR assays were developed to detect penaeid shrimp and blue crab, crustacean shellfish allergens. The method was tested using shrimp meat and crab meat spiked into several types of foods, including canned soups, deli foods, meat, seafood, and prepared seafood products. Foods were spiked with either shrimp or crab at levels ranging from 0.1 to 10⁶ parts per million (ppm) and analyzed either raw or cooked by a variety of methods. Real-time PCR data were used to generate linear standard curves, and assays were evaluated with respect to linear range and reaction efficiency. Results indicate that both assays performed well in a variety of food types. High reaction efficiencies were achieved across a linear range of 6-8 orders of magnitude. Limits of detection were generally between 0.1 and 1 ppm. Cooking methods used to simulate thermal processing of foods had little effect on assay performance. This work demonstrates that real-time PCR can be a valuable tool in the detection of crustacean shellfish.
Than, Leslie Thian Lung; Chong, Pei Pei; Ng, Kee Peng; Seow, Heng Fong
2015-01-01
The number of invasive candidiasis cases has risen especially with an increase in the number of immunosuppressed and immunocom promised patients. The early detection of Candida species which is specific and sensitive is important in determining the correct administration of antifungal drugs to patients. This study aims to develop a method for the detection, identification and quantitation of medically important Candida species through quantitative polymerase chain reaction (qPCR). The isocitrate lyase (ICL) gene which is not found in mammals was chosen as the target gene of real-time PCR. Absolute quantitation of the gene copy number was achieved by constructing the plasmid containing the ICL gene which is used to generate standard curve. Twenty fungal species, two bacterial species and human DNA were tested to check the specificity of the detection method. All eight Candida species were successfully detected, identified and quantitated based on the ICL gene. A seven-log range of the gene copy number and a minimum detection limit of 10(3) copies were achieved. A one-tube absolute quantification real-time PCR that differentiates medically important Candida species via individual unique melting temperature was achieved. Analytical sensitivity and specificity were not compromised.
International Nuclear Information System (INIS)
Huang, S-H; Tsai, M-H; Lin, C-W; Yang, T-C; Chuang, P-H; Tsai, I-S; Lu, H-C; Wan Lei; Lin, Y-J; Lai, C-H
2008-01-01
Virus isolation and antibody detection are routinely used for diagnosis of Japanese encephalitis virus (JEV) infection, but the low level of transient viremia in some JE patients makes JEV isolation from clinical and surveillance samples very difficult. We describe the use of gold nanoparticle-based RT-PCR and real-time quantitative RT-PCR assays for detection of JEV from its RNA genome. We tested the effect of gold nanoparticles on four different PCR systems, including conventional PCR, reverse-transcription PCR (RT-PCR), and SYBR green real-time PCR and RT-PCR assays for diagnosis in the acute phase of JEV infection. Gold nanoparticles increased the amplification yield of the PCR product and shortened the PCR time compared to the conventional reaction. In addition, nanogold-based real-time RT-PCR showed a linear relationship between Ct and template amount using ten-fold dilutions of JEV. The nanogold-based RT-PCR and real-time quantitative RT-PCR assays were able to detect low levels (1-10 000 copies) of the JEV RNA genomes extracted from culture medium or whole blood, providing early diagnostic tools for the detection of low-level viremia in the acute-phase infection. The assays described here were simple, sensitive, and rapid approaches for detection and quantitation of JEV in tissue cultured samples as well as clinical samples
Balachandran, Priya; Friberg, Maria; Vanlandingham, V; Kozak, K; Manolis, Amanda; Brevnov, Maxim; Crowley, Erin; Bird, Patrick; Goins, David; Furtado, Manohar R; Petrauskene, Olga V; Tebbs, Robert S; Charbonneau, Duane
2012-02-01
Reducing the risk of Salmonella contamination in pet food is critical for both companion animals and humans, and its importance is reflected by the substantial increase in the demand for pathogen testing. Accurate and rapid detection of foodborne pathogens improves food safety, protects the public health, and benefits food producers by assuring product quality while facilitating product release in a timely manner. Traditional culture-based methods for Salmonella screening are laborious and can take 5 to 7 days to obtain definitive results. In this study, we developed two methods for the detection of low levels of Salmonella in pet food using real-time PCR: (i) detection of Salmonella in 25 g of dried pet food in less than 14 h with an automated magnetic bead-based nucleic acid extraction method and (ii) detection of Salmonella in 375 g of composite dry pet food matrix in less than 24 h with a manual centrifugation-based nucleic acid preparation method. Both methods included a preclarification step using a novel protocol that removes food matrix-associated debris and PCR inhibitors and improves the sensitivity of detection. Validation studies revealed no significant differences between the two real-time PCR methods and the standard U.S. Food and Drug Administration Bacteriological Analytical Manual (chapter 5) culture confirmation method.
Gattuso, Antonietta; Gianfranceschi, Monica Virginia; Sonnessa, Michele; Delibato, Elisabetta; Marchesan, Massimo; Hernandez, Marta; De Medici, Dario; Rodriguez-Lazaro, David
2014-08-01
The aim of this study was to optimize a Real-Time PCR protocol for a rapid detection of Listeria monocytogenes in pork meat, using reduced volumes of primary selective enrichment broth and times of incubation to decrease the cost and time for analysis. Forty-five samples of pork meat were artificially contaminated with two different levels of L. monocytogenes (1-10 CFU per sample and 10-100 CFU per sample), homogenized in three different volumes of Half Fraser Broth (1:3; 1:5 and 1:10) and incubated at 30°C ± 1°C for 5h, 8h and 24h. The detection was conducted in parallel by Real-Time PCR and the ISO standard 11290-1 methods. L. monocytogenes was detected in all the samples after 24h by Real-Time PCR method, also using reduced volumes of Half Fraser Broth. This represents a clear advantage as the time to final detection and the inherent costs were significantly reduced compared to the ISO reference method. All samples artificially contaminated were correctly detected also after 8 of incubation at 30°C ± 1°C in Half Fraser Broth and 24h in Fraser Broth at 37°C ± 1°C using cultural method. Copyright © 2014 Elsevier B.V. All rights reserved.
The Prototype of Real-time Object Detection System Based on SMS
Directory of Open Access Journals (Sweden)
M. Hana Mirza
2010-08-01
Full Text Available The powerful algorithm to detect object movement in development of room monitoring system is very urgent. The commond algorithm needs complex computation. In this research, the prototype of real-time object detection system using simple algorithm is developed, i.e. using the determination of the max noise/pixel value and the tolerance threshold of image accurately, and then the system automatically send a SMS (short message services to user when the object movement is detected. The developed prototype used a Logitech QuickCam webcam, a Siemens C45 mobile phone and a data cable, and the Borland Delphi 7 with additional components and Serial PortNG Tvideo as system software. The application also includes a database to store the captured images whenever object movement is detected. The test results by varying conditions of light intensities using a 5-watt light bulb, fluorescent lamp 20 and 40 watts indicate that the application is able to automatically detect the presence of moving objects with 100% success rate. The success rate is strongly influenced by the determination of the max noise/pixel value and the tolerance threshold during system configuration. This application is also capable of sending SMS automatically when the system detects a moving object with an average time of 8.35 seconds.
The development and application of the two real-time RT-PCR assays to detect the pathogen of HFMD.
Directory of Open Access Journals (Sweden)
Aili Cui
Full Text Available Large-scale Hand, Foot, and Mouth Disease (HFMD outbreaks have frequently occurred in China since 2008, affecting more than one million children and causing several hundred children deaths every year. The pathogens of HFMD are mainly human enteroviruses (HEVs. Among them, human enterovirus 71 (HEV71 and coxsackievirus A16 (CVA16 are the most common pathogens of HFMD. However, other HEVs could also cause HFMD. To rapidly detect HEV71 and CVA16, and ensure detection of all HEVs causing HFMD, two real-time hybridization probe-based RT-PCR assays were developed in this study. One is a multiplex real-time RT-PCR assay, which was developed to detect and differentiate HEV71 specifically from CVA16 directly from clinical specimens within 1-2 h, and the other is a broad-spectrum real-time RT-PCR assay, which targeted almost all HEVs. The experiments confirmed that the two assays have high sensitivity and specificity, and the sensitivity was up to 0.1 TCID50/ml for detection of HEVs, HEV71, and CVA16, respectively. A total of 213 clinical specimens were simultaneously detected by three kinds of assays, including the two real-time RT-PCR assays, direct conventional RT-PCR assay, and virus isolation assay on human rhabdomyosarcoma cells (RD cells. The total positive rate of both HEV71 and CVA16 was 69.48% with real-time RT-PCR assay, 47.42% with RT-PCR assay, and 34.58% with virus isolation assay. One HFMD clinical specimen was positive for HEV, but negative for HEV71 or CVA16, which was identified as Echovirus 11 (Echo11 by virus isolation, RT-PCR, and sequencing for the VP1 gene. The two real-time RT-PCR assays had been applied in 31 provincial HFMD labs to detect the pathogens of HFMD, which has contributed to the rapid identification of the pathogens in the early stages of HFMD outbreaks, and helped to clarify the etiologic agents of HFMD in China.
Robust real-time change detection in high jitter.
Energy Technology Data Exchange (ETDEWEB)
Simonson, Katherine Mary; Ma, Tian J.
2009-08-01
A new method is introduced for real-time detection of transient change in scenes observed by staring sensors that are subject to platform jitter, pixel defects, variable focus, and other real-world challenges. The approach uses flexible statistical models for the scene background and its variability, which are continually updated to track gradual drift in the sensor's performance and the scene under observation. Two separate models represent temporal and spatial variations in pixel intensity. For the temporal model, each new frame is projected into a low-dimensional subspace designed to capture the behavior of the frame data over a recent observation window. Per-pixel temporal standard deviation estimates are based on projection residuals. The second approach employs a simple representation of jitter to generate pixelwise moment estimates from a single frame. These estimates rely on spatial characteristics of the scene, and are used gauge each pixel's susceptibility to jitter. The temporal model handles pixels that are naturally variable due to sensor noise or moving scene elements, along with jitter displacements comparable to those observed in the recent past. The spatial model captures jitter-induced changes that may not have been seen previously. Change is declared in pixels whose current values are inconsistent with both models.
Oresko, Joseph J; Duschl, Heather; Cheng, Allen C
2010-05-01
Cardiovascular disease (CVD) is the single leading cause of global mortality and is projected to remain so. Cardiac arrhythmia is a very common type of CVD and may indicate an increased risk of stroke or sudden cardiac death. The ECG is the most widely adopted clinical tool to diagnose and assess the risk of arrhythmia. ECGs measure and display the electrical activity of the heart from the body surface. During patients' hospital visits, however, arrhythmias may not be detected on standard resting ECG machines, since the condition may not be present at that moment in time. While Holter-based portable monitoring solutions offer 24-48 h ECG recording, they lack the capability of providing any real-time feedback for the thousands of heart beats they record, which must be tediously analyzed offline. In this paper, we seek to unite the portability of Holter monitors and the real-time processing capability of state-of-the-art resting ECG machines to provide an assistive diagnosis solution using smartphones. Specifically, we developed two smartphone-based wearable CVD-detection platforms capable of performing real-time ECG acquisition and display, feature extraction, and beat classification. Furthermore, the same statistical summaries available on resting ECG machines are provided.
Real-time detection and elimination of nonorthogonality error in interference fringe processing
International Nuclear Information System (INIS)
Hu Haijiang; Zhang Fengdeng
2011-01-01
In the measurement system of interference fringe, the nonorthogonality error is a main error source that influences the precision and accuracy of the measurement system. The detection and elimination of the error has been an important target. A novel method that only uses the cross-zero detection and the counting is proposed to detect and eliminate the nonorthogonality error in real time. This method can be simply realized by means of the digital logic device, because it does not invoke trigonometric functions and inverse trigonometric functions. And it can be widely used in the bidirectional subdivision systems of a Moire fringe and other optical instruments.
Development of a real-time quantitative assay for detection of Epstein-Barr virus
H.G.M. Niesters (Bert); E. Fries; K.C. Wolthers (Katja); A.D.M.E. Osterhaus (Albert); J.J. Cornelissen (Jan); J.W.J. van Esser (Joost)
2000-01-01
textabstractWith the use of real-time PCR, we developed and evaluated a rapid, sensitive, specific, and reproducible method for the detection of Epstein-Barr virus (EBV) DNA in plasma samples. This method allowed us to screen plasma and serum samples over a range between 100 and
Tian, Qian; Feng, Jian-Jun; Hu, Jie; Zhao, Wen-Jun
2016-10-14
In recent years, use of the DNA-intercalating dye propidium monoazide (PMA) in real-time PCR has been reported as a novel method to detect viable bacteria in different types of samples, such as food, environmental, and microbiological samples. In this study, viable cells of Acidovorax citrulli, the causal agent of bacterial seedling blight and fruit blotch, were selectively detected and differentiated from dead cells by real-time fluorescent polymerase chain reaction amplification after the bacterial solution was treated with the DNA-binding dye PMA. The primers and TaqMan probe were based on the A. citrulli genome (Aave_1909, Gene ID: 4669443) and were highly specific for A. citrulli. The detection threshold of this assay was 10 3 colony-forming units per mL (CFU/mL) in pure cell suspensions containing viable and dead cells and infected watermelon seeds. Application of this assay enables the selective detection of viable cells of A. citrulli and facilitates monitoring of the pathogen in watermelon and melon seeds.
Evaluation of two real time PCR assays for the detection of bacterial DNA in amniotic fluid.
Girón de Velasco-Sada, Patricia; Falces-Romero, Iker; Quiles-Melero, Inmaculada; García-Perea, Adela; Mingorance, Jesús
2018-01-01
The aim of this study was to evaluate two non-commercial Real-Time PCR assays for the detection of microorganisms in amniotic fluid followed by identification by pyrosequencing. We collected 126 amniotic fluids from 2010 to 2015 for the evaluation of two Real-Time PCR assays for detection of bacterial DNA in amniotic fluid (16S Universal PCR and Ureaplasma spp. specific PCR). The method was developed in the Department of Microbiology of the University Hospital La Paz. Thirty-seven samples (29.3%) were positive by PCR/pyrosequencing and/or culture, 4 of them were mixed cultures with Ureaplasma urealyticum. The Universal 16S Real-Time PCR was compared with the standard culture (81.8% sensitivity, 97.4% specificity, 75% positive predictive value, 98% negative predictive value). The Ureaplasma spp. specific Real-Time PCR was compared with the Ureaplasma/Mycoplasma specific culture (92.3% sensitivity, 89.4% specificity, 50% positive predictive value, 99% negative predictive value) with statistically significant difference (p=0.005). Ureaplasma spp. PCR shows a rapid response time (5h from DNA extraction until pyrosequencing) when comparing with culture (48h). So, the response time of bacteriological diagnosis in suspected chorioamnionitis is reduced. Copyright © 2017 Elsevier B.V. All rights reserved.
Directory of Open Access Journals (Sweden)
Kang Feng-feng
2012-03-01
Full Text Available Objective To investigate the clinical application of Real-Time PCR for rapid detection of methicillin-resistant Staphylococcus aureus (MRSA directly from nasopharyngeal swab specimens.
International Nuclear Information System (INIS)
Godinez, V.; Shu, F.; Finlayson, R.; O'Donnell, B.; Anastasopoulos, A.; Tsimogiannis, A.
2004-01-01
Early detection of mechanical failure in helicopter drive train components is a key safety and economical issue with both military and civil sectors of aviation. Of these components, couplings are particularly critical. The objective of this work is to demonstrate the feasibility of designing and developing a reliable, real time monitoring methodology based on Supervised Pattern Recognition (SPR) for early detection of cracks in couplings used in helicopter and engine drive systems. Within this framework, a portable Acoustic Emission (AE) system was used, equipped with a semi-real time SPR software package. Results from AE tests performed in a gearbox-testing bench at different speeds and different torque values are presented. These results indicate that the energy content of different frequency bands in the AE signals power spectra is strongly correlated with the introduction of EDM notches in the main gear. Further tests indicate that a strong shift in the frequency of the AE signals is observed after spalling occurred in the pinion gear. The variation of displacement and velocity between signal classes are discussed as a potential feature in characterizing crack severity. Finally, a scope of the work for optimizing the methodology in detecting and evaluating coupling cracking in real time will be presented. (author)
Real-time underwater object detection based on an electrically scanned high-resolution sonar
DEFF Research Database (Denmark)
Henriksen, Lars
1994-01-01
The paper describes an approach to real time detection and tracking of underwater objects, using image sequences from an electrically scanned high-resolution sonar. The use of a high resolution sonar provides a good estimate of the location of the objects, but strains the computers on board, beca...
Directory of Open Access Journals (Sweden)
I. Karthika Lakshmi
2018-04-01
Full Text Available Aim: The present study was designed to standardize real-time polymerase chain reaction (PCR for detecting the bluetongue virus from blood samples of sheep collected during outbreaks of bluetongue disease in the year 2014 in Andhra Pradesh and Telangana states of India. Materials and Methods: A 10-fold serial dilution of Plasmid PUC59 with bluetongue virus (BTV NS3 insert was used to plot the standard curve. BHK-21 and KC cells were used for in vitro propagation of virus BTV-9 at a TCID50/ml of 105 ml and RNA was isolated by the Trizol method. Both reverse transcription -PCR and real-time PCR using TaqMan probe were carried out with RNA extracted from virus-spiked culture medium and blood to compare the sensitivity by means of finding out the limit of detection (LoD. The results were verified by inoculating the detected and undetected dilutions onto cell cultures with further cytological (cytopathic effect and molecular confirmation (by BTV-NS1 group-specific PCR. The standardized technique was then applied to field samples (blood for detecting BTV. Results: The slope of the standard curve obtained was -3.23, and the efficiency was 103%. The LoD with RT-PCR was 8.269Ex103 number of copies of plasmid, whereas it was 13 with real-time PCR for plasmid dilutions. Similarly, LoD was determined for virus-spiked culture medium, and blood with both the types of PCR and the values were 103 TCID 50/ml and 104 TCID 50/ml with RT-PCR and 10° TCID 50/ml and 102 TCID 50/ml with real-time PCR, respectively. The standardized technique was applied to blood samples collected from BTV suspected animals; 10 among 20 samples were found positive with Cq values ranging from 27 to 39. The Cq value exhibiting samples were further processed in cell cultures and were confirmed to be BT positive. Likewise, Cq undetected samples on processing in cell cultures turned out to be BTV negative. Conclusion: Real-time PCR was found to be a very sensitive as well as reliable method
Directory of Open Access Journals (Sweden)
CHENG Fang
2013-04-01
Full Text Available Real-time PCR technique has been widely used in quantitative GMO detection in recent years.The accuracy of GMOs quantification based on the real-time PCR methods is still a difficult problem,especially for the quantification of high processed samples.To develop the suitable and accurate real-time PCR system for high processed GM samples,we made ameliorations to several real-time PCR parameters,including re-designed shorter target DNA fragment,similar lengths of amplified endogenous and exogenous gene targets,similar GC contents and melting temperatures of PCR primers and TaqMan probes.Also,one Heat-Treatment Processing Model (HTPM was established using soybean flour samples containing GM soybean GTS 40-3-2 to validate the effectiveness of the improved real-time PCR system.Tested results showed that the quantitative bias of GM content in heat processed samples were lowered using the new PCR system.The improved duplex real-time PCR was further validated using processed foods derived from GM soybean,and more accurate GM content values in these foods was also achieved.These results demonstrated that the improved duplex real-time PCR would be quite suitable in quantitative detection of high processed food products.
Energy Technology Data Exchange (ETDEWEB)
Ma Yingliang; Housden, R. James; Razavi, Reza; Rhode, Kawal S. [Division of Imaging Sciences and Biomedical Engineering, King' s College London, London SE1 7EH (United Kingdom); Gogin, Nicolas; Cathier, Pascal [Medisys Research Group, Philips Healthcare, Paris 92156 (France); Gijsbers, Geert [Interventional X-ray, Philips Healthcare, Best 5680 DA (Netherlands); Cooklin, Michael; O' Neill, Mark; Gill, Jaswinder; Rinaldi, C. Aldo [Department of Cardiology, Guys and St. Thomas' Hospitals NHS Foundation Trust, London SE1 7EH (United Kingdom)
2013-07-15
Purpose: X-ray fluoroscopically guided cardiac electrophysiology (EP) procedures are commonly carried out to treat patients with arrhythmias. X-ray images have poor soft tissue contrast and, for this reason, overlay of a three-dimensional (3D) roadmap derived from preprocedural volumetric images can be used to add anatomical information. It is useful to know the position of the catheter electrodes relative to the cardiac anatomy, for example, to record ablation therapy locations during atrial fibrillation therapy. Also, the electrode positions of the coronary sinus (CS) catheter or lasso catheter can be used for road map motion correction.Methods: In this paper, the authors present a novel unified computational framework for image-based catheter detection and tracking without any user interaction. The proposed framework includes fast blob detection, shape-constrained searching and model-based detection. In addition, catheter tracking methods were designed based on the customized catheter models input from the detection method. Three real-time detection and tracking methods are derived from the computational framework to detect or track the three most common types of catheters in EP procedures: the ablation catheter, the CS catheter, and the lasso catheter. Since the proposed methods use the same blob detection method to extract key information from x-ray images, the ablation, CS, and lasso catheters can be detected and tracked simultaneously in real-time.Results: The catheter detection methods were tested on 105 different clinical fluoroscopy sequences taken from 31 clinical procedures. Two-dimensional (2D) detection errors of 0.50 {+-} 0.29, 0.92 {+-} 0.61, and 0.63 {+-} 0.45 mm as well as success rates of 99.4%, 97.2%, and 88.9% were achieved for the CS catheter, ablation catheter, and lasso catheter, respectively. With the tracking method, accuracies were increased to 0.45 {+-} 0.28, 0.64 {+-} 0.37, and 0.53 {+-} 0.38 mm and success rates increased to 100%, 99
International Nuclear Information System (INIS)
Denman, S.E.; McSweeney, C.S.
2005-01-01
Many nucleic acid-based probe and PCR assays have been developed for the detection tracking of specific microbes within the rumen ecosystem. Conventional PCR assays detect PCR products at the end stage of each PCR reaction, where exponential amplification is no longer being achieved. This approach can result in different end product (amplicon) quantities being generated. In contrast, using quantitative, or real-time PCR, quantification of the amplicon is performed not at the end of the reaction, but rather during exponential amplification, where theoretically each cycle will result in a doubling of product being created. For real-time PCR, the cycle at which fluorescence is deemed to be detectable above the background during the exponential phase is termed the cycle threshold (Ct). The Ct values obtained are then used for quantitation, which will be discussed later
Real-time QRS detection using integrated variance for ECG gated cardiac MRI
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Schmidt Marcus
2016-09-01
Full Text Available During magnetic resonance imaging (MRI, a patient’s vital signs are required for different purposes. In cardiac MRI (CMR, an electrocardiogram (ECG of the patient is required for triggering the image acquisition process. However, a reliable QRS detection of an ECG signal acquired inside an MRI scanner is a challenging task due to the magnetohydrodynamic (MHD effect which interferes with the ECG. The aim of this work was to develop a reliable QRS detector usable inside the MRI which also fulfills the standards for medical devices (IEC 60601-2-27. Therefore, a novel real-time QRS detector based on integrated variance measurements is presented. The algorithm was trained on ANSI/AAMI EC13 test waveforms and was then applied to two databases with 12-lead ECG signals recorded inside and outside an MRI scanner. Reliable results for both databases were achieved for the ECG signals recorded inside (DBMRI: sensitivity Se = 99.94%, positive predictive value +P = 99.84% and outside (DBInCarT: Se = 99.29%, +P = 99.72% the MRI. Due to the accurate R-peak detection in real-time this can be used for monitoring and triggering in MRI exams.
Rapid quantitative detection of Lactobacillus sakei in meat and fermented sausages by real-time PCR.
Martín, Belén; Jofré, Anna; Garriga, Margarita; Pla, Maria; Aymerich, Teresa
2006-09-01
A quick and simple method for quantitative detection of Lactobacillus sakei in fermented sausages was successfully developed. It is based on Chelex-100-based DNA purification and real-time PCR enumeration using a TaqMan fluorescence probe. Primers and probes were designed in the L. sakei 16S-23S rRNA intergenic transcribed spacer region, and the assay was evaluated using L. sakei genomic DNA and an artificially inoculated sausage model. The detection limit of this technique was approximately 3 cells per reaction mixture using both purified DNA and the inoculated sausage model. The quantification limit was established at 30 cells per reaction mixture in both models. The assay was then applied to enumerate L. sakei in real samples, and the results were compared to the MRS agar count method followed by confirmation of the percentage of L. sakei colonies. The results obtained by real-time PCR were not statistically significantly different than those obtained by plate count on MRS agar (P > 0.05), showing a satisfactory agreement between both methods. Therefore, the real-time PCR assay developed can be considered a promising rapid alternative method for the quantification of L. sakei and evaluation of the implantation of starter strains of L. sakei in fermented sausages.
Improvement of a picking algorithm real-time P-wave detection by kurtosis
Ishida, H.; Yamada, M.
2016-12-01
Earthquake early warning (EEW) requires fast and accurate P-wave detection. The current EEW system in Japan uses the STA/LTAalgorithm (Allen, 1978) to detect P-wave arrival.However, some stations did not trigger during the 2011 Great Tohoku Earthquake due to the emergent onset. In addition, accuracy of the P-wave detection is very important: on August 1, 2016, the EEW issued a false alarm with M9 in Tokyo region due to a thunder noise.To solve these problems, we use a P-wave detection method using kurtosis statistics. It detects the change of statistic distribution of the waveform amplitude. This method was recently developed (Saragiotis et al., 2002) and used for off-line analysis such as making seismic catalogs. To apply this method for EEW, we need to remove an acausal calculation and enable a real-time processing. Here, we propose a real-time P-wave detection method using kurtosis statistics with a noise filter.To avoid false triggering by a noise, we incorporated a simple filter to classify seismic signal and noise. Following Kong et al. (2016), we used the interquartilerange and zero cross rate for the classification. The interquartile range is an amplitude measure that is equal to the middle 50% of amplitude in a certain time window. The zero cross rate is a simple frequency measure that counts the number of times that the signal crosses baseline zero. A discriminant function including these measures was constructed by the linear discriminant analysis.To test this kurtosis method, we used strong motion records for 62 earthquakes between April, 2005 and July, 2015, which recorded the seismic intensity greater equal to 6 lower in the JMA intensity scale. The records with hypocentral distance picks. It shows that the median error is 0.13 sec and 0.035 sec for STA/LTA and kurtosis method. The kurtosis method tends to be more sensitive to small changes in amplitude.Our approach will contribute to improve the accuracy of source location determination of
Rheem, Insoo; Park, Joowon; Kim, Tae-Hyun; Kim, Jong Wan
2012-11-01
In this study, we evaluated the analytical performance and clinical potential of a one-step multiplex real-time PCR assay for the simultaneous detection of 14 types of respiratory viruses using the AdvanSure RV real-time PCR Kit (LG Life Sciences, Korea). Three hundred and twenty clinical specimens were tested with the AdvanSure RV real-time PCR Kit and conventional multiplex reverse transcription (RT)-PCR assay. The assay results were analyzed and the one-step AdvanSure RV real-time PCR Kit was compared with the conventional multiplex RT-PCR assay with respect to the sensitivity and specificity of the detection of respiratory viruses. The limit of detection (LOD) was 1.31 plaque-forming units (PFU)/mL for human rhinoviruses (hRVs), 4.93 PFU/mL for human coronavirus HCoV-229E/NL63, 2.67 PFU/mL for human coronavirus HCoV-OC43, 18.20 PFU/mL for parainfluenza virus 1 (PIV)-1, 24.57 PFU/mL for PIV-2, 1.73 PFU/mL for PIV-3, 1.79 PFU/mL for influenza virus group (Flu) A, 59.51 PFU/mL for FluB, 5.46 PFU/mL for human respiratory syncytial virus (hRSV)-A, 17.23 PFU/mL for hRSV-B, 9.99 PFU/mL for human adenovirus (ADVs). The cross-reactivity test for this assay against 23 types of non-respiratory viruses showed negative results for all viruses tested. The agreement between the one-step AdvanSure multiplex real-time PCR assay and the conventional multiplex RT-PCR assay was 98%. The one-step AdvanSure RV multiplex real-time PCR assay is a simple assay with high potential for specific, rapid and sensitive laboratory diagnosis of respiratory viruses compared to conventional multiplex RT-PCR.
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Aline Lavado Tolardo
2016-06-01
Full Text Available Vesiculoviruses (VSV are zoonotic viruses that cause vesicular stomatitis disease in cattle, horses and pigs, as well as sporadic human cases of acute febrile illness. Therefore, diagnosis of VSV infections by reliable laboratory techniques is important to allow a proper case management and implementation of strategies for the containment of virus spread. We show here a sensitive and reproducible real-time reverse transcriptase polymerase chain reaction (RT-PCR for detection and quantification of VSV. The assay was evaluated with arthropods and serum samples obtained from horses, cattle and patients with acute febrile disease. The real-time RT-PCR amplified the Piry, Carajas, Alagoas and Indiana Vesiculovirus at a melting temperature 81.02 ± 0.8ºC, and the sensitivity of assay was estimated in 10 RNA copies/mL to the Piry Vesiculovirus. The viral genome has been detected in samples of horses and cattle, but not detected in human sera or arthropods. Thus, this assay allows a preliminary differential diagnosis of VSV infections.
A Precise and Real-Time Loop-closure Detection for SLAM Using the RSOM Tree
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Siyang Song
2015-06-01
Full Text Available In robotic applications of visual simultaneous localization and mapping (SLAM techniques, loop-closure detection detects whether or not a current location has previously been visited. We present an online and incremental approach to detect loops when images come from an already visited scene and learn new information from the environment. Instead of utilizing a bag-of-words model, the attributed graph model is applied to represent images and measure the similarity between pairs of images in our method. In order to position a camera in visual environments in real-time, the method demands retrieval of images from the database through a clustering tree that we call RSOM (recursive self-organizing feature map. As long as the match is found between the current graph and several graphs in the database, a threshold will be chosen to judge whether loop-closure is accepted or rejected. The results demonstrate the method's accuracy and real-time performance by testing several videos collected from a digital camera fixed on vehicles in indoor and outdoor environments.
Howe, Gerald B; Loveless, Bonnie M; Norwood, David; Craw, Philip; Waag, David; England, Marilyn; Lowe, John R; Courtney, Bernard C; Pitt, M Louise; Kulesh, David A
2009-01-01
Real-time PCR was used to analyze archived blood from non-human primates (NHP) and fluid samples originating from a well-controlled Q fever vaccine efficacy trial. The PCR targets were the IS1111 element and the com1 gene of Coxiella burnetii. Data from that previous study were used to evaluate real-time PCR as an alternative to the use of sero-conversion by mouse bioassay for both quantification and early detection of C. burnetii bacteria. Real-time PCR and the mouse bioassay exhibited no statistical difference in quantifying the number of microorganisms delivered in the aerosol challenge dose. The presence of C. burnetii in peripheral blood of non-human primates was detected by real-time PCR as early after exposure as the mouse bioassay with results available within hours instead of weeks. This study demonstrates that real-time PCR has the ability to replace the mouse bioassay to measure dosage and monitor infection of C. burnetii in a non-human primate model.
Fast real-time PCR for the detection of crustacean allergen in foods.
Herrero, Beatriz; Vieites, Juan M; Espiñeira, Montserrat
2012-02-29
Crustaceans are one of the most common allergens causing severe food reaction. These food allergens are a health problem, and they have become very important; there are various regulations that establish that labeling must be present regarding these allergens to warn consumers. In the present work a fast real-time PCR, by a LNA probe, was developed. This allows the detection of crustaceans in all kinds of products, including processed products in which very aggressive treatments of temperature and pressure during the manufacturing process are used. This methodology provides greater sensitivity and specificity and reduces the analysis time of real-time PCR to 40 min. This methodology was further validated by means of simulating products likely to contain this allergen. For this, products present on the market were spiked with crustacean cooking water. The assay is a potential tool in issues related to the labeling of products and food security to protect the allergic consumer.
Directory of Open Access Journals (Sweden)
Kwadwo S. Agyepong
2013-01-01
Full Text Available Time-course expression profiles and methods for spectrum analysis have been applied for detecting transcriptional periodicities, which are valuable patterns to unravel genes associated with cell cycle and circadian rhythm regulation. However, most of the proposed methods suffer from restrictions and large false positives to a certain extent. Additionally, in some experiments, arbitrarily irregular sampling times as well as the presence of high noise and small sample sizes make accurate detection a challenging task. A novel scheme for detecting periodicities in time-course expression data is proposed, in which a real-valued iterative adaptive approach (RIAA, originally proposed for signal processing, is applied for periodogram estimation. The inferred spectrum is then analyzed using Fisher’s hypothesis test. With a proper -value threshold, periodic genes can be detected. A periodic signal, two nonperiodic signals, and four sampling strategies were considered in the simulations, including both bursts and drops. In addition, two yeast real datasets were applied for validation. The simulations and real data analysis reveal that RIAA can perform competitively with the existing algorithms. The advantage of RIAA is manifested when the expression data are highly irregularly sampled, and when the number of cycles covered by the sampling time points is very reduced.
Sensitive detection of novel Indian isolate of BTV 21 using ns1 gene based real-time PCR assay
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Gaya Prasad
2013-06-01
Full Text Available Aim: The study was conducted to develop ns1 gene based sensitive real-time RT-PCR assay for diagnosis of India isolates of bluetongue virus (BTV. Materials and Methods: The BTV serotype 21 isolate (KMNO7 was isolated from Andhra Pradesh and propagated in BHK-21 cell line in our laboratory. The Nucleic acid (dsRNA of virus was extracted using Trizol method and cDNA was prepared using a standard protocol. The cDNA was allowed to ns1 gene based group specific PCR to confirm the isolate as BTV. The viral RNA was diluted 10 folds and the detection limit of ns1 gene based RT-PCR was determined. Finally the tenfold diluted viral RNA was subjected to real-time RT-PCR using ns1 gene primer and Taq man probe to standardized the reaction and determine the detection limit. Results: The ns1 gene based group specific PCR showed a single 366bp amplicon in agarose gel electrophoresis confirmed the sample as BTV. The ns1 gene RT-PCR using tenfold diluted viral RNA showed the detection limit of 70.0 fg in 1%agarose gel electrophoresis. The ns1 gene based real time RT-PCR was successfully standardized and the detection limit was found to be 7.0 fg. Conclusion: The ns1 gene based real-time RT-PCR was successfully standardized and it was found to be 10 times more sensitive than conventional RT-PCR. Key words: bluetongue, BTV21, RT-PCR, Real time RT-PCR, ns1 gene [Vet World 2013; 6(8.000: 554-557
Embedded and real-time vehicle detection system for challenging on-road scenes
Gu, Qin; Yang, Jianyu; Kong, Lingjiang; Yan, Wei Qi; Klette, Reinhard
2017-06-01
Vehicle detection is an important topic for advanced driver-assistance systems. This paper proposes an adaptive approach for an embedded system by focusing on monocular vehicle detection in real time, also aiming at being accurate under challenging conditions. Scene classification is accomplished by using a simplified convolution neural network with hypothesis generation by SoftMax regression. The output is consequently taken into account to optimize detection parameters for hypothesis generation and testing. Thus, we offer a sample-reorganization mechanism to improve the performance of vehicle hypothesis verification. A hypothesis leap mechanism is in use to improve the operating efficiency of the on-board system. A practical on-road test is employed to verify vehicle detection (i.e., accuracy) and also the performance of the designed on-board system regarding speed.
Real-time flight conflict detection and release based on Multi-Agent system
Zhang, Yifan; Zhang, Ming; Yu, Jue
2018-01-01
This paper defines two-aircrafts, multi-aircrafts and fleet conflict mode, sets up space-time conflict reservation on the basis of safety interval and conflict warning time in three-dimension. Detect real-time flight conflicts combined with predicted flight trajectory of other aircrafts in the same airspace, and put forward rescue resolutions for the three modes respectively. When accorded with the flight conflict conditions, determine the conflict situation, and enter the corresponding conflict resolution procedures, so as to avoid the conflict independently, as well as ensure the flight safety of aimed aircraft. Lastly, the correctness of model is verified with numerical simulation comparison.
Development of a real-time PCR to detect Demodex canis DNA in different tissue samples.
Ravera, Ivan; Altet, Laura; Francino, Olga; Bardagí, Mar; Sánchez, Armand; Ferrer, Lluís
2011-02-01
The present study reports the development of a real-time polymerase chain reaction (PCR) to detect Demodex canis DNA on different tissue samples. The technique amplifies a 166 bp of D. canis chitin synthase gene (AB 080667) and it has been successfully tested on hairs extracted with their roots and on formalin-fixed paraffin embedded skin biopsies. The real-time PCR amplified on the hairs of all 14 dogs with a firm diagnosis of demodicosis and consistently failed to amplify on negative controls. Eleven of 12 skin biopsies with a morphologic diagnosis of canine demodicosis were also positive. Sampling hairs on two skin points (lateral face and interdigital skin), D. canis DNA was detected on nine of 51 healthy dogs (17.6%) a much higher percentage than previously reported with microscopic studies. Furthermore, it is foreseen that if the number of samples were increased, the percentage of positive dogs would probably also grow. Moreover, in four of the six dogs with demodicosis, the samples taken from non-lesioned skin were positive. This finding, if confirmed in further studies, suggests that demodicosis is a generalized phenomenon in canine skin, due to proliferation of local mite populations, even though macroscopic lesions only appear in certain areas. The real-time PCR technique to detect D. canis DNA described in this work is a useful tool to advance our understanding of canine demodicosis.
Hwang, J Y; Kang, J M; Jang, Y W; Kim, H
2004-01-01
Novel algorithm and real-time ambulatory monitoring system for fall detection in elderly people is described. Our system is comprised of accelerometer, tilt sensor and gyroscope. For real-time monitoring, we used Bluetooth. Accelerometer measures kinetic force, tilt sensor and gyroscope estimates body posture. Also, we suggested algorithm using signals which obtained from the system attached to the chest for fall detection. To evaluate our system and algorithm, we experimented on three people aged over 26 years. The experiment of four cases such as forward fall, backward fall, side fall and sit-stand was repeated ten times and the experiment in daily life activity was performed one time to each subject. These experiments showed that our system and algorithm could distinguish between falling and daily life activity. Moreover, the accuracy of fall detection is 96.7%. Our system is especially adapted for long-time and real-time ambulatory monitoring of elderly people in emergency situation.
Real-time PCR improves Helicobacter pylori detection in patients with peptic ulcer bleeding.
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María José Ramírez-Lázaro
Full Text Available BACKGROUND AND AIMS: Histological and rapid urease tests to detect H. pylori in biopsy specimens obtained during peptic ulcer bleeding episodes (PUB often produce false-negative results. We aimed to examine whether immunohistochemistry and real-time PCR can improve the sensitivity of these biopsies. PATIENTS AND METHODS: We selected 52 histology-negative formalin-fixed paraffin-embedded biopsy specimens obtained during PUB episodes. Additional tests showed 10 were true negatives and 42 were false negatives. We also selected 17 histology-positive biopsy specimens obtained during PUB to use as controls. We performed immunohistochemistry staining and real-time PCR for 16S rRNA, ureA, and 23S rRNA for H. pylori genes on all specimens. RESULTS: All controls were positive for H. pylori on all PCR assays and immunohistochemical staining. Regarding the 52 initially negative biopsies, all PCR tests were significantly more sensitive than immunohistochemical staining (p<0.01. Sensitivity and specificity were 55% and 80% for 16S rRNA PCR, 43% and 90% for ureA PCR, 41% and 80% for 23S rRNA PCR, and 7% and 100% for immunohistochemical staining, respectively. Combined analysis of PCR assays for two genes were significantly more sensitive than ureA or 23S rRNA PCR tests alone (p<0.05 and marginally better than 16S rRNA PCR alone. The best combination was 16S rRNA+ureA, with a sensitivity of 64% and a specificity of 80%. CONCLUSIONS: Real-time PCR improves the detection of H. pylori infection in histology-negative formalin-fixed paraffin-embedded biopsy samples obtained during PUB episodes. The low reported prevalence of H. pylori in PUB may be due to the failure of conventional tests to detect infection.
Development of a real-time quantitative assay for detection of Epstein-Barr virus
Niesters, H. G.; van Esser, J.; Fries, E.; Wolthers, K. C.; Cornelissen, J.; Osterhaus, A. D.
2000-01-01
With the use of real-time PCR, we developed and evaluated a rapid, sensitive, specific, and reproducible method for the detection of Epstein-Barr virus (EBV) DNA in plasma samples. This method allowed us to screen plasma and serum samples over a range between 100 and 10(7) copies of DNA per ml using
Real-time PCR detection of Brucella spp. DNA in lesions and viscera of bovine carcasses.
Sola, Marília Cristina; da Veiga Jardim, Eurione A G; de Freitas, Marcius Ribeiro; de Mesquita, Albenones José
2014-09-01
This study reports a real-time PCR assay for the detection of Brucella spp. associated with the FTA® Elute method in lesions observed during sanitary inspections in beef slaughter. Of the total 276 samples, 78 (28.3%) tested positive and 198 (71.7%) negative for Brucella spp. The real-time PCR technique associated with the FTA® Elute method proved to be an important tool for the diagnosis, judgment about and disposal of carcasses and viscera of slaughtered animals. Copyright © 2014 Elsevier B.V. All rights reserved.
International Nuclear Information System (INIS)
Testa, D.; Carfantan, H.; Fasoli, A.; Goodyear, A.; King, Q.; Blanchard, P.; Klein, A.; Lavanchy, P.; Panis, T.
2011-01-01
We present the real-time VME system used to detect and track MHD instabilities, and particularly Alfven Eigenmodes, on the JET tokamak [J. Wesson, Tokamaks, 3rd ed., Oxford Science Publication, Oxford, 2003, p. 617]. This system runs on a 1 kHz clock cycle, and allows performing a real-time, unsupervised and blind detection, decomposition and tracking of the individual components in a frequency-degenerate, multi-harmonic spectrum, using a small number of input data which are unevenly sampled in the spatial domain. This makes it possible to follow in real-time the detected modes as the plasma background evolves, and measure in real-time their frequency, damping rate, toroidal mode-number and relative amplitude. The successful implementation of this system opens a clear path towards developing real-time control tools for electro-magnetic instabilities in future fusion devices aimed at achieving a net energy gain, such as ITER [J. Wesson, Tokamaks, 3rd ed., Oxford Science Publication, Oxford, 2003, p. 711].
Novel methods of cytokine detection: Real-time PCR, ELISPOT, and intracellular cytokine staining
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Eliza Turlej
2009-05-01
Full Text Available Cytokines are small hormone-like proteins that play important roles in immune system control. Cytokines regulate the proliferation and differentiation of cells and hematopoiesis and act as mediators in the inflammatory reaction. Changes in cytokine levels are found in many diseases, such as sepsis, bowel inflammatory disease, autoimmune diseases, as well as graft-versus-host disease. Cytokines levels can be detected using in vivo, in vitro, and ex vivo techniques. The level of cytokine produced can be measured by immunoenzymatic test (ELISA in supernatant after cell culture with the addition of stimulant and in plasma by techniques that measure the level of cytokine secretion in cells (e.g. immunohistochemical staining, ELISPOT, and intracellular cytokine staining, and by molecular biological methods (RPA, real-time PCR, in situ hybridization, and Northern blot. Detection of cytokine mRNA in tissues is useful in the direct determination of heterogenic populations of cytokine-producing cells. Nowadays the most frequently used methods for measuring cytokine level are ELISPOT, intracellular cytokine staining with flow cytometry detection, and real-time PCR. These methods have an important clinical role in vaccine efficacy, in viral, bacterial, and verminous diagnostics, and in determining the efficacy of cancer treatment.
Real-time instrument-failure detection in the LOFT pressurizer using functional redundancy
International Nuclear Information System (INIS)
Tylee, J.L.
1982-07-01
The functional redundancy approach to detecting instrument failures in a pressurized water reactor (PWR) pressurizer is described and evaluated. This real-time method uses a bank of Kalman filters (one for each instrument) to generate optimal estimates of the pressurizer state. By performing consistency checks between the output of each filter, failed instruments can be identified. Simulation results and actual pressurizer data are used to demonstrate the capabilities of the technique
Advanced real-time manipulation of video streams
Herling, Jan
2014-01-01
Diminished Reality is a new fascinating technology that removes real-world content from live video streams. This sensational live video manipulation actually removes real objects and generates a coherent video stream in real-time. Viewers cannot detect modified content. Existing approaches are restricted to moving objects and static or almost static cameras and do not allow real-time manipulation of video content. Jan Herling presents a new and innovative approach for real-time object removal with arbitrary camera movements.
Ha, Y; Fessehaie, A; Ling, K S; Wechter, W P; Keinath, A P; Walcott, R R
2009-06-01
To improve the simultaneous detection of two pathogens in cucurbit seed, a combination of magnetic capture hybridization (MCH) and multiplex real-time polymerase chain reaction (PCR) was developed. Single-stranded DNA hybridization capture probes targeting DNA of Acidovorax avenae subsp. citrulli, causal agent of bacterial fruit blotch, and Didymella bryoniae, causal agent of gummy stem blight, were covalently attached to magnetic particles and used to selectively concentrate template DNA from cucurbit seed samples. Sequestered template DNAs were subsequently amplified by multiplex real-time PCR using pathogen-specific TaqMan PCR assays. The MCH multiplex real-time PCR assay displayed a detection threshold of A. avenae subsp. citrulli at 10 CFU/ml and D. bryoniae at 10(5) conidia/ml in mixtures of pure cultures of the two pathogens, which was 10-fold more sensitive than the direct real-time PCR assays for the two pathogens separately. Although the direct real-time PCR assay displayed a detection threshold for A. avenae subsp. citrulli DNA of 100 fg/microl in 25% (1/4 samples) of the samples assayed, MCH real-time PCR demonstrated 100% detection frequency (4/4 samples) at the same DNA concentration. MCH did not improve detection sensitivity for D. bryoniae relative to direct real-time PCR using conidial suspensions or seed washes from D. bryoniae-infested cucurbit seed. However, MCH real-time PCR facilitated detection of both target pathogens in watermelon and melon seed samples (n = 5,000 seeds/sample) in which 0.02% of the seed were infested with A. avenae subsp. citrulli and 0.02% were infested with D. bryoniae.
International Nuclear Information System (INIS)
Ma Yingliang; Housden, R. James; Razavi, Reza; Rhode, Kawal S.; Gogin, Nicolas; Cathier, Pascal; Gijsbers, Geert; Cooklin, Michael; O'Neill, Mark; Gill, Jaswinder; Rinaldi, C. Aldo
2013-01-01
Purpose: X-ray fluoroscopically guided cardiac electrophysiology (EP) procedures are commonly carried out to treat patients with arrhythmias. X-ray images have poor soft tissue contrast and, for this reason, overlay of a three-dimensional (3D) roadmap derived from preprocedural volumetric images can be used to add anatomical information. It is useful to know the position of the catheter electrodes relative to the cardiac anatomy, for example, to record ablation therapy locations during atrial fibrillation therapy. Also, the electrode positions of the coronary sinus (CS) catheter or lasso catheter can be used for road map motion correction.Methods: In this paper, the authors present a novel unified computational framework for image-based catheter detection and tracking without any user interaction. The proposed framework includes fast blob detection, shape-constrained searching and model-based detection. In addition, catheter tracking methods were designed based on the customized catheter models input from the detection method. Three real-time detection and tracking methods are derived from the computational framework to detect or track the three most common types of catheters in EP procedures: the ablation catheter, the CS catheter, and the lasso catheter. Since the proposed methods use the same blob detection method to extract key information from x-ray images, the ablation, CS, and lasso catheters can be detected and tracked simultaneously in real-time.Results: The catheter detection methods were tested on 105 different clinical fluoroscopy sequences taken from 31 clinical procedures. Two-dimensional (2D) detection errors of 0.50 ± 0.29, 0.92 ± 0.61, and 0.63 ± 0.45 mm as well as success rates of 99.4%, 97.2%, and 88.9% were achieved for the CS catheter, ablation catheter, and lasso catheter, respectively. With the tracking method, accuracies were increased to 0.45 ± 0.28, 0.64 ± 0.37, and 0.53 ± 0.38 mm and success rates increased to 100%, 99.2%, and 96
Real-time bicycle detection at signalized intersections using thermal imaging technology
Collaert, Robin
2013-02-01
More and more governments and authorities around the world are promoting the use of bicycles in cities, as this is healthy for the bicyclist and improves the quality of life in general. Safety and efficiency of bicyclists has become a major focus. To achieve this, there is a need for a smarter approach towards the control of signalized intersections. Various traditional detection technologies, such as video, microwave radar and electromagnetic loops, can be used to detect vehicles at signalized intersections, but none of these can consistently separate bikes from other traffic, day and night and in various weather conditions. As bikes should get a higher priority and also require longer green time to safely cross the signalized intersection, traffic managers are looking for alternative detection systems that can make the distinction between bicycles and other vehicles near the stop bar. In this paper, the drawbacks of a video-based approach are presented, next to the benefits of a thermal-video-based approach for vehicle presence detection with separation of bicycles. Also, the specific technical challenges are highlighted in developing a system that combines thermal image capturing, image processing and output triggering to the traffic light controller in near real-time and in a single housing.
A generic method for real time detection of magnetic sensor failure on tokamaks
International Nuclear Information System (INIS)
Nouailletas, Rémy; Moreau, Philippe; Bremond, Sylvain
2012-01-01
Highlights: ► We propose a generic method to detect and correct in real time faults on magnetic sensor. ► This method is applied to Tore Supra and tested offline with real data. ► Then the method is modified to be applied to ITER ex-vessel sensor configuration. ► The method is tested on the ITER case with simulated data. - Abstract: In tokamaks, magnetic field probe sensors are used to measure the plasma position. If a sensor provides a wrong data, the error may propagate through the control loop and cause undesirable contact between the vessel wall and the plasma. In the case of a tokamak with water cooled walls, these types of event may be very serious. Despite of these unlikely faults, the potential damages call for a real time check of magnetic sensor data before using them for control. In this paper a simple and generic method based on the comparison of each sensor to a weighted sum of its neighbors is proposed. From the analysis of the residue (the result of the comparison), the fault can be detected and compensated. The method is tuned and tested against Tore Supra experimental data. Then, the method is adapted to ITER and assessed on a reference ITER scenario using simulated magnetic sensor data.
Pick- and waveform-based techniques for real-time detection of induced seismicity
Grigoli, Francesco; Scarabello, Luca; Böse, Maren; Weber, Bernd; Wiemer, Stefan; Clinton, John F.
2018-05-01
The monitoring of induced seismicity is a common operation in many industrial activities, such as conventional and non-conventional hydrocarbon production or mining and geothermal energy exploitation, to cite a few. During such operations, we generally collect very large and strongly noise-contaminated data sets that require robust and automated analysis procedures. Induced seismicity data sets are often characterized by sequences of multiple events with short interevent times or overlapping events; in these cases, pick-based location methods may struggle to correctly assign picks to phases and events, and errors can lead to missed detections and/or reduced location resolution and incorrect magnitudes, which can have significant consequences if real-time seismicity information are used for risk assessment frameworks. To overcome these issues, different waveform-based methods for the detection and location of microseismicity have been proposed. The main advantages of waveform-based methods is that they appear to perform better and can simultaneously detect and locate seismic events providing high-quality locations in a single step, while the main disadvantage is that they are computationally expensive. Although these methods have been applied to different induced seismicity data sets, an extensive comparison with sophisticated pick-based detection methods is still missing. In this work, we introduce our improved waveform-based detector and we compare its performance with two pick-based detectors implemented within the SeiscomP3 software suite. We test the performance of these three approaches with both synthetic and real data sets related to the induced seismicity sequence at the deep geothermal project in the vicinity of the city of St. Gallen, Switzerland.
Optical sensor for real-time weld defect detection
Ancona, Antonio; Maggipinto, Tommaso; Spagnolo, Vincenzo; Ferrara, Michele; Lugara, Pietro M.
2002-04-01
In this work we present an innovative optical sensor for on- line and non-intrusive welding process monitoring. It is based on the spectroscopic analysis of the optical VIS emission of the welding plasma plume generated in the laser- metal interaction zone. Plasma electron temperature has been measured for different chemical species composing the plume. Temperature signal evolution has been recorded and analyzed during several CO2-laser welding processes, under variable operating conditions. We have developed a suitable software able to real time detect a wide range of weld defects like crater formation, lack of fusion, excessive penetration, seam oxidation. The same spectroscopic approach has been applied for electric arc welding process monitoring. We assembled our optical sensor in a torch for manual Gas Tungsten Arc Welding procedures and tested the prototype in a manufacturing industry production line. Even in this case we found a clear correlation between the signal behavior and the welded joint quality.
Directory of Open Access Journals (Sweden)
Maurice Marcel Sandeu
Full Text Available BACKGROUND: An accurate method for detecting malaria parasites in the mosquito's vector remains an essential component in the vector control. The Enzyme linked immunosorbent assay specific for circumsporozoite protein (ELISA-CSP is the gold standard method for the detection of malaria parasites in the vector even if it presents some limitations. Here, we optimized multiplex real-time PCR assays to accurately detect minor populations in mixed infection with multiple Plasmodium species in the African malaria vectors Anopheles gambiae and Anopheles funestus. METHODS: Complementary TaqMan-based real-time PCR assays that detect Plasmodium species using specific primers and probes were first evaluated on artificial mixtures of different targets inserted in plasmid constructs. The assays were further validated in comparison with the ELISA-CSP on 200 field caught Anopheles gambiae and Anopheles funestus mosquitoes collected in two localities in southern Benin. RESULTS: The validation of the duplex real-time PCR assays on the plasmid mixtures demonstrated robust specificity and sensitivity for detecting distinct targets. Using a panel of mosquito specimen, the real-time PCR showed a relatively high sensitivity (88.6% and specificity (98%, compared to ELISA-CSP as the referent standard. The agreement between both methods was "excellent" (κ=0.8, P<0.05. The relative quantification of Plasmodium DNA between the two Anopheles species analyzed showed no significant difference (P=0, 2. All infected mosquito samples contained Plasmodium falciparum DNA and mixed infections with P. malariae and/or P. ovale were observed in 18.6% and 13.6% of An. gambiae and An. funestus respectively. Plasmodium vivax was found in none of the mosquito samples analyzed. CONCLUSION: This study presents an optimized method for detecting the four Plasmodium species in the African malaria vectors. The study highlights substantial discordance with traditional ELISA-CSP pointing out the
Young, Sean D; Rivers, Caitlin; Lewis, Bryan
2014-06-01
Recent availability of "big data" might be used to study whether and how sexual risk behaviors are communicated on real-time social networking sites and how data might inform HIV prevention and detection. This study seeks to establish methods of using real-time social networking data for HIV prevention by assessing 1) whether geolocated conversations about HIV risk behaviors can be extracted from social networking data, 2) the prevalence and content of these conversations, and 3) the feasibility of using HIV risk-related real-time social media conversations as a method to detect HIV outcomes. In 2012, tweets (N=553,186,061) were collected online and filtered to include those with HIV risk-related keywords (e.g., sexual behaviors and drug use). Data were merged with AIDSVU data on HIV cases. Negative binomial regressions assessed the relationship between HIV risk tweeting and prevalence by county, controlling for socioeconomic status measures. Over 9800 geolocated tweets were extracted and used to create a map displaying the geographical location of HIV-related tweets. There was a significant positive relationship (psocial networking data as a method for evaluating and detecting Human immunodeficiency virus (HIV) risk behaviors and outcomes. Copyright © 2014 Elsevier Inc. All rights reserved.
Shrivastava, Sajal; Sohn, Il-Yung; Son, Young-Min; Lee, Won-Il; Lee, Nae-Eung
2015-11-01
Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules.Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (r
DEFF Research Database (Denmark)
Kertzscher Schwencke, Gustavo Adolfo Vladimir; Andersen, Claus E.; Tanderup, Kari
2014-01-01
Purpose:This study presents an adaptive error detection algorithm (AEDA) for real-timein vivo point dosimetry during high dose rate (HDR) or pulsed dose rate (PDR) brachytherapy (BT) where the error identification, in contrast to existing approaches, does not depend on an a priori reconstruction ......, and the AEDA’s capacity to distinguish between true and false error scenarios. The study further shows that the AEDA can offer guidance in decision making in the event of potential errors detected with real-time in vivo point dosimetry....... of the dosimeter position reconstruction. Given its nearly exclusive dependence on stable dosimeter positioning, the AEDA allows for a substantially simplified and time efficient real-time in vivo BT dosimetry implementation. Methods:In the event of a measured potential treatment error, the AEDA proposes the most...
Leach, L; Zhu, Y; Chaturvedi, S
2018-02-01
Candida auris is an emerging multidrug-resistant yeast causing invasive health care-associated infection with high mortality worldwide. Rapid identification of C. auris is of primary importance for the implementation of public health measures to control the spread of infection. To achieve these goals, we developed and validated a TaqMan-based real-time PCR assay targeting the internal transcribed spacer 2 ( ITS 2) region of the ribosomal gene. The assay was highly specific, reproducible, and sensitive, with the detection limit of 1 C. auris CFU/PCR. The performance of the C. auris real-time PCR assay was evaluated by using 623 surveillance samples, including 365 patient swabs and 258 environmental sponges. Real-time PCR yielded positive results from 49 swab and 58 sponge samples, with 89% and 100% clinical sensitivity with regard to their respective culture-positive results. The real-time PCR also detected C. auris DNA from 1% and 12% of swab and sponge samples with culture-negative results, indicating the presence of dead or culture-impaired C. auris The real-time PCR yielded results within 4 h of sample processing, compared to 4 to 14 days for culture, reducing turnaround time significantly. The new real-time PCR assay allows for accurate and rapid screening of C. auris and can increase effective control and prevention of this emerging multidrug-resistant fungal pathogen in health care facilities. Copyright © 2018 Leach et al.
Real-time detection of natural objects using AM-coded spectral matching imager
Kimachi, Akira
2005-01-01
This paper describes application of the amplitude-modulation (AM)-coded spectral matching imager (SMI) to real-time detection of natural objects such as human beings, animals, vegetables, or geological objects or phenomena, which are much more liable to change with time than artificial products while often exhibiting characteristic spectral functions associated with some specific activity states. The AM-SMI produces correlation between spectral functions of the object and a reference at each pixel of the correlation image sensor (CIS) in every frame, based on orthogonal amplitude modulation (AM) of each spectral channel and simultaneous demodulation of all channels on the CIS. This principle makes the SMI suitable to monitoring dynamic behavior of natural objects in real-time by looking at a particular spectral reflectance or transmittance function. A twelve-channel multispectral light source was developed with improved spatial uniformity of spectral irradiance compared to a previous one. Experimental results of spectral matching imaging of human skin and vegetable leaves are demonstrated, as well as a preliminary feasibility test of imaging a reflective object using a test color chart.
International Nuclear Information System (INIS)
Mendell, D.S.
1978-01-01
This paper describes the basic design and philosophy of a real-time, interferometer phase-detection system used on the 2XIIB and TMX magnetic-fusion experiments at the Lawrence Livermore Laboratory. This diagnostics system is now a satellite to a host computer and uses high-speed, emitter-coupled logic techniques to derive data on real-time phase relationships. The system's input signals can be derived from interferometer outputs over a wide range of reference frequencies. An LSI-11 microcomputer is the interface between the high-speed phase-detection logic, buffer memory, human interaction, and host computer. Phase data on a storage CRT is immediately displayed after each experimental fusion shot. An operator can interrogate this phase data more closely from an interactive control panel, while the host computer is simultaneously examining the system's buffer memory or arming the system for the next shot
Stachelska, M A
2017-09-26
The aim of the present study was to establish a rapid and accurate real-time PCR method to detect pathogenic Yersinia enterocolitica in pork. Yersinia enterocolitica is considered to be a crucial zoonosis, which can provoke diseases both in humans and animals. The classical culture methods designated to detect Y. enterocolitica species in food matrices are often very time-consuming. The chromosomal locus _tag CH49_3099 gene, that appears in pathogenic Y. enterocolitica strains, was applied as DNA target for the 5' nuclease PCR protocol. The probe was labelled at the 5' end with the fluorescent reporter dye (FAM) and at the 3' end with the quencher dye (TAMRA). The real-time PCR cycling parameters included 41 cycles. A Ct value which reached a value higher than 40 constituted a negative result. The developed for the needs of this study qualitative real-time PCR method appeared to give very specific and reliable results. The detection rate of locus _tag CH49_3099 - positive Y. enterocolitica in 150 pig tonsils was 85 % and 32 % with PCR and culture methods, respectively. Both the Real-time PCR results and culture method results were obtained from material that was enriched during overnight incubation. The subject of the study were also raw pork meat samples. Among 80 samples examined, 7 ones were positive when real-time PCR was applied, and 6 ones were positive when classical culture method was applied. The application of molecular techniques based on the analysis of DNA sequences such as the Real-time PCR enables to detect this pathogenic bacteria very rapidly and with higher specificity, sensitivity and reliability in comparison to classical culture methods.
Radioactive aerosol detection station for near real-time atmospheric monitoring
International Nuclear Information System (INIS)
Mason, L.R.; Bohner, John D.
1997-01-01
A radionuclide aerosol detection station has been developed to measure radioactivity in the environment. The objective is to monitor the atmosphere for anthropogenic radioactivity that could be indicative of nuclear weapons tests to verify the Comprehensive Nuclear Test Ban Treaty. Eighty stations will form the backbone of the International Monitoring System in which stations are linked to a central analysis facility called the International Data Centre. Data are transmitted to this centre in near real-time to facilitate rapid detection. Principal process of the field measurement are collection, separation, and assay. Collection of airborne radioactivity is achieved through high-volume air sampling. Aerosols separation is accomplished by high-efficiency particulate filtration. Radionuclides assay is achieved by in-situ high resolution gamma spectrometry. These modules are integrated into a unit that provides power, control, and communication support subsystems. Station operation is semi-automatic requiring only minimal human interaction. (author). 6 refs., 3 figs., 3 tabs
International Nuclear Information System (INIS)
Saba, V.; Setayeshi, S.; Ghannadi-Maragheh, M.
2011-01-01
We have developed an algorithm for real-time detection and complete correction of the patient motion effects during single photon emission computed tomography. The algorithm is based on a linear prediction filter (LPC). The new prediction of projection data algorithm (PPDA) detects most motions-such as those of the head, legs, and hands-using comparison of the predicted and measured frame data. When the data acquisition for a specific frame is completed, the accuracy of the acquired data is evaluated by the PPDA. If patient motion is detected, the scanning procedure is stopped. After the patient rests in his or her true position, data acquisition is repeated only for the corrupted frame and the scanning procedure is continued. Various experimental data were used to validate the motion detection algorithm; on the whole, the proposed method was tested with approximately 100 test cases. The PPDA shows promising results. Using the PPDA enables us to prevent the scanner from collecting disturbed data during the scan and replaces them with motion-free data by real-time rescanning for the corrupted frames. As a result, the effects of patient motion is corrected in real time. (author)
Springer, Jan; Goldenberger, Daniel; Schmidt, Friderike; Weisser, Maja; Wehrle-Wieland, Elisabeth; Einsele, Hermann; Frei, Reno; Löffler, Jürgen
2016-03-01
PCR-based detection of Mucorales species could improve diagnosis of suspected invasive fungal infection, leading to a better patient outcome. This study describes two independent probe-based real-time PCR tests for detection of clinically relevant Mucorales, targeting specific fragments of the 18S and the 28S rRNA genes. Both assays have a short turnaround time, allow fast, specific and very sensitive detection of clinically relevant Mucorales and have the potential to be used as quantitative tests. They were validated on various clinical samples (fresh and formalin-fixed paraffin-embedded specimens, mainly biopsies, n = 17). The assays should be used as add-on tools to complement standard techniques; a combined approach of both real-time PCR assays has 100 % sensitivity. Genus identification by subsequent sequencing is possible for amplicons of the 18S PCR assay. In conclusion, combination of the two independent Mucorales assays described in this study, 18S and 28S, detected all clinical samples associated with proven Mucorales infection (n = 10). Reliable and specific identification of Mucorales is a prerequisite for successful antifungal therapy as these fungi show intrinsic resistance to voriconazole and caspofungin.
A MIQE-compliant real-time PCR assay for Aspergillus detection.
Directory of Open Access Journals (Sweden)
Gemma L Johnson
Full Text Available The polymerase chain reaction (PCR is widely used as a diagnostic tool in clinical laboratories and is particularly effective for detecting and identifying infectious agents for which routine culture and microscopy methods are inadequate. Invasive fungal disease (IFD is a major cause of morbidity and mortality in immunosuppressed patients, and optimal diagnostic criteria are contentious. Although PCR-based methods have long been used for the diagnosis of invasive aspergillosis (IA, variable performance in clinical practice has limited their value. This shortcoming is a consequence of differing sample selection, collection and preparation protocols coupled with a lack of standardisation of the PCR itself. Furthermore, it has become clear that the performance of PCR-based assays in general is compromised by the inadequacy of experimental controls, insufficient optimisation of assay performance as well as lack of transparency in reporting experimental details. The recently published "Minimum Information for the publication of real-time Quantitative PCR Experiments" (MIQE guidelines provide a blueprint for good PCR assay design and unambiguous reporting of experimental detail and results. We report the first real-time quantitative PCR (qPCR assay targeting Aspergillus species that has been designed, optimised and validated in strict compliance with the MIQE guidelines. The hydrolysis probe-based assay, designed to target the 18S rRNA DNA sequence of Aspergillus species, has an efficiency of 100% (range 95-107%, a dynamic range of at least six orders of magnitude and limits of quantification and detection of 6 and 0.6 Aspergillus fumigatus genomes, respectively. It does not amplify Candida, Scedosporium, Fusarium or Rhizopus species and its clinical sensitivity is demonstrated in histological material from proven IA cases, as well as concordant PCR and galactomannan data in matched broncho-alveolar lavage and blood samples. The robustness
Ferreira, HL; Spilki, FR; dos Santos, MMAB; de Almeida, RS; Arns, CW
2009-01-01
Avian metapneumovirus (AMPV) belongs to Metapneumovirus genus of Paramyxoviridae family. Virus isolation, serology, and detection of genomic RNA are used as diagnostic methods for AMPV. The aim of the present study was to compare the detection of six subgroup A AMPV isolates (AMPV/A) viral RNA by using different conventional and real time RT-PCR methods. Two new RT-PCR tests and two real time RT-PCR tests, both detecting fusion (F) gene and nucleocapsid (N) gene were compared with an establis...
First Real-Time Detection of Surface Dust in a Tokamak
International Nuclear Information System (INIS)
Skinner, C.; Rais, B.; Roquemore, A.L.; Kugel, H.W.; Marsala, R.; Provost, T.
2010-01-01
The first real-time detection of surface dust inside a tokamak was made using an electrostatic dust detector. A fine grid of interlocking circuit traces was installed in the NSTX vessel and biased to 50 v. Impinging dust particles created a temporary short circuit and the resulting current pulse was recorded by counting electronics. The techniques used to increase the detector sensitivity by a factor of x10,000 to match NSTX dust levels while suppressing electrical pickup are presented. The results were validated by comparison to lab measurements, by the null signal from a covered detector that was only sensitive to pickup, and by the dramatic increase in signal when Li particles were introduced for wall conditioning purposes.
Real-time pose invariant logo and pattern detection
Sidla, Oliver; Kottmann, Michal; Benesova, Wanda
2011-01-01
The detection of pose invariant planar patterns has many practical applications in computer vision and surveillance systems. The recognition of company logos is used in market studies to examine the visibility and frequency of logos in advertisement. Danger signs on vehicles could be detected to trigger warning systems in tunnels, or brand detection on transport vehicles can be used to count company-specific traffic. We present the results of a study on planar pattern detection which is based on keypoint detection and matching of distortion invariant 2d feature descriptors. Specifically we look at the keypoint detectors of type: i) Lowe's DoG approximation from the SURF algorithm, ii) the Harris Corner Detector, iii) the FAST Corner Detector and iv) Lepetit's keypoint detector. Our study then compares the feature descriptors SURF and compact signatures based on Random Ferns: we use 3 sets of sample images to detect and match 3 logos of different structure to find out which combinations of keypoint detector/feature descriptors work well. A real-world test tries to detect vehicles with a distinctive logo in an outdoor environment under realistic lighting and weather conditions: a camera was mounted on a suitable location for observing the entrance to a parking area so that incoming vehicles could be monitored. In this 2 hour long recording we can successfully detect a specific company logo without false positives.
Development of real-time PCR for detection of Mycoplasma hominis
DEFF Research Database (Denmark)
Baczynska, A.; Svenstrup, Helle Friis; Fedder, J.
2004-01-01
BACKGROUND: Mycoplasma hominis is associated with pelvic inflammatory disease, bacterial vaginosis, post partum fever, sepsis and infections of the central nervous system often leading to serious conditions. Association with development of female infertility has also been suggested, but different....... Information on bacterial load in genital swabs can be obtained. The assay allowed detection of M. hominis in a closed system reducing the risk of contamination by amplicon carry-over......., glyceraldehyde-3-phosphate dehydrogenase (gap), as a target. RESULTS: Real-time PCR was optimized to detect 10 copies of M. hominis PG21 genomic DNA. A fluorescence signal was measured for all 20 other M. hominis isolates, and melting curves analysis showed variations in the melting temperature in agreement...
Real-time portable system for fabric defect detection using an ARM processor
Fernandez-Gallego, J. A.; Yañez-Puentes, J. P.; Ortiz-Jaramillo, B.; Alvarez, J.; Orjuela-Vargas, S. A.; Philips, W.
2012-06-01
Modern textile industry seeks to produce textiles as little defective as possible since the presence of defects can decrease the final price of products from 45% to 65%. Automated visual inspection (AVI) systems, based on image analysis, have become an important alternative for replacing traditional inspections methods that involve human tasks. An AVI system gives the advantage of repeatability when implemented within defined constrains, offering more objective and reliable results for particular tasks than human inspection. Costs of automated inspection systems development can be reduced using modular solutions with embedded systems, in which an important advantage is the low energy consumption. Among the possibilities for developing embedded systems, the ARM processor has been explored for acquisition, monitoring and simple signal processing tasks. In a recent approach we have explored the use of the ARM processor for defects detection by implementing the wavelet transform. However, the computation speed of the preprocessing was not yet sufficient for real time applications. In this approach we significantly improve the preprocessing speed of the algorithm, by optimizing matrix operations, such that it is adequate for a real time application. The system was tested for defect detection using different defect types. The paper is focused in giving a detailed description of the basis of the algorithm implementation, such that other algorithms may use of the ARM operations for fast implementations.
ICARES: a real-time automated detection tool for clusters of infectious diseases in the Netherlands.
Groeneveld, Geert H; Dalhuijsen, Anton; Kara-Zaïtri, Chakib; Hamilton, Bob; de Waal, Margot W; van Dissel, Jaap T; van Steenbergen, Jim E
2017-01-01
Clusters of infectious diseases are frequently detected late. Real-time, detailed information about an evolving cluster and possible associated conditions is essential for local policy makers, travelers planning to visit the area, and the local population. This is currently illustrated in the Zika
Partial validation of a TaqMan real-time quantitative PCR for the detection of ranaviruses
DEFF Research Database (Denmark)
Stilwell, Natalie K.; Whittington, Richard J.; Hick, Paul M.
2018-01-01
Ranaviruses are globally emerging pathogens negatively impacting wild and cultured fish, amphibians, and reptiles. Although conventional and diagnostic real-time PCR (qPCR) assays have been developed to detect ranaviruses, these assays often have not been tested against the known diversity of ran...
Scheutz, Flemming; Lund, Ole; Hasman, Henrik; Kaas, Rolf S.; Nielsen, Eva M.; Aarestrup, Frank M.
2014-01-01
Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-producing Escherichia coli (VTEC). In Denmark, the Statens Serum Institut (SSI) routinely receives all suspected VTEC isolates. During a 7-week period in the fall of 2012, all incoming isolates were concurrently subjected to WGS using IonTorrent PGM. Real-time bioinformatics analysis was performed using web-tools (www.genomicepidemiology.org) for species determination, multilocus sequence type (MLST) typing, and determination of phylogenetic relationship, and a specific VirulenceFinder for detection of E. coli virulence genes was developed as part of this study. In total, 46 suspected VTEC isolates were characterized in parallel during the study. VirulenceFinder proved successful in detecting virulence genes included in routine typing, explicitly verocytotoxin 1 (vtx1), verocytotoxin 2 (vtx2), and intimin (eae), and also detected additional virulence genes. VirulenceFinder is also a robust method for assigning verocytotoxin (vtx) subtypes. A real-time clustering of isolates in agreement with the epidemiology was established from WGS, enabling discrimination between sporadic and outbreak isolates. Overall, WGS typing produced results faster and at a lower cost than the current routine. Therefore, WGS typing is a superior alternative to conventional typing strategies. This approach may also be applied to typing and surveillance of other pathogens. PMID:24574290
Joensen, Katrine Grimstrup; Scheutz, Flemming; Lund, Ole; Hasman, Henrik; Kaas, Rolf S; Nielsen, Eva M; Aarestrup, Frank M
2014-05-01
Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-producing Escherichia coli (VTEC). In Denmark, the Statens Serum Institut (SSI) routinely receives all suspected VTEC isolates. During a 7-week period in the fall of 2012, all incoming isolates were concurrently subjected to WGS using IonTorrent PGM. Real-time bioinformatics analysis was performed using web-tools (www.genomicepidemiology.org) for species determination, multilocus sequence type (MLST) typing, and determination of phylogenetic relationship, and a specific VirulenceFinder for detection of E. coli virulence genes was developed as part of this study. In total, 46 suspected VTEC isolates were characterized in parallel during the study. VirulenceFinder proved successful in detecting virulence genes included in routine typing, explicitly verocytotoxin 1 (vtx1), verocytotoxin 2 (vtx2), and intimin (eae), and also detected additional virulence genes. VirulenceFinder is also a robust method for assigning verocytotoxin (vtx) subtypes. A real-time clustering of isolates in agreement with the epidemiology was established from WGS, enabling discrimination between sporadic and outbreak isolates. Overall, WGS typing produced results faster and at a lower cost than the current routine. Therefore, WGS typing is a superior alternative to conventional typing strategies. This approach may also be applied to typing and surveillance of other pathogens.
Real-time radiography at the NECTAR facility
International Nuclear Information System (INIS)
Buecherl, T.; Lierse von Gostomski, Ch.
2011-01-01
A feasibility study has shown that real-time radiography using fission neutrons is possible at the NECTAR facility, when using an improved detection system for fast variations (Buecherl et al., 2009 ). Continuing this study, real-time measurements of slowly varying processes like the water uptake in medium sized trunks (diameter about 12 cm) and of slow periodic processes (e.g. a slowly rotating iron disk) are investigated successfully using the existing detection system.
Real-time radiography at the NECTAR facility
Bücherl, T.; Lierse von Gostomski, Ch.
2011-09-01
A feasibility study has shown that real-time radiography using fission neutrons is possible at the NECTAR facility, when using an improved detection system for fast variations (Bücherl et al., 2009 [1]). Continuing this study, real-time measurements of slowly varying processes like the water uptake in medium sized trunks (diameter about 12 cm) and of slow periodic processes (e.g. a slowly rotating iron disk) are investigated successfully using the existing detection system.
Real-time radiography at the NECTAR facility
Energy Technology Data Exchange (ETDEWEB)
Buecherl, T., E-mail: thomas.buecherl@radiochemie.de [Lehrstuhl fuer Radiochemie (RCM), Technische Universitaet Muenchen (TUM), Walther-Meissner-Str. 3, 85748 Garching (Germany); Lierse von Gostomski, Ch. [Lehrstuhl fuer Radiochemie (RCM), Technische Universitaet Muenchen (TUM), Walther-Meissner-Str. 3, 85748 Garching (Germany)
2011-09-21
A feasibility study has shown that real-time radiography using fission neutrons is possible at the NECTAR facility, when using an improved detection system for fast variations (Buecherl et al., 2009 ). Continuing this study, real-time measurements of slowly varying processes like the water uptake in medium sized trunks (diameter about 12 cm) and of slow periodic processes (e.g. a slowly rotating iron disk) are investigated successfully using the existing detection system.
International Nuclear Information System (INIS)
Wu, Lingfei; Wu, Kesheng; Sim, Alex; Churchill, Michael; Choi, Jong Youl
2016-01-01
A novel algorithm and implementation of real-time identification and tracking of blob-filaments in fusion reactor data is presented. Similar spatio-temporal features are important in many other applications, for example, ignition kernels in combustion and tumor cells in a medical image. This work presents an approach for extracting these features by dividing the overall task into three steps: local identification of feature cells, grouping feature cells into extended feature, and tracking movement of feature through overlapping in space. Through our extensive work in parallelization, we demonstrate that this approach can effectively make use of a large number of compute nodes to detect and track blob-filaments in real time in fusion plasma. Here, on a set of 30GB fusion simulation data, we observed linear speedup on 1024 processes and completed blob detection in less than three milliseconds using Edison, a Cray XC30 system at NERSC.
Alidjinou, Enagnon Kazali; Sane, Famara; Lefevre, Christine; Baras, Agathe; Moumna, Ilham; Engelmann, Ilka; Vantyghem, Marie-Christine; Hober, Didier
2017-11-01
Enteroviruses (EV) have been associated with type 1 diabetes (T1D), but EV RNA detection has been reported in only a small proportion of T1D patients. We studied whether integrated cell culture and reverse transcription real-time PCR could improve EV detection in blood samples from patients with T1D. Blood was collected from 13 patients with T1D. The presence of EV RNA in blood was investigated by using real-time RT-PCR. In addition, plasma and white blood cells (WBC) were inoculated to BGM and Vero cell line cultures. Culture supernatants and cells collected on day 7 and day 14 were tested for EV RNA by real-time RT-PCR. Enterovirus identification was performed through sequencing of the VP4/VP2 region. Enterovirus RNA was detected in blood by using real-time RT-PCR in only one out of 13 patients. The detection of EV RNA in cultures inoculated with clinical samples (plasma and/or WBC) gave positive results in five other patients. The viral loads were low, ranging from 45 to 4420 copies/ng of total RNA. One isolate was successfully identified as coxsackievirus B1. Integrated cell culture and reverse transcription real-time PCR can improve the detection rate of EV in blood samples of patients with T1D and can be useful to investigate further the relationship between EV and the disease.
Near-infrared high-resolution real-time omnidirectional imaging platform for drone detection
Popovic, Vladan; Ott, Beat; Wellig, Peter; Leblebici, Yusuf
2016-10-01
Recent technological advancements in hardware systems have made higher quality cameras. State of the art panoramic systems use them to produce videos with a resolution of 9000 x 2400 pixels at a rate of 30 frames per second (fps).1 Many modern applications use object tracking to determine the speed and the path taken by each object moving through a scene. The detection requires detailed pixel analysis between two frames. In fields like surveillance systems or crowd analysis, this must be achieved in real time.2 In this paper, we focus on the system-level design of multi-camera sensor acquiring near-infrared (NIR) spectrum and its ability to detect mini-UAVs in a representative rural Swiss environment. The presented results show the UAV detection from the trial that we conducted during a field trial in August 2015.
Directory of Open Access Journals (Sweden)
Sundeok Kwon
2018-06-01
Full Text Available Many healthcare problems are life threatening and need real-time detection to improve patient safety. Heart attack or ventricular fibrillation (VF is a common problem worldwide. Most previous research on VF detection has used ECG devices to capture data and sent to other higher performance units for processing and has relied on domain experts and/or sophisticated algorithms for detection. In this case, it delayed the response time and consumed much more energy of the ECG module. In this study, we propose a prototype that an embedded microcontroller where an ECG sensor is used to capture, filter and process data, run VF detection algorithms, and only transmit the detected event to the smartphone for alert and call for services. We discuss how to adapt a common filtering and scale process and five light-weighted algorithms from open literature to realize the idea. We also develop an integrated prototype, which emulates the VF process from existing data sets, to evaluate the detection capability of the framework and algorithms. Our results show that (1 TD outperforms the other four algorithms considered with sensitivity reaching 96.56% and specificity reaching 81.53% in the MIT-BIH dataset. Our evaluations confirm that with some adaptation the conventional filtering process and detection algorithms can be efficiently deployed in a microcontroller with good detection accuracy while saving battery power, shortening response time, and conserving the network bandwidth.
2015-06-01
CONFABULATION BASED REAL-TIME ANOMALY DETECTION FOR WIDE-AREA SURVEILLANCE USING HETEROGENEOUS HIGH PERFORMANCE COMPUTING ARCHITECTURE SYRACUSE...DETECTION FOR WIDE-AREA SURVEILLANCE USING HETEROGENEOUS HIGH PERFORMANCE COMPUTING ARCHITECTURE 5a. CONTRACT NUMBER FA8750-12-1-0251 5b. GRANT...processors including graphic processor units (GPUs) and Intel Xeon Phi processors. Experimental results showed significant speedups, which can enable
A method for real-time memory efficient implementation of blob detection in large images
Directory of Open Access Journals (Sweden)
Petrović Vladimir L.
2017-01-01
Full Text Available In this paper we propose a method for real-time blob detection in large images with low memory cost. The method is suitable for implementation on the specialized parallel hardware such as multi-core platforms, FPGA and ASIC. It uses parallelism to speed-up the blob detection. The input image is divided into blocks of equal sizes to which the maximally stable extremal regions (MSER blob detector is applied in parallel. We propose the usage of multiresolution analysis for detection of large blobs which are not detected by processing the small blocks. This method can find its place in many applications such as medical imaging, text recognition, as well as video surveillance or wide area motion imagery (WAMI. We explored the possibilities of usage of detected blobs in the feature-based image alignment as well. When large images are processed, our approach is 10 to over 20 times more memory efficient than the state of the art hardware implementation of the MSER.
Mao, Weihua; Riaz, Nadeem; Lee, Louis; Wiersma, Rodney; Xing, Lei
2008-08-01
The advantage of highly conformal dose techniques such as 3DCRT and IMRT is limited by intrafraction organ motion. A new approach to gain near real-time 3D positions of internally implanted fiducial markers is to analyze simultaneous onboard kV beam and treatment MV beam images (from fluoroscopic or electronic portal image devices). Before we can use this real-time image guidance for clinical 3DCRT and IMRT treatments, four outstanding issues need to be addressed. (1) How will fiducial motion blur the image and hinder tracking fiducials? kV and MV images are acquired while the tumor is moving at various speeds. We find that a fiducial can be successfully detected at a maximum linear speed of 1.6 cm/s. (2) How does MV beam scattering affect kV imaging? We investigate this by varying MV field size and kV source to imager distance, and find that common treatment MV beams do not hinder fiducial detection in simultaneous kV images. (3) How can one detect fiducials on images from 3DCRT and IMRT treatment beams when the MV fields are modified by a multileaf collimator (MLC)? The presented analysis is capable of segmenting a MV field from the blocking MLC and detecting visible fiducials. This enables the calculation of nearly real-time 3D positions of markers during a real treatment. (4) Is the analysis fast enough to track fiducials in nearly real time? Multiple methods are adopted to predict marker positions and reduce search regions. The average detection time per frame for three markers in a 1024 x 768 image was reduced to 0.1 s or less. Solving these four issues paves the way to tracking moving fiducial markers throughout a 3DCRT or IMRT treatment. Altogether, these four studies demonstrate that our algorithm can track fiducials in real time, on degraded kV images (MV scatter), in rapidly moving tumors (fiducial blurring), and even provide useful information in the case when some fiducials are blocked from view by the MLC. This technique can provide a gating signal or
A method for accurate detection of genomic microdeletions using real-time quantitative PCR
Directory of Open Access Journals (Sweden)
Bassett Anne S
2005-12-01
Full Text Available Abstract Background Quantitative Polymerase Chain Reaction (qPCR is a well-established method for quantifying levels of gene expression, but has not been routinely applied to the detection of constitutional copy number alterations of human genomic DNA. Microdeletions or microduplications of the human genome are associated with a variety of genetic disorders. Although, clinical laboratories routinely use fluorescence in situ hybridization (FISH to identify such cryptic genomic alterations, there remains a significant number of individuals in which constitutional genomic imbalance is suspected, based on clinical parameters, but cannot be readily detected using current cytogenetic techniques. Results In this study, a novel application for real-time qPCR is presented that can be used to reproducibly detect chromosomal microdeletions and microduplications. This approach was applied to DNA from a series of patient samples and controls to validate genomic copy number alteration at cytoband 22q11. The study group comprised 12 patients with clinical symptoms of chromosome 22q11 deletion syndrome (22q11DS, 1 patient trisomic for 22q11 and 4 normal controls. 6 of the patients (group 1 had known hemizygous deletions, as detected by standard diagnostic FISH, whilst the remaining 6 patients (group 2 were classified as 22q11DS negative using the clinical FISH assay. Screening of the patients and controls with a set of 10 real time qPCR primers, spanning the 22q11.2-deleted region and flanking sequence, confirmed the FISH assay results for all patients with 100% concordance. Moreover, this qPCR enabled a refinement of the region of deletion at 22q11. Analysis of DNA from chromosome 22 trisomic sample demonstrated genomic duplication within 22q11. Conclusion In this paper we present a qPCR approach for the detection of chromosomal microdeletions and microduplications. The strategic use of in silico modelling for qPCR primer design to avoid regions of repetitive
Sabrina, Rabehi; Mossadak, Hamdi Taha; Bakir, Mamache; Asma, Meghezzi; Khaoula, Boushaba
2018-01-01
Aim: The aim of this study was to detect Brucella spp. DNA in milk samples collected from seronegative cows using the real-time polymerase chain reaction (PCR) assay for diagnosis of brucellosis in seronegative dairy cows to prevent transmission of disease to humans and to reduce economic losses in animal production. Materials and Methods: In this study, 65 milk samples were investigated for the detection of Brucella spp. The detection of the IS711 gene in all samples was done by real-time PCR assay by comparative cycle threshold method. Results: The results show that of the 65 DNA samples tested, 2 (3.08%) were positive for Brucella infection. The mean cyclic threshold values of IS711 real-time PCR test were 37.97 and 40.48, indicating a positive reaction. Conclusion: The results of the present study indicated that the real-time PCR appears to offer several advantages over serological tests. For this reason, the real-time PCR should be validated on representative numbers of Brucella-infected and free samples before being implemented in routine diagnosis in human and animal brucellosis for controlling this disease. PMID:29657430
Effect of ionizing radiation on the quantitative detection of Salmonella using real-time PCR
Energy Technology Data Exchange (ETDEWEB)
Lim, Sangyong; Jung, Jinwoo [Radiation Research Center for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185 (Korea, Republic of); Kim, Minjeong; Ryu, Sangryeol [Department of Food and Animal Biotechnology, School of Agricultural Biotechnology, Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921 (Korea, Republic of); Kim, Dongho [Radiation Research Center for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185 (Korea, Republic of)], E-mail: fungikim@kaeri.re.kr
2008-09-15
Food irradiation is an economically viable technology for inactivating foodborne pathogens, but irradiation can mask pathogens in unhygienically prepared food. The aim of this study was to investigate the effect of irradiation treatment on the detection of Salmonella using real-time PCR. Three commercially available kits were tested, of which the InstaGene Matrix procedure was most effective in preparing template DNA from Salmonella exposed to radiation in broth culture. The minimum level of detection by real-time PCR combined with InstaGene Matrix was 3 log units of Salmonella per milliliter. However, when pure cultures of Salmonella were irradiated at 3 and 5 kGy, the cycle threshold (C{sub T}) increased 1-1.5-fold compared to irradiation at 0 and 1 kGy. This indicated that irradiation treatment may result in an underestimation of bacterial counts due to radiation-induced DNA lesions. We also compared C{sub T} values in inoculated chicken homogenates before and after irradiation, which in this model caused a 1.3-3.3-fold underestimation of bacterial counts with respect to irradiation dose.
Fischer, Christoph; Domer, Benno; Wibmer, Thomas; Penzel, Thomas
2017-03-01
Photoplethysmography has been used in a wide range of medical devices for measuring oxygen saturation, cardiac output, assessing autonomic function, and detecting peripheral vascular disease. Artifacts can render the photoplethysmogram (PPG) useless. Thus, algorithms capable of identifying artifacts are critically important. However, the published PPG algorithms are limited in algorithm and study design. Therefore, the authors developed a novel embedded algorithm for real-time pulse waveform (PWF) segmentation and artifact detection based on a contour analysis in the time domain. This paper provides an overview about PWF and artifact classifications, presents the developed PWF analysis, and demonstrates the implementation on a 32-bit ARM core microcontroller. The PWF analysis was validated with data records from 63 subjects acquired in a sleep laboratory, ergometry laboratory, and intensive care unit in equal parts. The output of the algorithm was compared with harmonized experts' annotations of the PPG with a total duration of 31.5 h. The algorithm achieved a beat-to-beat comparison sensitivity of 99.6%, specificity of 90.5%, precision of 98.5%, and accuracy of 98.3%. The interrater agreement expressed as Cohen's kappa coefficient was 0.927 and as F-measure was 0.990. In conclusion, the PWF analysis seems to be a suitable method for PPG signal quality determination, real-time annotation, data compression, and calculation of additional pulse wave metrics such as amplitude, duration, and rise time.
Day, J B; Basavanna, U
2015-01-01
To develop a rapid detection procedure for Listeria monocytogenes in infant formula and lettuce using a macrophage-based enrichment protocol and real-time PCR. A macrophage cell culture system was employed for the isolation and enrichment of L. monocytogenes from infant formula and lettuce for subsequent identification using real-time PCR. Macrophage monolayers were exposed to infant formula and lettuce contaminated with a serial dilution series of L. monocytogenes. As few as approx. 10 CFU ml(-1) or g(-1) of L. monocytogenes were detected in infant formula and lettuce after 16 h postinfection by real-time PCR. Internal positive PCR controls were utilized to eliminate the possibility of false-negative results. Co-inoculation with Listeria innocua did not reduce the L. monocytogenes detection sensitivity. Intracellular L. monocytogenes could also be isolated on Listeria selective media from infected macrophage lysates for subsequent confirmation. The detection method is highly sensitive and specific for L. monocytogenes in infant formula and lettuce and establishes a rapid identification time of 20 and 48 h for presumptive and confirmatory identification, respectively. The method is a promising alternative to many currently used q-PCR detection methods which employ traditional selective media for enrichment of contaminated food samples. Macrophage enrichment of L. monocytogenes eliminates PCR inhibitory food elements and contaminating food microflora which produce cleaner samples that increase the rapidity and sensitivity of detection. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.
Seo, K H; Valentin-Bon, I E; Brackett, R E
2006-03-01
Salmonellosis caused by Salmonella Enteritidis (SE) is a significant cause of foodborne illnesses in the United States. Consumption of undercooked eggs and egg-containing products has been the primary risk factor for the disease. The importance of the bacterial enumeration technique has been enormously stressed because of the quantitative risk analysis of SE in shell eggs. Traditional enumeration methods mainly depend on slow and tedious most-probable-number (MPN) methods. Therefore, specific, sensitive, and rapid methods for SE quantitation are needed to collect sufficient data for risk assessment and food safety policy development. We previously developed a real-time quantitative PCR assay for the direct detection and enumeration of SE and, in this study, applied it to naturally contaminated ice cream samples with and without enrichment. The detection limit of the real-time PCR assay was determined with artificially inoculated ice cream. When applied to the direct detection and quantification of SE in ice cream, the real-time PCR assay was as sensitive as the conventional plate count method in frequency of detection. However, populations of SE derived from real-time quantitative PCR were approximately 1 log higher than provided by MPN and CFU values obtained by conventional culture methods. The detection and enumeration of SE in naturally contaminated ice cream can be completed in 3 h by this real-time PCR method, whereas the cultural enrichment method requires 5 to 7 days. A commercial immunoassay for the specific detection of SE was also included in the study. The real-time PCR assay proved to be a valuable tool that may be useful to the food industry in monitoring its processes to improve product quality and safety.
Shrivastava, Sajal; Sohn, Il-Yung; Son, Young-Min; Lee, Won-Il; Lee, Nae-Eung
2015-12-14
Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules.
Dilek, Ufuk; Erol, Mustafa
2018-05-01
ARKit is a framework which allows developers to create augmented reality apps for the iPhone and iPad. In a previous study, we had shown that it could be used to detect position in educational physics experiments and emphasized that the ability to provide position data in real-time was one of the prominent features of this newly emerging technology. In this study, we demonstrate an example of how real-time data acquisition can be employed in educational settings, report some of the limitations of ARKit and how we have overcome these limitations. By means of ARKit or a similar framework, ordinary mobile devices can be adapted for use in microcomputer-based lab activities.
Magnetoresistive sensor for real-time single nucleotide polymorphism genotyping
DEFF Research Database (Denmark)
Rizzi, Giovanni; Østerberg, Frederik Westergaard; Dufva, Martin
2014-01-01
We demonstrate a magnetoresistive sensor platform that allows for the real-time detection of point mutations in DNA targets. Specifically, we detect point mutations at two sites in the human beta globin gene. For DNA detection, the present sensor technology has a detection limit of about 160p...... of magnetic beads, which enables real-time quantification of the specific binding of magnetic beads to the sensor surface under varying experimental conditions....
Multispectral fluorometric sensor for real time in-situ detection of marine petroleum spills
International Nuclear Information System (INIS)
Andrews, J.M.; Lieberman, S.H.
1998-01-01
This paper describes the development of a fluorescence based in-situ sensor system for real time monitoring and detection of petroleum hydrocarbon contaminants in the marine environment. The system consists of an array of underwater sensors deployed just below the water surface. The sensors can detect floating product (surface sheen) from below the surface as well as detect emulsified or dissolved phase petroleum in the water column. Data from each of the sensors is transmitted to a central base station computer for display, logging, and analysis. The primary intended use of the system is to protect marine facilities from accidental, petroleum discharges by providing responding authorities with immediate notification of the occurrence of a leak or spill. The detection of petroleum is based upon the fluorescence of polycyclic aromatic hydrocarbons found within petroleum derived products. The sensors utilize broadband ultraviolet excitation from a pulsed xenon lamp to generate fluorescence in contaminated sea water. The intensity of the resulting fluorescence emission is proportional to both the oil concentration in water, and/or the oil film thickness on the water surface. Multispectral fluorescence emission information is used to distinguish between several possible petroleum classes and eliminate false positive interference from non-petroleum based fluorophores such as chlorophyll. Real time qualitative identification yields an important advantage in terms of rapidly resolving questions of spill origin or in determining an appropriate response. To enable long term underwater deployment, the optical energy of the ultraviolet excitation source also serves to prevent the occurrence of biofouling on the surface of the optical window. The results of initial testing in San Diego Harbor and at the Ohmsett wave tank facility in New Jersey demonstrate the system's ability to detect petroleum products under a variety of conditions, including the presence of strong harbor
Gaydos, C. A.; Cartwright, C. P.; Colaninno, P.; Welsch, J.; Holden, J.; Ho, S. Y.; Webb, E. M.; Anderson, C.; Bertuzis, R.; Zhang, L.; Miller, T.; Leckie, G.; Abravaya, K.; Robinson, J.
2010-01-01
A multicenter clinical study was conducted to evaluate the performance characteristics of the Abbott RealTime CT/NG assay, a multiplex real-time PCR assay, for simultaneous detection of Chlamydia trachomatis and Neisseria gonorrhoeae. The specimens were collected from a total of 3,832 male and female subjects at 16 geographically diverse sites. Specimens included male and female urine samples, male urethral swabs, female endocervical swabs, and self-collected and clinician-collected vaginal swabs. Specimens were tested with the automated Abbott RealTime CT/NG assay, Aptima Combo 2 assay (Gen-Probe), ProbeTec ET CT/GC assay (Becton Dickinson), and culture for N. gonorrhoeae. The Aptima Combo 2 assay, the ProbeTec assay, and the N. gonorrhoeae culture were used as the reference assays. For each subject, a patient infected status (PIS) was determined based on the combined results from the reference assays. The overall prevalence in female subjects was 8.9% for C. trachomatis and 3.8% for N. gonorrhoeae. The overall male prevalence was 18.2% for C. trachomatis and 16.7% for N. gonorrhoeae. The overall sensitivity and specificity of the Abbott RealTime CT/NG assay were 92.4% and 99.2% for C. trachomatis and 96.9% and 99.7% for N. gonorrhoeae, respectively. In comparison, the sensitivity and specificity, respectively, for the Aptima Combo 2 assay were 94.5% and 99.0% for C. trachomatis and 96.1% and 99.5% for N. gonorrhoeae, and those for the ProbeTec ET assay were 90.3% and 99.5% for C. trachomatis and 92.0% and 97.3% for N. gonorrhoeae in this study. The Abbott RealTime CT/NG assay offers C. trachomatis and N. gonorrhoeae dual detection with high sensitivity and specificity. The automated assay provides a useful alternative nucleic acid amplification assay for clinical laboratories and clinicians. PMID:20668135
Gaydos, C A; Cartwright, C P; Colaninno, P; Welsch, J; Holden, J; Ho, S Y; Webb, E M; Anderson, C; Bertuzis, R; Zhang, L; Miller, T; Leckie, G; Abravaya, K; Robinson, J
2010-09-01
A multicenter clinical study was conducted to evaluate the performance characteristics of the Abbott RealTime CT/NG assay, a multiplex real-time PCR assay, for simultaneous detection of Chlamydia trachomatis and Neisseria gonorrhoeae. The specimens were collected from a total of 3,832 male and female subjects at 16 geographically diverse sites. Specimens included male and female urine samples, male urethral swabs, female endocervical swabs, and self-collected and clinician-collected vaginal swabs. Specimens were tested with the automated Abbott RealTime CT/NG assay, Aptima Combo 2 assay (Gen-Probe), ProbeTec ET CT/GC assay (Becton Dickinson), and culture for N. gonorrhoeae. The Aptima Combo 2 assay, the ProbeTec assay, and the N. gonorrhoeae culture were used as the reference assays. For each subject, a patient infected status (PIS) was determined based on the combined results from the reference assays. The overall prevalence in female subjects was 8.9% for C. trachomatis and 3.8% for N. gonorrhoeae. The overall male prevalence was 18.2% for C. trachomatis and 16.7% for N. gonorrhoeae. The overall sensitivity and specificity of the Abbott RealTime CT/NG assay were 92.4% and 99.2% for C. trachomatis and 96.9% and 99.7% for N. gonorrhoeae, respectively. In comparison, the sensitivity and specificity, respectively, for the Aptima Combo 2 assay were 94.5% and 99.0% for C. trachomatis and 96.1% and 99.5% for N. gonorrhoeae, and those for the ProbeTec ET assay were 90.3% and 99.5% for C. trachomatis and 92.0% and 97.3% for N. gonorrhoeae in this study. The Abbott RealTime CT/NG assay offers C. trachomatis and N. gonorrhoeae dual detection with high sensitivity and specificity. The automated assay provides a useful alternative nucleic acid amplification assay for clinical laboratories and clinicians.
A method of real-time detection for distant moving obstacles by monocular vision
Jia, Bao-zhi; Zhu, Ming
2013-12-01
In this paper, we propose an approach for detection of distant moving obstacles like cars and bicycles by a monocular camera to cooperate with ultrasonic sensors in low-cost condition. We are aiming at detecting distant obstacles that move toward our autonomous navigation car in order to give alarm and keep away from them. Method of frame differencing is applied to find obstacles after compensation of camera's ego-motion. Meanwhile, each obstacle is separated from others in an independent area and given a confidence level to indicate whether it is coming closer. The results on an open dataset and our own autonomous navigation car have proved that the method is effective for detection of distant moving obstacles in real-time.
WiFi-Based Real-Time Calibration-Free Passive Human Motion Detection
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Liangyi Gong
2015-12-01
Full Text Available With the rapid development of WLAN technology, wireless device-free passive human detection becomes a newly-developing technique and holds more potential to worldwide and ubiquitous smart applications. Recently, indoor fine-grained device-free passive human motion detection based on the PHY layer information is rapidly developed. Previous wireless device-free passive human detection systems either rely on deploying specialized systems with dense transmitter-receiver links or elaborate off-line training process, which blocks rapid deployment and weakens system robustness. In the paper, we explore to research a novel fine-grained real-time calibration-free device-free passive human motion via physical layer information, which is independent of indoor scenarios and needs no prior-calibration and normal profile. We investigate sensitivities of amplitude and phase to human motion, and discover that phase feature is more sensitive to human motion, especially to slow human motion. Aiming at lightweight and robust device-free passive human motion detection, we develop two novel and practical schemes: short-term averaged variance ratio (SVR and long-term averaged variance ratio (LVR. We realize system design with commercial WiFi devices and evaluate it in typical multipath-rich indoor scenarios. As demonstrated in the experiments, our approach can achieve a high detection rate and low false positive rate.
WiFi-Based Real-Time Calibration-Free Passive Human Motion Detection.
Gong, Liangyi; Yang, Wu; Man, Dapeng; Dong, Guozhong; Yu, Miao; Lv, Jiguang
2015-12-21
With the rapid development of WLAN technology, wireless device-free passive human detection becomes a newly-developing technique and holds more potential to worldwide and ubiquitous smart applications. Recently, indoor fine-grained device-free passive human motion detection based on the PHY layer information is rapidly developed. Previous wireless device-free passive human detection systems either rely on deploying specialized systems with dense transmitter-receiver links or elaborate off-line training process, which blocks rapid deployment and weakens system robustness. In the paper, we explore to research a novel fine-grained real-time calibration-free device-free passive human motion via physical layer information, which is independent of indoor scenarios and needs no prior-calibration and normal profile. We investigate sensitivities of amplitude and phase to human motion, and discover that phase feature is more sensitive to human motion, especially to slow human motion. Aiming at lightweight and robust device-free passive human motion detection, we develop two novel and practical schemes: short-term averaged variance ratio (SVR) and long-term averaged variance ratio (LVR). We realize system design with commercial WiFi devices and evaluate it in typical multipath-rich indoor scenarios. As demonstrated in the experiments, our approach can achieve a high detection rate and low false positive rate.
Real-Time MENTAT programming language and architecture
Grimshaw, Andrew S.; Silberman, Ami; Liu, Jane W. S.
1989-01-01
Real-time MENTAT, a programming environment designed to simplify the task of programming real-time applications in distributed and parallel environments, is described. It is based on the same data-driven computation model and object-oriented programming paradigm as MENTAT. It provides an easy-to-use mechanism to exploit parallelism, language constructs for the expression and enforcement of timing constraints, and run-time support for scheduling and exciting real-time programs. The real-time MENTAT programming language is an extended C++. The extensions are added to facilitate automatic detection of data flow and generation of data flow graphs, to express the timing constraints of individual granules of computation, and to provide scheduling directives for the runtime system. A high-level view of the real-time MENTAT system architecture and programming language constructs is provided.
SonoNet: Real-Time Detection and Localisation of Fetal Standard Scan Planes in Freehand Ultrasound.
Baumgartner, Christian F; Kamnitsas, Konstantinos; Matthew, Jacqueline; Fletcher, Tara P; Smith, Sandra; Koch, Lisa M; Kainz, Bernhard; Rueckert, Daniel
2017-11-01
Identifying and interpreting fetal standard scan planes during 2-D ultrasound mid-pregnancy examinations are highly complex tasks, which require years of training. Apart from guiding the probe to the correct location, it can be equally difficult for a non-expert to identify relevant structures within the image. Automatic image processing can provide tools to help experienced as well as inexperienced operators with these tasks. In this paper, we propose a novel method based on convolutional neural networks, which can automatically detect 13 fetal standard views in freehand 2-D ultrasound data as well as provide a localization of the fetal structures via a bounding box. An important contribution is that the network learns to localize the target anatomy using weak supervision based on image-level labels only. The network architecture is designed to operate in real-time while providing optimal output for the localization task. We present results for real-time annotation, retrospective frame retrieval from saved videos, and localization on a very large and challenging dataset consisting of images and video recordings of full clinical anomaly screenings. We found that the proposed method achieved an average F1-score of 0.798 in a realistic classification experiment modeling real-time detection, and obtained a 90.09% accuracy for retrospective frame retrieval. Moreover, an accuracy of 77.8% was achieved on the localization task.
A Novel Real-Time Feature Matching Scheme
Directory of Open Access Journals (Sweden)
Ying Liu
2014-02-01
Full Text Available Affine Scale Invariant Feature Transform (ASIFT can obtain fully affine invariance, however, its time cost reaches about twice that in Scale Invariant Feature Transform (SIFT. We propose an improved ASIFT algorithm based on feature points in scale space for real-time application. In order to detect the affine invariant feature point, we establish a second-order difference of Gaussian (DOG pyramid and replace the extreme detection in the DOG pyramid by zero detection in the proposed second-order DOG pyramid, which decreases the complexity of the scheme. Experimental results show that the proposed method has a big progress in the real-time performance compared to the traditional one, while preserving the fully affine invariance and precision.
Directory of Open Access Journals (Sweden)
Antonio Moccia
2012-01-01
Full Text Available This paper describes the target detection algorithm for the image processor of a vision-based system that is installed onboard an unmanned helicopter. It has been developed in the framework of a project of the French national aerospace research center Office National d’Etudes et de Recherches Aérospatiales (ONERA which aims at developing an air-to-ground target tracking mission in an unknown urban environment. In particular, the image processor must detect targets and estimate ground motion in proximity of the detected target position. Concerning the target detection function, the analysis has dealt with realizing a corner detection algorithm and selecting the best choices in terms of edge detection methods, filtering size and type and the more suitable criterion of detection of the points of interest in order to obtain a very fast algorithm which fulfills the computation load requirements. The compared criteria are the Harris-Stephen and the Shi-Tomasi, ones, which are the most widely used in literature among those based on intensity. Experimental results which illustrate the performance of the developed algorithm and demonstrate that the detection time is fully compliant with the requirements of the real-time system are discussed.
Franzo, G; Drigo, M; Lupini, C; Catelli, E; Laconi, A; Listorti, V; Bonci, M; Naylor, C J; Martini, M; Cecchinato, M
2014-06-01
Use of real-time PCR is increasing in the diagnosis of infectious disease due to its sensitivity, specificity, and speed of detection. These characteristics make it particularly suited for the diagnosis of viral infections, like avian metapneumovirus (AMPV), for which effective control benefits from continuously updated knowledge of the epidemiological situation. Other real-time reverse transcription (RT)-PCRs have been published based on highly specific fluorescent dye-labeled probes, but they have high initial cost, complex validation, and a marked susceptibility to the genetic variability of their target sequence. With this in mind, we developed and validated a SYBR Green I-based quantitative RT-PCR for the detection of the two most prevalent AMPV subtypes (i.e., subtypes A and B). The assay demonstrated an analytical sensitivity comparable with that of a previously published real-time RT-PCR and the ability to detect RNA equivalent to approximately 0.5 infectious doses for both A and B subtypes. The high efficiency and linearity between viral titer and crossing point displayed for both subtypes make it suited for viral quantification. Optimization of reaction conditions and the implementation of melting curve analysis guaranteed the high specificity of the assay. The stable melting temperature difference between the two subtypes indicated the possibility of subtyping through melting temperature analysis. These characteristics make our assay a sensitive, specific, and rapid tool, enabling contemporaneous detection, quantification, and discrimination of AMPV subtype A and B.
Sankuntaw, Nipaporn; Sukprasert, Saovaluk; Engchanil, Chulapan; Kaewkes, Wanlop; Chantratita, Wasun; Pairoj, Vantanit; Lulitanond, Viraphong
2011-01-01
Human herpesvirus infection of immunocompromised hosts may lead to central nervous system (CNS) infection and diseases. In this study, a single tube multiplex real-time PCR was developed for the detection of five herpesviruses (HSV-1, HSV-2, VZV, EBV and CMV) in clinical cerebrospinal fluid (CSF) specimens. Two primer pairs specific for the herpesvirus polymerase gene and five hybridization probe pairs for the specific identification of the herpesvirus types were used in a LightCycler multiplex real-time PCR. A singleplex real-time PCR was first optimized and then applied to the multiplex real-time PCR. The singleplex and multiplex real-time PCRs showed no cross-reactivity. The sensitivity of the singleplex real-time PCR was 1 copy per reaction for each herpesvirus, while that of the multiplex real-time PCR was 1 copy per reaction for HSV-1 and VZV and 10 copies per reaction for HSV-2, EBV and CMV. Intra and inter-assay variations of the single tube multiplex assay were in the range of 0.02%-3.67% and 0.79%-4.35%, respectively. The assay was evaluated by testing 62 clinical CSF samples and was found to have equivalent sensitivity, specificity and agreement as the routine real-time PCR, but reducing time, cost and amount of used sample. Copyright © 2011 Elsevier Ltd. All rights reserved.
Molenkamp, Richard; van der Ham, Alwin; Schinkel, Janke; Beld, Marcel
2007-01-01
One of the most interesting aspects of real-time PCR based on the detection of fluorophoric labeled oligonucleotides is the possibility of being able to detect conveniently multiple targets in the same PCR reaction. Recently, Roche Diagnostics launched a real-time PCR platform, the LightCycler480
Directory of Open Access Journals (Sweden)
Ma Mingxiao
Full Text Available Sacbrood virus (SBV is a picorna-like virus that affects honey bees (Apis mellifera and results in the death of the larvae. Several procedures are available to detect Chinese SBV (CSBV in clinical samples, but not to estimate the level of CSBV infection. The aim of this study was develop an assay for rapid detection and quantification of this virus. Primers and probes were designed that were specific for CSBV structural protein genes. A TaqMan minor groove binder (MGB probe-based, fluorescence real-time quantitative PCR was established. The specificity, sensitivity and stability of the assay were assessed; specificity was high and there were no cross-reactivity with healthy larvae or other bee viruses. The assay was applied to detect CSBV in 37 clinical samples and its efficiency was compared with clinical diagnosis, electron microscopy observation, and conventional RT-PCR. The TaqMan MGB-based probe fluorescence real-time quantitative PCR for CSBV was more sensitive than other methods tested. This assay was a reliable, fast, and sensitive method that was used successfully to detect CSBV in clinical samples. The technology can provide a useful tool for rapid detection of CSBV. This study has established a useful protocol for CSBV testing, epidemiological investigation, and development of animal models.
International Nuclear Information System (INIS)
J Zwan, B; Colvill, E; Booth, J; J O’Connor, D; Keall, P; B Greer, P
2016-01-01
Purpose: The added complexity of the real-time adaptive multi-leaf collimator (MLC) tracking increases the likelihood of undetected MLC delivery errors. In this work we develop and test a system for real-time delivery verification and error detection for MLC tracking radiotherapy using an electronic portal imaging device (EPID). Methods: The delivery verification system relies on acquisition and real-time analysis of transit EPID image frames acquired at 8.41 fps. In-house software was developed to extract the MLC positions from each image frame. Three comparison metrics were used to verify the MLC positions in real-time: (1) field size, (2) field location and, (3) field shape. The delivery verification system was tested for 8 VMAT MLC tracking deliveries (4 prostate and 4 lung) where real patient target motion was reproduced using a Hexamotion motion stage and a Calypso system. Sensitivity and detection delay was quantified for various types of MLC and system errors. Results: For both the prostate and lung test deliveries the MLC-defined field size was measured with an accuracy of 1.25 cm 2 (1 SD). The field location was measured with an accuracy of 0.6 mm and 0.8 mm (1 SD) for lung and prostate respectively. Field location errors (i.e. tracking in wrong direction) with a magnitude of 3 mm were detected within 0.4 s of occurrence in the X direction and 0.8 s in the Y direction. Systematic MLC gap errors were detected as small as 3 mm. The method was not found to be sensitive to random MLC errors and individual MLC calibration errors up to 5 mm. Conclusion: EPID imaging may be used for independent real-time verification of MLC trajectories during MLC tracking deliveries. Thresholds have been determined for error detection and the system has been shown to be sensitive to a range of delivery errors.
Energy Technology Data Exchange (ETDEWEB)
Xu, Fan; Wang, Yuanqing, E-mail: yqwang@nju.edu.cn; Li, Fenfang [School of Electronic Science and Engineering, Nanjing University, Nanjing 210046 (China)
2016-03-15
The avalanche-photodiode-array (APD-array) laser detection and ranging (LADAR) system has been continually developed owing to its superiority of nonscanning, large field of view, high sensitivity, and high precision. However, how to achieve higher-efficient detection and better integration of the LADAR system for real-time three-dimensional (3D) imaging continues to be a problem. In this study, a novel LADAR system using four linear mode APDs (LmAPDs) is developed for high-efficient detection by adopting a modulation and multiplexing technique. Furthermore, an automatic control system for the array LADAR system is proposed and designed by applying the virtual instrumentation technique. The control system aims to achieve four functions: synchronization of laser emission and rotating platform, multi-channel synchronous data acquisition, real-time Ethernet upper monitoring, and real-time signal processing and 3D visualization. The structure and principle of the complete system are described in the paper. The experimental results demonstrate that the LADAR system is capable of achieving real-time 3D imaging on an omnidirectional rotating platform under the control of the virtual instrumentation system. The automatic imaging LADAR system utilized only 4 LmAPDs to achieve 256-pixel-per-frame detection with by employing 64-bit demodulator. Moreover, the lateral resolution is ∼15 cm and range accuracy is ∼4 cm root-mean-square error at a distance of ∼40 m.
DEFF Research Database (Denmark)
Wang, Zhenyu; Sekulovic, Andrea; Kutter, Jörg Peter
2006-01-01
A novel real-time PCR microchip platform with integrated thermal system and polymer waveguides has been developed. By using the integrated optical system of the real-time PCR chip, cadF – a virulence gene of Campylobacter jejuni, could specifically be detected. Two different DNA binding dyes, SYTOX...
NEAR REAL-TIME AUTOMATIC MARINE VESSEL DETECTION ON OPTICAL SATELLITE IMAGES
Directory of Open Access Journals (Sweden)
G. Máttyus
2013-05-01
Full Text Available Vessel monitoring and surveillance is important for maritime safety and security, environment protection and border control. Ship monitoring systems based on Synthetic-aperture Radar (SAR satellite images are operational. On SAR images the ships made of metal with sharp edges appear as bright dots and edges, therefore they can be well distinguished from the water. Since the radar is independent from the sun light and can acquire images also by cloudy weather and rain, it provides a reliable service. Vessel detection from spaceborne optical images (VDSOI can extend the SAR based systems by providing more frequent revisit times and overcoming some drawbacks of the SAR images (e.g. lower spatial resolution, difficult human interpretation. Optical satellite images (OSI can have a higher spatial resolution thus enabling the detection of smaller vessels and enhancing the vessel type classification. The human interpretation of an optical image is also easier than as of SAR image. In this paper I present a rapid automatic vessel detection method which uses pattern recognition methods, originally developed in the computer vision field. In the first step I train a binary classifier from image samples of vessels and background. The classifier uses simple features which can be calculated very fast. For the detection the classifier is slided along the image in various directions and scales. The detector has a cascade structure which rejects most of the background in the early stages which leads to faster execution. The detections are grouped together to avoid multiple detections. Finally the position, size(i.e. length and width and heading of the vessels is extracted from the contours of the vessel. The presented method is parallelized, thus it runs fast (in minutes for 16000 × 16000 pixels image on a multicore computer, enabling near real-time applications, e.g. one hour from image acquisition to end user.
Near Real-Time Automatic Marine Vessel Detection on Optical Satellite Images
Máttyus, G.
2013-05-01
Vessel monitoring and surveillance is important for maritime safety and security, environment protection and border control. Ship monitoring systems based on Synthetic-aperture Radar (SAR) satellite images are operational. On SAR images the ships made of metal with sharp edges appear as bright dots and edges, therefore they can be well distinguished from the water. Since the radar is independent from the sun light and can acquire images also by cloudy weather and rain, it provides a reliable service. Vessel detection from spaceborne optical images (VDSOI) can extend the SAR based systems by providing more frequent revisit times and overcoming some drawbacks of the SAR images (e.g. lower spatial resolution, difficult human interpretation). Optical satellite images (OSI) can have a higher spatial resolution thus enabling the detection of smaller vessels and enhancing the vessel type classification. The human interpretation of an optical image is also easier than as of SAR image. In this paper I present a rapid automatic vessel detection method which uses pattern recognition methods, originally developed in the computer vision field. In the first step I train a binary classifier from image samples of vessels and background. The classifier uses simple features which can be calculated very fast. For the detection the classifier is slided along the image in various directions and scales. The detector has a cascade structure which rejects most of the background in the early stages which leads to faster execution. The detections are grouped together to avoid multiple detections. Finally the position, size(i.e. length and width) and heading of the vessels is extracted from the contours of the vessel. The presented method is parallelized, thus it runs fast (in minutes for 16000 × 16000 pixels image) on a multicore computer, enabling near real-time applications, e.g. one hour from image acquisition to end user.
Badr, Salah M.; Bruztman, Donald P.; Nelson, Michael L.; Byrnes, Ronald Benton
1992-01-01
This paper presents an introduction to the basic issues involved in real-time systems. Both real-time operating sys and real-time programming languages are explored. Concurrent programming and process synchronization and communication are also discussed. The real-time requirements of the Naval Postgraduate School Autonomous Under Vehicle (AUV) are then examined. Autonomous underwater vehicle (AUV), hard real-time system, real-time operating system, real-time programming language, real-time sy...
Real-time detection of antibiotic activity by measuring nanometer-scale bacterial deformation
Iriya, Rafael; Syal, Karan; Jing, Wenwen; Mo, Manni; Yu, Hui; Haydel, Shelley E.; Wang, Shaopeng; Tao, Nongjian
2017-12-01
Diagnosing antibiotic-resistant bacteria currently requires sensitive detection of phenotypic changes associated with antibiotic action on bacteria. Here, we present an optical imaging-based approach to quantify bacterial membrane deformation as a phenotypic feature in real-time with a nanometer scale (˜9 nm) detection limit. Using this approach, we found two types of antibiotic-induced membrane deformations in different bacterial strains: polymyxin B induced relatively uniform spatial deformation of Escherichia coli O157:H7 cells leading to change in cellular volume and ampicillin-induced localized spatial deformation leading to the formation of bulges or protrusions on uropathogenic E. coli CFT073 cells. We anticipate that the approach will contribute to understanding of antibiotic phenotypic effects on bacteria with a potential for applications in rapid antibiotic susceptibility testing.
von Hertwig, Aline Morgan; Sant'Ana, Anderson S; Sartori, Daniele; da Silva, Josué José; Nascimento, Maristela S; Iamanaka, Beatriz Thie; Pelegrinelli Fungaro, Maria Helena; Taniwaki, Marta Hiromi
2018-05-01
Some species from Aspergillus section Nigri are morphologically very similar and altogether have been called A. niger aggregate. Although the species included in this group are morphologically very similar, they differ in their ability to produce mycotoxins and other metabolites and their taxonomical status has evolved continuously. Among them, A. niger and A. welwitschiae are ochratoxin A and fumonisin B 2 producers and their detection and/or identification is of crucial importance for food safety. The aim of this study was the development of a real-time PCR-based method for simultaneous discrimination of A. niger and A. welwitschiae from other species of the A. niger aggregate isolated from coffee beans. One primer pair and a hybridization probe specific for detection of A. niger and A. welwitschiae strains were designed based on the BenA gene sequences, and used in a Real-time PCR assay for the rapid discrimination between both these species from all others of the A. niger aggregate. The Real-time PCR assay was shown to be 100% efficient in discriminating the 73 isolates of A. niger/A. welwitschiae from the other A. niger aggregate species analyzed as a negative control. This result testifies to the use of this technique as a good tool in the rapid detection of these important toxigenic species. Copyright © 2018 Elsevier B.V. All rights reserved.
Real-time Quaking-induced Conversion Assay for Detection of CWD Prions in Fecal Material.
Cheng, Yo Ching; Hannaoui, Samia; John, Theodore Ralph; Dudas, Sandor; Czub, Stefanie; Gilch, Sabine
2017-09-29
The RT-QuIC technique is a sensitive in vitro cell-free prion amplification assay based mainly on the seeded misfolding and aggregation of recombinant prion protein (PrP) substrate using prion seeds as a template for the conversion. RT-QuIC is a novel high-throughput technique which is analogous to real-time polymerase chain reaction (PCR). Detection of amyloid fibril growth is based on the dye Thioflavin T, which fluoresces upon specific interaction with ᵦ-sheet rich proteins. Thus, amyloid formation can be detected in real time. We attempted to develop a reliable non-invasive screening test to detect chronic wasting disease (CWD) prions in fecal extract. Here, we have specifically adapted the RT-QuIC technique to reveal PrP Sc seeding activity in feces of CWD infected cervids. Initially, the seeding activity of the fecal extracts we prepared was relatively low in RT-QuIC, possibly due to potential assay inhibitors in the fecal material. To improve seeding activity of feces extracts and remove potential assay inhibitors, we homogenized the fecal samples in a buffer containing detergents and protease inhibitors. We also submitted the samples to different methodologies to concentrate PrP Sc on the basis of protein precipitation using sodium phosphotungstic acid, and centrifugal force. Finally, the feces extracts were tested by optimized RT-QuIC which included substrate replacement in the protocol to improve the sensitivity of detection. Thus, we established a protocol for sensitive detection of CWD prion seeding activity in feces of pre-clinical and clinical cervids by RT-QuIC, which can be a practical tool for non-invasive CWD diagnosis.
Huhtamo, Eili; Hasu, Essi; Uzcátegui, Nathalie Y; Erra, Elina; Nikkari, Simo; Kantele, Anu; Vapalahti, Olli; Piiparinen, Heli
2010-01-01
The increased traveling to dengue endemic regions and the numerous epidemics have led to a rise in imported dengue. The laboratory diagnosis of acute dengue requires several types of tests and often paired samples are needed for obtaining reliable results. Although several diagnostic methods are available, proper comparative data on their performance are lacking. To compare the performance of novel methods including a novel pan-DENV real-time RT-PCR and a commercially available NS1 capture-EIA in regard to IgM detection for optimizing the early diagnosis of DENV in travelers. A panel of 99 selected early phase serum samples of dengue patients was studied by real-time RT-PCR, NS1 antigen ELISA, IgM-EIA, IgG-IFA and cell culture virus isolation. The novel real-time RT-PCR was shown specific and sensitive for detection of DENV-1-4 RNA and suitable for diagnostic use. The diagnostic rate using combination of RNA and IgM detection was 99% and using NS1 and IgM detection 95.9%. The results of RNA and NS1 antigen detection disagreed in 15.5% of samples that had only RNA or NS1 antigen detected. The diagnostic rates of early samples are higher when either RNA or NS1 antigen detection is combined with IgM detection. Besides the differences in the RNA and NS1 detection assays, the observed discrepancy of results could suggest individual variation or differences in timing of these markers in patient serum. Copyright (c) 2009 Elsevier B.V. All rights reserved.
Maas, L; Dorigo-Zetsma, J W; de Groot, C J; Bouter, S; Plötz, F B; van Ewijk, B E
2014-06-01
The performance of a multiplex real-time PCR for the detection of Blastocystis, Dientamoeba fragilis, Giardia lamblia, Cryptosporidium species and Entamoeba species in faecal samples was evaluated in an observational prospective study. Paediatric patients (0-18 years) presenting with gastrointestinal symptoms and suspected of having enteroparasitic disease were included. A questionnaire on gastrointestinal symptoms and the chosen treatment was completed at the start of the study and after 6 weeks. Of 163 paediatric patients (mean age, 7.8 years), 114 (70%) had a PCR-positive faecal sample. D. fragilis was detected most frequently, in 101 patients, followed by Blastocystis in 49. In faecal samples of 47 patients, more than one protozoan was detected, mainly the combination of D. fragilis and Blastocystis. Reported gastrointestinal symptoms were abdominal pain (78%), nausea (30%), and altered bowel habits (28%). Eighty-nine of the PCR-positive patients were treated with antibiotics. A significant reduction in abdominal pain was observed both in treated and in untreated patients. This study demonstrated that multiplex real-time PCR detects a high percentage of intestinal protozoa in paediatric patients with gastrointestinal symptoms. However, interpretation and determination of the clinical relevance of a positive PCR result in this population are still difficult. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.
Hwang, Seoyeon; Kang, Byunghak; Hong, Jiyoung; Kim, Ahyoun; Kim, Hyejin; Kim, Kisang; Cheon, Doo-Sung
2013-07-01
Human enterovirus (EV) 71 is the main etiological agent of hand, foot, and mouth disease (HFMD). It is associated with neurological complications, and caused fatalities during recent outbreaks in the Asia-Pacific region. Infections caused by EV71 could lead to many complications, ranging from brainstem encephalitis to pulmonary oedema, resulting in high mortality. In this study, a duplex real-time RT-PCR assay was developed in order to simultaneously detect pan-EV and EV71. EV71-specific primers and probes were designed based on the highly conserved VP1 region of EV71. Five EV71 strains were detected as positive, and no positive fluorescence signal was observed in the duplex real-time RT-PCR for other viral RNA, which showed 100% specificity for the selected panel, and no cross-reactions were observed in this duplex real-time RT-PCR. The EV71-specific duplex real-time RT-PCR was more sensitive than conventional RT-PCR, and detected viral titers that were 10-fold lower than those measured by the latter. Of the 381 HFMD clinical specimens, 196 (51.4%) cases were pan-EV-positive, of which 170 (86.7%) were EV71-positive when tested by pan-EV and EV71-specific duplex real-time RT-PCR. EV71-specific duplex real-time RT-PCR offers a rapid and sensitive method to detect EV71 from clinical specimens, and will allow quarantine measures to be taken more effectively during outbreaks. Copyright © 2013 Wiley Periodicals, Inc.
Guion, Chase E; Ochoa, Theresa J; Walker, Christopher M; Barletta, Francesca; Cleary, Thomas G
2008-05-01
Diarrheagenic Escherichia coli strains are important causes of diarrhea in children from the developing world and are now being recognized as emerging enteropathogens in the developed world. Current methods of detection are too expensive and labor-intensive for routine detection of these organisms to be practical. We developed a real-time fluorescence-based multiplex PCR for the detection of all six of the currently recognized classes of diarrheagenic E. coli. The primers were designed to specifically amplify eight different virulence genes in the same reaction: aggR for enteroaggregative E. coli, stIa/stIb and lt for enterotoxigenic E. coli, eaeA for enteropathogenic E. coli and Shiga toxin-producing E. coli (STEC), stx(1) and stx(2) for STEC, ipaH for enteroinvasive E. coli, and daaD for diffusely adherent E. coli (DAEC). Eighty-nine of ninety diarrheagenic E. coli and 36/36 nonpathogenic E. coli strains were correctly identified using this approach (specificity, 1.00; sensitivity, 0.99). The single false negative was a DAEC strain. The total time between preparation of DNA from E. coli colonies on agar plates and completion of PCR and melting-curve analysis was less than 90 min. The cost of materials was low. Melting-point analysis of real-time multiplex PCR is a rapid, sensitive, specific, and inexpensive method for detection of diarrheagenic E. coli.
Yang, Peng; Peng, Xiaomin; Cui, Shujuan; Shao, Junbin; Zhu, Xuping; Zhang, Daitao; Liang, Huijie; Wang, Quanyi
2013-07-30
Streptococcal superantigens (SAgs) are the major virulence factors of infection in humans for group A Streptococcus (GAS) bacteria. A panel consisting of seven duplex real-time PCR assays was developed to simultaneously detect 13 streptococcal SAgs and one internal control which may be important in the control of GAS-mediated diseases. Primer and probe sequences were selected based on the highly conserved region from an alignment of nucleotide sequences of the 13 streptococcal SAgs. The reaction conditions of the duplex real-time PCR were optimized and the specificity of the duplex assays was evaluated using SAg positive strains. The limit of detection of the duplex assays was determined by using 10-fold serial dilutions of the DNA of 13 streptococcal SAgs and compared to a conventional polymerase chain reaction (PCR) method for evaluating the duplex assays sensitivity. Using the duplex assays, we were able to differentiate between 13 SAgs from Streptococcus strains and other non-Streptococcus bacteria without cross-reaction. On the other hand, the limit of detection of the duplex assays was at least one or two log dilutions lower than that of the conventional PCR. The panel was highly specific (100%) and the limit of detection of these duplex groups was at least ten times lower than that obtained by using a conventional PCR method.
Real-Time Hazard Detection and Avoidance Demonstration for a Planetary Lander
Epp, Chirold D.; Robertson, Edward A.; Carson, John M., III
2014-01-01
The Autonomous Landing Hazard Avoidance Technology (ALHAT) Project is chartered to develop and mature to a Technology Readiness Level (TRL) of six an autonomous system combining guidance, navigation and control with terrain sensing and recognition functions for crewed, cargo, and robotic planetary landing vehicles. In addition to precision landing close to a pre-mission defined landing location, the ALHAT System must be capable of autonomously identifying and avoiding surface hazards in real-time to enable a safe landing under any lighting conditions. This paper provides an overview of the recent results of the ALHAT closed loop hazard detection and avoidance flight demonstrations on the Morpheus Vertical Testbed (VTB) at the Kennedy Space Center, including results and lessons learned. This effort is also described in the context of a technology path in support of future crewed and robotic planetary exploration missions based upon the core sensing functions of the ALHAT system: Terrain Relative Navigation (TRN), Hazard Detection and Avoidance (HDA), and Hazard Relative Navigation (HRN).
Tokarchuk, Laurissa; Wang, Xinyue; Poslad, Stefan
2017-01-01
In an age when people are predisposed to report real-world events through their social media accounts, many researchers value the benefits of mining user generated content from social media. Compared with the traditional news media, social media services, such as Twitter, can provide more complete and timely information about the real-world events. However events are often like a puzzle and in order to solve the puzzle/understand the event, we must identify all the sub-events or pieces. Existing Twitter event monitoring systems for sub-event detection and summarization currently typically analyse events based on partial data as conventional data collection methodologies are unable to collect comprehensive event data. This results in existing systems often being unable to report sub-events in real-time and often in completely missing sub-events or pieces in the broader event puzzle. This paper proposes a Sub-event detection by real-TIme Microblog monitoring (STRIM) framework that leverages the temporal feature of an expanded set of news-worthy event content. In order to more comprehensively and accurately identify sub-events this framework first proposes the use of adaptive microblog crawling. Our adaptive microblog crawler is capable of increasing the coverage of events while minimizing the amount of non-relevant content. We then propose a stream division methodology that can be accomplished in real time so that the temporal features of the expanded event streams can be analysed by a burst detection algorithm. In the final steps of the framework, the content features are extracted from each divided stream and recombined to provide a final summarization of the sub-events. The proposed framework is evaluated against traditional event detection using event recall and event precision metrics. Results show that improving the quality and coverage of event contents contribute to better event detection by identifying additional valid sub-events. The novel combination of
Directory of Open Access Journals (Sweden)
Laurissa Tokarchuk
Full Text Available In an age when people are predisposed to report real-world events through their social media accounts, many researchers value the benefits of mining user generated content from social media. Compared with the traditional news media, social media services, such as Twitter, can provide more complete and timely information about the real-world events. However events are often like a puzzle and in order to solve the puzzle/understand the event, we must identify all the sub-events or pieces. Existing Twitter event monitoring systems for sub-event detection and summarization currently typically analyse events based on partial data as conventional data collection methodologies are unable to collect comprehensive event data. This results in existing systems often being unable to report sub-events in real-time and often in completely missing sub-events or pieces in the broader event puzzle. This paper proposes a Sub-event detection by real-TIme Microblog monitoring (STRIM framework that leverages the temporal feature of an expanded set of news-worthy event content. In order to more comprehensively and accurately identify sub-events this framework first proposes the use of adaptive microblog crawling. Our adaptive microblog crawler is capable of increasing the coverage of events while minimizing the amount of non-relevant content. We then propose a stream division methodology that can be accomplished in real time so that the temporal features of the expanded event streams can be analysed by a burst detection algorithm. In the final steps of the framework, the content features are extracted from each divided stream and recombined to provide a final summarization of the sub-events. The proposed framework is evaluated against traditional event detection using event recall and event precision metrics. Results show that improving the quality and coverage of event contents contribute to better event detection by identifying additional valid sub-events. The
Energy Technology Data Exchange (ETDEWEB)
Ruiz, M.; Barrera, E.; Gonzalez, J.; Melendez, R. [Grupo de Investigacion en Instrumentacion y Acustica Aplicada - Universidad Politecnica de Madrid (Spain); Vega, J.; Ratta, G.; Gonzalez, S. [Asociacion EURATOM/CIEMAT para Fusion, Madrid (Spain); Murari, A. [Consorzio RFX - Associazione EURATOM ENEA per la Fusione, Padova (Italy)
2009-07-01
A basic requirement of the data acquisition systems used in long pulse fusion experiments is to detect events of interest in the acquired signals in real time. Developing such applications is usually a complex task, so it is necessary to develop a set of hardware and software tools that simplify their implementation. An example of these tools is the Intelligent Test and Measurement System (ITMS), which offers distributed data acquisition, distribution and real time processing capabilities with advanced, but easy to use, software tools that simplify application development and system setup. This poster presents the application of the ITMS platform to solve the problem of detecting L/H and H/L transitions in real time based on the use of efficient pattern recognition algorithms. The system architecture used to implement this solution and its performance evaluation are discussed. The system consists of the following elements: a) the ITMS, which is used both to implement the data acquisition and real time LH-HL detection, and to simulate the working environment by reproducing real signals obtained from JET database; b) an event detector, developed using advanced pattern recognition algorithms, that will continuously analyze the information of the acquired signals in order to detect the L/H and H/L transitions; and c) a host computer with several software tools developed with LabVIEW, JAVA and JINI to simplify the development of these complex experiments. These tools allow the user to describe data acquisition and processing tasks using state machines defined in SCXML. These state machines become part of the system setup information, so the behaviour of the system can be changed subsequently by simply modifying these state machines. All the events and key detected are stored by the host computer. This document is a poster. (authors)
Xiang, Guiming; Pu, Xiaoyun; Jiang, Dongneng; Liu, Linlin; Liu, Chang; Liu, Xiaobo
2013-01-01
The marine bacterium Vibrio parahaemolyticus (V. parahaemolyticus) causes gastroenteritis in humans via the ingestion of raw or undercooked contaminated seafood, and early diagnosis and prompt treatment are important for the prevention of V. parahaemolyticus-related diseases. In this study, a real-time resistance measurement based on loop-mediated isothermal amplification (LAMP), electrochemical ion bonding (Crystal violet and Mg2+), real-time monitoring, and derivative analysis was developed. V. parahaemolyticus DNA was first amplified by LAMP, and the products (DNA and pyrophosphate) represented two types of negative ions that could combine with a positive dye (Crystal violet) and positive ions (Mg2+) to increase the resistance of the reaction liquid. This resistance was measured in real-time using a specially designed resistance electrode, thus permitting the quantitative detection of V. parahaemolyticus. The results were obtained in 1–2 hours, with a minimum bacterial density of 10 CFU.mL−1 and high levels of accuracy (97%), sensitivity (96.08%), and specificity (97.96%) when compared to cultivation methods. Therefore, this simple and rapid method has a potential application in the detection of V. parahaemolyticus on a gene chip or in point-of-care testing. PMID:23991096
Frosth, Sara; König, Ulrika; Nyman, Ann-Kristin; Aspán, Anna
2017-09-01
Dichelobacter nodosus is the principal cause of ovine footrot and strain virulence is an important factor in disease severity. Therefore, detection and virulence determination of D. nodosus is important for proper diagnosis of the disease. Today this is possible by real-time PCR analysis. Analysis of large numbers of samples is costly and laborious; therefore, pooling of individual samples is common in surveillance programs. However, pooling can reduce the sensitivity of the method. The aim of this study was to develop a pooling method for real-time PCR analysis that would allow sensitive detection and simultaneous virulence determination of D. nodosus. A total of 225 sheep from 17 flocks were sampled using ESwabs within the Swedish Footrot Control Program in 2014. Samples were first analysed individually and then in pools of five by real-time PCR assays targeting the 16S rRNA and aprV2/B2 genes of D. nodosus. Each pool consisted of four negative and one positive D. nodosus samples with varying amounts of the bacterium. In the individual analysis, 61 (27.1%) samples were positive in the 16S rRNA and the aprV2/B2 PCR assays and 164 (72.9%) samples were negative. All samples positive in the aprV2/B2 PCR-assay were of aprB2 variant. The pooled analysis showed that all 41 pools were also positive for D. nodosus 16S rRNA and the aprB2 variant. The diagnostic sensitivity for pooled and individual samples was therefore similar. Our method includes concentration of the bacteria before DNA-extraction. This may account for the maintenance of diagnostic sensitivity. Diagnostic sensitivity in the real-time PCR assays of the pooled samples were comparable to the sensitivity obtained for individually analysed samples. Even sub-clinical infections were able to be detected in the pooled PCR samples which is important for control of the disease. This method may therefore be implemented in footrot control programs where it can replace analysis of individual samples.
Huang, Huali; Cheng, Fang; Wang, Ruoan; Zhang, Dabing; Yang, Litao
2013-01-01
Proper selection of endogenous reference genes and their real-time PCR assays is quite important in genetically modified organisms (GMOs) detection. To find a suitable endogenous reference gene and its real-time PCR assay for common wheat (Triticum aestivum L.) DNA content or copy number quantification, four previously reported wheat endogenous reference genes and their real-time PCR assays were comprehensively evaluated for the target gene sequence variation and their real-time PCR performance among 37 common wheat lines. Three SNPs were observed in the PKABA1 and ALMT1 genes, and these SNPs significantly decreased the efficiency of real-time PCR amplification. GeNorm analysis of the real-time PCR performance of each gene among common wheat lines showed that the Waxy-D1 assay had the lowest M values with the best stability among all tested lines. All results indicated that the Waxy-D1 gene and its real-time PCR assay were most suitable to be used as an endogenous reference gene for common wheat DNA content quantification. The validated Waxy-D1 gene assay will be useful in establishing accurate and creditable qualitative and quantitative PCR analysis of GM wheat.
Directory of Open Access Journals (Sweden)
Huali Huang
Full Text Available Proper selection of endogenous reference genes and their real-time PCR assays is quite important in genetically modified organisms (GMOs detection. To find a suitable endogenous reference gene and its real-time PCR assay for common wheat (Triticum aestivum L. DNA content or copy number quantification, four previously reported wheat endogenous reference genes and their real-time PCR assays were comprehensively evaluated for the target gene sequence variation and their real-time PCR performance among 37 common wheat lines. Three SNPs were observed in the PKABA1 and ALMT1 genes, and these SNPs significantly decreased the efficiency of real-time PCR amplification. GeNorm analysis of the real-time PCR performance of each gene among common wheat lines showed that the Waxy-D1 assay had the lowest M values with the best stability among all tested lines. All results indicated that the Waxy-D1 gene and its real-time PCR assay were most suitable to be used as an endogenous reference gene for common wheat DNA content quantification. The validated Waxy-D1 gene assay will be useful in establishing accurate and creditable qualitative and quantitative PCR analysis of GM wheat.
Huang, Huali; Cheng, Fang; Wang, Ruoan; Zhang, Dabing; Yang, Litao
2013-01-01
Proper selection of endogenous reference genes and their real-time PCR assays is quite important in genetically modified organisms (GMOs) detection. To find a suitable endogenous reference gene and its real-time PCR assay for common wheat (Triticum aestivum L.) DNA content or copy number quantification, four previously reported wheat endogenous reference genes and their real-time PCR assays were comprehensively evaluated for the target gene sequence variation and their real-time PCR performance among 37 common wheat lines. Three SNPs were observed in the PKABA1 and ALMT1 genes, and these SNPs significantly decreased the efficiency of real-time PCR amplification. GeNorm analysis of the real-time PCR performance of each gene among common wheat lines showed that the Waxy-D1 assay had the lowest M values with the best stability among all tested lines. All results indicated that the Waxy-D1 gene and its real-time PCR assay were most suitable to be used as an endogenous reference gene for common wheat DNA content quantification. The validated Waxy-D1 gene assay will be useful in establishing accurate and creditable qualitative and quantitative PCR analysis of GM wheat. PMID:24098735
A Wireless Sensor System for Real-Time Monitoring and Fault Detection of Motor Arrays.
Medina-García, Jonathan; Sánchez-Rodríguez, Trinidad; Galán, Juan Antonio Gómez; Delgado, Aránzazu; Gómez-Bravo, Fernando; Jiménez, Raúl
2017-02-25
This paper presents a wireless fault detection system for industrial motors that combines vibration, motor current and temperature analysis, thus improving the detection of mechanical faults. The design also considers the time of detection and further possible actions, which are also important for the early detection of possible malfunctions, and thus for avoiding irreversible damage to the motor. The remote motor condition monitoring is implemented through a wireless sensor network (WSN) based on the IEEE 802.15.4 standard. The deployed network uses the beacon-enabled mode to synchronize several sensor nodes with the coordinator node, and the guaranteed time slot mechanism provides data monitoring with a predetermined latency. A graphic user interface offers remote access to motor conditions and real-time monitoring of several parameters. The developed wireless sensor node exhibits very low power consumption since it has been optimized both in terms of hardware and software. The result is a low cost, highly reliable and compact design, achieving a high degree of autonomy of more than two years with just one 3.3 V/2600 mAh battery. Laboratory and field tests confirm the feasibility of the wireless system.
Real-time detection of metal ions using conjugated polymer composite papers.
Lee, Ji Eun; Shim, Hyeon Woo; Kwon, Oh Seok; Huh, Yang-Il; Yoon, Hyeonseok
2014-09-21
Cellulose, a natural polymeric material, has widespread technical applications because of its inherent structural rigidity and high surface area. As a conjugated polymer, polypyrrole shows practical potential for a diverse and promising range of future technologies. Here, we demonstrate a strategy for the real-time detection and removal of metal ions with polypyrrole/cellulose (PPCL) composite papers in solution. Simply, the conjugated polymer papers had different chemical/physical properties by applying different potentials to them, which resulted in differentiable response patterns and adsorption efficiencies for individual metal ions. First, large-area PPCL papers with a diameter of 5 cm were readily obtained via vapor deposition polymerization. The papers exhibited both mechanical flexibility and robustness, in which polypyrrole retained its redox property perfectly. The ability of the PPCL papers to recognize metal ions was examined in static and flow cells, in which real-time current change was monitored at five different applied potentials (+1, +0.5, 0, -0.5, and -1 V vs. Ag/AgCl). Distinguishable signals in the PPCL paper responses were observed for individual metal ions through principal component analysis. Particularly, the PPCL papers yielded unique signatures for three metal ions, Hg(ii), Ag(i), and Cr(iii), even in a real sample, groundwater. The sorption of metal ions by PPCL papers was examined in the flow system. The PPCL papers had a greatly superior adsorption efficiency for Hg(ii) compared to that of the other metal ions. With the strong demand for the development of inexpensive, flexible, light-weight, and environmentally friendly devices, the fascinating characteristics of these PPCL papers are likely to provide good opportunities for low-cost paper-based flexible or wearable devices.
Attention focussing and anomaly detection in real-time systems monitoring
Doyle, Richard J.; Chien, Steve A.; Fayyad, Usama M.; Porta, Harry J.
1993-01-01
In real-time monitoring situations, more information is not necessarily better. When faced with complex emergency situations, operators can experience information overload and a compromising of their ability to react quickly and correctly. We describe an approach to focusing operator attention in real-time systems monitoring based on a set of empirical and model-based measures for determining the relative importance of sensor data.
Directory of Open Access Journals (Sweden)
Thaer YASEEN
2015-12-01
Full Text Available A recent severe outbreak of Xylella fastidiosa associated with ‘olive quick decline syndrome’ (OQDS was reported in Apulia (Southern Italy. In this study an on-site real-time loop-mediated isothermal amplification (real-time LAMP was developed for detecting X. fastidiosa in host plants and insects. A marked simplification of the DNA extraction procedure was obtained by heating the samples in a portable Smart-Dart device and using an optimized enhancer reaction buffer. The connection to a tablet or Smartphone allowed to visualize the results of the reaction in real time. Compared to PCR and ELISA, with which it showed comparable results in terms of sensitivity and reliability in the X. fastidiosa detection, this simplified real-time LAMP procedure proved to be “user friendly”, displaying the advantages to be an on-site detection method of easy handling, rapid execution and low cost.
Real-time statistical quality control and ARM
International Nuclear Information System (INIS)
Blough, D.K.
1992-05-01
An important component of the Atmospheric Radiation Measurement (ARM) Program is real-time quality control of data obtained from meteorological instruments. It is the goal of the ARM program to enhance the predictive capabilities of global circulation models by incorporating in them more detailed information on the radiative characteristics of the earth's atmosphere. To this end, a number of Cloud and Radiation Testbeds (CART's) will be built at various locations worldwide. Each CART will consist of an array of instruments designed to collect radiative data. The large amount of data obtained from these instruments necessitates real-time processing in order to flag outliers and possible instrument malfunction. The Bayesian dynamic linear model (DLM) proves to be an effective way of monitoring the time series data which each instrument generates. It provides a flexible yet powerful approach to detecting in real-time sudden shifts in a non-stationary multivariate time series. An application of these techniques to data arising from a remote sensing instrument to be used in the CART is provided. Using real data from a wind profiler, the ability of the DLM to detect outliers is studied. 5 refs
Kaspar, A; Pfister, K; Nielsen, M K; Silaghi, C; Fink, H; Scheuerle, M C
2017-01-11
Strongylus vulgaris has become a rare parasite in Germany during the past 50 years due to the practice of frequent prophylactic anthelmintic therapy. To date, the emerging development of resistance in Cyathostominae and Parascaris spp. to numerous equine anthelmintics has changed deworming management and the frequency of anthelmintic usage. In this regard, reliable detection of parasitic infections, especially of the highly pathogenic S. vulgaris is essential. In the current study, two diagnostic methods for the detection of infections with S. vulgaris were compared and information on the occurrence of this parasite in German horses was gained. For this purpose, faecal samples of 501 horses were screened for S. vulgaris with real-time PCR and an additional larval culture was performed in samples of 278 horses. A subset of 26 horses underwent multiple follow-up examinations with both methods in order to evaluate both the persistence of S. vulgaris infections and the reproducibility of each diagnostic method. The real-time PCR revealed S. vulgaris-DNA in ten of 501 investigated equine samples (1.9%). The larval culture demonstrated larvae of S. vulgaris in three of the 278 samples (1.1%). A direct comparison of the two methods was possible in 321 samples including 43 follow-up examinations with the result of 11 S. vulgaris-positive samples by real-time PCR and 4 S. vulgaris-positive samples by larval culture. The McNemar's test (p-value = 0.016) revealed a significant difference and the kappa values (0.525) showed a moderate agreement between real-time PCR and larval culture. The real-time PCR detected a significantly higher proportion of positives of S. vulgaris compared to larval culture and should thus be considered as a routine diagnostic method for the detection of S. vulgaris in equine samples.
Krishnan, M.; Bhowmik, B.; Hazra, B.; Pakrashi, V.
2018-02-01
In this paper, a novel baseline free approach for continuous online damage detection of multi degree of freedom vibrating structures using Recursive Principal Component Analysis (RPCA) in conjunction with Time Varying Auto-Regressive Modeling (TVAR) is proposed. In this method, the acceleration data is used to obtain recursive proper orthogonal components online using rank-one perturbation method, followed by TVAR modeling of the first transformed response, to detect the change in the dynamic behavior of the vibrating system from its pristine state to contiguous linear/non-linear-states that indicate damage. Most of the works available in the literature deal with algorithms that require windowing of the gathered data owing to their data-driven nature which renders them ineffective for online implementation. Algorithms focussed on mathematically consistent recursive techniques in a rigorous theoretical framework of structural damage detection is missing, which motivates the development of the present framework that is amenable for online implementation which could be utilized along with suite experimental and numerical investigations. The RPCA algorithm iterates the eigenvector and eigenvalue estimates for sample covariance matrices and new data point at each successive time instants, using the rank-one perturbation method. TVAR modeling on the principal component explaining maximum variance is utilized and the damage is identified by tracking the TVAR coefficients. This eliminates the need for offline post processing and facilitates online damage detection especially when applied to streaming data without requiring any baseline data. Numerical simulations performed on a 5-dof nonlinear system under white noise excitation and El Centro (also known as 1940 Imperial Valley earthquake) excitation, for different damage scenarios, demonstrate the robustness of the proposed algorithm. The method is further validated on results obtained from case studies involving
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. Copyright © 2014 Elsevier B.V. All rights reserved.
Farcas, Gabriella A; Soeller, Rainer; Zhong, Kathleen; Zahirieh, Alireza; Kain, Kevin C
2006-03-01
Imported drug-resistant malaria is a growing problem in industrialized countries. Rapid and accurate diagnosis is essential to prevent malaria-associated mortality in returned travelers. However, outside of a limited number of specialized centers, the microscopic diagnosis of malaria is slow, unreliable, and provides little information about drug resistance. Molecular diagnostics have the potential to overcome these limitations. We developed and evaluated a rapid, real-time polymerase chain reaction (PCR) assay to detect Plasmodium falciparum malaria and chloroquine (CQ)-resistance determinants in returned travelers who are febrile. A real-time PCR assay based on detection of the K76T mutation in PfCRT (K76T) of P. falciparum was developed on a LightCycler platform (Roche). The performance characteristics of the real-time assay were compared with those of the nested PCR-restriction fragment-length polymorphism (RFLP) and the sequence analyses of samples obtained from 200 febrile returned travelers, who included 125 infected with P. falciparum (48 of whom were infected CQ-susceptible [K76] and 77 of whom were CQ-resistant [T76] P. falciparum), 22 infected with Plasmodium vivax, 10 infected with Plasmodium ovale, 3 infected with Plasmodium malariae malaria, and 40 infected with other febrile syndromes. All patient samples were coded, and all analyses were performed blindly. The real-time PCR assay detected multiple pfcrt haplotypes associated with CQ resistance in geographically diverse malaria isolates acquired by travelers. Compared with nested-PCR RFLP (the reference standard), the real-time assay was 100% sensitive and 96.2% specific for detection of the P. falciparum K76T mutation. This assay is rapid, sensitive, and specific for the detection and characterization of CQ-resistant P. falciparum malaria in returned travelers. This assay is automated, standardized, and suitable for routine use in clinical diagnostic laboratories.
Real time loss detection for SNM in process
International Nuclear Information System (INIS)
Candy, J.V.; Dunn, D.R.; Gavel, D.T.
1980-01-01
This paper discusses the basis of a design for real time special nuclear material (SNM) loss detectors. The design utilizes process measurements and signal processing techniques to produce a timely estimate of material loss. A state estimator is employed as the primary signal processing algorithm. Material loss is indicated by changes in the states or process innovations (residuals). The design philosophy is discussed in the context of these changes
DEFF Research Database (Denmark)
Nielsen, Linette Buxbom; Hjulsager, Charlotte Kristiane; Larsen, Helene
conventional PCR assays with real-time PCR assays to obtain a uniform assay palette. The present work describes the development of a novel real-time RT-qPCR assay for the dual detection of canine and phocine distemper virus. The assay is relevant for the future detection of outbreaks of canine distemper virus...... in e.g. in farmed mink and wildlife and phocine distemper in seals. A set of primers and dual labelled probe was designed based on an alignment of distemper sequences in GenBank from various species and in-house sequences from recent outbreaks in Danish farmed mink. The assay amplifies a segment of 151...... bp in the Phosphoprotein (P) gene of the distemper virus genome. The dynamic range and PCR efficiency (E) was experimentally determined using 10-fold dilutions of a specially designed distemper DNA-oligo in addition to extracted RNA from clinical samples. E of the real-time assay was shown to range...
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.
Energy Technology Data Exchange (ETDEWEB)
Solaimani, Mohiuddin [Univ. of Texas-Dallas, Richardson, TX (United States); Iftekhar, Mohammed [Univ. of Texas-Dallas, Richardson, TX (United States); Khan, Latifur [Univ. of Texas-Dallas, Richardson, TX (United States); Thuraisingham, Bhavani [Univ. of Texas-Dallas, Richardson, TX (United States); Ingram, Joey Burton [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2015-09-01
Anomaly detection refers to the identi cation of an irregular or unusual pat- tern which deviates from what is standard, normal, or expected. Such deviated patterns typically correspond to samples of interest and are assigned different labels in different domains, such as outliers, anomalies, exceptions, or malware. Detecting anomalies in fast, voluminous streams of data is a formidable chal- lenge. This paper presents a novel, generic, real-time distributed anomaly detection framework for heterogeneous streaming data where anomalies appear as a group. We have developed a distributed statistical approach to build a model and later use it to detect anomaly. As a case study, we investigate group anomaly de- tection for a VMware-based cloud data center, which maintains a large number of virtual machines (VMs). We have built our framework using Apache Spark to get higher throughput and lower data processing time on streaming data. We have developed a window-based statistical anomaly detection technique to detect anomalies that appear sporadically. We then relaxed this constraint with higher accuracy by implementing a cluster-based technique to detect sporadic and continuous anomalies. We conclude that our cluster-based technique out- performs other statistical techniques with higher accuracy and lower processing time.
Real time ultrasonography in obstructive jaundice
International Nuclear Information System (INIS)
Cho, Kyung Sik; Kim, Ho Kyun; Sung, Nak Kwan; Kim, Soon Yong
1982-01-01
Ultrasonography is a predominantly accurate, relatively simple unique diagnostic method of obstructive jaundice. The ultrasonographic findings of obstructive jaundice are dilated intra- and extrahepatic duct with intraluminal hyper reflective echo or mass in and/ or around the bile duct. The superiority of high resolution real time ultrasonography for the diagnosis of obstructive jaundice is bases on the easy detectability of extra- and intrahepatic bile ducts by its multiple sectional images in a short time, the flexibility of probe and small crystal size. Author evaluated real time sonographic findings 46 obstructive jaundice patients confirmed by surgery or radiographical examinations. The results were: 1. Diameter of extrahepatic duct in obstructive jaundice were varied from normal to 4.0 Cm, mostly 8 to 10 mm in diameter (26%). Degree of dilatation of biliary duct appeared more prominent in cancer patients than other causes of obstruction. 2. The site of obstruction was detected in 85% (39/46) and its common site was common bile duct in 63% (29/46). 3. The diagnostic accuracy of choledocholithiasis and cancer was 82% (22/27) and 44% (4/9), respectively. Diagnostic accuracy of the real time ultrasonography in obstructive jaundice was over all 75% (34/46)
Shell-vial culture and real-time PCR applied to Rickettsia typhi and Rickettsia felis detection.
Segura, Ferran; Pons, Immaculada; Pla, Júlia; Nogueras, María-Mercedes
2015-11-01
Murine typhus is a zoonosis transmitted by fleas, whose etiological agent is Rickettsia typhi. Rickettsia felis infection can produces similar symptoms. Both are intracellular microorganisms. Therefore, their diagnosis is difficult and their infections can be misdiagnosed. Early diagnosis prevents severity and inappropriate treatment regimens. Serology can't be applied during the early stages of infection because it requires seroconversion. Shell-vial (SV) culture assay is a powerful tool to detect Rickettsia. The aim of the study was to optimize SV using a real-time PCR as monitoring method. Moreover, the study analyzes which antibiotics are useful to isolate these microorganisms from fleas avoiding contamination by other bacteria. For the first purpose, SVs were inoculated with each microorganism. They were incubated at different temperatures and monitored by real-time PCR and classical methods (Gimenez staining and indirect immunofluorescence assay). R. typhi grew at all temperatures. R. felis grew at 28 and 32 °C. Real-time PCR was more sensitive than classical methods and it detected microorganisms much earlier. Besides, the assay sensitivity was improved by increasing the number of SV. For the second purpose, microorganisms and fleas were incubated and monitored in different concentrations of antibiotics. Gentamicin, sufamethoxazole, trimethoprim were useful for R. typhi isolation. Gentamicin, streptomycin, penicillin, and amphotericin B were useful for R. felis isolation. Finally, the optimized conditions were used to isolate R. felis from fleas collected at a veterinary clinic. R. felis was isolated at 28 and 32 °C. However, successful establishment of cultures were not possible probably due to sub-optimal conditions of samples.
Directory of Open Access Journals (Sweden)
Kosuke Nakamura
2016-06-01
Real-time polymerase chain reaction (PCR detection method for unauthorized genetically modified (GM papaya (Carica papaya L. line PRSV-YK (PRSV-YK detection method was developed using whole genome sequence data (DDBJ Sequenced Read Archive under accession No. PRJDB3976. Interlaboratory validation datasets for PRSV-YK detection method were provided. Data indicating homogeneity of samples prepared for interlaboratory validation were included. Specificity and sensitivity test data for PRSV-YK detection method were also provided.
WiFi-Based Real-Time Calibration-Free Passive Human Motion Detection †
Gong, Liangyi; Yang, Wu; Man, Dapeng; Dong, Guozhong; Yu, Miao; Lv, Jiguang
2015-01-01
With the rapid development of WLAN technology, wireless device-free passive human detection becomes a newly-developing technique and holds more potential to worldwide and ubiquitous smart applications. Recently, indoor fine-grained device-free passive human motion detection based on the PHY layer information is rapidly developed. Previous wireless device-free passive human detection systems either rely on deploying specialized systems with dense transmitter-receiver links or elaborate off-line training process, which blocks rapid deployment and weakens system robustness. In the paper, we explore to research a novel fine-grained real-time calibration-free device-free passive human motion via physical layer information, which is independent of indoor scenarios and needs no prior-calibration and normal profile. We investigate sensitivities of amplitude and phase to human motion, and discover that phase feature is more sensitive to human motion, especially to slow human motion. Aiming at lightweight and robust device-free passive human motion detection, we develop two novel and practical schemes: short-term averaged variance ratio (SVR) and long-term averaged variance ratio (LVR). We realize system design with commercial WiFi devices and evaluate it in typical multipath-rich indoor scenarios. As demonstrated in the experiments, our approach can achieve a high detection rate and low false positive rate. PMID:26703612
Use of real-time PCR to detect canine parvovirus in feces of free-ranging wolves
Mech, L. David; Almberg, Emily S.; Smith, Douglas; Goyal, Sagar; Singer, Randall S.
2012-01-01
Using real-time PCR, we tested 15 wolf (Canis lupus) feces from the Superior National Forest (SNF), Minnesota, USA, and 191 from Yellowstone National Park (YNP), USA, collected during summer and 13 during winter for canine parvovirus (CPV)-2 DNA. We also tested 20 dog feces for CPV-2 DNA. The PCR assay was 100% sensitive and specific with a minimum detection threshold of 104 50% tissue culture infective dose. Virus was detected in two winter specimens but none of the summer specimens. We suggest applying the technique more broadly especially with winter feces.
Use of real-time PCR to detect canine parvovirus in feces of free-ranging wolves.
Mech, L David; Almberg, Emily S; Smith, Douglas; Goyal, Sagar; Singer, Randall S
2012-04-01
Using real-time PCR, we tested 15 wolf (Canis lupus) feces from the Superior National Forest (SNF), Minnesota, USA, and 191 from Yellowstone National Park (YNP), USA, collected during summer and 13 during winter for canine parvovirus (CPV)-2 DNA. We also tested 20 dog feces for CPV-2 DNA. The PCR assay was 100% sensitive and specific with a minimum detection threshold of 10(4) 50% tissue culture infective dose. Virus was detected in two winter specimens but none of the summer specimens. We suggest applying the technique more broadly especially with winter feces.
Rapid detection of Van genes in rectal swabs by real time PCR in Southern Brazil
Directory of Open Access Journals (Sweden)
Vlademir Cantarelli
2011-10-01
Full Text Available INTRODUCTION: Laboratory-based surveillance is an important component in the control of vancomycin resistant enterococci (VRE. METHODS: The study aimed to evaluate real-time polymerase chain reaction (RT-PCR (genes vanA-vanB for VRE detection on 115 swabs from patients included in a surveillance program. RESULTS: Sensitivity of RT-PCR was similar to primary culture (75% and 79.5%, respectively when compared to broth enriched culture, whereas specificity was 83.1%. CONCLUSIONS: RT-PCR provides same day results, however it showed low sensitivity for VRE detection.
Ni, Yizhao; Lingren, Todd; Hall, Eric S; Leonard, Matthew; Melton, Kristin; Kirkendall, Eric S
2018-05-01
Timely identification of medication administration errors (MAEs) promises great benefits for mitigating medication errors and associated harm. Despite previous efforts utilizing computerized methods to monitor medication errors, sustaining effective and accurate detection of MAEs remains challenging. In this study, we developed a real-time MAE detection system and evaluated its performance prior to system integration into institutional workflows. Our prospective observational study included automated MAE detection of 10 high-risk medications and fluids for patients admitted to the neonatal intensive care unit at Cincinnati Children's Hospital Medical Center during a 4-month period. The automated system extracted real-time medication use information from the institutional electronic health records and identified MAEs using logic-based rules and natural language processing techniques. The MAE summary was delivered via a real-time messaging platform to promote reduction of patient exposure to potential harm. System performance was validated using a physician-generated gold standard of MAE events, and results were compared with those of current practice (incident reporting and trigger tools). Physicians identified 116 MAEs from 10 104 medication administrations during the study period. Compared to current practice, the sensitivity with automated MAE detection was improved significantly from 4.3% to 85.3% (P = .009), with a positive predictive value of 78.0%. Furthermore, the system showed potential to reduce patient exposure to harm, from 256 min to 35 min (P patient exposure to potential harm following MAE events.
van Doornum, G J J; Schutten, Martin; Voermans, J; Guldemeester, G J J; Niesters, H G M
2007-01-01
Several real-time PCR and nucleic acid sequence-based amplification (NASBA) primer pairs and a modified real-time PCR primer pair for the detection of enteroviruses were compared. The modified real-time PCR primer pair was evaluated on clinical samples in comparison with cell culture using the
A new comparison of hyperspectral anomaly detection algorithms for real-time applications
Díaz, María.; López, Sebastián.; Sarmiento, Roberto
2016-10-01
Due to the high spectral resolution that remotely sensed hyperspectral images provide, there has been an increasing interest in anomaly detection. The aim of anomaly detection is to stand over pixels whose spectral signature differs significantly from the background spectra. Basically, anomaly detectors mark pixels with a certain score, considering as anomalies those whose scores are higher than a threshold. Receiver Operating Characteristic (ROC) curves have been widely used as an assessment measure in order to compare the performance of different algorithms. ROC curves are graphical plots which illustrate the trade- off between false positive and true positive rates. However, they are limited in order to make deep comparisons due to the fact that they discard relevant factors required in real-time applications such as run times, costs of misclassification and the competence to mark anomalies with high scores. This last fact is fundamental in anomaly detection in order to distinguish them easily from the background without any posterior processing. An extensive set of simulations have been made using different anomaly detection algorithms, comparing their performances and efficiencies using several extra metrics in order to complement ROC curves analysis. Results support our proposal and demonstrate that ROC curves do not provide a good visualization of detection performances for themselves. Moreover, a figure of merit has been proposed in this paper which encompasses in a single global metric all the measures yielded for the proposed additional metrics. Therefore, this figure, named Detection Efficiency (DE), takes into account several crucial types of performance assessment that ROC curves do not consider. Results demonstrate that algorithms with the best detection performances according to ROC curves do not have the highest DE values. Consequently, the recommendation of using extra measures to properly evaluate performances have been supported and justified by
Directory of Open Access Journals (Sweden)
Brenden Jongman
2015-10-01
Full Text Available Humanitarian organizations have a crucial role in response and relief efforts after floods. The effectiveness of disaster response is contingent on accurate and timely information regarding the location, timing and impacts of the event. Here we show how two near-real-time data sources, satellite observations of water coverage and flood-related social media activity from Twitter, can be used to support rapid disaster response, using case-studies in the Philippines and Pakistan. For these countries we analyze information from disaster response organizations, the Global Flood Detection System (GFDS satellite flood signal, and flood-related Twitter activity analysis. The results demonstrate that these sources of near-real-time information can be used to gain a quicker understanding of the location, the timing, as well as the causes and impacts of floods. In terms of location, we produce daily impact maps based on both satellite information and social media, which can dynamically and rapidly outline the affected area during a disaster. In terms of timing, the results show that GFDS and/or Twitter signals flagging ongoing or upcoming flooding are regularly available one to several days before the event was reported to humanitarian organizations. In terms of event understanding, we show that both GFDS and social media can be used to detect and understand unexpected or controversial flood events, for example due to the sudden opening of hydropower dams or the breaching of flood protection. The performance of the GFDS and Twitter data for early detection and location mapping is mixed, depending on specific hydrological circumstances (GFDS and social media penetration (Twitter. Further research is needed to improve the interpretation of the GFDS signal in different situations, and to improve the pre-processing of social media data for operational use.
Real-Time WGS-based Typing of VTEC Isolates for Surveillance and Outbreak Detection
DEFF Research Database (Denmark)
Joensen, Katrine Grimstrup; Hasman, Henrik; Scheutz, F.
2013-01-01
the IonTorrent PGM benchtop sequencing technology. WGS-based typing was carried out using web-based tools, developed by the Center for Genomic Epidemiology (www.genomicepidemiology.org), for determination of MLST types, virulence genes and phylogenetic relationship between the isolates. The WGS-based...... a small outbreak occurred. For all isolates, apart from one resulting in poor sequence output, the WGS-based typing led to detection of the same virulence gene variants as the routine typing, and was also able to detect many other possible virulence features, and in most instances produce a useful typing...... result faster than routine typing. Also, the WGS-approach was able to correctly detect, according to the routine typing, the isolates belonging to the outbreak. Conclusion: The real-time WGS-based typing was able to produce typing results comparable to the routine typing, at least as fast as the routine...
EVA GREEN REAL-TIME PCR USED TO DETECT CELERY AS AN ALLERGEN IN FOOD
Directory of Open Access Journals (Sweden)
Ondrej Škultéty
2011-04-01
Full Text Available EvaGreen® Real-Time PCR method has been used for celery(Apium graveolens allergen detection. A primer designed in mannitol dehydrogenase gene region has been used for specific celery identification in sample. The results show possibility to create calibration curve using artificially adulterated samples. The increasing variability between parallel calibration of celery samples has been observed from 0.1 % to 100%. Detection limit has been set to value 0.1% in celery representing 1000 ppm. Fluorescent signal has been presented even in samples with lower percentage addition of celery but these samples have been excluded according to unspecific melting curve.doi:10.5219/138
Real-Time Detection of Staphylococcus Aureus Using Whispering Gallery Mode Optical Microdisks
Directory of Open Access Journals (Sweden)
Hala Ghali
2016-05-01
Full Text Available Whispering Gallery Mode (WGM microresonators have recently been studied as a means to achieve real-time label-free detection of biological targets such as virus particles, specific DNA sequences, or proteins. Due to their high quality (Q factors, WGM resonators can be highly sensitive. A biosensor also needs to be selective, requiring proper functionalization of its surface with the appropriate ligand that will attach the biomolecule of interest. In this paper, WGM microdisks are used as biosensors for detection of Staphylococcus aureus. The microdisks are functionalized with LysK, a phage protein specific for staphylococci at the genus level. A binding event on the surface shifts the resonance peak of the microdisk resonator towards longer wavelengths. This reactive shift can be used to estimate the surface density of bacteria that bind to the surface of the resonator. The limit of detection of a microdisk with a Q-factor around 104 is on the order of 5 pg/mL, corresponding to 20 cells. No binding of Escherichia coli to the resonators is seen, supporting the specificity of the functionalization scheme.
Martín, Maria Cruz; del Rio, Beatriz; Martínez, Noelia; Magadán, Alfonso H; Alvarez, Miguel A
2008-12-01
One of the main microbiological problems of the dairy industry is the susceptibility of starter bacteria to virus infections. Lactobacillus delbrueckii, a component of thermophilic starter cultures used in the manufacture of several fermented dairy products, including yogurt, is also sensitive to bacteriophage attacks. To avoid the problems associated with these viruses, quick and sensitive detection methods are necessary. In the present study, a fast real-time quantitative polymerase chain reaction assay for the direct detection and quantification of L. delbrueckii phages in milk was developed. A set of primers and a TaqMan MGB probe was designed, based on the lysin gene sequence of different L. delbrueckii phages. The results show the proposed method to be a rapid (total processing time 30 min), specific and highly sensitive technique for detecting L. delbrueckii phages in milk.
Benitez, Alvaro J; Winchell, Jonas M
2016-04-01
We developed a single tube multiplex real-time PCR assay that allows for the rapid detection and typing of 9 nonpneumophila Legionella spp. isolates that are clinically relevant. The multiplex assay is capable of simultaneously detecting and discriminating L. micdadei, L. bozemanii, L. dumoffii, L. longbeachae, L. feeleii, L. anisa, L. parisiensis, L. tucsonensis serogroup (sg) 1 and 3, and L. sainthelensis sg 1 and 2 isolates. Evaluation of the assay with nucleic acid from each of these species derived from both clinical and environmental isolates and typing strains demonstrated 100% sensitivity and 100% specificity when tested against 43 other Legionella spp. Typing of L. anisa, L. parisiensis, and L. tucsonensis sg 1 and 3 isolates was accomplished by developing a real-time PCR assay followed by high-resolution melt (HRM) analysis targeting the ssrA gene. Further typing of L. bozemanii, L. longbeachae, and L. feeleii isolates to the serogroup level was accomplished by developing a real-time PCR assay followed by HRM analysis targeting the mip gene. When used in conjunction with other currently available diagnostic tests, these assays may aid in rapidly identifying specific etiologies associated with Legionella outbreaks, clusters, sporadic cases, and potential environmental sources. Published by Elsevier Inc.
Kireev, SV; Petrov, NG; Podolyako, EM; Shnyrev, SL
The absorption of mercaptan mixtures used for odorizing natural gas and mixtures of natural gas is experimentally studied in the spectral range 2.5-20 mu m. An absorption method for the real-time detection of the odorant concentration is proposed. The method is based on intensity measurements of the
Becherer, Lisa; Bakheit, Mohammed; Frischmann, Sieghard; Stinco, Silvina; Borst, Nadine; Zengerle, Roland; von Stetten, Felix
2018-04-03
A variety of real-time detection techniques for loop-mediated isothermal amplification (LAMP) based on the change in fluorescence intensity during DNA amplification enable simultaneous detection of multiple targets. However, these techniques depend on fluorogenic probes containing target-specific sequences. That complicates the adaption to different targets leading to time-consuming assay optimization. Here, we present the first universal real-time detection technique for multiplex LAMP. The novel approach allows simple assay design and is easy to implement for various targets. The innovation features a mediator displacement probe and a universal reporter. During amplification of target DNA the mediator is displaced from the mediator displacement probe. Then it hybridizes to the reporter generating a fluorescence signal. The novel mediator displacement (MD) detection was validated against state-of-the-art molecular beacon (MB) detection by means of a HIV-1 RT-LAMP: MD surpassed MB detection by accelerated probe design (MD: 10 min, MB: 3-4 h), shorter times to positive (MD 4.1 ± 0.1 min shorter than MB, n = 36), improved signal-to-noise fluorescence ratio (MD: 5.9 ± 0.4, MB: 2.7 ± 0.4; n = 15), and showed equally good or better analytical performance parameters. The usability of one universal mediator-reporter set in different multiplex assays was successfully demonstrated for a biplex RT-LAMP of HIV-1 and HTLV-1 and a biplex LAMP of Haemophilus ducreyi and Treponema pallidum, both showing good correlation between target concentration and time to positive. Due to its simple implementation it is suggested to extend the use of the universal mediator-reporter sets to the detection of various other diagnostic panels.
Madani, Mehrdad; Subbotin, Sergei A; Moens, Maurice
2005-04-01
The potato cyst nematode Globodera pallida and the beet cyst nematode Heterodera schachtii are major nematode pests in world agriculture. Precise identification and knowledge about the number of nematodes in field soil are necessary to develop effective integrated pest control. Here we report the results of the Real-Time PCR assay for the rapid detection and quantification of G. pallida and H. schachtii. Using species specific primers and SYBR green I dye, we were able to detect a single second stage juvenile of cyst forming nematodes in samples. The specificity of the reaction was confirmed by the lack of amplification of DNAs from other Heterodera or Globodera species. Validation tests showed a rather high correlation between real numbers of second stage juveniles in a sample and expected numbers detected by Real-Time PCR. Reasons for observed differences in sensitivity and reliability of quantification detection for two species as well as other problems of Real-Time PCR are discussed. The Real-Time PCR assay with SYBR green I dye targeting fragments of the ITS-rDNA provided a sensitive means for the rapid and simultaneous detection and quantification of juveniles of these pests.
Li, Nan; Wang, Jiahui; Shen, Qing; Han, Chunhui; Zhang, Jing; Li, Fengqin; Xu, Jin; Jiang, Tao
2013-11-01
To develop a real-time PCR method for identification and detection of domestic horse meat (Equus caballus) in animal-origin products. The primer and TaqMan-probe was designed and synthesized according to the EU reference laboratory and 87 bp fragments was amplified for horse ingredients. The specificity and sensitivity was tested by artificially spiked horse meat into other domestic meat, such as cattle, sheep, pork, chicken, duck and rabbit. 122 samples of cattle and sheep products were random collected in Beijing market and the detection of horse meat was carried out. The real-time PCR in this study has high specificity and sensitivity for horse meat. No cross-reaction was observed between the horse and sheep, pork, chicken, duck and rabbit meat. There was little cross reaction between horse and cattle when the CT value reach 33. 81. The method can detect 0.1% of horse meat mixed with other domestic animal-origin products. No horse meat ingredients were detected in 122 samples in this survey. There was no horse meat mixed into cattle and sheep products in Beijing marked.
Directory of Open Access Journals (Sweden)
Indrawati Sendow
2014-05-01
Full Text Available Nipah is a dangerous zoonotic disease with a high social, economical and psychological impact. Fruitbat Pteropus sp. is one of the nipah virus reservoir host. As the virus is categorized as a dangerous zoonoticdisease that cause fatal in human, all works related to live virus should be conducted in a laboratory withBSL4 facilities. The detection of nipah virus using real time PCR to replace virus isolastion can thereforebe conducted in a laboratory without BSL4 facilities. The results was further confirmed at referencelaboratory at Australian Animal Health Laboratory ( AAHL Geelong, Australia, indicated that nipahvirus can be detected in saliva of fruit bat P. vampyrus in Medan North Sumatera.
Sroka-Oleksiak, Agnieszka; Ufir, Krzysztof; Salamon, Dominika; Bulanda, Malgorzata; Gosiewski, Tomasz
Lyme disease, caused by Borrelia burgdorferi, is a multisystem disease that often makes difficulties to recognize caused by their genetic heterogenity. Currently, the gold standard for the detection of Lyme disease (LD) is serologic diagnostics based mainly on tests: ELISA and Western blot (WB). These methods, however, are subject to consider- able defect, especially in the initial phase of infection due to the occurrence of so-called serological window period and low specificity. For this reason, they might be replaced by molecular methods, for example polymerase chain reaction (PCR), which should be more sensitivity and specificity. In the present study we attempt to optimize the PCR reaction conditions and enhance existing test sensitivity by applying the equivalent of real time PCR - nested PCR for detection B. burgdorferi DNA in the patient's blood. The study involved 94 blood samples of patients with suspected LD. From each sample, 1.5 ml of blood was used for the isolation of bacterial DNA and PCR real time am- plification and its equivalent, in nested version. The remaining part earmarked for serologi- cal testing. Optimization of the reaction conditions made experimentally, using gradient of the temperature and gradient of the magnesium ions concentration for reaction real time in nested-PCR and PCR version. The results show that the nested-PCR real time, has a much higher sensitivity 45 (47.8%) of positive results for the detection of B. burgdorferi compared to the single- variety, without a preceding pre-amplification 2 (2.1%). Serological methods allowed the detection of infection in 41 (43.6%) samples. These results support of the nested PCR method as a better molecular tool for the detection of B. burgdorferi infection than classical PCR real time reaction. The nested-PCR real time method may be considered as a complement to ELISA and WB mainly in the early stages of infection, when in the blood circulating B. burgdorferi cells. By contrast, the
Multiplex real-time PCR SYBR Green for detection and typing of group III Clostridium botulinum.
Anniballi, Fabrizio; Auricchio, Bruna; Delibato, Elisabetta; Antonacci, Monia; De Medici, Dario; Fenicia, Lucia
2012-01-27
Clostridium botulinum type C and type D belonging to the group III organisms, are mainly responsible for animal botulism outbreaks. Clinical signs alone are often insufficient to make a diagnosis of botulism and a laboratory confirmation is required. Laboratory confirmation can be performed by demonstrating the presence of botulinum neurotoxins in serum, gastrointestinal contents, liver, wound of sick or dead animals, or by demonstrating the presence of C. botulinum in gastrointestinal contents, liver, and wound. Demonstration of spores in gastrointestinal contents or tissue of animals with clinical signs indicative of botulism reinforces the clinical diagnosis. With the aim of detecting and typing C. botulinum group III organisms, a multiplex real-time PCR SYBR Green was developed and in-house validated. Selectivity, limit of detection, relative accuracy, relative specificity, relative sensitivity, and repeatability of the method were investigated. The multiplex real-time PCR SYBR green used showed a 100% selectivity, 100% relative accuracy, 100% relative specificity, 100% relative sensitivity and a limit of detection of 277 and 580 DNA copies for C. botulinum type C and C. botulinum type D, respectively. The method reported here represents a suitable tool for laboratory diagnosis of type C and D botulism and for testing a large number of samples collected during the animal botulism surveillance and prevention activities. Copyright © 2011 Elsevier B.V. All rights reserved.
Sensitive detection of porcine DNA in processed animal proteins using a TaqMan real-time PCR assay.
Pegels, N; González, I; Fernández, S; García, T; Martín, R
2012-01-01
A TaqMan real-time PCR method was developed for specific detection of porcine-prohibited material in industrial feeds. The assay combines the use of a porcine-specific primer pair, which amplifies a 79 bp fragment of the mitochondrial (mt) 12 S rRNA gene, and a locked nucleic acid (LNA) TaqMan probe complementary to a target sequence lying between the porcine-specific primers. The nuclear 18 S rRNA gene system, yielding a 77 bp amplicon, was employed as a positive amplification control to monitor the total content of amplifiable DNA in the samples. The specificity of the porcine primers-probe system was verified against different animal and plant species, including mammals, birds and fish. The applicability of the real-time PCR protocol to detect the presence of porcine mt DNA in feeds was determined through the analysis of 190 industrial feeds (19 known reference and 171 blind samples) subjected to stringent processing treatments. The performance of the method allows qualitative and highly sensitive detection of short fragments from porcine DNA in all the industrial feeds declared to contain porcine material. Although the method has quantitative potential, the real quantitative capability of the assay is limited by the existing variability in terms of composition and processing conditions of the feeds, which affect the amount and quality of amplifiable DNA.
Kotrotsiou, Tzimoula; Tzimoula, Kotrotsiou; Exindari, Maria; Maria, Exindari; Diza, Eudoxia; Eudoxia, Diza; Gioula, Georgia; Georgia, Gioula; Melidou, Angeliki; Angeliki, Melidou; Malisiovas, Nikolaos; Nikolaos, Malisiovas
2015-02-01
The study aimed to identify the proportion of tetM-positive Ureaplasma spp. isolates phenotypically susceptible to tetracycline by real-time PCR. Ureaplasma spp. strains of urogenital origin were isolated from 100 female or male adults on A7 agar plates. The presence of Ureaplasma was confirmed by the presence of urease gene by a novel real-time PCR method. Genotyping and sensitivity to tetracyclines were examined using commercial methods. The tetM gene was detected by a novel real-time PCR method especially designed for this study. Ureaplasma parvum was isolated from 87 of the specimens; Ureaplasma urealyticum, from 12; and both species were isolated from a single specimen. All isolates were phenotypically susceptible to tetracyclines. Thirty-five strains were tetM carriers; 29 (82.9%), U. parvum; 5 (14.3%), U. urealyticum; and 1 (2.9%), U. parvum/U. urealyticum. No statistically significant difference was observed between the 3 groups. Four (40%) tetM carriers were isolated from 10 symptomatic men; 11 (32.4%), from 34 symptomatic women; and 20 (35.7%), from 56 asymptomatic women. No statistically significant difference was observed between the 3 groups. The tetM determinant is detected in 35% of phenotypically susceptible to tetracycline Ureaplasma spp. Greek isolates. The use of a real-time PCR technique is particularly helpful, as it makes its detection easy; cost-effective; rapid; and, therefore, more convenient for the surveillance of the dissemination of the tetM resistance gene. Copyright © 2015 Elsevier Inc. All rights reserved.
Hinić, Vladimira; Feuz, Kinga; Turan, Selda; Berini, Andrea; Frei, Reno; Pfeifer, Karin; Goldenberger, Daniel
2017-05-01
Rapid and reliable diagnosis is crucial for correct management of tuberculosis. The Abbott RealTime MTB Assay represents a novel qualitative real-time PCR assay for direct detection of M. tuberculosis-complex (MTB) DNA from respiratory samples. The test targets two highly conserved sequences, the multi-copy insertion element IS6110 and the protein antigen B (PAB) gene of MTB, allowing even the detection of IS6610-deficient strains. We evaluated this commercial diagnostic test by analyzing 200 respiratory and, for the first time, 87 non-respiratory clinical specimens from our tertiary care institution and compared its results to our IS6110-based in-house real-time PCR for MTB as well as MTB culture. Overall sensitivity for Abbott RealTime MTB was 100% (19/19) in smear positive and 87.5% (7/8) in smear negative specimens, while the specificity of the assay was 100% (260/260). For both non-respiratory smear positive and smear negative specimens Abbott RealTime MTB tests showed 100% (8/8) sensitivity and 100% (8/8) specificity. Cycle threshold (Ct) value analysis of 16 MTB positive samples showed a slightly higher Ct value of the Abbott RealTime MTB test compared to our in-house MTB assay (mean delta Ct = 2.55). In conclusion, the performance of the new Abbott RealTime MTB Assay was highly similar to culture and in-house MTB PCR. We document successful analysis of 87 non-respiratory samples with the highly automated Abbott RealTime MTB test with no inhibition observed. Copyright © 2017 Elsevier Ltd. All rights reserved.
International Nuclear Information System (INIS)
Zhang Hong-Yan; Yang Li-Quan; Ning Ting-Yin; Liu Wei-Min; Sun Jia-Yu; Wang Peng-Fei; Meng Lan; Nie Jia-Cai
2012-01-01
A laser scanning confocal imaging-surface plasmon resonance (LSCI-SPR) instrument integrated with a wavelength-dependent surface plasmon resonance (SPR) sensor and a laser scanning confocal microscopy (LSCM) is built to detect the bonding process of human IgG and fluorescent-labeled affinity purified antibodies in real time. The shifts of resonant wavelength at different reaction time stages are obtained by SPR, corresponding well with the changes of the fluorescence intensity collected by using LSCM. The instrument shows the merits of the combination and complementation of the SPR and LSCM, with such advantages as quantificational analysis, high spatial resolution and real time monitor, which are of great importance for practical applications in biosensor and life science. (general)
Automatic near-real-time detection of CMEs in Mauna Loa K-Cor coronagraph images
Thompson, W. T.; St Cyr, O. C.; Burkepile, J.; Posner, A.
2017-12-01
A simple algorithm has been developed to detect the onset of coronal massejections (CMEs), together with an estimate of their speed, in near-real-timeusing images of the linearly polarized white-light solar corona taken by theK-Cor telescope at the Mauna Loa Solar Observatory (MLSO). The algorithm usedis a variation on the Solar Eruptive Event Detection System (SEEDS) developedat George Mason University. The algorithm was tested against K-Cor data takenbetween 29 April 2014 and 20 February 2017, on days which the MLSO websitemarked as containing CMEs. This resulted in testing of 139 days worth of datacontaining 171 CMEs. The detection rate varied from close to 80% in 2014-2015when solar activity was high, down to as low as 20-30% in 2017 when activitywas low. The difference in effectiveness with solar cycle is attributed to thedifference in relative prevalance of strong CMEs between active and quietperiods. There were also twelve false detections during this time period,leading to an average false detection rate of 8.6% on any given day. However,half of the false detections were clustered into two short periods of a fewdays each when special conditions prevailed to increase the false detectionrate. The K-Cor data were also compared with major Solar Energetic Particle(SEP) storms during this time period. There were three SEP events detectedeither at Earth or at one of the two STEREO spacecraft where K-Cor wasobserving during the relevant time period. The K-Cor CME detection algorithmsuccessfully generated alerts for two of these events, with lead times of 1-3hours before the SEP onset at 1 AU. The third event was not detected by theautomatic algorithm because of the unusually broad width of the CME in positionangle.
Development and validation of real-time PCR for rapid detection of Mecistocirrus digitatus.
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Subhra Subhadra
Full Text Available Hematophagous activity of Mecistocirrus digitatus, which causes substantial blood and weight loss in large ruminants, is an emerging challenge due to the economic loss it brings to the livestock industry. Infected animals are treated with anthelmintic drugs, based on the identification of helminth species and the severity of infection; however, traditional methods such as microscopic identification and the counting of eggs for diagnosis and determination of level of infection are laborious, cumbersome and unreliable. To facilitate the detection of this parasite, a SYBR green-based real-time PCR was standardized and validated for the detection of M. digitatus infection in cattle and buffaloes. Oligonucleotides were designed to amplify partial Internal Transcribed Spacer (ITS-1 sequence of M. digitatus. The specificity of the primers was confirmed by non-amplification of DNA extracted from other commonly occurring gastrointestinal nematodes in ruminants. Plasmids were ligated with partial ITS-1 sequence of M. digitatus, serially diluted (hundred fold and used as standards in the real-time PCR assay. The quantification cycle (Cq values were plotted against the standard DNA concentration to produce a standard curve. The assay was sensitive enough to detect one plasmid containing the M. digitatus DNA. Clinical application of this assay was validated by testing the DNA extracted from the faeces of naturally infected cattle (n = 40 and buffaloes (n = 25. The results were compared with our standard curve to calculate the quantity of M. digitatus in each faecal sample. The Cq value of the assay depicted a strong linear relationship with faecal DNA content, with a regression coefficient of 0.984 and efficiency of 99%. This assay has noteworthy advantages over the conventional methods of diagnosis because it is more specific, sensitive and reliable.
Real-Time PCR in Clinical Microbiology: Applications for Routine Laboratory Testing
Espy, M. J.; Uhl, J. R.; Sloan, L. M.; Buckwalter, S. P.; Jones, M. F.; Vetter, E. A.; Yao, J. D. C.; Wengenack, N. L.; Rosenblatt, J. E.; Cockerill, F. R.; Smith, T. F.
2006-01-01
Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory. PMID:16418529
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Kramme Stefanie
2008-05-01
Full Text Available Abstract Background Coxiella burnetii is the causative agent of Q-fever, a widespread zoonosis. Due to its high environmental stability and infectivity it is regarded as a category B biological weapon agent. In domestic animals infection remains either asymptomatic or presents as infertility or abortion. Clinical presentation in humans can range from mild flu-like illness to acute pneumonia and hepatitis. Endocarditis represents the most common form of chronic Q-fever. In humans serology is the gold standard for diagnosis but is inadequate for early case detection. In order to serve as a diagnostic tool in an eventual biological weapon attack or in local epidemics we developed a real-time 5'nuclease based PCR assay with an internal control system. To facilitate high-throughput an automated extraction procedure was evaluated. Results To determine the minimum number of copies that are detectable at 95% chance probit analysis was used. Limit of detection in blood was 2,881 copies/ml [95%CI, 2,188–4,745 copies/ml] with a manual extraction procedure and 4,235 copies/ml [95%CI, 3,143–7,428 copies/ml] with a fully automated extraction procedure, respectively. To demonstrate clinical application a total of 72 specimens of animal origin were compared with respect to manual and automated extraction. A strong correlation between both methods was observed rendering both methods suitable. Testing of 247 follow up specimens of animal origin from a local Q-fever epidemic rendered real-time PCR more sensitive than conventional PCR. Conclusion A sensitive and thoroughly evaluated real-time PCR was established. Its high-throughput mode may show a useful approach to rapidly screen samples in local outbreaks for other organisms relevant for humans or animals. Compared to a conventional PCR assay sensitivity of real-time PCR was higher after testing samples from a local Q-fever outbreak.
DEFF Research Database (Denmark)
Minero, Gabriel Khose Antonio; Nogueira, Catarina; Rizzi, Giovanni
2017-01-01
We report on an optomagnetic technique optimised for real-time molecular detection of Dengue fever virus under ideal as well as non-ideal laboratory conditions using two different detection approaches. The first approach is based on the detection of the hydrodynamic volume of streptavidin coated...... magnetic nanoparticles attached to biotinylated LAMP amplicons. We demonstrate detection of sub-femtomolar Dengue DNA target concentrations in the ideal contamination-free lab environment within 20 min. The second detection approach is based on sequence-specific binding of functionalised magnetic...... claim detection of down to 100 fM of Dengue target after 20 min of LAMP with a contamination background....
Integrated Oil spill detection and forecasting using MOON real time data
De Dominicis, M.; Pinardi, N.; Coppini, G.; Tonani, M.; Guarnieri, A.; Zodiatis, G.; Lardner, R.; Santoleri, R.
2009-01-01
MOON (Mediterranean Operational Oceanography Network) is an operational distributed system ready to provide quality controlled and timely marine observations (in situ and satellite) and environmental analyses and predictions for management of oil spill accidents. MOON operational systems are based upon the real time functioning of an integrated system composed of the Real Time Observing system, the regional, sub-regional and coastal forecasting systems and a products dissemination system. All...
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F.M. de Moraes
2018-05-01
Full Text Available Clinical manifestations of Zika, dengue, and chikungunya virus infections are very similar, making it difficult to reach a diagnosis based only on clinical grounds. In addition, there is an intense cross-reactivity between antibodies directed to Zika virus and other flaviviruses, and an accurate Zika diagnosis is best achieved by real-time RT-PCR. However, some real-time RT-PCR show better performance than others. To reach the best possible Zika diagnosis, the analytic sensitivity of some probe-based real-time RT-PCR amplifying Zika virus RNA was evaluated in spiked and clinical samples. We evaluated primers and probes to detect Zika virus, which had been published before, and tested sensitivity using serum spiked and patient samples by real-time RT-PCR. When tested against spiked samples, the previously described primers showed different sensitivity, with very similar results when samples from patients (serum and urine were analyzed. Real-time RT-PCR designed to amplify Zika virus NS1 showed the best analytical sensitivity for all samples.
Energy Technology Data Exchange (ETDEWEB)
Jothikumar, N., E-mail: jin2@cdc.gov; Hill, Vincent R.
2013-06-28
Highlights: •Uses a single-labeled fluorescent primer for real-time PCR. •The detection sensitivity of PET PCR was comparable to TaqMan PCR. •Melt curve analysis can be performed to confirm target amplicon production. •Conventional PCR primers can be converted to PET PCR primers. -- Abstract: We report the development of a fluorescently labeled oligonucleotide primer that can be used to monitor real-time PCR. The primer has two parts, the 3′-end of the primer is complimentary to the target and a universal 17-mer stem loop at the 5′-end forms a hairpin structure. A fluorescent dye is attached to 5′-end of either the forward or reverse primer. The presence of guanosine residues at the first and second position of the 3′ dangling end effectively quenches the fluorescence due to the photo electron transfer (PET) mechanism. During the synthesis of nucleic acid, the hairpin structure is linearized and the fluorescence of the incorporated primer increases several-fold due to release of the fluorescently labeled tail and the absence of guanosine quenching. As amplicons are synthesized during nucleic acid amplification, the fluorescence increase in the reaction mixture can be measured with commercially available real-time PCR instruments. In addition, a melting procedure can be performed to denature the double-stranded amplicons, thereby generating fluorescence peaks that can differentiate primer dimers and other non-specific amplicons if formed during the reaction. We demonstrated the application of PET-PCR for the rapid detection and quantification of Cryptosporidium parvum DNA. Comparison with a previously published TaqMan® assay demonstrated that the two real-time PCR assays exhibited similar sensitivity for a dynamic range of detection of 6000–0.6 oocysts per reaction. PET PCR primers are simple to design and less-expensive than dual-labeled probe PCR methods, and should be of interest for use by laboratories operating in resource
International Nuclear Information System (INIS)
Jothikumar, N.; Hill, Vincent R.
2013-01-01
Highlights: •Uses a single-labeled fluorescent primer for real-time PCR. •The detection sensitivity of PET PCR was comparable to TaqMan PCR. •Melt curve analysis can be performed to confirm target amplicon production. •Conventional PCR primers can be converted to PET PCR primers. -- Abstract: We report the development of a fluorescently labeled oligonucleotide primer that can be used to monitor real-time PCR. The primer has two parts, the 3′-end of the primer is complimentary to the target and a universal 17-mer stem loop at the 5′-end forms a hairpin structure. A fluorescent dye is attached to 5′-end of either the forward or reverse primer. The presence of guanosine residues at the first and second position of the 3′ dangling end effectively quenches the fluorescence due to the photo electron transfer (PET) mechanism. During the synthesis of nucleic acid, the hairpin structure is linearized and the fluorescence of the incorporated primer increases several-fold due to release of the fluorescently labeled tail and the absence of guanosine quenching. As amplicons are synthesized during nucleic acid amplification, the fluorescence increase in the reaction mixture can be measured with commercially available real-time PCR instruments. In addition, a melting procedure can be performed to denature the double-stranded amplicons, thereby generating fluorescence peaks that can differentiate primer dimers and other non-specific amplicons if formed during the reaction. We demonstrated the application of PET-PCR for the rapid detection and quantification of Cryptosporidium parvum DNA. Comparison with a previously published TaqMan® assay demonstrated that the two real-time PCR assays exhibited similar sensitivity for a dynamic range of detection of 6000–0.6 oocysts per reaction. PET PCR primers are simple to design and less-expensive than dual-labeled probe PCR methods, and should be of interest for use by laboratories operating in resource
Near real time detection of deforestation in the Brazilian Amazon using MODIS imagery
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Egídio Arai
2007-06-01
Full Text Available The objective of this paper is to provide near real time information about deforestation detection (DETER in the entire Brazilian Amazon using MODIS high temporal resolution images. It is part of the operational deforestation monitoring project to estimate the annual deforestation rate in the Brazilian Amazon (PRODES. A rapid deforestation detection method was designed to support land use policies in this region. In order to evaluate the proposed method a test site was selected covering a Landsat ETM+ scene (227/68 located in Mato Grosso State. For this purpose a multitemporal series of MODIS surface reflectance images (MOD09 and the corresponding ETM+ images from June to October 2002 were analyzed. It was found that small deforested areas (lower than 15 ha were detected by MODIS images with lower accuracy when compared with ETM+ images. As the deforested areas increase MODIS and ETM+ results tend to converge. This procedure showed to be adequate to operationally detect and monitor deforested areas and has been used since 2004 as part of a government plan to control the Amazon deforestation.
Velasco, Valeria; Sherwood, Julie S.; Rojas-García, Pedro P.; Logue, Catherine M.
2014-01-01
The aim of this study was to compare a real-time PCR assay, with a conventional culture/PCR method, to detect S. aureus, mecA and Panton-Valentine Leukocidin (PVL) genes in animals and retail meat, using a two-step selective enrichment protocol. A total of 234 samples were examined (77 animal nasal swabs, 112 retail raw meat, and 45 deli meat). The multiplex real-time PCR targeted the genes: nuc (identification of S. aureus), mecA (associated with methicillin resistance) and PVL (virulence factor), and the primary and secondary enrichment samples were assessed. The conventional culture/PCR method included the two-step selective enrichment, selective plating, biochemical testing, and multiplex PCR for confirmation. The conventional culture/PCR method recovered 95/234 positive S. aureus samples. Application of real-time PCR on samples following primary and secondary enrichment detected S. aureus in 111/234 and 120/234 samples respectively. For detection of S. aureus, the kappa statistic was 0.68–0.88 (from substantial to almost perfect agreement) and 0.29–0.77 (from fair to substantial agreement) for primary and secondary enrichments, using real-time PCR. For detection of mecA gene, the kappa statistic was 0–0.49 (from no agreement beyond that expected by chance to moderate agreement) for primary and secondary enrichment samples. Two pork samples were mecA gene positive by all methods. The real-time PCR assay detected the mecA gene in samples that were negative for S. aureus, but positive for Staphylococcus spp. The PVL gene was not detected in any sample by the conventional culture/PCR method or the real-time PCR assay. Among S. aureus isolated by conventional culture/PCR method, the sequence type ST398, and multi-drug resistant strains were found in animals and raw meat samples. The real-time PCR assay may be recommended as a rapid method for detection of S. aureus and the mecA gene, with further confirmation of methicillin-resistant S. aureus (MRSA) using
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Valeria Velasco
Full Text Available The aim of this study was to compare a real-time PCR assay, with a conventional culture/PCR method, to detect S. aureus, mecA and Panton-Valentine Leukocidin (PVL genes in animals and retail meat, using a two-step selective enrichment protocol. A total of 234 samples were examined (77 animal nasal swabs, 112 retail raw meat, and 45 deli meat. The multiplex real-time PCR targeted the genes: nuc (identification of S. aureus, mecA (associated with methicillin resistance and PVL (virulence factor, and the primary and secondary enrichment samples were assessed. The conventional culture/PCR method included the two-step selective enrichment, selective plating, biochemical testing, and multiplex PCR for confirmation. The conventional culture/PCR method recovered 95/234 positive S. aureus samples. Application of real-time PCR on samples following primary and secondary enrichment detected S. aureus in 111/234 and 120/234 samples respectively. For detection of S. aureus, the kappa statistic was 0.68-0.88 (from substantial to almost perfect agreement and 0.29-0.77 (from fair to substantial agreement for primary and secondary enrichments, using real-time PCR. For detection of mecA gene, the kappa statistic was 0-0.49 (from no agreement beyond that expected by chance to moderate agreement for primary and secondary enrichment samples. Two pork samples were mecA gene positive by all methods. The real-time PCR assay detected the mecA gene in samples that were negative for S. aureus, but positive for Staphylococcus spp. The PVL gene was not detected in any sample by the conventional culture/PCR method or the real-time PCR assay. Among S. aureus isolated by conventional culture/PCR method, the sequence type ST398, and multi-drug resistant strains were found in animals and raw meat samples. The real-time PCR assay may be recommended as a rapid method for detection of S. aureus and the mecA gene, with further confirmation of methicillin-resistant S. aureus (MRSA
Akiyama, Hiroshi; Sakata, Kozue; Makiyma, Daiki; Nakamura, Kosuke; Teshima, Reiko; Nakashima, Akie; Ogawa, Asako; Yamagishi, Toru; Futo, Satoshi; Oguchi, Taichi; Mano, Junichi; Kitta, Kazumi
2011-01-01
In many countries, the labeling of grains, feed, and foodstuff is mandatory if the genetically modified (GM) organism content exceeds a certain level of approved GM varieties. We previously developed an individual kernel detection system consisting of grinding individual kernels, DNA extraction from the individually ground kernels, GM detection using multiplex real-time PCR, and GM event detection using multiplex qualitative PCR to analyze the precise commingling level and varieties of GM maize in real sample grains. We performed the interlaboratory study of the DNA extraction with multiple ground samples, multiplex real-time PCR detection, and multiplex qualitative PCR detection to evaluate its applicability, practicality, and ruggedness for the individual kernel detection system of GM maize. DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR were evaluated by five laboratories in Japan, and all results from these laboratories were consistent with the expected results in terms of the commingling level and event analysis. Thus, the DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR for the individual kernel detection system is applicable and practicable in a laboratory to regulate the commingling level of GM maize grain for GM samples, including stacked GM maize.
Directory of Open Access Journals (Sweden)
Hany Sady
2015-07-01
Full Text Available The present study describes a real-time PCR approach with high resolution melting-curve (HRM assay developed for the detection and differentiation of Schistosoma mansoni and S. haematobium in fecal and urine samples collected from rural Yemen. The samples were screened by microscopy and PCR for the Schistosoma species infection. A pair of degenerate primers were designed targeting partial regions in the cytochrome oxidase subunit I (cox1 gene of S. mansoni and S. haematobium using real-time PCR-HRM assay. The overall prevalence of schistosomiasis was 31.8%; 23.8% of the participants were infected with S. haematobium and 9.3% were infected with S. mansoni. With regards to the intensity of infections, 22.1% and 77.9% of S. haematobium infections were of heavy and light intensities, respectively. Likewise, 8.1%, 40.5% and 51.4% of S. mansoni infections were of heavy, moderate and light intensities, respectively. The melting points were distinctive for S. mansoni and S. haematobium, categorized by peaks of 76.49 ± 0.25 °C and 75.43 ± 0.26 °C, respectively. HRM analysis showed high detection capability through the amplification of Schistosoma DNA with as low as 0.0001 ng/µL. Significant negative correlations were reported between the real-time PCR-HRM cycle threshold (Ct values and microscopic egg counts for both S. mansoni in stool and S. haematobium in urine (p < 0.01. In conclusion, this closed-tube HRM protocol provides a potentially powerful screening molecular tool for the detection of S. mansoni and S. haematobium. It is a simple, rapid, accurate, and cost-effective method. Hence, this method is a good alternative approach to probe-based PCR assays.
Schwenk, Kurt; Willburger, Katharina; Pless, Sebastian
2017-10-01
Motivated by politics and economy, the monitoring of the world wide ship traffic is a field of high topicality. To detect illegal activities like piracy, illegal fishery, ocean dumping and refugee transportation is of great value. The analysis of satellite images on the ground delivers a great contribution to situation awareness. However, for many applications the up-to-dateness of the data is crucial. With ground based processing, the time between image acquisition and delivery of the data to the end user is in the range of several hours. The highest influence to the duration of ground based processing is the delay caused by the transmission of the large amount of image data from the satellite to the processing centre on the ground. One expensive solution to this issue is the usage of data relay satellites systems like EDRS. Another approach is to analyse the image data directly on-board of the satellite. Since the product data (e.g. ship position, heading, velocity, characteristics) is very small compared to the input image data, real-time connections provided by satellite telecommunication services like Iridium or Orbcomm can be used to send small packets of information directly to the end user without significant delay. The AMARO (Autonomous real-time detection of moving maritime objects) project at DLR is a feasibility study of an on-board ship detection system involving a real-time low bandwidth communication. The operation of a prototype on-board ship detection system will be demonstrated on an airborne platform. In this article, the scope, aim and design of a flight experiment for an on-board ship detection system scheduled for mid of 2018 is presented. First, the scope and the constraints of the experiment are explained in detail. The main goal is to demonstrate the operability of an automatic ship detection system on board of an airplane. For data acquisition the optical high resolution DLR MACS-MARE camera (VIS/NIR) is used. The system will be able to
Detecting subsurface fluid leaks in real-time using injection and production rates
Singh, Harpreet; Huerta, Nicolas J.
2017-12-01
CO2 injection into geologic formations for either enhanced oil recovery or carbon storage introduces a risk for undesired fluid leakage into overlying groundwater or to the surface. Despite decades of subsurface CO2 production and injection, the technologies and methods for detecting CO2 leaks are still costly and prone to large uncertainties. This is especially true for pressure-based monitoring methods, which require the use of simplified geological and reservoir flow models to simulate the pressure behavior as well as background noise affecting pressure measurements. In this study, we propose a method to detect the time and volume of fluid leakage based on real-time measurements of well injection and production rates. The approach utilizes analogies between fluid flow and capacitance-resistance modeling. Unlike other leak detection methods (e.g. pressure-based), the proposed method does not require geological and reservoir flow models to simulate the behavior that often carry significant sources of uncertainty; therefore, with our approach the leak can be detected with greater certainty. The method can be applied to detect when a leak begins by tracking a departure in fluid production rate from the expected pattern. The method has been tuned to detect the effect of boundary conditions and fluid compressibility on leakage. To highlight the utility of this approach we use our method to detect leaks for two scenarios. The first scenario simulates a fluid leak from the storage formation into an above-zone monitoring interval. The second scenario simulates intra-reservoir migration between two compartments. We illustrate this method to detect fluid leakage in three different reservoirs with varying levels of geological and structural complexity. The proposed leakage detection method has three novelties: i) requires only readily-available data (injection and production rates), ii) accounts for fluid compressibility and boundary effects, and iii) in addition to
Real-time computational photon-counting LiDAR
Edgar, Matthew; Johnson, Steven; Phillips, David; Padgett, Miles
2018-03-01
The availability of compact, low-cost, and high-speed MEMS-based spatial light modulators has generated widespread interest in alternative sampling strategies for imaging systems utilizing single-pixel detectors. The development of compressed sensing schemes for real-time computational imaging may have promising commercial applications for high-performance detectors, where the availability of focal plane arrays is expensive or otherwise limited. We discuss the research and development of a prototype light detection and ranging (LiDAR) system via direct time of flight, which utilizes a single high-sensitivity photon-counting detector and fast-timing electronics to recover millimeter accuracy three-dimensional images in real time. The development of low-cost real time computational LiDAR systems could have importance for applications in security, defense, and autonomous vehicles.
A real-time PCR assay for the detection of atypical strains of Chlamydiaceae from pigeons.
Directory of Open Access Journals (Sweden)
Aleksandar Zocevic
Full Text Available Recent evidence of the occurrence of atypical Chlamydiaceae strains in pigeons, different from the established Chlamydiaceae, requires the development of a specific and rapid detection tool to investigate their prevalence and significance. Here is described a new real-time PCR assay that allows specific detection of atypical Chlamydiaceae from pigeons. The assay has been used to assess the dissemination of these strains in field samples collected from Parisian pigeon populations in 2009. The results suggest a limited dissemination compared to the usually higher prevalence of Chlamydia psittaci that is the main species associated with avian chlamydiosis.
Joensen, Katrine Grimstrup; Scheutz, Flemming; Lund, Ole; Hasman, Henrik; Kaas, Rolf Sommer; Nielsen, Eva M.; Aarestrup, Frank Møller
2014-01-01
Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-prod...
Joensen, Katrine Grimstrup; Scheutz, Flemming; Lund, Ole; Hasman, Henrik; Kaas, Rolf S.; Nielsen, Eva M.; Aarestrup, Frank M.
2014-01-01
Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-prod...
Directory of Open Access Journals (Sweden)
Tianpeng Feng
2016-01-01
Full Text Available An auto fabric defect detection system via computer vision is used to replace manual inspection. In this paper, we propose a hardware accelerated algorithm based on a small-scale over-completed dictionary (SSOCD via sparse coding (SC method, which is realized on a parallel hardware platform (TMS320C6678. In order to reduce computation, the image patches projections in the training SSOCD are taken as features and the proposed features are more robust, and exhibit obvious advantages in detection results and computational cost. Furthermore, we introduce detection ratio and false ratio in order to measure the performance and reliability of the hardware accelerated algorithm. The experiments show that the proposed algorithm can run with high parallel efficiency and that the detection speed meets the real-time requirements of industrial inspection.
Directory of Open Access Journals (Sweden)
Elisha Khandker
2016-07-01
Full Text Available Background and objectives:Cervical cancer due to Human papillomavirus (HPV is one of the leading causes of morbidity and mortality in women. Testing of HPV can identify women who are at risk of cervical cancer. Nowadays, molecular methods like real time polymerase chain reaction (PCR and hybrid capture technique are applied for detecting HPV in cervical specimens. The objective of the present study was to determine the rate of HPV infection in women with chronic cervicitis and cervical intraepithelial neoplasia (CIN by a commercial real time polymerase chain reaction test kit and by a hybrid capture HPV DNA test. Methods:Women aged between 20 to 55 years with chronic cervicitis and CIN were enrolled in the study after obtaining informed consent. Cervical specimen was collected by using cervical brush and stored in transport medium until used. HPV was detected by High Risk Screen Real-TM Quant 2x (Sacace, Biotechnologies SrI, Italy real time PCR kit (HR RT-PCR and by Hybrid Capture-2 High-Risk HPV DNA (Hc-2; Digene Corporation, USA test. Results: Total 72 women with chronic cervicitis and CIN of different grades were included in the study. Out of this, HPV infection detected by HR RT-PCR was 31 (43% and by Hc-2 was 14 (19.4%. Both the tests were able to detect HPV infection in all the CIN 3 cases and in most of the CIN 2 cases. However, HR RT-PCR detected higher number of HPV in chronic cervicitis and CIN1 cases. Conclusion:The study has shown that HR RT-PCR and Hc-2 tests are equally effective in detecting HPV infection in patients with CIN 2 and CIN 3 lesions. However, HR RT-PCR is more sensitive test for detecting HPV in chronic cervicitis and early CIN lesions and, therefore can be used in epidemiological study to detect presence of HPV in general population. IMC J Med Sci 2016; 10(2: 45-48
Modeling and Implementing Two-Stage AdaBoost for Real-Time Vehicle License Plate Detection
Directory of Open Access Journals (Sweden)
Moon Kyou Song
2014-01-01
Full Text Available License plate (LP detection is the most imperative part of the automatic LP recognition system. In previous years, different methods, techniques, and algorithms have been developed for LP detection (LPD systems. This paper proposes to automatical detection of car LPs via image processing techniques based on classifier or machine learning algorithms. In this paper, we propose a real-time and robust method for LPD systems using the two-stage adaptive boosting (AdaBoost algorithm combined with different image preprocessing techniques. Haar-like features are used to compute and select features from LP images. The AdaBoost algorithm is used to classify parts of an image within a search window by a trained strong classifier as either LP or non-LP. Adaptive thresholding is used for the image preprocessing method applied to those images that are of insufficient quality for LPD. This method is of a faster speed and higher accuracy than most of the existing methods used in LPD. Experimental results demonstrate that the average LPD rate is 98.38% and the computational time is approximately 49 ms.
International Nuclear Information System (INIS)
Shirato, Hiroki; Suzuki, Keishiro; Sharp, Gregory C.; Fujita, Katsuhisa R.T.; Onimaru, Rikiya; Fujino, Masaharu; Kato, Norio; Osaka, Yasuhiro; Kinoshita, Rumiko; Taguchi, Hiroshi; Onodera, Shunsuke; Miyasaka, Kazuo
2006-01-01
Background: To reduce the uncertainty of registration for lung tumors, we have developed a four-dimensional (4D) setup system using a real-time tumor-tracking radiotherapy system. Methods and Materials: During treatment planning and daily setup in the treatment room, the trajectory of the internal fiducial marker was recorded for 1 to 2 min at the rate of 30 times per second by the real-time tumor-tracking radiotherapy system. To maximize gating efficiency, the patient's position on the treatment couch was adjusted using the 4D setup system with fine on-line remote control of the treatment couch. Results: The trajectory of the marker detected in the 4D setup system was well visualized and used for daily setup. Various degrees of interfractional and intrafractional changes in the absolute amplitude and speed of the internal marker were detected. Readjustments were necessary during each treatment session, prompted by baseline shifting of the tumor position. Conclusion: The 4D setup system was shown to be useful for reducing the uncertainty of tumor motion and for increasing the efficiency of gated irradiation. Considering the interfractional and intrafractional changes in speed and amplitude detected in this study, intercepting radiotherapy is the safe and cost-effective method for 4D radiotherapy using real-time tracking technology
The real-time quaking-induced conversion (RT-QuIC) is a rapid, specific, and sensitive prion seeding activity detection assay that uses recombinant prion protein (rPrPSen) to detect sub-infectious levels of the abnormal isoforms of the prion protein (PrPSc). Although RT-QuIC has been successfully us...
Zemtsova, Galina E; Montgomery, Merrill; Levin, Michael L
2015-01-01
Studies on the natural transmission cycles of zoonotic pathogens and the reservoir competence of vertebrate hosts require methods for reliable diagnosis of infection in wild and laboratory animals. Several PCR-based applications have been developed for detection of infections caused by Spotted Fever group Rickettsia spp. in a variety of animal tissues. These assays are being widely used by researchers, but they differ in their sensitivity and reliability. We compared the sensitivity of five previously published conventional PCR assays and one SYBR green-based real-time PCR assay for the detection of rickettsial DNA in blood and tissue samples from Rickettsia- infected laboratory animals (n = 87). The real-time PCR, which detected rickettsial DNA in 37.9% of samples, was the most sensitive. The next best were the semi-nested ompA assay and rpoB conventional PCR, which detected as positive 18.4% and 14.9% samples respectively. Conventional assays targeting ompB, gltA and hrtA genes have been the least sensitive. Therefore, we recommend the SYBR green-based real-time PCR as a tool for the detection of rickettsial DNA in animal samples due to its higher sensitivity when compared to more traditional assays.
Cornelissen, Jan B.W.J.; Bree, de Freddy M.; Wal, van der Fimme J.; Kooij, Engbert A.; Koene, Miriam G.J.; Bossers, Alex; Smid, Bregtje; Antonis, Adriaan F.; Wisselink, Henk J.
2017-01-01
Background: In this study we evaluated the RespoCheck Mycoplasma triplex real-time PCR for the detection in bronchoalveolar lavage fluid (BALF) of Mycoplasma (M.) dispar, M. bovis and M. bovirhinis, all three associated with bovine respiratory disease (BRD). Primers and probes of the RespoCheck
DEFF Research Database (Denmark)
Efunshile, Michael A; Ngwu, Bethrand A F; Kurtzhals, Jørgen A L
2015-01-01
Diarrhea remains the second largest killer of children worldwide, and Nigeria ranks number two on the list of global deaths attributable to diarrhea. Meanwhile, prevalence studies on potentially diarrheagenic protozoa in asymptomatic carriers using molecular detection methods remain scarce in sub......-Saharan countries. To overcome sensitivity issues related to microscopic detection and identification of cysts in stool concentrates, real-time polymerase chain reaction (PCR) was used to analyze genomic DNAs extracted from stool samples from 199 healthy school children for Entamoeba histolytica, E. dispar, Giardia...
Pantchev, Alexandra; Sting, Reinhard; Bauerfeind, Rolf; Tyczka, Judith; Sachse, Konrad
2010-12-01
The aim of the present study was to analyse the occurrence of chlamydiae in several mammalian host species. Clinical samples that previously tested positive in a Chlamydiaceae-specific real-time PCR were retested using six species-specific real-time PCR assays to identify the chlamydial species involved. Chlamydophila (Cp.) abortus was the agent most frequently found in cattle, sheep, horses, goats, and pigs. Detection in cattle of Cp. psittaci (11% of samples) and Chlamydia (C.) suis (9%), as well as Cp. psittaci in a goat sample was somewhat unexpected. DNA of two different chlamydiae was identified in 56 (12.7%) of 440 samples tested. Cp. felis was the predominant species found in cats, while in guinea pigs and rabbits only Cp. caviae was detected. Interestingly, the latter two pathogens were also identified in samples from dogs. The data show that mixed chlamydial infections are not rare and suggest an extended host range of individual species. Copyright © 2009 Elsevier Ltd. All rights reserved.
National Research Council Canada - National Science Library
Jaw, Link
2003-01-01
In this Phase I STTR, SMI and ARL have developed a Real Time Supervisor for fault detection and system reconfiguration in a team of micro UAVs, that are tasked to perform a team mission like surveillance or rendezvous...
Developments in real-time monitoring for geologic hazard warnings (Invited)
Leith, W. S.; Mandeville, C. W.; Earle, P. S.
2013-12-01
Real-time data from global, national and local sensor networks enable prompt alerts and warnings of earthquakes, tsunami, volcanic eruptions, geomagnetic storms , broad-scale crustal deformation and landslides. State-of-the-art seismic systems can locate and evaluate earthquake sources in seconds, enabling 'earthquake early warnings' to be broadcast ahead of the damaging surface waves so that protective actions can be taken. Strong motion monitoring systems in buildings now support near-real-time structural damage detection systems, and in quiet times can be used for state-of-health monitoring. High-rate GPS data are being integrated with seismic strong motion data, allowing accurate determination of earthquake displacements in near-real time. GPS data, combined with rainfall, groundwater and geophone data, are now used for near-real-time landslide monitoring and warnings. Real-time sea-floor water pressure data are key for assessing tsunami generation by large earthquakes. For monitoring remote volcanoes that lack local ground-based instrumentation, the USGS uses new technologies such as infrasound arrays and the worldwide lightning detection array to detect eruptions in progress. A new real-time UV-camera system for measuring the two dimensional SO2 flux from volcanic plumes will allow correlations with other volcano monitoring data streams to yield fundamental data on changes in gas flux as an eruption precursor, and how magmas de-gas prior to and during eruptions. Precision magnetic field data support the generation of real-time indices of geomagnetic disturbances (Dst, K and others), and can be used to model electrical currents in the crust and bulk power system. Ground-induced electrical current monitors are used to track those currents so that power grids can be effectively managed during geomagnetic storms. Beyond geophysical sensor data, USGS is using social media to rapidly detect possible earthquakes and to collect firsthand accounts of the impacts of
Real-time, high frequency QRS electrocardiograph with reduced amplitude zone detection
Schlegel, Todd T. (Inventor); DePalma, Jude L. (Inventor); Moradi, Saeed (Inventor)
2009-01-01
Real time cardiac electrical data are received from a patient, manipulated to determine various useful aspects of the ECG signal, and displayed in real time in a useful form on a computer screen or monitor. The monitor displays the high frequency data from the QRS complex in units of microvolts, juxtaposed with a display of conventional ECG data in units of millivolts or microvolts. The high frequency data are analyzed for their root mean square (RMS) voltage values and the discrete RMS values and related parameters are displayed in real time. The high frequency data from the QRS complex are analyzed with imbedded algorithms to determine the presence or absence of reduced amplitude zones, referred to herein as ''RAZs''. RAZs are displayed as ''go, no-go'' signals on the computer monitor. The RMS and related values of the high frequency components are displayed as time varying signals, and the presence or absence of RAZs may be similarly displayed over time.
Real-Time in Vivo Detection of H2O2 Using Hyperpolarized 13C-Thiourea.
Wibowo, Arif; Park, Jae Mo; Liu, Shie-Chau; Khosla, Chaitan; Spielman, Daniel M
2017-07-21
Reactive oxygen species (ROS) are essential cellular metabolites widely implicated in many diseases including cancer, inflammation, and cardiovascular and neurodegenerative disorders. Yet, ROS signaling remains poorly understood, and their measurements are a challenge due to high reactivity and instability. Here, we report the development of 13 C-thiourea as a probe to detect and measure H 2 O 2 dynamics with high sensitivity and spatiotemporal resolution using hyperpolarized 13 C magnetic resonance spectroscopic imaging. In particular, we show 13 C-thiourea to be highly polarizable and to possess a long spin-lattice relaxation time (T 1 ), which enables real-time monitoring of ROS-mediated transformation. We also demonstrate that 13 C-thiourea reacts readily with H 2 O 2 to give chemically distinguishable products in vitro and validate their detection in vivo in a mouse liver. This study suggests that 13 C-thiourea is a promising agent for noninvasive detection of H 2 O 2 in vivo. More broadly, our findings outline a viable clinical application for H 2 O 2 detection in patients with a range of diseases.
Real-time multiplexed digital cavity-enhanced spectroscopy
International Nuclear Information System (INIS)
Boyson, Toby K.; Dagdigian, Paul J.; Pavey, Karl D.; Fitzgerald, Nicholas J.; Spence, Thomas G.; Moore, David S.; Harb, Charles C.
2015-01-01
Cavity-enhanced spectroscopy is a sensitive optical absorption technique but one where the practical applications have been limited to studying small wavelength ranges. In addition, this Letter shows that wideband operation can be achieved by combining techniques usually reserved for the communications community with that of cavity-enhanced spectroscopy, producing a multiplexed real-time cavity-enhanced spectrometer. We use multiple collinear laser sources operating asynchronously and simultaneously while being detected on a single photodetector. This is synonymous with radio frequency (RF) cellular systems in which signals are detected on a single antenna but decoded uniquely. Here, we demonstrate results with spectra of methyl salicylate and show parts-per-billion per root hertz sensitivity measured in real-time
Nakamura, Kosuke; Akiyama, Hiroshi; Kawano, Noriaki; Kobayashi, Tomoko; Yoshimatsu, Kayo; Mano, Junichi; Kitta, Kazumi; Ohmori, Kiyomi; Noguchi, Akio; Kondo, Kazunari; Teshima, Reiko
2013-12-01
Genetically modified (GM) rice (Oryza sativa) lines, such as insecticidal Kefeng and Kemingdao, have been developed and found unauthorised in processed rice products in many countries. Therefore, qualitative detection methods for the GM rice are required for the GM food regulation. A transgenic construct for expressing cowpea (Vigna unguiculata) trypsin inhibitor (CpTI) was detected in some imported processed rice products contaminated with Kemingdao. The 3' terminal sequence of the identified transgenic construct for expression of CpTI included an endoplasmic reticulum retention signal coding sequence (KDEL) and nopaline synthase terminator (T-nos). The sequence was identical to that in a report on Kefeng. A novel construct-specific real-time polymerase chain reaction (PCR) detection method for detecting the junction region sequence between the CpTI-KDEL and T-nos was developed. The imported processed rice products were evaluated for the contamination of the GM rice using the developed construct-specific real-time PCR methods, and detection frequency was compared with five event-specific detection methods. The construct-specific detection methods detected the GM rice at higher frequency than the event-specific detection methods. Therefore, we propose that the construct-specific detection method is a beneficial tool for screening the contamination of GM rice lines, such as Kefeng, in processed rice products for the GM food regulation. Copyright © 2013 Elsevier Ltd. All rights reserved.
SMA Diagnosis: Detection of SMN1 Deletion with Real-Time mCOP-PCR System Using Fresh Blood DNA.
Niba, Emma Tabe Eko; Ar Rochmah, Mawaddah; Harahap, Nur Imma Fatimah; Awano, Hiroyuki; Morioka, Ichiro; Iijima, Kazumoto; Saito, Toshio; Saito, Kayoko; Takeuchi, Atsuko; Lai, Poh San; Bouike, Yoshihiro; Nishio, Hisahide; Shinohara, Masakazu
2017-12-18
Spinal muscular atrophy (SMA) is one of the most common autosomal recessive disorders. The symptoms are caused by defects of lower motor neurons in the spinal cord. More than 95% of SMA patients are homozygous for survival motor neuron 1 (SMN1) deletion. We previously developed a screening system for SMN1 deletion based on a modified competitive oligonucleotide priming-PCR (mCOP-PCR) technique using dried blood spot (DBS) on filter paper. This system is convenient for mass screening in the large population and/or first-tier diagnostic method of the patients in the remote areas. However, this system was still time-consuming and effort-taking, because it required pre-amplification procedure to avoid non-specific amplification and gel-electrophoresis to detect the presence or absence of SMN1 deletion. When the fresh blood samples are used instead of DBS, or when the gel-electrophoresis is replaced by real-time PCR, we may have a simpler and more rapid diagnostic method for SMA. To establish a simpler and more rapid diagnostic method of SMN1 deletion using fresh blood DNA. DNA samples extracted from fresh blood and stored at 4 ℃ for 1 month. The samples were assayed using a real-time mCOP-PCR system without pre-amplification procedures. DNA samples had already been genotyped by PCR-restriction fragment length polymorphism (PCR-RFLP), showing the presence or absence of SMN1 exon 7. The DNA samples were directly subjected to the mCOP-PCR step. The amplification of mCOP-PCR was monitored in a real-time PCR apparatus. The genotyping results of the real-time mCOP-PCR system using fresh blood DNA were completely matched with those of PCR-RFLP. In this real-time mCOP-PCR system using fresh blood-DNA, it took only four hours from extraction of DNA to detection of the presence or absence of SMN1 deletion, while it took more than 12 hours in PCR-RFLP. Our real-time mCOP-PCR system using fresh blood DNA was rapid and accurate, suggesting it may be useful for the first
[Quantitative fluorogenic real-time PCR assay for respiratory syncytial virus detection].
Zhang, Qi-wei; You, Shang-you; Sun, Ji-min; Wu, Qi; Yu, Chun-hua; Zhang, Chu-yu
2005-07-01
To Establish a rapid and objective quantitative fluorogenic real-time PCR assay for early detection of human respiratory syncytial virus (hRSV). Two pairs of primers and one TaqMan Fluorogenic probe that are specific for the recognition of the most conservative N gene of hRSV for virus detection with LighCycler PCR in 93 nasopharyngeal secretion specimens collected from infants and young children. The assay was compared with virus isolation, routine PCR, nested PCR, and enzyme-linked immunosorbent assay (ELISA). This TaqMan assay had a sensitivity of 1 x 10(2) cDNA copies/microl with a dynamic range between 1 x 10(2) and 1 x 10(7) cDNA copies/microl, which was the same as that of nested PCR, but 10 times more sensitive than routine PCR. The specificity of the assay was evaluated by comparing hRSV with polivirus type 1, coxsackie virus type 2, influenza A, influenza B and adenovirus type 7. A PCR product of the expected size (195 bp) was produced and fluorescence signal detected for hRSV, but not for any of the other viruses. The results in LightCycler and Rotor-Gene instrument were consistent. Forty-four specimens (43.9%) were hRSV-positive with this assay and 4 (4/93,4.3%) were hRSV-positive with ELISA, showing rather low correlation between the two methods. No visible relation was found between the concentration of hRSV RNA and severity of the disease. This assay is rapid, sensitive, specific and quantitative, and has the potential of wide application for early diagnosis of hRSV infection and evaluation of the therapeutic effect.
Sadeghi, Saman; MacKay, William A.; van Dam, R. Michael; Thompson, Michael
2011-02-01
Real-time analysis of multi-channel spatio-temporal sensor data presents a considerable technical challenge for a number of applications. For example, in brain-computer interfaces, signal patterns originating on a time-dependent basis from an array of electrodes on the scalp (i.e. electroencephalography) must be analyzed in real time to recognize mental states and translate these to commands which control operations in a machine. In this paper we describe a new technique for recognition of spatio-temporal patterns based on performing online discrimination of time-resolved events through the use of correlation of phase dynamics between various channels in a multi-channel system. The algorithm extracts unique sensor signature patterns associated with each event during a training period and ranks importance of sensor pairs in order to distinguish between time-resolved stimuli to which the system may be exposed during real-time operation. We apply the algorithm to electroencephalographic signals obtained from subjects tested in the neurophysiology laboratories at the University of Toronto. The extension of this algorithm for rapid detection of patterns in other sensing applications, including chemical identification via chemical or bio-chemical sensor arrays, is also discussed.
Murphy, Helen R; Lee, Seulgi; da Silva, Alexandre J
2017-07-01
Cyclospora cayetanensis is a protozoan parasite that causes human diarrheal disease associated with the consumption of fresh produce or water contaminated with C. cayetanensis oocysts. In the United States, foodborne outbreaks of cyclosporiasis have been linked to various types of imported fresh produce, including cilantro and raspberries. An improved method was developed for identification of C. cayetanensis in produce at the U.S. Food and Drug Administration. The method relies on a 0.1% Alconox produce wash solution for efficient recovery of oocysts, a commercial kit for DNA template preparation, and an optimized TaqMan real-time PCR assay with an internal amplification control for molecular detection of the parasite. A single laboratory validation study was performed to assess the method's performance and compare the optimized TaqMan real-time PCR assay and a reference nested PCR assay by examining 128 samples. The samples consisted of 25 g of cilantro or 50 g of raspberries seeded with 0, 5, 10, or 200 C. cayetanensis oocysts. Detection rates for cilantro seeded with 5 and 10 oocysts were 50.0 and 87.5%, respectively, with the real-time PCR assay and 43.7 and 94.8%, respectively, with the nested PCR assay. Detection rates for raspberries seeded with 5 and 10 oocysts were 25.0 and 75.0%, respectively, with the real-time PCR assay and 18.8 and 68.8%, respectively, with the nested PCR assay. All unseeded samples were negative, and all samples seeded with 200 oocysts were positive. Detection rates using the two PCR methods were statistically similar, but the real-time PCR assay is less laborious and less prone to amplicon contamination and allows monitoring of amplification and analysis of results, making it more attractive to diagnostic testing laboratories. The improved sample preparation steps and the TaqMan real-time PCR assay provide a robust, streamlined, and rapid analytical procedure for surveillance, outbreak response, and regulatory testing of foods for
Network-Based Real-time Integrated Fire Detection and Alarm (FDA) System with Building Automation
Anwar, F.; Boby, R. I.; Rashid, M. M.; Alam, M. M.; Shaikh, Z.
2017-11-01
Fire alarm systems have become increasingly an important lifesaving technology in many aspects, such as applications to detect, monitor and control any fire hazard. A large sum of money is being spent annually to install and maintain the fire alarm systems in buildings to protect property and lives from the unexpected spread of fire. Several methods are already developed and it is improving on a daily basis to reduce the cost as well as increase quality. An integrated Fire Detection and Alarm (FDA) systems with building automation was studied, to reduce cost and improve their reliability by preventing false alarm. This work proposes an improved framework for FDA system to ensure a robust intelligent network of FDA control panels in real-time. A shortest path algorithmic was chosen for series of buildings connected by fiber optic network. The framework shares information and communicates with each fire alarm panels connected in peer to peer configuration and declare the network state using network address declaration from any building connected in network. The fiber-optic connection was proposed to reduce signal noises, thus increasing large area coverage, real-time communication and long-term safety. Based on this proposed method an experimental setup was designed and a prototype system was developed to validate the performance in practice. Also, the distributed network system was proposed to connect with an optional remote monitoring terminal panel to validate proposed network performance and ensure fire survivability where the information is sequentially transmitted. The proposed FDA system is different from traditional fire alarm and detection system in terms of topology as it manages group of buildings in an optimal and efficient manner.Introduction
Bougot-Robin, Kristelle
2013-12-20
2D imaging of biochips is particularly interesting for multiplex biosensing. Resonant properties allow label-free detection using the change of refractive index at the chip surface. We demonstrate a new principle of Scanning Of Resonance on Chip by Imaging (SORCI) based on spatial profiles of nanopatterns of resonant waveguide gratings (RWGs) and its embodiment in a fluidic chip for real-time biological studies. This scheme allows multiplexing of the resonance itself by providing nanopattern sensing areas in a bioarray format. Through several chip designs we discuss resonance spatial profiles, dispersion and electric field distribution for optimal light-matter interaction with biological species of different sizes. Fluidic integration is carried out with a black anodized aluminum chamber, advantageous in term of mechanical stability, multiple uses of the chip, temperature control and low optical background. Real-time hybridization experiments are illustrated by SNP (Single Nucleotide Polymorphism) detection in gyrase A of E. coli K12, observed in evolution studies of resistance to the antibiotic ciprofloxacin. We choose a 100 base pairs (bp) DNA target (∼30 kDa) including the codon of interest and demonstrate the high specificity of our technique for probes and targets with close affinity constants. This work validates the safe applicability of our unique combination of RWGs and simple instrumentation for real-time biosensing with sensitivity in buffer solution of ∼10 pg/mm2. Paralleling the success of RWGs sensing for cells sensing, our work opens new avenues for a large number of biological studies. © 2013 Springer Science+Business Media.
Gasparic, M.B.; Cankar, K.; Zel, J.; Gruden, K.
2008-01-01
Background: The real-time polymerase chain reaction is currently the method of choice for quantifying nucleic acids in different DNA based quantification applications. It is widely used also for detecting and quantifying genetically modified components in food and feed, predominantly employing
Allen, Phillip G.
1985-12-01
The call for abolishing photo reconnaissance in favor of real time is once more being heard. Ten years ago the same cries were being heard with the introduction of the Charge Coupled Device (CCD). The real time system problems that existed then and stopped real time proliferation have not been solved. The lack of an organized program by either DoD or industry has hampered any efforts to solve the problems, and as such, very little has happened in real time in the last ten years. Real time is not a replacement for photo, just as photo is not a replacement for infra-red or radar. Operational real time sensors can be designed only after their role has been defined and improvements made to the weak links in the system. Plodding ahead on a real time reconnaissance suite without benefit of evaluation of utility will allow this same paper to be used ten years from now.
Chase, D.M.; Elliott, D.G.; Pascho, R.J.
2006-01-01
Renibacterium salmoninarum is an important salmonid pathogen that is difficult to culture. We developed and assessed a real-time, quantitative, polymerase chain reaction (qPCR) assay for the detection and enumeration of R. salmoninarum. The qPCR is based on TaqMan technology and amplifies a 69-base pair (bp) region of the gene encoding the major soluble antigen (MSA) of R. salmoninarum. The qPCR assay consistently detected as few as 5 R. salmoninarum cells per reaction in kidney tissue. The specificity of the qPCR was confirmed by testing the DNA extracts from a panel of microorganisms that were either common fish pathogens or reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA). Kidney samples from 38 juvenile Chinook salmon (Oncorhynchus tshawytscha) in a naturally infected population were examined by real-time qPCR, a nested PCR, and ELISA, and prevalences of R. salmoninarum detected were 71, 66, and 71%, respectively. The qPCR should be a valuable tool for evaluating the R. salmoninarum infection status of salmonids.
Directory of Open Access Journals (Sweden)
Hasan Ozturk
2010-01-01
Full Text Available Bending fatigue crack is a dangerous and insidious mode of failure in gears. As it produces no debris in its early stages, it gives little warning during its progression, and usually results in either immediate loss of serviceability or greatly reduced power transmitting capacity. This paper presents the applications of vibration-based techniques (i.e. conventional time and frequency domain analysis, cepstrum, and continuous wavelet transform to real gear vibrations in the early detection, diagnosis and advancement monitoring of a real tooth fatigue crack and compares their detection and diagnostic capabilities on the basis of experimental results. Gear fatigue damage is achieved under heavy-loading conditions and the gearbox is allowed to run until the gears suffer badly from complete tooth breakage. It has been found that the initiation and progression of fatigue crack cannot be easily detected by conventional time and frequency domain approaches until the fault is significantly developed. On the contrary, the wavelet transform is quite sensitive to any change in gear vibration and reveals fault features earlier than other methods considered.
MARCELINO-GUIMARÃES, F. C.; GUIMARÃES, M. F. M.; DE-BARROS, E. G.
2009-01-01
The increasing presence of products derived from genetically modified (GM) plants in human and animal diets has led to the development of detection methods to distinguish biotechnology-derived foods from conventional ones. The conventional and real-time PCR have been used, respectively, to detect and quantify GM residues in highly processed foods. DNA extraction is a critical step during the analysis process. Some factors such as DNA degradation, matrix effects, and the presence of PCR inhibi...
Mackay, Ian M.; Arden, Katherine E.; Nitsche, Andreas
2002-01-01
The use of the polymerase chain reaction (PCR) in molecular diagnostics has increased to the point where it is now accepted as the gold standard for detecting nucleic acids from a number of origins and it has become an essential tool in the research laboratory. Real-time PCR has engendered wider acceptance of the PCR due to its improved rapidity, sensitivity, reproducibility and the reduced risk of carry-over contamination. There are currently five main chemistries used for the detection of P...
Fischer, Melina; Schirrmeier, Horst; Wernike, Kerstin; Wegelt, Anne; Beer, Martin; Hoffmann, Bernd
2013-11-05
Schmallenberg virus (SBV), a novel orthobunyavirus of the Simbu serogroup, was first identified in October 2011 in dairy cattle in Germany, where it caused fever, diarrhea and a drop in milk yield. Since then, SBV additionally has been detected in adult sheep and goats. Although symptoms of acute infection were not observed, infection during a vulnerable phase of pregnancy caused congenital malformations and stillbirths. In view of the current situation and the possible emergence of further Simbu serogroup members, a pan-Simbu real-time reverse transcriptase (RT) PCR system for the reliable detection of Simbu serogroup viruses should be developed. In this study a pan-Simbu real-time RT-PCR system was established and compared to several SBV real-time RT-PCR assays. All PCR-systems were tested using a panel of different Simbu serogroup viruses as well as several field samples from diseased cattle, sheep and goats originating from all over Germany. Several pan-Simbu real-time RT-PCR products were sequenced via Sanger sequencing. Furthermore, in silico analyses were performed to investigate suitability for the detection of further orthobunyaviruses. All tested members of the Simbu serogroup (n = 14) as well as most of the field samples were successfully detected by the pan-Simbu real-time RT-PCR system. The comparison of this intercalating dye assay with different TaqMan probe-based assays developed for SBV diagnostics confirmed the functionality of the pan-Simbu assay for screening purposes. However, the SBV-TaqMan-assay SBV-S3 delivered the highest analytical sensitivity of less than ten copies per reaction for duplex systems including an internal control. In addition, for confirmation of SBV-genome detection the highly specific SBV-M1 assay was established. The pan-Simbu real-time RT-PCR system was able to detect all tested members of the Simbu serogroup, most of the SBV field samples as well as three tested Bunyamwera serogroup viruses with a suitable
Sharifdini, Meysam; Mirhendi, Hossein; Ashrafi, Keyhan; Hosseini, Mostafa; Mohebali, Mehdi; Khodadadi, Hossein; Kia, Eshrat Beigom
2015-01-01
This study was performed to evaluate nested polymerase chain reaction (PCR) and real-time PCR methods for detection of Strongyloides stercoralis in fecal samples compared with parasitological methods. A total of 466 stool samples were examined by conventional parasitological methods (formalin ether concentration [FEC] and agar plate culture [APC]). DNA was extracted using an in-house method, and mitochondrial cytochrome c oxidase subunit 1 and 18S ribosomal genes were amplified by nested PCR and real-time PCR, respectively. Among 466 samples, 12.7% and 18.2% were found infected with S. stercoralis by FEC and APC, respectively. DNA of S. stercoralis was detected in 18.9% and 25.1% of samples by real-time PCR and nested PCR, respectively. Considering parasitological methods as the diagnostic gold standard, the sensitivity and specificity of nested PCR were 100% and 91.6%, respectively, and that of real-time PCR were 84.7% and 95.8%, respectively. However, considering sequence analyzes of the selected nested PCR products, the specificity of nested PCR is increased. In general, molecular methods were superior to parasitological methods. They were more sensitive and more reliable in detection of S. stercoralis in comparison with parasitological methods. Between the two molecular methods, the sensitivity of nested PCR was higher than real-time PCR. PMID:26350449
Filipiak, Anna; Hasiów-Jaroszewska, Beata
2016-04-01
The real-time PCR-HRM analysis was developed for the detection and discrimination of the quarantine nematode Bursaphelenchus xylophilus and Bursaphelenchus mucronatus. A set of primers was designed to target the ITS region of rDNA. The results have demonstrated that this analysis is a valuable tool for differentiation of these both species. Copyright © 2016 Elsevier Ltd. All rights reserved.
Feathered Detectives: Real-Time GPS Tracking of Scavenging Gulls Pinpoints Illegal Waste Dumping.
Directory of Open Access Journals (Sweden)
Joan Navarro
Full Text Available Urban waste impacts human and environmental health, and waste management has become one of the major challenges of humanity. Concurrently with new directives due to manage this human by-product, illegal dumping has become one of the most lucrative activities of organized crime. Beyond economic fraud, illegal waste disposal strongly enhances uncontrolled dissemination of human pathogens, pollutants and invasive species. Here, we demonstrate the potential of novel real-time GPS tracking of scavenging species to detect environmental crime. Specifically, we were able to detect illegal activities at an officially closed dump, which was visited recurrently by 5 of 19 GPS-tracked yellow-legged gulls (Larus michahellis. In comparison with conventional land-based surveys, GPS tracking allows a much wider and cost-efficient spatiotemporal coverage, even of the most hazardous sites, while GPS data accessibility through the internet enables rapid intervention. Our results suggest that multi-species guilds of feathered detectives equipped with GPS and cameras could help fight illegal dumping at continental scales. We encourage further experimental studies, to infer waste detection thresholds in gulls and other scavenging species exploiting human waste dumps.
Energy Technology Data Exchange (ETDEWEB)
Yokoyama, Akihito, E-mail: yokoyama.akihito@jaea.go.jp [Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515 (Japan); Takasaki Advanced Radiation Research Institute (TARRI), Japan Atomic Energy Agency (JAEA), 1233 Watanuki-machi, Takasaki, Gunma 370-1292 (Japan); Kada, Wataru [Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515 (Japan); Satoh, Takahiro; Koka, Masashi [Takasaki Advanced Radiation Research Institute (TARRI), Japan Atomic Energy Agency (JAEA), 1233 Watanuki-machi, Takasaki, Gunma 370-1292 (Japan); Shimada, Keisuke; Yokoata, Yuya; Miura, Kenta; Hanaizumi, Osamu [Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515 (Japan)
2016-03-15
In this paper, we propose and test a real-time detection system for single-ion hits using mega-electronvolt (MeV)-heavy ions. The system was constructed using G2000 and G9 glass scintillators, as well as an electron-multiplying charge-coupled device (EMCCD) camera combined with an inverted microscope with a 10× objective lens. Commercially available G2000 and G9 glass scintillators, which have been reported to exhibit strong photoluminescence at 489, 543, 585, and 622 nm as a result of the Tb{sup 3+} f–f transition, were employed for highly accurate ionized particle detection. The EMCCD camera had a resolution of 512 × 512 pixels, each with a size of 16 μm × 16 μm, and a maximum linear gain of 8 × 10{sup 5} electrons. For 260-MeV Ne, 3 ion hits/s were detected by our system. The intensity of the ionoluminescence (IL) peak induced by the heavy ions was 140 times the noise intensity. In contrast, the luminous diameter at the full width at half maximum (FWHM) in both the horizontal and vertical directions was calculated to be approximately 4.5 μm. These results suggest that our detection system can accurately detect single-ion hits with a diameter of the order of 1 μm.
Powerful conveyer belt real-time online detection system based on x-ray
Rong, Feng; Miao, Chang-yun; Meng, Wei
2009-07-01
The powerful conveyer belt is widely used in the mine, dock, and so on. After used for a long time, internal steel rope of the conveyor belt may fracture, rust, joints moving, and so on .This would bring potential safety problems. A kind of detection system based on x-ray is designed in this paper. Linear array detector (LDA) is used. LDA cost is low, response fast; technology mature .Output charge of LDA is transformed into differential voltage signal by amplifier. This kind of signal have great ability of anti-noise, is suitable for long-distance transmission. The processor is FPGA. A IP core control 4-channel A/D convertor, achieve parallel output data collection. Soft-core processor MicroBlaze which process tcp/ip protocol is embedded in FPGA. Sampling data are transferred to a computer via Ethernet. In order to improve the image quality, algorithm of getting rid of noise from the measurement result and taking gain normalization for pixel value is studied and designed. Experiments show that this system work well, can real-time online detect conveyor belt of width of 2.0m and speed of 5 m/s, does not affect the production. Image is clear, visual and can easily judge the situation of conveyor belt.
Mandappa, I M; Joglekar, Prasanna; Manonmani, H K
2015-07-01
A multiplex real-time isothermal amplification assay was developed using molecular beacons for the detection of Bacillus cereus and Staphylococcus aureus by targeting four important virulence genes. A correlation between targeting highly accessible DNA sequences and isothermal amplification based molecular beacon efficiency and sensitivity was demonstrated using phi(Φ)29 DNA polymerase at a constant isothermal temperature of 30 °C. It was very selective and consistently detected down to 10(1) copies of DNA. The specificity and sensitivity of this assay, when tested with pure culture were high, surpassing those of currently used PCR assays for the detection of these organisms. The molecular beacon based real-time isothermal amplification (MBRTIA) assay could be carried out entirely in 96 well plates or well strips, enabling a rapid and high-throughput detection of food borne pathogens.
Detection of Mycoplasma genitalium in female cervical samples by Multitarget Real-Time PCR
Directory of Open Access Journals (Sweden)
Sabina Mahmutović-Vranić
2007-05-01
Full Text Available Mycoplasma genitalum (MG is associated with variety of urogenital infections such as non-gonococcal urethritis (NGU, endometritis and cervicitis. The objective of this study was to demonstrate and evaluate a research polymerase chain reaction (PCR assay, for the detection of MG in cervical samples of a tested population of women attending gynecology clinics in Bosnia and Herzegovina. The Multitarget Real-Time (MTRT PCR, utilizing the ABI 7900HT, the sequence detection system, was performed for the detection of MG. Cervical samples (N=97 from females were divided into three types of patient groups: Group 1: patients who had known abnormal clinical cytology reports (N=34; Group 2: patients who reported a history of genitourinary infections (N=22; and Group 3: patients not in either groups 1 or 2 (N=41. Overall, 14,43% (14/97 of those tested were positive for MG. A positive sample was defined as having a cycle threshold cross point (Ct < 40,0 with a fluorescent detection comparable to the low positive control utilized during the run. This study validated the use of MTRT PCR as a reliable method for the detection of MG in clinical specimens and should facilitate large-scale screening for this organism.
Bottari, Benedetta; Agrimonti, Caterina; Gatti, Monica; Neviani, Erasmo; Marmiroli, Nelson
2013-01-01
A multiplex real time PCR (mRealT-PCR) useful to rapidly screen microbial composition of thermophilic starter cultures for hard cooked cheeses and to compare samples with potentially different technological properties was developed. Novel primers directed toward pheS gene were designed and optimized for multiple detection of Lactobacillus helveticus, Lactobacillus delbrueckii, Streptococcus thermophilus and Lactobacillus fermentum. The assay was based on SYBR Green chemistry followed by melting curves analysis. The method was then evaluated for applications in the specific detection of the 4 lactic acid bacteria (LAB) in 29 different natural whey starters for Parmigiano Reggiano cheese production. The results obtained by mRealT-PCR were also compared with those obtained on the same samples by Fluorescence in Situ Hybridization (FISH) and Length-Heterogeneity PCR (LH-PCR). The mRealT-PCR developed in this study, was found to be effective for analyzing species present in the samples with an average sensitivity down to less than 600 copies of DNA and therefore sensitive enough to detect even minor LAB community members of thermophilic starter cultures. The assay was able to describe the microbial population of all the different natural whey starter samples analyzed, despite their natural variability. A higher number of whey starter samples with S. thermophilus and L. fermentum present in their microbial community were revealed, suggesting that these species could be more frequent in Parmigiano Reggiano natural whey starter samples than previously shown. The method was more effective than LH-PCR and FISH and, considering that these two techniques have to be used in combination to detect the less abundant species, the mRealT-PCR was also faster. Providing a single step sensitive detection of L. helveticus, L. delbrueckii, S. thermophilus and L. fermentum, the developed mRealT-PCR could be used for screening thermophilic starter cultures and to follow the presence of
Directory of Open Access Journals (Sweden)
Galina E Zemtsova
Full Text Available Studies on the natural transmission cycles of zoonotic pathogens and the reservoir competence of vertebrate hosts require methods for reliable diagnosis of infection in wild and laboratory animals. Several PCR-based applications have been developed for detection of infections caused by Spotted Fever group Rickettsia spp. in a variety of animal tissues. These assays are being widely used by researchers, but they differ in their sensitivity and reliability. We compared the sensitivity of five previously published conventional PCR assays and one SYBR green-based real-time PCR assay for the detection of rickettsial DNA in blood and tissue samples from Rickettsia- infected laboratory animals (n = 87. The real-time PCR, which detected rickettsial DNA in 37.9% of samples, was the most sensitive. The next best were the semi-nested ompA assay and rpoB conventional PCR, which detected as positive 18.4% and 14.9% samples respectively. Conventional assays targeting ompB, gltA and hrtA genes have been the least sensitive. Therefore, we recommend the SYBR green-based real-time PCR as a tool for the detection of rickettsial DNA in animal samples due to its higher sensitivity when compared to more traditional assays.
Real-Time Eye Detection and Tracking under Various Light Conditions
Directory of Open Access Journals (Sweden)
Feng Jiao
2007-10-01
Full Text Available This paper describes a real-time online prototype automobile and truck driver-fatigue monitor. It uses remotely located charge-coupled-device cameras equipped with active infrared illuminators to acquire video images of the driver. Various visual cues that typically characterize the level of alertness of a person are extracted in real time and systematically combined to infer the fatigue level of the driver. The visual cues employed characterize eyelid movement, gaze movement, head movement, and facial expression. A probabilistic model is developed to model human fatigue and to predict fatigue based on the visual cues obtained. The simultaneous use of multiple visual cues and their systematic combination yields a much more robust and accurate fatigue characterization than using a single visual cue. This system was validated under real-life fatigue conditions with human subjects of different ethnic backgrounds, genders, and ages; with/without glasses; and under different illumination conditions. It was found to be reasonably robust, reliable, and accurate in fatigue characterization.
Quantitative detection of Campylobacter jejuni on fresh chicken carcasses by real-time PCR.
Rönner, Anna-Clara; Lindmark, Hans
2007-06-01
Campylobacter jejuni infection is a significant cause of foodborne gastroenteritis worldwide. Consumption and handling of poultry products is believed to be the primary risk factor for campylobacteriosis. Risk assessments require quantitative data, and C. jejuni is enumerated usually by direct plating, which sometimes allows growth of non-Campylobacter bacteria. The objective of the present study was to develop a quantitative real-time PCR method (q-PCR) for enumerating C. jejuni in chicken rinse without a culturing step. The procedure to obtain the template for the PCR assay involved (i) filtration of 10 ml of chicken rinse, (ii) centrifugation of the sample, and (iii) total DNA extraction from the pellet obtained using a commercial DNA extraction kit. The detection limit of the method was comparable to that for plating 100 microl of chicken rinse on modified charcoal cefoperazone deoxycholate agar, and the detection limit could be further improved 10-fold by concentrating the DNA eluate by ethanol precipitation. A close correlation for spiked chicken rinse was obtained for the results of the quantitative real-time PCR method and direct plating (r = 0.99). The coefficient of correlation for the methods was 0.87 when samples from chicken carcasses on the slaughter line were analyzed, whereas a lower correlation (r = 0.76) was obtained when samples from retail carcasses were analyzed. Greater variation in the proportion of dead and/or viable but not culturable Campylobacter types in the retail samples may explain the decreased correlation between the methods. Overall, the new method is simple and fast and the results obtained are closely correlated with those for direct plating for samples containing a low proportion of dead Campylobacter cells.
DEFF Research Database (Denmark)
de Knegt, Victoria Elizabeth; Kristiansen, Gitte Qvist; Schønning, Kristian
2017-01-01
BACKGROUND: We aimed to evaluate the relevance of dual target real-time polymerase chain (PCR) assays targeting the rtxA and cpn60 genes of the paediatric pathogen Kingella kingae. We also studied for the first time the clinical and epidemiological features of K. kingae infections in a Danish pop......-value: peak in autumn. CONCLUSION: Dual target-specific real-time PCR markedly improved the detection of K. kingae in clinical specimens when compared to culture methods....
Chen, J H K; She, K K K; Kwong, T-C; Wong, O-Y; Siu, G K H; Leung, C-C; Chang, K-C; Tam, C-M; Ho, P-L; Cheng, V C C; Yuen, K-Y; Yam, W-C
2015-09-01
The automated high-throughput Abbott RealTime MTB real-time PCR assay has been recently launched for Mycobacterium tuberculosis complex (MTBC) clinical diagnosis. This study would like to evaluate its performance. We first compared its diagnostic performance with the Roche Cobas TaqMan MTB assay on 214 clinical respiratory specimens. Prospective analysis of a total 520 specimens was then performed to further evaluate the Abbott assay. The Abbott assay showed a lower limit of detection at 22.5 AFB/ml, which was more sensitive than the Cobas assay (167.5 AFB/ml). The two assays demonstrated a significant difference in diagnostic performance (McNemar's test; P = 0.0034), in which the Abbott assay presented significantly higher area under curve (AUC) than the Cobas assay (1.000 vs 0.880; P = 0.0002). The Abbott assay demonstrated extremely low PCR inhibition on clinical respiratory specimens. The automated Abbott assay required only very short manual handling time (0.5 h), which could help to improve the laboratory management. In the prospective analysis, the overall estimates for sensitivity and specificity of the Abbott assay were both 100 % among smear-positive specimens, whereas the smear-negative specimens were 96.7 and 96.1 %, respectively. No cross-reactivity with non-tuberculosis mycobacterial species was observed. The superiority in sensitivity of the Abbott assay for detecting MTBC in smear-negative specimens could further minimize the risk in MTBC false-negative detection. The new Abbott RealTime MTB assay has good diagnostic performance which can be a useful diagnostic tool for rapid MTBC detection in clinical laboratories.
Rapid, Real-time Methane Detection in Ground Water Using a New Gas-Water Equilibrator Design
Ruybal, C. J.; DiGiulio, D. C.; Wilkin, R. T.; Hargrove, K. D.; McCray, J. E.
2014-12-01
Recent increases in unconventional gas development have been accompanied by public concern for methane contamination in drinking water wells near production areas. Although not a regulated pollutant, methane may be a marker contaminant for others that are less mobile in groundwater and thus may be detected later, or at a location closer to the source. In addition, methane poses an explosion hazard if exsolved concentrations reach 5 - 15% volume in air. Methods for determining dissolved gases, such as methane, have evolved over 60 years. However, the response time of these methods is insufficient to monitor trends in methane concentration in real-time. To enable rapid, real-time monitoring of aqueous methane concentrations during ground water purging, a new gas-water equilibrator (GWE) was designed that increases gas-water mass exchange rates of methane for measurement. Monitoring of concentration trends allows a comparison of temporal trends between sampling events and comparison of baseline conditions with potential post-impact conditions. These trends may be a result of removal of stored casing water, pre-purge ambient borehole flow, formation physical and chemical heterogeneity, or flow outside of well casing due to inadequate seals. Real-time information in the field can help focus an investigation, aid in determining when to collect a sample, save money by limiting costs (e.g. analytical, sample transport and storage), and provide an immediate assessment of local methane concentrations. Four domestic water wells, one municipal water well, and one agricultural water well were sampled for traditional laboratory analysis and compared to the field GWE results. Aqueous concentrations measured on the GWE ranged from non-detect to 1,470 μg/L methane. Some trends in aqueous methane concentrations measured on the GWE were observed during purging. Applying a paired t-test comparing the new GWE method and traditional laboratory analysis yielded a p-value 0
Real-time Human Activity Recognition
Albukhary, N.; Mustafah, Y. M.
2017-11-01
The traditional Closed-circuit Television (CCTV) system requires human to monitor the CCTV for 24/7 which is inefficient and costly. Therefore, there’s a need for a system which can recognize human activity effectively in real-time. This paper concentrates on recognizing simple activity such as walking, running, sitting, standing and landing by using image processing techniques. Firstly, object detection is done by using background subtraction to detect moving object. Then, object tracking and object classification are constructed so that different person can be differentiated by using feature detection. Geometrical attributes of tracked object, which are centroid and aspect ratio of identified tracked are manipulated so that simple activity can be detected.
DEFF Research Database (Denmark)
Bui, Thanh Xuan; Wolff, Anders; Madsen, Mogens
2012-01-01
Campylobacter spp. is the most common cause of bacterial diarrhoea in humans worldwide. Therefore, rapid and reliable methods fordetection and quantification of this pathogen are required. In this study, we have developed a reverse transcription quantitative real-time PCR(RT-qPCR) for detection a...
International Nuclear Information System (INIS)
Goddard, Braden; Charlton, William S.; McDeavitt, Sean M.
2010-01-01
Research highlights: → HPGe detectors are suitable for UREX+3a real-time spectroscopy. → HPGe N-type detectors may be suitable for a reprocessing facility. → Gamma ray self-shielding does not occur for pipe diameters less than 2 in. - Abstract: Reprocessing nuclear fuel is becoming more viable in the United States due to the anticipated increase in construction of nuclear power plants, the growing stockpile of existing used nuclear fuel, and a public desire to reduce the amount of this fuel. A new reprocessing facility will likely have state of the art controls and monitoring methods to safeguard special nuclear materials, as well as to provide real-time monitoring for process control. The focus of this research was to create a proof of concept to enable the development of a detection strategy that uses well established gamma and neutron measurement methods to characterize samples from the Uranium Extraction Plus 3a (UREX+3a) reprocessing method using a variety of detector types and measurement times. A facility that implemented real-time gamma detection equipment could improve product quality control and provide additional benefits, such as waste volume reduction. In addition to the spectral analyses, it was determined by Monte Carlo N Particle (MCNP) simulations that there is no noticeable self-shielding for internal pipe diameters less than 5.08 cm, indicating that no self-shielding correction factors are needed. Further, it was determined that High Purity Germanium (HPGe) N-type detectors have the high gamma ray energy resolution and neutron damage resistance that would be required in a reprocessing facility. Finally, the gamma ray spectra for the measured samples were simulated using MCNP and then the model was extended to predict the responses from an actual reprocessing scenario from UREX+3a applied to fuel that had a decay time of 3 years. The 3-year decayed fuel was more representative of commercially reprocessed fuel than the acquired UREX+3a
Real Time Fire Reconnaissance Satellite Monitoring System Failure Model
Nino Prieto, Omar Ariosto; Colmenares Guillen, Luis Enrique
2013-09-01
In this paper the Real Time Fire Reconnaissance Satellite Monitoring System is presented. This architecture is a legacy of the Detection System for Real-Time Physical Variables which is undergoing a patent process in Mexico. The methodologies for this design are the Structured Analysis for Real Time (SA- RT) [8], and the software is carried out by LACATRE (Langage d'aide à la Conception d'Application multitâche Temps Réel) [9,10] Real Time formal language. The system failures model is analyzed and the proposal is based on the formal language for the design of critical systems and Risk Assessment; AltaRica. This formal architecture uses satellites as input sensors and it was adapted from the original model which is a design pattern for physical variation detection in Real Time. The original design, whose task is to monitor events such as natural disasters and health related applications, or actual sickness monitoring and prevention, as the Real Time Diabetes Monitoring System, among others. Some related work has been presented on the Mexican Space Agency (AEM) Creation and Consultation Forums (2010-2011), and throughout the International Mexican Aerospace Science and Technology Society (SOMECYTA) international congress held in San Luis Potosí, México (2012). This Architecture will allow a Real Time Fire Satellite Monitoring, which will reduce the damage and danger caused by fires which consumes the forests and tropical forests of Mexico. This new proposal, permits having a new system that impacts on disaster prevention, by combining national and international technologies and cooperation for the benefit of humankind.
Real-Time Detection of Sporadic Meteors in the Intensified TV Imaging Systems.
Vítek, Stanislav; Nasyrova, Maria
2017-12-29
The automatic observation of the night sky through wide-angle video systems with the aim of detecting meteor and fireballs is currently among routine astronomical observations. The observation is usually done in multi-station or network mode, so it is possible to estimate the direction and the speed of the body flight. The high velocity of the meteorite flying through the atmosphere determines the important features of the camera systems, namely the high frame rate. Thanks to high frame rates, such imaging systems produce a large amount of data, of which only a small fragment has scientific potential. This paper focuses on methods for the real-time detection of fast moving objects in the video sequences recorded by intensified TV systems with frame rates of about 60 frames per second. The goal of our effort is to remove all unnecessary data during the daytime and make free hard-drive capacity for the next observation. The processing of data from the MAIA (Meteor Automatic Imager and Analyzer) system is demonstrated in the paper.
Real Time Speed Measure while Automobile Braking on Soft Sensing Technique
Energy Technology Data Exchange (ETDEWEB)
Zhu, W B; Li, D S; Lu, Y [China Jiliang University, Hangzhou, Zhejiang province, 310018 (China)
2006-10-15
Because the braking performance of automobile has close relationship to traffic safety, it is important to detect that. Focusing on the problem that the real time speed is difficult to obtain in detection process, soft sensing technique is introduced in this paper. According to analyzing the relationship of the dynamics equation of a moving automobile, a module of real time speed of braking is set up. By using imitation method with experiment data to get the pressure function of cylinder and analyzing the relationship between the trigging moment of a wheel and the pressure function of brake cylinder, the real time speed is confirmed in good precision. The maximal measurement error of real time speed is 8.7% and the precision can satisfy engineering request.
Real Time Speed Measure while Automobile Braking on Soft Sensing Technique
International Nuclear Information System (INIS)
Zhu, W B; Li, D S; Lu, Y
2006-01-01
Because the braking performance of automobile has close relationship to traffic safety, it is important to detect that. Focusing on the problem that the real time speed is difficult to obtain in detection process, soft sensing technique is introduced in this paper. According to analyzing the relationship of the dynamics equation of a moving automobile, a module of real time speed of braking is set up. By using imitation method with experiment data to get the pressure function of cylinder and analyzing the relationship between the trigging moment of a wheel and the pressure function of brake cylinder, the real time speed is confirmed in good precision. The maximal measurement error of real time speed is 8.7% and the precision can satisfy engineering request
Directory of Open Access Journals (Sweden)
Yi eWang
2016-05-01
Full Text Available We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA, which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5’ end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labelled at the 5’ end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5’ end short sequences and their complementary sequences, which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 minutes, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.
Wang, Yi; Wang, Yan; Zhang, Lu; Liu, Dongxin; Luo, Lijuan; Li, Hua; Cao, Xiaolong; Liu, Kai; Xu, Jianguo; Ye, Changyun
2016-01-01
We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA), which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5' end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labeled at the 5' end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5' end short sequences and their complementary sequences), which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 min, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here, we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.
DEFF Research Database (Denmark)
Zor, Kinga; Heiskanen, Arto; Caviglia, Claudia
2014-01-01
and electrochemical analysis platform with in-built fluid handling and detection, enabling complete cell based assays comprising on-line electrode cleaning, sterilization, surface functionalization, cell seeding, cultivation and electrochemical real-time monitoring of cellular dynamics. To demonstrate the versatility...... capability. The here presented platform is aimed at applications utilizing cell based assays, ranging from e.g. monitoring of drug effects in pharmacological studies, characterization of neural stem cell differentiation, and screening of genetically modified microorganisms to environmental monitoring....
Shrestha, Nabin K; Tuohy, Marion J; Hall, Gerri S; Reischl, Udo; Gordon, Steven M; Procop, Gary W
2003-11-01
Mycobacteria cause a variety of illnesses that differ in severity and public health implications. The differentiation of Mycobacterium tuberculosis from nontuberculous mycobacteria (NTM) is of primary importance for infection control and choice of antimicrobial therapy. Despite advances in molecular diagnostics, the ability to rapidly diagnose M. tuberculosis infections by PCR is still inadequate, largely because of the possibility of false-negative reactions. We designed and validated a real-time PCR for mycobacteria by using the LightCycler system with 18 reference strains and 168 clinical mycobacterial isolates. All clinically significant mycobacteria were detected; the mean melting temperatures (with 99.9% confidence intervals [99.9% CI] in parentheses) for the different mycobacteria were as follows: M. tuberculosis, 64.35 degrees C (63.27 to 65.42 degrees C); M. kansasii, 59.20 degrees C (58.07 to 60.33 degrees C); M. avium, 57.82 degrees C (57.05 to 58.60 degrees C); M. intracellulare, 54.46 degrees C (53.69 to 55.23 degrees C); M. marinum, 58.91 degrees C (58.28 to 59.55 degrees C); rapidly growing mycobacteria, 53.09 degrees C (50.97 to 55.20 degrees C) or 43.19 degrees C (42.19 to 44.49 degrees C). This real-time PCR assay with melting curve analysis consistently accurately detected and differentiated M. tuberculosis from NTM. Detection of an NTM helps ensure that the negative result for M. tuberculosis is a true negative. The specific melting temperature also provides a suggestion of the identity of the NTM present, when the most commonly encountered mycobacterial species are considered. In a parallel comparison, both the LightCycler assay and the COBAS Amplicor M. tuberculosis assay correctly categorized 48 of 50 specimens that were proven by culture to contain M. tuberculosis, and the LightCycler assay correctly characterized 3 of 3 specimens that contained NTM.
LENUS (Irish Health Repository)
Grogan, Juanita A
2011-06-01
Novel real-time PCR assays targeting the Bordetella pertussis insertion sequence IS481, the toxin promoter region and Bordetella parapertussis insertion sequence IS1001 were designed. PCR assays were capable of detecting ≤10 copies of target DNA per reaction, with an amplification efficiency of ≥90 %. From September 2003 to December 2009, per-nasal swabs and nasopharyngeal aspirates submitted for B. pertussis culture from patients ≤1 month to >15 years of age were examined by real-time PCR. Among 1324 patients, 76 (5.7 %) were B. pertussis culture positive and 145 (10.95 %) were B. pertussis PCR positive. Of the B. pertussis PCR-positive patients, 117 (81 %) were aged 6 months or less. A total of 1548 samples were examined, of which 87 (5.6 %) were culture positive for B. pertussis and 169 (10.92 %) were B. pertussis PCR positive. All culture-positive samples were PCR positive. Seven specimens (0.5 %) were B. parapertussis culture positive and 10 (0.8 %) were B. parapertussis PCR positive, with all culture-positive samples yielding PCR-positive results. A review of patient laboratory records showed that of the 1324 patients tested for pertussis 555 (42 %) had samples referred for respiratory syncytial virus (RSV) testing and 165 (30 %) were positive, as compared to 19.4 % of the total 5719 patients tested for RSV in this period. Analysis of the age distribution of RSV-positive patients identified that 129 (78 %) were aged 6 months or less, similar to the incidence observed for pertussis in that patient age group. In conclusion, the introduction of the real-time PCR assays for the routine detection of B. pertussis resulted in a 91 % increase in the detection of the organism as compared to microbiological culture. The incidence of infection with B. parapertussis is low while the incidence of RSV infection in infants suspected of having pertussis is high, with a similar age distribution to B. pertussis infection.
Fu, Yung-Chieh; Liao, I-Chuang; Chen, Hung-Mo; Yan, Jing-Jou
2016-07-01
The Abbott RealTime MTB assay, launched in June 2014, has been shown to have a competitive performance in the detection of the Mycobacterium tuberculosis (MTB) complex in respiratory specimens. The present study was conducted to investigate the usefulness of the Abbott MTB Realtime assay in the detection of MTB in formalin-fixed paraffin-embedded (FFPE) tissues. A total of 96 FFPE specimens obtained from microbiologically proven MTB cases (N=60) and nontuberculous Mycobacterium cases (N=36) were analyzed. The performance of the Abbott MTB Realtime assay was compared with that of the Roche Cobas TaqMan MTB assay. The overall sensitivity and specificity of the Abbott assay were 63.3% and 97.2%, respectively, compared with 11.7% and 100% for the Cobas assay. The detection rate of the Abbott assay was much higher among 37 acid-fast-positive specimens than among 23 acid-fast-negative specimens (89.3% versus 21.7%, respectively). The detection rate of the assay was higher among 29 resection specimens than among 31 small biopsy specimens (86.2% versus 41.9%, respectively). Our results suggest that the Abbott RealTime MTB assay can be used to differentiate MTB from nontuberculous mycobacterial infections in acid-fast-positive FFPE tissues. © 2016 by the Association of Clinical Scientists, Inc.
Detection of HPV and co-infecting pathogens in healthy Italian women by multiplex real-time PCR.
Camporiondo, Maria Pia; Farchi, Francesca; Ciccozzi, Massimo; Denaro, Aurelia; Gallone, Domenica; Maracchioni, Fabio; Favalli, Cartesio; Ciotti, Marco
2016-01-01
Several pathogens can be transmitted sexually and are an important cause of morbidity among sexually active women. The aim of the study was to detect the presence of human papillomavirus (HPV), Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Trichomonas vaginalis (TV), Mycoplasma hominis (MH), Mycoplasma genitalium (MG), Ureaplasma urealyticum (UU), and Ureaplasma parvum (UP) in a group of 309 healthy women enrolled at the San Camillo - Forlanini hospital of Rome by using two multiplex real-time PCR assays based on TOCE® technology. The women's ages ranged from 34 to 60 years, median 49 [IQR 45-54]. Of the 309 women tested, HPV DNA was detected in 77/309 (24.9%) patients. Of these, 44 (14.2%) harboured a single infection while 33 (10.7%) were infected by multiple genotypes. Prevalence of HPV infection was highest among females aged 40-50 years (15.2%). Of the other pathogens sought, CT, MG and NG were not detected while positive results were found for MH (12/309, 3.9%), TV (4/309, 1.3%), UP (89/309, 28.8%) and UU (14/309, 4.5%). Co-infections were as follows: 5 MH/HPV, 4 TV/HPV, 34 UP/HPV and 9 UU/HPV. In HPV-positive women, the probability of being infected by UP and UU was 2.5 (p=0.00045) and 6 fold higher (p=0.0016) than in HPV-negative women. The study supports the use of multiplex real-time PCR assays in a routine diagnostic setting. The high sensitivity and specificity of these assays along with the simultaneous detection of the most common sexually transmitted pathogens confers an advantage with respect to more obsolete methods reducing costs and time to diagnosis.
FRB microstructure revealed by the real-time detection of FRB170827
Farah, W.; Flynn, C.; Bailes, M.; Jameson, A.; Bannister, K. W.; Barr, E. D.; Bateman, T.; Bhandari, S.; Caleb, M.; Campbell-Wilson, D.; Chang, S.-W.; Deller, A.; Green, A. J.; Hunstead, R.; Jankowski, F.; Keane, E.; Macquart, J.-P.; Möller, A.; Onken, C. A.; Osłowski, S.; Parthasarathy, A.; Plant, K.; Ravi, V.; Shannon, R.; Tucker, B. E.; Venkatraman Krishnan, V.; Wolf, C.
2018-05-01
We report a new Fast Radio Burst (FRB) discovered in real-time as part of the UTMOST project at the Molonglo Observatory Synthesis Radio Telescope (MOST). FRB170827 is the first detected with our low-latency ( 20 ± 7 Jy ms, and is narrow, with a width of ˜ 400 μs at 10% of its maximum amplitude. However, the burst shows three temporal components, the narrowest of which is ˜ 30 μs, and a scattering timescale of 4.1 ± 2.7 μs. The FRB shows spectral modulations on frequency scales of 1.5 MHz and 0.1 MHz. Both are prominent in the dynamic spectrum, which shows a very bright region of emission between 841 and 843 MHz, and weaker, patchy emission across the entire band. We show the fine spectral structure could arise in the FRB host galaxy, or its immediate vicinity.
Real time RT-PCR assay for detection of different serotypes of FMDV in Egypt
Directory of Open Access Journals (Sweden)
Laila El-Shehawy
Full Text Available Aim: The present study indicated that rRT-PCR could be provided for the detection of FMDV in infected, contact and carrier cattle and also provide a rapid sensitive tool aiming to aid in rapid disease detection and control. Foot and Mouth disease virus serotypes O and A still existing in Egypt. In January 2012, sever outbreaks struck the animal population in most Egyptian 1 governorates. The causative virus was identified as FMDV SAT2. Material and Methods: Five samples of tongue epithelium (ET and five oesophageal-pharyngeal (OP fluid samples were collected from FMD suspected cattle in infected farm at El-Fayoum and 20 OP samples from in-contact cattle at the same farm in addition to 30 OP samples from apparently healthy cattle at three different localities in El-Fayoum governorate (12 from Fayoum; 9 from Sinoras and 9 from Edsa in order to detect carrier cattle. All of these samples were collected during November and December 2011 and January 2012. Results: All the ET and OP samples were inoculated on BHK cell culture and baby mice. The obtained results were identified using complement fixation test in addition to real-time reverse transcriptase polymerase chain reaction (rRT-PCR. In the infected farm at El-Fayoum FMDV type SAT2 was detected in cattle which are considered as the first introduction of this type while FMDV type O and SAT2 were detected in the in-contact cattle in the same farm. The sensitivity of rRT-PCR was cleared in the in-contact cattle as 13 out of 20 OP samples were positive to FMDV by rRT-PCR while 11 out of 20 OP samples were positive to FMDV by CFT. The OP samples collected from apparently healthy cattle from Fayoum, Sinoras and Edsa localities in Fayoum governorate demonstrate the circulation of the FMDV type A, O and the recent SAT2 in carrier cattle which threaten cattle population in Fayoum governorate. Also the sensitivity of real time RT-PCR over the CFT in detection of FMDV carrier cattle was clearly noticed in
Hung, Min-Sheng; Ho, Chia-Chin; Chen, Chih-Pin
2016-08-01
This study developed a microfluidic platform for replicating and detecting DNA in real time by integrating a laser and a microfluidic device composed of polydimethylsiloxane. The design of the microchannels consisted of a laser-heating area and a detection area. An infrared laser was used as the heating source for DNA replication, and the laser power was adjusted to heat the solutions directly. In addition, strong biotin-avidin binding was used to capture and detect the replicated products. The biotin on one end was bound to avidin and anchored to the surface of the microchannels, whereas the biotin on the other end was bound to the quantum dots (Qdots). The results showed that the fluorescent intensity of the Qdots bound to the replicated products in the detection area increased with the number of thermal cycles created by the laser. When the number of thermal cycles was ≥10, the fluorescent intensity of the Qdots was directly detectable on the surface of the microchannels. The proposed method is more sensitive than detection methods entailing gel electrophoresis.
Real time 1.55 μm VCSEL-based coherent detection link
DEFF Research Database (Denmark)
Rodes Lopez, Roberto; Parekh, D.; Jensen, Jesper Bevensee
2012-01-01
This paper presents an experimental demonstration of VCSEL-based PON with simplified real-time coherent receiver at 2.5 Gbps. Receiver sensitivity of −37 dBm is achieved proving splitting ratio up to 2048 after 17 km fiber transmission.......This paper presents an experimental demonstration of VCSEL-based PON with simplified real-time coherent receiver at 2.5 Gbps. Receiver sensitivity of −37 dBm is achieved proving splitting ratio up to 2048 after 17 km fiber transmission....
DEFF Research Database (Denmark)
Fachmann, Mette Sofie Rousing; Josefsen, Mathilde Hasseldam; Hoorfar, Jeffrey
2015-01-01
bacterial cells in two validated real-time PCR assays for Campylobacter and Salmonella. The five best performing (based on: limit of detection (LOD), maximum fluorescence, shape of amplification curves, and amplification efficiency) were subsequently applied to meat and fecal samples. The VeriQuest q......PCR master mix performed best for both meat and fecal samples (LODs of 102 and 104 CFU ml-1 in the purest and crudest DNA extractions, respectively) compared with Tth (LOD=102 -103 and 105 -106 CFU ml-1 ). AmpliTaqGold and HotMasterTaq both performed well (LOD=102 -104 CFU ml-1 ) with meat samples and poorly...... (LOD=103 -106 CFU ml-1 /not detected) with fecal samples. CONCLUSIONS: Applying the VeriQuest qPCR master mix in the two tested real-time PCR assays could allow for simpler sample preparation and thus a reduction in cost. SIGNIFICANCE AND IMPACT OF STUDY: This work exemplifies a cost-effective strategy...
CUDA-based real time surgery simulation.
Liu, Youquan; De, Suvranu
2008-01-01
In this paper we present a general software platform that enables real time surgery simulation on the newly available compute unified device architecture (CUDA)from NVIDIA. CUDA-enabled GPUs harness the power of 128 processors which allow data parallel computations. Compared to the previous GPGPU, it is significantly more flexible with a C language interface. We report implementation of both collision detection and consequent deformation computation algorithms. Our test results indicate that the CUDA enables a twenty times speedup for collision detection and about fifteen times speedup for deformation computation on an Intel Core 2 Quad 2.66 GHz machine with GeForce 8800 GTX.
Comparison between digital PCR and real-time PCR in detection of Salmonella typhimurium in milk.
Wang, Meng; Yang, Junjie; Gai, Zhongtao; Huo, Shengnan; Zhu, Jianhua; Li, Jun; Wang, Ranran; Xing, Sheng; Shi, Guosheng; Shi, Feng; Zhang, Lei
2018-02-02
As a kind of zero-tolerance foodborne pathogens, Salmonella typhimurium poses a great threat to quality of food products and public health. Hence, rapid and efficient approaches to identify Salmonella typhimurium are urgently needed. Combined with PCR and fluorescence technique, real-time PCR (qPCR) and digital PCR (ddPCR) are regarded as suitable tools for detecting foodborne pathogens. To compare the effect between qPCR and ddPCR in detecting Salmonella typhimurium, a series of nucleic acid, pure strain culture and spiking milk samples were applied and the resistance to inhibitors referred in this article as well. Compared with qPCR, ddPCR exhibited more sensitive (10 -4 ng/μl or 10 2 cfu/ml) and less pre-culturing time (saving 2h). Moreover, ddPCR had stronger resistance to inhibitors than qPCR, yet absolute quantification hardly performed when target's concentration over 1ng/μl or 10 6 cfu/ml. This study provides an alternative strategy in detecting foodborne Salmonella typhimurium. Copyright © 2018 Elsevier B.V. All rights reserved.
Andergassen, Ulrich; Kölbl, Alexandra C; Mahner, Sven; Jeschke, Udo
2016-04-01
Cells, which detach from a primary epithelial tumour and migrate through lymphatic vessels and blood stream are called 'circulating tumour cells'. These cells are considered to be the main root of remote metastasis and are correlated to a worse prognosis concerning progression-free and overall survival of the patients. Therefore, the detection of the minimal residual disease is of great importance regarding therapeutic decisions. Many different detection strategies are already available, but only one method, the CellSearch® system, reached FDA approval. The present review focusses on the detection of circulating tumour cells by means of real-time PCR, a highly sensitive method based on differences in gene expression between normal and malignant cells. Strategies for an enrichment of tumour cells are mentioned, as well as a large panel of potential marker genes. Drawbacks and advantages of the technique are elucidated, whereas, the greatest advantage might be, that by selection of appropriate marker genes, also tumour cells, which have already undergone epithelial to mesenchymal transition can be detected. Finally, the application of real-time PCR in different gynaecological malignancies is described, with breast cancer being the most studied cancer entity.
A real-time radiation mapping system
International Nuclear Information System (INIS)
Scoggins, W.A.; VanEtten, D.M.
1988-01-01
A prototype of a real-time radiation mapping system, Ranger, was developed to respond to an accident involving the release of plutonium for the Department of Energy's Accident Response Group. In 1987 Ranger demonstrated that it can provide an efficient method of monitoring large areas of land for radioactive contamination. With the experience gained from the operation of the prototype, the external computer and software are being upgraded in order to obtain a fully operational system. The new system uses the prototype's commercially available line-of-sight microwave system for determining position and the same radiation detection instruments. The data obtained from the radiation detection instrument(s) are linked back to the external computer along with the relative position of the measurement through the ranging system. The data are displayed on a gridded map as colored circles and permanently stored in real-time. The different colors represent different contamination levels. Contours can be drawn using the permanently stored data. 4 figs
Robust Real-Time Tracking for Visual Surveillance
Directory of Open Access Journals (Sweden)
Aguilera Josep
2007-01-01
Full Text Available This paper describes a real-time multi-camera surveillance system that can be applied to a range of application domains. This integrated system is designed to observe crowded scenes and has mechanisms to improve tracking of objects that are in close proximity. The four component modules described in this paper are (i motion detection using a layered background model, (ii object tracking based on local appearance, (iii hierarchical object recognition, and (iv fused multisensor object tracking using multiple features and geometric constraints. This integrated approach to complex scene tracking is validated against a number of representative real-world scenarios to show that robust, real-time analysis can be performed.
Imaging gene expression in real-time using aptamers
Energy Technology Data Exchange (ETDEWEB)
Shin, Il Chung [Iowa State Univ., Ames, IA (United States)
2011-01-01
Signal transduction pathways are usually activated by external stimuli and are transient. The downstream changes such as transcription of the activated genes are also transient. Real-time detection of promoter activity is useful for understanding changes in gene expression, especially during cell differentiation and in development. A simple and reliable method for viewing gene expression in real time is not yet available. Reporter proteins such as fluorescent proteins and luciferase allow for non-invasive detection of the products of gene expression in living cells. However, current reporter systems do not provide for real-time imaging of promoter activity in living cells. This is because of the long time period after transcription required for fluorescent protein synthesis and maturation. We have developed an RNA reporter system for imaging in real-time to detect changes in promoter activity as they occur. The RNA reporter uses strings of RNA aptamers that constitute IMAGEtags (Intracellular MultiAptamer GEnetic tags), which can be expressed from a promoter of choice. The tobramycin, neomycin and PDC RNA aptamers have been utilized for this system and expressed in yeast from the GAL1 promoter. The IMAGEtag RNA kinetics were quantified by RT-qPCR. In yeast precultured in raffinose containing media the GAL1 promoter responded faster than in yeast precultured in glucose containing media. IMAGEtag RNA has relatively short half-life (5.5 min) in yeast. For imaging, the yeast cells are incubated with their ligands that are labeled with fluorescent dyes. To increase signal to noise, ligands have been separately conjugated with the FRET (Förster resonance energy transfer) pairs, Cy3 and Cy5. With these constructs, the transcribed aptamers can be imaged after activation of the promoter by galactose. FRET was confirmed with three different approaches, which were sensitized emission, acceptor photobleaching and donor lifetime by FLIM (fluorescence lifetime imaging
Imaging gene expression in real-time using aptamers
Energy Technology Data Exchange (ETDEWEB)
Shin, Ilchung [Iowa State Univ., Ames, IA (United States)
2012-01-01
Signal transduction pathways are usually activated by external stimuli and are transient. The downstream changes such as transcription of the activated genes are also transient. Real-time detection of promoter activity is useful for understanding changes in gene expression, especially during cell differentiation and in development. A simple and reliable method for viewing gene expression in real time is not yet available. Reporter proteins such as fluorescent proteins and luciferase allow for non-invasive detection of the products of gene expression in living cells. However, current reporter systems do not provide for real-time imaging of promoter activity in living cells. This is because of the long time period after transcription required for fluorescent protein synthesis and maturation. We have developed an RNA reporter system for imaging in real-time to detect changes in promoter activity as they occur. The RNA reporter uses strings of RNA aptamers that constitute IMAGEtags (Intracellular MultiAptamer GEnetic tags), which can be expressed from a promoter of choice. The tobramycin, neomycin and PDC RNA aptamers have been utilized for this system and expressed in yeast from the GAL1 promoter. The IMAGEtag RNA kinetics were quantified by RT-qPCR. In yeast precultured in raffinose containing media the GAL1 promoter responded faster than in yeast precultured in glucose containing media. IMAGEtag RNA has relatively short half-life (5.5 min) in yeast. For imaging, the yeast cells are incubated with their ligands that are labeled with fluorescent dyes. To increase signal to noise, ligands have been separately conjugated with the FRET (Förster resonance energy transfer) pairs, Cy3 and Cy5. With these constructs, the transcribed aptamers can be imaged after activation of the promoter by galactose. FRET was confirmed with three different approaches, which were sensitized emission, acceptor photobleaching and donor lifetime by FLIM (fluorescence lifetime imaging
Implementation of a General Real-Time Visual Anomaly Detection System Via Soft Computing
Dominguez, Jesus A.; Klinko, Steve; Ferrell, Bob; Steinrock, Todd (Technical Monitor)
2001-01-01
The intelligent visual system detects anomalies or defects in real time under normal lighting operating conditions. The application is basically a learning machine that integrates fuzzy logic (FL), artificial neural network (ANN), and generic algorithm (GA) schemes to process the image, run the learning process, and finally detect the anomalies or defects. The system acquires the image, performs segmentation to separate the object being tested from the background, preprocesses the image using fuzzy reasoning, performs the final segmentation using fuzzy reasoning techniques to retrieve regions with potential anomalies or defects, and finally retrieves them using a learning model built via ANN and GA techniques. FL provides a powerful framework for knowledge representation and overcomes uncertainty and vagueness typically found in image analysis. ANN provides learning capabilities, and GA leads to robust learning results. An application prototype currently runs on a regular PC under Windows NT, and preliminary work has been performed to build an embedded version with multiple image processors. The application prototype is being tested at the Kennedy Space Center (KSC), Florida, to visually detect anomalies along slide basket cables utilized by the astronauts to evacuate the NASA Shuttle launch pad in an emergency. The potential applications of this anomaly detection system in an open environment are quite wide. Another current, potentially viable application at NASA is in detecting anomalies of the NASA Space Shuttle Orbiter's radiator panels.
Kodera, Yuki
2018-01-01
Large earthquakes with long rupture durations emit P wave energy throughout the rupture period. Incorporating late-onset P waves into earthquake early warning (EEW) algorithms could contribute to robust predictions of strong ground motion. Here I describe a technique to detect in real time P waves from growing ruptures to improve the timeliness of an EEW algorithm based on seismic wavefield estimation. The proposed P wave detector, which employs a simple polarization analysis, successfully detected P waves from strong motion generation areas of the 2011 Mw 9.0 Tohoku-oki earthquake rupture. An analysis using 23 large (M ≥ 7) events from Japan confirmed that seismic intensity predictions based on the P wave detector significantly increased lead times without appreciably decreasing the prediction accuracy. P waves from growing ruptures, being one of the fastest carriers of information on ongoing rupture development, have the potential to improve the performance of EEW systems.
Wang, Zhouli; Cai, Rui; Yuan, Yahong; Niu, Chen; Hu, Zhongqiu; Yue, Tianli
2014-04-03
Alicyclobacillus acidoterrestris is the most important spoilage species within the Alicyclobacillus genus and has become a major issue in the pasteurized fruit juice industry. The aim of this study was to develop a method combining immunomagnetic separation (IMS) with real-time PCR system (IMS-PCR) for rapid and specific detection of A. acidoterrestris in fruit products. A real-time PCR with the TaqMan system was designed to target the 16S rDNA genes with specific primer and probe set. The specificity of the assay was confirmed using 9 A. acidoterrestris strains and 21 non-A. acidoterrestris strains. The results indicated that no combination of the designed primers and probe was found in any Alicyclobacillus genus except A. acidoterrestris. The detection limit of the established IMS-PCR was less than 10CFU/mL and the testing process was accomplished in 2-3h. For the three types of samples (sterile water, apple juice and kiwi juice), the correlation coefficient of standard curves was greater than 0.991, and the calculated PCR efficiencies were from 108% to 109%. As compared with the standard culture method performed concurrently on the same set of samples, the sensitivity, specificity and accuracy of IMS-PCR for 196 naturally contaminated fruit products were 90.0%, 98.3% and 97.5%, respectively. The results exhibited that the proposed IMS-PCR method was effective for the rapid detection of A. acidoterrestris in fruit products. Copyright © 2014. Published by Elsevier B.V.
Singh, Prashant; Pfeifer, Yvonne; Mustapha, Azlin
2016-05-01
Real-time PCR melt curve assays for the detection of β-lactamase, extended-spectrum β-lactamase and carbapenemase genes in Gram-negative bacteria were developed. Two multiplex real-time PCR melt curve assays were developed for the detection of ten common β-lactamase genes: blaKPC-like, blaOXA-48-like, blaNDM-like, blaVIM-like, blaIMP-like, blaCTX-M-1+2-group, blaCMY-like, blaACC-like, blaSHV-like and blaTEM-like. The assays were evaluated using 25 bacterial strains and 31 DNA samples (total n=56) comprising different Enterobacteriaceae genera and Pseudomonas spp. These strains were previously characterized at five research institutes. Each resistance gene targeted in this study generated a non-overlapping and distinct melt curve peak. The assay worked effectively and detected the presence of additional resistance genes in 23 samples. The assays developed in this study offer a simple, low cost method for the detection of prevalent β-lactamase, ESBL and carbapenemase genes among Gram-negative pathogens. Copyright © 2016 Elsevier B.V. All rights reserved.
Robène, Isabelle; Perret, Marion; Jouen, Emmanuel; Escalon, Aline; Maillot, Marie-Véronique; Chabirand, Aude; Moreau, Aurélie; Laurent, Annie; Chiroleu, Frédéric; Pruvost, Olivier
2015-07-01
Bacterial blight of onion is an emerging disease threatening world onion production. The causal agent Xanthomonas axonopodis pv. allii is seed transmitted and a reliable and sensitive tool is needed to monitor seed exchanges. A triplex quantitative real-time PCR assay was developed targeting two X. axonopodis pv. allii-specific markers and an internal control chosen in 5.8S rRNA gene from Alliaceae. Amplification of at least one marker indicates the presence of the bacterium in seed extracts. This real-time PCR assay detected all the 79 X. axonopodis pv. allii strains tested and excluded 85.2% of the 135 non-target strains and particularly all 39 saprophytic and pathogenic bacteria associated with onion. Cross-reactions were mainly obtained for strains assigned to nine phylogenetically related X. axonopodis pathovars. The cycle cut-off was estimated statistically at 36.3 considering a risk of false positive of 1%. The limit of detection obtained in at least 95% of the time (LOD 95%) was 5×10(3) CFU/g (colony forming unit/g). The sensitivity threshold was found to be 1 infected seed in 32,790 seeds. This real-time PCR assay should be useful for preventing the long-distance spread of X. axonopodis pv. allii via contaminated seed lots and determining the epidemiology of the bacterium. Copyright © 2015 Elsevier B.V. All rights reserved.
Detection of viable Escherichia coli O157:H7 in ground beef by propidium monoazide real-time PCR.
Liu, Yarui; Mustapha, Azlin
2014-01-17
Escherichia coli O157:H7 associated with food has caused many serious public health problems in recent years. However, only viable cells of this pathogen can cause infections, and false-positive detection caused by dead cells can lead to unnecessary product recalls. The objective of this study was to develop and optimize a method that combines propidium monoazide (PMA) staining with real-time PCR to detect only viable cells of E. coli O157:H7 in ground beef. PMA is a DNA intercalating dye that can penetrate compromised membranes of dead cells and bind to cellular DNA, preventing its amplification via a subsequent PCR. Three strains of E. coli O157:H7 (505B, G5310 and C7927) at concentrations of 10(0) to 10(8)CFU/mL were used as live cells. Dead cells were obtained by heating cell suspensions at 85°C for 15 min. Suspensions were treated with PMA and the optimized assay was applied to artificially contaminated ground beef with two different fat contents (10% and 27%). DNA was extracted and amplified by TaqMan® real-time PCR assay targeting the uidA gene for detection of E. coli O157:H7. Plasmid pUC19 was added as an internal amplification control (IAC). A treatment of 25 μM PMA with a 10-min light exposure on ice was sufficient to eliminate DNA from 10(8) dead E. coli O157:H7 cells/mL. The optimized assay could detect as low as 10(2) CFU/mL viable E. coli O157:H7 in pure culture and 10(5) CFU/g in ground beef, in the presence of 10(6)/mL or g of dead cells. With an 8-h enrichment, 1 CFU/g viable E. coli O157:H7 in ground beef was detectable without interference from 10(6) dead cells/g. In conclusion, the PMA real-time PCR could effectively detect viable E. coli O157:H7 without being compromised by dead cells. Copyright © 2013 Elsevier B.V. All rights reserved.
López-Calleja, Inés María; de la Cruz, Silvia; González, Isabel; García, Teresa; Martín, Rosario
2015-06-15
Two real-time polymerase chain reaction (PCR)-based assays for detection of walnut (Juglans regia) and pecan (Carya illinoinensis) traces in a wide range of processed foods are described here. The method consists on a real-time PCR assay targeting the ITS1 region, using a nuclease (TaqMan) probe labeled with FAM and BBQ. The method was positive for walnut and pecan respectively, and negative for all other heterologous plants and animals tested. Using a series of model samples with defined raw walnut in wheat flour and heat-treated walnut in wheat flour with a range of concentrations of 0.1-100,000 mg kg(-1), a practical detection limit of 0.1 mg kg(-1) of walnut content was estimated. Identical binary mixtures were done for pecan, reaching the same limit of detection of 0.1 mg kg(-1). The assay was successfully trialed on a total of 232 commercial foodstuffs. Copyright © 2015 Elsevier Ltd. All rights reserved.
Multiplex real-time PCR assay for Legionella species.
Kim, Seung Min; Jeong, Yoojung; Sohn, Jang Wook; Kim, Min Ja
2015-12-01
Legionella pneumophila serogroup 1 (sg1) accounts for the majority of infections in humans, but other Legionella species are also associated with human disease. In this study, a new SYBR Green I-based multiplex real-time PCR assay in a single reaction was developed to allow the rapid detection and differentiation of Legionella species by targeting specific gene sequences. Candidate target genes were selected, and primer sets were designed by referring to comparative genomic hybridization data of Legionella species. The Legionella species-specific groES primer set successfully detected all 30 Legionella strains tested. The xcpX and rfbA primers specifically detected L. pneumophila sg1-15 and L. pneumophila sg1, respectively. In addition, this assay was validated by testing clinical samples and isolates. In conclusion, this novel multiplex real-time PCR assay might be a useful diagnostic tool for the rapid detection and differentiation of Legionella species in both clinical and epidemiological studies. Copyright © 2015 Elsevier Ltd. All rights reserved.
Van Beeck, Kristof; Goedemé, Toon; Tuytelaars, Tinne
2012-01-01
Van Beeck K., Goedemé T., Tuytelaars T., ''A warping window approach to real-time vision-based pedestrian detection in a truck’s blind spot zone'', Proceedings 9th international conference on informatics in control, automation and robotics - ICINCO 2012, vol. 2, pp. 561-568, July 28-31, 2012, Rome, Italy.
Yu, Haijie; Huang, Bin; Zhuo, Xunhui; Chen, Xueqiu; Du, Aifang
2013-11-08
Real-time PCR-based detection of Toxoplasma gondii is very sensitive and convenient for diagnosing toxoplasmosis. However, the performance of the PCR assays could be influenced by the target gene chosen. Here we evaluate a real-time PCR assay using double-stranded DNA dyes (SYBR(®) Green I assay) with a new set of primers targeting the SAG1 gene for the fast and specific detection of T. gondii. The assay showed higher sensitivity than conventional PCR protocols using T. gondii DNA as template. The detection limit of the developed real-time PCR assay was in the order of 1 tachyzoite. The assay was also assessed by experimentally infected mice and showed positive results for blood (25%), spleen (50%) and lung (50%) as early as 1 dpi. The specificity of the assay was confirmed by using DNA from Neospora caninum, Escherichia coli, Babesia bovis, Trypanosoma brucei, Cryptosporidium parvum, and Toxocara canis. Assay applicability was successfully tested in blood samples collected from slaughtered pigs. These results indicate that, based on SYBR(®) green I, the quantitative SAG1 assay may also be useful in the study of the pathogenicity, immunoprophylaxis, and treatment of T. gondii. Copyright © 2013 Elsevier B.V. All rights reserved.
Shariati, Laleh; Validi, Majid; Tabatabaiefar, Mohammad Amin; Karimi, Ali; Nafisi, Mohammad Reza
2010-12-01
Methicillin-resistant Staphylococcus aureus (MRSA) is a nosocomial pathogen. Our main objective was to compare oxacillin disk test, oxacillin E-test, and oxacillin agar screen for detection of methicillin resistance in S. aureus, using real-time PCR for mecA as the "gold standard" comparison assay. 196 S. aureus isolates were identified out of 284 Staphylococcus isolates. These isolates were screened for MRSA with several methods: disk diffusion, agar screen (6.0 μg/ml), oxacillin E-test, and real-time PCR for detection of mecA gene. Of the 196 S. aureus isolates tested, 96 isolates (49%) were mecA-positive and 100 isolates (51%) mecA-negative. All methods tested had a statistically significant agreement with real-time PCR. E-test was 100% sensitive and specific for mecA presence. The sensitivity and specificity of oxacillin agar screen method were 98 and 99%, respectively and sensitivity and specificity of oxacillin disk diffusion method were 95 and 93%, respectively. In the present study, oxacillin E-test is proposed as the best phenotypic method. For economic reasons, the oxacillin agar screen method (6.0 μg/ml), which is suitable for the detection of MRSA, is recommended due to its accuracy and low cost.
A noninvasive technique for real-time detection of bruises in apple surface based on machine vision
Zhao, Juan; Peng, Yankun; Dhakal, Sagar; Zhang, Leilei; Sasao, Akira
2013-05-01
Apple is one of the highly consumed fruit item in daily life. However, due to its high damage potential and massive influence on taste and export, the quality of apple has to be detected before it reaches the consumer's hand. This study was aimed to develop a hardware and software unit for real-time detection of apple bruises based on machine vision technology. The hardware unit consisted of a light shield installed two monochrome cameras at different angles, LED light source to illuminate the sample, and sensors at the entrance of box to signal the positioning of sample. Graphical Users Interface (GUI) was developed in VS2010 platform to control the overall hardware and display the image processing result. The hardware-software system was developed to acquire the images of 3 samples from each camera and display the image processing result in real time basis. An image processing algorithm was developed in Opencv and C++ platform. The software is able to control the hardware system to classify the apple into two grades based on presence/absence of surface bruises with the size of 5mm. The experimental result is promising and the system with further modification can be applicable for industrial production in near future.
Qu, X S; Wanner, L A; Christ, B J
2011-03-01
To develop a multiplex real-time PCR assay using TaqMan probes for the simultaneous detection and discrimination of potato powdery scab and common scab, two potato tuber diseases with similar symptoms, and the causal pathogens Spongospora subterranea and plant pathogenic Streptomyces spp. Real-time PCR primers and a probe for S. subterranea were designed based on the DNA sequence of the ribosomal RNA ITS2 region. Primers and a probe for pathogenic Streptomyces were designed based on the DNA sequence of the txtAB genes. The two sets of primer pairs and probes were used in a single real-time PCR assay. The multiplex real-time PCR assay was confirmed to be specific for S. subterranea and pathogenic Streptomyces. The assay detected DNA quantities of 100 fg for each of the two pathogens and linear responses and high correlation coefficients between the amount of DNA and C(t) values for each pathogen were achieved. The presence of two sets of primer pairs and probes and of plant extracts did not alter the sensitivity and efficiency of multiplex PCR amplification. Using the PCR assay, we could discriminate between powdery scab and common scab tubers with similar symptoms. Common scab and powdery scab were detected in some tubers with no visible symptoms. Mixed infections of common scab and powdery scab on single tubers were also revealed. This multiplex real-time PCR assay is a rapid, cost efficient, specific and sensitive tool for the simultaneous detection and discrimination of the two pathogens on infected potato tubers when visual symptoms are inconclusive or not present. Accurate and quick identification and discrimination of the cause of scab diseases on potatoes will provide critical information to potato growers and researchers for disease management. This is important because management strategies for common and powdery scab diseases are very different. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.
Real-Time PCR Detection of Dogwood Anthracnose Fungus in Historical Herbarium Specimens from Asia.
Miller, Stephen; Masuya, Hayato; Zhang, Jian; Walsh, Emily; Zhang, Ning
2016-01-01
Cornus species (dogwoods) are popular ornamental trees and important understory plants in natural forests of northern hemisphere. Dogwood anthracnose, one of the major diseases affecting the native North American Cornus species, such as C. florida, is caused by the fungal pathogen Discula destructiva. The origin of this fungus is not known, but it is hypothesized that it was imported to North America with its host plants from Asia. In this study, a TaqMan real-time PCR assay was used to detect D. destructiva in dried herbarium and fresh Cornus samples. Several herbarium specimens from Japan and China were detected positive for D. destructiva, some of which were collected before the first report of the dogwood anthracnose in North America. Our findings further support that D. destructiva was introduced to North America from Asia where the fungus likely does not cause severe disease.
A TaqMan real-time PCR assay for detection of Meloidogyne hapla in root galls and in soil
DEFF Research Database (Denmark)
Sapkota, Rumakanta; Skantar, Andrea M.; Nicolaisen, Mogens
2016-01-01
. haplaand showed no significant amplification of DNA from non-target nematodes. The assay was able to detect M. haplain a background of plant and soil DNA. A dilution series of M. haplaeggs in soil showed a high correlation ( R 2 = 0 . 95 , P ...Early detection and quantification of Meloidogyne haplain soil is essential for effective disease management. The purpose of this study was to develop a real-time PCR assay for detection of M. haplain soil. Primers and a TaqMan probe were designed for M. hapladetection. The assay detected M......-knot development in carrots by testing soils before planting. The assay could be useful for management decisions in carrot cultivation....
Real-Time Head Pose Estimation on Mobile Platforms
Directory of Open Access Journals (Sweden)
Jianfeng Ren
2010-06-01
Full Text Available Many computer vision applications such as augmented reality require head pose estimation. As far as the real-time implementation of head pose estimation on relatively resource limited mobile platforms is concerned, it is required to satisfy real-time constraints while maintaining reasonable head pose estimation accuracy. The introduced head pose estimation approach in this paper is an attempt to meet this objective. The approach consists of the following components: Viola-Jones face detection, color-based face tracking using an online calibration procedure, and head pose estimation using Hu moment features and Fisher linear discriminant. Experimental results running on an actual mobile device are reported exhibiting both the real- time and accuracy aspects of the developed approach.
Dolz, Sandra; Barragán, Eva; Fuster, Óscar; Llop, Marta; Cervera, José; Such, Esperanza; De Juan, Inmaculada; Palanca, Sarai; Murria, Rosa; Bolufer, Pascual; Luna, Irene; Gómez, Inés; López, María; Ibáñez, Mariam; Sanz, Miguel A
2013-09-01
The recent World Health Organization classification recognizes different subtypes of acute myeloid leukemia (AML) according to the presence of several recurrent genetic abnormalities. Detection of these abnormalities and other molecular changes is of increasing interest because it contributes to a refined diagnosis and prognostic assessment in AML and enables monitoring of minimal residual disease. These genetic abnormalities can be detected using single RT-PCR, although the screening is still labor intensive and costly. We have developed a novel real-time RT-PCR assay to simultaneously detect 15 AML-associated rearrangements that is a simple and easily applicable method for use in clinical diagnostic laboratories. This method showed 100% specificity and sensitivity (95% confidence interval, 91% to 100% and 92% to 100%, respectively). The procedure was validated in a series of 105 patients with AML. The method confirmed all translocations detected using standard cytogenetics and fluorescence in situ hybridization and some additional undetected rearrangements. Two patients demonstrated two molecular rearrangements simultaneously, with BCR-ABL1 implicated in both, in addition to RUNX1-MECOM in one patient and PML-RARA in another. In conclusion, this novel real-time RT-PCR assay for simultaneous detection of multiple AML-associated fusion genes is a versatile and sensitive method for reliable screening of recurrent rearrangements in AML. Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.
A timed-automata approach for critical path detection in a soft real-time application
Yildiz, Bugra Mehmet; Bockisch, Christoph; Rensink, Arend; Aksit, Mehmet
In this paper, we report preliminary ideas from our project called “Time Performance Improvement With Parallel Processing Systems‿ (TIPS). In the TIPS project, we plan to take advantage of multi-core platforms for performance improvement by parallelizing a complex soft real-time application. In
DEFF Research Database (Denmark)
Brasen, Claus Lohman; Frischknecht, Lone; Ørnskov, Dorthe
2017-01-01
in the probe-binding site may cause errors in analysis. The aim of this study was to determine the prevalence of the variants in a Danish cohort examined for lactose intolerance as well as to improve the real-time PCR analysis for detection of the different variants. METHODS: We genotyped 3395 routine samples...
Detection of exogenous gene doping of IGF-I by a real-time quantitative PCR assay.
Zhang, Jin-Ju; Xu, Jing-Feng; Shen, Yong-Wei; Ma, Shi-Jiao; Zhang, Ting-Ting; Meng, Qing-Lin; Lan, Wen-Jun; Zhang, Chun; Liu, Xiao-Mei
2017-07-01
Gene doping can be easily concealed since its product is similar to endogenous protein, making its effective detection very challenging. In this study, we selected insulin-like growth factor I (IGF-I) exogenous gene for gene doping detection. First, the synthetic IGF-I gene was subcloned to recombinant adeno-associated virus (rAAV) plasmid to produce recombinant rAAV2/IGF-I-GFP vectors. Second, in an animal model, rAAV2/IGF-I-GFP vectors were injected into the thigh muscle tissue of mice, and then muscle and blood specimens were sampled at different time points for total DNA isolation. Finally, real-time quantitative PCR was employed to detect the exogenous gene doping of IGF-I. In view of the characteristics of endogenous IGF-I gene sequences, a TaqMan probe was designed at the junction of exons 2 and 3 of IGF-I gene to distinguish it from the exogenous IGF-I gene. In addition, an internal reference control plasmid and its probe were used in PCR to rule out false-positive results through comparison of their threshold cycle (Ct) values. Thus, an accurate exogenous IGF-I gene detection approach was developed in this study. © 2016 International Union of Biochemistry and Molecular Biology, Inc.
Vautrin, Sonia; Zhang, David
2007-01-01
A species-specific endogenous reference gene system was developed for polymerase chain reaction (PCR)-based analysis in common wheat (Triticum aestivum L.) by targeting the ALMT1 gene, an aluminium-activated malate transporter. The primers and probe were elaborated for real-time PCR-based qualitative and quantitative assay. The size of amplified product is 95 base pairs. The specificity was assessed on 17 monocot and dicot plant species. The established real-time PCR assay amplified only T. aestivum-derived DNA; no amplification occurred on other phylogenetically related species, including durum wheat (T. durum). The robustness of the system was tested on the DNA of 15 common wheat cultivars using 20 000 genomic copies per PCR the mean cycle threshold (Ct) values of 24.02 +/- 0.251 were obtained. The absolute limits of detection and quantification of the real-time PCR assay were estimated to 2 and 20 haploid genome copies of common wheat, respectively. The linearity was experimentally validated on 2-fold serial dilutions of DNA from 650 to 20 000 haploid genome copies. All these results show that the real-time PCR assay developed on the ALMT1 gene is suitable to be used as an endogenous reference gene for PCR-based specific detection and quantification of T. aestivum-derived DNA in various applications, in particular for the detection and quantification of genetically modified materials in common wheat.
Paudel, Damodar; Jarman, Richard; Limkittikul, Kriengsak; Klungthong, Chonticha; Chamnanchanunt, Supat; Nisalak, Ananda; Gibbons, Robert; Chokejindachai, Watcharee
2011-01-01
Background: Dengue fever and dengue hemorrhagic fever are caused by dengue virus. Dengue infection remains a burning problem of many countries. To diagnose acute dengue in the early phase we improve the low cost, rapid SYBR green real time assay and compared the sensitivity and specificity with real time Taqman® assay and conventional nested PCR assay. Aims: To develop low cost, rapid and reliable real time SYBR green diagnostic dengue assay and compare with Taqman real-time assay and conventional nested PCR (modified Lanciotti). Materials and Methods: Eight cultured virus strains were diluted in tenth dilution down to undetectable level by the PCR to optimize the primer, temperature (annealing, and extension and to detect the limit of detection of the assay. Hundred and ninety three ELISA and PCR proved dengue clinical samples were tested with real time SYBR® Green assay, real time Taqman® assay to compare the sensitivity and specificity. Results: Sensitivity and specificity of real time SYBR® green dengue assay (84% and 66%, respectively) was almost comparable to those (81% and 74%) of Taqman real time PCR dengue assay. Real time SYBR® green RT-PCR was equally sensitive in primary and secondary infection while real time Taqman was less sensitive in the secondary infection. Sensitivity of real time Taqman on DENV3 (87%) was equal to SYBR green real time PCR dengue assay. Conclusion: We developed low cost rapid diagnostic SYBR green dengue assay. Further study is needed to make duplex primer assay for the serotyping of dengue virus. PMID:22363089
Towards Real-Time Facial Landmark Detection in Depth Data Using Auxiliary Information
Directory of Open Access Journals (Sweden)
Connah Kendrick
2018-06-01
Full Text Available Modern facial motion capture systems employ a two-pronged approach for capturing and rendering facial motion. Visual data (2D is used for tracking the facial features and predicting facial expression, whereas Depth (3D data is used to build a series of expressions on 3D face models. An issue with modern research approaches is the use of a single data stream that provides little indication of the 3D facial structure. We compare and analyse the performance of Convolutional Neural Networks (CNN using visual, Depth and merged data to identify facial features in real-time using a Depth sensor. First, we review the facial landmarking algorithms and its datasets for Depth data. We address the limitation of the current datasets by introducing the Kinect One Expression Dataset (KOED. Then, we propose the use of CNNs for the single data stream and merged data streams for facial landmark detection. We contribute to existing work by performing a full evaluation on which streams are the most effective for the field of facial landmarking. Furthermore, we improve upon the existing work by extending neural networks to predict into 3D landmarks in real-time with additional observations on the impact of using 2D landmarks as auxiliary information. We evaluate the performance by using Mean Square Error (MSE and Mean Average Error (MAE. We observe that the single data stream predicts accurate facial landmarks on Depth data when auxiliary information is used to train the network. The codes and dataset used in this paper will be made available.
Directory of Open Access Journals (Sweden)
Burgos Lorenzo
2010-07-01
Full Text Available Abstract Background The routine generation of transgenic plants involves analysis of transgene integration into the host genome by means of Southern blotting. However, this technique cannot distinguish between uniformly transformed tissues and the presence of a mixture of transgenic and non-transgenic cells in the same tissue. On the other hand, the use of reporter genes often fails to accurately detect chimerical tissues because their expression can be affected by several factors, including gene silencing and plant development. So, new approaches based on the quantification of the amount of the transgene are needed urgently. Results We show here that chimeras are a very frequent phenomenon observed after regenerating transgenic plants. Spatial and temporal analyses of transformed tobacco and apricot plants with a quantitative, real-time PCR amplification of the neomycin phosphotransferase (nptII transgene as well as of an internal control (β-actin, used to normalise the amount of target DNA at each reaction, allowed detection of chimeras at unexpected rates. The amount of the nptII transgene differed greatly along with the sub-cultivation period of these plants and was dependent on the localisation of the analysed leaves; being higher in roots and basal leaves, while in the apical leaves it remained at lower levels. These data demonstrate that, unlike the use of the gus marker gene, real-time PCR is a powerful tool for detection of chimeras. Although some authors have proposed a consistent, positive Southern analysis as an alternative methodology for monitoring the dissociation of chimeras, our data show that it does not provide enough proof of uniform transformation. In this work, however, real-time PCR was applied successfully to monitor the dissociation of chimeras in tobacco plants and apricot callus. Conclusions We have developed a rapid and reliable method to detect and estimate the level of chimeras in transgenic tobacco and apricot
Fast Real-Time PCR for the Detection of Crustacean Allergens in Foods.
Santaclara, Francisco J; Espiñeira, Montserrat
2017-01-01
Crustaceans are one of the most common allergens causing severe food reaction. Hypersensitivity reactions associated with seafood intake are one of the most common food allergies in adults. Crustaceans including shrimps, prawns, crabs, lobster, and crayfish are a common cause of anaphylaxis or hypersensitivity, with shrimps and crabs being the most common causes of allergy. Symptoms occur most often when food or cooking water are ingested.These food allergens are a health problem, and they have become very important; as evidenced by the existence of several regulations that establish that labeling must be present regarding these allergens to warn consumers.The methodology herein exposed allows the detection of crustaceans in any type of product, including those where very aggressive treatments of temperature and pressure are used during the manufacturing process.The main features of this method are its high sensitivity and specificity, and reduced analysis time of real-time PCR (40 min). This assay is a potential tool in issues related to the labeling of products and food security to protect the allergic consumer.
Self-Powered Implantable Skin-Like Glucometer for Real-Time Detection of Blood Glucose Level In Vivo
Zhang, Wanglinhan; Zhang, Linlin; Gao, Huiling; Yang, Wenyan; Wang, Shuai; Xing, Lili; Xue, Xinyu
2018-06-01
Implantable bioelectronics for analyzing physiological biomarkers has recently been recognized as a promising technique in medical treatment or diagnostics. In this study, we developed a self-powered implantable skin-like glucometer for real-time detection of blood glucose level in vivo. Based on the piezo-enzymatic-reaction coupling effect of GOx@ZnO nanowire, the device under an applied deformation can actively output piezoelectric signal containing the glucose-detecting information. No external electricity power source or battery is needed for this device, and the outputting piezoelectric voltage acts as both the biosensing signal and electricity power. A practical application of the skin-like glucometer implanted in mouse body for detecting blood glucose level has been simply demonstrated. These results provide a new technique path for diabetes prophylaxis and treatment.
Van Beeck, Kristof; Goedemé, Toon; Tuytelaars, Tinne
2014-01-01
Van Beeck K., Goedemé G., Tuytelaars T., ''Real-time vision-based pedestrian detection in a truck’s blind spot zone using a warping window approach'', Informatics in control, automation and robotics - lecture notes in electrical engineering, vol. 283, pp. 251-264, Ferrier J.-L., Bernard A., Gusikhin O. and Madani K., eds., 2014.
Can Real-Time Data Also Be Climate Quality?
Brewer, M.; Wentz, F. J.
2015-12-01
GMI, AMSR-2 and WindSat herald a new era of highly accurate and timely microwave data products. Traditionally, there has been a large divide between real-time and re-analysis data products. What if these completely separate processing systems could be merged? Through advanced modeling and physically based algorithms, Remote Sensing Systems (RSS) has narrowed the gap between real-time and research-quality. Satellite microwave ocean products have proven useful for a wide array of timely Earth science applications. Through cloud SST capabilities have enormously benefited tropical cyclone forecasting and day to day fisheries management, to name a few. Oceanic wind vectors enhance operational safety of shipping and recreational boating. Atmospheric rivers are of import to many human endeavors, as are cloud cover and knowledge of precipitation events. Some activities benefit from both climate and real-time operational data used in conjunction. RSS has been consistently improving microwave Earth Science Data Records (ESDRs) for several decades, while making near real-time data publicly available for semi-operational use. These data streams have often been produced in 2 stages: near real-time, followed by research quality final files. Over the years, we have seen this time delay shrink from months or weeks to mere hours. As well, we have seen the quality of near real-time data improve to the point where the distinction starts to blur. We continue to work towards better and faster RFI filtering, adaptive algorithms and improved real-time validation statistics for earlier detection of problems. Can it be possible to produce climate quality data in real-time, and what would the advantages be? We will try to answer these questions…
Nelson, Matthew P.; Tazik, Shawna K.; Bangalore, Arjun S.; Treado, Patrick J.; Klem, Ethan; Temple, Dorota
2017-05-01
Hyperspectral imaging (HSI) systems can provide detection and identification of a variety of targets in the presence of complex backgrounds. However, current generation sensors are typically large, costly to field, do not usually operate in real time and have limited sensitivity and specificity. Despite these shortcomings, HSI-based intelligence has proven to be a valuable tool, thus resulting in increased demand for this type of technology. By moving the next generation of HSI technology into a more adaptive configuration, and a smaller and more cost effective form factor, HSI technologies can help maintain a competitive advantage for the U.S. armed forces as well as local, state and federal law enforcement agencies. Operating near the physical limits of HSI system capability is often necessary and very challenging, but is often enabled by rigorous modeling of detection performance. Specific performance envelopes we consistently strive to improve include: operating under low signal to background conditions; at higher and higher frame rates; and under less than ideal motion control scenarios. An adaptable, low cost, low footprint, standoff sensor architecture we have been maturing includes the use of conformal liquid crystal tunable filters (LCTFs). These Conformal Filters (CFs) are electro-optically tunable, multivariate HSI spectrometers that, when combined with Dual Polarization (DP) optics, produce optimized spectral passbands on demand, which can readily be reconfigured, to discriminate targets from complex backgrounds in real-time. With DARPA support, ChemImage Sensor Systems (CISS™) in collaboration with Research Triangle Institute (RTI) International are developing a novel, real-time, adaptable, compressive sensing short-wave infrared (SWIR) hyperspectral imaging technology called the Reconfigurable Conformal Imaging Sensor (RCIS) based on DP-CF technology. RCIS will address many shortcomings of current generation systems and offer improvements in
Towards real-time intrusion detection for NetFlow and IPFIX
Hofstede, R.J.; Bartos, Vaclav; Sperotto, Anna; Pras, Aiko
2013-01-01
DDoS attacks bring serious economic and technical damage to networks and enterprises. Timely detection and mitigation are therefore of great importance. However, when flow monitoring systems are used for intrusion detection, as it is often the case in campus, enterprise and backbone networks, timely
Qiu, Feng; Cao, Jingyuan; Su, Qiudong; Yi, Yao; Bi, Shengli
2014-05-30
Detection of hepatitis viral infections has traditionally relied on the circulating antibody test using the enzyme-linked immunosorbent assay. However, multiplex real-time PCR has been increasingly used for a variety of viral nucleic acid detections and has proven to be superior to traditional methods. Hepatitis A virus (HAV) and hepatitis E virus (HEV) are the major causes of acute hepatitis worldwide; both HAV and HEV infection are a main public health problem. In the present study, a one-step multiplex reverse transcriptase quantitative polymerase chain reaction assay using hydrolysis probes was developed for simultaneously detecting HAV and HEV. This novel detection system proved specific to the target viruses, to be highly sensitive and to be applicable to clinical sera samples, making it useful for rapid, accurate and feasible identification of HAV and HEV.
Directory of Open Access Journals (Sweden)
Qin E-de
2010-06-01
Full Text Available Abstract A duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR assay was improved for simultaneous detection of highly pathogenic H5N1 avian influenza virus and pandemic H1N1 (2009 influenza virus, which is suitable for early diagnosis of influenza-like patients and for epidemiological surveillance. The sensitivity of this duplex real-time RT-PCR assay was 0.02 TCID50 (50% tissue culture infective dose for H5N1 and 0.2 TCID50 for the pandemic H1N1, which was the same as that of each single-target RT-PCR for pandemic H1N1 and even more sensitive for H5N1 with the same primers and probes. No cross reactivity of detecting other subtype influenza viruses or respiratory tract viruses was observed. Two hundred and thirty-six clinical specimens were tested by comparing with single real-time RT-PCR and result from the duplex assay was 100% consistent with the results of single real-time RT-PCR and sequence analysis.
Automated real time constant-specificity surveillance for disease outbreaks
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Brownstein John S
2007-06-01
Full Text Available Abstract Background For real time surveillance, detection of abnormal disease patterns is based on a difference between patterns observed, and those predicted by models of historical data. The usefulness of outbreak detection strategies depends on their specificity; the false alarm rate affects the interpretation of alarms. Results We evaluate the specificity of five traditional models: autoregressive, Serfling, trimmed seasonal, wavelet-based, and generalized linear. We apply each to 12 years of emergency department visits for respiratory infection syndromes at a pediatric hospital, finding that the specificity of the five models was almost always a non-constant function of the day of the week, month, and year of the study (p Conclusion Modeling the variance of visit patterns enables real-time detection with known, constant specificity at all times. With constant specificity, public health practitioners can better interpret the alarms and better evaluate the cost-effectiveness of surveillance systems.
Erdősi, Orsolya; Szakmár, Katalin; Reichart, Olivér; Szili, Zsuzsanna; László, Noémi; Székely Körmöczy, Péter; Laczay, Péter
2014-09-01
The incidence of outbreaks of foodborne listeriosis has indicated the need for a reliable and rapid detection of the microbe in different foodstuffs. A method combining redox potential measurement and real-time polymerase chain reaction (PCR) was developed to detect Listeria monocytogenes in artificially contaminated raw milk and soft cheese. Food samples of 25 g or 25 ml were homogenised in 225 ml of Listeria Enrichment Broth (LEB) with Oxford supplement, and the redox potential measurement technique was applied. For Listeria species the measuring time was maximum 34 h. The absence of L. monocytogenes could reliably be proven by the redox potential measurement method, but Listeria innocua and Bacillus subtilis could not be differentiated from L. monocytogenes on the basis of the redox curves. The presence of L. monocytogenes had to be confirmed by real-time PCR. The combination of these two methods proved to detect < 10 cfu/g of L. monocytogenes in a cost- and time-effective manner. This method can potentially be used as an alternative to the standard nutrient method for the rapid detection of L. monocytogenes in food.
Jaravata, Carmela V; Smith, Wayne L; Rensen, Gabriel J; Ruzante, Juliana M; Cullor, James S
2006-01-01
A modified forensic DNA extraction and real-time fluorescent polymerase chain reaction assay has been evaluated for the detection of Mycobacterium avium subsp. paratuberculosis (MAP) in bovine fecal samples using primers and fluorescent resonance energy transfer (FRET) probes targeting the IS900 gene sequence of MAP. DNA was successfully extracted from manure samples by utilizing the Whatman FTA card technology, which allows for simple processing and storage of samples at room temperature. The FTA cards were washed and subjected to a Chelex-100 incubation to remove any remaining polymerase chain reaction (PCR) inhibitors and to elute the DNA from the FTA card. This isolated DNA was then subjected to direct real time fluorescent PCR analysis. Detection of MAP DNA from bovine fecal samples spiked with known concentrations of viable MAP cells was obtained. The detection limits of the assay was consistently found to be between 10(2) and 10(4) colony forming units [CFU]/g, with some samples containing as low as 10 CFU/g, yielding positive assay results. This cost-efficient assay allows reporting of results as early as 4 h after fecal collection, which can be particularly useful in highthroughput herd screening.
Directory of Open Access Journals (Sweden)
Wen-Pin Chou
2017-02-01
Full Text Available Polymerase chain reaction (PCR has been one of the principal techniques of molecular biology and diagnosis for decades. Conventional PCR platforms, which work by rapidly heating and cooling the whole vessel, need complicated hardware designs, and cause energy waste and high cost. On the other hand, partial heating on the various locations of vessels to induce convective solution flows by buoyancy have been used for DNA amplification in recent years. In this research, we develop a new convective PCR platform, capillary loop convective polymerase chain reaction (clcPCR, which can generate one direction flow and make the PCR reaction more stable. The U-shaped loop capillaries with 1.6 mm inner diameter are designed as PCR reagent containers. The clcPCR platform utilizes one isothermal heater for heating the bottom of the loop capillary and a CCD device for detecting real-time amplifying fluorescence signals. The stable flow was generated in the U-shaped container and the amplification process could be finished in 25 min. Our experiments with different initial concentrations of DNA templates demonstrate that clcPCR can be applied for precise quantification. Multiple sample testing and real-time quantification will be achieved in future studies.
Detection of infusate leakage in the brain using real-time imaging of convection-enhanced delivery.
Varenika, Vanja; Dickinson, Peter; Bringas, John; LeCouteur, Richard; Higgins, Robert; Park, John; Fiandaca, Massimo; Berger, Mitchel; Sampson, John; Bankiewicz, Krystof
2008-11-01
The authors have shown that convection-enhanced delivery (CED) of gadoteridol-loaded liposomes (GDLs) into different regions of normal monkey brain results in predictable, widespread distribution of this tracking agent as detected by real-time MR imaging. They also have found that this tracking technique allows monitoring of the distribution of similar nanosized agents such as therapeutic liposomes and viral vectors. A limitation of this procedure is the unexpected leakage of liposomes out of targeted parenchyma or malignancies into sulci and ventricles. The aim of the present study was to evaluate the efficacy of CED after the onset of these types of leakage. The authors documented this phenomenon in a study of 5 nonhuman primates and 7 canines, comprising 54 CED infusion sessions. Approximately 20% of these infusions resulted in leakage into cerebral ventricles or sulci. All of the infusions and leakage events were monitored with real-time MR imaging. The authors created volume-distributed versus volume-infused graphs for each infusion session. These graphs revealed the rate of distribution of GDL over the course of each infusion and allowed the authors to evaluate the progress of CED before and after leakage. The distribution of therapeutics within the target structure ceased to increase or resulted in significant attenuation after the onset of leakage. An analysis of the cases in this study revealed that leakage undermines the efficacy of CED. These findings reiterate the importance of real-time MR imaging visualization during CED to ensure an accurate, robust distribution of therapeutic agents.
Sisco, Edward; Dake, Jeffrey
2016-04-14
Direct Analysis in Real Time Mass Spectrometry (DART-MS) has been used to detect the presence of non-narcotic adulterants in beverages. The non-narcotic adulterants that were examined in this work incorporated a number low molecular weight alcohols, acetone, ammonium hydroxide, and sodium hypochlorite. Analysis of the adulterants was completed by pipetting 1 µL deposits onto glass microcapillaries along with an appropriate dopant species followed by introduction into the DART gas stream. It was found that detection of these compounds in the complex matrices of common beverages (soda, energy drinks, etc.) was simplified through the use of a dopant species to allow for adduct formation with the desired compound(s) of interest. Other parameters that were investigated included DART gas stream temperature, in source collision induced dissociation, ion polarity, and DART needle voltage. Sensitivities of the technique were found to range from 0.001 % volume fraction to 0.1 % volume fraction, comparable to traditional analyses completed using headspace gas chromatography mass spectrometry (HS-GC/MS). Once a method was established using aqueous solutions, , fifteen beverages were spiked with each of the nine adulterants, to simulate real world detection, and in nearly all cases the adulterant could be detected either in pure form, or complexed with the added dopant species. This technique provides a rapid way to directly analyze beverages believed to be contaminated with non-narcotic adulterants at sensitivities similar to or exceeding those of traditional confirmatory analyses.
Coffey, Lee; Owens, Erica; Tambling, Karen; O'Neill, David; O'Connor, Laura; O'Reilly, Catherine
2010-11-01
Nitriles are widespread in the environment as a result of biological and industrial activity. Nitrile hydratases catalyse the hydration of nitriles to the corresponding amide and are often associated with amidases, which catalyze the conversion of amides to the corresponding acids. Nitrile hydratases have potential as biocatalysts in bioremediation and biotransformation applications, and several successful examples demonstrate the advantages. In this work a real-time PCR assay was designed for the detection of Fe-type nitrile hydratase genes from environmental isolates purified from nitrile-enriched soils and seaweeds. Specific PCR primers were also designed for amplification and sequencing of the genes. Identical or highly homologous nitrile hydratase genes were detected from isolates of numerous genera from geographically diverse sites, as were numerous novel genes. The genes were also detected from isolates of genera not previously reported to harbour nitrile hydratases. The results provide further evidence that many bacteria have acquired the genes via horizontal gene transfer. The real-time PCR assay should prove useful in searching for nitrile hydratases that could have novel substrate specificities and therefore potential in industrial applications.
Automated real time peg and tool detection for the FLS trainer box.
Nemani, Arun; Sankaranarayanan, Ganesh
2012-01-01
This study proposes a method that effectively tracks trocar tool and peg positions in real time to allow real time assessment of the peg transfer task of the Fundamentals of Laparoscopic Surgery (FLS). By utilizing custom code along with OpenCV libraries, tool and peg positions can be accurately tracked without altering the original setup conditions of the FLS trainer box. This is achieved via a series of image filtration sequences, thresholding functions, and Haar training methods.
A Novel Real-Time DDoS Attack Detection Mechanism Based on MDRA Algorithm in Big Data
Directory of Open Access Journals (Sweden)
Bin Jia
2016-01-01
Full Text Available In the wake of the rapid development and wide application of information technology and Internet, our society has come into the information explosion era. Meanwhile, it brings in new and severe challenges to the field of network attack behavior detection due to the explosive growth and high complexity of network traffic. Therefore, an effective and efficient detection mechanism that can detect attack behavior from large scale of network traffic plays an important role. In this paper, we focus on how to distinguish the attack traffic from normal data flows in Big Data and propose a novel real-time DDoS attack detection mechanism based on Multivariate Dimensionality Reduction Analysis (MDRA. In this mechanism, we first reduce the dimensionality of multiple characteristic variables in a network traffic record by Principal Component Analysis (PCA. Then, we analyze the correlation of the lower dimensional variables. Finally, the attack traffic can be differentiated from the normal traffic by MDRA and Mahalanobis distance (MD. Compared with previous research methods, our experimental results show that higher precision rate is achieved and it approximates to 100% in True Negative Rate (TNR for detection; CPU computing time is one-eightieth and memory resource consumption is one-third of the previous detection method based on Multivariate Correlation Analysis (MCA; computing complexity is constant.
Wang, Jianchang; Wang, Jinfeng; Cui, Yuan; Nan, Huizhu; Yuan, Wanzhe
2017-08-01
A real-time PCR assay was developed for specific detection of novel duck-origin goose parvovirus (N-GPV), the etiological agent of duck beak atrophy and dwarfism syndrome (BADS). The detection limit of the assay was 10 2 copies. The assay was useful in the prevention and control of BADS. Copyright © 2017 Elsevier Ltd. All rights reserved.
DEFF Research Database (Denmark)
Kowalczyk, Andrzej; Markowska-Daniel, Iwona; Rasmussen, Thomas Bruun
2013-01-01
Swine influenza virus (SIV) causes a contagious and requiring official notification disease of pigs and humans. In this study, a real-time reverse transcription-polymerase chain reaction (RT-PCR) assay based on primer–probe energy transfer (PriProET) for the detection of SIV RNA was developed...... of the specific product amplification. The assay is specific for influenza virus with a sensitivity of detection limit of approximately 10 copies of RNA by PCR. Based on serial dilutions of SIV, the detection limit of the assay was approximately 0.003 TCID50/ml for H1N1 A/Swine/Poland/KPR9/2004 virus. The Pri...
Directory of Open Access Journals (Sweden)
Žel Jana
2008-03-01
Full Text Available Abstract Background The real-time polymerase chain reaction is currently the method of choice for quantifying nucleic acids in different DNA based quantification applications. It is widely used also for detecting and quantifying genetically modified components in food and feed, predominantly employing TaqMan® and SYBR® Green real-time PCR chemistries. In our study four alternative chemistries: Lux™, Plexor™, Cycling Probe Technology and LNA® were extensively evaluated and compared using TaqMan® chemistry as a reference system. Results Amplicons were designed on the maize invertase gene and the 5'-junction of inserted transgene and plant genomic DNA in MON 810 event. Real-time assays were subsequently compared for their efficiency in PCR amplification, limits of detection and quantification, repeatability and accuracy to test the performance of the assays. Additionally, the specificity of established assays was checked on various transgenic and non-transgenic plant species. The overall applicability of the designed assays was evaluated, adding practicability and costs issues to the performance characteristics. Conclusion Although none of the chemistries significantly outperformed the others, there are certain characteristics that suggest that LNA® technology is an alternative to TaqMan® when designing assays for quantitative analysis. Because LNA® probes are much shorter they might be especially appropriate when high specificity is required and where the design of a common TaqMan® probe is difficult or even impossible due to sequence characteristics. Plexor™ on the other hand might be a method of choice for qualitative analysis when sensitivity, low cost and simplicity of use prevail.
Real-Time Visualization System for Deep-Sea Surveying
Directory of Open Access Journals (Sweden)
Yujie Li
2014-01-01
Full Text Available Remote robotic exploration holds vast potential for gaining knowledge about extreme environments, which is difficult to be accessed by humans. In the last two decades, various underwater devices were developed for detecting the mines and mine-like objects in the deep-sea environment. However, there are some problems in recent equipment, like poor accuracy of mineral objects detection, without real-time processing, and low resolution of underwater video frames. Consequently, the underwater objects recognition is a difficult task, because the physical properties of the medium, the captured video frames, are distorted seriously. In this paper, we are considering use of the modern image processing methods to determine the mineral location and to recognize the mineral actually within a little computation complex. We firstly analyze the recent underwater imaging models and propose a novel underwater optical imaging model, which is much closer to the light propagation model in the underwater environment. In our imaging system, we remove the electrical noise by dual-tree complex wavelet transform. And then we solve the nonuniform illumination of artificial lights by fast guided trilateral bilateral filter and recover the image color through automatic color equalization. Finally, a shape-based mineral recognition algorithm is proposed for underwater objects detection. These methods are designed for real-time execution on limited-memory platforms. This pipeline is suitable for detecting underwater objects in practice by our experiences. The initial results are presented and experiments demonstrate the effectiveness of the proposed real-time visualization system.
Sommer, D; Enderlein, D; Antakli, A; Schönenbrücher, H; Slaghuis, J; Redmann, T; Lierz, M
2012-01-01
The efficiency of two commercial PCR methods based on real-time technology, the foodproof® Salmonella detection system and the BAX® PCR Assay Salmonella system was compared to standardized culture methods (EN ISO 6579:2002 - Annex D) for the detection of Salmonella spp. in poultry samples. Four sample matrices (feed, dust, boot swabs, feces) obtained directly from poultry flocks, as well as artificially spiked samples of the same matrices, were used. All samples were tested for Salmonella spp. using culture methods first as the gold standard. In addition samples spiked with Salmonella Enteridis were tested to evaluate the sensitivity of both PCR methods. Furthermore all methods were evaluated in an annual ring-trial of the National Salmonella Reference Laboratory of Germany. Salmonella detection in the matrices feed, dust and boot swabs were comparable in both PCR systems whereas the results from feces differed markedly. The quality, especially the freshness, of the fecal samples had an influence on the sensitivity of the real-time PCR and the results of the culture methods. In fresh fecal samples an initial spiking level of 100cfu/25g Salmonella Enteritidis was detected. Two-days-dried fecal samples allowed the detection of 14cfu/25g. Both real- time PCR protocols appear to be suitable for the detection of Salmonella spp. in all four matrices. The foodproof® system detected eight samples more to be positive compared to the BAX® system, but had a potential false positive result in one case. In 7-days-dried samples none of the methods was able to detect Salmonella likely through letal cell damage. In general the advantage of PCR analyses over the culture method is the reduction of working time from 4-5 days to only 2 days. However, especially for the analysis of fecal samples official validation should be conducted according to the requirement of EN ISO6579:2002 - Annex D.
Improving a real-time object detector with compact temporal information
DEFF Research Database (Denmark)
Ahrnbom, Martin; Jensen, Morten Bornø; Åström, Kalle
2017-01-01
Neural networks designed for real-time object detection have recently improved significantly, but in practice, look- ing at only a single RGB image at the time may not be ideal. For example, when detecting objects in videos, a foreground detection algorithm can be used to obtain compact temporal......, a problem this approach is well suited for. The ac- curacy was found to improve significantly (up to 66%), with a roughly 40% increase in computational time....
Energy Technology Data Exchange (ETDEWEB)
Newby, Deborah Trishelle; Hadfield, Ted; Roberto, Francisco Figueroa
2003-08-01
Real-time PCR provides a means of detecting and quantifying DNA targets by monitoring PCR product accumulation during cycling as indicated by increased fluorescence. A number of different approaches can be used to generate the fluorescence signal. Three approaches—SYBR Green I (a double-stranded DNA intercalating dye), 5'-exonuclease (enzymatically released fluors), and hybridization probes (fluorescence resonance energy transfer)—were evaluated for use in a real-time PCR assay to detect Brucella abortus. The three assays utilized the same amplification primers to produce an identical amplicon. This amplicon spans a region of the B. abortus genome that includes portions of the alkB gene and the IS711 insertion element. All three assays were of comparable sensitivity, providing a linear assay over 7 orders of magnitude (from 7.5 ng down to 7.5 fg). However, the greatest specificity was achieved with the hybridization probe assay.
Rapid diagnosis of sepsis with TaqMan-Based multiplex real-time PCR.
Liu, Chang-Feng; Shi, Xin-Ping; Chen, Yun; Jin, Ye; Zhang, Bing
2018-02-01
The survival rate of septic patients mainly depends on a rapid and reliable diagnosis. A rapid, broad range, specific and sensitive quantitative diagnostic test is the urgent need. Thus, we developed a TaqMan-Based Multiplex real-time PCR assays to identify bloodstream pathogens within a few hours. Primers and TaqMan probes were designed to be complementary to conserved regions in the 16S rDNA gene of different kinds of bacteria. To evaluate accurately, sensitively, and specifically, the known bacteria samples (Standard strains, whole blood samples) are determined by TaqMan-Based Multiplex real-time PCR. In addition, 30 blood samples taken from patients with clinical symptoms of sepsis were tested by TaqMan-Based Multiplex real-time PCR and blood culture. The mean frequency of positive for Multiplex real-time PCR was 96% at a concentration of 100 CFU/mL, and it was 100% at a concentration greater than 1000 CFU/mL. All the known blood samples and Standard strains were detected positively by TaqMan-Based Multiplex PCR, no PCR products were detected when DNAs from other bacterium were used in the multiplex assay. Among the 30 patients with clinical symptoms of sepsis, 18 patients were confirmed positive by Multiplex real-time PCR and seven patients were confirmed positive by blood culture. TaqMan-Based Multiplex real-time PCR assay with highly sensitivity, specificity and broad detection range, is a rapid and accurate method in the detection of bacterial pathogens of sepsis and should have a promising usage in the diagnosis of sepsis. © 2017 Wiley Periodicals, Inc.
Automated real time constant-specificity surveillance for disease outbreaks.
Wieland, Shannon C; Brownstein, John S; Berger, Bonnie; Mandl, Kenneth D
2007-06-13
For real time surveillance, detection of abnormal disease patterns is based on a difference between patterns observed, and those predicted by models of historical data. The usefulness of outbreak detection strategies depends on their specificity; the false alarm rate affects the interpretation of alarms. We evaluate the specificity of five traditional models: autoregressive, Serfling, trimmed seasonal, wavelet-based, and generalized linear. We apply each to 12 years of emergency department visits for respiratory infection syndromes at a pediatric hospital, finding that the specificity of the five models was almost always a non-constant function of the day of the week, month, and year of the study (p accounting for not only the expected number of visits, but also the variance of the number of visits. The expectation-variance model achieves constant specificity on all three time scales, as well as earlier detection and improved sensitivity compared to traditional methods in most circumstances. Modeling the variance of visit patterns enables real-time detection with known, constant specificity at all times. With constant specificity, public health practitioners can better interpret the alarms and better evaluate the cost-effectiveness of surveillance systems.
Ring trial 2016 for Bluetongue virus detection by real-time RT-PCR in France.
Sailleau, Corinne; Viarouge, Cyril; Breard, Emmanuel; Vitour, Damien; Zientara, Stephan
2017-05-01
Since the unexpected emergence of BTV-8 in Northern Europe and the incursion of BTV-8 and 1 in France in 2006-2007, molecular diagnosis has considerably evolved. Several real-time RT-PCR (rtRT-PCR) methods have been developed and published, and are currently being used in many countries across Europe for BTV detection and typing. In France, the national reference laboratory (NRL) for orbiviruses develops and validates 'ready-to-use' kits with private companies for viral RNA detection. The regional laboratories network that was set up to deal with a heavy demand for analyses has used these available kits. From 2007, ring tests were organized to monitor the performance of the French laboratories. This study presents the results of 63 regional laboratories in the ring trial organized in 2016. Blood samples were sent to the laboratories. Participants were asked to use the rtRT-PCR methods in place in their laboratory, for detection of all BTV serotypes and specifically BTV-8. The French regional laboratories are able to detect and genotype BTV in affected animals. Despite the use of several methods (i.e. RNA extraction and different commercial rtRT-PCRs), the network is homogeneous. The ring trial demonstrated that the French regional veterinary laboratories have reliable and robust BTV diagnostic tools for BTV genome detection.
A real-time PCR antibiogram for drug-resistant sepsis.
Directory of Open Access Journals (Sweden)
John R Waldeisen
Full Text Available Current molecular diagnostic techniques for susceptibility testing of septicemia rely on genotyping for the presence of known resistance cassettes. This technique is intrinsically vulnerable due to the inability to detect newly emergent resistance genes. Traditional phenotypic susceptibility testing has always been a superior method to assay for resistance; however, relying on the multi-day growth period to determine which antimicrobial to administer jeopardizes patient survival. These factors have resulted in the widespread and deleterious use of broad-spectrum antimicrobials. The real-time PCR antibiogram, described herein, combines universal phenotypic susceptibility testing with the rapid diagnostic capabilities of PCR. We have developed a procedure that determines susceptibility by monitoring pathogenic load with the highly conserved 16S rRNA gene in blood samples exposed to different antimicrobial drugs. The optimized protocol removes heme and human background DNA from blood, which allows standard real-time PCR detection systems to be employed with high sensitivity (<100 CFU/mL. Three strains of E. coli, two of which were antimicrobial resistant, were spiked into whole blood and exposed to three different antibiotics. After real-time PCR-based determination of pathogenic load, a ΔC(t<3.0 between untreated and treated samples was found to indicate antimicrobial resistance (P<0.01. Minimum inhibitory concentration was determined for susceptible bacteria and pan-bacterial detection was demonstrated with 3 gram-negative and 2 gram-positive bacteria. Species identification was performed via analysis of the hypervariable amplicons. In summary, we have developed a universal diagnostic phenotyping technique that assays for the susceptibility of drug-resistant septicemia with the speed of PCR. The real-time PCR antibiogram achieves detection, susceptibility testing, minimum inhibitory concentration determination, and identification in less than 24
Real-time resource allocation for tracking systems
Satsangi, Y.; Whiteson, S.; Oliehoek, F.A.; Bouma, H.
2017-01-01
Automated tracking is key to many computer vision applications. However, many tracking systems struggle to perform in real-time due to the high computational cost of detecting people, especially in ultra high resolution images. We propose a new algorithm called PartiMax that greatly reduces this
Improvement of sampling plans for Salmonella detection in pooled table eggs by use of real-time PCR
DEFF Research Database (Denmark)
Pasquali, Frédérique; De Cesare, Alessandra; Valero, Antonio
2014-01-01
Eggs and egg products have been described as the most critical food vehicles of salmonellosis. The prevalence and level of contamination of Salmonella on table eggs are low, which severely affects the sensitivity of sampling plans applied voluntarily in some European countries, where one to five...... pools of 10 eggs are tested by the culture based reference method ISO 6579:2004. In the current study we have compared the testing-sensitivity of the reference culture method ISO 6579:2004 and an alternative real-time PCR method on Salmonella contaminated egg-pool of different sizes (4-9 uninfected eggs...... mixed with one contaminated egg) and contamination levels (10°-10(1), 10(1)-10(2), 10(2)-10(3)CFU/eggshell). Two hundred and seventy samples corresponding to 15 replicates per pool size and inoculum level were tested. At the lowest contamination level real-time PCR detected Salmonella in 40...
Development of quantitative real-time PCR for detection and enumeration of Enterobacteriaceae.
Takahashi, Hajime; Saito, Rumi; Miya, Satoko; Tanaka, Yuichiro; Miyamura, Natsumi; Kuda, Takashi; Kimura, Bon
2017-04-04
The family Enterobacteriaceae, members of which are widely distributed in the environment, includes many important human pathogens. In this study, a rapid real-time PCR method targeting rplP, coding for L16 protein, a component of the ribosome large subunit, was developed for enumerating Enterobacteriaceae strains, and its efficiency was evaluated using naturally contaminated food products. The rplP-targeted real-time PCR amplified Enterobacteriaceae species with Ct values of 14.0-22.8, whereas the Ct values for non-Enterobacteriaceae species were >30, indicating the specificity of this method for the Enterobacteriaceae. Using a calibration curve of Ct=-3.025 (log CFU/g)+37.35, which was calculated from individual plots of the cell numbers in different concentrations of 5 Enterobacteriaceae species, the rplP-targeted real-time PCR was applied to 51 food samples. A Enterobacteriaceae species in foods rapidly and accurately, and therefore, it can be used for the microbiological risk analysis of foods. Copyright © 2017 Elsevier B.V. All rights reserved.
Psifidi, Androniki; Dovas, Chrysostomos; Banos, Georgios
2011-01-01
Background Single nucleotide polymorphisms (SNP) have proven to be powerful genetic markers for genetic applications in medicine, life science and agriculture. A variety of methods exist for SNP detection but few can quantify SNP frequencies when the mutated DNA molecules correspond to a small fraction of the wild-type DNA. Furthermore, there is no generally accepted gold standard for SNP quantification, and, in general, currently applied methods give inconsistent results in selected cohorts. In the present study we sought to develop a novel method for accurate detection and quantification of SNP in DNA pooled samples. Methods The development and evaluation of a novel Ligase Chain Reaction (LCR) protocol that uses a DNA-specific fluorescent dye to allow quantitative real-time analysis is described. Different reaction components and thermocycling parameters affecting the efficiency and specificity of LCR were examined. Several protocols, including gap-LCR modifications, were evaluated using plasmid standard and genomic DNA pools. A protocol of choice was identified and applied for the quantification of a polymorphism at codon 136 of the ovine PRNP gene that is associated with susceptibility to a transmissible spongiform encephalopathy in sheep. Conclusions The real-time LCR protocol developed in the present study showed high sensitivity, accuracy, reproducibility and a wide dynamic range of SNP quantification in different DNA pools. The limits of detection and quantification of SNP frequencies were 0.085% and 0.35%, respectively. Significance The proposed real-time LCR protocol is applicable when sensitive detection and accurate quantification of low copy number mutations in DNA pools is needed. Examples include oncogenes and tumour suppressor genes, infectious diseases, pathogenic bacteria, fungal species, viral mutants, drug resistance resulting from point mutations, and genetically modified organisms in food. PMID:21283808
Application of reverse transcription-PCR and real-time PCR in nanotoxicity research.
Mo, Yiqun; Wan, Rong; Zhang, Qunwei
2012-01-01
Reverse transcription-polymerase chain reaction (RT-PCR) is a relatively simple and inexpensive technique to determine the expression level of target genes and is widely used in biomedical science research including nanotoxicology studies for semiquantitative analysis. Real-time PCR allows for the detection of PCR amplification in the exponential growth phase of the reaction and is much more quantitative than traditional RT-PCR. Although a number of kits and reagents for RT-PCR and real-time PCR are commercially available, the basic principles are the same. Here, we describe the procedures for total RNA isolation by using TRI Reagent, for reverse transcription (RT) by M-MLV reverse transcriptase, and for PCR by GoTaq(®) DNA Polymerase. And real-time PCR will be performed on an iQ5 multicolor real-time PCR detection system by using iQ™ SYBR Green Supermix.
Yip, Cyril C Y; Sridhar, Siddharth; Cheng, Andrew K W; Fung, Ami M Y; Cheng, Vincent C C; Chan, Kwok-Hung; Yuen, Kwok-Yung
2017-08-01
HHV-6 reactivation in immunocompromised patients is common and may be associated with serious morbidity and mortality; therefore, early detection and initiation of therapy might be of benefit. Real-time PCR assays allow for early identification of HHV-6 reactivation to assist in providing a timely response. Thus, we compared the performance of an in-house developed HHV-6 quantitative PCR assay with a commercially available kit, the RealStar ® HHV-6 PCR Kit. The analytical sensitivity, analytical specificity, linearity, precision and accuracy of the in-house developed HHV-6 qPCR assay were evaluated. The diagnostic performance of the in-house HHV-6 qPCR assay was compared with the RealStar ® HHV-6 PCR Kit, using 72 clinical specimens and 17 proficiency testing samples. Linear regression analysis of the quantitative results showed a dynamic range from 2 to 10 log 10 copies/ml and a coefficient of determination (R 2 ) of 0.999 for the in-house assay. A dilution series demonstrated a limit of detection and a limit of quantification of 1.7 log 10 and 2 log 10 copies/ml, respectively. The precision of the assay was highly reproducible among runs with coefficients of variance (CV) ranging from 0.27% to 4.37%. A comparison of 27 matched samples showed an excellent correlation between the quantitative viral loads measured by the in-house HHV-6 qPCR assay and the RealStar ® HHV-6 PCR Kit (R 2 =0.926; PPCR Kit. Copyright © 2017 Elsevier B.V. All rights reserved.
Specification and Test of Real-Time Systems
DEFF Research Database (Denmark)
Nielsen, Brian
of the system, and a set of constraint patterns which describes and enforces the timing and synchronization constraints among components. We propose new techniques for automated black box conformance testing of real-time systems against densely timed speci cations. A test generator tool examines a specification......Distributed real-time computer based systems are very complex and intrinsically difficult to specify and implement correctly; in part this is caused by the overwhelming number of possible interactions between system components, but especially by a lack of adequate methods and tools to deal...... of the desired system behavior and generates the necessary test cases. A main problem is to construct a reasonably small test suite that can be executed within allotted resources, while having a high likelihood of detecting unknown errors. Our goal has been to treat the time dimension of this problem thoroughly...
Real-Time Detection Methods to Monitor TRU Compositions in UREX+Process Streams
Energy Technology Data Exchange (ETDEWEB)
McDeavitt, Sean; Charlton, William; Indacochea, J Ernesto; taleyarkhan, Rusi; Pereira, Candido
2013-03-01
The U.S. Department of Energy has developed advanced methods for reprocessing spent nuclear fuel. The majority of this development was accomplished under the Advanced Fuel Cycle Initiative (AFCI), building on the strong legacy of process development R&D over the past 50 years. The most prominent processing method under development is named UREX+. The name refers to a family of processing methods that begin with the Uranium Extraction (UREX) process and incorporate a variety of other methods to separate uranium, selected fission products, and the transuranic (TRU) isotopes from dissolved spent nuclear fuel. It is important to consider issues such as safeguards strategies and materials control and accountability methods. Monitoring of higher actinides during aqueous separations is a critical research area. By providing on-line materials accountability for the processes, covert diversion of the materials streams becomes much more difficult. The importance of the nuclear fuel cycle continues to rise on national and international agendas. The U.S. Department of Energy is evaluating and developing advanced methods for safeguarding nuclear materials along with instrumentation in various stages of the fuel cycle, especially in material balance areas (MBAs) and during reprocessing of used nuclear fuel. One of the challenges related to the implementation of any type of MBA and/or reprocessing technology (e.g., PUREX or UREX) is the real-time quantification and control of the transuranic (TRU) isotopes as they move through the process. Monitoring of higher actinides from their neutron emission (including multiplicity) and alpha signatures during transit in MBAs and in aqueous separations is a critical research area. By providing on-line real-time materials accountability, diversion of the materials becomes much more difficult. The objective of this consortium was to develop real time detection methods to monitor the efficacy of the UREX+ process and to safeguard the separated
International Nuclear Information System (INIS)
Khan, S. A.; Ahmed, S.; Khan, F. A.; Shamshad, G. U.; Joyia, Z.; Mushahid, N.; Saeed, S.
2013-01-01
Objective: To determine the sensitivity of a real time polymerase chain reaction (PCR) for malaria diagnosis and to compare its accuracy with microscopy and an antigen based rapid diagnostic test (OptiMal). Study Design: Cross-sectional analytical study. Place and Duration of Study: Military Hospital, Armed Forces Institute of Transfusion and Armed Forces Institute of Pathology, Rawalpindi, from July to December 2011. Methodology: Venous blood samples of 300 clinically suspected patients of malaria were tested for malaria parasite by microscopy and OptiMal; and malaria parasite index was calculated for the positive samples. Plasmodium genus specific real time PCR was performed on all specimens, targeting small subunit rRNA gene. Diagnostic accuracy of three tests was compared and cost analysis was done. Results: Out of 300 patients, malaria parasite was detected in 110, 106 and 123 patients by microscopy, OptiMAL and PCR respectively. Real time PCR was 100% sensitive while microscopy and OptiMal had sensitivity of 89.4% and 86.2% respectively. All methods were 100% specific. The cost per test was calculated to be 0.2, 2.75 and 3.30 US dollar by microscopy, OptiMal and PCR respectively, excluding the once capital cost on PCR equipment. Conclusion: Genus specific real time PCR for the diagnosis of malaria was successfully established as a highly sensitive and affordable technology that should be incorporated in the diagnostic algorithm in this country. (author)
Eisemann, Elmar; Assarsson, Ulf; Wimmer, Michael
2011-01-01
Important elements of games, movies, and other computer-generated content, shadows are crucial for enhancing realism and providing important visual cues. In recent years, there have been notable improvements in visual quality and speed, making high-quality realistic real-time shadows a reachable goal. Real-Time Shadows is a comprehensive guide to the theory and practice of real-time shadow techniques. It covers a large variety of different effects, including hard, soft, volumetric, and semi-transparent shadows.The book explains the basics as well as many advanced aspects related to the domain
Parametric Roll - Risk Reduction through Real-time Detection
DEFF Research Database (Denmark)
Galeazzi, Roberto
2014-01-01
PAROLL is an innovative condition-monitoring system for the timely detection of parametric roll on merchant vessels. It has been invented and developed by the Technical University of Denmark. DNV GL and Wallenius Marine have supported the development and full-scale validation of this monitoring...
1991-09-30
0196 or 413 545-0720 PI E-mail Address: krithi@nirvan.cs.umass.edu, stankovic(ocs.umass.edu Grant or Contract Title: Dependable Real - Time Systems Grant...Dependable Real - Time Systems " Grant or Contract Number: N00014-85-k-0398 L " Reporting Period: 1 Oct 87 - 30 Sep 91 , 2. Summary of Accomplishments ’ 2.1 Our...in developing a sound approach to scheduling tasks in complex real - time systems , (2) developed a real-time operating system kernel, a preliminary
Telemetric real-time sensor for the detection of acute upper gastrointestinal bleeding.
Schostek, Sebastian; Zimmermann, Melanie; Keller, Jan; Fode, Mario; Melbert, Michael; Schurr, Marc O; Gottwald, Thomas; Prosst, Ruediger L
2016-04-15
Acute upper gastrointestinal bleedings from ulcers or esophago-gastric varices are life threatening medical conditions which require immediate endoscopic therapy. Despite successful endoscopic hemostasis, there is a significant risk of rebleeding often requiring close surveillance of these patients in the intensive care unit (ICU). Any time delay to recognize bleeding may lead to a high blood loss and increases the risk of death. A novel telemetric real-time bleeding sensor can help indicate blood in the stomach: the sensor is swallowed to detect active bleeding or is anchored endoscopically on the gastrointestinal wall close to the potential bleeding source. By telemetric communication with an extra-corporeal receiver, information about the bleeding status is displayed. In this study the novel sensor, which measures characteristic optical properties of blood, has been evaluated in an ex-vivo setting to assess its clinical applicability and usability. Human venous blood of different concentrations, various fluids, and liquid food were tested. The LED-based sensor was able to reliably distinguish between concentrated blood and other liquids, especially red-colored fluids. In addition, the spectrometric quality of the small sensor (size: 6.5mm in diameter, 25.5mm in length) was comparable to a much larger and technically more complex laboratory spectrophotometer. The experimental data confirm the capability of a miniaturized sensor to identify concentrated blood, which could help in the very near future the detection of upper gastrointestinal bleeding and to survey high-risk patients for rebleeding. Copyright © 2015 Elsevier B.V. All rights reserved.
Development of real-time PCR tests for the detection of Tenebrio molitor in food and feed.
Debode, Frédéric; Marien, Aline; Gérard, Amaury; Francis, Frédéric; Fumière, Olivier; Berben, Gilbert
2017-08-01
Insects are rich in proteins and could be an alternative source of proteins to feed animals and humans. Numerous companies have started the production of insects for feed purposes. In Europe, these processed animal proteins are not yet authorised by legislation as many questions still need to be answered concerning this 'novel food'. Authorisations will be possible when methods of authentication of the products are available. In this study we propose real-time PCR methods for the specific detection of the mealworm (Tenebriomolitor), one of the most widely used insects for food and feed production. Two PCR assays are proposed: the first based on the wingless gene and the second based on the cadherin gene. The PCR tests amplify fragments of 87 bp. These qualitative methods were tested according to several performance criteria. The specificity was tested on 34 insect species' DNA, but also on non-insect species including crustacean, mammals, birds and plants. The limit of detection was determined and was below 20 copies for the two PCR tests. The applicability of the tests was demonstrated by the analysis of real-life processed samples containing T. molitor.
A real-time PCR approach to detect predation on anchovy and sardine early life stages
Cuende, Elsa; Mendibil, Iñaki; Bachiller, Eneko; Álvarez, Paula; Cotano, Unai; Rodriguez-Ezpeleta, Naiara
2017-12-01
Recruitment of sardine (Sardina pilchardus Walbaum, 1792) and anchovy (Engraulis encrasicolus Linnaeus, 1758) is thought to be regulated by predation of their eggs and larvae. Predators of sardine and anchovy can be identified by visual taxonomic identification of stomach contents, but this method is time consuming, tedious and may underestimate predation, especially in small predators such as fish larvae. Alternatively, genetic tools may offer a more cost-effective and accurate alternative. Here, we have developed a multiplex real-time polymerase chain reaction (RT-PCR) assay based on TaqMan probes to simultaneously detect sardine and anchovy remains in gut contents of potential predators. The assay combines previously described and newly generated species-specific primers and probes for anchovy and sardine detection respectively, and allows the detection of 0,001 ng of target DNA (which corresponds to about one hundredth of the total DNA present in a single egg). We applied the method to candidate anchovy and sardine egg predators in the Bay of Biscay, Atlantic Mackerel (Scomber scombrus) larvae. Egg predation observed was limited primarily to those stations where sardine and/or anchovy eggs were present. Our developed assay offers a suitable tool to understand the effects of predation on the survival of anchovy and sardine early life stages.
CERN. Geneva; Flockhart, Ronald Bruce; Seppey, P
2003-01-01
With LabVIEW Real-Time, you can choose from a variety of RT Series hardware. Add a real-time data acquisition component into a larger measurement and automation system or create a single stand-alone real-time solution with data acquisition, signal conditioning, motion control, RS-232, GPIB instrumentation, and Ethernet connectivity. With the various hardware options, you can create a system to meet your precise needs today, while the modularity of the system means you can add to the solution as your system requirements grow. If you are interested in Reliable and Deterministic systems for Measurement and Automation, you will profit from this seminar. Agenda: Real-Time Overview LabVIEW RT Hardware Platforms - Linux on PXI Programming with LabVIEW RT Real-Time Operating Systems concepts Timing Applications Data Transfer
DEFF Research Database (Denmark)
McKillan, John; McMenamy, Michael; Hjertner, Bernt
2010-01-01
sensitive than the conventional PCR recommended by the OIE. Linear range was ten logs from 2 × 101 to 2 × 1010. The assay is rapid with an amplification time just over 2 h. The development of this assay provides a useful tool for the specific diagnosis of ASF in statutory or emergency testing programs......The design of a 5′ conjugated minor groove binder (MGB) probe real-time PCR assay is described for the rapid, sensitive and specific detection of African swine fever virus (ASFV) DNA. The assay is designed against the 9GL region and is capable of detecting 20 copies of a DNA standard. It does...
Concepts of real time and semi-real time material control
International Nuclear Information System (INIS)
Lovett, J.E.
1975-01-01
After a brief consideration of the traditional material balance accounting on an MBA basis, this paper explores the basic concepts of real time and semi-real time material control, together with some of the major problems to be solved. Three types of short-term material control are discussed: storage, batch processing, and continuous processing. (DLC)
Detection and Characterization of Equatorial Scintillation for Real-Time Operational Support
National Research Council Canada - National Science Library
McNeil, W
1997-01-01
The Phillips Laboratory Scintillation Network Decision Aid (PL-SCINDA) is a software tool which uses real-time data from remote sites to model ionospheric plasma depletions in the equatorial region...
DEFF Research Database (Denmark)
Christensen, Knud Smed
2000-01-01
Describes fundamentals of parallel programming and a kernel for that. Describes methods for modelling and checking parallel problems. Real time problems.......Describes fundamentals of parallel programming and a kernel for that. Describes methods for modelling and checking parallel problems. Real time problems....
International Nuclear Information System (INIS)
Asami, Tohru; Hashimoto, Kazuo; Yamamoto, Seiichi
1992-01-01
Recently, aiming at the application to the plant control for nuclear reactors and traffic and communication control, the research and the practical use of the expert system suitable to real time processing have become conspicuous. In this report, the condition for the required function to control the object that dynamically changes within a limited time is presented, and the technical difference between the real time expert system developed so as to satisfy it and the expert system of conventional type is explained with the actual examples and from theoretical aspect. The expert system of conventional type has the technical base in the problem-solving equipment originating in STRIPS. The real time expert system is applied to the fields accompanied by surveillance and control, to which conventional expert system is hard to be applied. The requirement for the real time expert system, the example of the real time expert system, and as the techniques of realizing real time processing, the realization of interruption processing, dispersion processing, and the mechanism of maintaining the consistency of knowledge are explained. (K.I.)
Pandey, Parul; Lee, Eun Kyung; Pompili, Dario
2016-11-01
Stress is one of the key factor that impacts the quality of our daily life: From the productivity and efficiency in the production processes to the ability of (civilian and military) individuals in making rational decisions. Also, stress can propagate from one individual to other working in a close proximity or toward a common goal, e.g., in a military operation or workforce. Real-time assessment of the stress of individuals alone is, however, not sufficient, as understanding its source and direction in which it propagates in a group of people is equally-if not more-important. A continuous near real-time in situ personal stress monitoring system to quantify level of stress of individuals and its direction of propagation in a team is envisioned. However, stress monitoring of an individual via his/her mobile device may not always be possible for extended periods of time due to limited battery capacity of these devices. To overcome this challenge a novel distributed mobile computing framework is proposed to organize the resources in the vicinity and form a mobile device cloud that enables offloading of computation tasks in stress detection algorithm from resource constrained devices (low residual battery, limited CPU cycles) to resource rich devices. Our framework also supports computing parallelization and workflows, defining how the data and tasks divided/assigned among the entities of the framework are designed. The direction of propagation and magnitude of influence of stress in a group of individuals are studied by applying real-time, in situ analysis of Granger Causality. Tangible benefits (in terms of energy expenditure and execution time) of the proposed framework in comparison to a centralized framework are presented via thorough simulations and real experiments.
Real-time, single-step bioassay using nanoplasmonic resonator with ultra-high sensitivity
Energy Technology Data Exchange (ETDEWEB)
Zhang, Xiang; Ellman, Jonathan A; Chen, Fanqing Frank; Su, Kai-Hang; Wei, Qi-Huo; Sun, Cheng
2014-04-01
A nanoplasmonic resonator (NPR) comprising a metallic nanodisk with alternating shielding layer(s), having a tagged biomolecule conjugated or tethered to the surface of the nanoplasmonic resonator for highly sensitive measurement of enzymatic activity. NPRs enhance Raman signals in a highly reproducible manner, enabling fast detection of protease and enzyme activity, such as Prostate Specific Antigen (paPSA), in real-time, at picomolar sensitivity levels. Experiments on extracellular fluid (ECF) from paPSA-positive cells demonstrate specific detection in a complex bio-fluid background in real-time single-step detection in very small sample volumes.
Son, Na Ry; Seo, Dong Joo; Lee, Min Hwa; Seo, Sheungwoo; Wang, Xiaoyu; Lee, Bog-Hieu; Lee, Jeong-Su; Joo, In-Sun; Hwang, In-Gyun; Choi, Changsun
2014-09-01
The aim of this study was to develop an optimal technique for detecting hepatitis E virus (HEV) in swine livers. Here, three elution buffers and two concentration methods were compared with respect to enhancing recovery of HEV from swine liver samples. Real-time reverse transcription-polymerase chain reaction (RT-PCR) and nested RT-PCR were performed to detect HEV RNA. When phosphate-buffered saline (PBS, pH 7.4) was used to concentrate HEV in swine liver samples using ultrafiltration, real-time RT-PCR detected HEV in 6 of the 26 samples. When threonine buffer was used to concentrate HEV using polyethylene glycol (PEG) precipitation and ultrafiltration, real-time RT-PCR detected HEV in 1 and 3 of the 26 samples, respectively. When glycine buffer was used to concentrate HEV using ultrafiltration and PEG precipitation, real-time RT-PCR detected HEV in 1 and 3 samples of the 26 samples, respectively. When nested RT-PCR was used to detect HEV, all samples tested negative regardless of the type of elution buffer or concentration method used. Therefore, the combination of real-time RT-PCR and ultrafiltration with PBS buffer was the most sensitive and reliable method for detecting HEV in swine livers. Copyright © 2014 Elsevier B.V. All rights reserved.
Zhang, Chi; Fang, Xin; Qiu, Haopu; Li, Ning
2015-01-01
Real-time PCR amplification of mitochondria gene could not be used for DNA quantification, and that of single copy DNA did not allow an ideal sensitivity. Moreover, cross-reactions among similar species were commonly observed in the published methods amplifying repetitive sequence, which hindered their further application. The purpose of this study was to establish a short interspersed nuclear element (SINE)-based real-time PCR approach having high specificity for species detection that could be used in DNA quantification. After massive screening of candidate Sus scrofa SINEs, one optimal combination of primers and probe was selected, which had no cross-reaction with other common meat species. LOD of the method was 44 fg DNA/reaction. Further, quantification tests showed this approach was practical in DNA estimation without tissue variance. Thus, this study provided a new tool for qualitative detection of porcine component, which could be promising in the QC of meat products.
3D Printed "Earable" Smart Devices for Real-Time Detection of Core Body Temperature.
Ota, Hiroki; Chao, Minghan; Gao, Yuji; Wu, Eric; Tai, Li-Chia; Chen, Kevin; Matsuoka, Yasutomo; Iwai, Kosuke; Fahad, Hossain M; Gao, Wei; Nyein, Hnin Yin Yin; Lin, Liwei; Javey, Ali
2017-07-28
Real-time detection of basic physiological parameters such as blood pressure and heart rate is an important target in wearable smart devices for healthcare. Among these, the core body temperature is one of the most important basic medical indicators of fever, insomnia, fatigue, metabolic functionality, and depression. However, traditional wearable temperature sensors are based upon the measurement of skin temperature, which can vary dramatically from the true core body temperature. Here, we demonstrate a three-dimensional (3D) printed wearable "earable" smart device that is designed to be worn on the ear to track core body temperature from the tympanic membrane (i.e., ear drum) based on an infrared sensor. The device is fully integrated with data processing circuits and a wireless module for standalone functionality. Using this smart earable device, we demonstrate that the core body temperature can be accurately monitored regardless of the environment and activity of the user. In addition, a microphone and actuator are also integrated so that the device can also function as a bone conduction hearing aid. Using 3D printing as the fabrication method enables the device to be customized for the wearer for more personalized healthcare. This smart device provides an important advance in realizing personalized health care by enabling real-time monitoring of one of the most important medical parameters, core body temperature, employed in preliminary medical screening tests.
Szarka, Mate; Guttman, Andras
2017-10-17
We present the application of a smartphone anatomy based technology in the field of liquid phase bioseparations, particularly in capillary electrophoresis. A simple capillary electrophoresis system was built with LED induced fluorescence detection and a credit card sized minicomputer to prove the concept of real time fluorescent imaging (zone adjustable time-lapse fluorescence image processor) and separation controller. The system was evaluated by analyzing under- and overloaded aminopyrenetrisulfonate (APTS)-labeled oligosaccharide samples. The open source software based image processing tool allowed undistorted signal modulation (reprocessing) if the signal was inappropriate for the actual detection system settings (too low or too high). The novel smart detection tool for fluorescently labeled biomolecules greatly expands dynamic range and enables retrospective correction for injections with unsuitable signal levels without the necessity to repeat the analysis.
International Nuclear Information System (INIS)
Jin, Hui; Gui, Rijun; Sun, Jie; Wang, Yanfeng
2016-01-01
Probe-donor integrated nanocomposites were developed from conjugating silica-coated Mn"2"+:ZnS quantum dots (QDs) with MoS_2 QDs and photosensitive nitric oxide (NO) donors (Fe_4S_3(NO)_7"−, RBS). Under excitation with near-infrared (NIR) light at 808 nm, the Mn"2"+:ZnS@SiO_2/MoS_2-RBS nanocomposites showed the dual-emissive two-photon excited photoluminescence (TPEPL) that induced RBS photolysis to release NO in situ. NO caused TPEPL quenching of Mn"2"+:ZnS QDs, but it produced almost no impact on the TPEPL of MoS_2 QDs. Hence, the nanocomposites were developed as a novel QDs-based ratiometric TPEPL probe for real-time detection of NO release in situ. The ratiometric TPEPL intensity is nearly linear (R"2 = 0.9901) with NO concentration in the range of 0.01∼0.8 μM, which corresponds to the range of NO release time (0∼15 min). The detection limit was calculated to be approximately 4 nM of NO. Experimental results confirmed that this novel ratiometric TPEPL probe possessed high selectivity and sensitivity for the detection of NO against potential competitors, and especially showed high detection performance for NIR-light triggered NO release in tumor intracellular microenvironments. These results would promote the development of versatile probe-donor integrated systems, also providing a facile and efficient strategy to real-time detect the highly controllable drug release in situ, especially in physiological microenvironments. - Highlights: • Mn"2"+:ZnS@SiO_2/MoS_2-RBS nanocomposites were developed as a novel ratiometric two-photon excited fluorescence probe. • This probe could conduct real-time detection of nitric oxide release in situ. • High feasibility of this probe was confirmed in tumor intracellular microenvironments.
Wadhwa, Ashutosh; Wilkins, Kimberly; Gao, Jinxin; Condori Condori, Rene Edgar; Gigante, Crystal M; Zhao, Hui; Ma, Xiaoyue; Ellison, James A; Greenberg, Lauren; Velasco-Villa, Andres; Orciari, Lillian; Li, Yu
2017-01-01
Rabies, resulting from infection by Rabies virus (RABV) and related lyssaviruses, is one of the most deadly zoonotic diseases and is responsible for up to 70,000 estimated human deaths worldwide each year. Rapid and accurate laboratory diagnosis of rabies is essential for timely administration of post-exposure prophylaxis in humans and control of the disease in animals. Currently, only the direct fluorescent antibody (DFA) test is recommended for routine rabies diagnosis. Reverse-transcription polymerase chain reaction (RT-PCR) based diagnostic methods have been widely adapted for the diagnosis of other viral pathogens, but there is currently no widely accepted rapid real-time RT-PCR assay for the detection of all lyssaviruses. In this study, we demonstrate the validation of a newly developed multiplex real-time RT-PCR assay named LN34, which uses a combination of degenerate primers and probes along with probe modifications to achieve superior coverage of the Lyssavirus genus while maintaining sensitivity and specificity. The primers and probes of the LN34 assay target the highly conserved non-coding leader region and part of the nucleoprotein (N) coding sequence of the Lyssavirus genome to maintain assay robustness. The probes were further modified by locked nucleotides to increase their melting temperature to meet the requirements for an optimal real-time RT-PCR assay. The LN34 assay was able to detect all RABV variants and other lyssaviruses in a validation panel that included representative RABV isolates from most regions of the world as well as representatives of 13 additional Lyssavirus species. The LN34 assay was successfully used for both ante-mortem and post-mortem diagnosis of over 200 clinical samples as well as field derived surveillance samples. This assay represents a major improvement over previously published rabies specific RT-PCR and real-time RT-PCR assays because of its ability to universally detect RABV and other lyssaviruses, its high
Directory of Open Access Journals (Sweden)
Ashutosh Wadhwa
2017-01-01
Full Text Available Rabies, resulting from infection by Rabies virus (RABV and related lyssaviruses, is one of the most deadly zoonotic diseases and is responsible for up to 70,000 estimated human deaths worldwide each year. Rapid and accurate laboratory diagnosis of rabies is essential for timely administration of post-exposure prophylaxis in humans and control of the disease in animals. Currently, only the direct fluorescent antibody (DFA test is recommended for routine rabies diagnosis. Reverse-transcription polymerase chain reaction (RT-PCR based diagnostic methods have been widely adapted for the diagnosis of other viral pathogens, but there is currently no widely accepted rapid real-time RT-PCR assay for the detection of all lyssaviruses. In this study, we demonstrate the validation of a newly developed multiplex real-time RT-PCR assay named LN34, which uses a combination of degenerate primers and probes along with probe modifications to achieve superior coverage of the Lyssavirus genus while maintaining sensitivity and specificity. The primers and probes of the LN34 assay target the highly conserved non-coding leader region and part of the nucleoprotein (N coding sequence of the Lyssavirus genome to maintain assay robustness. The probes were further modified by locked nucleotides to increase their melting temperature to meet the requirements for an optimal real-time RT-PCR assay. The LN34 assay was able to detect all RABV variants and other lyssaviruses in a validation panel that included representative RABV isolates from most regions of the world as well as representatives of 13 additional Lyssavirus species. The LN34 assay was successfully used for both ante-mortem and post-mortem diagnosis of over 200 clinical samples as well as field derived surveillance samples. This assay represents a major improvement over previously published rabies specific RT-PCR and real-time RT-PCR assays because of its ability to universally detect RABV and other lyssaviruses
Real-Time Human Detection for Aerial Captured Video Sequences via Deep Models
Directory of Open Access Journals (Sweden)
Nouar AlDahoul
2018-01-01
Full Text Available Human detection in videos plays an important role in various real life applications. Most of traditional approaches depend on utilizing handcrafted features which are problem-dependent and optimal for specific tasks. Moreover, they are highly susceptible to dynamical events such as illumination changes, camera jitter, and variations in object sizes. On the other hand, the proposed feature learning approaches are cheaper and easier because highly abstract and discriminative features can be produced automatically without the need of expert knowledge. In this paper, we utilize automatic feature learning methods which combine optical flow and three different deep models (i.e., supervised convolutional neural network (S-CNN, pretrained CNN feature extractor, and hierarchical extreme learning machine for human detection in videos captured using a nonstatic camera on an aerial platform with varying altitudes. The models are trained and tested on the publicly available and highly challenging UCF-ARG aerial dataset. The comparison between these models in terms of training, testing accuracy, and learning speed is analyzed. The performance evaluation considers five human actions (digging, waving, throwing, walking, and running. Experimental results demonstrated that the proposed methods are successful for human detection task. Pretrained CNN produces an average accuracy of 98.09%. S-CNN produces an average accuracy of 95.6% with soft-max and 91.7% with Support Vector Machines (SVM. H-ELM has an average accuracy of 95.9%. Using a normal Central Processing Unit (CPU, H-ELM’s training time takes 445 seconds. Learning in S-CNN takes 770 seconds with a high performance Graphical Processing Unit (GPU.
Real-Time Earthquake Monitoring with Spatio-Temporal Fields
Whittier, J. C.; Nittel, S.; Subasinghe, I.
2017-10-01
With live streaming sensors and sensor networks, increasingly large numbers of individual sensors are deployed in physical space. Sensor data streams are a fundamentally novel mechanism to deliver observations to information systems. They enable us to represent spatio-temporal continuous phenomena such as radiation accidents, toxic plumes, or earthquakes almost as instantaneously as they happen in the real world. Sensor data streams discretely sample an earthquake, while the earthquake is continuous over space and time. Programmers attempting to integrate many streams to analyze earthquake activity and scope need to write code to integrate potentially very large sets of asynchronously sampled, concurrent streams in tedious application code. In previous work, we proposed the field stream data model (Liang et al., 2016) for data stream engines. Abstracting the stream of an individual sensor as a temporal field, the field represents the Earth's movement at the sensor position as continuous. This simplifies analysis across many sensors significantly. In this paper, we undertake a feasibility study of using the field stream model and the open source Data Stream Engine (DSE) Apache Spark(Apache Spark, 2017) to implement a real-time earthquake event detection with a subset of the 250 GPS sensor data streams of the Southern California Integrated GPS Network (SCIGN). The field-based real-time stream queries compute maximum displacement values over the latest query window of each stream, and related spatially neighboring streams to identify earthquake events and their extent. Further, we correlated the detected events with an USGS earthquake event feed. The query results are visualized in real-time.
Directory of Open Access Journals (Sweden)
Ho KC
2005-01-01
Full Text Available We propose a real-time software system for landmine detection using ground-penetrating radar (GPR. The system includes an efficient and adaptive preprocessing component; a hidden Markov model- (HMM- based detector; a corrective training component; and an incremental update of the background model. The preprocessing is based on frequency-domain processing and performs ground-level alignment and background removal. The HMM detector is an improvement of a previously proposed system (baseline. It includes additional pre- and postprocessing steps to improve the time efficiency and enable real-time application. The corrective training component is used to adjust the initial model parameters to minimize the number of misclassification sequences. This component could be used offline, or online through feedback to adapt an initial model to specific sites and environments. The background update component adjusts the parameters of the background model to adapt it to each lane during testing. The proposed software system is applied to data acquired from three outdoor test sites at different geographic locations, using a state-of-the-art array GPR prototype. The first collection was used as training, and the other two (contain data from more than 1200 m of simulated dirt and gravel roads for testing. Our results indicate that, on average, the corrective training can improve the performance by about 10% for each site. For individual lanes, the performance gain can reach 50%.
Real-time multiplex PCR assay for detection of Yersinia pestis and Yersinia pseudotuberculosis.
Matero, Pirjo; Pasanen, Tanja; Laukkanen, Riikka; Tissari, Päivi; Tarkka, Eveliina; Vaara, Martti; Skurnik, Mikael
2009-01-01
A multiplex real-time polymerase chain reaction (PCR) assay was developed for the detection of Yersinia pestis and Yersinia pseudotuberculosis. The assay includes four primer pairs, two of which are specific for Y. pestis, one for Y. pestis and Y. pseudotuberculosis and one for bacteriophage lambda; the latter was used as an internal amplification control. The Y. pestis-specific target genes in the assay were ypo2088, a gene coding for a putative methyltransferase, and the pla gene coding for the plasminogen activator. In addition, the wzz gene was used as a target to specifically identify both Y. pestis and the closely related Y. pseudotuberculosis group. The primer and probe sets described for the different genes can be used either in single or in multiplex PCR assays because the individual probes were designed with different fluorochromes. The assays were found to be both sensitive and specific; the lower limit of the detection was 10-100 fg of extracted Y. pestis or Y. pseudotuberculosis total DNA. The sensitivity of the tetraplex assay was determined to be 1 cfu for the ypo2088 and pla probe labelled with FAM and JOE fluorescent dyes, respectively.
[Real-time PCR in rapid diagnosis of Aeromonas hydrophila necrotizing soft tissue infections].
Kohayagawa, Yoshitaka; Izumi, Yoko; Ushita, Misuzu; Niinou, Norio; Koshizaki, Masayuki; Yamamori, Yuji; Kaneko, Sakae; Fukushima, Hiroshi
2009-11-01
We report a case of rapidly progressive necrotizing soft tissue infection and sepsis followed by a patient's death. We suspected Vibrio vulnificus infection because the patient's underlying disease was cirrhosis and the course extremely rapid. No microbe had been detected at death. We extracted DNA from a blood culture bottle. SYBR green I real-time PCR was conducted but could not detect V. vulnificus vvh in the DNA sample. Aeromonas hydrophila was cultured and identified in blood and necrotized tissue samples. Real-time PCR was conducted to detect A. hydrophila ahh1, AHCYTOEN and aerA in the DNA sample extracted from the blood culture bottle and an isolated necrotized tissue strain, but only ahh1 was positive. High-mortality in necrotizing soft tissue infections makes it is crucial to quickly detect V. vulnificus and A. hydrophila. We found real-time PCR for vvh, ahh1, AHCYTOEN, and aerA useful in detecting V. vulnificus and A. hydrophila in necrotizing soft tissue infections.
Buelow, Daelynn; Sun, Yilun; Tang, Li; Gu, Zhengming; Pounds, Stanley; Hayden, Randall
2016-07-01
Monitoring of Epstein-Barr virus (EBV) load in immunocompromised patients has become integral to their care. An increasing number of reagents are available for quantitative detection of EBV; however, there are little published comparative data. Four real-time PCR systems (one using laboratory-developed reagents and three using analyte-specific reagents) were compared with one another for detection of EBV from whole blood. Whole blood specimens seeded with EBV were used to determine quantitative linearity, analytical measurement range, lower limit of detection, and CV for each assay. Retrospective testing of 198 clinical samples was performed in parallel with all methods; results were compared to determine relative quantitative and qualitative performance. All assays showed similar performance. No significant difference was found in limit of detection (3.12-3.49 log10 copies/mL; P = 0.37). A strong qualitative correlation was seen with all assays that used clinical samples (positive detection rates of 89.5%-95.8%). Quantitative correlation of clinical samples across assays was also seen in pairwise regression analysis, with R(2) ranging from 0.83 to 0.95. Normalizing clinical sample results to IU/mL did not alter the quantitative correlation between assays. Quantitative EBV detection by real-time PCR can be performed over a wide linear dynamic range, using three different commercially available reagents and laboratory-developed methods. EBV was detected with comparable sensitivity and quantitative correlation for all assays. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.
Biris, Alexandru S.; Galanzha, Ekaterina I.; Li, Zhongrui; Mahmood, Meena; Xu, Yang; Zharov, Vladimir P.
2009-03-01
Nanoparticles are intensively being explored as contrast agents for medical diagnostics and therapies using various optical methods. We present the first demonstration of the use of time-resolved Raman spectroscopy for in vivo real-time detection of circulating carbon nanotubes (CNTs) or cancer cells labeled with CNTs in the lymph, blood, and tissues of live animals with fast spectral acquisition times of down to few milliseconds. After intravenously administering CNTs in the tail vein of the rat, this technique provides the ability to detect the circulation of CNTs in the blood microvessels of the intact rat ear. The capability of Raman spectroscopy is also demonstrated to monitor, identify, and image the CNTs during their transportation by lymphatics in the rat ear and mesentery. The strong and specific Raman scattering properties of CNTs make it possible to detect in vitro and in vivo single cancer cells (HeLa) tagged with CNTs. In vivo Raman flow cytometry opens a new avenue for multiparameter analysis of circulating nanoparticles with strong Raman scattering properties and their pharmokinetics in blood and lymph systems. Moreover, this technology has the potential for molecular detection and identification of circulating tumor cells, and infections labeled with CNTs.
Detection of 12 respiratory viruses by duplex real time PCR assays in respiratory samples.
Arvia, Rosaria; Corcioli, Fabiana; Ciccone, Nunziata; Della Malva, Nunzia; Azzi, Alberta
2015-12-01
Different viruses can be responsible for similar clinical manifestations of respiratory infections. Thus, the etiological diagnosis of respiratory viral diseases requires the detection of a large number of viruses. In this study, 6 duplex real-time PCR assays, using EvaGreen intercalating dye, were developed to detect 12 major viruses responsible for respiratory diseases: influenza A and B viruses, enteroviruses (including enterovirus spp, and rhinovirus spp), respiratory syncytial virus, human metapneumovirus, coronaviruses group I (of which CoV 229E and CoV NL63 are part) and II (including CoV OC43 and CoV HKU1), parainfluenza viruses type 1, 2, 3 and 4, human adenoviruses and human bocaviruses. The 2 target viruses of each duplex reaction were distinguishable by the melting temperatures of their amplicons. The 6 duplex real time PCR assays were applied for diagnostic purpose on 202 respiratory samples from 157 patients. One hundred fifty-seven samples were throat swabs and 45 were bronchoalveolar lavages. The results of the duplex PCR assays were confirmed by comparison with a commercial, validated, assay; in addition, the positive results were confirmed by sequencing. The analytical sensitivity of the duplex PCR assays varied from 10(3) copies/ml to 10(4) copies/ml. For parainfluenza virus 2 only it was 10(5) copies/ml. Seventy clinical samples (35%) from 55 patients (30 children and 25 adults) were positive for 1 or more viruses. In adult patients, influenza A virus was the most frequently detected respiratory virus followed by rhinoviruses. In contrast, respiratory syncytial virus was the most common virus in children, followed by enteroviruses, influenza A virus and coronavirus NL63. The small number of samples/patients does not allow us to draw any epidemiological conclusion. Altogether, the results of this study indicate that the 6 duplex PCR assays described in this study are sensitive, specific and cost-effective. Thus, this assay could be
Deep neural networks to enable real-time multimessenger astrophysics
George, Daniel; Huerta, E. A.
2018-02-01
Gravitational wave astronomy has set in motion a scientific revolution. To further enhance the science reach of this emergent field of research, there is a pressing need to increase the depth and speed of the algorithms used to enable these ground-breaking discoveries. We introduce Deep Filtering—a new scalable machine learning method for end-to-end time-series signal processing. Deep Filtering is based on deep learning with two deep convolutional neural networks, which are designed for classification and regression, to detect gravitational wave signals in highly noisy time-series data streams and also estimate the parameters of their sources in real time. Acknowledging that some of the most sensitive algorithms for the detection of gravitational waves are based on implementations of matched filtering, and that a matched filter is the optimal linear filter in Gaussian noise, the application of Deep Filtering using whitened signals in Gaussian noise is investigated in this foundational article. The results indicate that Deep Filtering outperforms conventional machine learning techniques, achieves similar performance compared to matched filtering, while being several orders of magnitude faster, allowing real-time signal processing with minimal resources. Furthermore, we demonstrate that Deep Filtering can detect and characterize waveform signals emitted from new classes of eccentric or spin-precessing binary black holes, even when trained with data sets of only quasicircular binary black hole waveforms. The results presented in this article, and the recent use of deep neural networks for the identification of optical transients in telescope data, suggests that deep learning can facilitate real-time searches of gravitational wave sources and their electromagnetic and astroparticle counterparts. In the subsequent article, the framework introduced herein is directly applied to identify and characterize gravitational wave events in real LIGO data.
Novel methods for real-time 3D facial recognition
Rodrigues, Marcos; Robinson, Alan
2010-01-01
In this paper we discuss our approach to real-time 3D face recognition. We argue the need for real time operation in a realistic scenario and highlight the required pre- and post-processing operations for effective 3D facial recognition. We focus attention to some operations including face and eye detection, and fast post-processing operations such as hole filling, mesh smoothing and noise removal. We consider strategies for hole filling such as bilinear and polynomial interpolation and Lapla...
On-line diagnostics for a real time system
International Nuclear Information System (INIS)
Sreenivasan, P.
1976-01-01
The purpose of an on-line diagnostics is to infuse the ability of self diagnosing in an online computer to enhance its dependability in a real time system. Such a diagnostics evolved for the CDPS of the Fast Breeder Test Reactor at Kalpakkam is reported. The two phases of the diagnostics, i.e., the malfunction detection and post detection action are described in some detail. (A.K.)
Management of threatened abortion with real-time sonography.
Anderson, S G
1980-02-01
Real-time sonography was used to evaluate 158 patients with threatened abortion. Fetal motion was first detected during the seventh gestational week and with increasing frequency thereafter in 73 patients with viable pregnancies continuing to term. Only 2 of 65 patients who aborted demonstrated fetal motion. The presence or absence of fetal motion was most reliable after 7 weeks' gestation for establishing a prognosis for a given pregnancy. Seventy-two of 74 pregnancies with fetal motion continued to term, whereas 63 of 64 pregnancies without fetal motion aborted. A method for using real-time sonography in the management of threatened abortion is presented.
Khandelwal, Siddhartha; Wickstrom, Nicholas
2016-12-01
Detecting gait events is the key to many gait analysis applications that would benefit from continuous monitoring or long-term analysis. Most gait event detection algorithms using wearable sensors that offer a potential for use in daily living have been developed from data collected in controlled indoor experiments. However, for real-word applications, it is essential that the analysis is carried out in humans' natural environment; that involves different gait speeds, changing walking terrains, varying surface inclinations and regular turns among other factors. Existing domain knowledge in the form of principles or underlying fundamental gait relationships can be utilized to drive and support the data analysis in order to develop robust algorithms that can tackle real-world challenges in gait analysis. This paper presents a novel approach that exhibits how domain knowledge about human gait can be incorporated into time-frequency analysis to detect gait events from long-term accelerometer signals. The accuracy and robustness of the proposed algorithm are validated by experiments done in indoor and outdoor environments with approximately 93 600 gait events in total. The proposed algorithm exhibits consistently high performance scores across all datasets in both, indoor and outdoor environments.
Directory of Open Access Journals (Sweden)
Natividad-Sancho Angels
2005-08-01
Full Text Available Abstract Background Herpes Simplex Virus (HSV Genital Ulcer Disease (GUD is an important public health problem, whose interaction with HIV results in mutually enhancing epidemics. Conventional methods for detecting HSV tend to be slow and insensitive. We designed a rapid PCR-based assay to quantify and type HSV in cervicovaginal lavage (CVL fluid of subjects attending a Genito-Urinary Medicine (GUM clinic. Vaginal swabs, CVL fluid and venous blood were collected. Quantitative detection of HSV was conducted using real time PCR with HSV specific primers and SYBR Green I. Fluorogenic TaqMan Minor Groove Binder (MGB probes designed around a single base mismatch in the HSV DNA polymerase I gene were used to type HSV in a separate reaction. The Kalon test was used to detect anti-HSV-2 IgG antibodies in serum. Testing for HIV, other Sexually Transmitted Infections (STI and related infections was based on standard clinical and laboratory methods. Results Seventy consecutive GUM clinic attendees were studied. Twenty-seven subjects (39% had detectable HSV DNA in CVL fluid; HSV-2 alone was detected in 19 (70% subjects, HSV-1 alone was detected in 4 (15% subjects and both HSV types were detected in 4 (15% subjects. Eleven out of 27 subjects (41% with anti-HSV-2 IgG had detectable HSV-2 DNA in CVL fluid. Seven subjects (10% were HIV-positive. Three of seven (43% HIV-infected subjects and two of five subjects with GUD (40% were secreting HSV-2. None of the subjects in whom HSV-1 was detected had GUD. Conclusion Quantitative real-time PCR and Taqman MGB probes specific for HSV-1 or -2 were used to develop an assay for quantification and typing of HSV. The majority of subjects in which HSV was detected had low levels of CVL fluid HSV, with no detectable HSV-2 antibodies and were asymptomatic.