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Sample records for advanced detection isolation

  1. Advanced detection, isolation, and accommodation of sensor failures in turbofan engines: Real-time microcomputer implementation

    NASA Technical Reports Server (NTRS)

    Delaat, John C.; Merrill, Walter C.

    1990-01-01

    The objective of the Advanced Detection, Isolation, and Accommodation Program is to improve the overall demonstrated reliability of digital electronic control systems for turbine engines. For this purpose, an algorithm was developed which detects, isolates, and accommodates sensor failures by using analytical redundancy. The performance of this algorithm was evaluated on a real time engine simulation and was demonstrated on a full scale F100 turbofan engine. The real time implementation of the algorithm is described. The implementation used state-of-the-art microprocessor hardware and software, including parallel processing and high order language programming.

  2. Operations management system advanced automation: Fault detection isolation and recovery prototyping

    NASA Technical Reports Server (NTRS)

    Hanson, Matt

    1990-01-01

    The purpose of this project is to address the global fault detection, isolation and recovery (FDIR) requirements for Operation's Management System (OMS) automation within the Space Station Freedom program. This shall be accomplished by developing a selected FDIR prototype for the Space Station Freedom distributed processing systems. The prototype shall be based on advanced automation methodologies in addition to traditional software methods to meet the requirements for automation. A secondary objective is to expand the scope of the prototyping to encompass multiple aspects of station-wide fault management (SWFM) as discussed in OMS requirements documentation.

  3. A real-time implementation of an advanced sensor failure detection, isolation, and accommodation algorithm

    NASA Technical Reports Server (NTRS)

    Delaat, J. C.; Merrill, W. C.

    1983-01-01

    A sensor failure detection, isolation, and accommodation algorithm was developed which incorporates analytic sensor redundancy through software. This algorithm was implemented in a high level language on a microprocessor based controls computer. Parallel processing and state-of-the-art 16-bit microprocessors are used along with efficient programming practices to achieve real-time operation.

  4. Visual and efficient immunosensor technique for advancing biomedical applications of quantum dots on Salmonella detection and isolation

    NASA Astrophysics Data System (ADS)

    Tang, Feng; Pang, Dai-Wen; Chen, Zhi; Shao, Jian-Bo; Xiong, Ling-Hong; Xiang, Yan-Ping; Xiong, Yan; Wu, Kai; Ai, Hong-Wu; Zhang, Hui; Zheng, Xiao-Li; Lv, Jing-Rui; Liu, Wei-Yong; Hu, Hong-Bing; Mei, Hong; Zhang, Zhen; Sun, Hong; Xiang, Yun; Sun, Zi-Yong

    2016-02-01

    It is a great challenge in nanotechnology for fluorescent nanobioprobes to be applied to visually detect and directly isolate pathogens in situ. A novel and visual immunosensor technique for efficient detection and isolation of Salmonella was established here by applying fluorescent nanobioprobes on a specially-designed cellulose-based swab (a solid-phase enrichment system). The selective and chromogenic medium used on this swab can achieve the ultrasensitive amplification of target bacteria and form chromogenic colonies in situ based on a simple biochemical reaction. More importantly, because this swab can serve as an attachment site for the targeted pathogens to immobilize and immunologically capture nanobioprobes, our mAb-conjugated QD bioprobes were successfully applied on the solid-phase enrichment system to capture the fluorescence of targeted colonies under a designed excitation light instrument based on blue light-emitting diodes combined with stereomicroscopy or laser scanning confocal microscopy. Compared with the traditional methods using 4-7 days to isolate Salmonella from the bacterial mixture, this method took only 2 days to do this, and the process of initial screening and preliminary diagnosis can be completed in only one and a half days. Furthermore, the limit of detection can reach as low as 101 cells per mL Salmonella on the background of 105 cells per mL non-Salmonella (Escherichia coli, Proteus mirabilis or Citrobacter freundii, respectively) in experimental samples, and even in human anal ones. The visual and efficient immunosensor technique may be proved to be a favorable alternative for screening and isolating Salmonella in a large number of samples related to public health surveillance.It is a great challenge in nanotechnology for fluorescent nanobioprobes to be applied to visually detect and directly isolate pathogens in situ. A novel and visual immunosensor technique for efficient detection and isolation of Salmonella was established here

  5. Visual and efficient immunosensor technique for advancing biomedical applications of quantum dots on Salmonella detection and isolation.

    PubMed

    Tang, Feng; Pang, Dai-Wen; Chen, Zhi; Shao, Jian-Bo; Xiong, Ling-Hong; Xiang, Yan-Ping; Xiong, Yan; Wu, Kai; Ai, Hong-Wu; Zhang, Hui; Zheng, Xiao-Li; Lv, Jing-Rui; Liu, Wei-Yong; Hu, Hong-Bing; Mei, Hong; Zhang, Zhen; Sun, Hong; Xiang, Yun; Sun, Zi-Yong

    2016-02-28

    It is a great challenge in nanotechnology for fluorescent nanobioprobes to be applied to visually detect and directly isolate pathogens in situ. A novel and visual immunosensor technique for efficient detection and isolation of Salmonella was established here by applying fluorescent nanobioprobes on a specially-designed cellulose-based swab (a solid-phase enrichment system). The selective and chromogenic medium used on this swab can achieve the ultrasensitive amplification of target bacteria and form chromogenic colonies in situ based on a simple biochemical reaction. More importantly, because this swab can serve as an attachment site for the targeted pathogens to immobilize and immunologically capture nanobioprobes, our mAb-conjugated QD bioprobes were successfully applied on the solid-phase enrichment system to capture the fluorescence of targeted colonies under a designed excitation light instrument based on blue light-emitting diodes combined with stereomicroscopy or laser scanning confocal microscopy. Compared with the traditional methods using 4-7 days to isolate Salmonella from the bacterial mixture, this method took only 2 days to do this, and the process of initial screening and preliminary diagnosis can be completed in only one and a half days. Furthermore, the limit of detection can reach as low as 10(1) cells per mL Salmonella on the background of 10(5) cells per mL non-Salmonella (Escherichia coli, Proteus mirabilis or Citrobacter freundii, respectively) in experimental samples, and even in human anal ones. The visual and efficient immunosensor technique may be proved to be a favorable alternative for screening and isolating Salmonella in a large number of samples related to public health surveillance. PMID:26853517

  6. Advanced Technology for Isolating Payloads in Microgravity

    NASA Technical Reports Server (NTRS)

    Alhorn, Dean C.

    1997-01-01

    advances in isolation technology for that particular component. The final section presents some concluding thoughts and a summary of anticipated advances in research and development for isolating microgravity experiments.

  7. Fault Detection and Isolation for Hydraulic Control

    NASA Technical Reports Server (NTRS)

    1987-01-01

    Pressure sensors and isolation valves act to shut down defective servochannel. Redundant hydraulic system indirectly senses failure in any of its electrical control channels and mechanically isolates hydraulic channel controlled by faulty electrical channel so flat it cannot participate in operating system. With failure-detection and isolation technique, system can sustains two failed channels and still functions at full performance levels. Scheme useful on aircraft or other systems with hydraulic servovalves where failure cannot be tolerated.

  8. Advancing Explosives Detection Capabilities: Vapor Detection

    ScienceCinema

    Atkinson, David

    2016-07-12

    A new, PNNL-developed method provides direct, real-time detection of trace amounts of explosives such as RDX, PETN and C-4. The method selectively ionizes a sample before passing the sample through a mass spectrometer to detect explosive vapors. The method could be used at airports to improve aviation security.

  9. Advancing Explosives Detection Capabilities: Vapor Detection

    SciTech Connect

    Atkinson, David

    2012-10-15

    A new, PNNL-developed method provides direct, real-time detection of trace amounts of explosives such as RDX, PETN and C-4. The method selectively ionizes a sample before passing the sample through a mass spectrometer to detect explosive vapors. The method could be used at airports to improve aviation security.

  10. Recent advances in nonlinear passive vibration isolators

    NASA Astrophysics Data System (ADS)

    Ibrahim, R. A.

    2008-07-01

    The theory of nonlinear vibration isolation has witnessed significant developments due to pressing demands for the protection of structural installations, nuclear reactors, mechanical components, and sensitive instruments from earthquake ground motion, shocks, and impact loads. In view of these demands, engineers and physicists have developed different types of nonlinear vibration isolators. This article presents a comprehensive assessment of recent developments of nonlinear isolators in the absence of active control means. It does not deal with other means of linear or nonlinear vibration absorbers. It begins with the basic concept and features of nonlinear isolators and inherent nonlinear phenomena. Specific types of nonlinear isolators are then discussed, including ultra-low-frequency isolators. For vertical vibration isolation, the treatment of the Euler spring isolator is based on the post-buckling dynamic characteristics of the column elastica and axial stiffness. Exact and approximate analyses of axial stiffness of the post-buckled Euler beam are outlined. Different techniques of reducing the resonant frequency of the isolator are described. Another group is based on the Gospodnetic-Frisch-Fay beam, which is free to slide on two supports. The restoring force of this beam resembles to a great extent the restoring roll moment of biased ships. The base isolation of buildings, bridges, and liquid storage tanks subjected to earthquake ground motion is then described. Base isolation utilizes friction elements, laminated-rubber bearings, and the friction pendulum. Nonlinear viscoelastic and composite material springs, and smart material elements are described in terms of material mechanical characteristics and the dependence of their transmissibility on temperature and excitation amplitude. The article is closed by conclusions, which highlight resolved and unresolved problems and recommendations for future research directions.

  11. AIDE - Advanced Intrusion Detection Environment

    SciTech Connect

    Smith, Cathy L.

    2013-04-28

    Would you like to know when someone has dropped an undesirable executable binary on our system? What about something less malicious such as a software installation by a user? What about the user who decides to install a newer version of mod_perl or PHP on your web server without letting you know beforehand? Or even something as simple as when an undocumented config file change is made by another member of the admin group? Do you even want to know about all the changes that happen on a daily basis on your server? The purpose of an intrusion detection system (IDS) is to detect unauthorized, possibly malicious activity. The purpose of a host-based IDS, or file integrity checker, is check for unauthorized changes to key system files, binaries, libraries, and directories on the system. AIDE is an Open Source file and directory integrity checker. AIDE will let you know when a file or directory has been added, deleted, modified. It is included with the Red Hat Enterprise 6. It is available for other Linux distros. This is a case study describing the process of configuring AIDE on an out of the box RHEL6 installation. Its goal is to illustrate the thinking and the process by which a useful AIDE configuration is built.

  12. Reference-free detection of isolated SNPs

    PubMed Central

    Uricaru, Raluca; Rizk, Guillaume; Lacroix, Vincent; Quillery, Elsa; Plantard, Olivier; Chikhi, Rayan; Lemaitre, Claire; Peterlongo, Pierre

    2015-01-01

    Detecting single nucleotide polymorphisms (SNPs) between genomes is becoming a routine task with next-generation sequencing. Generally, SNP detection methods use a reference genome. As non-model organisms are increasingly investigated, the need for reference-free methods has been amplified. Most of the existing reference-free methods have fundamental limitations: they can only call SNPs between exactly two datasets, and/or they require a prohibitive amount of computational resources. The method we propose, discoSnp, detects both heterozygous and homozygous isolated SNPs from any number of read datasets, without a reference genome, and with very low memory and time footprints (billions of reads can be analyzed with a standard desktop computer). To facilitate downstream genotyping analyses, discoSnp ranks predictions and outputs quality and coverage per allele. Compared to finding isolated SNPs using a state-of-the-art assembly and mapping approach, discoSnp requires significantly less computational resources, shows similar precision/recall values, and highly ranked predictions are less likely to be false positives. An experimental validation was conducted on an arthropod species (the tick Ixodes ricinus) on which de novo sequencing was performed. Among the predicted SNPs that were tested, 96% were successfully genotyped and truly exhibited polymorphism. PMID:25404127

  13. Advanced Atmospheric Water Vapor DIAL Detection System

    NASA Technical Reports Server (NTRS)

    Refaat, Tamer F.; Elsayed-Ali, Hani E.; DeYoung, Russell J. (Technical Monitor)

    2000-01-01

    Measurement of atmospheric water vapor is very important for understanding the Earth's climate and water cycle. The remote sensing Differential Absorption Lidar (DIAL) technique is a powerful method to perform such measurement from aircraft and space. This thesis describes a new advanced detection system, which incorporates major improvements regarding sensitivity and size. These improvements include a low noise advanced avalanche photodiode detector, a custom analog circuit, a 14-bit digitizer, a microcontroller for on board averaging and finally a fast computer interface. This thesis describes the design and validation of this new water vapor DIAL detection system which was integrated onto a small Printed Circuit Board (PCB) with minimal weight and power consumption. Comparing its measurements to an existing DIAL system for aerosol and water vapor profiling validated the detection system.

  14. An advanced ISOL facility based on ATLAS.

    SciTech Connect

    Nolen, J. A.

    1999-02-24

    The Argonne concept for an accelerator complex for efficiently producing high-quality radioactive beams from ion source energy up to 6-15 MeV/u is described. The Isotope-Separator-On-Line (ISOL) method is used. A high-power driver accelerator produces radionuclides in a target that is closely coupled to an ion source and mass separator. By using a driver accelerator which can deliver a variety of beams and energies the radionuclide production mechanisms can be chosen to optimize yields for the species of interest. To effectively utilize the high beam power of the driver two-step target/ion source geometries are proposed (1) Neutron production with intermediate energy deuterons on a primary target to produce neutron-rich fission products in a secondary {sup 238}U target, and (2) Fragmentation of neutron-rich heavy ion rich fission products in a secondary beams such as {sup 18}O in a target/catcher geometry. Heavy ion beams with total energies in the 1-10 GcV range are also available for radionuclide production via high-energy spallation reactions. At the present time R and D is in progress to develop superconducting resonator structures for a driver linac to cover the energy range up to 100 MeV per nucleon for heavy ions and 200 MeV for protons. The post accelerator scheme is based on using existing ISOL-type 1+ ion source technology followed by CW Radio Frequency Quadruple (RFQ) accelerators and superconducting linacs including the present ATLAS accelerator. A full-scale prototype of the first-stage RFQ has been successfully tested with RF at full design voltage and tests with ion beams are in progress. A benchmark beam, {sup 132}Sn {at} 7 MeV/u, requires two stripping stages, one a gas stripper at very low velocity after the first RFQ section, and one a foil stripper at higher velocity after a superconducting-linac injector.

  15. Advances in noninvasive detection of CAD

    SciTech Connect

    Kahn, J.K. )

    1991-04-01

    Advances in the noninvasive detection of myocardial ischemia are increasing our ability to diagnose coronary artery disease (CAD). Tomographic (SPECT) thallium imaging provides better identification of coronary arteries with atherosclerotic narrowing. Increased lung thallium uptake and transient ischemic dilatation of the heart are additional markers of severe CAD. Late thallium imaging, as well as reinjection imaging, provides more accurate identification of myocardial ischemia. Finally, new myocardial imaging agents, such as technetium Tc 99m sestamibi (Cardiolite), should improve detection of CAD by noninvasive methods.10 references.

  16. Advanced technologies for perimeter intrusion detection sensors

    SciTech Connect

    Williams, J.D.

    1995-03-01

    The development of integrated circuit fabrication techniques and the resulting devices have contributed more to the advancement of exterior intrusion detectors and alarm assessment devices than any other technology. The availability of this technology has led to the improvements in and further development of smaller more powerful computers, microprocessors, solid state memories, solid state cameras, thermal imagers, low-power lasers, and shorter pulse width and higher frequency electronic circuitry. This paper presents information on planning a perimeter intrusion detection system, identifies the site characteristics that affect its performance, and describes improvements to perimeter intrusion detection sensors and assessment devices that have been achieved by using integrated circuit technology.

  17. Advanced endoscopic imaging to improve adenoma detection

    PubMed Central

    Neumann, Helmut; Nägel, Andreas; Buda, Andrea

    2015-01-01

    Advanced endoscopic imaging is revolutionizing our way on how to diagnose and treat colorectal lesions. Within recent years a variety of modern endoscopic imaging techniques was introduced to improve adenoma detection rates. Those include high-definition imaging, dye-less chromoendoscopy techniques and novel, highly flexible endoscopes, some of them equipped with balloons or multiple lenses in order to improve adenoma detection rates. In this review we will focus on the newest developments in the field of colonoscopic imaging to improve adenoma detection rates. Described techniques include high-definition imaging, optical chromoendoscopy techniques, virtual chromoendoscopy techniques, the Third Eye Retroscope and other retroviewing devices, the G-EYE endoscope and the Full Spectrum Endoscopy-system. PMID:25789092

  18. Advanced glycation end-products inhibitors isolated from Schisandra grandiflora.

    PubMed

    Poornima, B; Kumar, D Anand; Siva, Bandi; Venkanna, A; Vadaparthi, P R Rao; Kumar, K; Tiwari, Ashok K; Babu, K Suresh

    2016-01-01

    Free radicals scavenging and advanced glycation end-products (AGEs) inhibitory potentials in crude chloroform extract of Schisandra grandiflora were evaluated. Bioassay-guided isolation of the chloroform extract led to the identification of 24 compounds. Among the isolates, ( ± ) gomisin M1, arisantetralone C and D, macelignan, saurulignan B and SZ-MO displayed potent-free radical scavenging as well as AGEs inhibitory potentials. This is the first report identifying the presence of AGEs inhibitory activity and assigning AGEs inhibitory activity to these compounds. Therefore, our research finds new application of traditional medicinal plant S. grandiflora having capacity to reduce formation and accumulation of AGEs in diabetes.

  19. Isolation and analysis of ginseng: advances and challenges

    PubMed Central

    Wang, Chong-Zhi

    2011-01-01

    Ginseng occupies a prominent position in the list of best-selling natural products in the world. Because of its complex constituents, multidisciplinary techniques are needed to validate the analytical methods that support ginseng’s use worldwide. In the past decade, rapid development of technology has advanced many aspects of ginseng research. The aim of this review is to illustrate the recent advances in the isolation and analysis of ginseng, and to highlight their new applications and challenges. Emphasis is placed on recent trends and emerging techniques. The current article reviews the literature between January 2000 and September 2010. PMID:21258738

  20. Selection of advanced technologies for detection of trucks

    NASA Astrophysics Data System (ADS)

    Middleton, Dan

    1998-01-01

    The North American Free Trade Agreement is anticipated an already increasing trend in highway freight movement across the international border between Texas and Mexico. The Texas Department of Transportation is concerned about safeguarding its motoring public and protection of its highway infrastructure. By sponsoring this research, it hopes to improve traffic signal operations, especially at isolated intersections. Recent advances in sensing technologies and signalization enable safer and more efficient intersection control. This research evaluated advanced detection technologies that can be used to increase green time to trucks and reduce their stops and delays. Equipment selection criteria required devices that were reasonably accurate in classification of vehicles under all weather and lighting conditions and determination of vehicle speeds. The research team selected active IR and passive acoustic technologies. Components of the detection system include: an Industrial PC, proprietary boards inside the computer, IR and acoustic detectors, a pole for mounting the selected systems, and a classifier system using pavement sensors for verification purposes. The purpose of the node computer was to interpret signals from detectors, store data, and communicate with the controller cabinet upon detection of a truck.

  1. Robust Fault Detection and Isolation for Stochastic Systems

    NASA Technical Reports Server (NTRS)

    George, Jemin; Gregory, Irene M.

    2010-01-01

    This paper outlines the formulation of a robust fault detection and isolation scheme that can precisely detect and isolate simultaneous actuator and sensor faults for uncertain linear stochastic systems. The given robust fault detection scheme based on the discontinuous robust observer approach would be able to distinguish between model uncertainties and actuator failures and therefore eliminate the problem of false alarms. Since the proposed approach involves precise reconstruction of sensor faults, it can also be used for sensor fault identification and the reconstruction of true outputs from faulty sensor outputs. Simulation results presented here validate the effectiveness of the robust fault detection and isolation system.

  2. Robust detection, isolation and accommodation for sensor failures

    NASA Technical Reports Server (NTRS)

    Emami-Naeini, A.; Akhter, M. M.; Rock, S. M.

    1986-01-01

    The objective is to extend the recent advances in robust control system design of multivariable systems to sensor failure detection, isolation, and accommodation (DIA), and estimator design. This effort provides analysis tools to quantify the trade-off between performance robustness and DIA sensitivity, which are to be used to achieve higher levels of performance robustness for given levels of DIA sensitivity. An innovations-based DIA scheme is used. Estimators, which depend upon a model of the process and process inputs and outputs, are used to generate these innovations. Thresholds used to determine failure detection are computed based on bounds on modeling errors, noise properties, and the class of failures. The applicability of the newly developed tools are demonstrated on a multivariable aircraft turbojet engine example. A new concept call the threshold selector was developed. It represents a significant and innovative tool for the analysis and synthesis of DiA algorithms. The estimators were made robust by introduction of an internal model and by frequency shaping. The internal mode provides asymptotically unbiased filter estimates.The incorporation of frequency shaping of the Linear Quadratic Gaussian cost functional modifies the estimator design to make it suitable for sensor failure DIA. The results are compared with previous studies which used thresholds that were selcted empirically. Comparison of these two techniques on a nonlinear dynamic engine simulation shows improved performance of the new method compared to previous techniques

  3. Recent advances in microfluidic detection systems

    PubMed Central

    Baker, Christopher A; Duong, Cindy T; Grimley, Alix; Roper, Michael G

    2009-01-01

    There are numerous detection methods available for methods are being put to use for detection on these miniaturized systems, with the analyte of interest driving the choice of detection method. In this article, we summarize microfluidic 2 years. More focus is given to unconventional approaches to detection routes and novel strategies for performing high-sensitivity detection. PMID:20414455

  4. A highly selective fluorescent probe for direct detection and isolation of mouse embryonic stem cells.

    PubMed

    Chandran, Yogeswari; Kang, Nam-Young; Park, Sung-Jin; Alamudi, Samira Husen; Kim, Jun-Young; Sahu, Srikanta; Su, Dongdong; Lee, Jungyeol; Vendrell, Marc; Chang, Young-Tae

    2015-11-01

    Stem cell research has gathered immense attention in the past decade due to the remarkable ability of stem cells for self-renewal and tissue-specific differentiation. Despite having numerous advancements in stem cell isolation and manipulation techniques, there is a need for highly reliable probes for the specific detection of live stem cells. Herein we developed a new fluorescence probe (CDy9) with high selectivity for mouse embryonic stem cells. CDy9 allows the detection and isolation of intact stem cells with marginal impact on their function and capabilities. PMID:26115574

  5. ADVANCED SEISMIC BASE ISOLATION METHODS FOR MODULAR REACTORS

    SciTech Connect

    E. Blanford; E. Keldrauk; M. Laufer; M. Mieler; J. Wei; B. Stojadinovic; P.F. Peterson

    2010-09-20

    Advanced technologies for structural design and construction have the potential for major impact not only on nuclear power plant construction time and cost, but also on the design process and on the safety, security and reliability of next generation of nuclear power plants. In future Generation IV (Gen IV) reactors, structural and seismic design should be much more closely integrated with the design of nuclear and industrial safety systems, physical security systems, and international safeguards systems. Overall reliability will be increased, through the use of replaceable and modular equipment, and through design to facilitate on-line monitoring, in-service inspection, maintenance, replacement, and decommissioning. Economics will also receive high design priority, through integrated engineering efforts to optimize building arrangements to minimize building heights and footprints. Finally, the licensing approach will be transformed by becoming increasingly performance based and technology neutral, using best-estimate simulation methods with uncertainty and margin quantification. In this context, two structural engineering technologies, seismic base isolation and modular steel-plate/concrete composite structural walls, are investigated. These technologies have major potential to (1) enable standardized reactor designs to be deployed across a wider range of sites, (2) reduce the impact of uncertainties related to site-specific seismic conditions, and (3) alleviate reactor equipment qualification requirements. For Gen IV reactors the potential for deliberate crashes of large aircraft must also be considered in design. This report concludes that base-isolated structures should be decoupled from the reactor external event exclusion system. As an example, a scoping analysis is performed for a rectangular, decoupled external event shell designed as a grillage. This report also reviews modular construction technology, particularly steel-plate/concrete construction using

  6. Artificial-neural-network-based failure detection and isolation

    NASA Astrophysics Data System (ADS)

    Sadok, Mokhtar; Gharsalli, Imed; Alouani, Ali T.

    1998-03-01

    This paper presents the design of a systematic failure detection and isolation system that uses the concept of failure sensitive variables (FSV) and artificial neural networks (ANN). The proposed approach was applied to tube leak detection in a utility boiler system. Results of the experimental testing are presented in the paper.

  7. Robust fault detection and isolation in stochastic systems

    NASA Astrophysics Data System (ADS)

    George, Jemin

    2012-07-01

    This article outlines the formulation of a robust fault detection and isolation (FDI) scheme that can precisely detect and isolate simultaneous actuator and sensor faults for uncertain linear stochastic systems. The given robust fault detection scheme based on the discontinuous robust observer approach would be able to distinguish between model uncertainties and actuator failures and therefore eliminate the problem of false alarms. Since the proposed approach involves estimating sensor faults, it can also be used for sensor fault identification and the reconstruction of true outputs from faulty sensor outputs. Simulation results presented here validate the effectiveness of the proposed robust FDI system.

  8. Recent advances in biosensor based endotoxin detection.

    PubMed

    Das, A P; Kumar, P S; Swain, S

    2014-01-15

    Endotoxins also referred to as pyrogens are chemically lipopolysaccharides habitually found in food, environment and clinical products of bacterial origin and are unavoidable ubiquitous microbiological contaminants. Pernicious issues of its contamination result in high mortality and severe morbidities. Standard traditional techniques are slow and cumbersome, highlighting the pressing need for evoking agile endotoxin detection system. The early and prompt detection of endotoxin assumes prime importance in health care, pharmacological and biomedical sectors. The unparalleled recognition abilities of LAL biosensors perched with remarkable sensitivity, high stability and reproducibility have bestowed it with persistent reliability and their possible fabrication for commercial applicability. This review paper entails an overview of various trends in current techniques available and other possible alternatives in biosensor based endotoxin detection together with its classification, epidemiological aspects, thrust areas demanding endotoxin control, commercially available detection sensors and a revolutionary unprecedented approach narrating the influence of omics for endotoxin detection. PMID:23934306

  9. Recent advances in biosensor based endotoxin detection.

    PubMed

    Das, A P; Kumar, P S; Swain, S

    2014-01-15

    Endotoxins also referred to as pyrogens are chemically lipopolysaccharides habitually found in food, environment and clinical products of bacterial origin and are unavoidable ubiquitous microbiological contaminants. Pernicious issues of its contamination result in high mortality and severe morbidities. Standard traditional techniques are slow and cumbersome, highlighting the pressing need for evoking agile endotoxin detection system. The early and prompt detection of endotoxin assumes prime importance in health care, pharmacological and biomedical sectors. The unparalleled recognition abilities of LAL biosensors perched with remarkable sensitivity, high stability and reproducibility have bestowed it with persistent reliability and their possible fabrication for commercial applicability. This review paper entails an overview of various trends in current techniques available and other possible alternatives in biosensor based endotoxin detection together with its classification, epidemiological aspects, thrust areas demanding endotoxin control, commercially available detection sensors and a revolutionary unprecedented approach narrating the influence of omics for endotoxin detection.

  10. Advances in mechanical detection of magnetic resonance

    PubMed Central

    Kuehn, Seppe; Hickman, Steven A.; Marohn, John A.

    2008-01-01

    The invention and initial demonstration of magnetic resonance force microscopy (MRFM) in the early 1990s launched a renaissance of mechanical approaches to detecting magnetic resonance. This article reviews progress made in MRFM in the last decade, including the demonstration of scanned probe detection of magnetic resonance (electron spin resonance, ferromagnetic resonance, and nuclear magnetic resonance) and the mechanical detection of electron spin resonance from a single spin. Force and force-gradient approaches to mechanical detection are reviewed and recent related work using attonewton sensitivity cantilevers to probe minute fluctuating electric fields near surfaces is discussed. Given recent progress, pushing MRFM to single proton sensitivity remains an exciting possibility. We will survey some practical and fundamental issues that must be resolved to meet this challenge. PMID:18266413

  11. Nanofluidic transport through isolated carbon nanotube channels: Advances, controversies, and challenges

    DOE PAGES

    Guo, Shirui; Meshot, Eric R.; Kuykendall, Tevye; Cabrini, Stefano; Fornasiero, Francesco

    2015-06-02

    Owing to their simple chemistry and structure, controllable geometry, and a plethora of unusual yet exciting transport properties, carbon nanotubes (CNTs) have emerged as exceptional channels for fundamental nanofluidic studies, as well as building blocks for future fluidic devices that can outperform current technology in many applications. Leveraging the unique fluidic properties of CNTs in advanced systems requires a full understanding of their physical origin. Recent advancements in nanofabrication technology enable nanofluidic devices to be built with a single, nanometer-wide CNT as a fluidic pathway. These novel platforms with isolated CNT nanochannels offer distinct advantages for establishing quantitative structure–transport correlationsmore » in comparison with membranes containing many CNT pores. In addition, they are promising components for single-molecule sensors as well as for building nanotube-based circuits wherein fluidics and electronics can be coupled. With such advanced device architecture, molecular and ionic transport can be manipulated with vastly enhanced control for applications in sensing, separation, detection, and therapeutic delivery. Recent achievements in fabricating isolated-CNT nanofluidic platforms are highlighted, along with the most-significant findings each platform enables for water, ion, and molecular transport. Furthermore, the implications of these findings and remaining open questions on the exceptional fluidic properties of CNTs are also discussed.« less

  12. Nanofluidic transport through isolated carbon nanotube channels: Advances, controversies, and challenges

    SciTech Connect

    Guo, Shirui; Meshot, Eric R.; Kuykendall, Tevye; Cabrini, Stefano; Fornasiero, Francesco

    2015-06-02

    Owing to their simple chemistry and structure, controllable geometry, and a plethora of unusual yet exciting transport properties, carbon nanotubes (CNTs) have emerged as exceptional channels for fundamental nanofluidic studies, as well as building blocks for future fluidic devices that can outperform current technology in many applications. Leveraging the unique fluidic properties of CNTs in advanced systems requires a full understanding of their physical origin. Recent advancements in nanofabrication technology enable nanofluidic devices to be built with a single, nanometer-wide CNT as a fluidic pathway. These novel platforms with isolated CNT nanochannels offer distinct advantages for establishing quantitative structure–transport correlations in comparison with membranes containing many CNT pores. In addition, they are promising components for single-molecule sensors as well as for building nanotube-based circuits wherein fluidics and electronics can be coupled. With such advanced device architecture, molecular and ionic transport can be manipulated with vastly enhanced control for applications in sensing, separation, detection, and therapeutic delivery. Recent achievements in fabricating isolated-CNT nanofluidic platforms are highlighted, along with the most-significant findings each platform enables for water, ion, and molecular transport. Furthermore, the implications of these findings and remaining open questions on the exceptional fluidic properties of CNTs are also discussed.

  13. Towards Certification of a Space System Application of Fault Detection and Isolation

    NASA Technical Reports Server (NTRS)

    Feather, Martin S.; Markosian, Lawrence Z.

    2008-01-01

    Advanced fault detection, isolation and recovery (FDIR) software is being investigated at NASA as a means to the improve reliability and availability of its space systems. Certification is a critical step in the acceptance of such software. Its attainment hinges on performing the necessary verification and validation to show that the software will fulfill its requirements in the intended setting. Presented herein is our ongoing work to plan for the certification of a pilot application of advanced FDIR software in a NASA setting. We describe the application, and the key challenges and opportunities it offers for certification.

  14. MPI Runtime Error Detection with MUST: Advances in Deadlock Detection

    DOE PAGES

    Hilbrich, Tobias; Protze, Joachim; Schulz, Martin; de Supinski, Bronis R.; Müller, Matthias S.

    2013-01-01

    The widely used Message Passing Interface (MPI) is complex and rich. As a result, application developers require automated tools to avoid and to detect MPI programming errors. We present the Marmot Umpire Scalable Tool (MUST) that detects such errors with significantly increased scalability. We present improvements to our graph-based deadlock detection approach for MPI, which cover future MPI extensions. Our enhancements also check complex MPI constructs that no previous graph-based detection approach handled correctly. Finally, we present optimizations for the processing of MPI operations that reduce runtime deadlock detection overheads. Existing approaches often require 𝒪( p ) analysis timemore » per MPI operation, for p processes. We empirically observe that our improvements lead to sub-linear or better analysis time per operation for a wide range of real world applications.« less

  15. Advances in Significance Testing for Cluster Detection

    NASA Astrophysics Data System (ADS)

    Coleman, Deidra Andrea

    Over the past two decades, much attention has been given to data driven project goals such as the Human Genome Project and the development of syndromic surveillance systems. A major component of these types of projects is analyzing the abundance of data. Detecting clusters within the data can be beneficial as it can lead to the identification of specified sequences of DNA nucleotides that are related to important biological functions or the locations of epidemics such as disease outbreaks or bioterrorism attacks. Cluster detection techniques require efficient and accurate hypothesis testing procedures. In this dissertation, we improve upon the hypothesis testing procedures for cluster detection by enhancing distributional theory and providing an alternative method for spatial cluster detection using syndromic surveillance data. In Chapter 2, we provide an efficient method to compute the exact distribution of the number and coverage of h-clumps of a collection of words. This method involves defining a Markov chain using a minimal deterministic automaton to reduce the number of states needed for computation. We allow words of the collection to contain other words of the collection making the method more general. We use our method to compute the distributions of the number and coverage of h-clumps in the Chi motif of H. influenza.. In Chapter 3, we provide an efficient algorithm to compute the exact distribution of multiple window discrete scan statistics for higher-order, multi-state Markovian sequences. This algorithm involves defining a Markov chain to efficiently keep track of probabilities needed to compute p-values of the statistic. We use our algorithm to identify cases where the available approximation does not perform well. We also use our algorithm to detect unusual clusters of made free throw shots by National Basketball Association players during the 2009-2010 regular season. In Chapter 4, we give a procedure to detect outbreaks using syndromic

  16. Recent advances in resonant optothermalacoustic detection

    NASA Astrophysics Data System (ADS)

    Doty, James H., III; Kosterev, Anatoliy A.; Tittel, Frank K.

    2011-01-01

    Optothermal detection is a spectroscopic technique where the energy input into a gas or other media caused by absorption of optical radiation is measured directly by means of a thermal detector.1-3 A fraction of the absorbed energy is transported to the thermal detector by heat conduction or molecular diffusion. In this work a conventional thermal sensor was replaced by a quartz tuning fork (QTF), and the optical power input into the gas was modulated at the QTF resonant frequency. We call this approach "resonant optothermoacoustic detection", or ROTADE. The same experimental setup can be used to conduct a closely related technique, quartz enhanced photoacoustic spectroscopy (QEPAS).4 QEPAS relies on energy transfer from the initially excited molecular vibrational state to the translational degrees of freedom. In some cases this process is too slow to follow the modulation required for QEPAS. In other cases, the resonant energy transfer can result in vibrational excitation of nitrogen, which relaxes very slowly. ROTADE, on the other hand, detects the energy delivered by molecules even if this energy is still in the form of vibrational excitation. The molecules will then release their energy to the QTF upon collision with its surface. Experimental investigations of ROTADE and its comparison with QEPAS were performed in pure CO2 and 0.5% acetylene in N2 using near-infrared diode lasers. A fiber collimator and a refocusing lens were used to focus the laser to a ~15 μm diameter waist. Its position was scanned in the QTF plane using a 3D translation stage with computer-controlled actuators. Different QTFs were used to compare the effect of modulation frequency on the ROTADE signal.

  17. Fault detection and isolation of sensors in aeration control systems.

    PubMed

    Carlsson, Bengt; Zambrano, Jesús

    2016-01-01

    In this paper, we consider the problem of fault detection (FD) and isolation in the aeration system of an activated sludge process. For this study, the dissolved oxygen in each aerated zone is assumed to be controlled automatically. As the basis for an FD method we use the ratio of air flow rates into different zones. The method is evaluated in two scenarios: using the Benchmark Simulation Model no. 1 (BSM1) by Monte Carlo simulations and using data from a wastewater treatment plant. The FD method shows good results for a correct and early FD and isolation.

  18. Review on Recent Advances in the Analysis of Isolated Organelles

    PubMed Central

    Satori, Chad P.; Kostal, Vratislav; Arriaga, Edgar A.

    2012-01-01

    The analysis of isolated organelles is one of the pillars of modern bioanalytical chemistry. This review describes recent developments on the isolation and characterization of isolated organelles both from living organisms and cell cultures. Salient reports on methods to release organelles focused on reproducibility and yield, membrane isolation, and integrated devices for organelle release. New developments on organelle fractionation after their isolation were on the topics of centrifugation, immunocapture, free flow electrophoresis, flow field-flow fractionation, fluorescence activated organelle sorting, laser capture microdissection, and dielectrophoresis. New concepts on characterization of isolated organelles included atomic force microscopy, optical tweezers combined with Raman spectroscopy, organelle sensors, flow cytometry, capillary electrophoresis, and microfluidic devices. PMID:23107131

  19. Advanced Water Vapor Lidar Detection System

    NASA Technical Reports Server (NTRS)

    Elsayed-Ali, Hani

    1998-01-01

    In the present water vapor lidar system, the detected signal is sent over long cables to a waveform digitizer in a CAMAC crate. This has the disadvantage of transmitting analog signals for a relatively long distance, which is subjected to pickup noise, leading to a decrease in the signal to noise ratio. Generally, errors in the measurement of water vapor with the DIAL method arise from both random and systematic sources. Systematic errors in DIAL measurements are caused by both atmospheric and instrumentation effects. The selection of the on-line alexandrite laser with a narrow linewidth, suitable intensity and high spectral purity, and its operation at the center of the water vapor lines, ensures minimum influence in the DIAL measurement that are caused by the laser spectral distribution and avoid system overloads. Random errors are caused by noise in the detected signal. Variability of the photon statistics in the lidar return signal, noise resulting from detector dark current, and noise in the background signal are the main sources of random error. This type of error can be minimized by maximizing the signal to noise ratio. The increase in the signal to noise ratio can be achieved by several ways. One way is to increase the laser pulse energy, by increasing its amplitude or the pulse repetition rate. Another way, is to use a detector system with higher quantum efficiency and lower noise, on the other hand, the selection of a narrow band optical filter that rejects most of the day background light and retains high optical efficiency is an important issue. Following acquisition of the lidar data, we minimize random errors in the DIAL measurement by averaging the data, but this will result in the reduction of the vertical and horizontal resolutions. Thus, a trade off is necessary to achieve a balance between the spatial resolution and the measurement precision. Therefore, the main goal of this research effort is to increase the signal to noise ratio by a factor of

  20. Documentation of the current fault detection, isolation and reconfiguration software of the AIPS fault-tolerant processor

    NASA Technical Reports Server (NTRS)

    Lanning, David T.; Shepard, Allen W.; Johnson, Sally C.

    1987-01-01

    Documentation is presented of the December 1986 version of the ADA code for the fault detection, isolation, and reconfiguration (FDIR) functions of the Advanced Information processing System (AIPS) Fault-Tolerant Processor (FTP). Because the FTP is still under development and the software is constantly undergoing changes, this should not be considered final documentation of the FDIR software of the FTP.

  1. Detection and molecular characterization of Egyptian isolates of grapevine viruses.

    PubMed

    Fattouh, F; Ratti, C; El-Ahwany, A M D; Aleem, E Abdel; Babini, A R; Autonell, C Rubies

    2014-01-01

    Selected commercial and/or local vineyards and nurseries in three different governorates of Egypt (Alexandria, El-Beheira and El-Menofia) were surveyed for symptoms indicative of infection by grapevine viruses. Leaf samples from red-fruited and white-fruited Vitis vinefera were tested for grapevine leafroll associated viruses (GLRaV-1, GLRaV-2, and GLRaV-3), grapevine viruses A and B (GVA, GVB), grapevine rupestris stem pitting virus (GRSPaV), grapevine fanleaf virus (GFLV), and grapevine fleck virus (GFKV) from early April to late October 2010. Incidence of these viruses was assessed by RT-PCR in 60 different samples. Selected amplicons were sequenced. While GVA was the most wide spread (30%), GLRaV-1, GVB, GFLV, and GFKV were not detected during the survey. However, GVA, GLRaV-2, GLRaV-3, and GRSPaV were detected in the form of single infection or in mixed infections of 2 to 4 viruses. Phylogenetic analysis was performed on all Egyptian isolates of GLRaV-2 (4), GLRaV-3 (7), GVA (3), and GRSPaV (6). GRSPaV was detected for the first time in Egypt. Phylogenetic analysis provided insights into the evolutionary relationship between the reported Egyptian isolates and other previously reported isolates. PMID:24957718

  2. Detecting and isolating abrupt changes in linear switching systems

    NASA Astrophysics Data System (ADS)

    Nazari, Sohail; Zhao, Qing; Huang, Biao

    2015-04-01

    In this paper, a novel fault detection and isolation (FDI) method for switching linear systems is developed. All input and output signals are assumed to be corrupted with measurement noises. In the proposed method, a 'lifted' linear model named as stochastic hybrid decoupling polynomial (SHDP) is introduced. The SHDP model governs the dynamics of the switching linear system with all different modes, and is independent of the switching sequence. The error-in-variable (EIV) representation of SHDP is derived, and is used for the fault residual generation and isolation following the well-adopted local approach. The proposed FDI method can detect and isolate the fault-induced abrupt changes in switching models' parameters without estimating the switching modes. Furthermore, in this paper, the analytical expressions of the gradient vector and Hessian matrix are obtained based on the EIV SHDP formulation, so that they can be used to implement the online fault detection scheme. The performance of the proposed method is then illustrated by simulation examples.

  3. Detection and isolation of circulating tumor cells: principles and methods.

    PubMed

    Esmaeilsabzali, Hadi; Beischlag, Timothy V; Cox, Michael E; Parameswaran, Ash M; Park, Edward J

    2013-11-15

    Efforts to improve the clinical management of several cancers include finding better methods for the quantitative and qualitative analysis of circulating tumor cells (CTCs). However, detection and isolation of CTCs from the blood circulation is not a trivial task given their scarcity and the lack of reliable markers to identify these cells. With a variety of emerging technologies, a thorough review of the exploited principles and techniques as well as the trends observed in the development of these technologies can assist researchers to recognize the potential improvements and alternative approaches. To help better understand the related biological concepts, a simplified framework explaining cancer formation and its spread to other organs as well as how CTCs contribute to this process has been presented first. Then, based on their basic working-principles, the existing methods for detection and isolation of CTCs have been classified and reviewed as nucleic acid-based, physical properties-based and antibody-based methods. The review of literature suggests that antibody-based methods, particularly in conjunction with a microfluidic lab-on-a-chip setting, offer the highest overall performance for detection and isolation of CTCs. Further biological and engineering-related research is required to improve the existing methods. These include finding more specific markers for CTCs as well as enhancing the throughput, sensitivity, and analytic functionality of current devices.

  4. Seismic isolation of Advanced LIGO: Review of strategy, instrumentation and performance

    NASA Astrophysics Data System (ADS)

    Matichard, F.; Lantz, B.; Mittleman, R.; Mason, K.; Kissel, J.; Abbott, B.; Biscans, S.; McIver, J.; Abbott, R.; Abbott, S.; Allwine, E.; Barnum, S.; Birch, J.; Celerier, C.; Clark, D.; Coyne, D.; DeBra, D.; DeRosa, R.; Evans, M.; Foley, S.; Fritschel, P.; Giaime, J. A.; Gray, C.; Grabeel, G.; Hanson, J.; Hardham, C.; Hillard, M.; Hua, W.; Kucharczyk, C.; Landry, M.; Le Roux, A.; Lhuillier, V.; Macleod, D.; Macinnis, M.; Mitchell, R.; O'Reilly, B.; Ottaway, D.; Paris, H.; Pele, A.; Puma, M.; Radkins, H.; Ramet, C.; Robinson, M.; Ruet, L.; Sarin, P.; Shoemaker, D.; Stein, A.; Thomas, J.; Vargas, M.; Venkateswara, K.; Warner, J.; Wen, S.

    2015-09-01

    The new generation of gravitational waves detectors require unprecedented levels of isolation from seismic noise. This article reviews the seismic isolation strategy and instrumentation developed for the Advanced LIGO observatories. It summarizes over a decade of research on active inertial isolation and shows the performance recently achieved at the Advanced LIGO observatories. The paper emphasizes the scientific and technical challenges of this endeavor and how they have been addressed. An overview of the isolation strategy is given. It combines multiple layers of passive and active inertial isolation to provide suitable rejection of seismic noise at all frequencies. A detailed presentation of the three active platforms that have been developed is given. They are the hydraulic pre-isolator, the single-stage internal isolator and the two-stage internal isolator. The architecture, instrumentation, control scheme and isolation results are presented for each of the three systems. Results show that the seismic isolation sub-system meets Advanced LIGO’s stringent requirements and robustly supports the operation of the two detectors.

  5. Detection of dengue virus in platelets isolated from dengue patients.

    PubMed

    Noisakran, Sansanee; Gibbons, Robert V; Songprakhon, Pucharee; Jairungsri, Aroonroong; Ajariyakhajorn, Chuanpis; Nisalak, Ananda; Jarman, Richard G; Malasit, Prida; Chokephaibulkit, Kulkanya; Perng, Guey Chuen

    2009-03-01

    Though thrombocytopenia or dysfunction of platelets is common in dengue virus infection, the role of platelets has not been established. We enrolled 33 hospitalized children with serologically confirmed dengue virus infection. Blood specimens were collected during hospitalization. Platelets and plasma were isolated from the whole blood. Detection of dengue virus in plasma and platelets was carried out by RT-PCR with primers that can differentiate different dengue serotypes simultaneously, and by electron transmission microscopy (EM). Dengue viral RNA was detected in the platelets and plasma by conventional RT-PCR. A significantly higher percentage of dengue viral RNA was detected in platelets than in plasma (p = 0.03). Platelets isolated 5 days after onset of fever were most likely positive for viral RNA. Concurrent infection or co-circulation with multiple dengue serotypes was observed in 12% of patients. Infrequently, negative-stranded dengue viral RNA was detected in platelets and in plasma. Importantly, EM confirmed the presence of dengue viral-like particles inside platelets prepared from dengue patients. Our findings suggest the presence of dengue virus in platelets may be associated with the dysfunction of platelets observed in dengue patients.

  6. Multiple Pathogen Detection Using Biosensors: Advancements and Challenges

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Advancements in biosensor research have considerably impacted clinical diagnostics for human health. Efforts in capitalizing on the sensitivity of biosensors for food pathogen detection are evident in the food safety/security research community. For practical application with foods that normally h...

  7. Edge Detection to Isolate Motion in Adaptive Optics Systems

    SciTech Connect

    Chan, C W

    2003-07-11

    Adaptive optics uses signal processing techniques and deformable mirrors to minimize image degradation caused by phase aberrations. In the case of telescope imaging, the atmosphere causes phase aberrations. In the case of satellite imaging, errors due to the ultra-light-weight characteristics of the primary mirror cause phase aberrations. Scene-based Shack-Hartmann Wave Front Sensing takes the correlation between successive wavelets to determine these phase aberrations. A large problem with the scene-based approach is that motion, such as a moving car, can cause the correlation of two lenslets to peak, not where the scenes align, but where the moving object in each frame aligns. As such, the continued use of scene-based Wave Front Sensing necessitates successful isolation of moving objects from a stationary background scene. With the knowledge of which pixels are immobile, one should avoid the problem of locking onto a moving object when taking the correlation of two successive frames in time. Two main requirements of isolation are consistency and efficiency. In this document I will discuss the different edge detection algorithms explored for moving object isolation and how I came to the conclusion that, for our purposes of scene-based Shack-Hartmann WFS, edge detection is too inconsistent to be of any use. Because the Shack-Hartmann lenslets limits us to low resolutions, edge detection that works on higher resolution images will not work on our images. The results of each algorithm will show that with so few pixels per subaperature, edge detection is a poor method of identifying moving objects.

  8. Advances in nucleic acid-based detection methods.

    PubMed Central

    Wolcott, M J

    1992-01-01

    Laboratory techniques based on nucleic acid methods have increased in popularity over the last decade with clinical microbiologists and other laboratory scientists who are concerned with the diagnosis of infectious agents. This increase in popularity is a result primarily of advances made in nucleic acid amplification and detection techniques. Polymerase chain reaction, the original nucleic acid amplification technique, changed the way many people viewed and used nucleic acid techniques in clinical settings. After the potential of polymerase chain reaction became apparent, other methods of nucleic acid amplification and detection were developed. These alternative nucleic acid amplification methods may become serious contenders for application to routine laboratory analyses. This review presents some background information on nucleic acid analyses that might be used in clinical and anatomical laboratories and describes some recent advances in the amplification and detection of nucleic acids. PMID:1423216

  9. Incipient fault detection study for advanced spacecraft systems

    NASA Technical Reports Server (NTRS)

    Milner, G. Martin; Black, Michael C.; Hovenga, J. Mike; Mcclure, Paul F.

    1986-01-01

    A feasibility study to investigate the application of vibration monitoring to the rotating machinery of planned NASA advanced spacecraft components is described. Factors investigated include: (1) special problems associated with small, high RPM machines; (2) application across multiple component types; (3) microgravity; (4) multiple fault types; (5) eight different analysis techniques including signature analysis, high frequency demodulation, cepstrum, clustering, amplitude analysis, and pattern recognition are compared; and (6) small sample statistical analysis is used to compare performance by computation of probability of detection and false alarm for an ensemble of repeated baseline and faulted tests. Both detection and classification performance are quantified. Vibration monitoring is shown to be an effective means of detecting the most important problem types for small, high RPM fans and pumps typical of those planned for the advanced spacecraft. A preliminary monitoring system design and implementation plan is presented.

  10. Isolated heart models: cardiovascular system studies and technological advances.

    PubMed

    Olejnickova, Veronika; Novakova, Marie; Provaznik, Ivo

    2015-07-01

    Isolated heart model is a relevant tool for cardiovascular system studies. It represents a highly reproducible model for studying broad spectrum of biochemical, physiological, morphological, and pharmaceutical parameters, including analysis of intrinsic heart mechanics, metabolism, and coronary vascular response. Results obtained in this model are under no influence of other organ systems, plasma concentration of hormones or ions and influence of autonomic nervous system. The review describes various isolated heart models, the modes of heart perfusion, and advantages and limitations of various experimental setups. It reports the improvements of perfusion setup according to Langendorff introduced by the authors.

  11. A real-time FORTRAN implementation of a sensor failure detection, isolation and accommodation algorithm

    NASA Technical Reports Server (NTRS)

    Delaat, J. C.

    1984-01-01

    An advanced, sensor failure detection, isolation, and accomodation algorithm has been developed by NASA for the F100 turbofan engine. The algorithm takes advantage of the analytical redundancy of the sensors to improve the reliability of the sensor set. The method requires the controls computer, to determine when a sensor failure has occurred without the help of redundant hardware sensors in the control system. The controls computer provides an estimate of the correct value of the output of the failed sensor. The algorithm has been programmed in FORTRAN using a real-time microprocessor-based controls computer. A detailed description of the algorithm and its implementation on a microprocessor is given.

  12. Advances in Magnetic Resonance Imaging Contrast Agents for Biomarker Detection

    NASA Astrophysics Data System (ADS)

    Sinharay, Sanhita; Pagel, Mark D.

    2016-06-01

    Recent advances in magnetic resonance imaging (MRI) contrast agents have provided new capabilities for biomarker detection through molecular imaging. MRI contrast agents based on the T2 exchange mechanism have more recently expanded the armamentarium of agents for molecular imaging. Compared with T1 and T2* agents, T2 exchange agents have a slower chemical exchange rate, which improves the ability to design these MRI contrast agents with greater specificity for detecting the intended biomarker. MRI contrast agents that are detected through chemical exchange saturation transfer (CEST) have even slower chemical exchange rates. Another emerging class of MRI contrast agents uses hyperpolarized 13C to detect the agent with outstanding sensitivity. These hyperpolarized 13C agents can be used to track metabolism and monitor characteristics of the tissue microenvironment. Together, these various MRI contrast agents provide excellent opportunities to develop molecular imaging for biomarker detection.

  13. Advances in Magnetic Resonance Imaging Contrast Agents for Biomarker Detection

    PubMed Central

    Sinharay, Sanhita; Pagel, Mark D.

    2016-01-01

    Recent advances in magnetic resonance imaging (MRI) contrast agents have provided new capabilities for biomarker detection through molecular imaging. MRI contrast agents based on the T2 exchange mechanism have more recently expanded the armamentarium of agents for molecular imaging. Compared with T1 and T2* agents, T2 exchange agents have a slower chemical exchange rate, which improves the ability to design these MRI contrast agents with greater specificity for detecting the intended biomarker. MRI contrast agents that are detected through chemical exchange saturation transfer (CEST) have even slower chemical exchange rates. Another emerging class of MRI contrast agents uses hyperpolarized 13C to detect the agent with outstanding sensitivity. These hyperpolarized 13C agents can be used to track metabolism and monitor characteristics of the tissue microenvironment. Together, these various MRI contrast agents provide excellent opportunities to develop molecular imaging for biomarker detection. PMID:27049630

  14. Recent Advances In Science Support For Isolated Droplet Combustion Experiments

    NASA Technical Reports Server (NTRS)

    Dryer, F. L.; Kazakov, A.; Urban, B. D.; Kroenlein, K.

    2003-01-01

    In a joint program involving Prof. F.A. Williams of the University of California, San Diego and Dr. V. Nayagam of the National Center for Microgravity Research, the combustion characteristics of isolated liquid fuel droplets of n-heptane, n-decane, methanol, methanol-water, ethanol and ethanol-water having initial diameters between about 1 mm and 6 mm continues to be investigated. The objectives of the work are to improve fundamental knowledge of droplet combustion dynamics for pure fuels and fuel-water mixtures through microgravity experiments and theoretical analyses. The Princeton contributions support the engineering design, data analysis, and data interpretation requirements for the study of initially single component, spherically symmetric, isolated droplet combustion studies through experiments and numerical modeling. UCSD contributions are described in a companion communication in this conference. The Princeton effort also addresses the analyses of Fiber Supported Droplet Combustion (FSDC) experiments conducted with the above fuels and collaborative work with others who are investigating droplet combustion in the presence of steady convection. A thorough interpretation of droplet burning behavior for n-heptane and n-decane over a relatively wide range of conditions also involves the influences of sooting on the combustion behavior, and this particular aspect on isolated burning of droplets is under consideration in a collaborative program underway with Drexel University. This collaboration is addressed in another communication at this conference. The one-dimensional, time-dependent, numerical modeling approach that we have continued to evolve for analyzing isolated, quiescent droplet combustion data has been further applied to investigate several facets of isolated droplet burning of simple alcohols, n-heptane, and n-decane. Some of the new results are described below.

  15. Guaranteed robust fault detection and isolation techniques for small satellites

    NASA Astrophysics Data System (ADS)

    Valavani, L.; Tantouris, N.

    2013-12-01

    The paper presents two generic fault detection and isolation (FDI) techniques which have shown remarkable robustness when applied to the SIMULINK model of a small satellite for thruster failures. While fundamentally different in their design approach, they both generate ʽstructured residuals' which accurately capture the failure mode. The diagnosis criterion in both methods relies on residuals direction rather than magnitude, which avoids the delays and expense of setting accurate thresholds for residuals magnitudes. Most importantly, this fact can account for the enhanced robustness to disturbances and sensor noise, as well as to significant parametric variations. Extensive Monte Carlo simulations are presented validating the robust performance of the two algorithms.

  16. Detecting Gear Tooth Fatigue Cracks in Advance of Complete Fracture

    NASA Technical Reports Server (NTRS)

    Zakrajsek, James J.; Lewicki, David G.

    1996-01-01

    Results of using vibration-based methods to detect gear tooth fatigue cracks are presented. An experimental test rig was used to fail a number of spur gear specimens through bending fatigue. The gear tooth fatigue crack in each test was initiated through a small notch in the fillet area of a tooth on the gear. The primary purpose of these tests was to verify analytical predictions of fatigue crack propagation direction and rate as a function of gear rim thickness. The vibration signal from a total of three tests was monitored and recorded for gear fault detection research. The damage consisted of complete rim fracture on the two thin rim gears and single tooth fracture on the standard full rim test gear. Vibration-based fault detection methods were applied to the vibration signal both on-line and after the tests were completed. The objectives of this effort were to identify methods capable of detecting the fatigue crack and to determine how far in advance of total failure positive detection was given. Results show that the fault detection methods failed to respond to the fatigue crack prior to complete rim fracture in the thin rim gear tests. In the standard full rim gear test all of the methods responded to the fatigue crack in advance of tooth fracture; however, only three of the methods responded to the fatigue crack in the early stages of crack propagation.

  17. Advances in Isolation Methods for Spermatogonial Stem Cells.

    PubMed

    Zhang, Rui; Sun, Jin; Zou, Kang

    2016-02-01

    Stem cell research has led to many remarkable achievements in recent years, but progress in the study of spermatogonial stem cells (SSCs) has been relatively slow, partly due to the slow development of techniques for spermatogonial stem cell isolation. The major accomplishments of SSC sorting and identification occurred approximately 10 years ago, and since that time, these techniques have been widely used without major improvements. In this article, we briefly introduce the biological properties of SSCs before reviewing the development of sorting techniques for SSCs in the past decades. We then summarize recent achievements in SSC sorting and finally discuss the advantages and disadvantages of SSC isolation methods, to provide new insight into techniques and research related to spermatogonial stem cells and promote the development of reproductive biology.

  18. Distributed fault detection and isolation resilient to network model uncertainties.

    PubMed

    Teixeira, Andre; Shames, Iman; Sandberg, Henrik; Johansson, Karl H

    2014-11-01

    The ability to maintain state awareness in the face of unexpected and unmodeled errors and threats is a defining feature of a resilient control system. Therefore, in this paper, we study the problem of distributed fault detection and isolation (FDI) in large networked systems with uncertain system models. The linear networked system is composed of interconnected subsystems and may be represented as a graph. The subsystems are represented by nodes, while the edges correspond to the interconnections between subsystems. Considering faults that may occur on the interconnections and subsystems, as our first contribution, we propose a distributed scheme to jointly detect and isolate faults occurring in nodes and edges of the system. As our second contribution, we analyze the behavior of the proposed scheme under model uncertainties caused by the addition or removal of edges. Additionally, we propose a novel distributed FDI scheme based on local models and measurements that is resilient to changes outside of the local subsystem and achieves FDI. Our third contribution addresses the complexity reduction of the distributed FDI method, by characterizing the minimum amount of model information and measurements needed to achieve FDI and by reducing the number of monitoring nodes. The proposed methods can be fused to design a scalable and resilient distributed FDI architecture that achieves local FDI despite unknown changes outside the local subsystem. The proposed approach is illustrated by numerical experiments on the IEEE 118-bus power network benchmark.

  19. Advanced Strain-Isolation-Pad Material with Bonded Fibrous Construction

    NASA Technical Reports Server (NTRS)

    Seibold, R. W.; Saito, C. A.; Buller, B. W.

    1982-01-01

    The feasibility of utilizing air lay and liquid lay felt deposition techniques to fabricate strain isolation pad (SIP) materials for the Space Shuttle Orbiter was demonstrated. These materials were developed as candidate replacements for the present needled felt SIP used between the ceramic tiles and the aluminum skin on the undersurface of the Orbiter. The SIP materials that were developed consisted of high temperature aramid fibers deposited by controlled fluid (air or liquid) carriers to form low density unbonded felts. The deposited felts were then bonded at the fiber intersections with a small amount of high temperature polyimide resin. This type of bonded felt construction can potentially eliminate two of the problems associated with the present SIP, viz., transmittal of localized stresses into the tiles and load history dependent mechanical response. However, further work is needed to achieve adequate through thickness tensile strength in the bonded felts.

  20. [A Case of Isolated Leptomeningeal Carcinomatosis from Advanced Gastric Cancer].

    PubMed

    Ji, Jung Geun; Chung, Joo Won; Nam, Seung Woo; Choi, Seung Kyu; Lee, Dong Won; Kim, Dae In; Jeon, Byung Gwan; Shin, Yun Jae

    2016-08-25

    Leptomeningeal carcinomatosis (LMC) is rare metastatic form of gastric cancer. Most cases are diagnosed in the final stage after multiple distant metastasis. An 84-year-old woman was admitted with melena, headache and vomiting. Esophagogastroduodenoscopy showed an ulceroinfiltrating lesion at the stomach (Borrmann class III), and biopsy revealed a signet ring cell carcinoma. The abdominal-pelvic CT showed no evidence of metastasis. A sudden decrease of consciousness was noted, but the brain CT showed no active lesion while the brain MRI revealed enhancement of leptomeninges. A lumbar puncture was performed and the cerebrospinal fluid study revealed malignant neoplastic cells. With family consent, no further evaluation and treatment were administered and she died six weeks after the diagnosis of gastric cancer. We report an extremely rare case of a patient who initially presented with neurologic symptoms, and was diagnosed LMC from advanced gastric cancer without any evidence of metastasis in abdomen and pelvis. PMID:27554216

  1. Isolation, Detection, and Characterization of Enterotoxigenic Bacteroides fragilis in Clinical Samples

    PubMed Central

    Fathi, Payam; Wu, Shaoguang

    2016-01-01

    Bacteroides fragilis is an extensively studied anaerobic bacterium comprising the normal flora of the human gut. B. fragilis is known to be one of the most commonly isolated species from clinical samples and has been shown to cause a wide range of pathologies in humans [1, 2]. As an opportunistic pathogen B. fragilis can cause abscess formation and bacteremia [2]. Additionally in its enterotoxigenic form, B. fragilis is a known cause of diarrheal illness, is associated with inflammatory bowel disease, and has been recently characterized in patients with colon cancer [3 - 5]. As research in the field of the gut microbiome continues to expand at an ever increasing rate due to advances in the availability of next generation sequencing and analysis tools it is important to outline various molecular methods that can be employed in quickly detecting and isolating relevant strains of B. fragilis. This review outlines methods that are routinely employed in the isolation and detection of B. fragilis, with an emphasis on characterizing enterotoxigenic B. fragilis (ETBF) strains. PMID:27335618

  2. Optimal Sensor Allocation for Fault Detection and Isolation

    NASA Technical Reports Server (NTRS)

    Azam, Mohammad; Pattipati, Krishna; Patterson-Hine, Ann

    2004-01-01

    Automatic fault diagnostic schemes rely on various types of sensors (e.g., temperature, pressure, vibration, etc) to measure the system parameters. Efficacy of a diagnostic scheme is largely dependent on the amount and quality of information available from these sensors. The reliability of sensors, as well as the weight, volume, power, and cost constraints, often makes it impractical to monitor a large number of system parameters. An optimized sensor allocation that maximizes the fault diagnosibility, subject to specified weight, volume, power, and cost constraints is required. Use of optimal sensor allocation strategies during the design phase can ensure better diagnostics at a reduced cost for a system incorporating a high degree of built-in testing. In this paper, we propose an approach that employs multiple fault diagnosis (MFD) and optimization techniques for optimal sensor placement for fault detection and isolation (FDI) in complex systems. Keywords: sensor allocation, multiple fault diagnosis, Lagrangian relaxation, approximate belief revision, multidimensional knapsack problem.

  3. Detection of Staphylococcus aureus with an intermediate profile to vancomycin (VISA) isolate from Santa Maria, RS.

    PubMed

    Marques, Jaciane Baggiotto; Dalmolin, Tanise Vendruscolo; Bonez, Pauline Cordenonsi; Agertt, Vanessa Albertina; de Campos, Marli Matiko Anraku; Santos, Roberto Christ Vianna

    2013-01-01

    Twenty-three isolates of Staphylococcus aureus resistant to methicillin have been analyzed, being found a clinical isolate of VISA through microdilution technique. The others techniques were unable to detect such isolates. This is the first study that shows the presence of VISA in clinical isolates in the city of Santa Maria-RS.

  4. Advanced Ship Detection For Spaceborne Based Maritime Awareness

    NASA Astrophysics Data System (ADS)

    Radius, Andrea; Ferreira, Joao; Carmo, Paulo; Marques, Paulo

    2013-12-01

    In the last years the increase in marine traffic generated the necessity of global monitoring for marine environment management in terms of safety, security and fisheries. The increasing number of new satellite-based Synthetic Aperture Radar (SAR) systems, and the intrinsic capability of the transmitted electromagnetic pulses to interact with the ships and to retrieve its cinematic characteristics, made this instrument particularly fit to improve global maritime awareness through the fusion with cooperative data (AIS, VMS, LRIT). The growing need of global maritime awareness gave a push to the realization of different projects in the European context, each one focused on a different particular objective. Particularly useful is the synergy between the operational and research aspects, being the goal of the last to improve the state of the art in the field of ship detection. Two European projects are the key to strive this synergy: the project MARitime Security Service (MARISS), which implements the operational capability, and the R&D Dolphin projects, which is focused on the deep exploitation of remote sensing data and on the technological development of advanced techniques for ship detection and classification purposes, and Seabilla project, which is also dedicated to improve the current ship detection capability and to fuse all the available information from different data sources for border surveillance optimization. This paper introduces the multipurpose Edisoft Vessel Detection software (EdiVDC) implemented by the EDISOFT company, which comes from the necessity to respect increasingly stringent requirements in terms of ship detection. The EdiVDC software is being operationally used in the framework of the MARISS project and it integrates advanced processing algorithms, developed in the scope of the Dolphin project with the cooperation of ISEL-IT (Instituto de Telecomunicações), and data simulators, developed in the context of the Seabilla project, improving

  5. A low loss Faraday isolator for squeezed vacuum injection in Advanced LIGO

    NASA Astrophysics Data System (ADS)

    Goetz, Ryan; Tanner, David; Mueller, Guido

    2016-03-01

    Using conventional interferometry, the strain sensitivity of Advanced LIGO is limited by a quantum noise floor known as the standard quantum limit (SQL). Injecting squeezed vacuum states into the output port of the interferometer allows for detector sensitivities below the SQL at frequencies within a band of observational interest. The effectiveness of squeezing in reducing quantum noise is strongly dependent upon the optical loss in the squeezed path. Thus, to combine the squeezed vacuum state with the interferometer output we require a Faraday isolator with both high power-throughput efficiency and high isolation ratio. A prototype isolator is currently being developed, and we will discuss the design goals and current status.

  6. Detection and isolation of Bluetongue virus from commercial vaccine batches.

    PubMed

    Bumbarov, Velizar; Golender, Natalia; Erster, Oran; Khinich, Yevgeny

    2016-06-14

    In this report we describe the detection and identification of Bluetongue virus (BTV) contaminations in commercial vaccines. BTV RNA was detected in vaccine batches of Lumpy skin disease (LSD) and Sheep pox (SP) using quantitative PCR (qPCR) for VP1 and NS3 genes. Both batches were positive for VP1 and NS3 in qPCR. The LSD vaccine-derived sample was positive for VP1 and VP2 in conventional PCR. The SP vaccine-derived sample was examined by amplification of VP1, VP4, VP6, VP7, NS2 and NS3 gene segments in conventional PCR. The SP vaccine-derived sample was further propagated in embryonated chicken eggs (ECE) and Vero cells. Preliminary sequence analysis showed that the LSD vaccine-derived sequence was 98-99% similar to BTV9. Analysis of the six genomic segments from the SP vaccine-derived isolate showed the highest similarity to BTV26 (66.3-97.8%). These findings are particularly important due to the effect of BTV on cattle and sheep, for which the vaccines are intended. They also demonstrate the necessity of rigorous vaccine inspection and strict vaccine production control. PMID:27171751

  7. Recent advances in immunosensor for narcotic drug detection

    PubMed Central

    Gandhi, Sonu; Suman, Pankaj; Kumar, Ashok; Sharma, Prince; Capalash, Neena; Suri, C. Raman

    2015-01-01

    Introduction: Immunosensor for illicit drugs have gained immense interest and have found several applications for drug abuse monitoring. This technology has offered a low cost detection of narcotics; thereby, providing a confirmatory platform to compliment the existing analytical methods. Methods: In this minireview, we define the basic concept of transducer for immunosensor development that utilizes antibodies and low molecular mass hapten (opiate) molecules. Results: This article emphasizes on recent advances in immunoanalytical techniques for monitoring of opiate drugs. Our results demonstrate that high quality antibodies can be used for immunosensor development against target analyte with greater sensitivity, specificity and precision than other available analytical methods. Conclusion: In this review we highlight the fundamentals of different transducer technologies and its applications for immunosensor development currently being developed in our laboratory using rapid screening via immunochromatographic kit, label free optical detection via enzyme, fluorescence, gold nanoparticles and carbon nanotubes based immunosensing for sensitive and specific monitoring of opiates. PMID:26929925

  8. Integrated Seismic Event Detection and Location by Advanced Array Processing

    SciTech Connect

    Kvaerna, T; Gibbons, S J; Ringdal, F; Harris, D B

    2007-02-09

    The principal objective of this two-year study is to develop and test a new advanced, automatic approach to seismic detection/location using array processing. We address a strategy to obtain significantly improved precision in the location of low-magnitude events compared with current fully-automatic approaches, combined with a low false alarm rate. We have developed and evaluated a prototype automatic system which uses as a basis regional array processing with fixed, carefully calibrated, site-specific parameters in conjuction with improved automatic phase onset time estimation. We have in parallel developed tools for Matched Field Processing for optimized detection and source-region identification of seismic signals. This narrow-band procedure aims to mitigate some of the causes of difficulty encountered using the standard array processing system, specifically complicated source-time histories of seismic events and shortcomings in the plane-wave approximation for seismic phase arrivals at regional arrays.

  9. Detection and isolation of circulating melanoma cells using photoacoustic flowmetry.

    PubMed

    O'Brien, Christine M; Rood, Kyle; Sengupta, Shramik; Gupta, Sagar K; DeSouza, Thiago; Cook, Aaron; Viator, John A

    2011-01-01

    Circulating tumor cells (CTCs) are those cells that have separated from a macroscopic tumor and spread through the blood and lymph systems to seed secondary tumors(1,2,3). CTCs are indicators of metastatic disease and their detection in blood samples may be used to diagnose cancer and monitor a patient's response to therapy. Since CTCs are rare, comprising about one tumor cell among billions of normal blood cells in advanced cancer patients, their detection and enumeration is a difficult task. We exploit the presence of pigment in most melanoma cells to generate photoacoustic, or laser induced ultrasonic waves in a custom flow cytometer for detection of circulating melanoma cells (CMCs)(4,5). This process entails separating a whole blood sample using centrifugation and obtaining the white blood cell layer. If present in whole blood, CMCs will separate with the white blood cells due to similar density. These cells are resuspended in phosphate buffered saline (PBS) and introduced into the flowmeter. Rather than a continuous flow of the blood cell suspension, we induced two phase flow in order to capture these cells for further study. In two phase flow, two immiscible liquids in a microfluidic system meet at a junction and form alternating slugs of liquid(6,7). PBS suspended white blood cells and air form microliter slugs that are sequentially irradiated with laser light. The addition of a surfactant to the liquid phase allows uniform slug formation and the user can create different sized slugs by altering the flow rates of the two phases. Slugs of air and slugs of PBS with white blood cells contain no light absorbers and hence, do not produce photoacoustic waves. However, slugs of white blood cells that contain even single CMCs absorb laser light and produce high frequency acoustic waves. These slugs that generate photoacoustic waves are sequestered and collected for cytochemical staining for verification of CMCs. PMID:22143421

  10. Sensing parasites: Proteomic and advanced bio-detection alternatives.

    PubMed

    Sánchez-Ovejero, Carlos; Benito-Lopez, Fernando; Díez, Paula; Casulli, Adriano; Siles-Lucas, Mar; Fuentes, Manuel; Manzano-Román, Raúl

    2016-03-16

    Parasitic diseases have a great impact in human and animal health. The gold standard for the diagnosis of the majority of parasitic infections is still conventional microscopy, which presents important limitations in terms of sensitivity and specificity and commonly requires highly trained technicians. More accurate molecular-based diagnostic tools are needed for the implementation of early detection, effective treatments and massive screenings with high-throughput capacities. In this respect, sensitive and affordable devices could greatly impact on sustainable control programmes which exist against parasitic diseases, especially in low income settings. Proteomics and nanotechnology approaches are valuable tools for sensing pathogens and host alteration signatures within microfluidic detection platforms. These new devices might provide novel solutions to fight parasitic diseases. Newly described specific parasite derived products with immune-modulatory properties have been postulated as the best candidates for the early and accurate detection of parasitic infections as well as for the blockage of parasite development. This review provides the most recent methodological and technological advances with great potential for bio-sensing parasites in their hosts, showing the newest opportunities offered by modern "-omics" and platforms for parasite detection and control.

  11. Detection of Polyclonality among Clinical Isolates from Prosthetic Joint Infections

    PubMed Central

    De-la-Fuente, Marta; Martinez-Perez, Marta; Gonzalez-Pallares, Iris

    2015-01-01

    Prosthetic joint infection (PJI) is an increasingly important health concern in the Western world due to the rising number of joint arthroplasties. Although most infections are considered to be monomicrobial, the introduction of sonication procedures has led to an increase in the detection of polymicrobial infections. To date, no published studies have investigated the presence of different clones of the same species in the infected patient. The objective of this study was to analyze whether the phenomenon of polyclonality, or the appearance of different clones in the same sample, occurs in PJI. Bacteria isolated by sonication of the retrieved implant from patients with theoretically monomicrobial PJI were included in the study. Two techniques (random amplified polymorphic DNA [RAPD] and matrix-assisted laser desorption ionization–time of flight [MALDI-TOF] mass spectrometry) were used to determine the presence of several clones in the same sample. Results were analyzed to determine bacterial species and infection type (acute versus chronic). RAPD showed a predominance of polyclonal cases (16 of 19). However, when performing the analysis with MALDI-TOF, all cases were shown to be polyclonal. We were unable to establish any relationship between the two methodologies. Polyclonality is a common phenomenon in acute and chronic PJI. Further studies are needed to establish the potential implications of this phenomenon on patient outcomes. PMID:26378278

  12. Costas loop lock detection in the advanced receiver

    NASA Astrophysics Data System (ADS)

    Mileant, A.; Hinedi, S.

    1989-11-01

    The advanced receiver currently being developed uses a Costas digital loop to demodulate the subcarrier. Previous analyses of lock detector algorithms for Costas loops have ignored the effects of the inherent correlation between the samples of the phase-error process. Accounting for this correlation is necessary to achieve the desired lock-detection probability for a given false-alarm rate. Both analysis and simulations are used to quantify the effects of phase correlation on lock detection for the square-law and the absolute-value type detectors. Results are obtained which depict the lock-detection probability as a function of loop signal-to-noise ratio for a given false-alarm rate. The mathematical model and computer simulation show that the square-law detector experiences less degradation due to phase jitter than the absolute-value detector and that the degradation in detector signal-to-noise ratio is more pronounced for square-wave than for sine-wave signals.

  13. Costas loop lock detection in the advanced receiver

    NASA Technical Reports Server (NTRS)

    Mileant, A.; Hinedi, S.

    1989-01-01

    The advanced receiver currently being developed uses a Costas digital loop to demodulate the subcarrier. Previous analyses of lock detector algorithms for Costas loops have ignored the effects of the inherent correlation between the samples of the phase-error process. Accounting for this correlation is necessary to achieve the desired lock-detection probability for a given false-alarm rate. Both analysis and simulations are used to quantify the effects of phase correlation on lock detection for the square-law and the absolute-value type detectors. Results are obtained which depict the lock-detection probability as a function of loop signal-to-noise ratio for a given false-alarm rate. The mathematical model and computer simulation show that the square-law detector experiences less degradation due to phase jitter than the absolute-value detector and that the degradation in detector signal-to-noise ratio is more pronounced for square-wave than for sine-wave signals.

  14. Bringing isolated dark matter out of isolation: Late-time reheating and indirect detection

    NASA Astrophysics Data System (ADS)

    Erickcek, Adrienne L.; Sinha, Kuver; Watson, Scott

    2016-09-01

    In standard cosmology, the growth of structure becomes significant following matter-radiation equality. In nonthermal histories, where an effectively matter-dominated phase occurs due to scalar oscillations prior to big bang nucleosynthesis, a new scale at smaller wavelengths appears in the matter power spectrum. Density perturbations that enter the horizon during the early matter-dominated era (EMDE) grow linearly with the scale factor prior to the onset of radiation domination, which leads to enhanced inhomogeneity on small scales if dark matter (DM) thermally and kinetically decouples during the EMDE. The microhalos that form from these enhanced perturbations significantly boost the self-annihilation rate for dark matter. This has important implications for indirect detection experiments: the larger annihilation rate may result in observable signals from dark matter candidates that are usually deemed untestable. As a proof of principle, we consider binos in heavy supersymmetry with an intermediate extended Higgs sector and all other superpartners decoupled. We find that these isolated binos, which lie under the neutrino floor, can account for the dark matter relic density and decouple from the standard model early enough to preserve the enhanced small-scale inhomogeneity generated during the EMDE. If early forming microhalos survive as subhalos within larger microhalos, the resulting boost to the annihilation rate for bino dark matter near the pseudoscalar resonance exceeds the upper limit established by Fermi-LAT's observations of dwarf spheroidal galaxies. These DM candidates motivate the N -body simulations required to eliminate uncertainties in the microhalos' internal structure by exemplifying how an EMDE can enable Fermi-LAT to probe isolated dark matter.

  15. Development of the Vibration Isolation System for the Advanced Resistive Exercise Device

    NASA Technical Reports Server (NTRS)

    Niebuhr, Jason H.; Hagen, Richard A.

    2011-01-01

    This paper describes the development of the Vibration Isolation System for the Advanced Resistive Exercise Device from conceptual design to lessons learned. Maintaining a micro-g environment on the International Space Station requires that experiment racks and major vibration sources be isolated. The challenge in characterizing exercise loads and testing the system in the presence of gravity led to a decision to qualify the system by analysis. Available data suggests that the system is successful in attenuating loads, yet there has been a major component failure and several procedural issues during its 3 years of operational use.

  16. Advances in Electrostatic Dust Detection on Remote Surfaces

    SciTech Connect

    Voinier, C; Skinner, C H; Roquemore, A L

    2005-02-09

    The inventory of dust in next-step magnetic fusion devices will be regulated for safety reasons, however diagnostics to measure in-vessel dust are still in their infancy. Advances in dust particle detection on remote surfaces are reported. Two grids of interlocking circuit traces with spacing in the range 125 mu m to 25 mu m are biased to 30 V. Impinging dust creates a short circuit and the result current pulse is recorded. The detector response was measured with particles scraped from a carbon fiber composite tile and sorted by size category. The finest 25 mu m grid showed a sensitivity more than an order of magnitude higher than the 125 mu m grid. The response to the finest particle categories (5 30 mu m) was two orders of magnitude higher than the largest (125 250 mu m) category. Longer duration current pulses were observed from the coarser particles. The results indicate a detection threshold for fine particles below 1 mu g/cm^2.

  17. Survey of pedestrian detection for advanced driver assistance systems.

    PubMed

    Gerónimo, David; López, Antonio M; Sappa, Angel D; Graf, Thorsten

    2010-07-01

    Advanced driver assistance systems (ADASs), and particularly pedestrian protection systems (PPSs), have become an active research area aimed at improving traffic safety. The major challenge of PPSs is the development of reliable on-board pedestrian detection systems. Due to the varying appearance of pedestrians (e.g., different clothes, changing size, aspect ratio, and dynamic shape) and the unstructured environment, it is very difficult to cope with the demanded robustness of this kind of system. Two problems arising in this research area are the lack of public benchmarks and the difficulty in reproducing many of the proposed methods, which makes it difficult to compare the approaches. As a result, surveying the literature by enumerating the proposals one--after-another is not the most useful way to provide a comparative point of view. Accordingly, we present a more convenient strategy to survey the different approaches. We divide the problem of detecting pedestrians from images into different processing steps, each with attached responsibilities. Then, the different proposed methods are analyzed and classified with respect to each processing stage, favoring a comparative viewpoint. Finally, discussion of the important topics is presented, putting special emphasis on the future needs and challenges. PMID:20489227

  18. Survey of pedestrian detection for advanced driver assistance systems.

    PubMed

    Gerónimo, David; López, Antonio M; Sappa, Angel D; Graf, Thorsten

    2010-07-01

    Advanced driver assistance systems (ADASs), and particularly pedestrian protection systems (PPSs), have become an active research area aimed at improving traffic safety. The major challenge of PPSs is the development of reliable on-board pedestrian detection systems. Due to the varying appearance of pedestrians (e.g., different clothes, changing size, aspect ratio, and dynamic shape) and the unstructured environment, it is very difficult to cope with the demanded robustness of this kind of system. Two problems arising in this research area are the lack of public benchmarks and the difficulty in reproducing many of the proposed methods, which makes it difficult to compare the approaches. As a result, surveying the literature by enumerating the proposals one--after-another is not the most useful way to provide a comparative point of view. Accordingly, we present a more convenient strategy to survey the different approaches. We divide the problem of detecting pedestrians from images into different processing steps, each with attached responsibilities. Then, the different proposed methods are analyzed and classified with respect to each processing stage, favoring a comparative viewpoint. Finally, discussion of the important topics is presented, putting special emphasis on the future needs and challenges.

  19. Safe, Advanced, Adaptable Isolation System Eliminates the Need for Critical Lifts

    NASA Technical Reports Server (NTRS)

    Ginn, Starr

    2011-01-01

    The Starr Soft Support isolation system incorporates an automatically reconfigurable aircraft jack into NASA's existing 1-Hertz isolators. This enables an aircraft to float in mid-air without the need for a critical lift during ground vibration testing (GVT), significantly reducing testing risk, time, and costs. Currently incorporating the most advanced technology available, the 60,000-poundcapacity (27-metric-ton) isolation system is used for weight and measurement tests, control-surface free-play tests, and structural mode interaction tests without the need for any major reconfiguration, often saving days of time and significantly reducing labor costs. The Starr Soft Support isolation system consists of an aircraft-jacking device with three jacking points, each of which has an individual motor and accommodates up to 20,000 pounds (9 metric tons) for a total 60,000-pound (27-metric-ton) capacity. The system can be transported to the aircraft by forklift and placed at its jacking points using a pallet jack. The motors power the electric actuators, raising the aircraft above the ground until the landing gear can retract. Inflatable isolators then deploy, enabling the aircraft to float in mid-air, simulating a 1-Hertz free-free boundary condition. Inflatable isolators have been in use at NASA for years, enabling aircraft to literally float unsupported for highly accurate GVT. These isolators must be placed underneath the aircraft for this to occur. Traditionally, this is achieved by a critical lift a high-risk procedure in which a crane and flexible cord system are used to lift the aircraft. In contrast, the Starr Soft Support isolation system eliminates the need for critical lift by integrating the inflatable isolators into an aircraft jacking system. The system maintains vertical and horizontal isolating capabilities. The aircraft can be rolled onto the system, jacked up, and then the isolators can be inflated and positioned without any personnel needing to work

  20. Detection, isolation, and characterization of acidophilic methanotrophs from Sphagnum mosses.

    PubMed

    Kip, Nardy; Ouyang, Wenjing; van Winden, Julia; Raghoebarsing, Ashna; van Niftrik, Laura; Pol, Arjan; Pan, Yao; Bodrossy, Levente; van Donselaar, Elly G; Reichart, Gert-Jan; Jetten, Mike S M; Damsté, Jaap S Sinninghe; Op den Camp, Huub J M

    2011-08-15

    Sphagnum peatlands are important ecosystems in the methane cycle. Methane-oxidizing bacteria in these ecosystems serve as a methane filter and limit methane emissions. Yet little is known about the diversity and identity of the methanotrophs present in and on Sphagnum mosses of peatlands, and only a few isolates are known. The methanotrophic community in Sphagnum mosses, originating from a Dutch peat bog, was investigated using a pmoA microarray. A high biodiversity of both gamma- and alphaproteobacterial methanotrophs was found. With Sphagnum mosses as the inoculum, alpha- and gammaproteobacterial acidophilic methanotrophs were isolated using established and newly designed media. The 16S rRNA, pmoA, pxmA, and mmoX gene sequences showed that the alphaproteobacterial isolates belonged to the Methylocystis and Methylosinus genera. The Methylosinus species isolated are the first acid-tolerant members of this genus. Of the acidophilic gammaproteobacterial strains isolated, strain M5 was affiliated with the Methylomonas genus, and the other strain, M200, may represent a novel genus, most closely related to the genera Methylosoma and Methylovulum. So far, no acidophilic or acid-tolerant methanotrophs in the Gammaproteobacteria class are known. All strains showed the typical features of either type I or II methanotrophs and are, to the best of our knowledge, the first isolated (acidophilic or acid-tolerant) methanotrophs from Sphagnum mosses.

  1. Advanced nanoelectronic architectures for THz-based biological agent detection

    NASA Astrophysics Data System (ADS)

    Woolard, Dwight L.; Jensen, James O.

    2009-02-01

    The U.S. Army Research Office (ARO) and the U.S. Army Edgewood Chemical Biological Center (ECBC) jointly lead and support novel research programs that are advancing the state-of-the-art in nanoelectronic engineering in application areas that have relevance to national defense and security. One fundamental research area that is presently being emphasized by ARO and ECBC is the exploratory investigation of new bio-molecular architectural concepts that can be used to achieve rapid, reagent-less detection and discrimination of biological warfare (BW) agents, through the control of multi-photon and multi-wavelength processes at the nanoscale. This paper will overview an ARO/ECBC led multidisciplinary research program presently under the support of the U.S. Defense Threat Reduction Agency (DTRA) that seeks to develop new devices and nanoelectronic architectures that are effective for extracting THz signatures from target bio-molecules. Here, emphasis will be placed on the new nanosensor concepts and THz/Optical measurement methodologies for spectral-based sequencing/identification of genetic molecules.

  2. Model-based fault detection and isolation for intermittently active faults with application to motion-based thruster fault detection and isolation for spacecraft

    NASA Technical Reports Server (NTRS)

    Wilson, Edward (Inventor)

    2008-01-01

    The present invention is a method for detecting and isolating fault modes in a system having a model describing its behavior and regularly sampled measurements. The models are used to calculate past and present deviations from measurements that would result with no faults present, as well as with one or more potential fault modes present. Algorithms that calculate and store these deviations, along with memory of when said faults, if present, would have an effect on the said actual measurements, are used to detect when a fault is present. Related algorithms are used to exonerate false fault modes and finally to isolate the true fault mode. This invention is presented with application to detection and isolation of thruster faults for a thruster-controlled spacecraft. As a supporting aspect of the invention, a novel, effective, and efficient filtering method for estimating the derivative of a noisy signal is presented.

  3. Immunochemical detection of a common antigen among Streptococcus uberis isolates.

    PubMed Central

    Jones, K F; Norcross, N L

    1983-01-01

    Fifty-three isolates of Streptococcus uberis from various sources were examined for the presence of a common antigen. Initially, a serum was produced in rabbits which, by using rocket line immunoelectrophoresis, proved to react with identity to all of the S. uberis crude extracts as well as group B and E streptococcal extracts. The antigen(s) responsible for this cross-reactivity was partially purified by Sephacryl S-200 gel chromatography and analyzed by fused rocket immunoelectrophoresis. Further analysis by immunodiffusion showed that probably two antigens in the gel chromatography-consolidated fractions were common to the S. uberis and group B and E isolates, but that one of the antigens present was unique to S. uberis. Trypsin destroyed the immunoreactivity of this antigen. Isolation of this common antigen could possibly alleviate some of the tedium associated with the identification of this organism. Images PMID:6408120

  4. [Detection of genetic variability in Cercospora kikuchii isolates from a single soybean field].

    PubMed

    Lurá, M C; Di Conza, J A; González, A M; Latorre Rapela, M G; Turino, L; Ibáñez, M M; Iacona, V

    2007-01-01

    Detection of genetic variability in Cercospora kikuchii isolates from a single soybean field. Current knowledge about epidemiology and population structure of Cercospora kikuchii is little developed and no studies regarding this subject have been reported in Argentina. The aim of this work was to select primers to study genetic variability in C. kikuchii isolated from the same soybean field using RAPD (Random Amplified Polymorphism DNA). RAPD was applied to the DNA of 5 C. kikuchii, isolated from diseased tissue of the soybean in the same field, another isolate, from a strain collection. Out of seven primers, five of them proved to be useful to study the population of C. kikuchii isolates.

  5. UIO design for singular delayed LPV systems with application to actuator fault detection and isolation

    NASA Astrophysics Data System (ADS)

    Hassanabadi, Amir Hossein; Shafiee, Masoud; Puig, Vicenc

    2016-01-01

    In this paper, the unknown input observer (UIO) design for singular delayed linear parameter varying (LPV) systems is considered regarding its application to actuator fault detection and isolation. The design procedure assumes that the LPV system is represented in the polytopic framework. Existence and convergence conditions for the UIO are established. The design procedure is formulated by means of linear matrix inequalities (LMIs). Actuator fault detection and isolation is based on using the UIO approach for designing a residual generator that is completely decoupled from unknown inputs and exclusively sensitive to faults. Fault isolation is addressed considering two different strategies: dedicated and generalised bank of observers' schemes. The applicability of these two schemes for the fault isolation is discussed. An open flow canal system is considered as a case study to illustrate the performance and usefulness of the proposed fault detection and isolation method in different fault scenarios.

  6. A hybrid fault detection and isolation strategy for a team of cooperating unmanned vehicles

    NASA Astrophysics Data System (ADS)

    Tousi, M. M.; Khorasani, K.

    2015-01-01

    In this paper, a hybrid fault detection and isolation (FDI) methodology is developed for a team of cooperating unmanned vehicles. The proposed approach takes advantage of the cooperative nature of the team to detect and isolate relatively low-severity actuator faults that are otherwise not detectable and isolable by the vehicles themselves individually. The approach is hybrid and consists of both low-level (agent/team level) and high-level [discrete-event systems (DES) level] FDI modules. The high-level FDI module is formulated in the DES supervisory control framework, whereas the low-level FDI module invokes classical FDI techniques. By properly integrating the two FDI modules, a larger class of faults can be detected and isolated as compared to the existing techniques in the literature that rely on each level separately. Simulation results for a team of five unmanned aerial vehicles are also presented to demonstrate the effectiveness and capabilities of our proposed methodology.

  7. Lessons Learned on Implementing Fault Detection, Isolation, and Recovery (FDIR) in a Ground Launch Environment

    NASA Technical Reports Server (NTRS)

    Ferell, Bob; Lewis, Mark; Perotti, Jose; Oostdyk, Rebecca; Goerz, Jesse; Brown, Barbara

    2010-01-01

    This paper's main purpose is to detail issues and lessons learned regarding designing, integrating, and implementing Fault Detection Isolation and Recovery (FDIR) for Constellation Exploration Program (CxP) Ground Operations at Kennedy Space Center (KSC).

  8. Advances in isolation and characterization of homogeneous cell populations using laser microdissection.

    PubMed

    Mizuarai, S; Takahashi, K; Kobayashi, T; Kotani, H

    2005-01-01

    The isolation and characterization of homogeneous cell populations are of great importance for the analysis of gene expression, because normal tissues contain various types of cells, and the differences in the populations of isolated cells exert significant effects on gene expression analysis. Researchers have attempted to develop methods for the isolation of homogeneous cell populations, such as flow cytometry and mechanical dissection. However, the recent emergence of laser-assisted microdissection has revolutionized the isolation of single-cell populations from solid tissues. With the help of a cutting laser, laser microdissection can isolate tissues (cells) of interest without contamination from surrounding tissues with the microscopic visualization field. By combining laser microdissection and subsequent microarray technology, several studies have resulted in the identification of disease-related genes. In this review, we summarize the principle of laser microdissection and provide several successful examples of target-gene identification using the conventional method combining laser microdissection and microarray. Next, we discuss the practical drawbacks of the combinational method, such as the need for a large number of cells and the disturbance of the relative abundance of transcripts during RNA amplification. We introduce our modifications to combined laser microdissection and microarray for detection of disease-related genes; the technique is simple, yet practical and accurate. Finally, versatile applications of laser microdissection, not only to transcript expression analysis, but also to other genomics and proteomics analyses are, also presented.

  9. Evaluation of Group B Streptococcus Differential Agar for detection and isolation of Streptococcus agalactiae.

    PubMed

    Bou, G; Figueira, M; Canle, D; Cartelle, M; Eiros, J M; Villanueva, R

    2005-08-01

    In total, 320 vaginal or rectal swabs were cultured on Granada medium (GM) or Group B Streptococcus Differential Agar (GBSDA), and were also inoculated into LIM broth (Todd-Hewitt broth supplemented with selective antibiotics), for detection of group B Streptococcus (GBS). Overall, GBS isolates were detected on 53 of the 320 swabs; 47 of these isolates grew on both GM and GBSDA, five only on GBSDA, and one only following subculture from LIM broth. GBSDA appears to be a valid alternative to GM for the growth of GBS isolates from pregnant women.

  10. Detection of rDNA ITS polymorphism in Rhizoctonia solani AG 2-1 isolates.

    PubMed

    Pannecoucque, Joke; Höfte, Monica

    2009-01-01

    The sequence variability of the ribosomal internal transcribed spacer regions ITS1 and ITS2, including the 5.8S gene, was investigated for Rhizoctonia solani isolates of anastomosis group (AG) 2-1. During PCR RFLP analysis of eight isolates, the restriction patterns of four isolates showed an excess of bands after restriction with the enzymes AvaII and/or HincII, which suggested the presence of more than one ITS region. By cloning the ITS region of six isolates sequence heterogeneity was detected in the isolates that showed an excess of bands in the PCR RFLP analysis; up to nine different ITS regions were identified within one isolate. The same level of diversity was found within the same isolate as among isolates. In the phylogenetic tree based on the rDNA ITS sequences of several AG 2-1 isolates, sequences derived from the same isolate did not form distinct clusters, questioning the relevance of further subdivision of heterogeneous AG 2-1 isolates based on the ITS region.

  11. Methods and apparatus using commutative error detection values for fault isolation in multiple node computers

    DOEpatents

    Almasi, Gheorghe [Ardsley, NY; Blumrich, Matthias Augustin [Ridgefield, CT; Chen, Dong [Croton-On-Hudson, NY; Coteus, Paul [Yorktown, NY; Gara, Alan [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Heidelberger, Philip [Cortlandt Manor, NY; Hoenicke, Dirk I [Ossining, NY; Singh, Sarabjeet [Mississauga, CA; Steinmacher-Burow, Burkhard D [Wernau, DE; Takken, Todd [Brewster, NY; Vranas, Pavlos [Bedford Hills, NY

    2008-06-03

    Methods and apparatus perform fault isolation in multiple node computing systems using commutative error detection values for--example, checksums--to identify and to isolate faulty nodes. When information associated with a reproducible portion of a computer program is injected into a network by a node, a commutative error detection value is calculated. At intervals, node fault detection apparatus associated with the multiple node computer system retrieve commutative error detection values associated with the node and stores them in memory. When the computer program is executed again by the multiple node computer system, new commutative error detection values are created and stored in memory. The node fault detection apparatus identifies faulty nodes by comparing commutative error detection values associated with reproducible portions of the application program generated by a particular node from different runs of the application program. Differences in values indicate a possible faulty node.

  12. Detection, isolation, and persistence of viruses within bivalve mollusks

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Norovirus (NV), hepatitis A virus (HAV), and other virus transmission by molluscan shellfish is a significant issue. Research at the ARS-Dover DE laboratory has led to the development of improved methods for detecting these viruses. To identify pathogenic viruses within mollusks, a rapid highly-se...

  13. Specific detection of avian pneumovirus (APV) US isolates by RT-PCR.

    PubMed

    Shin, H J; Rajashekara, G; Jirjis, F F; Shaw, D P; Goyal, S M; Halvorson, D A; Nagaraja, K V

    2000-01-01

    This report details the development of an RT-PCR assay for the specific detection of US isolates of avian pneumovirus (APV). Of the several primer pairs tested, two sets of primers derived from the matrix gene of APV were able to specifically detect the viral RNA of APV. The nucleotide sequence comparison of the PCR products of APV isolates from Minnesota suggested that these viruses were closely related to the Colorado strain of APV, but were distinct from subtypes A and B European isolates of turkey APV (turkey rhinotracheitis: TRT). This M gene-based PCR was found to be very specific and sensitive. APV as low as 8 x 10(-5) TCID50 (0.0323 microg/ml) could be detected using this assay. In addition, the two primers were able to differentiate isolates from turkeys in Minnesota.

  14. Improved isolation protocol to detect high molecular weight polysaccharide structures of Campylobacter jejuni.

    PubMed

    Kovács, Judit K; Felső, Péter; Emődy, Levente; Schneider, György; Kocsis, Béla

    2014-12-01

    Simple detection of high molecular weight, LPS-like structures of Campylobacter jejuni is still an unsolved problem. A phenol-free extraction method for the detection of HMW polysaccharide was developed without the need for Western blot. This method provides a reliable technique for large-scale screening and comparative characterization study of different isolates.

  15. Inverted pendulum as low-frequency pre-isolation for advanced gravitational wave detectors

    NASA Astrophysics Data System (ADS)

    Takamori, A.; Raffai, P.; Márka, S.; DeSalvo, R.; Sannibale, V.; Tariq, H.; Bertolini, A.; Cella, G.; Viboud, N.; Numata, K.; Takahashi, R.; Fukushima, M.

    2007-11-01

    We have developed advanced seismic attenuation systems for Gravitational Wave (GW) detectors. The design consists of an Inverted Pendulum (IP) holding stages of Geometrical Anti-Spring Filters (GASF) and pendula, which isolate the test mass suspension from ground noise. The ultra-low-frequency IP suppresses the horizontal seismic noise, while the GASF suppresses the vertical ground vibrations. The three legs of the IP are supported by cylindrical maraging steel flexural joints. The IP can be tuned to very low frequencies by carefully adjusting its load. As a best result, we have achieved an ultra low, ˜12 mHz pendulum frequency for the system prototype made for Advanced LIGO (Laser Interferometer Gravitational Wave Observatory). The measured quality factor, Q, of this IP, ranging from Q˜2500 (at 0.45 Hz) to Q˜2 (at 12 mHz), is compatible with structural damping, and is proportional to the square of the pendulum frequency. Tunable counterweights allow for precise center-of-percussion tuning to achieve the required attenuation up to the first leg internal resonance (˜60 Hz for advanced LIGO prototype). All measurements are in good agreement with our analytical models. We therefore expect good attenuation in the low-frequency region, from ˜0.1to ˜50 Hz, covering the micro-seismic peak. The extremely soft IP requires minimal control force, which simplifies any needed actuation.

  16. Usage of Fault Detection Isolation & Recovery (FDIR) in Constellation (CxP) Launch Operations

    NASA Technical Reports Server (NTRS)

    Ferrell, Rob; Lewis, Mark; Perotti, Jose; Oostdyk, Rebecca; Spirkovska, Lilly; Hall, David; Brown, Barbara

    2010-01-01

    This paper will explore the usage of Fault Detection Isolation & Recovery (FDIR) in the Constellation Exploration Program (CxP), in particular Launch Operations at Kennedy Space Center (KSC). NASA's Exploration Technology Development Program (ETDP) is currently funding a project that is developing a prototype FDIR to demonstrate the feasibility of incorporating FDIR into the CxP Ground Operations Launch Control System (LCS). An architecture that supports multiple FDIR tools has been formulated that will support integration into the CxP Ground Operation's Launch Control System (LCS). In addition, tools have been selected that provide fault detection, fault isolation, and anomaly detection along with integration between Flight and Ground elements.

  17. Fault detection and isolation for a nonlinear railway vehicle suspension with a Hybrid Extended Kalman filter

    NASA Astrophysics Data System (ADS)

    Jesussek, Mathias; Ellermann, Katrin

    2013-10-01

    Fault detection is considered to be one way to improve system reliability and dependability for railway vehicles. The secondary lateral and anti-yaw dampers are the most critical parts in railway suspension systems. So far, the dampers have been modelled as linear components in the fault detection and isolation observer design. In this work, a Hybrid Extended Kalman filter is used to capture the nonlinear characteristics of the dampers. In order to detect and isolate faults, a nonlinear residual generator is developed, which can distinguish clearly between different types of faults. A lateral half train model serves as an example for the proposed technique. The results show that failures in the nonlinear suspension system can be detected and isolated accurately.

  18. [Study advance on formation, transformation and detection of masked deoxynivalenol].

    PubMed

    Yu, Chuanchuan; Yu, Hongxia; Li, Fengqin

    2009-03-01

    Conjugated deoxynivalenol, in which the toxins were usually bound to a more polar substance like glucose in crops, is referred to as masked deoxynivalenol. It could not detected with routine detection methods, but could release its toxic precursor after hydrolysis in gastrointestinal tract. In this paper, summarizes the formation, transformation and detection of masked deoxynivalenol as well as its relationship with human health were reviewed.

  19. Gene detection, virus isolation, and sequence analysis of avian leukosis viruses in Taiwan country chickens.

    PubMed

    Chang, Shu-Wei; Hsu, Meng-Fang; Wang, Ching-Ho

    2013-06-01

    Avian leukosis virus (ALV) infection in Taiwan Country chickens (TCCs) was investigated by using gene detection, virus isolation, and sequence analysis. The blood samples of 61 TCC flocks at market ages from a slaughter house were screened for exogenous ALVs using polymerase chain reaction to investigate the ALV infection status. The buffy coats from three breeder and four commercial chicken flocks were cocultured with DF-1 cells to isolate the virus. The full proviral DNA genomes of two ALV isolates were sequenced, analyzed, and compared with reference ALV strains. The gene detection results showed that 60 and 43 of the 61 flocks were infected with subgroup A of ALV (ALV-A) and subgroup J of ALV (ALV-J), respectively. Virus isolation results showed that five ALV-As and two ALV-Js were isolated from those seven TCC flocks. The full sequences of the isolates showed that isolate TW-3577 possessed a myeloblastosis-associated virus 1 gp85 coding region and an ALV-J 3'-untranslated region (3'UTR) and was similar to ordinary ALV-A. However, TW-3593 was unique. The 3'UTR of this isolate displayed high identity to endogenous counterpart sequence and its gp85 was different from all subgroups. This unique ALV is common in Taiwan.

  20. Detection and isolation of nucleic acid sequences using a bifunctional hybridization probe

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    2000-01-01

    A method for detecting and isolating a target sequence in a sample of nucleic acids is provided using a bifunctional hybridization probe capable of hybridizing to the target sequence that includes a detectable marker and a first complexing agent capable of forming a binding pair with a second complexing agent. A kit is also provided for detecting a target sequence in a sample of nucleic acids using a bifunctional hybridization probe according to this method.

  1. QPSK loop lock detection in the advanced receiver

    NASA Technical Reports Server (NTRS)

    Mileant, A.; Hinedi, S.

    1990-01-01

    The Advanced Receiver (ARX 2) currently being developed uses a Costas crossover loop to acquire and track the phase of an incoming quadrature phase-shift-keyed (QPSK) signal. The performance is described for the QPSK lock detector to be implemented, taking into account the phase jitter in the tracking loop. Simulations are used to verify the results of the analysis.

  2. QPSK loop lock detection in the advanced receiver

    NASA Astrophysics Data System (ADS)

    Mileant, A.; Hinedi, S.

    1990-05-01

    The Advanced Receiver (ARX 2) currently being developed uses a Costas crossover loop to acquire and track the phase of an incoming quadrature phase-shift-keyed (QPSK) signal. The performance is described for the QPSK lock detector to be implemented, taking into account the phase jitter in the tracking loop. Simulations are used to verify the results of the analysis.

  3. Recent Advances in Nanoplasmonic Sensors for Environmental Detection and Monitoring.

    PubMed

    Choi, Inhee

    2016-05-01

    The great attention in environmental pollution urges the development of innovative monitoring system enabling rapid, sensitive, specific detection and easy operation. Recent progress in nanoplasmonic sensors allowing real-time, highly-sensitive, label-free and multiplex detection provides a promising alternative to conventional environmental analyzing techniques. This review summarizes novel nanoplasmonic approaches categorized by optical detection technologies, which include surface plasmon resonance spectroscopy, dark-field nanospectroscopy, Raman spectroscopy, and even naked eyes. The focus of this review will be on how plasmonic nanostructures can be utilized to detect environmental pollutants, and remarkable accomplishments to enhance the detection performances. In addition, we discuss current challenge and future direction for ubiquitous environmental sensing and monitoring. PMID:27483747

  4. Recent Advances for the Detection of Ochratoxin A

    PubMed Central

    Ha, Tai Hwan

    2015-01-01

    Ochratoxin A (OTA) is one of the mycotoxins secreted by Aspergillus and Penicillium that can easily colonize various grains like coffee, peanut, rice, and maize. Since OTA is a chemically stable compound that can endure the physicochemical conditions of modern food processing, additional research efforts have been devoted to develop sensitive and cost-effective surveillance solutions. Although traditional chromatographic and immunoassays appear to be mature enough to attain sensitivity up to the regulation levels, alternative detection schemes are still being enthusiastically pursued in an attempt to meet the requirements of rapid and cost-effective detections. Herein, this review presents recent progresses in OTA detections with minimal instrumental usage, which have been facilitated by the development of OTA aptamers and by the innovations in functional nanomaterials. In addition to the introduction of aptamer-based OTA detection techniques, OTA-specific detection principles are also presented, which exclusively take advantage of the unique chemical structure and related physicochemical characteristics. PMID:26690216

  5. Robust detection-isolation-accommodation for sensor failures

    NASA Technical Reports Server (NTRS)

    Weiss, J. L.; Pattipati, K. R.; Willsky, A. S.; Eterno, J. S.; Crawford, J. T.

    1985-01-01

    The results of a one year study to: (1) develop a theory for Robust Failure Detection and Identification (FDI) in the presence of model uncertainty, (2) develop a design methodology which utilizes the robust FDI ththeory, (3) apply the methodology to a sensor FDI problem for the F-100 jet engine, and (4) demonstrate the application of the theory to the evaluation of alternative FDI schemes are presented. Theoretical results in statistical discrimination are used to evaluate the robustness of residual signals (or parity relations) in terms of their usefulness for FDI. Furthermore, optimally robust parity relations are derived through the optimization of robustness metrics. The result is viewed as decentralization of the FDI process. A general structure for decentralized FDI is proposed and robustness metrics are used for determining various parameters of the algorithm.

  6. Advances in Anthrax Detection: Overview of Bioprobes and Biosensors.

    PubMed

    Kim, Joungmok; Gedi, Vinayakumar; Lee, Sang-Choon; Cho, Jun-Haeng; Moon, Ji-Young; Yoon, Moon-Young

    2015-06-01

    Anthrax is an infectious disease caused by Bacillus anthracis. Although anthrax commonly affects domestic and wild animals, it causes a rare but lethal infection in humans. A variety of techniques have been introduced and evaluated to detect anthrax using cultures, polymerase chain reaction, and immunoassays to address the potential threat of anthrax being used as a bioweapon. The high-potential harm of anthrax in bioterrorism requires sensitive and specific detection systems that are rapid, field-ready, and real-time monitoring. Here, we provide a systematic overview of anthrax detection probes with their potential applications in various ultra-sensitive diagnostic systems. PMID:25987133

  7. Advances in the detection capability on actinic blank inspection

    NASA Astrophysics Data System (ADS)

    Yamane, Takeshi; Amano, Tsuyoshi; Takagi, Noriaki; Watanabe, Hidehiro; Mori, Ichro; Ino, Tomohisa; Suzuki, Tomohiro; Takehisa, Kiwamu; Miyai, Hiroki; Kusunose, Haruhiko

    2016-03-01

    Improvements in the detection capability of a high-volume-manufacturing (HVM) actinic blank inspection (ABI) prototype for native defects caused by illumination numerical aperture (NA) enlargement were evaluated. A mask blank was inspected by varying the illumination NA. The defect signal intensity increased with illumination NA enlargement as predicted from simulation. The mask blank was also inspected with optical tools, and no additional phase defect was detected. All of the printable phase defects were verified to have been detected by the HVM ABI prototype.

  8. Advances in Anthrax Detection: Overview of Bioprobes and Biosensors.

    PubMed

    Kim, Joungmok; Gedi, Vinayakumar; Lee, Sang-Choon; Cho, Jun-Haeng; Moon, Ji-Young; Yoon, Moon-Young

    2015-06-01

    Anthrax is an infectious disease caused by Bacillus anthracis. Although anthrax commonly affects domestic and wild animals, it causes a rare but lethal infection in humans. A variety of techniques have been introduced and evaluated to detect anthrax using cultures, polymerase chain reaction, and immunoassays to address the potential threat of anthrax being used as a bioweapon. The high-potential harm of anthrax in bioterrorism requires sensitive and specific detection systems that are rapid, field-ready, and real-time monitoring. Here, we provide a systematic overview of anthrax detection probes with their potential applications in various ultra-sensitive diagnostic systems.

  9. Developments in advanced and energy saving thermal isolations for cryogenic applications

    NASA Astrophysics Data System (ADS)

    Shu, Q. S.; Demko, J. A.; Fesmire, J. E.

    2015-12-01

    The cooling power consumption in large scale superconducting systems is huge and cryogenic devices used in space applications often require an extremely long cryogen holding time. To economically maintain the device at its operating temperature and minimize the refrigeration losses, high performance of thermal isolation is essential. The radiation from warm surrounding surfaces and conducting heat leaks through supports and penetrations are the dominant heat loads to the cold mass under vacuum condition. The advanced developments in various cryogenic applications to successfully reduce the heat loads through radiation and conduction are briefly and systematically discussed and evaluated in this review paper. These include: (1) thermal Insulation for different applications (foams, perlites, glass bubbles, aerogel and MLI), (2) sophisticated low-heat-leak support (cryogenic tension straps, trolley bars and posts with dedicated thermal intercepts), and (3) novel cryogenic heat switches.

  10. [Isolation and identification methods of enterobacteria group and its technological advancement].

    PubMed

    Furuta, Itaru

    2007-08-01

    In the last half-century, isolation and identification methods of enterobacteria groups have markedly improved by technological advancement. Clinical microbiology tests have changed overtime from tube methods to commercial identification kits and automated identification. Tube methods are the original method for the identification of enterobacteria groups, that is, a basically essential method to recognize bacterial fermentation and biochemical principles. In this paper, traditional tube tests are discussed, such as the utilization of carbohydrates, indole, methyl red, and citrate and urease tests. Commercial identification kits and automated instruments by computer based analysis as current methods are also discussed, and those methods provide rapidity and accuracy. Nonculture techniques of nucleic acid typing methods using PCR analysis, and immunochemical methods using monoclonal antibodies can be further developed.

  11. ASCS online fault detection and isolation based on an improved MPCA

    NASA Astrophysics Data System (ADS)

    Peng, Jianxin; Liu, Haiou; Hu, Yuhui; Xi, Junqiang; Chen, Huiyan

    2014-09-01

    Multi-way principal component analysis (MPCA) has received considerable attention and been widely used in process monitoring. A traditional MPCA algorithm unfolds multiple batches of historical data into a two-dimensional matrix and cut the matrix along the time axis to form subspaces. However, low efficiency of subspaces and difficult fault isolation are the common disadvantages for the principal component model. This paper presents a new subspace construction method based on kernel density estimation function that can effectively reduce the storage amount of the subspace information. The MPCA model and the knowledge base are built based on the new subspace. Then, fault detection and isolation with the squared prediction error (SPE) statistic and the Hotelling ( T 2) statistic are also realized in process monitoring. When a fault occurs, fault isolation based on the SPE statistic is achieved by residual contribution analysis of different variables. For fault isolation of subspace based on the T 2 statistic, the relationship between the statistic indicator and state variables is constructed, and the constraint conditions are presented to check the validity of fault isolation. Then, to improve the robustness of fault isolation to unexpected disturbances, the statistic method is adopted to set the relation between single subspace and multiple subspaces to increase the corrective rate of fault isolation. Finally fault detection and isolation based on the improved MPCA is used to monitor the automatic shift control system (ASCS) to prove the correctness and effectiveness of the algorithm. The research proposes a new subspace construction method to reduce the required storage capacity and to prove the robustness of the principal component model, and sets the relationship between the state variables and fault detection indicators for fault isolation.

  12. Flight test results of failure detection and isolation algorithms for a redundant strapdown inertial measurement unit

    NASA Technical Reports Server (NTRS)

    Morrell, F. R.; Motyka, P. R.; Bailey, M. L.

    1990-01-01

    Flight test results for two sensor fault-tolerant algorithms developed for a redundant strapdown inertial measurement unit are presented. The inertial measurement unit (IMU) consists of four two-degrees-of-freedom gyros and accelerometers mounted on the faces of a semi-octahedron. Fault tolerance is provided by edge vector test and generalized likelihood test algorithms, each of which can provide dual fail-operational capability for the IMU. To detect the wide range of failure magnitudes in inertial sensors, which provide flight crucial information for flight control and navigation, failure detection and isolation are developed in terms of a multi level structure. Threshold compensation techniques, developed to enhance the sensitivity of the failure detection process to navigation level failures, are presented. Four flight tests were conducted in a commercial transport-type environment to compare and determine the performance of the failure detection and isolation methods. Dual flight processors enabled concurrent tests for the algorithms. Failure signals such as hard-over, null, or bias shift, were added to the sensor outputs as simple or multiple failures during the flights. Both algorithms provided timely detection and isolation of flight control level failures. The generalized likelihood test algorithm provided more timely detection of low-level sensor failures, but it produced one false isolation. Both algorithms demonstrated the capability to provide dual fail-operational performance for the skewed array of inertial sensors.

  13. Detection and Antimicrobial Resistance of Vibrio Isolates in Aquaculture Environments: Implications for Public Health.

    PubMed

    Igbinosa, Etinosa O

    2016-04-01

    The aim of this study was to evaluate the presence of Vibrio isolates recovered from four different fish pond facilities in Benin City, Nigeria, determine their antibiogram profiles, and evaluate the public health implications of these findings. Fish pond water samples were collected from four sampling sites between March and September 2014. A total of 56 samples were collected and screened for the isolation of Vibrio species using standard culture-based methods. Polymerase chain reaction (PCR) was used to confirm the identities of the Vibrio species using the genus-specific and species-specific primers. Vibrio species were detected at all the study sites at a concentration on the order of 10(3) and 10(6) CFU/100 ml. A total of 550 presumptive Vibrio isolates were subjected to PCR confirmation. Of these isolates, 334 isolates tested positive, giving an overall Vibrio prevalence rate of 60.7%. The speciation of the 334 Vibrio isolates from fish ponds yielded 32.63% Vibrio fluvialis, 20.65% Vibrio parahaemolyticus, 18.26% Vibrio vulnificus, and 28.44% other Vibrio species. In all, 167 confirmed Vibrio isolates were selected from a pool of 334 confirmed Vibrio isolates for antibiogram profiling. The susceptibility profiles of 20 antimicrobial agents on the isolates revealed a high level of resistance for AMP(R), ERY(R), NAL(R), SUL(R), TMP(R), SXT(R), TET(R), OTC(R), and CHL(R). The percentage of multiple drug resistance Vibrio isolates was 67.6%. The multiple antibiotic resistance index mean value of 0.365 for the Vibrio isolates found in this study indicated that the Vibrio isolates were exposed to high-risk sources of contamination when antibiotics were frequently used. The resistant Vibrio strains could be transmitted through the food chain to humans and therefore constitutes a risk to public health.

  14. Detection of Carbapenemases in Clinical Enterobacteriaceae Isolates Using the VITEK AST-N202 Card

    PubMed Central

    Bae, Il Kwon; Kang, Hyun-Kyung; Jang, In-Ho; Lee, Woonhyoung; Kim, Keonhan; Jeong, Seok Hoon; Lee, Kyungwon

    2015-01-01

    Background The rapid and accurate detection of carbapenemase-producing Enterobacteriaceae (CPE) in clinical microbiology laboratories is essential for the treatment and control of infections caused by these microorganisms. This study was performed to evaluate the ability of the VITEK AST-N202 card to detect CPE isolates. Materials and Methods A total of 43 (Klebsiella pneumoniae, n = 37; Escherichia coli, n = 3; and Enterobacter cloacae, n = 3) CPE isolates and 79 carbapenemase-non-producing Enterobacteriaceae (CNE) isolates were included in this study. The CPE isolates harbored KPC-2 (n = 11), KPC-3 (n = 20), GES-5 (n = 5), VIM-2 (n = 2), IMP-1 (n = 1), NDM-1 (n = 2), or OXA-232 (n = 2). Of the 79 CNE isolates, eight K. pneumoniae isolates were resistant to ertapenem, imipenem, and meropenem, while the remaining 71 isolates were susceptible to the carbapenems. Antimicrobial susceptibilities were tested using the VITEK AST-N202 card, and the results were interpreted as positive when the isolates showed resistant or intermediate results. Modified-Hodge tests (MHTs) were performed using ertapenem or meropenem disks for the screening of carbapenemase production. Polymerase chain reaction (PCR) and direct sequencing were used to identify β-lactamase genes. Results Sensitivity of MHT with ertapenem and meropenem disks for the detection of carbapenemase was 81.4% (35/43) and 81.4% (35/43), respectively, and a combination with both antibiotic disks increased the sensitivity to 88.4% (38/43). Specificity of the MHT was 100% (79/79) for the CNE isolates. Sensitivity of ertapenem, imipenem, and meropenem as assessed by the VITEK AST-N202 card was 100% (43/43), 93% (40/43), and 95.3% (41/43), respectively. Specificity (89.8%, 71/79) of the test with each carbapenem was improved to 100% (71/71) when eight carbapenem-resistant CNE isolates were excluded from the testing. Conclusion The VITEK AST-N202 card showed high sensitivity for the detection of carbapenemases in

  15. Antimicrobial Susceptibility of Bordetella bronchiseptica Isolates from Swine and Companion Animals and Detection of Resistance Genes.

    PubMed

    Prüller, Sandra; Rensch, Ulrike; Meemken, Diana; Kaspar, Heike; Kopp, Peter A; Klein, Günter; Kehrenberg, Corinna

    2015-01-01

    Bordetella bronchiseptica causes infections of the respiratory tract in swine and other mammals and is a precursor for secondary infections with Pasteurella multocida. Treatment of B. bronchiseptica infections is conducted primarily with antimicrobial agents. Therefore it is essential to get an overview of the susceptibility status of these bacteria. The aim of this study was to comparatively analyse broth microdilution susceptibility testing according to CLSI recommendations with an incubation time of 16 to 20 hours and a longer incubation time of 24 hours, as recently proposed to obtain more homogenous MICs. Susceptibility testing against a panel of 22 antimicrobial agents and two fixed combinations was performed with 107 porcine isolates from different farms and regions in Germany and 43 isolates obtained from companion animals in Germany and other European countries. Isolates with increased MICs were investigated by PCR assays for the presence of resistance genes. For ampicillin, all 107 porcine isolates were classified as resistant, whereas only a single isolate was resistant to florfenicol. All isolates obtained from companion animals showed elevated MICs for β-lactam antibiotics and demonstrated an overall low susceptibility to cephalosporines. Extension of the incubation time resulted in 1-2 dilution steps higher MIC50 values of porcine isolates for seven antimicrobial agents tested, while isolates from companion animals exhibited twofold higher MIC50/90 values only for tetracycline and cefotaxime. For three antimicrobial agents, lower MIC50 and MIC90 values were detected for both, porcine and companion animal isolates. Among the 150 isolates tested, the resistance genes blaBOR-1 (n = 147), blaOXA-2, (n = 4), strA and strB (n = 17), sul1 (n = 10), sul2 (n = 73), dfrA7 (n = 3) and tet(A) (n = 8) were detected and a plasmid localisation was identified for several of the resistance genes.

  16. Antimicrobial Susceptibility of Bordetella bronchiseptica Isolates from Swine and Companion Animals and Detection of Resistance Genes.

    PubMed

    Prüller, Sandra; Rensch, Ulrike; Meemken, Diana; Kaspar, Heike; Kopp, Peter A; Klein, Günter; Kehrenberg, Corinna

    2015-01-01

    Bordetella bronchiseptica causes infections of the respiratory tract in swine and other mammals and is a precursor for secondary infections with Pasteurella multocida. Treatment of B. bronchiseptica infections is conducted primarily with antimicrobial agents. Therefore it is essential to get an overview of the susceptibility status of these bacteria. The aim of this study was to comparatively analyse broth microdilution susceptibility testing according to CLSI recommendations with an incubation time of 16 to 20 hours and a longer incubation time of 24 hours, as recently proposed to obtain more homogenous MICs. Susceptibility testing against a panel of 22 antimicrobial agents and two fixed combinations was performed with 107 porcine isolates from different farms and regions in Germany and 43 isolates obtained from companion animals in Germany and other European countries. Isolates with increased MICs were investigated by PCR assays for the presence of resistance genes. For ampicillin, all 107 porcine isolates were classified as resistant, whereas only a single isolate was resistant to florfenicol. All isolates obtained from companion animals showed elevated MICs for β-lactam antibiotics and demonstrated an overall low susceptibility to cephalosporines. Extension of the incubation time resulted in 1-2 dilution steps higher MIC50 values of porcine isolates for seven antimicrobial agents tested, while isolates from companion animals exhibited twofold higher MIC50/90 values only for tetracycline and cefotaxime. For three antimicrobial agents, lower MIC50 and MIC90 values were detected for both, porcine and companion animal isolates. Among the 150 isolates tested, the resistance genes blaBOR-1 (n = 147), blaOXA-2, (n = 4), strA and strB (n = 17), sul1 (n = 10), sul2 (n = 73), dfrA7 (n = 3) and tet(A) (n = 8) were detected and a plasmid localisation was identified for several of the resistance genes. PMID:26275219

  17. Antimicrobial Susceptibility of Bordetella bronchiseptica Isolates from Swine and Companion Animals and Detection of Resistance Genes

    PubMed Central

    Prüller, Sandra; Rensch, Ulrike; Meemken, Diana; Kaspar, Heike; Kopp, Peter A.; Klein, Günter; Kehrenberg, Corinna

    2015-01-01

    Bordetella bronchiseptica causes infections of the respiratory tract in swine and other mammals and is a precursor for secondary infections with Pasteurella multocida. Treatment of B. bronchiseptica infections is conducted primarily with antimicrobial agents. Therefore it is essential to get an overview of the susceptibility status of these bacteria. The aim of this study was to comparatively analyse broth microdilution susceptibility testing according to CLSI recommendations with an incubation time of 16 to 20 hours and a longer incubation time of 24 hours, as recently proposed to obtain more homogenous MICs. Susceptibility testing against a panel of 22 antimicrobial agents and two fixed combinations was performed with 107 porcine isolates from different farms and regions in Germany and 43 isolates obtained from companion animals in Germany and other European countries. Isolates with increased MICs were investigated by PCR assays for the presence of resistance genes. For ampicillin, all 107 porcine isolates were classified as resistant, whereas only a single isolate was resistant to florfenicol. All isolates obtained from companion animals showed elevated MICs for β-lactam antibiotics and demonstrated an overall low susceptibility to cephalosporines. Extension of the incubation time resulted in 1–2 dilution steps higher MIC50 values of porcine isolates for seven antimicrobial agents tested, while isolates from companion animals exhibited twofold higher MIC50/90 values only for tetracycline and cefotaxime. For three antimicrobial agents, lower MIC50 and MIC90 values were detected for both, porcine and companion animal isolates. Among the 150 isolates tested, the resistance genes blaBOR-1 (n = 147), blaOXA-2, (n = 4), strA and strB (n = 17), sul1 (n = 10), sul2 (n = 73), dfrA7 (n = 3) and tet(A) (n = 8) were detected and a plasmid localisation was identified for several of the resistance genes. PMID:26275219

  18. Detection of mutations associated with isoniazid resistance in Mycobacterium tuberculosis isolates from China.

    PubMed

    Zhang, Min; Yue, Jun; Yang, Yan-Ping; Zhang, Hong-Mei; Lei, Jian-Qiang; Jin, Rui-Liang; Zhang, Xue-Lian; Wang, Hong-Hai

    2005-11-01

    Nine structural genes (furA, katG, inhA, kasA, Rv0340, iniB, iniA, iniC, and efpA) and two regulatory regions (the oxyR-ahpC intergenic region and the promoter of mabA-inhA) in 87 isoniazid (INH)-monoresistant and 50 INH-susceptible Mycobacterium tuberculosis isolates collected from five provinces of China were analyzed by sequencing. Eighty-two (94.3%) INH-resistant isolates had mutations in the katG gene, with the katG Ser315Thr mutation predominant (55.2%). No mutation at codon 463 of katG was detected among the 50 INH-susceptible isolates with different IS6110 fingerprints. In addition, there were 35 (40.2%) INH-resistant isolates that had a mutation at codon 463 of katG. Of the INH-resistant strains, 20 (23.0%) isolates harbored double mutations at two separate loci of katG. Mutations in the inhA promoter region occurred in 13 (14.9%) isolates; 4.6% of the isolates had inhA structural gene mutations, and 11.5% harbored mutations in the oxyR-ahpC intergenic region. Drug resistance-associated mutations were detected in the iniBAC region and efpA. PMID:16272473

  19. Rapid identification of mycobacteria and rapid detection of drug resistance in Mycobacterium tuberculosis in cultured isolates and in respiratory specimens.

    PubMed

    Yam, Wing-Cheong; Siu, Kit-Hang Gilman

    2013-01-01

    Recent advances in molecular biology and better understanding of the genetic basis of drug resistance have allowed rapid identification of mycobacteria and rapid detection of drug resistance of Mycobacterium tuberculosis present in cultured isolates or in respiratory specimens. In this chapter, several simple nucleic acid amplification-based techniques are introduced as molecular approach for clinical diagnosis of tuberculosis. A one-tube nested IS6110-based polymerase chain reaction (PCR) is used for M. tuberculosis complex identification; the use of a multiplex allele-specific PCR is demonstrated to detect the isoniazid resistance; PCR-sequencing assays are applied for rifampicin and ofloxacin resistance detection and 16S rDNA sequencing is utilized for identification of mycobacterial species from cultures of acid fast bacilli (AFB). Despite the high specificity and sensitivity of the molecular techniques, mycobacterial culture remains the "Gold Standard" for tuberculosis diagnosis. Negative results of molecular tests never preclude the infection or the presence of drug resistance. These technological advancements are, therefore, not intended to replace the conventional tests, but rather have major complementary roles in tuberculosis diagnosis.

  20. Prospects and advancements in C-reactive protein detection

    PubMed Central

    Chandra, Pranjal; Suman, Pankaj; Airon, Himangi; Mukherjee, Monalisa; Kumar, Prabhanshu

    2014-01-01

    C-reactive protein (CRP) is one of the earliest proteins that appear in the blood circulation in most systemic inflammatory conditions and this is the reason for its significance, even after identification of many organ specific inflammatory markers which appear relatively late during the course of disease. Earlier methods of CRP detection were based on the classical methods of antigen-antibody interaction through precipitation and agglutination reactions. Later on, CRP based enzymatic assays came into the picture which were further modified by integration of an antigen-antibody detection system with surface plasma spectroscopy. Then came the time for the development of electrochemical biosensors where nanomaterials were used to make a highly sensitive and portable detection system based on silicon nanowire, metal-oxide-semiconductor field-effect transistor/bipolar junction transistor, ZnS nanoparticle, aptamer, field emission transmitter, vertical flow immunoassay etc. This editorial attempts to summarize developments in the field of CRP detection, with a special emphasis on biosensor technology. This would help in translating the latest development in CRP detection in the clinical diagnosis of inflammatory conditions at an early onset of the diseases. PMID:25237625

  1. Advanced terahertz techniques for quality control and counterfeit detection

    NASA Astrophysics Data System (ADS)

    Ahi, Kiarash; Anwar, Mehdi

    2016-04-01

    This paper reports our invented methods for detection of counterfeit electronic. These versatile techniques are also handy in quality control applications. Terahertz pulsed laser systems are capable of giving the material characteristics and thus make it possible to distinguish between the materials used in authentic components and their counterfeit clones. Components with material defects can also be distinguished in section in this manner. In this work different refractive indices and absorption coefficients were observed for counterfeit components compared to their authentic counterparts. Existence of unexpected ingredient materials was detected in counterfeit components by Fourier Transform analysis of the transmitted terahertz pulse. Thicknesses of different layers are obtainable by analyzing the reflected terahertz pulse. Existence of unexpected layers is also detectable in this manner. Recycled, sanded and blacktopped counterfeit electronic components were detected as a result of these analyses. Counterfeit ICs with die dislocations were detected by depicting the terahertz raster scanning data in a coordinate plane which gives terahertz images. In the same manner, raster scanning of the reflected pulse gives terahertz images of the surfaces of the components which were used to investigate contaminant materials and sanded points on the surfaces. The results of the later technique, reveals the recycled counterfeit components.

  2. Prospects and advancements in C-reactive protein detection.

    PubMed

    Chandra, Pranjal; Suman, Pankaj; Airon, Himangi; Mukherjee, Monalisa; Kumar, Prabhanshu

    2014-03-26

    C-reactive protein (CRP) is one of the earliest proteins that appear in the blood circulation in most systemic inflammatory conditions and this is the reason for its significance, even after identification of many organ specific inflammatory markers which appear relatively late during the course of disease. Earlier methods of CRP detection were based on the classical methods of antigen-antibody interaction through precipitation and agglutination reactions. Later on, CRP based enzymatic assays came into the picture which were further modified by integration of an antigen-antibody detection system with surface plasma spectroscopy. Then came the time for the development of electrochemical biosensors where nanomaterials were used to make a highly sensitive and portable detection system based on silicon nanowire, metal-oxide-semiconductor field-effect transistor/bipolar junction transistor, ZnS nanoparticle, aptamer, field emission transmitter, vertical flow immunoassay etc. This editorial attempts to summarize developments in the field of CRP detection, with a special emphasis on biosensor technology. This would help in translating the latest development in CRP detection in the clinical diagnosis of inflammatory conditions at an early onset of the diseases. PMID:25237625

  3. Recent advances and progress in the detection of bisphenol A.

    PubMed

    Sun, Fengxia; Kang, Lichao; Xiang, Xiaoli; Li, Hongmin; Luo, Xiaoling; Luo, Ruifeng; Lu, Chunxia; Peng, Xiayu

    2016-10-01

    Bisphenol A (BPA) is an important industrial chemical used as a plasticizer in polycarbonate and epoxy resins in the plastic and paper industries. Because of its estrogenic properties, BPA has attracted increasing attention from many researchers. This review focuses primarily on analytical methods for BPA detection that have emerged in recent years. We present and discuss the advantages and disadvantages of sample preparation techniques (e.g., solvent extraction, solid-phase extraction, molecularly imprinted polymer solid-phase extraction, and micro-extraction techniques) and analytical methods (e.g., liquid chromatography, liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, capillary electrophoresis, immunoassay, and several novel sensors). We also discuss expected future developments for the detection of BPA. Graphical Abstract This review focuses primarily on the recent development in the detection of bisphenol A including sample pre-treatment and analytical methods. PMID:27485626

  4. Detection of toxigenic isolates of Aspergillus flavus and related species on coconut cream agar.

    PubMed

    Dyer, S K; McCammon, S

    1994-01-01

    A new readily-prepared medium, coconut cream agar, was developed for the detection of aflatoxin production by isolates of Aspergillus flavus and related species. Coconut cream agar, which comprised coconut cream (50%) and agar (1.5%), detected isolates of A. flavus more effectively than the synthetic media tested and was as effective as media containing desiccated coconut. Fluorescence colouring of colonies grown on coconut cream agar could be used to differentiate A. flavus from A. parasiticus and A. nomius. In addition, conidial colour of A. flavus and A. nomius was quite distinct from that of A. parasiticus.

  5. Advances in Assays and Analytical Approaches for Botulinum Toxin Detection

    SciTech Connect

    Grate, Jay W.; Ozanich, Richard M.; Warner, Marvin G.; Bruckner-Lea, Cindy J.; Marks, James D.

    2010-08-04

    Methods to detect botulinum toxin, the most poisonous substance known, are reviewed. Current assays are being developed with two main objectives in mind: 1) to obtain sufficiently low detection limits to replace the mouse bioassay with an in vitro assay, and 2) to develop rapid assays for screening purposes that are as sensitive as possible while requiring an hour or less to process the sample an obtain the result. This review emphasizes the diverse analytical approaches and devices that have been developed over the last decade, while also briefly reviewing representative older immunoassays to provide background and context.

  6. Semi-active control of isolated and damaged structures using online damage detection

    NASA Astrophysics Data System (ADS)

    Amini, Fereidoun; Mohajeri, Seyed Ahmad; Javanbakht, Majd

    2015-10-01

    The idea of using semi-active or active control devices within a base isolation system has been developed recently, since applying this system to building structures has some shortcomings such as the creation of large displacements at the base level and the system's lack of adaptability to different seismic excitations. In this study, an integrated structural health monitoring and semi-active control scheme is proposed to enhance the seismic behavior of damaged isolated structures. The nonlinear behavior of an isolated structure is limited to the isolator level and the superstructure is assumed to remain linear. Then, using an online damage detection algorithm based on identified system Markov parameters and a semi-active fuzzy controller, the damage in the base isolator is mitigated and the seismic response of the structure is reduced. In addition, a magnetorheological damper is utilized as a well-studied semi-active actuator in the control system. The effectiveness of the proposed control system is evaluated through the numerical study of a six-degrees-of-freedom model of base-isolated buildings excited by various near-fault and far-field earthquake records. The results of the simulation show that the integrated algorithm is substantially effective in improving the dynamic behavior of isolated structures and reducing the damage in the isolator.

  7. Analytical evaluation for somatic mutation detection in circulating tumor cells isolated using a lateral magnetophoretic microseparator.

    PubMed

    Cho, Hyungseok; Kim, Jinho; Han, Song-I; Han, Ki-Ho

    2016-10-01

    CTCs are currently in the spotlight because provide comprehensive genetic information that enables monitoring of the evolution of cancer and selection of appropriate therapeutic strategies that cannot be obtained from a single-site tumor biopsy. Despite their importance, current techniques for isolating CTCs are limited in terms of their ability to yield high-quality CTCs from peripheral blood for use in profiling cancer genetic mutations by DNA sequencing technologies. This paper introduces a lateral magnetophoretic microseparator (the 'CTC-μChip') for isolating highly pure CTCs from blood, which facilitates the detection of somatic mutations in isolated CTCs. To isolate CTCs from peripheral blood, nucleated cells were first prepared by red blood cell lysis. Then, CTCs were isolated from nucleated cells within 30 min using the CTC-μChip. Analytical evaluation using 5 mL blood samples spiked with 5-50 MCF7 breast cancer cells demonstrated that the average recovery rate of the CTC-μChip was 99.08 %. The average number of residual white blood cells (WBCs) in isolated samples was 53, meaning that the WBC depletion rate is 472,000-fold (5.67 log), assuming that blood contains 5 × 10(6) WBCs per milliliter. The isolated MCF7 cells had a purity of 6.9 - 67.9 %, depending on the spiked MCF7 concentration. Using next-generation sequencing technology, heterozygous somatic mutations (PIK3CA and APC) of MCF7 cells were evaluated in the isolated samples. The results showed that somatic mutations could be detected in as few as two MCF7 cells per milliliter of blood, indicating that the CTC-μChip facilitates the detection of somatic variants in CTCs. PMID:27628059

  8. The advance of non-invasive detection methods in osteoarthritis

    NASA Astrophysics Data System (ADS)

    Dai, Jiao; Chen, Yanping

    2011-06-01

    Osteoarthritis (OA) is one of the most prevalent chronic diseases which badly affected the patients' living quality and economy. Detection and evaluation technology can provide basic information for early treatment. A variety of imaging methods in OA were reviewed, such as conventional X-ray, computed tomography (CT), ultrasound (US), magnetic resonance imaging (MRI) and near-infrared spectroscopy (NIRS). Among the existing imaging modalities, the spatial resolution of X-ray is extremely high; CT is a three-dimensional method, which has high density resolution; US as an evaluation method of knee OA discriminates lesions sensitively between normal cartilage and degenerative one; as a sensitive and nonionizing method, MRI is suitable for the detection of early OA, but the cost is too expensive for routine use; NIRS is a safe, low cost modality, and is also good at detecting early stage OA. In a word, each method has its own advantages, but NIRS is provided with broader application prospect, and it is likely to be used in clinical daily routine and become the golden standard for diagnostic detection.

  9. LEADERS: Lightweight Epidemiology Advanced Detection and Emergency Response System

    NASA Astrophysics Data System (ADS)

    Ritter, Todd A.

    2002-06-01

    Technological advancements in molecular biology now offer a wide-range of applications for bio-warfare defense, medical surveillance, agricultural surveillance and pure research. Idaho Technology has designed and produced the world's fastest DNA-based identifiers. The R.A.P.I.D. TM (Ruggedized Advanced Pathogen Identification Device) provides several options for using sensitive and specific molecular biology-based technology One of the key features of the RAPID is a software package called Detector*. Detector* allows Minimally Trained Care Providers (MTCP) to operate the instrument by automating the steps of running PCR and automatically analyzing the sample data. Pathogen identification is carried out automatically using positive and negative controls to protect against false positive and false negative results. As part of the LEADER system, the Remote RAPID Viewer (RRV) component allows for real-time remote monitoring of PCR reactions run on the RAPID, thus giving the Subject Matter Expert (SME) the ability to request specific tests when triggered by the auto-analysis system. In addition the RRV component facilitates in result verification of tests run by MTCP, assists in tracking outbreaks, and helps coordinate large scale real-time crisis management. The system will allow access to epidemiological data from thin client (i.e. web browser), thus allowing the SME to connect from anywhere with an internet connection. In addition the LEADER system will automatically contact and alert SME when threshold criteria are met, helping reduce the time to first response.

  10. Detection and tracking of drones using advanced acoustic cameras

    NASA Astrophysics Data System (ADS)

    Busset, Joël.; Perrodin, Florian; Wellig, Peter; Ott, Beat; Heutschi, Kurt; Rühl, Torben; Nussbaumer, Thomas

    2015-10-01

    Recent events of drones flying over city centers, official buildings and nuclear installations stressed the growing threat of uncontrolled drone proliferation and the lack of real countermeasure. Indeed, detecting and tracking them can be difficult with traditional techniques. A system to acoustically detect and track small moving objects, such as drones or ground robots, using acoustic cameras is presented. The described sensor, is completely passive, and composed of a 120-element microphone array and a video camera. The acoustic imaging algorithm determines in real-time the sound power level coming from all directions, using the phase of the sound signals. A tracking algorithm is then able to follow the sound sources. Additionally, a beamforming algorithm selectively extracts the sound coming from each tracked sound source. This extracted sound signal can be used to identify sound signatures and determine the type of object. The described techniques can detect and track any object that produces noise (engines, propellers, tires, etc). It is a good complementary approach to more traditional techniques such as (i) optical and infrared cameras, for which the object may only represent few pixels and may be hidden by the blooming of a bright background, and (ii) radar or other echo-localization techniques, suffering from the weakness of the echo signal coming back to the sensor. The distance of detection depends on the type (frequency range) and volume of the noise emitted by the object, and on the background noise of the environment. Detection range and resilience to background noise were tested in both, laboratory environments and outdoor conditions. It was determined that drones can be tracked up to 160 to 250 meters, depending on their type. Speech extraction was also experimentally investigated: the speech signal of a person being 80 to 100 meters away can be captured with acceptable speech intelligibility.

  11. How Does Sampling Methodology Influence Molecular Detection and Isolation Success in Influenza A Virus Field Studies?

    PubMed

    Latorre-Margalef, Neus; Avril, Alexis; Tolf, Conny; Olsen, Björn; Waldenström, Jonas

    2016-02-01

    Wild waterfowl are important reservoir hosts for influenza A virus (IAV) and a potential source of spillover infections in other hosts, including poultry and swine. The emergence of highly pathogenic avian influenza (HPAI) viruses, such as H5N1 and H5N8, and subsequent spread along migratory flyways prompted the initiation of several programs in Europe, North America, and Africa to monitor circulation of HPAI and low-pathogenicity precursor viruses (low-pathogenicity avian influenza [LPAI] viruses). Given the costs of maintaining such programs, it is essential to establish best practice for field methodologies to provide robust data for epidemiological interpretation. Here, we use long-term surveillance data from a single site to evaluate the influence of a number of parameters on virus detection and isolation of LPAI viruses. A total of 26,586 samples (oropharyngeal, fecal, and cloacal) collected from wild mallards were screened by real-time PCR, and positive samples were subjected to isolation in embryonated chicken eggs. The LPAI virus detection rate was influenced by the sample type: cloacal/fecal samples showed a consistently higher detection rate and lower cycle threshold (Ct) value than oropharyngeal samples. Molecular detection was more sensitive than isolation, and virus isolation success was proportional to the number of RNA copies in the sample. Interestingly, for a given Ct value, the isolation success was lower in samples from adult birds than in those from juveniles. Comparing the results of specific real-time reverse transcriptase (RRT)-PCRs and of isolation, it was clear that coinfections were common in the investigated birds. The effects of sample type and detection methods warrant some caution in interpretation of the surveillance data. PMID:26655759

  12. How Does Sampling Methodology Influence Molecular Detection and Isolation Success in Influenza A Virus Field Studies?

    PubMed Central

    Avril, Alexis; Tolf, Conny; Olsen, Björn

    2015-01-01

    Wild waterfowl are important reservoir hosts for influenza A virus (IAV) and a potential source of spillover infections in other hosts, including poultry and swine. The emergence of highly pathogenic avian influenza (HPAI) viruses, such as H5N1 and H5N8, and subsequent spread along migratory flyways prompted the initiation of several programs in Europe, North America, and Africa to monitor circulation of HPAI and low-pathogenicity precursor viruses (low-pathogenicity avian influenza [LPAI] viruses). Given the costs of maintaining such programs, it is essential to establish best practice for field methodologies to provide robust data for epidemiological interpretation. Here, we use long-term surveillance data from a single site to evaluate the influence of a number of parameters on virus detection and isolation of LPAI viruses. A total of 26,586 samples (oropharyngeal, fecal, and cloacal) collected from wild mallards were screened by real-time PCR, and positive samples were subjected to isolation in embryonated chicken eggs. The LPAI virus detection rate was influenced by the sample type: cloacal/fecal samples showed a consistently higher detection rate and lower cycle threshold (Ct) value than oropharyngeal samples. Molecular detection was more sensitive than isolation, and virus isolation success was proportional to the number of RNA copies in the sample. Interestingly, for a given Ct value, the isolation success was lower in samples from adult birds than in those from juveniles. Comparing the results of specific real-time reverse transcriptase (RRT)-PCRs and of isolation, it was clear that coinfections were common in the investigated birds. The effects of sample type and detection methods warrant some caution in interpretation of the surveillance data. PMID:26655759

  13. Continuing issues with Lead: Recent Advances in Detection

    PubMed Central

    Deibler, Kristine

    2014-01-01

    In the past Pb2+ has been used in many industries, including gasoline, piping, toys, paints, and more. The use of lead has led to a natural increase of lead concentration in the environment especially in air and water. According to the U.S. CDC “no level of lead in blood is considered safe.” Exposure to very low amounts of lead can cause several health complications including developmental and neurological disorders. Over the past several years an emphasis has been placed in developing systems that can detect lead at a very low concentration. A great deal of work has been accomplished in the development of Pb2+ sensors that can not only detect but also quantify the amount and in some cases in the presence of other metal ions. Herein, we describe current regulations, mode of exposure and recent development of sensing techniques. PMID:25089117

  14. A simplified hydroethidine method for fast and accurate detection of superoxide production in isolated mitochondria.

    PubMed

    Back, Patricia; Matthijssens, Filip; Vanfleteren, Jacques R; Braeckman, Bart P

    2012-04-01

    Because superoxide is involved in various physiological processes, many efforts have been made to improve its accurate quantification. We optimized and validated a superoxide-specific and -sensitive detection method. The protocol is based on fluorescence detection of the superoxide-specific hydroethidine (HE) oxidation product, 2-hydroxyethidium. We established a method for the quantification of superoxide production in isolated mitochondria without the need for acetone extraction and purification chromatography as described in previous studies.

  15. Polarization control for enhanced defect detection on advanced memory devices

    NASA Astrophysics Data System (ADS)

    Lee, Byoung-Ho; Ihm, Dong-Chul; Yeo, Jeong-Ho; Gluk, Yael; Meshulach, Doron

    2006-03-01

    Dense repetitive wafer structures, such as memory cells, with a pitch below the wavelength of the illumination light may take on effective birefringent properties, especially in layers of high refractive index materials such as silicon or conductors. Such induced "form birefringence" effects may result in dependency of the optical response on the illumination polarization and direction. In such structures, control over the polarization of the light becomes important to enhance signal-to-noise ratio (SNR) of pattern defects. We present defect detection results and analysis using DUV laser illumination for different polarization configurations and collection perspectives on Flash RAM devices. Improvement in detection SNR of bridge defect type is observed with linear illumination polarization perpendicular to the pattern lines. Generally, for small design rules (smaller than wavelength) polarization effects become more evident. Also, for smaller defect sizes, detection strongly depends on control of the illumination polarization. Linear polarization perpendicular to the pattern showed penetration into the structure even though the pitch is smaller than the illumination wavelength.

  16. The effect of different isolation protocols on detection and molecular characterization of Campylobacter from poultry.

    PubMed

    Ugarte-Ruiz, M; Wassenaar, T M; Gómez-Barrero, S; Porrero, M C; Navarro-Gonzalez, N; Domínguez, L

    2013-11-01

    We determined whether different methods to isolate Campylobacter (including the ISO standard 10272:2006-1) affected the genotypes detectable from poultry, at three points during slaughter: caecal content, neck skin and meat. Carcasses from 28 independent flocks were thus sampled (subset A). In addition, ten neck skin samples from four flocks, ten caecal samples from ten different flocks and ten unrelated meat samples obtained from local supermarkets were collected (subset B). Campylobacter was isolated using eight different protocols: with and without enrichment using Bolton broth, Preston broth or Campyfood broth (CFB), followed by culture on either modified Charcoal Cefoperazone Deoxycholate Agar (mCCDA) or Campyfood agar (CFA). All obtained isolates were genotyped for flaA-SVR, and over half of the isolates were also typed by MLST. The strain richness, as a measure of number of detected fla-genotypes, obtained from subset A neck skin and caecal samples was higher than that of meat samples. In half of the cases, within a flock, at least one identical fla-genotype was obtained at all three slaughter stages, suggestive of autologous contamination of carcasses. Enrichment reduced the observed richness of isolates, while CFA plates increased richness compared to mCCDA plates, irrespective of inclusion of an enrichment step. Because the isolation protocol used influences both the yield and the fla-genotype richness obtained from poultry, this variable should be taken into account when different studies are being compared.

  17. Detection and quantification of human adenovirus genomes in Acanthamoeba isolated from swimming pools.

    PubMed

    Staggemeier, Rodrigo; Arantes, Thalita; Caumo, Karin S; Rott, Marilise B; Spilki, Fernando R

    2016-01-01

    Acanthamoeba is the most common free-living environmental amoeba, it may serve as an important vehicle for various microorganisms living in the same environment, such as viruses, being pathogenic to humans. This study aimed to detect and quantify human adenoviruses (HAdV) in Acanthamoebas isolated from water samples collected from swimming pools in the city of Porto Alegre, Southern Brazil. Free-living amoebae of the genus Acanthamoeba were isolated from water samples, and isolates (n=16) were used to investigate the occurrence of HAdVs. HAdV detection was performed by quantitative real-time polymerase chain reaction (qPCR). HAdVs were detected in 62.5% (10/16) of Acanthamoeba isolates, ranging from 3.24x103 to 5.14x105 DNA copies per milliliter of isolate. HAdV viral loads found in this study are not negligible, especially because HAdV infections are associated with several human diseases, including gastroenteritis, respiratory distress, and ocular diseases. These findings reinforce the concept that Acanthamoeba may act as a reservoir and promote HAdV transmission through water. PMID:27142544

  18. Detection and sequence analysis of accessory gene regulator genes of Staphylococcus pseudintermedius isolates

    PubMed Central

    Chitra, M. Ananda; Jayanthy, C.; Nagarajan, B.

    2015-01-01

    Background: Staphylococcus pseudintermedius (SP) is the major pathogenic species of dogs involved in a wide variety of skin and soft tissue infections. The accessory gene regulator (agr) locus of Staphylococcus aureus has been extensively studied, and it influences the expression of many virulence genes. It encodes a two-component signal transduction system that leads to down-regulation of surface proteins and up-regulation of secreted proteins during in vitro growth of S. aureus. The objective of this study was to detect and sequence analyzing the AgrA, B, and D of SP isolated from canine skin infections. Materials and Methods: In this study, we have isolated and identified SP from canine pyoderma and otitis cases by polymerase chain reaction (PCR) and confirmed by PCR-restriction fragment length polymorphism. Primers for SP agrA and agrBD genes were designed using online primer designing software and BLAST searched for its specificity. Amplification of the agr genes was carried out for 53 isolates of SP by PCR and sequencing of agrA, B, and D were carried out for five isolates and analyzed using DNAstar and Mega5.2 software. Results: A total of 53 (59%) SP isolates were obtained from 90 samples. 15 isolates (28%) were confirmed to be methicillin-resistant SP (MRSP) with the detection of the mecA gene. Accessory gene regulator A, B, and D genes were detected in all the SP isolates. Complete nucleotide sequences of the above three genes for five isolates were submitted to GenBank, and their accession numbers are from KJ133557 to KJ133571. AgrA amino acid sequence analysis showed that it is mainly made of alpha-helices and is hydrophilic in nature. AgrB is a transmembrane protein, and AgrD encodes the precursor of the autoinducing peptide (AIP). Sequencing of the agrD gene revealed that the 5 canine SP strains tested could be divided into three Agr specificity groups (RIPTSTGFF, KIPTSTGFF, and RIPISTGFF) based on the putative AIP produced by each strain. The AIP of

  19. Detection of proteases from Sporosarcina aquimarina and Algoriphagus antarcticus isolated from Antarctic soil.

    PubMed

    Santos, Anderson F; Pires, Fabiano; Jesus, Hugo E; Santos, André L S; Peixoto, Raquel; Rosado, Alexandre S; D'Avila-Levy, Claudia M; Branquinha, Marta H

    2015-03-01

    Two psychrophilic bacterial samples were isolated from King George Island soil, in Antarctica. The phylogenetic analysis based on the 16S rRNA (rrs) gene led to the correlation with the closest related isolates as Sporosarcina aquimarina (99%) and Algoriphagus antarcticus (99%), with query coverage of 99% and 98%, respectively. The spent culture media from both isolates displayed proteolytic activities detected by sodium dodecyl sulfate polyacrylamide gel electrophoresis containing gelatin as protein substrate. Under the employed conditions, S. aquimarina showed a 55 kDa protease with the best activity detected at pH 7.0 and at 27°C. A. antarcticus also showed a single extracellular protease, however its molecular mass was around 90kDa and its best activity was detected at pH 9.0 and at 37°C. The proteases from both isolates were inhibited by 1,10-phenanthroline and EDTA, two metalloprotease inhibitors. This is the first record of protease detection in both species, and our results may contribute to broaden the basic knowledge of proteases from the Antarctica environment and may help prospecting future biotechnological applications of these enzymes.

  20. [Advances of NIR spectroscopy technology applied in seed quality detection].

    PubMed

    Zhu, Li-wei; Ma, Wen-guang; Hu, Jin; Zheng, Yun-ye; Tian, Yi-xin; Guan, Ya-jing; Hu, Wei-min

    2015-02-01

    Near infrared spectroscopy (NIRS) technology developed fast in recent years, due to its rapid speed, less pollution, high-efficiency and other advantages. It has been widely used in many fields such as food, chemical industry, pharmacy, agriculture and so on. The seed is the most basic and important agricultural capital goods, and seed quality is important for agricultural production. Most methods presently used for seed quality detecting were destructive, slow and needed pretreatment, therefore, developing one kind of method that is simple and rapid has great significance for seed quality testing. This article reviewed the application and trends of NIRS technology in testing of seed constituents, vigor, disease and insect pests etc. For moisture, starch, protein, fatty acid and carotene content, the model identification rates were high as their relative contents were high; for trace organic, the identification rates were low as their relative content were low. The heat-damaged seeds with low vigor were discriminated by NIRS, the seeds stored for different time could also been identified. The discrimination of frost-damaged seeds was impossible. The NIRS could be used to identify health and infected disease seeds, and did the classification for the health degree; it could identify parts of the fungal pathogens. The NIRS could identify worm-eaten and health seeds, and further distinguished the insect species, however the identification effects for small larval and low injury level of insect pests was not good enough. Finally, in present paper existing problems and development trends for NIRS in seed quality detection was discussed, especially the single seed detecting technology which was characteristic of the seed industry, the standardization of its spectral acquisition accessories will greatly improve its applicability.

  1. Recent Advances in Model-Assisted Probability of Detection

    NASA Technical Reports Server (NTRS)

    Thompson, R. Bruce; Brasche, Lisa J.; Lindgren, Eric; Swindell, Paul; Winfree, William P.

    2009-01-01

    The increased role played by probability of detection (POD) in structural integrity programs, combined with the significant time and cost associated with the purely empirical determination of POD, provides motivation for alternate means to estimate this important metric of NDE techniques. One approach to make the process of POD estimation more efficient is to complement limited empirical experiments with information from physics-based models of the inspection process or controlled laboratory experiments. The Model-Assisted Probability of Detection (MAPOD) Working Group was formed by the Air Force Research Laboratory, the FAA Technical Center, and NASA to explore these possibilities. Since the 2004 inception of the MAPOD Working Group, 11 meetings have been held in conjunction with major NDE conferences. This paper will review the accomplishments of this group, which includes over 90 members from around the world. Included will be a discussion of strategies developed to combine physics-based and empirical understanding, draft protocols that have been developed to guide application of the strategies, and demonstrations that have been or are being carried out in a number of countries. The talk will conclude with a discussion of future directions, which will include documentation of benefits via case studies, development of formal protocols for engineering practice, as well as a number of specific technical issues.

  2. Advanced fatigue-crack detection system in steel bridges

    NASA Astrophysics Data System (ADS)

    Fleming, Marvin F.; Hersh, S.; Chase, Steven B.

    1995-05-01

    The Federal Highway Administration has sponsored the development of a new system for fatigue crack detection and quantification of fatigue cracks in steel bridges. The NDE technology selected for the new system is based on earlier studies that have identified the best methods for this task. The new system that has been developed is based on previous work which produced two portable instruments that were field tested but were not widely accepted. The best characteristics from these systems have been integrated into a single instrument, using portable computer technology and adapted to the bridge inspection environment. The new system, which has come to be known as the New Ultrasonic-Magnetic Detection System (NUMAC), is configured as a backpack with a heads-up display that leaves the inspectors hands free to climb the structure and to view the inspection site simultaneously while viewing the ultrasonic or magnetic signals. The operation of the system controlled with a mouse or a keyboard. Importantly, the accuracy and repeatability of the NUMAC is combined with the ability to store inspection data. The stored data can be used to document condition, demonstrate and identity important trends, and efficiently channel resources. The flexibility of the portable computer based NDE system is intended to provide a basic, reliable and cost- effective instrument for steel bridge inspection.

  3. Advanced signal processing technique for damage detection in steel tubes

    NASA Astrophysics Data System (ADS)

    Amjad, Umar; Yadav, Susheel Kumar; Dao, Cac Minh; Dao, Kiet; Kundu, Tribikram

    2016-04-01

    In recent years, ultrasonic guided waves gained attention for reliable testing and characterization of metals and composites. Guided wave modes are excited and detected by PZT (Lead Zirconate Titanate) transducers either in transmission or reflection mode. In this study guided waves are excited and detected in the transmission mode and the phase change of the propagating wave modes are recorded. In most of the other studies reported in the literature, the change in the received signal strength (amplitude) is investigated with varying degrees of damage while in this study the change in phase is correlated with the extent of damage. Feature extraction techniques are used for extracting phase and time-frequency information. The main advantage of this approach is that the bonding condition between the transducer and the specimen does not affect the phase while it can affect the strength of recorded signal. Therefore, if the specimen is not damaged but the transducer-specimen bonding is deteriorated then the received signal strength is altered but the phase remains same and thus false positive predictions for damage can be avoided.

  4. Final LDRD report : advanced plastic scintillators for neutron detection.

    SciTech Connect

    Vance, Andrew L.; Mascarenhas, Nicholas; O'Bryan, Greg; Mrowka, Stanley

    2010-09-01

    This report summarizes the results of a one-year, feasibility-scale LDRD project that was conducted with the goal of developing new plastic scintillators capable of pulse shape discrimination (PSD) for neutron detection. Copolymers composed of matrix materials such as poly(methyl methacrylate) (PMMA) and blocks containing trans-stilbene (tSB) as the scintillator component were prepared and tested for gamma/neutron response. Block copolymer synthesis utilizing tSBMA proved unsuccessful so random copolymers containing up to 30% tSB were prepared. These copolymers were found to function as scintillators upon exposure to gamma radiation; however, they did not exhibit PSD when exposed to a neutron source. This project, while falling short of its ultimate goal, demonstrated the possible utility of single-component, undoped plastics as scintillators for applications that do not require PSD.

  5. Detection of Methicillin Resistance and Various Virulence Factors in Staphylococcus aureus Strains Isolated from Nasal Carriers

    PubMed Central

    Dağı, Hatice Türk; Fındık, Duygu; Demirel, Gamze; Arslan, Uğur

    2015-01-01

    Background: Staphylococus aureus can be found as a commensal on skin and nasal flora or it may cause local and invasive infections. S. aureus has a large number of virulence factors. Aims: To investigate the methicillin resistance and frequency of various virulence factors in S. aureus nasal isolates. Study Design: Descriptive study. Methods: Nasal samples collected from university students were cultured in media. S. aureus was identified by conventional methods and the Staphyloslide latex test (Becton Dickinson, Sparks, USA). Antibiotic susceptibility tests were conducted, and the methicillin resistance was determined. The mecA, nuc, pvl and staphylococcal toxin genes were examined by polymerase chain reaction (PCR). Results: S. aureus was isolated in 104 of 600 (17.3%) nasal samples. In total, 101 (97.1%) S. aureus isolates were methicillin-sensitive and the remaining 3 (2.9%) were methicillin-resistant. Furthermore, all but five isolates carried at least one staphylococcal enterotoxin gene, with seg being predominant. The tst and eta genes were determined in 29 (27.9%), and 3 (2.9%) isolates, respectively. None of the S. aureus isolates harbored see, etb, and pvl genes. Conclusion: A moderate rate of S. aureus carriage and low frequency of MRSA were detected in healthy students. S. aureus isolates had a high prevalence of staphylococcal enterotoxin genes and the tst gene. In this study, a large number of virulence factors were examined in S. aureus nasal isolates, and the data obtained from this study can be used for monitoring the prevalence of virulence genes in S. aureus strains isolated from nasal carriers. PMID:26167341

  6. Fault detection and isolation in manufacturing systems with an identified discrete event model

    NASA Astrophysics Data System (ADS)

    Roth, Matthias; Schneider, Stefan; Lesage, Jean-Jacques; Litz, Lothar

    2012-10-01

    In this article a generic method for fault detection and isolation (FDI) in manufacturing systems considered as discrete event systems (DES) is presented. The method uses an identified model of the closed-loop of plant and controller built on the basis of observed fault-free system behaviour. An identification algorithm known from literature is used to determine the fault detection model in form of a non-deterministic automaton. New results of how to parameterise this algorithm are reported. To assess the fault detection capability of an identified automaton, probabilistic measures are proposed. For fault isolation, the concept of residuals adapted for DES is used by defining appropriate set operations representing generic fault symptoms. The method is applied to a case study system.

  7. New Multiplex PCR for Rapid Detection of Isoniazid-Resistant Mycobacterium tuberculosis Clinical Isolates

    PubMed Central

    Herrera-León, Laura; Molina, Tamara; Saíz, Pilar; Sáez-Nieto, Juan Antonio; Soledad Jiménez, Maria

    2005-01-01

    In this study, we describe a multiplex PCR to detect a AGC→ACC (serine to threonine) mutation in the katG gene and a −15 C-to-T substitution (inhAC−15T) at the 5′ end of a presumed ribosome binding site in the promoter of the mabA-inhA operon. These mutations have been reported in the majority of previous studies as the most frequent mutations involved in the resistance to isoniazid (INH) of Mycobacterium tuberculosis clinical strains with high levels of resistance. The method was optimized and validated after an analysis of 30 M. tuberculosis clinical isolates with known sequences of the relevant part of the katG gene and the regulatory region of the mabA-inhA operon. We analyzed 297 INH-resistant M. tuberculosis isolates collected in Spain from 1996 to 2003 by PCR-restriction fragment length polymorphism (using the katG gene), DNA sequencing, and the newly developed multiplex PCR. The results were concordant for all 297 isolates tested. The analysis revealed that 204 (68.7%) of the isolates carried one or both of the mutations. This finding suggests that with further development this multiplex PCR will be able to detect the majority of the INH-resistant M. tuberculosis clinical isolates from Spain and other countries where a high frequency of similar mutations occur. PMID:15616288

  8. Set-theoretic methods in robust detection and isolation of sensor faults

    NASA Astrophysics Data System (ADS)

    Xu, Feng; Puig, Vicenç; Ocampo-Martinez, Carlos; Olaru, Sorin; Stoican, Florin

    2015-10-01

    This paper proposes a sensorfault detection and isolation (FDI) approach based on interval observers and invariant sets. In fault detection (FD), both interval observer-based and invariant set-based mechanisms are used to provide real-time fault alarms. In fault isolation (FI), the proposed approach also uses these two different mechanisms. The former, based on interval observers, aims to isolate faults during the transient-state operation induced by faults. If the former does not succeed, the latter, based on both interval observers and invariant sets, is started to guarantee FI after the system enters into steady state. Besides, a collection of invariant set-based FDI conditions are established by using all available system-operating information provided by all interval observers. In order to reduce computational complexity, a method to remove all available but redundant/unnecessary system-operating information is incorporated into this approach. If the considered faults satisfy the proposed FDI conditions, it can be guaranteed that they are detectable and isolable after their occurrences. This paper concludes with a case study based on a subsystem of a wind turbine benchmark, which can illustrate the effectiveness of this FDI technique.

  9. A Unified Nonlinear Adaptive Approach for Detection and Isolation of Engine Faults

    NASA Technical Reports Server (NTRS)

    Tang, Liang; DeCastro, Jonathan A.; Zhang, Xiaodong; Farfan-Ramos, Luis; Simon, Donald L.

    2010-01-01

    A challenging problem in aircraft engine health management (EHM) system development is to detect and isolate faults in system components (i.e., compressor, turbine), actuators, and sensors. Existing nonlinear EHM methods often deal with component faults, actuator faults, and sensor faults separately, which may potentially lead to incorrect diagnostic decisions and unnecessary maintenance. Therefore, it would be ideal to address sensor faults, actuator faults, and component faults under one unified framework. This paper presents a systematic and unified nonlinear adaptive framework for detecting and isolating sensor faults, actuator faults, and component faults for aircraft engines. The fault detection and isolation (FDI) architecture consists of a parallel bank of nonlinear adaptive estimators. Adaptive thresholds are appropriately designed such that, in the presence of a particular fault, all components of the residual generated by the adaptive estimator corresponding to the actual fault type remain below their thresholds. If the faults are sufficiently different, then at least one component of the residual generated by each remaining adaptive estimator should exceed its threshold. Therefore, based on the specific response of the residuals, sensor faults, actuator faults, and component faults can be isolated. The effectiveness of the approach was evaluated using the NASA C-MAPSS turbofan engine model, and simulation results are presented.

  10. Detecting Genetic Isolation in Human Populations: A Study of European Language Minorities

    PubMed Central

    Capocasa, Marco; Battaggia, Cinzia; Anagnostou, Paolo; Montinaro, Francesco; Boschi, Ilaria; Ferri, Gianmarco; Alù, Milena; Coia, Valentina; Crivellaro, Federica; Bisol, Giovanni Destro

    2013-01-01

    The identification of isolation signatures is fundamental to better understand the genetic structure of human populations and to test the relations between cultural factors and genetic variation. However, with current approaches, it is not possible to distinguish between the consequences of long-term isolation and the effects of reduced sample size, selection and differential gene flow. To overcome these limitations, we have integrated the analysis of classical genetic diversity measures with a Bayesian method to estimate gene flow and have carried out simulations based on the coalescent. Combining these approaches, we first tested whether the relatively short history of cultural and geographical isolation of four “linguistic islands” of the Eastern Alps (Lessinia, Sauris, Sappada and Timau) had left detectable signatures in their genetic structure. We then compared our findings to previous studies of European population isolates. Finally, we explored the importance of demographic and cultural factors in shaping genetic diversity among the groups under study. A combination of small initial effective size and continued genetic isolation from surrounding populations seems to provide a coherent explanation for the diversity observed among Sauris, Sappada and Timau, which was found to be substantially greater than in other groups of European isolated populations. Simulations of micro-evolutionary scenarios indicate that ethnicity might have been important in increasing genetic diversity among these culturally related and spatially close populations. PMID:23418562

  11. Detecting genetic isolation in human populations: a study of European language minorities.

    PubMed

    Capocasa, Marco; Battaggia, Cinzia; Anagnostou, Paolo; Montinaro, Francesco; Boschi, Ilaria; Ferri, Gianmarco; Alù, Milena; Coia, Valentina; Crivellaro, Federica; Destro Bisol, Giovanni

    2013-01-01

    The identification of isolation signatures is fundamental to better understand the genetic structure of human populations and to test the relations between cultural factors and genetic variation. However, with current approaches, it is not possible to distinguish between the consequences of long-term isolation and the effects of reduced sample size, selection and differential gene flow. To overcome these limitations, we have integrated the analysis of classical genetic diversity measures with a bayesian method to estimate gene flow and have carried out simulations based on the coalescent. Combining these approaches, we first tested whether the relatively short history of cultural and geographical isolation of four "linguistic islands" of the Eastern Alps (Lessinia, Sauris, Sappada and Timau) had left detectable signatures in their genetic structure. We then compared our findings to previous studies of European population isolates. Finally, we explored the importance of demographic and cultural factors in shaping genetic diversity among the groups under study. A combination of small initial effective size and continued genetic isolation from surrounding populations seems to provide a coherent explanation for the diversity observed among Sauris, Sappada and Timau, which was found to be substantially greater than in other groups of European isolated populations. Simulations of micro-evolutionary scenarios indicate that ethnicity might have been important in increasing genetic diversity among these culturally related and spatially close populations.

  12. Biosensor technology: recent advances in threat agent detection and medicine.

    PubMed

    Kirsch, Jeffrey; Siltanen, Christian; Zhou, Qing; Revzin, Alexander; Simonian, Aleksandr

    2013-11-21

    Biosensors are of great significance because of their capability to resolve a potentially large number of analytical problems and challenges in very diverse areas such as defense, homeland security, agriculture and food safety, environmental monitoring, medicine, pharmacology, industry, etc. The expanding role of biosensing in society and a real-world environment has led to an exponential growth of the R&D efforts around the world. The world market for biosensor devices, according to Global Industry Analysts, Inc., is expected to reach $12 billion by 2015. Such expedient growth is driven by several factors including medical and health problems, such as a growing population with a high risk of diabetes and obesity, and the rising incidence of chronic diseases such as heart disease, stroke, cancer, chronic respiratory diseases, tuberculosis, etc.; significant problems with environmental monitoring; and of course serious challenges in security and military applications and agriculture/food safety. A review paper in the biosensor technology area may be structured based on (i) the principles of detection, such as the type of transducer platform, bioanalytical principles (affinity or kinetic), and biorecognition elements origin/properties (i.e. antibodies, enzymes, cells, aptamers, etc.), and (ii) the application area. This review follows the latter strategy and focuses on the applications. This allows discussion on how different sensing strategies are brought to bear on the same problem and highlights advantages/disadvantages of these sensing strategies. Given the broad range of biosensor related applications, several particularly relevant areas of application were selected for review: biological threat agents, chemical threat agents, and medicine.

  13. Evaluation of Surrogate Disk Tests for Detection of Ciprofloxacin and Levofloxacin Resistance in Clinical Isolates of Salmonella enterica

    PubMed Central

    Deak, Eszter; Skov, Robert; Hindler, Janet A.

    2015-01-01

    Detection of fluoroquinolone resistance in Salmonella enterica has become increasingly difficult due to evolving resistance mechanisms to this antimicrobial class in this organism. We evaluated two quinolone disks and five fluoroquinolone disks for their ability to act as a surrogate agent for the detection of fluoroquinolone resistance in a collection of 136 S. enterica isolates, including 111 with intermediate or resistant ciprofloxacin MICs mediated by a variety of resistance mechanisms. Ciprofloxacin, ofloxacin, and pefloxacin disks detected all isolates resistant to ciprofloxacin (0% very major error) and yielded false resistance (major error) in 8, 4, and 12% of susceptible isolates, respectively. Ciprofloxacin and pefloxacin provided clearer differentiation of susceptible and resistant isolates. PMID:26292293

  14. Broad-spectrum detection and quantitation methods of Soil-borne cereal mosaic virus isolates.

    PubMed

    Vaïanopoulos, Céline; Legrève, Anne; Moreau, Virginie; Bragard, Claude

    2009-08-01

    A broad-spectrum reverse transcription-polymerase chain reaction (RT-PCR) protocol was developed for detecting Soil-borne cereal mosaic virus (SBCMV) isolates, responsible for mosaic diseases in Europe, using primers targeting the highly conserved 3'-untranslated region of RNA-1 and RNA-2 of SBCMV. The 3'-end region is a privileged target for the detection of a wide range of isolates, because of sequence conservation, of the tRNA-like structure, the major role in viral replication and the signal amplification due to the presence of numerous genomic and subgenomic RNAs. The primers were also designed for virus quantitation using real-time RT-PCR with SYBR-Green chemistry. No cross-reaction with Wheat spindle streak mosaic virus, frequently associated with SBCMV, was observed. The use of RT-PCR and real-time quantitative RT-PCR allowed a more sensitive detection and quantitation of SBCMV to be made than was the case with ELISA. The methods enabled European isolates of SBCMV from Belgium, France, Germany, Italy and the UK to be detected and quantified. Real-time RT-PCR represents a new tool for comparing soil inoculum potential as well as cultivar resistance to SBCMV.

  15. The evaluation of failure detection and isolation algorithms for restructurable control

    NASA Technical Reports Server (NTRS)

    Motyka, P.; Bonnice, W.; Hall, S.; Wagner, E.

    1984-01-01

    Three failure detection and identification techniques were compared to determine their usefulness in detecting and isolating failures in an aircraft flight control system; excluding sensor and flight control computer failures. The algorithms considered were the detection filter, the Generalized Likelihood Ratio test and the Orthogonal Series Generalized Likelihood Ratio test. A modification to the basic detection filter is also considered which uses secondary filtering of the residuals to produce unidirectional failure signals. The algorithms were evaluated by testing their ability to detect and isolate control surface failures in a nonlinear simulation of a C-130 aircraft. It was found that failures of some aircraft controls are difficult to distinguish because they have a similar effect on the dynamics of the vehicle. Quantitative measures for evaluating the distinguishability of failures are considered. A system monitoring strategy for implementing the failure detection and identification techniques was considered. This strategy identified the mix of direct measurement of failures versus the computation of failure necessary for implementation of the technology in an aircraft system.

  16. Development of advanced host cell protein enrichment and detection strategies to enable process relevant spike challenge studies.

    PubMed

    Soderquist, Ryan G; Trumbo, Mihaela; Hart, Roger A; Zhang, Qingchun; Flynn, Gregory C

    2015-01-01

    An orthogonal chromatography methodology for the enrichment of host cell protein (HCP) species relative to monoclonal antibody (mAb) products was developed and applied for the successful enrichment of HCP from post-Protein A process pools for seven different mAb products. An advanced two-dimensional liquid chromatography/mass spectrometry platform (2D-LC/MS(E) ) was utilized to demonstrate that the HCP enriched material was representative, in terms of species content, to pre-enriched process pools. The HCP enrichment methodology was scaled up for two different mAb products, and this process relevant enriched HCP material was used to conduct advanced spike challenge studies to demonstrate the utility of the approach for the understanding of (1) quantitative HCP clearance, (2) individual species clearance, and (3) species clearance redundancy across polishing chromatography steps. The combined ability to enrich process relevant HCP, detect individual HCP species with 2D-LC/MS(E) technology, and conduct advanced challenge studies with process relevant material surmounts prior limitations to high integrity process challenge study implementation, and facilitates significant process understanding for development of risk-based control strategies and strategic process design. This also demonstrates implementation of a foundational strategy for conducting spike-challenge studies using process-relevant impurities isolated from processes of interest using orthogonal approaches. PMID:26014278

  17. Development of advanced host cell protein enrichment and detection strategies to enable process relevant spike challenge studies.

    PubMed

    Soderquist, Ryan G; Trumbo, Mihaela; Hart, Roger A; Zhang, Qingchun; Flynn, Gregory C

    2015-01-01

    An orthogonal chromatography methodology for the enrichment of host cell protein (HCP) species relative to monoclonal antibody (mAb) products was developed and applied for the successful enrichment of HCP from post-Protein A process pools for seven different mAb products. An advanced two-dimensional liquid chromatography/mass spectrometry platform (2D-LC/MS(E) ) was utilized to demonstrate that the HCP enriched material was representative, in terms of species content, to pre-enriched process pools. The HCP enrichment methodology was scaled up for two different mAb products, and this process relevant enriched HCP material was used to conduct advanced spike challenge studies to demonstrate the utility of the approach for the understanding of (1) quantitative HCP clearance, (2) individual species clearance, and (3) species clearance redundancy across polishing chromatography steps. The combined ability to enrich process relevant HCP, detect individual HCP species with 2D-LC/MS(E) technology, and conduct advanced challenge studies with process relevant material surmounts prior limitations to high integrity process challenge study implementation, and facilitates significant process understanding for development of risk-based control strategies and strategic process design. This also demonstrates implementation of a foundational strategy for conducting spike-challenge studies using process-relevant impurities isolated from processes of interest using orthogonal approaches.

  18. First Detection of Metallo-β-Lactamase VIM-2 in Pseudomonas aeruginosa Isolates from Colombia

    PubMed Central

    Villegas, Maria Virginia; Lolans, Karen; del Rosario Olivera, Maria; Suarez, Carlos José; Correa, Adriana; Queenan, Anne Marie; Quinn, John P.

    2006-01-01

    Carbapenem resistance rates in Pseudomonas aeruginosa isolates in Colombia, as in many South American countries, are high for reasons that remain unclear. From our nationwide network, we describe the first detection of the metallo-β-lactamase VIM-2 in clinical isolates of P. aeruginosa from multiple cities within Colombia. Metallo-β-lactamases were not detected in the two centers with the highest imipenem resistance rates. Clonality was noted in five of the eight centers with strains meeting the criteria for molecular typing. The high carbapenem resistance in P. aeruginosa in Colombia may be attributable to a combination of factors, including the presence of metallo-β-lactamases and nosocomial transmission. PMID:16377690

  19. Failure detection and isolation methods for redundant gimballed inertial measurement units.

    NASA Technical Reports Server (NTRS)

    Solov, E. G.; Thibodeau, J. R., III

    1973-01-01

    Skewed alignment of two redundant conventional inertial measuring units permits nonambiguous detection and isolation of hard and soft failures in real time by an airborne computer. Accelerometer outputs and gimbal readouts are monitored periodically, and attitude rate and velocity error vectors are computed from these data. Magnitudes of these vectors provide failure detection, and projection of these error vectors onto the coordinate axes of the two clusters permits isolation. A detailed Monte Carlo simulation of one version of the mechanization as applied to Space Shuttle boost trajectories demonstrates effectiveness down to very low levels of inertial instrument performance failures. The results indicate that worst case overall navigation performance occurs when accelerometer failures are of the order of 20 sigma and gyro failures are about 100 sigma for conventional state-of-the-art IMU instruments.

  20. Molecular identification of Salmonella Infantis isolated from backyard chickens and detection of their resistance genesby PCR.

    PubMed

    Ghoddusi, A; Nayeri Fasaei, B; Karimi, V; Ashrafi Tamai, I; Moulana, Z; Zahraei Salehi, T

    2015-01-01

    This study aims at molecular identification of Salmonella Infantis isolated from backyard chickens and the detection of their antibiotic resistance genes. A total of 46 Salmonella-suspected samples isolated from backyard chickens of northern Iran were collected. Serotyping was done by the traditional method and then confirmed by PCR. Antimicrobial susceptibility of the isolates against 13 antimicrobial agents was determined by the standard disk diffusion method. There were 44 samples identified as Salmonella. Serotyping results showed that all 44 isolates belonged to serogroup C1 and serovar Infantis. The most resistance observed was to tetracycline and doxycycline (100%), chloramphenicol (79%) and florfenicol (72%). The floR, catI, tetA and tetG genes were used for the detection of florfenicol chloramphenicol and tetracycline resistance. In order to identify the phenotypic resistance in strains which showed resistance genes by PCR, colony PCR and culture on plates each containing antibiotic was performed simultaneously. All the Salmonella Infantis resistant to florfenicol and chloramphenicol harbored floR and catI. None of the Salmonella resistant to tetracycline carried tetA or tetG. The result of colony PCR and culture in antibiotic medium confirmed the results of PCR and indicated phenotypic resistance in these samples. PMID:27175192

  1. Detection and subtype identification of Blastocystis isolates from wastewater samples in the Philippines.

    PubMed

    Banaticla, Jan Ervin G; Rivera, Windell L

    2011-03-01

    To provide further evidence of waterborne transmission of Blastocystis, a total of 31 wastewater treatment plants from geographically distinct locations across the Philippines were sampled for influent and effluent sewage samples. In vitro cultivation was the method of choice to increase sensitivity of detection. Blastocystis cysts were detected in 15% (9/62) of the samples using in vitro culture. Moreover, influent and effluent samples were 23% (7/31) and 7% (2/31) positive for the parasite, respectively. The presence of viable cysts in treated samples may be an indication of the inefficiency of the treatment process in preventing Blastocystis from entering the environment. Polymerase chain reaction and sequencing of the full-length small subunit ribosomal RNA (SSU rRNA) genes of the nine wastewater isolates were performed. The SSU rRNA gene sequences of the isolates showed very high similarity (98 to 99%) to homologous sequences of Blastocystis described previously. The phylogenetic tree constructed showed that the wastewater isolates clustered with each other with good bootstrap support and belonged to two subtypes (ST) - ST1 and ST2. This is the first report of subtyping Blastocystis isolates from wastewater samples and gives further emphasis to the remarkable genetic diversity of the parasite. PMID:21301121

  2. A polymerase chain reaction protocol for the detection of various geographical isolates of white spot virus.

    PubMed

    Tapay, L M; Nadala, E C; Loh, P C

    1999-09-01

    Polymerase chain reaction (PCR) primers were designed based on the sequence of a cloned fragment of the white spot virus (WSV) genome and were used to detect at least four geographic isolates of WSV from both experimentally- and naturally-infected shrimp. In addition to high specificity, the one-step and two-step PCR protocols were determined to have sensitivities of 10-100 pg and 100 femtograms respectively. The two-step PCR protocol is recommended as a very sensitive and specific alternative protocol to Western blot assay for the detection of WSV.

  3. Detection of toxigenic Bacillus cereus strains isolated from vegetables in Mexico City.

    PubMed

    Flores-Urbán, Karen A; Natividad-Bonifacio, Iván; Vázquez-Quiñones, Carlos R; Vázquez-Salinas, Carlos; Quiñones-Ramírez, Elsa Irma

    2014-12-01

    Bacillus cereus can cause diarrhea and emetic syndromes after ingestion of food contaminated with it. This ability is due to the production of enterotoxins by this microorganism, these being the hemolysin BL complex, which is involved in the diarrheal syndrome, and cereulide, which is responsible for the emetic syndrome. The detection of genes associated with the production of these toxins can predict the virulence of strains isolated from contaminated food. In this paper, we analyzed 100 samples of vegetables, 25 of each kind (broccoli, coriander, carrot, and lettuce) obtained from different markets in Mexico City and its metropolitan area. B. cereus was isolated in 32, 44, 84, and 68% of the samples of broccoli, carrot, lettuce, and coriander, respectively. The hblA gene (encoding one of the three subunits of hemolysin BL) was amplified in 100% of the B. cereus isolates, and the ces gene (encoding the cereulide) could not be amplified from any of them. This is the first report of B. cereus isolation from the vegetables analyzed in this work and, also, the first report in Mexico of the isolation from vegetables of strains with potential virulence. The results should serve as evidence of the potential risk of consuming these foods without proper treatment. PMID:25474064

  4. Detection of toxigenic Bacillus cereus strains isolated from vegetables in Mexico City.

    PubMed

    Flores-Urbán, Karen A; Natividad-Bonifacio, Iván; Vázquez-Quiñones, Carlos R; Vázquez-Salinas, Carlos; Quiñones-Ramírez, Elsa Irma

    2014-12-01

    Bacillus cereus can cause diarrhea and emetic syndromes after ingestion of food contaminated with it. This ability is due to the production of enterotoxins by this microorganism, these being the hemolysin BL complex, which is involved in the diarrheal syndrome, and cereulide, which is responsible for the emetic syndrome. The detection of genes associated with the production of these toxins can predict the virulence of strains isolated from contaminated food. In this paper, we analyzed 100 samples of vegetables, 25 of each kind (broccoli, coriander, carrot, and lettuce) obtained from different markets in Mexico City and its metropolitan area. B. cereus was isolated in 32, 44, 84, and 68% of the samples of broccoli, carrot, lettuce, and coriander, respectively. The hblA gene (encoding one of the three subunits of hemolysin BL) was amplified in 100% of the B. cereus isolates, and the ces gene (encoding the cereulide) could not be amplified from any of them. This is the first report of B. cereus isolation from the vegetables analyzed in this work and, also, the first report in Mexico of the isolation from vegetables of strains with potential virulence. The results should serve as evidence of the potential risk of consuming these foods without proper treatment.

  5. Detection of a new insect flavivirus and isolation of Aedes flavivirus in Northern Italy

    PubMed Central

    2012-01-01

    Background During recent years, numerous novel ‘insect flaviviruses’ have been discovered in natural mosquito populations. In a previous study we described the presence of flavivirus DNA sequences integrated in Aedes albopictus (Asian tiger mosquito) populations from Northern Italy in 2007. Methods During 2008 we collected and tested Aedes females for flavivirus presence and developed phylogenetic analysis, virus isolation, electron microscopy studies and RNAse treatments. Results We detected a high prevalence of flavivirus in Ae. albopictus (77.5%). The phylogenetic analysis identified the insect flavivirus sequences as Aedes flavivirus (AEFV) recently described in Japan, and that may have been introduced in Italy travelling with the tiger mosquito. Some of these pools grew in C6/36 cells, producing cytopathic effects, and the RNase treatment results showed the presence of the detected sequences in RNA forms. Furthermore, we detected a new insect flavivirus in one pool of Aedes cinereus/geminus mosquitoes. Phylogenetic analysis of this virus shows that it forms a distinct cluster within the clade of insect flavivirus. Conclusions This is the first study to report a high prevalence, to describe the seasonal activity and an isolation of the insect flavivirus Aedes flavivirus in Europe. Moreover we describe the detection of a new insect flavivirus detected from Ae. cinereus mosquitoes from Italy. These flavivirus may be common, ubiquitous and diverse in nature and we discuss the implications of the insect flavivirus group in virus evolution and transmission. PMID:23043958

  6. Fault detection and isolation for a full-scale railway vehicle suspension with multiple Kalman filters

    NASA Astrophysics Data System (ADS)

    Jesussek, Mathias; Ellermann, Katrin

    2014-12-01

    Reliability and dependability in complex mechanical systems can be improved by fault detection and isolation (FDI) methods. These techniques are key elements for maintenance on demand, which could decrease service cost and time significantly. This paper addresses FDI for a railway vehicle: the mechanical model is described as a multibody system, which is excited randomly due to track irregularities. Various parameters, like masses, spring- and damper-characteristics, influence the dynamics of the vehicle. Often, the exact values of the parameters are unknown and might even change over time. Some of these changes are considered critical with respect to the operation of the system and they require immediate maintenance. The aim of this work is to detect faults in the suspension system of the vehicle. A Kalman filter is used in order to estimate the states. To detect and isolate faults the detection error is minimised with multiple Kalman filters. A full-scale train model with nonlinear wheel/rail contact serves as an example for the described techniques. Numerical results for different test cases are presented. The analysis shows that for the given system it is possible not only to detect a failure of the suspension system from the system's dynamic response, but also to distinguish clearly between different possible causes for the changes in the dynamical behaviour.

  7. Design and evaluation of a failure detection and isolation algorithm for restructurable control systems

    NASA Technical Reports Server (NTRS)

    Weiss, Jerold L.; Hsu, John Y.

    1986-01-01

    The use of a decentralized approach to failure detection and isolation for use in restructurable control systems is examined. This work has produced: (1) A method for evaluating fundamental limits to FDI performance; (2) Application using flight recorded data; (3) A working control element FDI system with maximal sensitivity to critical control element failures; (4) Extensive testing on realistic simulations; and (5) A detailed design methodology involving parameter optimization (with respect to model uncertainties) and sensitivity analyses. This project has concentrated on detection and isolation of generic control element failures since these failures frequently lead to emergency conditions and since knowledge of remaining control authority is essential for control system redesign. The failures are generic in the sense that no temporal failure signature information was assumed. Thus, various forms of functional failures are treated in a unified fashion. Such a treatment results in a robust FDI system (i.e., one that covers all failure modes) but sacrifices some performance when detailed failure signature information is known, useful, and employed properly. It was assumed throughout that all sensors are validated (i.e., contain only in-spec errors) and that only the first failure of a single control element needs to be detected and isolated. The FDI system which has been developed will handle a class of multiple failures.

  8. Detection and isolation of single tumor cells containing mutated DNA sequences

    NASA Astrophysics Data System (ADS)

    Leary, James F.; He, Feng; Reece, Lisa M.

    1999-04-01

    One of the problems in treating breast cancer patients is discovering the gene rearrangements that are occurring while the patient is in apparent remission. Spontaneous mutations in DNA sequences, particularly in tumor suppressor genes, can lead to the evolution of new clones of tumor cells that may be able to evade both clinical treatments and the patient's immune surveillance system. Isolation of these tumor clones is extremely difficult. Rare-event analysis and single-cell sorting techniques must be used to successfully detect and isolate these tumor clones. PCR amplification of selected gene sequences followed by TA cloning techniques can then be used to perform single-cell DNA sequencing in those gene regions. In this paper we present preliminary data showing successful detection and single-cell sorting of rare tumor clones from defined cell mixtures. Using TA cloning techniques and PCR we have been able to detect a single base-pair mutation in the PTEN tumor suppressor gene in single cells from a breast cancer cell line. Thus, while extremely difficult, it should in the future be possible to isolate tumor clones form a patient for subsequent molecular analyses of DNA mutations in critical gene regions.

  9. Failure detection and isolation investigation for strapdown skew redundant tetrad laser gyro inertial sensor arrays

    NASA Technical Reports Server (NTRS)

    Eberlein, A. J.; Lahm, T. G.

    1976-01-01

    The degree to which flight-critical failures in a strapdown laser gyro tetrad sensor assembly can be isolated in short-haul aircraft after a failure occurrence has been detected by the skewed sensor failure-detection voting logic is investigated along with the degree to which a failure in the tetrad computer can be detected and isolated at the computer level, assuming a dual-redundant computer configuration. The tetrad system was mechanized with two two-axis inertial navigation channels (INCs), each containing two gyro/accelerometer axes, computer, control circuitry, and input/output circuitry. Gyro/accelerometer data is crossfed between the two INCs to enable each computer to independently perform the navigation task. Computer calculations are synchronized between the computers so that calculated quantities are identical and may be compared. Fail-safe performance (identification of the first failure) is accomplished with a probability approaching 100 percent of the time, while fail-operational performance (identification and isolation of the first failure) is achieved 93 to 96 percent of the time.

  10. Aptamer-nanobody based ELASA for specific detection of Acinetobacter baumannii isolates.

    PubMed

    Rasoulinejad, Samaneh; Gargari, Seyed Latif Mousavi

    2016-08-10

    Acinetobacter baumannii has turned into an important threat in nosocomial outbreak infections and multidrug resistance leading to high mortality rates in the 21st century. In recent years its mortality has increased by 15% which in part could be due to lack of a rapid and sensitive diagnostic test. In this work we introduced a new detection test for A. baumannii with two highly specific aptamer and nanobody molecules. High binding affinity DNA oligonucleotide aptamers toward A. baumannii were selected through 12 rounds of whole cell System Evolution of Ligands by EXponential enrichment process (SELEX). The SELEX procedures was monitored by flow cytometry. The dissociation constant and binding efficiency of the selected aptamer Aci49 was 7.547±1:353pM and 47.50%, respectively. A sandwich enzyme linked aptamer sorbent assay (ELASA) was designed with the biotinylated Aci49 aptamer and our previously developed nanobody against biofilm associated protein (Bap). The assay system was optimized with A. baumannii (ATCC 19606) and 47 clinical isolates of A. baumannii were tested. The threshold of detection in sandwich ELASA process was10(3) CFU/ml. The sensitivity of test toward the clinical isolates was 95.47%. Our results reveal that the sandwich ELASA is sensitive and specific enough for the rapid detection of A. baumannii from clinical isolates. PMID:27234880

  11. Development of cost effective fenceline monitoring approaches to support advanced leak detection and repair strategies

    EPA Science Inventory

    Cost-effective fence line and process monitoring systems to support advanced leak detection and repair (LDAR) strategies can enhance protection of public health, facilitate worker safety, and help companies realize cost savings by reducing lost product. The U.S. EPA Office of Re...

  12. Detection of First- and Second-Line Drug Resistance in Mycobacterium tuberculosis Clinical Isolates by Pyrosequencing

    PubMed Central

    Morcillo, Nora; Imperiale, Belen; Hoffner, Sven E.; Juréen, Pontus

    2012-01-01

    Conventional phenotypic drug susceptibility testing (DST) methods for Mycobacterium tuberculosis are laborious and very time-consuming. Early detection of drug-resistant tuberculosis (TB) is essential for prevention and control of TB transmission. We have developed a pyrosequencing method for simultaneous detection of mutations associated with resistance to rifampin, isoniazid, ethambutol, amikacin, kanamycin, capreomycin, and ofloxacin. Seven pyrosequencing assays were optimized for following loci: rpoB, katG, embB, rrs, gyrA, and the promoter regions of inhA and eis. The molecular method was evaluated on a panel of 290 clinical isolates of M. tuberculosis. In comparison to phenotypic DST, the pyrosequencing method demonstrated high specificity (100%) and sensitivity (94.6%) for detection of multidrug-resistant M. tuberculosis as well as high specificity (99.3%) and sensitivity (86.9%) for detection of extensively drug-resistant M. tuberculosis. The short turnaround time combined with multilocus sequencing of several isolates in parallel makes pyrosequencing an attractive method for drug resistance screening in M. tuberculosis. PMID:22461677

  13. Phenotypic Tests for the Detection of β-Lactamase-Producing Enterobacteriaceae Isolated from Different Environments.

    PubMed

    de Oliveira, Daniele V; Van Der Sand, Sueli T

    2016-07-01

    Some bacteria from the Enterobacteriaceae family are showing a significant capability to disseminate β-lactams resistance mechanisms among them, and these same mechanisms can be carried out from the hospital environment to superficial water. The aim of this study was to evaluate different phenotypic methods for the detection β-lactamases production by enterobacteria isolated from the anthropogenic environment: hospital wastewater and from a stream that cross the city of Porto Alegre. The applied tests were the modified Hodge test (MHT) and phenotypic tests with the following inhibitors: carbapenemase-phenylboronic acid (APB), metallo-β-lactamase-EDTA, AmpC β-lactamase-cloxacillin, and the confirmatory test for extended-spectrum β-lactamase (ESBL)-clavulanic acid. For this evaluation, 131 isolates were initially subjected to antibiogram using the following antimicrobials: cefotaxime (30 µg), cefpodoxime (10 μg), ceftazidime (30 µg), ertapenem (10 μg), meropenem (10 μg), and aztreonam (30 μg). After this first screening, 62 isolates showed a profile resistance for at least one antimicrobial. These isolates were subjected to all phenotypic tests. Of those, 40 isolates were positive for at least one phenotypic test. In MHT test, one isolate was positive and five were with inconclusive results. The results achieved with the inhibitors are as follows: APB 25/40 positive strains; EDTA 8/40 positive strains; and with CLOXA 2/40 positive strains. ESBL production was observed for 34/40 strains. This assessment shows a high level of bacteria which can produce enzymes that inactivate β-lactams present in the different environment like the stream waters and from the hospital settings. PMID:27071981

  14. Salivary biomarkers for detection of oral squamous cell carcinoma – current state and recent advances

    PubMed Central

    Yakob, Maha; Fuentes, Laurel; Wang, Marilene B.; Abemayor, Elliot; Wong, David T.W.

    2014-01-01

    Oral squamous cell carcinoma (OSCC) is the most common malignant neoplasm of the oral cavity. Detection of OSCC is currently based on thorough clinical oral examination combined with biopsy for histological analysis. Most cases of OSCC are not detected until the cancer has developed into advanced stages; thus, a reliable early stage diagnostic marker is needed. This literature review presents an overview of the status of current advances in salivary diagnostics for OSCC. Though many protein and mRNA salivary biomarkers have been identified that can detect OSCC with high sensitivity and specificity, the most discernable findings occur with the use of multiple markers. Studies that incorporate proteomic, transcriptomic, and potentially additional “omics”, including methylomics, need to be initiated to bring technology to clinical applications and allow the best use of saliva in diagnosing OSCC. PMID:24883261

  15. Failure detection and isolation analysis of a redundant strapdown inertial measurement unit

    NASA Technical Reports Server (NTRS)

    Motyka, P.; Landey, M.; Mckern, R.

    1981-01-01

    The objective of this study was to define and develop techniques for failure detection and isolation (FDI) algorithms for a dual fail/operational redundant strapdown inertial navigation system are defined and developed. The FDI techniques chosen include provisions for hard and soft failure detection in the context of flight control and navigation. Analyses were done to determine error detection and switching levels for the inertial navigation system, which is intended for a conventional takeoff or landing (CTOL) operating environment. In addition, investigations of false alarms and missed alarms were included for the FDI techniques developed, along with the analyses of filters to be used in conjunction with FDI processing. Two specific FDI algorithms were compared: the generalized likelihood test and the edge vector test. A deterministic digital computer simulation was used to compare and evaluate the algorithms and FDI systems.

  16. Duplex PCR Methods for the Molecular Detection of Escherichia fergusonii Isolates from Broiler Chickens

    PubMed Central

    Simmons, Karen; Rempel, Heidi; Block, Glenn; Forgetta, Vincenzo; Vaillancourt, Rolland; Malouin, François; Topp, Edward; Delaquis, Pascal

    2014-01-01

    Escherichia fergusonii is an emerging pathogen that has been isolated from a wide range of infections in animals and humans. Primers targeting specific genes, including yliE (encoding a conserved hypothetical protein of the cellulose synthase and regulator of cellulose synthase island), EFER_1569 (encoding a hypothetical protein, putative transcriptional activator for multiple antibiotic resistance), and EFER_3126 (encoding a putative triphosphoribosyl-dephospho-coenzyme A [CoA]), were designed for the detection of E. fergusonii by conventional and real-time PCR methods. Primers were screened by in silico PCR against 489 bacterial genomic sequences and by both PCR methods on 55 reference and field strains. Both methods were specific and sensitive for E. fergusonii, showing amplification only for this bacterium. Conventional PCR required a minimum bacterial concentration of approximately 102 CFU/ml, while real-time PCR required a minimum of 0.3 pg of DNA for consistent detection. Standard curves showed an efficiency of 98.5%, with an R2 value of 0.99 for the real-time PCR assay. Cecal and cloacal contents from 580 chickens were sampled from broiler farms located in the Fraser Valley (British Columbia, Canada). Presumptive E. fergusonii isolates were recovered by enrichment and plating on differential and selective media. Of 301 total presumptive isolates, 140 (46.5%) were identified as E. fergusonii by biochemical profiling with the API 20E system and 268 (89.0%) using PCR methods. E. fergusonii detection directly from cecal and cloacal samples without preenrichment was achieved with both PCR methods. Hence, the PCR methods developed in this work significantly improve the detection of E. fergusonii. PMID:24441160

  17. Detection and isolation of Listeria monocytogenes from food samples: implications of sublethal injury.

    PubMed

    Donnelly, Catherine W

    2002-01-01

    Detection of L. monocytogenes is often limited by the performance of the enrichment media used to support bacterial growth to detectable levels. Because Listeria may exist at extremely low levels in foods, sample enrichment protocols must amplify these low initial populations to detectable limits. Listeria may also exist in an injured state in food products as a result of processing treatments such as heating, freezing, exposure to acids, or exposure to sanitizing compounds. Selective agents in enrichment media normally used for recovery of Listeria may inhibit repair and detection of sublethally injured Listeria, which may go on to repair, grow, and regain pathogenicity. Simple modifications to existing regulatory protocols, such as those that use more than one enrichment broth, raise sensitivity of detection to 90%. This review shows the efficacy of repair/enrichment strategies, which increase sensitivity of detection to 97.5-98.8% compared with 65-70% by standard regulatory protocols. Ribotype analysis of isolates obtained from meat samples reveals a complex microbial ecology, with striking differences in both number and distribution of distinct genetic types of Listeria, depending upon whether samples are enriched in selective or repair/enrichment media. In studies on enrichment of dairy environmental samples in University of Vermont medium and Listeria repair broth (UVM and LRB), combining these 2 primary enrichment media into a single tube of Fraser broth for dual secondary enrichment yielded a significantly higher percentage (p < 0.05) of Listeria-positive samples than did use of either LRB or UVM alone. Refinement of conventional Listeria recovery methods should consider the importance of the enrichment step, the nutritional needs of specific genetic types, and the physiological condition of Listeria isolates in foods.

  18. Advancing the speed, sensitivity and accuracy of biomolecular detection using multi-length-scale engineering

    NASA Astrophysics Data System (ADS)

    Kelley, Shana O.; Mirkin, Chad A.; Walt, David R.; Ismagilov, Rustem F.; Toner, Mehmet; Sargent, Edward H.

    2014-12-01

    Rapid progress in identifying disease biomarkers has increased the importance of creating high-performance detection technologies. Over the last decade, the design of many detection platforms has focused on either the nano or micro length scale. Here, we review recent strategies that combine nano- and microscale materials and devices to produce large improvements in detection sensitivity, speed and accuracy, allowing previously undetectable biomarkers to be identified in clinical samples. Microsensors that incorporate nanoscale features can now rapidly detect disease-related nucleic acids expressed in patient samples. New microdevices that separate large clinical samples into nanocompartments allow precise quantitation of analytes, and microfluidic systems that utilize nanoscale binding events can detect rare cancer cells in the bloodstream more accurately than before. These advances will lead to faster and more reliable clinical diagnostic devices.

  19. Advanced Ground Systems Maintenance Functional Fault Models For Fault Isolation Project

    NASA Technical Reports Server (NTRS)

    Perotti, Jose M. (Compiler)

    2014-01-01

    This project implements functional fault models (FFM) to automate the isolation of failures during ground systems operations. FFMs will also be used to recommend sensor placement to improve fault isolation capabilities. The project enables the delivery of system health advisories to ground system operators.

  20. Detection of volatile metabolites of moulds isolated from a contaminated library.

    PubMed

    Micheluz, Anna; Manente, Sabrina; Rovea, Manuela; Slanzi, Debora; Varese, Giovanna Cristina; Ravagnan, Giampietro; Formenton, Gianmaria

    2016-09-01

    The principal fungal species isolated from a contaminated library environment were tested for their microbial volatile organic compound (MVOC) production ability. Aspergillus creber, A. penicillioides, Cladosporium cladosporioides, Eurotium chevalieri, E. halophilicum, Penicillium brevicompactum and P. chrysogenum were cultivated on suitable culture media inside sample bottles specifically designed and created for direct MVOC injection to a GC-MS instrument. The fungal emissions were monitored over several weeks to detect changes with the aging of the colonies, monitored also by respirometric tests. A total of 55 different MVOCs were detected and isopropyl alcohol, 3-methyl-1-butanol and 2-butanone were the principal compounds in common between the selected fungal species. Moreover, 2,4-dimethylheptane, 1,4-pentadiene, styrene, ethanol, 2-methyl-1-butanol, acetone, furan and 2-methylfuran were the most detected compounds. For the first time, the MVOC production for particular fungal species was detected. The species A. creber, which belongs to the recently revised group Aspergillus section Versicolores, was characterized by the production of ethanol, furan and 1,4-pentadiene. For the xerophilic fungus E. halophilicum, specific production of acetone, 2-butanone and 1,4-pentadiene was detected, supported also by respirometric data. The results demonstrated the potential use of this method for the detection of fungal contamination phenomena inside Cultural Heritage's preservation environments. PMID:27392938

  1. NanoFlares for the detection, isolation, and culture of live tumor cells from human blood.

    PubMed

    Halo, Tiffany L; McMahon, Kaylin M; Angeloni, Nicholas L; Xu, Yilin; Wang, Wei; Chinen, Alyssa B; Malin, Dmitry; Strekalova, Elena; Cryns, Vincent L; Cheng, Chonghui; Mirkin, Chad A; Thaxton, C Shad

    2014-12-01

    Metastasis portends a poor prognosis for cancer patients. Primary tumor cells disseminate through the bloodstream before the appearance of detectable metastatic lesions. The analysis of cancer cells in blood—so-called circulating tumor cells (CTCs)—may provide unprecedented opportunities for metastatic risk assessment and investigation. NanoFlares are nanoconstructs that enable live-cell detection of intracellular mRNA. NanoFlares, when coupled with flow cytometry, can be used to fluorescently detect genetic markers of CTCs in the context of whole blood. They allow one to detect as few as 100 live cancer cells per mL of blood and subsequently culture those cells. This technique can also be used to detect CTCs in a murine model of metastatic breast cancer. As such, NanoFlares provide, to our knowledge, the first genetic-based approach for detecting, isolating, and characterizing live cancer cells from blood and may provide new opportunities for cancer diagnosis, prognosis, and personalized therapy.

  2. Detection and characterization of a Trichomonas isolate from a rehabilitated bald eagle (Haliaeetus leucocephalus).

    PubMed

    Kelly-Clark, Whitney K; McBurney, Scott; Forzán, María J; Desmarchelier, Marion; Greenwood, Spencer J

    2013-12-01

    A hatching-year bald eagle (Haliaeetus leucocephalus) was presented for clinical examination after being found unable to fly. Upon admission, routine wet-mount microscopy detected no trichomonads. Five months later, oral cavity inspection found no abnormalities, but the eagle was swabbed for research on trichomonosis in maritime birds. The swab was used to inoculate an InPouch TF culture and trichomonads were visible within 24 hr. Genotyping (ITS) revealed a Trichomonas isolate that was 100% identical to an isolate from a bearded vulture (Gypaetus barbatus) from the Czech Republic. The eagle was treated with metronidazole (50 mg/kg q 12h PO for 5 consecutive days). Following treatment, the eagle was swabbed and the inoculated InPouch TF culture was monitored daily for 1 wk. No trichomonads were observed. Rehabilitation centers interested in surveillance should consider combining the InPouch TF technique with clinical inspection of live birds to confirm trichomonosis and for future research.

  3. Analysis of Space Shuttle Ground Support System Fault Detection, Isolation, and Recovery Processes and Resources

    NASA Technical Reports Server (NTRS)

    Gross, Anthony R.; Gerald-Yamasaki, Michael; Trent, Robert P.

    2009-01-01

    As part of the FDIR (Fault Detection, Isolation, and Recovery) Project for the Constellation Program, a task was designed within the context of the Constellation Program FDIR project called the Legacy Benchmarking Task to document as accurately as possible the FDIR processes and resources that were used by the Space Shuttle ground support equipment (GSE) during the Shuttle flight program. These results served as a comparison with results obtained from the new FDIR capability. The task team assessed Shuttle and EELV (Evolved Expendable Launch Vehicle) historical data for GSE-related launch delays to identify expected benefits and impact. This analysis included a study of complex fault isolation situations that required a lengthy troubleshooting process. Specifically, four elements of that system were considered: LH2 (liquid hydrogen), LO2 (liquid oxygen), hydraulic test, and ground special power.

  4. Molecular detection and isolation from antarctica of methylotrophic bacteria able to grow with methylated sulfur compounds.

    PubMed

    Moosvi, S Azra; McDonald, Ian R; Pearce, David A; Kelly, Donovan P; Wood, Ann P

    2005-08-01

    This study is the first demonstration that a diverse facultatively methylotrophic microbiota exists in some Antarctic locations. PCR amplification of genes diagnostic for methylotrophs was carried out with bacterial DNA isolated from 14 soil and sediment samples from ten locations on Signy Island, South Orkney Islands, Antarctica. Genes encoding the mxaF of methanol dehydrogenase, the fdxA for Afipia ferredoxin, the msmA of methanesulfonate monooxygenase, and the 16S rRNA gene of Methylobacterium were detected in all samples tested. The mxaF gene sequences corresponded to those of Hyphomicrobium, Methylobacterium, and Methylomonas. Over 30 pure cultures of methylotrophs were isolated on methanesulfonate, dimethylsulfone, or dimethylsulfide from ten Signy Island lakes. Some were identified from 16S rRNA gene sequences (and morphology) as Hyphomicrobium species, strains of Afipia felis, and a methylotrophic Flavobacterium strain. Antarctic environments thus contain diverse methylotrophic bacteria, growing on various C1-substrates, including C1-sulfur compounds. PMID:16104352

  5. In-flight Fault Detection and Isolation in Aircraft Flight Control Systems

    NASA Technical Reports Server (NTRS)

    Azam, Mohammad; Pattipati, Krishna; Allanach, Jeffrey; Poll, Scott; Patterson-Hine, Ann

    2005-01-01

    In this paper we consider the problem of test design for real-time fault detection and isolation (FDI) in the flight control system of fixed-wing aircraft. We focus on the faults that are manifested in the control surface elements (e.g., aileron, elevator, rudder and stabilizer) of an aircraft. For demonstration purposes, we restrict our focus on the faults belonging to nine basic fault classes. The diagnostic tests are performed on the features extracted from fifty monitored system parameters. The proposed tests are able to uniquely isolate each of the faults at almost all severity levels. A neural network-based flight control simulator, FLTZ(Registered TradeMark), is used for the simulation of various faults in fixed-wing aircraft flight control systems for the purpose of FDI.

  6. Detection and characterization of a Trichomonas isolate from a rehabilitated bald eagle (Haliaeetus leucocephalus).

    PubMed

    Kelly-Clark, Whitney K; McBurney, Scott; Forzán, María J; Desmarchelier, Marion; Greenwood, Spencer J

    2013-12-01

    A hatching-year bald eagle (Haliaeetus leucocephalus) was presented for clinical examination after being found unable to fly. Upon admission, routine wet-mount microscopy detected no trichomonads. Five months later, oral cavity inspection found no abnormalities, but the eagle was swabbed for research on trichomonosis in maritime birds. The swab was used to inoculate an InPouch TF culture and trichomonads were visible within 24 hr. Genotyping (ITS) revealed a Trichomonas isolate that was 100% identical to an isolate from a bearded vulture (Gypaetus barbatus) from the Czech Republic. The eagle was treated with metronidazole (50 mg/kg q 12h PO for 5 consecutive days). Following treatment, the eagle was swabbed and the inoculated InPouch TF culture was monitored daily for 1 wk. No trichomonads were observed. Rehabilitation centers interested in surveillance should consider combining the InPouch TF technique with clinical inspection of live birds to confirm trichomonosis and for future research. PMID:24450084

  7. Unexpected detection of animal VP7 genes among common rotavirus strains isolated from children in Mexico.

    PubMed

    Laird, A R; Ibarra, V; Ruiz-Palacios, G; Guerrero, M L; Glass, R I; Gentsch, J R

    2003-09-01

    In the course of characterizing 103 rotaviruses from children in Mexico, we found that the majority of strains were globally common types (55.4% of total), while uncommon types represented 5.7%, mixed infections with common types represented 14.8%, and partially or fully nontypeable isolates represented about 24%. Serotype G9 was detected for the first time in Mexico. We sequenced a subset of strains that were G nontypeable by reverse transcriptase PCR and found surprisingly that two strains having common human rotavirus P genotypes (8 and 6) had serotype G3 and G4 VP7 gene sequences that shared closer homology with canine and porcine strains, respectively, than with human strains, suggesting that these isolates represented reassortants between human and animal rotaviruses.

  8. Methods for the detection and isolation of Shiga toxin-producing Escherichia coli.

    PubMed

    De Boer E; Heuvelink, A E

    2000-01-01

    Shiga toxin-producing Escherichia coli (STEC) are an important cause of haemorrhagic colitis and the diarrhoea-associated form of the haemolytic uraemic syndrome. Of the numerous serotypes of E. coli that have been shown to produce Shiga toxin (Stx), E. coli O157:H7 and E. coli O157:NM (non-motile) are most frequently implicated in human disease. Early recognition of STEC infections is critical for effective treatment of patients. Furthermore, rapid microbiological diagnosis of individual patients enables the prompt notification of outbreaks and implementation of control measures to prevent more cases. Most human infections caused by STEC have been acquired by the consumption of contaminated foods, especially those of bovine origin such as undercooked ground beef and unpasteurized cows' milk, and by person-to-person contacts. To identify the reservoirs of STEC and the routes of transmission to man, sensitive methods are needed as these pathogens may only be present in food, environmental and faecal samples in small numbers. In addition, sensitive and rapid detection methods are necessary for the food industry to ensure a safe supply of foods. Sensitive methods are also needed for surveillance programmes in risk assessment studies, and for studies on survival and growth of STEC strains. Cultural methods for the enrichment, isolation and confirmation of O157 STEC are still evolving. Several selective enrichment media have been described, of which modified tryptone soy broth with novobiocin and modified E. coli broth with novobiocin, seem to be the most appropriate. These media are minimally-selective broths that give a somewhat limited differential specificity favouring isolation of O157 STEC, as opposed to other Gram-negative bacteria, in the sample. An incubation temperature of 41-42 degrees C further enhances selectivity. The occurrence of heat-, freeze-, acid- or salt-stressed STEC in foods means that it is important to be able to detect cells that are in a

  9. Unexpected detection of animal VP7 genes among common rotavirus strains isolated from children in Mexico.

    PubMed

    Laird, A R; Ibarra, V; Ruiz-Palacios, G; Guerrero, M L; Glass, R I; Gentsch, J R

    2003-09-01

    In the course of characterizing 103 rotaviruses from children in Mexico, we found that the majority of strains were globally common types (55.4% of total), while uncommon types represented 5.7%, mixed infections with common types represented 14.8%, and partially or fully nontypeable isolates represented about 24%. Serotype G9 was detected for the first time in Mexico. We sequenced a subset of strains that were G nontypeable by reverse transcriptase PCR and found surprisingly that two strains having common human rotavirus P genotypes (8 and 6) had serotype G3 and G4 VP7 gene sequences that shared closer homology with canine and porcine strains, respectively, than with human strains, suggesting that these isolates represented reassortants between human and animal rotaviruses. PMID:12958276

  10. Functional Fault Modeling of a Cryogenic System for Real-Time Fault Detection and Isolation

    NASA Technical Reports Server (NTRS)

    Ferrell, Bob; Lewis, Mark; Perotti, Jose; Oostdyk, Rebecca; Brown, Barbara

    2010-01-01

    The purpose of this paper is to present the model development process used to create a Functional Fault Model (FFM) of a liquid hydrogen (L H2) system that will be used for realtime fault isolation in a Fault Detection, Isolation and Recover (FDIR) system. The paper explains th e steps in the model development process and the data products required at each step, including examples of how the steps were performed fo r the LH2 system. It also shows the relationship between the FDIR req uirements and steps in the model development process. The paper concl udes with a description of a demonstration of the LH2 model developed using the process and future steps for integrating the model in a live operational environment.

  11. Advanced power system protection and incipient fault detection and protection of spaceborne power systems

    NASA Technical Reports Server (NTRS)

    Russell, B. Don

    1989-01-01

    This research concentrated on the application of advanced signal processing, expert system, and digital technologies for the detection and control of low grade, incipient faults on spaceborne power systems. The researchers have considerable experience in the application of advanced digital technologies and the protection of terrestrial power systems. This experience was used in the current contracts to develop new approaches for protecting the electrical distribution system in spaceborne applications. The project was divided into three distinct areas: (1) investigate the applicability of fault detection algorithms developed for terrestrial power systems to the detection of faults in spaceborne systems; (2) investigate the digital hardware and architectures required to monitor and control spaceborne power systems with full capability to implement new detection and diagnostic algorithms; and (3) develop a real-time expert operating system for implementing diagnostic and protection algorithms. Significant progress has been made in each of the above areas. Several terrestrial fault detection algorithms were modified to better adapt to spaceborne power system environments. Several digital architectures were developed and evaluated in light of the fault detection algorithms.

  12. Detectability of eccentric compact binary coalescences with advanced gravitational-wave detectors

    NASA Astrophysics Data System (ADS)

    Coughlin, M.; Meyers, P.; Thrane, E.; Luo, J.; Christensen, N.

    2015-03-01

    Compact binary coalescences are a promising source of gravitational waves for second-generation interferometric gravitational-wave detectors such as advanced LIGO and advanced Virgo. While most binaries are expected to possess circular orbits, some may be eccentric, for example, if they are formed through dynamical capture. Eccentric orbits can create difficulty for matched filtering searches due to the challenges of creating effective template banks to detect these signals. In previous work, we showed how seedless clustering can be used to detect low-mass (Mtotal≤10 M⊙) compact binary coalescences for both spinning and eccentric systems, assuming a circular post-Newtonian expansion. Here, we describe a parametrization that is designed to maximize sensitivity to low-eccentricity (0 ≤ɛ ≤0.6 ) systems, derived from the analytic equations. We show that this parametrization provides a robust and computationally efficient method for detecting eccentric low-mass compact binaries. Based on these results, we conclude that advanced detectors will have a chance of detecting eccentric binaries if optimistic models prove true. However, a null observation is unlikely to firmly rule out models of eccentric binary populations.

  13. Fault detection, isolation, and diagnosis of self-validating multifunctional sensors

    NASA Astrophysics Data System (ADS)

    Yang, Jing-li; Chen, Yin-sheng; Zhang, Li-li; Sun, Zhen

    2016-06-01

    A novel fault detection, isolation, and diagnosis (FDID) strategy for self-validating multifunctional sensors is presented in this paper. The sparse non-negative matrix factorization-based method can effectively detect faults by using the squared prediction error (SPE) statistic, and the variables contribution plots based on SPE statistic can help to locate and isolate the faulty sensitive units. The complete ensemble empirical mode decomposition is employed to decompose the fault signals to a series of intrinsic mode functions (IMFs) and a residual. The sample entropy (SampEn)-weighted energy values of each IMFs and the residual are estimated to represent the characteristics of the fault signals. Multi-class support vector machine is introduced to identify the fault mode with the purpose of diagnosing status of the faulty sensitive units. The performance of the proposed strategy is compared with other fault detection strategies such as principal component analysis, independent component analysis, and fault diagnosis strategies such as empirical mode decomposition coupled with support vector machine. The proposed strategy is fully evaluated in a real self-validating multifunctional sensors experimental system, and the experimental results demonstrate that the proposed strategy provides an excellent solution to the FDID research topic of self-validating multifunctional sensors.

  14. Fault detection, isolation, and diagnosis of self-validating multifunctional sensors.

    PubMed

    Yang, Jing-Li; Chen, Yin-Sheng; Zhang, Li-Li; Sun, Zhen

    2016-06-01

    A novel fault detection, isolation, and diagnosis (FDID) strategy for self-validating multifunctional sensors is presented in this paper. The sparse non-negative matrix factorization-based method can effectively detect faults by using the squared prediction error (SPE) statistic, and the variables contribution plots based on SPE statistic can help to locate and isolate the faulty sensitive units. The complete ensemble empirical mode decomposition is employed to decompose the fault signals to a series of intrinsic mode functions (IMFs) and a residual. The sample entropy (SampEn)-weighted energy values of each IMFs and the residual are estimated to represent the characteristics of the fault signals. Multi-class support vector machine is introduced to identify the fault mode with the purpose of diagnosing status of the faulty sensitive units. The performance of the proposed strategy is compared with other fault detection strategies such as principal component analysis, independent component analysis, and fault diagnosis strategies such as empirical mode decomposition coupled with support vector machine. The proposed strategy is fully evaluated in a real self-validating multifunctional sensors experimental system, and the experimental results demonstrate that the proposed strategy provides an excellent solution to the FDID research topic of self-validating multifunctional sensors. PMID:27370486

  15. Automatic Myonuclear Detection in Isolated Single Muscle Fibers Using Robust Ellipse Fitting and Sparse Representation.

    PubMed

    Su, Hai; Xing, Fuyong; Lee, Jonah D; Peterson, Charlotte A; Yang, Lin

    2014-01-01

    Accurate and robust detection of myonuclei in isolated single muscle fibers is required to calculate myonuclear domain size. However, this task is challenging because: 1) shape and size variations of the nuclei, 2) overlapping nuclear clumps, and 3) multiple z-stack images with out-of-focus regions. In this paper, we have proposed a novel automatic detection algorithm to robustly quantify myonuclei in isolated single skeletal muscle fibers. The original z-stack images are first converted into one all-in-focus image using multi-focus image fusion. A sufficient number of ellipse fitting hypotheses are then generated from the myonuclei contour segments using heteroscedastic errors-in-variables (HEIV) regression. A set of representative training samples and a set of discriminative features are selected by a two-stage sparse model. The selected samples with representative features are utilized to train a classifier to select the best candidates. A modified inner geodesic distance based mean-shift clustering algorithm is used to produce the final nuclei detection results. The proposed method was extensively tested using 42 sets of z-stack images containing over 1,500 myonuclei. The method demonstrates excellent results that are better than current state-of-the-art approaches.

  16. Automatic Myonuclear Detection in Isolated Single Muscle Fibers Using Robust Ellipse Fitting and Sparse Representation

    PubMed Central

    Su, Hai; Xing, Fuyong; Lee, Jonah D.; Peterson, Charlotte A.; Yang, Lin

    2015-01-01

    Accurate and robust detection of myonuclei in isolated single muscle fibers is required to calculate myonuclear domain size. However, this task is challenging because: 1) shape and size variations of the nuclei, 2) overlapping nuclear clumps, and 3) multiple z-stack images with out-of-focus regions. In this paper, we have proposed a novel automatic detection algorithm to robustly quantify myonuclei in isolated single skeletal muscle fibers. The original z-stack images are first converted into one all-in-focus image using multi-focus image fusion. A sufficient number of ellipse fitting hypotheses are then generated from them yonuclei contour segments using heteroscedastic errors-invariables (HEIV) regression. A set of representative training samples and a set of discriminative features are selected by a two-stage sparse model. The selected samples with representative features are utilized to train a classifier to select the best candidates. A modified inner geodesic distance based mean-shift clustering algorithm is used to produce the final nuclei detection results. The proposed method was extensively tested using 42 sets of z-stack images containing over 1,500 myonuclei. The method demonstrates excellent results that are better than current state-of-the-art approaches. PMID:26356342

  17. Fault detection, isolation, and diagnosis of self-validating multifunctional sensors.

    PubMed

    Yang, Jing-Li; Chen, Yin-Sheng; Zhang, Li-Li; Sun, Zhen

    2016-06-01

    A novel fault detection, isolation, and diagnosis (FDID) strategy for self-validating multifunctional sensors is presented in this paper. The sparse non-negative matrix factorization-based method can effectively detect faults by using the squared prediction error (SPE) statistic, and the variables contribution plots based on SPE statistic can help to locate and isolate the faulty sensitive units. The complete ensemble empirical mode decomposition is employed to decompose the fault signals to a series of intrinsic mode functions (IMFs) and a residual. The sample entropy (SampEn)-weighted energy values of each IMFs and the residual are estimated to represent the characteristics of the fault signals. Multi-class support vector machine is introduced to identify the fault mode with the purpose of diagnosing status of the faulty sensitive units. The performance of the proposed strategy is compared with other fault detection strategies such as principal component analysis, independent component analysis, and fault diagnosis strategies such as empirical mode decomposition coupled with support vector machine. The proposed strategy is fully evaluated in a real self-validating multifunctional sensors experimental system, and the experimental results demonstrate that the proposed strategy provides an excellent solution to the FDID research topic of self-validating multifunctional sensors.

  18. PCR detection of cytK gene in Bacillus cereus group strains isolated from food samples.

    PubMed

    Oltuszak-Walczak, Elzbieta; Walczak, Piotr

    2013-11-01

    A method for detection of the cytotoxin K cytK structural gene and its active promoter preceded by the PlcR-binding box, controlling the expression level of this enterotoxin, was developed. The method was applied for the purpose of the analysis of 47 bacterial strains belonging to the Bacillus cereus group isolated from different food products. It was found that the majority of the analyzed strains carried the fully functional cytK gene with its PlcR regulated promoter. The cytK gene was not detected in four emetic strains of Bacillus cereus carrying the cesB gene and potentially producing an emetic toxin - cereulide. The cytotoxin K gene was detected in 4 isolates classified as Bacillus mycoides and one reference strain B. mycoides PCM 2024. The promoter region and the N-terminal part of the cytK gene from two strains of B. mycoides (5D and 19E) showed similarities to the corresponding sequences of Bacillus cereus W23 and Bacillus thuringiensis HD-789, respectively. It was shown for the first time that the cytK gene promoter region from strains 5D and 19E of Bacillus mycoides had a similar arrangement to the corresponding sequence of Bacillus cereus ATCC 14579. The presence of the cytK gene in Bacillus mycoides shows that this species, widely recognized as nonpathogenic, may pose potential biohazard to human beings.

  19. Detection of Salmonella enterica in pigs at slaughter and comparison with human isolates in Italy.

    PubMed

    Bonardi, Silvia; Alpigiani, Irene; Bruini, Ilaria; Barilli, Elena; Brindani, Franco; Morganti, Marina; Cavallini, Pierugo; Bolzoni, Luca; Pongolini, Stefano

    2016-02-01

    In 2013-2014, 201 pigs belonging to 67 batches were tested for Salmonella in their mesenteric lymph nodes (MLN) in one abattoir of Northern Italy. For each batch, faecal material was collected at lairage by swabbing the pen floor for approximately 1600 cm(2). The aim of this study was to investigate the prevalence of Salmonella in MLN of pigs at slaughter, to assess Salmonella contamination at lairage and to evaluate the effect of lairage duration on its prevalence. Serotyping, XbaI PFGE typing and antimicrobial testing of the isolates were performed. Pig and human Salmonella isolates of the same region of Italy were compared to evaluate possible correlations. Salmonella enterica was isolated from 19.9% of the MLN and 49.3% of the environmental faecal samples. Nine different serovars were identified among 75 S. enterica isolates. In MLN Salmonella Derby was the most common (52.5%), followed by S. enterica 4,[5],12:i:- (17.5%) and Salmonella Rissen (10.0%). In faecal samples S. Derby was prevalent (51.4%), followed by S. enterica 4,[5], 12:i:- (20.0%) and Salmonella Brandenburg (14.3%). Lairage holding varied between 1 and ≥ 12 h (median value: 2.5h). In pigs held for 1-3h, 14.1% were positive for Salmonella in MLN but the prevalence reached 31.8% when they were held for ≥ 12 h. The contamination of MLN was statistically different (p=0.0045) between the two groups, thus confirming the role of long-lasting lairage in Salmonella contamination of pigs. XbaI PFGE typing detected 36 PFGE types. Twenty-three PFGE types were identified among the 40 MLN isolates and 22 PFGE types among the 35 faecal isolates. A total of 11 PFGE types were shared between the MLN of pigs and the lairage environment. Among S. Derby, 6 shared PFGE types between MLN and faeces were found and among S. enterica 4,[5],12:i:- one PFGE type was common between MLN and the faecal samples. Shared profiles between human and swine isolates of S. Derby, S. enterica 4,[5],12:i:-, S. Rissen, Salmonella

  20. Comparison of sensitivities of virus isolation, antigen detection, and nucleic acid amplification for detection of equine influenza virus.

    PubMed

    Quinlivan, Michelle; Cullinane, Ann; Nelly, Maura; Van Maanen, Kees; Heldens, Jacco; Arkins, Sean

    2004-02-01

    Four seronegative foals aged 6 to 7 months were exposed to an aerosol of influenza strain A/Equi/2/Kildare/89 at 10(6) 50% egg infective doses (EID(50))/ml. Nasopharyngeal swabs were collected for 10 consecutive days after challenge. Virus isolation was performed in embryonated eggs, and the EID(50) was determined for all positive samples. The 50% tissue culture infective dose was determined using Madin-Darby canine kidney (MDCK) cells. Samples were also tested by an in vitro enzyme immunoassay test, Directigen Flu A, and by reverse transcription-PCR (RT-PCR) using nested primers from the nucleoprotein gene and a single set of primers from the matrix gene. RT-PCR using the matrix primers and virus isolation in embryonated eggs proved to be the most sensitive methods for the detection of virus. The Directigen Flu A test was the least sensitive method. The inclusion of 2% fetal calf serum in the viral transport medium inhibited the growth of virus from undiluted samples in MDCK cells but was essential for the maintenance of the virus titer in samples subjected to repeated freeze-thaw cycles. PMID:14766849

  1. Detection and Whole-Genome Sequencing of Carbapenemase-Producing Aeromonas hydrophila Isolates from Routine Perirectal Surveillance Culture

    PubMed Central

    Hughes, Heather Y.; Lau, Anna F.; Dekker, John P.; Michelin, Angela V.; Youn, Jung-Ho; Henderson, David K.; Frank, Karen M.; Segre, Julia A.

    2016-01-01

    Perirectal surveillance cultures and a stool culture grew Aeromonas species from three patients over a 6-week period and were without epidemiological links. Detection of the blaKPC-2 gene in one isolate prompted inclusion of non-Enterobacteriaceae in our surveillance culture workup. Whole-genome sequencing confirmed that the isolates were unrelated and provided data for Aeromonas reference genomes. PMID:26888898

  2. Clinical comparison of the Isolator 1. 5 microbial tube and the BACTEC radiometric system for detection of bacteremia in children

    SciTech Connect

    Carey, R.B.

    1984-05-01

    The Isolator 1.5 microbial tube was compared with the BACTEC radiometric detection system for the detection of bacteremia in children. The Isolator 1.5 is a blood culture system designed for small volumes of blood (0.5 to 1.5 ml). The method involves lysis of the cells of the patient and the direct plating of the entire blood lysate on agar media appropriate for the growth of fastidious microorganisms. Of 1,500 paired samples inoculated into the two systems, 68 were positive for 73 clinically significant organisms. The Isolator 1.5 recovered 81% of the positive cultures compared with 84% recovered by the BACTEC system. The contamination rates were 8.7 and 3.1% for the Isolator 1.5 and the BACTEC system, respectively. In cultures positive by both systems, the mean time to detection was 4.1 h faster with the Isolator 1.5. The mean time to obtain isolated colonies was 26.6 h faster with the Isolator 1.5. These data indicate the potential value of the Isolator 1.5 microbial tube as a simple, rapid, and sensitive method for the detection of bacteremia in children.

  3. ISOLATION AND DETECTION OF GIARDIA CYSTS FROM WATER USING DIRECT IMMUNOFLUORESCENCE.

    USGS Publications Warehouse

    Sorenson, Stephen K.; Riggs, John L.; Dileanis, Peter D.; Suk, Thomas J.

    1986-01-01

    A water-sampling apparatus used for the isolation and detection of Giardia cysts in water has been designed and tested. The sampling apparatus uses one of a variety of pumps or waterline pressure to move water through a filter. Two of the optional pumps are lightweight enough to make the apparatus portable and thus suitable for sampling in remote areas. This technique of sample processing produces good cyst recovery in much less time than is required with previously established methods. Giardia cysts are identified using direct immunofluorescence.

  4. First detection of oqxAB in Salmonella spp. isolated from food.

    PubMed

    Wong, Marcus Ho Yin; Chen, Sheng

    2013-01-01

    Food-borne salmonellosis is an important public health problem worldwide and the second leading cause of food-borne illnesses in Hong Kong. In this study, the prevalence and antimicrobial resistance of Salmonella in meat products in Hong Kong were determined. Interestingly, a plasmid-mediated quinolone resistance (PMQR) gene combination, oqxAB, which mediates resistance to nalidixic acid, chloramphenicol, and olaquindox, was for the first time detectable on the chromosomes of two Salmonella enterica serovar Derby isolates. Further surveillance of oqxAB in Salmonella will be needed.

  5. Recent Advancements in Nanobioassays and Nanobiosensors for Foodborne Pathogenic Bacteria Detection.

    PubMed

    Chen, Jing; Park, Bosoon

    2016-06-01

    Bacterial pathogens are one of the leading causes of food safety incidents and product recalls worldwide. Timely detection and identification of microbial contamination in agricultural and food products is crucial for disease prevention and outbreak investigation. In efforts to improve and/or replace time-consuming and laborious "gold standards" for pathogen detection, numerous alternative rapid methods have been proposed in the past 15 years, with a trend toward incorporating nanotechnology and nanomaterials in food pathogen detection. This article is a review of the use of nanotechnology in various detection and sample preparation techniques and advancements in nanotechnology applications in food matrices. Some practical considerations in nanobioassay design are discussed, and the gaps between research status quo and market demands are identified.

  6. Recent Advancements in Nanobioassays and Nanobiosensors for Foodborne Pathogenic Bacteria Detection.

    PubMed

    Chen, Jing; Park, Bosoon

    2016-06-01

    Bacterial pathogens are one of the leading causes of food safety incidents and product recalls worldwide. Timely detection and identification of microbial contamination in agricultural and food products is crucial for disease prevention and outbreak investigation. In efforts to improve and/or replace time-consuming and laborious "gold standards" for pathogen detection, numerous alternative rapid methods have been proposed in the past 15 years, with a trend toward incorporating nanotechnology and nanomaterials in food pathogen detection. This article is a review of the use of nanotechnology in various detection and sample preparation techniques and advancements in nanotechnology applications in food matrices. Some practical considerations in nanobioassay design are discussed, and the gaps between research status quo and market demands are identified. PMID:27296612

  7. Multifunctional magnetic nanowires: A novel breakthrough for ultrasensitive detection and isolation of rare cancer cells from non-metastatic early breast cancer patients using small volumes of blood.

    PubMed

    Hong, Wooyoung; Lee, Sooyeon; Chang, Hee Jin; Lee, Eun Sook; Cho, Youngnam

    2016-11-01

    Circulating tumor cells (CTCs) are recognized as promising biomarkers for diagnosis and indication of the prognosis of several epithelial cancers. However, at present, CTC monitoring is available only for advanced-stage patients rather than for those at an early stage of cancer. This is because of the extraordinary rarity of CTCs and the limited sensitivity of current methods. Herein, we report the development of multifunctional magnetic nanowires for the efficient isolation and detection of CTCs from the blood of patients, especially those with non-metastatic early-stage cancer. The nanowires, which are equipped with a high density of magnetic nanoparticles and five different types of antibodies (Ab mixture_mPpyNWs), offer a significant improvement in cell-isolation efficiency, even from very small amounts of blood (250 μL-1 mL). Notably, CTCs were isolated and identified in 29 out of 29 patients (100%) with non-metastatic early breast cancer, indicating that this procedure allowed detection of CTCs with greater accuracy, sensitivity, and specificity. In addition, we demonstrated in situ "naked eye" identification of the captured cancer cells via a simple colorimetric immunoassay. Our results show that antibody-functionalized magnetic nanowires offer great potential for a broad range of practical clinical applications, including early detection, diagnosis, and treatment of cancer. PMID:27552318

  8. Multifunctional magnetic nanowires: A novel breakthrough for ultrasensitive detection and isolation of rare cancer cells from non-metastatic early breast cancer patients using small volumes of blood.

    PubMed

    Hong, Wooyoung; Lee, Sooyeon; Chang, Hee Jin; Lee, Eun Sook; Cho, Youngnam

    2016-11-01

    Circulating tumor cells (CTCs) are recognized as promising biomarkers for diagnosis and indication of the prognosis of several epithelial cancers. However, at present, CTC monitoring is available only for advanced-stage patients rather than for those at an early stage of cancer. This is because of the extraordinary rarity of CTCs and the limited sensitivity of current methods. Herein, we report the development of multifunctional magnetic nanowires for the efficient isolation and detection of CTCs from the blood of patients, especially those with non-metastatic early-stage cancer. The nanowires, which are equipped with a high density of magnetic nanoparticles and five different types of antibodies (Ab mixture_mPpyNWs), offer a significant improvement in cell-isolation efficiency, even from very small amounts of blood (250 μL-1 mL). Notably, CTCs were isolated and identified in 29 out of 29 patients (100%) with non-metastatic early breast cancer, indicating that this procedure allowed detection of CTCs with greater accuracy, sensitivity, and specificity. In addition, we demonstrated in situ "naked eye" identification of the captured cancer cells via a simple colorimetric immunoassay. Our results show that antibody-functionalized magnetic nanowires offer great potential for a broad range of practical clinical applications, including early detection, diagnosis, and treatment of cancer.

  9. Detection of Multi-drug Resistant Acinetobacter Lwoffii Isolated from Soil of Mink Farm.

    PubMed

    Sun, Na; Wen, Yong Jun; Zhang, Shu Qin; Zhu, Hong Wei; Guo, Li; Wang, Feng Xue; Chen, Qiang; Ma, Hong Xia; Cheng, Shi Peng

    2016-07-01

    There were 4 Acinetobacter lwoffii obtained from soil samples. The antimicrobial susceptibility of the strains to 16 antimicrobial agents was investigated using K-B method. Three isolates showed the multi-drug resistance. The presence of resistance genes and integrons was determined using PCR. The aadA1, aac(3')-IIc, aph(3')-VII, aac(6')-Ib, sul2, cat2, floR, and tet(K) genes were detected, respectively. Three class 1 integrons were obtained. The arr-3-aacA4 and blaPSE-1 gene cassette, which cause resistance to aminoglycoside and beta-lactamase antibiotics. Our results reported the detection of multi-drug resistant and carried resistant genes Acinetobacter lwoffii from soil. The findings suggested that we should pay close attention to the prevalence of multi-drug resistant bacterial species of environment. PMID:27554122

  10. a New Online Distributed Process Fault Detection and Isolation Approach Using Potential Clustering Technique

    NASA Astrophysics Data System (ADS)

    Bahrampour, Soheil; Moshiri, Behzad; Salahshoor, Karim

    2009-08-01

    Most of process fault monitoring systems suffer from offline computations and confronting with novel faults that limit their applicabilities. This paper presents a new online fault detection and isolation (FDI) algorithm based on distributed online clustering approach. In the proposed approach, clustering algorithm is used for online detection of a new trend of time series data which indicates faulty condition. On the other hand, distributed technique is used to decompose the overall monitoring task into a series of local monitoring sub-tasks so as to locally track and capture the process faults. This algorithm not only solves the problem of online FDI, but also can handle novel faults. The diagnostic performances of the proposed FDI approach is evaluated on the Tennessee Eastman process plant as a large-scale benchmark problem.

  11. Evaluation of the LightCycler methicillin-resistant Staphylococcus aureus (MRSA) advanced test for detection of MRSA nasal colonization.

    PubMed

    Yam, W C; Siu, Gilman K H; Ho, P L; Ng, T K; Que, T L; Yip, K T; Fok, Cathie P K; Chen, Jonathan H K; Cheng, Vincent C C; Yuen, K Y

    2013-09-01

    Rapid detection of methicillin-resistant Staphylococcus aureus (MRSA) nasal colonization is crucial for the prevention and control of MRSA infections in health care settings. The LightCycler MRSA Advanced Test (Roche Diagnostics) is a commercially available real-time PCR assay for direct detection of MRSA nasal colonization by targeting of the staphylococcal cassette chromosome mec (SCCmec)-orfX junction. The diagnostic performance of the assay was compared with that of ChromID MRSA agar (bioMérieux) culture and an in-house duplex real-time PCR assay. Among 1,246 nasal swab specimens collected from 2 general hospitals in Hong Kong, 174 (14%) were considered true positive for MRSA. Chromogenic culture and the in-house real-time PCR assay identified 147 (84.5%) and 133 (76.4%) true-positive cases with specificities of 100% and 98.6%, respectively. Based on the target melting temperature (Tm) values (57.0 to 62.0 °C) defined by the manufacturer, the LightCycler MRSA Advanced Test identified only 85 (48.9%) true-positive specimens. Interestingly, an additional 60 (34.5%) true-positive specimens were detected despite atypical Tm values of 55 °C, providing overall sensitivity and specificity values of 83.3% and 99%, respectively. Among isolates with Tm values of 55 °C, most were typed as clonal complex 45 (CC45). By sequence analysis of the SCCmec-orfX junction, characteristic single-nucleotide polymorphisms (SNPs) were identified only in isolates with Tm values of 55°C and not in those with typical Tm values. It is conceivable that those SNPs were located inside the target region of the proprietary hybridization probes, which resulted in a Tm shift in the melting curve analysis. Our study highlights the importance of a global evaluation of commercial kits so that the interpretation algorithm covers different lineages of MRSA clones prevalent in various geographical regions.

  12. An insight into the isolation, enumeration, and molecular detection of Listeria monocytogenes in food.

    PubMed

    Law, Jodi Woan-Fei; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan; Lee, Learn-Han

    2015-01-01

    Listeria monocytogenes, a foodborne pathogen that can cause listeriosis through the consumption of food contaminated with this pathogen. The ability of L. monocytogenes to survive in extreme conditions and cause food contaminations have become a major concern. Hence, routine microbiological food testing is necessary to prevent food contamination and outbreaks of foodborne illness. This review provides insight into the methods for cultural detection, enumeration, and molecular identification of L. monocytogenes in various food samples. There are a number of enrichment and plating media that can be used for the isolation of L. monocytogenes from food samples. Enrichment media such as buffered Listeria enrichment broth, Fraser broth, and University of Vermont Medium (UVM) Listeria enrichment broth are recommended by regulatory agencies such as Food and Drug Administration-bacteriological and analytical method (FDA-BAM), US Department of Agriculture-Food and Safety (USDA-FSIS), and International Organization for Standardization (ISO). Many plating media are available for the isolation of L. monocytogenes, for instance, polymyxin acriflavin lithium-chloride ceftazidime aesculin mannitol, Oxford, and other chromogenic media. Besides, reference methods like FDA-BAM, ISO 11290 method, and USDA-FSIS method are usually applied for the cultural detection or enumeration of L. monocytogenes. most probable number technique is applied for the enumeration of L. monocytogenes in the case of low level contamination. Molecular methods including polymerase chain reaction, multiplex polymerase chain reaction, real-time/quantitative polymerase chain reaction, nucleic acid sequence-based amplification, loop-mediated isothermal amplification, DNA microarray, and next generation sequencing technology for the detection and identification of L. monocytogenes are discussed in this review. Overall, molecular methods are rapid, sensitive, specific, time- and labor-saving. In future, there are

  13. An insight into the isolation, enumeration, and molecular detection of Listeria monocytogenes in food.

    PubMed

    Law, Jodi Woan-Fei; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan; Lee, Learn-Han

    2015-01-01

    Listeria monocytogenes, a foodborne pathogen that can cause listeriosis through the consumption of food contaminated with this pathogen. The ability of L. monocytogenes to survive in extreme conditions and cause food contaminations have become a major concern. Hence, routine microbiological food testing is necessary to prevent food contamination and outbreaks of foodborne illness. This review provides insight into the methods for cultural detection, enumeration, and molecular identification of L. monocytogenes in various food samples. There are a number of enrichment and plating media that can be used for the isolation of L. monocytogenes from food samples. Enrichment media such as buffered Listeria enrichment broth, Fraser broth, and University of Vermont Medium (UVM) Listeria enrichment broth are recommended by regulatory agencies such as Food and Drug Administration-bacteriological and analytical method (FDA-BAM), US Department of Agriculture-Food and Safety (USDA-FSIS), and International Organization for Standardization (ISO). Many plating media are available for the isolation of L. monocytogenes, for instance, polymyxin acriflavin lithium-chloride ceftazidime aesculin mannitol, Oxford, and other chromogenic media. Besides, reference methods like FDA-BAM, ISO 11290 method, and USDA-FSIS method are usually applied for the cultural detection or enumeration of L. monocytogenes. most probable number technique is applied for the enumeration of L. monocytogenes in the case of low level contamination. Molecular methods including polymerase chain reaction, multiplex polymerase chain reaction, real-time/quantitative polymerase chain reaction, nucleic acid sequence-based amplification, loop-mediated isothermal amplification, DNA microarray, and next generation sequencing technology for the detection and identification of L. monocytogenes are discussed in this review. Overall, molecular methods are rapid, sensitive, specific, time- and labor-saving. In future, there are

  14. An insight into the isolation, enumeration, and molecular detection of Listeria monocytogenes in food

    PubMed Central

    Law, Jodi Woan-Fei; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan; Lee, Learn-Han

    2015-01-01

    Listeria monocytogenes, a foodborne pathogen that can cause listeriosis through the consumption of food contaminated with this pathogen. The ability of L. monocytogenes to survive in extreme conditions and cause food contaminations have become a major concern. Hence, routine microbiological food testing is necessary to prevent food contamination and outbreaks of foodborne illness. This review provides insight into the methods for cultural detection, enumeration, and molecular identification of L. monocytogenes in various food samples. There are a number of enrichment and plating media that can be used for the isolation of L. monocytogenes from food samples. Enrichment media such as buffered Listeria enrichment broth, Fraser broth, and University of Vermont Medium (UVM) Listeria enrichment broth are recommended by regulatory agencies such as Food and Drug Administration-bacteriological and analytical method (FDA-BAM), US Department of Agriculture-Food and Safety (USDA-FSIS), and International Organization for Standardization (ISO). Many plating media are available for the isolation of L. monocytogenes, for instance, polymyxin acriflavin lithium-chloride ceftazidime aesculin mannitol, Oxford, and other chromogenic media. Besides, reference methods like FDA-BAM, ISO 11290 method, and USDA-FSIS method are usually applied for the cultural detection or enumeration of L. monocytogenes. most probable number technique is applied for the enumeration of L. monocytogenes in the case of low level contamination. Molecular methods including polymerase chain reaction, multiplex polymerase chain reaction, real-time/quantitative polymerase chain reaction, nucleic acid sequence-based amplification, loop-mediated isothermal amplification, DNA microarray, and next generation sequencing technology for the detection and identification of L. monocytogenes are discussed in this review. Overall, molecular methods are rapid, sensitive, specific, time- and labor-saving. In future, there are

  15. Flight test results of a vector-based failure detection and isolation algorithm for a redundant strapdown inertial measurement unit

    NASA Technical Reports Server (NTRS)

    Morrell, F. R.; Bailey, M. L.; Motyka, P. R.

    1988-01-01

    Flight test results of a vector-based fault-tolerant algorithm for a redundant strapdown inertial measurement unit are presented. Because the inertial sensors provide flight-critical information for flight control and navigation, failure detection and isolation is developed in terms of a multi-level structure. Threshold compensation techniques for gyros and accelerometers, developed to enhance the sensitivity of the failure detection process to low-level failures, are presented. Four flight tests, conducted in a commercial transport type environment, were used to determine the ability of the failure detection and isolation algorithm to detect failure signals, such a hard-over, null, or bias shifts. The algorithm provided timely detection and correct isolation of flight control- and low-level failures. The flight tests of the vector-based algorithm demonstrated its capability to provide false alarm free dual fail-operational performance for the skewed array of inertial sensors.

  16. New uncooled thermal IR detector using silicon-diode-micromachined isolated silicon diode for IR detection (MISIR)

    NASA Astrophysics Data System (ADS)

    Kim, Jae-Kwan; Han, Chul-Hi

    2000-12-01

    A new thermal infrared detector using temperature characteristics of a diode has been developed. This micromachined isolated silicon diode for IR detection (MISIR) utilizes an electrochemical etching technique to achieve the thermal isolation of the diode. Experimental dependence of the diode current on the junction temperature enables a high responsivity of the MISIR and the electrochemical etch stop provides an effective isolation at simple and low-cost. The fabricated MISIR has demonstrated a detectivity of 1.2x1010(cm(DOT)HzHLF/W) at room temperature in air ambient.

  17. Fault Detection, Isolation and Recovery (FDIR) Portable Liquid Oxygen Hardware Demonstrator

    NASA Technical Reports Server (NTRS)

    Oostdyk, Rebecca L.; Perotti, Jose M.

    2011-01-01

    The Fault Detection, Isolation and Recovery (FDIR) hardware demonstration will highlight the effort being conducted by Constellation's Ground Operations (GO) to provide the Launch Control System (LCS) with system-level health management during vehicle processing and countdown activities. A proof-of-concept demonstration of the FDIR prototype established the capability of the software to provide real-time fault detection and isolation using generated Liquid Hydrogen data. The FDIR portable testbed unit (presented here) aims to enhance FDIR by providing a dynamic simulation of Constellation subsystems that feed the FDIR software live data based on Liquid Oxygen system properties. The LO2 cryogenic ground system has key properties that are analogous to the properties of an electronic circuit. The LO2 system is modeled using electrical components and an equivalent circuit is designed on a printed circuit board to simulate the live data. The portable testbed is also be equipped with data acquisition and communication hardware to relay the measurements to the FDIR application running on a PC. This portable testbed is an ideal capability to perform FDIR software testing, troubleshooting, training among others.

  18. Novel Aminoglycoside Resistance Transposons and Transposon-Derived Circular Forms Detected in Carbapenem-Resistant Acinetobacter baumannii Clinical Isolates

    PubMed Central

    Dwibedi, Chinmay Kumar; Sjöström, Karin; Edquist, Petra; Wai, Sun Nyunt; Uhlin, Bernt Eric

    2016-01-01

    Acinetobacter baumannii has emerged as an important opportunistic pathogen equipped with a growing number of antibiotic resistance genes. Our study investigated the molecular epidemiology and antibiotic resistance features of 28 consecutive carbapenem-resistant clinical isolates of A. baumannii collected throughout Sweden in 2012 and 2013. The isolates mainly belonged to clonal complexes (CCs) with an extensive international distribution, such as CC2 (n = 16) and CC25 (n = 7). Resistance to carbapenems was related to blaOXA-23 (20 isolates), blaOXA-24/40-like (6 isolates), blaOXA-467 (1 isolate), and ISAba1-blaOXA-69 (1 isolate). Ceftazidime resistance was associated with blaPER-7 in the CC25 isolates. Two classical point mutations were responsible for resistance to quinolones in all the isolates. Isolates with high levels of resistance to aminoglycosides carried the 16S rRNA methylase armA gene. The isolates also carried a variety of genes encoding aminoglycoside-modifying enzymes. Several novel structures involved in aminoglycoside resistance were identified, including Tn6279, ΔTn6279, Ab-ST3-aadB, and different assemblies of Tn6020 and TnaphA6. Importantly, a number of circular forms related to the IS26 or ISAba125 composite transposons were detected. The frequent occurrence of these circular forms in the populations of several isolates indicates a potential role of these circular forms in the dissemination of antibiotic resistance genes. PMID:26824943

  19. Stillbirth Risk Among Fetuses With Ultrasound-Detected Isolated Congenital Anomalies

    PubMed Central

    Frey, Heather A.; Odibo, Anthony O.; Dicke, Jeffrey M.; Shanks, Anthony L.; Macones, George A.; Cahill, Alison G.

    2014-01-01

    Objective To estimate the risk of stillbirth among pregnancies complicated by a major isolated congenital anomaly detected by antenatal ultrasound, and the influence of incidental growth restriction. Methods A retrospective cohort study of all consecutive singleton pregnancies undergoing routine anatomic survey between 1990 and 2009 was performed. Stillbirth rates among fetuses with an ultrasound-detected isolated major congenital anomaly were compared to fetuses without major anomalies. Stillbirth rates were calculated per 1,000 ongoing pregnancies. Exclusion criteria included delivery prior to 24 weeks of gestation, multiple fetal anomalies, minor anomalies and chromosomal abnormalities. Analyses were stratified by gestational age at delivery (prior to 32 weeks vs. 32 weeks of gestation or after) and birth weight less than the 10th percentile. We adjusted for confounders using logistic regression. Results Among 65,308 singleton pregnancies delivered at 24 weeks of gestation or after, 873 pregnancies with an isolated major congenital anomaly (1.3%) were identified. The overall stillbirth rate among fetuses with a major anomaly was 55/1,000 compared to 4/1,000 in nonanomalous fetuses (aOR 15.17, 95% CI 11.03–20.86). Stillbirth risk in anomalous fetuses was similar prior to 32 weeks of gestation (26/1,000) and 32 weeks of gestation or after (31/1,000). Among growth-restricted fetuses, the stillbirth rate increased among anomalous (127/1,000) and nonanomalous fetuses (18/1,000), and congenital anomalies remained associated with higher rates of stillbirth (aOR 8.20, 95% CI 5.27–12.74). Conclusion The stillbirth rate is increased in anomalous fetuses regardless of incidental growth restriction. These risks can assist practitioners designing care plans for anomalous fetuses who have elevated and competing risks of stillbirth and neonatal death. PMID:24901272

  20. Detection and Molecular Characterization of Mycobacterium microti Isolates in Wild Boar from Northern Italy

    PubMed Central

    Gaffuri, Alessandra; Gelmetti, Daniela; Tagliabue, Silvia; Chiari, Mario; Mangeli, Anna; Spisani, Matteo; Nassuato, Claudia; Gibelli, Lucia; Sacchi, Cristina; Zanoni, Mariagrazia; Pacciarini, M. Lodovica

    2014-01-01

    Approximately 23,000 hunter-harvested wild boars from the pre-Alpine area of northern Italy were examined for tuberculosis over a 9-year period (2003 to 2011). Retropharyngeal and mandibular lymph nodes from the wild boars were examined grossly, and 1,151 of the lymph nodes were analyzed in our laboratory by histology (728 samples) and culture isolation (819 samples). Mycobacterium tuberculosis complex (MTBC)-specific PCR (1,142 samples) was used for molecular-level detection in tissue samples, as was a gyrB restriction fragment length polymorphism (RFLP) assay (322 samples). Lesions compatible with tuberculosis and indistinguishable from those described in cases of Mycobacterium bovis infection had been observed since 2003. Mycobacterium microti was identified directly in 256 tissue samples by the adopted molecular approaches. However, only 26 M. microti strains were obtained by culture isolation due to the well-known difficulties in isolating this slow-growing mycobacterium. During 2006, a prevalence study was performed in two provinces of the area, and the diffusion of M. microti was calculated to be 5.8% (95% confidence intervals surrounding the estimated prevalences [CIP95%], 3.94 to 7.68%). Over the following years (2007 to 2011), the presence of M. microti appeared to be stable. All isolates were genotyped by spoligotyping and exact tandem repeat analysis (ETR types A to F). In addition to the typical vole type (SB0118), a new spoligotype lacking the 43 spacers was found. Spoligotyping was also applied directly to tissue samples, and a geographical cluster distribution of the two spoligotypes was observed. This is the first report studying the diffusion and genetic variability of M. microti in wild boar. PMID:24871212

  1. Detection and Isolation Techniques for Methanogens from Microbial Mats (in the El Tatio Geyser Field, Chile)

    NASA Astrophysics Data System (ADS)

    Pearson, E. Z.; Franks, M. A.; Bennett, P.

    2010-12-01

    Isolating methanogenic archea from an extreme environment such as El Tatio (high altitude, arid climate) gives insight to the methanogenic taxas able to adapt and grow under extreme conditions. The hydrothermal waters at El Tatio geyser field demonstrate extreme geochemical conditions, with discharge water from springs and geysers at local boiling temperature (85° C) with high levels of arsenic and low DIC levels. Despite these challenges, many of El Tatio’s hundred plus hydrothermal features host extensive microbial mat communities, many showing evidence of methanogenesis. When trying to isolate methanogens unique to this area, various approaches and techniques were used. To detect the presence of methanogens in samples taken from the field, dissolved methane concentrations were determined via gas chromatography (GC) analysis. Samples were then selected for culturing and most probable number (MPN) enumeration, where growth was assessed using both methane production and observations of fluorescence under UV light. PCR was used to see if the archeal DNA was apparent directly from the field, and shotgun cloning was done to determine phylogenetic affiliation. Several culturing techniques were carried out in an attempt to isolate methanogens from samples that showed evidence of methanogenesis. The slant culturing method was used because of the increased surface area for colonization combined with the relative ease of keeping anaerobic. After a few weeks, when colonies were apparent, some were aseptically selected and inoculated to observe growth in a liquid media containing ampicillin to inhibit bacterial growth. Culturing techniques proved successful after inoculation, showing a slow growth of methanogens via GC and autofluorescence. Further PCR tests and subsequent sequencing were done to confirm and identify isolates.

  2. Assessment of environmental DNA for detecting presence of imperiled aquatic amphibian species in isolated wetlands

    USGS Publications Warehouse

    Mckee, Anna; Calhoun, Daniel L.; Barichivich, William J.; Spear, Stephen F.; Goldberg, Caren S.; Glenn, Travis C

    2015-01-01

    Environmental DNA (eDNA) is an emerging tool that allows low-impact sampling for aquatic species by isolating DNA from water samples and screening for DNA sequences specific to species of interest. However, researchers have not tested this method in naturally acidic wetlands that provide breeding habitat for a number of imperiled species, including the frosted salamander (Ambystoma cingulatum), reticulated flatwoods salamanders (Ambystoma bishopi), striped newt (Notophthalmus perstriatus), and gopher frog (Lithobates capito). Our objectives for this study were to develop and optimize eDNA survey protocols and assays to complement and enhance capture-based survey methods for these amphibian species. We collected three or more water samples, dipnetted or trapped larval and adult amphibians, and conducted visual encounter surveys for egg masses for target species at 40 sites on 12 different longleaf pine (Pinus palustris) tracts. We used quantitative PCRs to screen eDNA from each site for target species presence. We detected flatwoods salamanders at three sites with eDNA but did not detect them during physical surveys. Based on the sample location we assumed these eDNA detections to indicate the presence of frosted flatwoods salamanders. We did not detect reticulated flatwoods salamanders. We detected striped newts with physical and eDNA surveys at two wetlands. We detected gopher frogs at 12 sites total, three with eDNA alone, two with physical surveys alone, and seven with physical and eDNA surveys. We detected our target species with eDNA at 9 of 11 sites where they were present as indicated from traditional surveys and at six sites where they were not detected with traditional surveys. It was, however, critical to use at least three water samples per site for eDNA. Our results demonstrate eDNA surveys can be a useful complement to traditional survey methods for detecting imperiled pond-breeding amphibians. Environmental DNA may be particularly useful in situations

  3. DETECTION OF MOLECULAR GAS IN VOID GALAXIES: IMPLICATIONS FOR STAR FORMATION IN ISOLATED ENVIRONMENTS

    SciTech Connect

    Das, M.; Honey, M.; Saito, T.; Iono, D.; Ramya, S.

    2015-12-10

    We present the detection of molecular gas from galaxies located in nearby voids using the CO(1–0) line emission as a tracer. The observations were performed using the 45 m single dish radio telescope of the Nobeyama Radio Observatory. Void galaxies lie in the most underdense parts of our universe and a significant fraction of them are gas rich, late-type spiral galaxies. Although isolated, they have ongoing star formation but appear to be slowly evolving compared to galaxies in denser environments. Not much is known about their star formation properties or cold gas content. In this study, we searched for molecular gas in five void galaxies. The galaxies were selected based on their relatively high IRAS fluxes or Hα line luminosities, both of which signify ongoing star formation. All five galaxies appear to be isolated and two lie within the Bootes void. We detected CO(1–0) emission from four of the five galaxies in our sample and their molecular gas masses lie between 10{sup 8} and 10{sup 9} M{sub ⊙}. We conducted follow-up Hα imaging observations of three detected galaxies using the Himalayan Chandra Telescope and determined their star formation rates (SFRs) from their Hα fluxes. The SFR varies from 0.2 to 1 M{sub ⊙} yr{sup −1}; which is similar to that observed in local galaxies. Our study indicates that although void galaxies reside in underdense regions, their disks contain molecular gas and have SFRs similar to galaxies in denser environments. We discuss the implications of our results.

  4. Advances in Optical Adjunctive Aids for Visualisation and Detection of Oral Malignant and Potentially Malignant Lesions

    PubMed Central

    Bhatia, Nirav; Lalla, Yastira; Vu, An N.; Farah, Camile S.

    2013-01-01

    Traditional methods of screening for oral potentially malignant disorders and oral malignancies involve a conventional oral examination with digital palpation. Evidence indicates that conventional examination is a poor discriminator of oral mucosal lesions. A number of optical aids have been developed to assist the clinician to detect oral mucosal abnormalities and to differentiate benign lesions from sinister pathology. This paper discusses advances in optical technologies designed for the detection of oral mucosal abnormalities. The literature regarding such devices, VELscope and Identafi, is critically analysed, and the novel use of Narrow Band Imaging within the oral cavity is also discussed. Optical aids are effective in assisting with the detection of oral mucosal abnormalities; however, further research is required to evaluate the usefulness of these devices in differentiating benign lesions from potentially malignant and malignant lesions. PMID:24078812

  5. Advances in ground vehicle-based LADAR for standoff detection of road-side hazards

    NASA Astrophysics Data System (ADS)

    Hollinger, Jim; Vessey, Alyssa; Close, Ryan; Middleton, Seth; Williams, Kathryn; Rupp, Ronald; Nguyen, Son

    2016-05-01

    Commercial sensor technology has the potential to bring cost-effective sensors to a number of U.S. Army applications. By using sensors built for a widespread of commercial application, such as the automotive market, the Army can decrease costs of future systems while increasing overall capabilities. Additional sensors operating in alternate and orthogonal modalities can also be leveraged to gain a broader spectrum measurement of the environment. Leveraging multiple phenomenologies can reduce false alarms and make detection algorithms more robust to varied concealment materials. In this paper, this approach is applied to the detection of roadside hazards partially concealed by light-to-medium vegetation. This paper will present advances in detection algorithms using a ground vehicle-based commercial LADAR system. The benefits of augmenting a LADAR with millimeter-wave automotive radar and results from relevant data sets are also discussed.

  6. Advancements of Data Anomaly Detection Research in Wireless Sensor Networks: A Survey and Open Issues

    PubMed Central

    Rassam, Murad A.; Zainal, Anazida; Maarof, Mohd Aizaini

    2013-01-01

    Wireless Sensor Networks (WSNs) are important and necessary platforms for the future as the concept “Internet of Things” has emerged lately. They are used for monitoring, tracking, or controlling of many applications in industry, health care, habitat, and military. However, the quality of data collected by sensor nodes is affected by anomalies that occur due to various reasons, such as node failures, reading errors, unusual events, and malicious attacks. Therefore, anomaly detection is a necessary process to ensure the quality of sensor data before it is utilized for making decisions. In this review, we present the challenges of anomaly detection in WSNs and state the requirements to design efficient and effective anomaly detection models. We then review the latest advancements of data anomaly detection research in WSNs and classify current detection approaches in five main classes based on the detection methods used to design these approaches. Varieties of the state-of-the-art models for each class are covered and their limitations are highlighted to provide ideas for potential future works. Furthermore, the reviewed approaches are compared and evaluated based on how well they meet the stated requirements. Finally, the general limitations of current approaches are mentioned and further research opportunities are suggested and discussed. PMID:23966182

  7. Advanced infrared sounder subpixel cloud detection with imagers and its impact on radiance assimilation in NWP

    NASA Astrophysics Data System (ADS)

    Wang, Pei; Li, Jun; Li, Jinlong; Li, Zhenglong; Schmit, Timothy J.; Bai, Wenguang

    2014-03-01

    Accurate cloud detection is very important for infrared (IR) radiance assimilation; improved cloud detection could reduce cloud contamination and hence improve the assimilation. Although operational numerical weather prediction (NWP) centers are using IR sounder radiance data for cloud detection, collocated high spatial resolution imager data could help sounder subpixel cloud detection and characterization. IR sounder radiances with improved cloud detection using Atmospheric Infrared Sounder (AIRS)/Moderate Resolution Imaging Spectroradiometer (MODIS) were assimilated for Hurricane Sandy (2012). Forecast experiments were run with Weather Research and Forecasting (WRF) as the forecast model and the Three-Dimensional Variational Assimilation (3DVAR)-based Gridpoint Statistical Interpolation (GSI) as the analysis system. Results indicate that forecasts of both hurricane track and intensity are substantially improved when the collocated high spatial resolution MODIS cloud mask is used for AIRS subpixel cloud detection for assimilating radiances. This methodology can be applied to process Crosstrack Infrared Sounder (CRIS)/Visible Infrared Imaging Radiometer Suite (VIIRS) onboard Suomi-NPOESS Preparatory Project (NPP)/Joint Polar Satellite System (JPSS) and Infrared Atmospheric Sounding Interferometer (IASI)/Advanced Very High Resolution Radiometer (AVHRR) onboard the Metop series for improved radiance assimilation in NWP.

  8. Detection of landmines and UXO using advanced synthetic aperture radar technology

    NASA Astrophysics Data System (ADS)

    Schreiber, Eric; Peichl, Markus; Dill, Stephan; Heinzel, Andreas; Bischeltsrieder, Florian

    2016-05-01

    A main problem of effective landmine and UXO decontamination is efficient and reliable detection and localization of suspicious objects in reasonable time. This requirement demands for fast sensors investigating large areas with sufficient spatial resolution and sensitivity. Ground penetrating radar (GPR) is a suitable tool and is considered as a complementing sensor since nearly two decades. However, most GPRs operate in very close distance to ground in a rather punctual method of operation. In contrast, synthetic aperture radar (SAR) is a technique allowing fast and laminar stand-off investigation of an area. TIRAMI-SAR is imaging radar at lower microwaves for fast close-in detection of buried and unburied objects on a larger area. This allows efficient confirmation of a threat by investigating such regions of detection by other sensors. For proper object detection sufficient spatial resolution is required. Hence the SAR principle is applied. SAR for landmine/UXO detection can be applied by side-looking radar moved on safe ground along the area of interest, being typically the un-safe ground. Additionally, reliable detection of buried and unburied objects requires sufficient suppression of background clutter. For that purpose TIRAMI-SAR is using several antennas in multi-static configuration and wave polarization together with advanced SAR processing. The advantages and necessity of a multi-static antenna configuration for this kind of GPR approach is illustrated in the paper.

  9. Far-infrared pedestrian detection for advanced driver assistance systems using scene context

    NASA Astrophysics Data System (ADS)

    Wang, Guohua; Liu, Qiong; Wu, Qingyao

    2016-04-01

    Pedestrian detection is one of the most critical but challenging components in advanced driver assistance systems. Far-infrared (FIR) images are well-suited for pedestrian detection even in a dark environment. However, most current detection approaches just focus on pedestrian patterns themselves, where robust and real-time detection cannot be well achieved. We propose a fast FIR pedestrian detection approach, called MAP-HOGLBP-T, to explicitly exploit the scene context for the driver assistance system. In MAP-HOGLBP-T, three algorithms are developed to exploit the scene contextual information from roads, vehicles, and background objects of high homogeneity, and we employ the Bayesian approach to build a classifier learner which respects the scene contextual information. We also develop a multiframe approval scheme to enhance the detection performance based on spatiotemporal continuity of pedestrians. Our empirical study on real-world datasets has demonstrated the efficiency and effectiveness of the proposed method. The performance is shown to be better than that of state-of-the-art low-level feature-based approaches.

  10. Assessment of the Utility of the Advanced Himawari Imager to Detect Active Fire Over Australia

    NASA Astrophysics Data System (ADS)

    Hally, B.; Wallace, L.; Reinke, K.; Jones, S.

    2016-06-01

    Wildfire detection and attribution is an issue of importance due to the socio-economic impact of fires in Australia. Early detection of fires allows emergency response agencies to make informed decisions in order to minimise loss of life and protect strategic resources in threatened areas. Until recently, the ability of land management authorities to accurately assess fire through satellite observations of Australia was limited to those made by polar orbiting satellites. The launch of the Japan Meteorological Agency (JMA) Himawari-8 satellite, with the 16-band Advanced Himawari Imager (AHI-8) onboard, in October 2014 presents a significant opportunity to improve the timeliness of satellite fire detection across Australia. The near real-time availability of images, at a ten minute frequency, may also provide contextual information (background temperature) leading to improvements in the assessment of fire characteristics. This paper investigates the application of the high frequency observation data supplied by this sensor for fire detection and attribution. As AHI-8 is a new sensor we have performed an analysis of the noise characteristics of the two spectral bands used for fire attribution across various land use types which occur in Australia. Using this information we have adapted existing algorithms, based upon least squares error minimisation and Kalman filtering, which utilise high frequency observations of surface temperature to detect and attribute fire. The fire detection and attribution information provided by these algorithms is then compared to existing satellite based fire products as well as in-situ information provided by land management agencies. These comparisons were made Australia-wide for an entire fire season - including many significant fire events (wildfires and prescribed burns). Preliminary detection results suggest that these methods for fire detection perform comparably to existing fire products and fire incident reporting from relevant

  11. An integrated, self-contained microfluidic cassette for isolation, amplification, and detection of nucleic acids

    PubMed Central

    Chen, Dafeng; Mauk, Michael; Qiu, Xianbo; Liu, Changchun; Kim, Jitae; Ramprasad, Sudhir; Ongagna, Serge; Abrams, William R.; Malamud, Daniel; Corstjens, Paul L. A. M.

    2010-01-01

    A self-contained, integrated, disposable, sample-to-answer, polycarbonate microfluidic cassette for nucleic acid—based detection of pathogens at the point of care was designed, constructed, and tested. The cassette comprises on-chip sample lysis, nucleic acid isolation, enzymatic amplification (polymerase chain reaction and, when needed, reverse transcription), amplicon labeling, and detection. On-chip pouches and valves facilitate fluid flow control. All the liquids and dry reagents needed for the various reactions are pre-stored in the cassette. The liquid reagents are stored in flexible pouches formed on the chip surface. Dry (RT-)PCR reagents are pre-stored in the thermal cycling, reaction chamber. The process operations include sample introduction; lysis of cells and viruses; solid-phase extraction, concentration, and purification of nucleic acids from the lysate; elution of the nucleic acids into a thermal cycling chamber and mixing with pre-stored (RT-)PCR dry reagents; thermal cycling; and detection. The PCR amplicons are labeled with digoxigenin and biotin and transmitted onto a lateral flow strip, where the target analytes bind to a test line consisting of immobilized avidin-D. The immobilized nucleic acids are labeled with up-converting phosphor (UCP) reporter particles. The operation of the cassette is automatically controlled by an analyzer that provides pouch and valve actuation with electrical motors and heating for the thermal cycling. The functionality of the device is demonstrated by detecting the presence of bacterial B.Cereus, viral armored RNA HIV, and HIV I virus in saliva samples. The cassette and actuator described here can be used to detect other diseases as well as the presence of bacterial and viral pathogens in the water supply and other fluids. PMID:20401537

  12. New technology for ultrasensitive detection and isolation of rare cells for clinical diagnostics and therapeutics

    NASA Astrophysics Data System (ADS)

    Leary, James F.; McLaughlin, Scott R.

    1995-04-01

    A high-speed, 11-parameter, 6-color fluorescence, laser flow cytometer/cell sorter with a number of special and unique features has been built for ultrasensitive detection and isolation of rare cells for clinical diagnostics and therapeutics. The software for real-time data acquisition and sort control, written as C++ programming language modules with a WindowsTM graphical user interface, runs on a 66-MHz 80486 computer joined by an extended bus to 23 sophisticated multi-layered boards of special data acquisition and sorting electronics. Special features include: high-speed (> 100,000 cells/sec) real-time data classification module (U.S. Patent 5,204,884 (1993)); real-time principal component cell sorting; multi-queue signal-processing system with multiple hardware and software event buffers to reduce instrument dead time, LUT charge-pulse definition, high-resolution `flexible' sorting for optimal yield/purity sort strategies (U.S. Patent 5,199,576); pre-focusing optical wavelength correction for a second laser beam; and two trains of three fluorescence detectors-- each adjustable for spatial separation to interrogate only one of two laser beams, syringe- driven or pressure-driven fluidics, and time-windowed parameters. The system has been built to be both expandable and versatile through the use of LUT's and a modular hardware and software design. The instrument is especially useful at detection and isolation of rare cell subpopulations for which our laboratory is well-known. Cell subpopulations at frequencies as small as 10-7 have been successfully studied with this system. Current applications in clinical diagnostics and therapeutics include detection and isolation of (1) fetal cells from material blood for prenatal diagnosis of birth defects, (2) hematopoietic stem and precursor cells for autologous bone marrow transplantation, (3) metastatic breast cancer cells for molecular characterization, and (4) HIV-infected maternal cells in newborn blood to study mother

  13. Comparison of rapid methods of detection of cytomegalovirus in saliva with virus isolation in tissue culture.

    PubMed

    Warren, W P; Balcarek, K; Smith, R; Pass, R F

    1992-04-01

    Two rapid methods for the detection of cytomegalovirus (CMV) in saliva from congenitally and perinatally infected children were assessed by comparison with traditional virus isolation in tissue culture (TC). The polymerase chain reaction (PCR) was used to amplify a 300-bp segment of the CMV gB gene which was detected in ethidium bromide-stained agarose gels. A centrifugation-enhanced microtiter culture method with a monoclonal antibody for the detection of early-antigen fluorescent foci (DEAFF) was also used. Saliva specimens were collected with mouth swabs from children who were between the ages of 1 month and 14 years and who had either prenatal or perinatal CMV infection. One hundred sixty samples were tested by PCR and TC; 65 (40.6%) were found positive by TC, and 58 (36.8%) were found positive by PCR. Although four samples were found positive by PCR and negative by TC, saliva from seronegative and seropositive TC-negative adults were never found positive by PCR. One hundred fifty-two samples were tested by DEAFF and TC; 64 (42.1%) were found positive by TC, and 58 (38.2%) were found positive by DEAFF. With TC results as a standard, the sensitivity and specificity of DEAFF were, respectively, 90.6 and 97.7%. Because of the greater ease of collecting saliva than urine from newborns, both of these rapid methods merit evaluation in screening for congenital infection.

  14. Detection, isolation, and capture of circulating breast cancer cells with photoacoustic flow cytometry

    NASA Astrophysics Data System (ADS)

    Bhattacharyya, Kiran; Njoroge, Martin; Goldschmidt, Benjamin S.; Gaffigan, Brian; Rood, Kyle; Viator, John A.

    2013-03-01

    According to the CDC, breast cancer is the most common cancer and the second leading cause of cancer related deaths among women. Metastasis, or the presence of secondary tumors caused by the spread of cancer cells via the circulatory or lymphatic systems, significantly worsens the prognosis of any breast cancer patient. In this study, a technique is developed to detect circulating breast cancer cells in human blood using a photoacoustic flow cytometry method. A Q-switched laser with a 5 ns pulse at 532 nm is used to interrogate thousands of cells with one pulse as they flow through the beam path. Cells which are pigmented, either naturally or artificially, emit an ultrasound wave as a result of the photoacoustic (PA) effect. Breast cancer cells are targeted with chromophores through immunochemistry in order to provide pigment. After which, the device is calibrated to demonstrate a single-cell detection limit. Cultured breast cancer cells are added to whole blood to reach a biologically relevant concentration of about 25-45 breast cancer cells per 1 mL of blood. An in vitro photoacoustic flow cytometer is used to detect and isolate these cells followed by capture with the use of a micromanipulator. This method can not only be used to determine the disease state of the patient and the response to therapy, it can also be used for genetic testing and in vitro drug trials since the circulating cell can be captured and studied.

  15. Application of immobilized synthetic anti-lipopolysaccharide peptides for the isolation and detection of bacteria.

    PubMed

    Sandetskaya, N; Engelmann, B; Brandenburg, K; Kuhlmeier, D

    2015-08-01

    The molecular detection of microorganisms in liquid samples generally requires their enrichment or isolation. The aim of our study was to evaluate the capture and pre-concentration of bacteria by immobilized particular cationic antimicrobial peptides, called synthetic anti-lipopolysaccharide peptides (SALP). For the proof-of-concept and screening of different SALP, the peptides were covalently immobilized on glass slides, and the binding of bacteria was confirmed by microscopic examination of the slides or their scanning, in case of fluorescent bacterial cells. The most efficient SALP was further tethered to magnetic beads. SALP beads were used for the magnetic capture of Escherichia coli in liquid samples. The efficiency of this strategy was evaluated using polymerase chain reaction (PCR). Covalently immobilized SALP were capable of capturing bacteria in liquid samples. However, PCR was hampered by the unspecific binding of DNA to the positively charged peptide. We developed a method for DNA recovery by the enzymatic digestion of the peptide, which allowed for a successful PCR, though the method had its own adverse impact on the detection and, thus, did not allow for the reliable quantitative analysis of the pathogen enrichment. Immobilized SALP can be used as capture molecules for bacteria in liquid samples and can be recommended for the design of the assays or decontamination of the fluids. For the accurate subsequent detection of bacteria, DNA-independent methods should be used.

  16. Development of Advanced Electrochemical Sensors for DNA Detection at the Point of Care

    NASA Astrophysics Data System (ADS)

    Hsieh, Kuangwen

    In the post-genomic era, ever-advancing capabilities in DNA detection and analysis have become vital to the detection of infectious diseases and the diagnosis of genetic abnormalities and inheritable diseases. The benefit of such capabilities, however, has yet to reach patients outside of centralized facilities. There thus exists an increasing need to decentralize DNA detection methods and to administer such diagnostics at the "point of care." Electrochemical-based DNA sensors present a compelling approach, but have yet to deliver satisfactory sensitivity, specificity, miniaturization, and real-time monitoring capability to meet the demand of point-of-care diagnostics. Motivated by their potential and their current limitations, in this dissertation, we present a series of strategies that we have undertaken in order to address the key shortcomings of electrochemical DNA sensors and advance them toward point-of-care applications. First, we report a single-step, single reagent, label-free, isothermal electrochemical DNA sensor based on the phenomenon of enzyme catalyzed target recycling amplification. Using this technique, we achieve improved detection limit in comparison to hybridization-based sensors without amplification. We also demonstrate greater than 16-fold amplification of signal at low target concentrations. Next, we present a novel electrochemical DNA sensor that detects single-nucleotide mismatched targets with unprecedented "polarity-switching" responses. This "bipolar" sensor employs a surface-bound and redox-modified (methylene blue) DNA probe architecture, and outputs a decreased Faradaic current when hybridized to a perfectly matched (PM) target, but conversely reports an increased Faradaic current when hybridized to a single-base mismatched (SM) target. Third, we describe the microfluidic electrochemical dynamic allele specific hybridization (microE-DASH) platform for versatile and rapid detection of single-nucleotide polymorphisms. Implementing

  17. A vector-based failure detection and isolation algorithm for a dual fail-operational redundant strapdown inertial measurement unit

    NASA Technical Reports Server (NTRS)

    Morrell, Frederick R.; Bailey, Melvin L.

    1987-01-01

    A vector-based failure detection and isolation technique for a skewed array of two degree-of-freedom inertial sensors is developed. Failure detection is based on comparison of parity equations with a threshold, and isolation is based on comparison of logic variables which are keyed to pass/fail results of the parity test. A multi-level approach to failure detection is used to ensure adequate coverage for the flight control, display, and navigation avionics functions. Sensor error models are introduced to expose the susceptibility of the parity equations to sensor errors and physical separation effects. The algorithm is evaluated in a simulation of a commercial transport operating in a range of light to severe turbulence environments. A bias-jump failure level of 0.2 deg/hr was detected and isolated properly in the light and moderate turbulence environments, but not detected in the extreme turbulence environment. An accelerometer bias-jump failure level of 1.5 milli-g was detected over all turbulence environments. For both types of inertial sensor, hard-over, and null type failures were detected in all environments without incident. The algorithm functioned without false alarm or isolation over all turbulence environments for the runs tested.

  18. Isolated Hepatic Perfusion with 200 mg Melphalan for Advanced Noncolorectal Liver Metastases

    PubMed Central

    Hoekman, Ellen J.; Gelderblom, Hans; Vahrmeijer, Alexander L.; van Persijn van Meerten, Els L.; Tijl, Fred G. J.; Hartgrink, Henk H.; Kuppen, Peter J. K.; Nortier, Johan W. R.; Tollenaar, Rob A. E. M.; van de Velde, Cornelis J. H.

    2008-01-01

    Purpose The liver is one of the most common sites for metastatic solid tumors. If the liver is the only site of metastatic disease, regional treatment options can offer the benefit of high local exposure with limited systemic toxicity, especially for patients without (further) systemic treatment options. We report the results of our experience with isolated hepatic perfusion (IHP) in patients with isolated liver metastases from a variety of primary tumors. Patients and Methods Nineteen patients with isolated unresectable liver metastases from a variety of tumors (13 uveal melanomas, 2 neuroendocrine carcinomas, 2 gastrointestinal stromal tumors, 1 hepatocellular carcinoma, and 1 high-grade sarcoma) were treated with a 60-min IHP using 200 mg melphalan. Patients were monitored for toxicity, response according to response evaluation criteria in solid tumors (RECIST) criteria, and survival. Results One melanoma patient was not perfused due to insufficient isolation of the liver. There was no treatment-related mortality. Reversible grade 3 or 4 hepatoxicity occurred in 10 (56%) patients, while veno-occlusive disease occurred in 4 (22%) patients. Of the 12 uveal melanoma patients who were perfused, 4 (33%) patients had a partial hepatic response, 6 (50%) patients had stable hepatic disease, and 2 (17%) patients were immediately progressive. Median disease-free survival was 6.6 months with a median overall survival of 10.0 months. Fifty percent of other primary tumors showed at least partial remission, including one complete remission in a high-grade sarcoma patient. Conclusion IHP with melphalan shows activity in patients with liver metastases from a variety of primary tumors, but other or additional drugs may improve therapeutic outcome. PMID:18470571

  19. Detection of new paternal dystrophin gene mutations in isolated cases of dystrophinopathy in females

    SciTech Connect

    Pegoraro, E.; Wessel, H.B.; Schwartz, L.; Hoffman, E.P. ); Schimke, R.N. ); Arahata, Kiichi; Hayashi, Yukiko ); Stern, H. ); Marks, H. ); Glasberg, M.R. )

    1994-06-01

    Duchenne muscular dystrophy is one of the most common lethal monogenic disorders and is caused by dystrophin deficiency. The disease is transmitted as an X-linked recessive trait; however, recent biochemical and clinical studies have shown that many girls and women with a primary myopathy have an underlying dystrophinopathy, despite a negative family history for Duchenne dystrophy. These isolated female dystrophinopathy patients carried ambiguous diagnoses with presumed autosomal recessive inheritance (limb-girdle muscular dystrophy) prior to biochemical detection of dystrophin abnormalities in their muscle biopsy. It has been assumed that these female dystrophinopathy patients are heterozygous carries who show preferential inactivation of the X chromosome harboring the normal dystrophin gene, although this has been shown for only a few X:autosome translocations and for two cases of discordant monozygotic twin female carriers. Here the authors study X-inactivation patterns of 13 female dystrophinopathy patients - 10 isolated cases and 3 cases with a positive family history for Duchenne dystrophy in males. They show that all cases have skewed X-inactivation patterns in peripheral blood DNA. Of the nine isolated cases informative in the assay, eight showed inheritance of the dystrophin gene mutation from the paternal germ line. Only a single case showed maternal inheritance. The 10-fold higher incidence of paternal transmission of dystrophin gene mutations in these cases is at 30-fold variance with Bayesian predictions and gene mutation rates. Thus, the results suggest some mechanistic interaction between new dystrophin gene mutations, paternal inheritance, and skewed X inactivation. The results provide both empirical risk data and a molecular diagnostic test method, which permit genetic counseling and prenatal diagnosis of this new category of patients. 58 refs., 7 figs., 2 tabs.

  20. Detection of Staphylococcus aureus Isolates with Heterogeneous Intermediate-Level Resistance to Vancomycin in the United States▿

    PubMed Central

    Richter, Sandra S.; Satola, Sarah W.; Crispell, Emily K.; Heilmann, Kristopher P.; Dohrn, Cassie L.; Riahi, Fathollah; Costello, Andrew J.; Diekema, Daniel J.; Doern, Gary V.

    2011-01-01

    The prevalence of heterogeneous intermediate-level resistance to vancomycin (hVISA) in Staphylococcus aureus was assessed by screening a large collection of recent isolates. Susceptibility testing by the Clinical and Laboratory Standards Institute broth microdilution method and the Etest GRD (glycopeptide resistance detection) method (bioMérieux) was performed on 4,210 clinically significant S. aureus isolates obtained in 2009 from 43 U.S. centers. Isolates with Etest GRD-positive results for hVISA were evaluated further by repeat GRD testing and population analysis profiling–area under the curve (PAP-AUC) analysis. No VISA (vancomycin MIC, 4 to 8 μg/ml) or vancomycin-resistant (MIC ≥ 16 μg/ml) strains were detected. The Etest GRD screen for hVISA was initially positive for 68 isolates (1.6%; all by teicoplanin MIC ≥ 8 μg/ml at 24 or 48 h). Among those 68 isolates, 45 were reproducibly GRD positive. PAP-AUC testing confirmed only 11 isolates as hVISA (all had reproducible GRD-positive results). The 11 hVISA isolates were from nine medical centers and appeared genetically diverse (ten different PFGE types). The rates of resistance (including intermediate) for hVISA were as follows: oxacillin, 82%; erythromycin, 82%; clindamycin, 73%; levofloxacin, 73%; trimethoprim-sulfamethoxazole, 9%; and daptomycin, 9%. All hVISA isolates were susceptible to linezolid, tigecycline, and ceftaroline. Our data suggest that the overall prevalence of hVISA in the United States is low (0.3%). The hVISA isolates represented 10.5% of isolates with vancomycin MICs of 2 μg/ml and 0.1% of isolates with vancomycin MICs of 1 μg/ml. The positive predictive value of GRD Etest for hVISA was 16.2% for initial screen positive and 24.4% for reproducibly positive results. PMID:21976769

  1. Design of a novel knowledge-based fault detection and isolation scheme.

    PubMed

    Zhao, Qing; Xu, Zhihan

    2004-04-01

    In this paper, a real-time fault detection and isolation (FDI) scheme for dynamical systems is developed, by integrating the signal processing technique with neural network design. Wavelet analysis is applied to capture the fault-induced transients of the measured signals in real-time, and the decomposed signals are pre-processed to extract details about a fault. A Regional Self-Organizing feature Map (R-SOM) neural network is synthesized to classify the fault types. The R-SOM neural network adopts two regions adjustment in the learning algorithm, thus it has high precision in clustering and matching, especially when the noise, disturbance and other uncertainties exist in the systems. As a result, the proposed FDI scheme is robust and accurate. The design is implemented on a stirred tank system and satisfactory online testing results are obtained.

  2. Fault detection and isolation of aircraft air data/inertial system

    NASA Astrophysics Data System (ADS)

    Berdjag, D.; Cieslak, J.; Zolghadri, A.

    2013-12-01

    A method for failure detection and isolation (FDI) for redundant aircraft sensors is presented. The outputs of the concerned sensors are involved in the computation of flight control laws, and the objective is to eliminate any fault before propagation in the control loop when selecting a unique flight parameter among a set (generally, three) of redundant measurements. The particular case of an oscillatory failure is investigated. The proposed method allows an accurate FDI of erroneous sensor and computes a consolidated parameter based on the fusion of data from remaining valid sensors. The benefits of the presented method are to enhance the data fusion process with FDI techniques which improve the performance of the fusion when only few sources (less than three) are initially valid.

  3. Evaluation of an expert system for fault detection, isolation, and recovery in the manned maneuvering unit

    NASA Technical Reports Server (NTRS)

    Rushby, John; Crow, Judith

    1990-01-01

    The authors explore issues in the specification, verification, and validation of artificial intelligence (AI) based software, using a prototype fault detection, isolation and recovery (FDIR) system for the Manned Maneuvering Unit (MMU). They use this system as a vehicle for exploring issues in the semantics of C-Language Integrated Production System (CLIPS)-style rule-based languages, the verification of properties relating to safety and reliability, and the static and dynamic analysis of knowledge based systems. This analysis reveals errors and shortcomings in the MMU FDIR system and raises a number of issues concerning software engineering in CLIPs. The authors came to realize that the MMU FDIR system does not conform to conventional definitions of AI software, despite the fact that it was intended and indeed presented as an AI system. The authors discuss this apparent disparity and related questions such as the role of AI techniques in space and aircraft operations and the suitability of CLIPS for critical applications.

  4. Tandem Mass Spectrometry Detection of Quorum Sensing Activity in Multidrug Resistant Clinical Isolate Acinetobacter baumannii

    PubMed Central

    Chan, Kok-Gan; Cheng, Huey Jia; Chen, Jian Woon; Yin, Wai-Fong; Ngeow, Yun Fong

    2014-01-01

    Many Proteobacteria communicate via production followed by response of quorum sensing molecules, namely, N-acyl homoserine lactones (AHLs). These molecules consist of a lactone moiety with N-acyl side chain with various chain lengths and degrees of saturation at C-3 position. AHL-dependent QS is often associated with regulation of diverse bacterial phenotypes including the expression of virulence factors. With the use of biosensor and high resolution liquid chromatography tandem mass spectrometry, the AHL production of clinical isolate A. baumannii 4KT was studied. Production of short chain AHL, namely, N-hexanoyl-homoserine lactone (C6-HSL) and N-octanoyl-homoserine lactone (C8-HSL), was detected. PMID:25101326

  5. Detection and isolation of plant-associated bacteria scavenging atmospheric molecular hydrogen.

    PubMed

    Kanno, Manabu; Constant, Philippe; Tamaki, Hideyuki; Kamagata, Yoichi

    2016-09-01

    High-affinity hydrogen (H2 )-oxidizing bacteria possessing group 5 [NiFe]-hydrogenase genes are important contributors to atmospheric H2 uptake in soil environments. Although previous studies reported the occurrence of a significant H2 uptake activity in vegetation, there has been no report on the identification and diversity of the responsible microorganisms. Here, we show the existence of plant-associated bacteria with the ability to consume atmospheric H2 that may be a potential energy source required for their persistence in plants. Detection of the gene hhyL - encoding the large subunit of group 5 [NiFe]-hydrogenase - in plant tissues showed that plant-associated high-affinity H2 -oxidizing bacteria are widely distributed in herbaceous plants. Among a collection of 145 endophytic isolates, seven Streptomyces strains were shown to possess hhyL gene and exhibit high- or intermediate-affinity H2 uptake activity. Inoculation of Arabidopsis thaliana (thale cress) and Oryza sativa (rice) seedlings with selected isolates resulted in an internalization of the bacteria in plant tissues. H2 uptake activity per bacterial cells was comparable between plant and soil, demonstrating that both environments are favourable for the H2 uptake activity of streptomycetes. This study first demonstrated the occurrence of plant-associated high-affinity H2 -oxidizing bacteria and proposed their potential contribution as atmospheric H2 sink.

  6. Using Decision Trees to Detect and Isolate Simulated Leaks in the J-2X Rocket Engine

    NASA Technical Reports Server (NTRS)

    Schwabacher, Mark A.; Aguilar, Robert; Figueroa, Fernando F.

    2009-01-01

    The goal of this work was to use data-driven methods to automatically detect and isolate faults in the J-2X rocket engine. It was decided to use decision trees, since they tend to be easier to interpret than other data-driven methods. The decision tree algorithm automatically "learns" a decision tree by performing a search through the space of possible decision trees to find one that fits the training data. The particular decision tree algorithm used is known as C4.5. Simulated J-2X data from a high-fidelity simulator developed at Pratt & Whitney Rocketdyne and known as the Detailed Real-Time Model (DRTM) was used to "train" and test the decision tree. Fifty-six DRTM simulations were performed for this purpose, with different leak sizes, different leak locations, and different times of leak onset. To make the simulations as realistic as possible, they included simulated sensor noise, and included a gradual degradation in both fuel and oxidizer turbine efficiency. A decision tree was trained using 11 of these simulations, and tested using the remaining 45 simulations. In the training phase, the C4.5 algorithm was provided with labeled examples of data from nominal operation and data including leaks in each leak location. From the data, it "learned" a decision tree that can classify unseen data as having no leak or having a leak in one of the five leak locations. In the test phase, the decision tree produced very low false alarm rates and low missed detection rates on the unseen data. It had very good fault isolation rates for three of the five simulated leak locations, but it tended to confuse the remaining two locations, perhaps because a large leak at one of these two locations can look very similar to a small leak at the other location.

  7. An ensemble of dynamic neural network identifiers for fault detection and isolation of gas turbine engines.

    PubMed

    Amozegar, M; Khorasani, K

    2016-04-01

    In this paper, a new approach for Fault Detection and Isolation (FDI) of gas turbine engines is proposed by developing an ensemble of dynamic neural network identifiers. For health monitoring of the gas turbine engine, its dynamics is first identified by constructing three separate or individual dynamic neural network architectures. Specifically, a dynamic multi-layer perceptron (MLP), a dynamic radial-basis function (RBF) neural network, and a dynamic support vector machine (SVM) are trained to individually identify and represent the gas turbine engine dynamics. Next, three ensemble-based techniques are developed to represent the gas turbine engine dynamics, namely, two heterogeneous ensemble models and one homogeneous ensemble model. It is first shown that all ensemble approaches do significantly improve the overall performance and accuracy of the developed system identification scheme when compared to each of the stand-alone solutions. The best selected stand-alone model (i.e., the dynamic RBF network) and the best selected ensemble architecture (i.e., the heterogeneous ensemble) in terms of their performances in achieving an accurate system identification are then selected for solving the FDI task. The required residual signals are generated by using both a single model-based solution and an ensemble-based solution under various gas turbine engine health conditions. Our extensive simulation studies demonstrate that the fault detection and isolation task achieved by using the residuals that are obtained from the dynamic ensemble scheme results in a significantly more accurate and reliable performance as illustrated through detailed quantitative confusion matrix analysis and comparative studies. PMID:26881999

  8. An ensemble of dynamic neural network identifiers for fault detection and isolation of gas turbine engines.

    PubMed

    Amozegar, M; Khorasani, K

    2016-04-01

    In this paper, a new approach for Fault Detection and Isolation (FDI) of gas turbine engines is proposed by developing an ensemble of dynamic neural network identifiers. For health monitoring of the gas turbine engine, its dynamics is first identified by constructing three separate or individual dynamic neural network architectures. Specifically, a dynamic multi-layer perceptron (MLP), a dynamic radial-basis function (RBF) neural network, and a dynamic support vector machine (SVM) are trained to individually identify and represent the gas turbine engine dynamics. Next, three ensemble-based techniques are developed to represent the gas turbine engine dynamics, namely, two heterogeneous ensemble models and one homogeneous ensemble model. It is first shown that all ensemble approaches do significantly improve the overall performance and accuracy of the developed system identification scheme when compared to each of the stand-alone solutions. The best selected stand-alone model (i.e., the dynamic RBF network) and the best selected ensemble architecture (i.e., the heterogeneous ensemble) in terms of their performances in achieving an accurate system identification are then selected for solving the FDI task. The required residual signals are generated by using both a single model-based solution and an ensemble-based solution under various gas turbine engine health conditions. Our extensive simulation studies demonstrate that the fault detection and isolation task achieved by using the residuals that are obtained from the dynamic ensemble scheme results in a significantly more accurate and reliable performance as illustrated through detailed quantitative confusion matrix analysis and comparative studies.

  9. Study on the Integrated Geophysic Methods and Application of Advanced Geological Detection for Complicated Tunnel

    NASA Astrophysics Data System (ADS)

    Zhou, L.; Xiao, G.

    2014-12-01

    The engineering geological and hydrological conditions of current tunnels are more and more complicated, as the tunnels are elongated with deeper depth. In constructing these complicated tunnels, geological hazards prone to occur as induced by unfavorable geological bodies, such as fault zones, karst or hydrous structures, etc. The working emphasis and difficulty of the advanced geological exploration for complicated tunnels are mainly focused on the structure and water content of these unfavorable geological bodies. The technical aspects of my paper systematically studied the advanced geological exploration theory and application aspects for complicated tunnels, with discussion on the key technical points and useful conclusions. For the all-aroundness and accuracy of advanced geological exploration results, the objective of my paper is targeted on the comprehensive examination on the structure and hydrous characteristic of the unfavorable geological bodies in complicated tunnels. By the multi-component seismic modeling on a more real model containing the air medium, the wave field response characteristics of unfavorable geological bodies can be analyzed, thus providing theoretical foundation for the observation system layout, signal processing and interpretation of seismic methods. Based on the tomographic imaging theory of seismic and electromagnetic method, 2D integrated seismic and electromagnetic tomographic imaging and visualization software was designed and applied in the advanced drilling hole in the tunnel face, after validation of the forward and inverse modeling results on theoretical models. The transmission wave imaging technology introduced in my paper can be served as a new criterion for detection of unfavorable geological bodies. After careful study on the basic theory, data processing and interpretation, practical applications of TSP and ground penetrating radar (GPR) method, as well as serious examination on their application examples, my paper

  10. Development, Implementation, and Testing of Fault Detection Strategies on the National Wind Technology Center's Controls Advanced Research Turbines

    SciTech Connect

    Johnson, K. E.; Fleming, P. A.

    2011-06-01

    The National Renewable Energy Laboratory's National Wind Technology Center dedicates two 600 kW turbines for advanced control systems research. A fault detection system for both turbines has been developed, analyzed, and improved across years of experiments to protect the turbines as each new controller is tested. Analysis of field data and ongoing fault detection strategy improvements have resulted in a system of sensors, fault definitions, and detection strategies that have thus far been effective at protecting the turbines. In this paper, we document this fault detection system and provide field data illustrating its operation while detecting a range of failures. In some cases, we discuss the refinement process over time as fault detection strategies were improved. The purpose of this article is to share field experience obtained during the development and field testing of the existing fault detection system, and to offer a possible baseline for comparison with more advanced turbine fault detection controllers.

  11. Technological advancements for the detection of and protection against biological and chemical warfare agents.

    PubMed

    Eubanks, Lisa M; Dickerson, Tobin J; Janda, Kim D

    2007-03-01

    There is a growing need for technological advancements to combat agents of chemical and biological warfare, particularly in the context of the deliberate use of a chemical and/or biological warfare agent by a terrorist organization. In this tutorial review, we describe methods that have been developed both for the specific detection of biological and chemical warfare agents in a field setting, as well as potential therapeutic approaches for treating exposure to these toxic species. In particular, nerve agents are described as a typical chemical warfare agent, and the two potent biothreat agents, anthrax and botulinum neurotoxin, are used as illustrative examples of potent weapons for which countermeasures are urgently needed.

  12. Detection and Sizing of Fatigue Cracks in Steel Welds with Advanced Eddy Current Techniques

    NASA Astrophysics Data System (ADS)

    Todorov, E. I.; Mohr, W. C.; Lozev, M. G.

    2008-02-01

    Butt-welded specimens were fatigued to produce cracks in the weld heat-affected zone. Advanced eddy current (AEC) techniques were used to detect and size the cracks through a coating. AEC results were compared with magnetic particle and phased-array ultrasonic techniques. Validation through destructive crack measurements was also conducted. Factors such as geometry, surface treatment, and crack tightness interfered with depth sizing. AEC inspection techniques have the potential of providing more accurate and complete sizing flaw data for manufacturing and in-service inspections.

  13. Comparative analysis of EV isolation procedures for miRNAs detection in serum samples

    PubMed Central

    Andreu, Zoraida; Rivas, Eva; Sanguino-Pascual, Aitana; Lamana, Amalia; Marazuela, Mónica; González-Alvaro, Isidoro; Sánchez-Madrid, Francisco; de la Fuente, Hortensia; Yáñez-Mó, María

    2016-01-01

    Extracellular vesicles (EVs) are emerging as potent non-invasive biomarkers. However, current methodologies are time consuming and difficult to translate to clinical practice. To analyse EV-encapsulated circulating miRNA, we searched for a quick, easy and economic method to enrich frozen human serum samples for EV. We compared the efficiency of several protocols and commercial kits to isolate EVs. Different methods based on precipitation, columns or filter systems were tested and compared with ultracentrifugation, which is the most classical protocol to isolate EVs. EV samples were assessed for purity and quantity by nanoparticle tracking analysis and western blot or cytometry against major EV protein markers. For biomarker validation, levels of a set of miRNAs were determined in EV fractions and compared with their levels in total serum. EVs isolated with precipitation-based methods were enriched for a subgroup of miRNAs that corresponded to miRNAs described to be encapsulated into EVs (miR-126, miR-30c and miR-143), while the detection of miR-21, miR-16-5p and miR-19a was very low compared with total serum. Our results point to precipitation using polyethylene glycol (PEG) as a suitable method for an easy and cheap enrichment of serum EVs for miRNA analyses. The overall performance of PEG was very similar, or better than other commercial precipitating reagents, in both protein and miRNA yield, but in comparison to them PEG is much cheaper. Other methods presented poorer results, mostly when assessing miRNA by qPCR analyses. Using PEG precipitation in a longitudinal study with human samples, we demonstrated that miRNA could be assessed in frozen samples up to 8 years of storage. We report a method based on a cut-off value of mean of fold EV detection versus serum that provides an estimate of the degree of encapsulation of a given miRNA. PMID:27330048

  14. Allele-specific duplex polymerase chain reaction to differentiate Mycobacterium abscessus subspecies and to detect highly clarithromycin-resistant isolates.

    PubMed

    Kim, H Y; Lee, S Y; Kim, B J; Kook, Y H

    2016-01-01

    On the basis of the structural differences of erm, we used a duplex polymerase chain reaction (PCR) to differentiate Mycobacterium abscessus subsp. abscessus and subsp. massiliense isolates and to detect the point mutations of 23S rRNA gene that confer a high level of resistance to clarithromycin. Subsp. massiliense strains occupying almost half of the clinical isolates can be simply identified, and their clarithromycin susceptibility can be rapidly determined. PMID:27514964

  15. Detection of galectin-3 and localization of advanced glycation end products (AGE) in human chronic skin wounds.

    PubMed

    Pepe, Daniel; Elliott, Christopher G; Forbes, Thomas L; Hamilton, Douglas W

    2014-02-01

    The matricellular protein galectin-3 (Gal-3) is upregulated in excisional skin repair in rats where it has been shown to modulate the inflammatory phase of repair. Recent research into kidney pathology has implicated Gal-3 as a receptor for advanced glycation end products (AGE), resulting in the binding and clearance of these molecules. AGEs are thought to contribute to defective skin repair in diabetic patients as well as a result of the normal aging process. However, the distribution and localization of Gal-3 and AGEs has never been performed in human chronic skin wound tissue. Using immunohistochemistry, the localization of Gal-3 and AGEs in tissue isolated from chronic wounds and non-involved skin from the same patient was investigated. Of the 16 patients from which tissue was isolated, 13 had type II diabetes, one had type I diabetes and 2 patients without diabetes were also examined. In non-involved dermis, Gal-3 was detected strongly in the epidermis and in the vasculature. However, at the wound edge and in the wound bed, the level of Gal-3 labelling was greatly reduced in both the epidermis and vasculature. Labelling of serial sections for Gal-3 and AGE demonstrated that where Gal-3 immunoreactivity is reduced in the epidermis and vasculature, there is a concomitant increase in the level of AGE staining. Interestingly, similar labelling patterns were evident in diabetic and non-diabetic patients. The results from our study demonstrate an inverse correlation between Gal-3 and AGEs localization, suggesting that Gal-3 may protect against accumulation of AGEs in wound healing.

  16. Distribution and phenotypic and genotypic detection of a metallo-β-lactamase, CphA, among bacteraemic Aeromonas isolates.

    PubMed

    Wu, Chi-Jung; Chen, Po-Lin; Wu, Jiunn-Jong; Yan, Jing-Jou; Lee, Chin-Chi; Lee, Hsin-Chun; Lee, Nan-Yao; Chang, Chia-Ming; Lin, Yu-Tzu; Chiu, Yen-Cheng; Ko, Wen-Chien

    2012-05-01

    The objectives of the study were to investigate the distribution of cphA-related genes (cphA) encoding a CphA metallo-β-lactamase (MBL) among 51 consecutive Aeromonas blood isolates and to compare different phenotypic methods for detecting CphA. The presence of cphA was detected by PCR. Four phenotypic methods, the imipenem-EDTA combined disc test, imipenem-EDTA MBL Etest, agar dilution test and modified Hodge test (MHT), were used to detect imipenem susceptibility and MBL production. The results showed that 35 (69%) blood isolates had cphA. All (100%) of 16 Aeromonas aquariorum isolates and 12 Aeromonas veronii isolates, and 4 (80%) of 5 Aeromonas hydrophila isolates, carried cphA, but none of 15 Aeromonas caviae isolates did. With the standard inocula, irrespective of the presence or absence of cphA, all but one (50, 98%) isolates were susceptible to imipenem tested by disc diffusion, Etest and agar dilution (10(4) c.f.u. spot inocula), and did not exhibit MBL production by the imipenem-EDTA combined disc test and MBL Etest. By the agar dilution test using large inocula (10(7) c.f.u.), 34 (97%) of 35 cphA(+) isolates had imipenem MICs of ≥16 µg ml(-1), higher than the susceptible breakpoint (4 µg ml(-1)), and demonstrated positive results for the MHT, while one cphA(+) and all 17 cphA(-) isolates had imipenem MICs of ≤4 µg ml(-1). In conclusion, the distribution of cphA among aeromonads is species-specific, found in A. aquariorum, A. veronii and A. hydrophila, and the MHT may be a phenotypic screening test for CphA production.

  17. Rapid Detection of Rifampin Resistance in Mycobacterium tuberculosis Isolates from India and Mexico by a Molecular Beacon Assay

    PubMed Central

    Varma-Basil, Mandira; El-Hajj, Hiyam; Colangeli, Roberto; Hazbón, Manzour Hernando; Kumar, Sujeet; Bose, Mridula; Bobadilla-del-Valle, Miriam; García, Lourdes García; Hernández, Araceli; Kramer, Fred Russell; Osornio, Jose Sifuentes; Ponce-de-León, Alfredo; Alland, David

    2004-01-01

    We assessed the performance of a rapid, single-well, real-time PCR assay for the detection of rifampin-resistant Mycobacterium tuberculosis by using clinical isolates from north India and Mexico, regions with a high incidence of tuberculosis. The assay uses five differently colored molecular beacons to determine if a short region of the M. tuberculosis rpoB gene contains mutations that predict rifampin resistance in most isolates. Until now, the assay had not been sufficiently tested on samples from countries with a high incidence of tuberculosis. In the present study, the assay detected mutations in 16 out of 16 rifampin-resistant isolates from north India (100%) and in 55 of 64 rifampin-resistant isolates from Mexico (86%) compared to results with standard susceptibility testing. The assay did not detect mutations (a finding predictive of rifampin susceptibility) in 37 out of 37 rifampin-susceptible isolates from India (100%) and 125 out of 126 rifampin-susceptible isolates from Mexico (99%). DNA sequencing revealed that none of the nine rifampin-resistant isolates from Mexico, which were misidentified as rifampin susceptible by the molecular beacon assay, contained a mutation in the region targeted by the molecular beacons. The one rifampin-susceptible isolate from Mexico that appeared to be rifampin resistant by the molecular beacon assay contained an S531W mutation, which is usually associated with rifampin resistance. Of the rifampin-resistant isolates that were correctly identified in the molecular beacon assay, one contained a novel L530A mutation and another contained a novel deletion between codons 511 and 514. Overall, the molecular beacon assay appears to have sufficient sensitivity (89%) and specificity (99%) for use in countries with a high prevalence of tuberculosis. PMID:15583274

  18. Rapid detection of rifampin resistance in Mycobacterium tuberculosis isolates from India and Mexico by a molecular beacon assay.

    PubMed

    Varma-Basil, Mandira; El-Hajj, Hiyam; Colangeli, Roberto; Hazbón, Manzour Hernando; Kumar, Sujeet; Bose, Mridula; Bobadilla-del-Valle, Miriam; García, Lourdes García; Hernández, Araceli; Kramer, Fred Russell; Osornio, Jose Sifuentes; Ponce-de-León, Alfredo; Alland, David

    2004-12-01

    We assessed the performance of a rapid, single-well, real-time PCR assay for the detection of rifampin-resistant Mycobacterium tuberculosis by using clinical isolates from north India and Mexico, regions with a high incidence of tuberculosis. The assay uses five differently colored molecular beacons to determine if a short region of the M. tuberculosis rpoB gene contains mutations that predict rifampin resistance in most isolates. Until now, the assay had not been sufficiently tested on samples from countries with a high incidence of tuberculosis. In the present study, the assay detected mutations in 16 out of 16 rifampin-resistant isolates from north India (100%) and in 55 of 64 rifampin-resistant isolates from Mexico (86%) compared to results with standard susceptibility testing. The assay did not detect mutations (a finding predictive of rifampin susceptibility) in 37 out of 37 rifampin-susceptible isolates from India (100%) and 125 out of 126 rifampin-susceptible isolates from Mexico (99%). DNA sequencing revealed that none of the nine rifampin-resistant isolates from Mexico, which were misidentified as rifampin susceptible by the molecular beacon assay, contained a mutation in the region targeted by the molecular beacons. The one rifampin-susceptible isolate from Mexico that appeared to be rifampin resistant by the molecular beacon assay contained an S531W mutation, which is usually associated with rifampin resistance. Of the rifampin-resistant isolates that were correctly identified in the molecular beacon assay, one contained a novel L530A mutation and another contained a novel deletion between codons 511 and 514. Overall, the molecular beacon assay appears to have sufficient sensitivity (89%) and specificity (99%) for use in countries with a high prevalence of tuberculosis.

  19. Lung Cancer Workshop XI: Tobacco-Induced Disease: Advances in Policy, Early Detection and Management.

    PubMed

    Mulshine, James L; Avila, Rick; Yankelevitz, David; Baer, Thomas M; Estépar, Raul San Jose; Ambrose, Laurie Fenton; Aldigé, Carolyn R

    2015-05-01

    The Prevent Cancer Foundation Lung Cancer Workshop XI: Tobacco-Induced Disease: Advances in Policy, Early Detection and Management was held in New York, NY on May 16 and 17, 2014. The two goals of the Workshop were to define strategies to drive innovation in precompetitive quantitative research on the use of imaging to assess new therapies for management of early lung cancer and to discuss a process to implement a national program to provide high quality computed tomography imaging for lung cancer and other tobacco-induced disease. With the central importance of computed tomography imaging for both early detection and volumetric lung cancer assessment, strategic issues around the development of imaging and ensuring its quality are critical to ensure continued progress against this most lethal cancer. PMID:25898957

  20. Design of Advanced Atmospheric Water Vapor Differential Absorption Lidar (DIAL) Detection System

    NASA Technical Reports Server (NTRS)

    Refaat, Tamer F.; Luck, William S., Jr.; DeYoung, Russell J.

    1999-01-01

    The measurement of atmospheric water vapor is very important for understanding the Earth's climate and water cycle. The lidar atmospheric sensing experiment (LASE) is an instrument designed and operated by the Langley Research Center for high precision water vapor measurements. The design details of a new water vapor lidar detection system that improves the measurement sensitivity of the LASE instrument by a factor of 10 are discussed. The new system consists of an advanced, very low noise, avalanche photodiode (APD) and a state-of-the-art signal processing circuit. The new low-power system is also compact and lightweight so that it would be suitable for space flight and unpiloted atmospheric vehicles (UAV) applications. The whole system is contained on one small printed circuit board (9 x 15 sq cm). The detection system is mounted at the focal plane of a lidar receiver telescope, and the digital output is read by a personal computer with a digital data acquisition card.

  1. Advanced In-Situ Detection and Chemical Analysis of Interstellar Dust Particles

    NASA Astrophysics Data System (ADS)

    Sternovsky, Z.; Gemer, A.; Gruen, E.; Horanyi, M.; Kempf, S.; Maute, K.; Postberg, F.; Srama, R.; Williams, E.; O'brien, L.; Rocha, J. R. R.

    2015-12-01

    The Ulysses dust detector discovered that interstellar dust particles pass through the solar system. The Hyperdsut instrument is developed for the in-situ detection and analysis of these particles to determine the elemental, chemical and isotopic compositions. Hyperdust builds on the heritage of previous successful instruments, e.g. the Cosmic Dust Analyzer (CDA) on Cassini. Hyperdust combines a highly sensitive Dust Trajectory Sensor (DTS) and the high mass resolution Chemical Analyzer (CA). The DTS will detect dust particles as small as 0.3 μm in radius, and the velocity vector information is used to confirm the interstellar origin and/or reveal the dynamics from the interactions within the solar system. The effective target area of the CA is > 600 cm2 achieves mass resolution in excess of 200, which is considerably higher than that of CDA, and is acheved by advanced ion optics design. The Hyperdust instrument is in the final phases of development to TRL 6.

  2. Lung Cancer Workshop XI: Tobacco-Induced Disease: Advances in Policy, Early Detection and Management.

    PubMed

    Mulshine, James L; Avila, Rick; Yankelevitz, David; Baer, Thomas M; Estépar, Raul San Jose; Ambrose, Laurie Fenton; Aldigé, Carolyn R

    2015-05-01

    The Prevent Cancer Foundation Lung Cancer Workshop XI: Tobacco-Induced Disease: Advances in Policy, Early Detection and Management was held in New York, NY on May 16 and 17, 2014. The two goals of the Workshop were to define strategies to drive innovation in precompetitive quantitative research on the use of imaging to assess new therapies for management of early lung cancer and to discuss a process to implement a national program to provide high quality computed tomography imaging for lung cancer and other tobacco-induced disease. With the central importance of computed tomography imaging for both early detection and volumetric lung cancer assessment, strategic issues around the development of imaging and ensuring its quality are critical to ensure continued progress against this most lethal cancer.

  3. Method for detection and reconstruction of gravitational wave transients with networks of advanced detectors

    NASA Astrophysics Data System (ADS)

    Klimenko, S.; Vedovato, G.; Drago, M.; Salemi, F.; Tiwari, V.; Prodi, G. A.; Lazzaro, C.; Ackley, K.; Tiwari, S.; Da Silva, C. F.; Mitselmakher, G.

    2016-02-01

    We present a method for detection and reconstruction of the gravitational wave (GW) transients with the networks of advanced detectors. Originally designed to search for transients with the initial GW detectors, it uses significantly improved algorithms, which enhance both the low-latency searches with rapid localization of GW events for the electromagnetic follow-up and high confidence detection of a broad range of the transient GW sources. In this paper, we present the analytic framework of the method. Following a short description of the core analysis algorithms, we introduce a novel approach to the reconstruction of the GW polarization from a pattern of detector responses to a GW signal. This polarization pattern is a unique signature of an arbitrary GW signal that can be measured independently from the other source parameters. The polarization measurements enable rapid reconstruction of the GW waveforms, sky localization, and helps identification of the source origin.

  4. Staphylococcus aureus Isolates from Goat and Sheep Milk Seem to Be Closely Related and Differ from Isolates Detected from Bovine Milk.

    PubMed

    Merz, Axel; Stephan, Roger; Johler, Sophia

    2016-01-01

    Dairy goat and sheep farms suffer severe economic losses due to intramammary infections, with Staphylococcus aureus representing the main cause of clinical mastitis in small ruminants. In addition, S. aureus contamination of goat and sheep milk may cause staphylococcal food poisoning, as many traditional caprine and ovine milk products are not subjected to pasteurization. Data on virulence and antimicrobial resistance genes, as well as on the clonality of S. aureus detected in goat and sheep milk is scarce. Therefore, it was the aim of this study to determine (i) spa types and clonal complexes (CC) and (ii) virulence and resistance gene profiles of S. aureus isolated from goat and sheep milk. A total of 162 milk samples from sheep and goats presenting signs of an intramammary infection and 104 bulk milk samples were collected. While low prevalence rates of S. aureus was detected on single animal level, 46% of the bulk tank milk samples from small ruminants were positive for S. aureus. All isolates were spa typed and CC and virulence and resistance gene patterns were determined using a DNA microarray. Data from 49 S. aureus isolates was included in the statistical analysis and the construction of a SplitsTree. The analyzed isolates could be assigned to eleven CC, with the large majority of goat and sheep isolates being assigned to CC130 and CC133. The findings of this study suggest that S. aureus shows pronounced adaptation to small ruminants in general, but not to sheep or goats in particular. Although some common characteristics among S. aureus from caprine, ovine, and bovine milk samples were observed, S. aureus from small ruminants seem to form a distinct population. As 67% of the detected S. aureus strains exhibited at least one enterotoxin gene, many caprine, or ovine raw milk products may be contaminated with low levels of enterotoxigenic S. aureus, stressing the importance of strict maintenance of the cold chain. PMID:27014240

  5. Ex vivo detection of histone H1 modified with advanced glycation end products.

    PubMed

    Pashikanti, Srinath; Boissonneault, Gilbert A; Cervantes-Laurean, Daniel

    2011-05-15

    A number of oxidative stress agents cause DNA and protein damage, which may compromise genomic integrity. Whereas oxidant-induced DNA damage has been extensively studied, much less is known concerning the occurrence and fate of nuclear protein damage, particularly of proteins involved in the regulation and maintenance of chromatin structure. Protein damage may be caused by the formation of reactive carbonyl species such as glyoxal, which forms after lipid peroxide degradation. It may also result from degradation of early protein glycation adducts and from methylglyoxal, formed in the process of glycolytic intermediate degradation. Major adducts indicative of protein damage include the advanced glycation end product (AGE) carboxymethyllysine (CML) and argpyrimidine protein adducts. Thus, the formation of CML and argpyrimidine protein adducts represents potential biomarkers for nuclear protein damage deriving from a variety of sources. The purpose of this study was to identify and quantify AGE adducts formed in vivo in a nuclear protein, specifically histone H1, using CML and argpyrimidine as biomarkers. Histone H1 was isolated from calf thymus collected immediately after slaughter under conditions designed to minimize AGE formation before isolation. Using antibodies directed against oxidative protein adducts, we identified CML, argpyrimidine, and protein crosslinks present in the freshly isolated histone H1. Detailed mass spectroscopy analysis of histone H1 revealed the presence of two specific lysine residues modified by CML adducts. Our results strongly suggest that glycation of important nuclear protein targets such as histone H1 occurs in vivo and that these oxidative changes may alter chromatin structure, ultimately contributing to chronic changes associated with aging and diseases such as diabetes. PMID:21315148

  6. Identification of Anaplasma marginale long-term carrier cattle by detection of serum antibody to isolated MSP-3.

    PubMed Central

    McGuire, T C; Davis, W C; Brassfield, A L; McElwain, T F; Palmer, G H

    1991-01-01

    Rapid and accurate detection of Anaplasma marginale-infected cattle would enhance anaplasmosis control procedures and evaluation of vaccines. Current tests based on detection of antibodies in serum are not widely used for several reasons, including the occurrence of either false-positive or false-negative results. We evaluated binding of antibodies in serum to a subunit antigen isolated from A. marginale initial bodies--major surface protein 3 (MSP-3). MSP-3 was detected in lysates of eight geographically different isolates of A. marginale and purified by affinity chromatography with monoclonal antibody AmG75C2. Antibodies from cattle infected with any of five geographically different isolates of A. marginale reacted in immunoblots with MSP-3. Sera from uninfected cattle and cattle infected with another rickettsial organism and two hemoprotozoal organisms failed to react with MSP-3. Six carrier cattle infected with the Florida isolate of A. marginale had antibody titers to MSP-3 ranging from 10(3) to 10(6) during a 5-year evaluation period. Since specific antibodies to isolated MSP-3 persist in high titers in long-term carrier cattle sera and MSP-3 is common among A. marginale isolates, it is recommended as a subunit antigen for an anaplasmosis test. Images PMID:1890178

  7. Fault detection and fault tolerant control of a smart base isolation system with magneto-rheological damper

    NASA Astrophysics Data System (ADS)

    Wang, Han; Song, Gangbing

    2011-08-01

    Fault detection and isolation (FDI) in real-time systems can provide early warnings for faulty sensors and actuator signals to prevent events that lead to catastrophic failures. The main objective of this paper is to develop FDI and fault tolerant control techniques for base isolation systems with magneto-rheological (MR) dampers. Thus, this paper presents a fixed-order FDI filter design procedure based on linear matrix inequalities (LMI). The necessary and sufficient conditions for the existence of a solution for detecting and isolating faults using the H_{\\infty } formulation is provided in the proposed filter design. Furthermore, an FDI-filter-based fuzzy fault tolerant controller (FFTC) for a base isolation structure model was designed to preserve the pre-specified performance of the system in the presence of various unknown faults. Simulation and experimental results demonstrated that the designed filter can successfully detect and isolate faults from displacement sensors and accelerometers while maintaining excellent performance of the base isolation technology under faulty conditions.

  8. Contribution of dfrA and inhA mutations to the detection of isoniazid-resistant Mycobacterium tuberculosis isolates.

    PubMed

    Ho, Yu Min; Sun, Yong-Jiang; Wong, Sin-Yew; Lee, Ann S G

    2009-09-01

    Screening of 127 isoniazid (INH)-resistant Mycobacterium tuberculosis isolates from Singapore for mutations within the dfrA and inhA genes revealed mutations in 0 and 5 (3.9%) isolates respectively, implying that mutations in dfrA do not contribute to the detection of INH-resistant M. tuberculosis and that mutations within inhA are rare. Thirty-seven (29%) of the 127 isolates had no mutations in any of the genes implicated in INH resistance (katG, kasA, and ndh; inhA and ahpC promoters), suggesting that there are new INH targets yet to be discovered. PMID:19581462

  9. Recent advances in isolation, synthesis, and evaluation of bioactivities of bispyrroloquinone alkaloids of marine origin.

    PubMed

    Nijampatnam, Bhavitavya; Dutta, Shilpa; Velu, Sadanandan E

    2015-08-01

    The ocean continues to provide a plethora of unique scaffolds capable of remarkable biological applications. A large number of pyrroloiminoquinone alkaloids, including discorhabdins, epinardins, batzellines, makaluvamines, and veiutamine, have been isolated from various marine organisms. A class of pyrroloiminoquinone-related alkaloids, known as bispyrroloquinones, is the focus of this review article. This family of marine alkaloids, which contain an aryl substituted bispyrroloquinone ring system, includes three subclasses of alkaloids namely, wakayin, tsitsikammamines A-B, and zyzzyanones A-D. Both wakayin and the tsitsikammamines contain a tetracyclic fused bispyrroloiminoquinone ring system, while zyzzyanones contain a fused tricyclic bispyrroloquinone ring system. The unique chemical structures of these marine natural products and their diverse biological properties, including antifungal and antimicrobial activity, as well as the potent, albeit generally nonspecific and universal cytotoxicities, have attracted great interest of synthetic chemists over the past three decades. Tsitsikammamines, wakayin, and several of their analogs show inhibition of topoisomerases. One additional possible mechanism of anticancer activity of tsitsikammamines analogs that has been discovered recently is through the inhibition of indoleamine 2, 3-dioxygenase, an enzyme involved in tumoral immune resistance. This review discusses the isolation, synthesis, and evaluation of bioactivities of bispyrroloquinone alkaloids and their analogs.

  10. Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production.

    PubMed

    Haitjema, Charles H; Solomon, Kevin V; Henske, John K; Theodorou, Michael K; O'Malley, Michelle A

    2014-08-01

    Anaerobic gut fungi are an early branching family of fungi that are commonly found in the digestive tract of ruminants and monogastric herbivores. It is becoming increasingly clear that they are the primary colonizers of ingested plant biomass, and that they significantly contribute to the decomposition of plant biomass into fermentable sugars. As such, anaerobic fungi harbor a rich reservoir of undiscovered cellulolytic enzymes and enzyme complexes that can potentially transform the conversion of lignocellulose into bioenergy products. Despite their unique evolutionary history and cellulolytic activity, few species have been isolated and studied in great detail. As a result, their life cycle, cellular physiology, genetics, and cellulolytic metabolism remain poorly understood compared to aerobic fungi. To help address this limitation, this review briefly summarizes the current body of knowledge pertaining to anaerobic fungal biology, and describes progress made in the isolation, cultivation, molecular characterization, and long-term preservation of these microbes. We also discuss recent cellulase- and cellulosome-discovery efforts from gut fungi, and how these interesting, non-model microbes could be further adapted for biotechnology applications.

  11. Detection of Integrase Gene in E. coli Isolated from Pigs at Different Stages of Production System

    PubMed Central

    Colello, Rocío; Padola, Nora Lía; Etcheverría, Analía; Rodríguez, Edgardo; Amanto, Fabián; Tapia, María Ofelia; Soraci, Alejandro Luis

    2014-01-01

    Integrons are one of the genetic elements involved in the acquisition of antibiotic resistance. The aim of the present research is to investigate the presence of integrons in commensal Escherichia coli (E. coli) strains, isolated from pigs at different stages of production system and from the environment in an Argentinian farm. Five sows postpartum and five randomly chosen piglets from each litter were sampled by rectal swabs. They were sampled again at day 21 and at day 70. Environmental samples from the farm were also obtained. E. coli containing any integron class or combination of both integrons was detected by polymerase chain reaction in 100% of sows and in piglets at different stages of production: farrowing pen stage 68.1%;, weaning 60%, and growing/finishing 85.8%, showing an increase along the production system. From environmental samples 78.4% of E. coli containing any integron class was detected. We conclude that animals and farm environment can act as reservoirs for potential spread of resistant bacteria by means of mobile genetic elements as integrons, which has a major impact on production of food animals and that can reach man through the food chain, constituting a problem for public health. PMID:24734046

  12. Isolation and molecular detection of methylotrophic bacteria occurring in the human mouth.

    PubMed

    Anesti, Vasiliki; McDonald, Ian R; Ramaswamy, Meghna; Wade, William G; Kelly, Donovan P; Wood, Ann P

    2005-08-01

    Diverse methylotrophic bacteria were isolated from the tongue, and supra- and subgingival plaque in the mouths of volunteers and patients with periodontitis. One-carbon compounds such as dimethylsulfide in the mouth are likely to be used as growth substrates for these organisms. Methylotrophic strains of Bacillus, Brevibacterium casei, Hyphomicrobium sulfonivorans, Methylobacterium, Micrococcus luteus and Variovorax paradoxus were characterized physiologically and by their 16S rRNA gene sequences. The type strain of B. casei was shown to be methylotrophic. Enzymes of methylotrophic metabolism were characterized in some strains, and activities consistent with growth using known pathways of C1-compound metabolism demonstrated. Genomic DNA from 18 tongue and dental plaque samples from nine volunteers was amplified by the polymerase chain reaction using primers for the 16S rRNA gene of Methylobacterium and the mxaF gene of methanol dehydrogenase. MxaF was detected in all nine volunteers, and Methylobacterium was detected in seven. Methylotrophic activity is thus a feature of the oral bacterial community. PMID:16011760

  13. Avian host range of Chlamydophila spp. based on isolation, antigen detection and serology.

    PubMed

    Kaleta, E F; Taday, Eva M A

    2003-10-01

    Published reports and our own diagnostic data on the avian host range of avian Chlamydophila spp. are presented in an attempt to provide evidence for the large number of bird species that have been naturally infected with chlamydia. The term 'chlamydia-positive' is based on either isolation of the organism and antigen detection or on serological detection of circulating antibodies. The list of chlamydia-positive birds contains the six major domestic species (chicken, turkey, Pekin duck, Muscovy duck, goose, and pigeon), the three minor domestic species (Japanese quail, bobwhite quail, and peafowl) and a total of 460 free-living or pet bird species in 30 orders. The order Psittaciformes contains by far the most (153 of 342; 45%) chlamydia-positive bird species. More than 20% of all species per order are positive for chlamydia in the orders Lariformes (gulls, 26 of 92 species; 28%), Alciformes (alks, six of 23 species; 26%), Sphenisciformes (penguins, four of 16 species; 25%), and Anseriformes (ducks and geese, 33 of 157 species; 21%). Only 5% of all bird species (14 of 259 species) in the order Phasianiformes (gallinaceus birds) are chlamydia-positive. The different percentages of chlamydia-positive bird species reflect: (i) a high rate of investigations (e.g. of domestic birds) compared with infrequent testing (e.g. of Charadriiformes or Cuculiformes), (ii) frequent zoonotic implications (e.g. psittacine and columbiform birds), and (iii) an assumed high susceptibility to infection and subsequent seroconversion (e.g. waterfowl).

  14. Optically-Detected Magnetic Resonance of Alkali Atoms Isolated on Helium Nano-Droplets

    NASA Astrophysics Data System (ADS)

    Koch, Markus; Callegari, Carlo; Ernst, Wolfgang E.

    2009-06-01

    Sharp, hyperfine-resolved, ESR spectra of alkali atoms isolated on helium nanodroplets are measured by optically-detected magnetic resonance (ODMR). A net spin polarization is created inside a magnetic field (B=0.2 to 4.2 T) by a pump laser beam. Microwave radiation in a resonant cavity at 9.4 GHz causes a spin transition which is detected by a probe laser beam. For ultimate precision the spectrum of free atoms is concurrently measured and serves as a reference. The shift of the ESR lines on the droplet with respect to free atoms directly reflects the distortion of the valence-electron wavefunction due to the He nanodroplet. While the electron g-factor remains unchanged within experimental uncertainties (<5 ppm), the increase of the hyperfine constant (typically +400 ppm) is consistent with an increase of the Fermi contact interaction. We are able to follow this change as a function of droplet size attesting the sensitivity of the method for the measurement of chemical shifts. The observation of Rabi oscillations indicates a long decoherence time and proves our ability to perform coherent manipulation of the spin.

  15. Comparative analyses of different genetic markers for the detection of Acanthamoeba spp. isolates.

    PubMed

    Derda, Monika; Wojtkowiak-Giera, Agnieszka; Hadaś, Edward

    2014-09-01

    Acanthamoeba are widespread free-living amoebae which may cause granulomatous amoebic encephalitis (GAE), keratitis, skin ulcerations and disseminated tissue infection. An important diagnostic and prognostic factor for the treatment of infection is a quick and correct diagnosis of amoebae strains. The aim of our study was to develop a rapid method for detection and identification of pathogenic Acanthamoeba spp. strains from diagnostic material collected from water. In this study we analysed five amplification-based genetic markers (Aca 16S, Ac6/210, GP, JDP, Nelson) used for identification of pathogenic Acanthamoeba spp. strains isolated in water sources in Poland, Iceland and Sweden. Our results demonstrated the presence of pathogenic Acanthamoeba strains in tap water. PCR assay appeared to be a more rapid and sensitive method to detect the presence of amoebae than the limited conventional techniques. Based on our observations, we can confirm that the use of four out of five genetic markers (Aca 16S, Ac 6/210, JDP, GP, Nelson) may be helpful in identification of Acanthamoeba spp. strains, but only one Aca 16S primer pair is a highly specific marker that distinguishes between pathogenic strains of Acanthamoeba and other free-living amoeba families.

  16. Avian host range of Chlamydophila spp. based on isolation, antigen detection and serology.

    PubMed

    Kaleta, E F; Taday, Eva M A

    2003-10-01

    Published reports and our own diagnostic data on the avian host range of avian Chlamydophila spp. are presented in an attempt to provide evidence for the large number of bird species that have been naturally infected with chlamydia. The term 'chlamydia-positive' is based on either isolation of the organism and antigen detection or on serological detection of circulating antibodies. The list of chlamydia-positive birds contains the six major domestic species (chicken, turkey, Pekin duck, Muscovy duck, goose, and pigeon), the three minor domestic species (Japanese quail, bobwhite quail, and peafowl) and a total of 460 free-living or pet bird species in 30 orders. The order Psittaciformes contains by far the most (153 of 342; 45%) chlamydia-positive bird species. More than 20% of all species per order are positive for chlamydia in the orders Lariformes (gulls, 26 of 92 species; 28%), Alciformes (alks, six of 23 species; 26%), Sphenisciformes (penguins, four of 16 species; 25%), and Anseriformes (ducks and geese, 33 of 157 species; 21%). Only 5% of all bird species (14 of 259 species) in the order Phasianiformes (gallinaceus birds) are chlamydia-positive. The different percentages of chlamydia-positive bird species reflect: (i) a high rate of investigations (e.g. of domestic birds) compared with infrequent testing (e.g. of Charadriiformes or Cuculiformes), (ii) frequent zoonotic implications (e.g. psittacine and columbiform birds), and (iii) an assumed high susceptibility to infection and subsequent seroconversion (e.g. waterfowl). PMID:14522700

  17. Isolate-Specific Detection of Grapevine fanleaf virus from Xiphinema index Through DNA-Based Molecular Probes.

    PubMed

    Finetti-Sialer, M M; Ciancio, A

    2005-03-01

    ABSTRACT Tests with a real-time reverse transcription-polymerase chain reaction (RT-PCR) were performed on specimens of Xiphinema index collected from the rhizosphere of Grapevine fanleaf virus (GFLV)-infected grapevines at Palagiano, Italy. A 1,157-bp fragment of the GFLV RNA-2 coat protein (CP) gene was amplified and sequenced. A fluorescent Scorpion probe was designed to detect a highly conserved CP region. A second region with isolate-specific multiple nucleotide polymorphisms was used to detect GFLV isolates using molecular beacons (MB). The Scorpion probe allowed quantitative estimation of GFLV RNA-2 in single nematodes, using a dilution series of a 692-nucleotide transcript of the CP gene. The assay allowed detection of GFLV RNA-2 in individual X. index, with a minimum template threshold of 800 fg or 2.8 x 10(6) RNA-2 molecules per nematode. The CP fragment used for GFLV detection with the Scorpion probe appeared highly conserved among isolates. The probes were tested against other GFLV isolates, which were recognized by the species-specific Scorpion probe and by the corresponding MB specific to the particular isolate. Both tests appeared useful as diagnostic tools or for studies on GFLV in acquisition, retention, and transmission experiments.

  18. Acquisition and processing of advanced sensor data for ERW and UXO detection and classification

    NASA Astrophysics Data System (ADS)

    Schultz, Gregory M.; Keranen, Joe; Miller, Jonathan S.; Shubitidze, Fridon

    2014-06-01

    The remediation of explosive remnants of war (ERW) and associated unexploded ordnance (UXO) has seen improvements through the injection of modern technological advances and streamlined standard operating procedures. However, reliable and cost-effective detection and geophysical mapping of sites contaminated with UXO such as cluster munitions, abandoned ordnance, and improvised explosive devices rely on the ability to discriminate hazardous items from metallic clutter. In addition to anthropogenic clutter, handheld and vehicle-based metal detector systems are plagued by natural geologic and environmental noise in many post conflict areas. We present new and advanced electromagnetic induction (EMI) technologies including man-portable and towed EMI arrays and associated data processing software. While these systems feature vastly different form factors and transmit-receive configurations, they all exhibit several fundamental traits that enable successful classification of EMI anomalies. Specifically, multidirectional sampling of scattered magnetic fields from targets and corresponding high volume of unique data provide rich information for extracting useful classification features for clutter rejection analysis. The quality of classification features depends largely on the extent to which the data resolve unique physics-based parameters. To date, most of the advanced sensors enable high quality inversion by producing data that are extremely rich in spatial content through multi-angle illumination and multi-point reception.

  19. A hybrid method for damage detection and quantification in advanced X-COR composite structures

    NASA Astrophysics Data System (ADS)

    Neerukatti, Rajesh Kumar; Rajadas, Abhishek; Borkowski, Luke; Chattopadhyay, Aditi; Huff, Daniel W.

    2016-04-01

    Advanced composite structures, such as foam core carbon fiber reinforced polymer composites, are increasingly being used in applications which require high strength, high in-plane and flexural stiffness, and low weight. However, the presence of in situ damage due to manufacturing defects and/or service conditions can complicate the failure mechanisms and compromise their strength and reliability. In this paper, the capability of detecting damages such as delaminations and foam-core separations in X-COR composite structures using non-destructive evaluation (NDE) and structural health monitoring (SHM) techniques is investigated. Two NDE techniques, flash thermography and low frequency ultrasonics, were used to detect and quantify the damage size and locations. Macro fiber composites (MFCs) were used as actuators and sensors to study the interaction of Lamb waves with delaminations and foam-core separations. The results indicate that both flash thermography and low frequency ultrasonics were capable of detecting damage in X-COR sandwich structures, although low frequency ultrasonic methods were capable of detecting through thickness damages more accurately than flash thermography. It was also observed that the presence of foam-core separations significantly changes the wave behavior when compared to delamination, which complicates the use of wave based SHM techniques. Further, a wave propagation model was developed to model the wave interaction with damages at different locations on the X-COR sandwich plate.

  20. Advanced Imaging Technologies for the Detection of Dysplasia and Early Cancer in Barrett Esophagus

    PubMed Central

    Espino, Alberto; Cirocco, Maria; DaCosta, Ralph

    2014-01-01

    Advanced esophageal adenocarcinomas arising from Barrett esophagus (BE) are tumors with an increasing incidence and poor prognosis. The aim of endoscopic surveillance of BE is to detect dysplasia, particularly high-grade dysplasia and intramucosal cancers that can subsequently be treated endoscopically before progression to invasive cancer with lymph node metastases. Current surveillance practice standards require the collection of random 4-quadrant biopsy specimens over every 1 to 2 cm of BE (Seattle protocol) to detect dysplasia with the assistance of white light endoscopy, in addition to performing targeted biopsies of recognizable lesions. This approach is labor-intensive but should currently be considered state of the art. Chromoendoscopy, virtual chromoendoscopy (e.g., narrow band imaging), and confocal laser endomicroscopy, in addition to high-definition standard endoscopy, might increase the diagnostic yield for the detection of dysplastic lesions. Until these modalities have been demonstrated to enhance efficiency or cost effectiveness, the standard protocol will remain careful examination using conventional off the shelf high-resolution endoscopes, combined with as longer inspection time which is associated with increased detection of dysplasia. PMID:24570883

  1. Summary of the ACS symposium on Advances in Food Allergen Detection.

    PubMed

    Ross, Mark M; Jackson, Lauren

    2013-06-19

    A symposium titled "Advances in Food Allergen Detection" was held at the 243rd National Meeting of the American Chemical Society (ACS) in March 2012 in San Diego, CA, and was sponsored by the ACS Division of Agricultural and Food Chemistry. The purpose of the symposium was to convene the leaders in the food allergen analysis field for presentations on, and discussions of, the state of the art, new developments, and critical challenges in the detection and quantitation of allergenic proteins in foods. Twenty-five presentations were delivered by speakers representing academic, government, and industrial institutions in 10 countries. The presentations covered all aspects of food allergens, including a historical progress review, regulatory policies, clinical practices, food-processing effects, food production equipment cross-contamination and cleaning, and the performance of several food allergen analytical strategies and technologies. This paper is intended to provide a brief summary of the presentations as well as a record of the proceedings of the symposium, which was deemed a great success in advancing food allergen analysis.

  2. Fault detection and isolation of PEM fuel cell system based on nonlinear analytical redundancy. An application via parity space approach

    NASA Astrophysics Data System (ADS)

    Aitouche, A.; Yang, Q.; Ould Bouamama, B.

    2011-05-01

    This paper presents a procedure dealing with the issue of fault detection and isolation (FDI) using nonlinear analytical redundancy (NLAR) technique applied in a proton exchange membrane (PEM) fuel cell system based on its mathematic model. The model is proposed and simplified into a five orders state space representation. The transient phenomena captured in the model include the compressor dynamics, the flow characteristics, mass and energy conservation and manifold fluidic mechanics. Nonlinear analytical residuals are generated based on the elimination of the unknown variables of the system by an extended parity space approach to detect and isolate actuator and sensor faults. Finally, numerical simulation results are given corresponding to a faults signature matrix.

  3. Optimal DNA isolation method for detection of bacteria in clinical specimens by broad-range PCR.

    PubMed

    Rantakokko-Jalava, Kaisu; Jalava, Jari

    2002-11-01

    Broad-range amplification of bacterial DNA from clinical specimens has proved useful for the diagnosis of various bacterial infections, especially during antimicrobial treatment of the patient. Optimal sample processing protocols for diagnostic broad-range bacterial PCR should release DNA from an array of target organisms with equal efficiencies and wash out inhibitory factors from various sample types without introducing bacterial DNA contamination to the amplification reaction. In the present study, two physical cell wall disintegration methods, bead beating and sonication, for enhanced detection of organisms with difficult-to-lyse cell walls were studied. The analytical sensitivities of several commercially available DNA purification kits, which were used with and without additional cell disintegration steps, were compared by using dilution series of model bacteria. Selected purification methods were used to process routine clinical specimens in parallel with the standard phenol-ether DNA extraction, and the results obtained by bacterial PCR and sequencing with the two template preparations were compared. The method with the DNA isolation kit with the lowest detection limits from the bacterial suspensions (Masterpure) did not prove to be superior to the standard method when the two methods were applied to 69 clinical specimens. For another set of 68 clinical specimens, DNA purified with a glass fiber filter column (High Pure) with an additional sonication step yielded results well in accord with those obtained by the standard method. Furthermore, bacterial DNA was detected in four samples that remained PCR negative by the standard method, and three of these contained DNA from gram-positive pathogens. Three samples were positive by the standard method only, indicating the limitations of applying any single method to all samples.

  4. [Application of chemiluminescence immunoassay method in detection of serum index for liver fibrosis in patients with advanced schistosomiasis].

    PubMed

    Luo, Jiang-Long

    2011-02-01

    The method of chemiluminescence immunoassay (CLIA) was adopted to detect the levels of hyaluronic acid (HA), laminin (LN), III procollagen (CP III), IV collagen (IV-C) in the sera of 102 cases of advanced schistosomiasis. The results showed that the levels of the 4 indexes of advanced schistosomiasis patients were significantly higher than those of healthy people. It is suggested that the application of CLIA to detect the related serum indexes in patients with advanced schistosomiasis is useful in the diagnosis of liver fibrosis. PMID:22164394

  5. A decentralized fault detection and isolation scheme for spacecraft: bridging the gap between model-based fault detection and isolation research and practice

    NASA Astrophysics Data System (ADS)

    Indra, S.; Travé-Massuyès, L.; Chanthery, E.

    2013-12-01

    This paper introduces a decentralized fault diagnosis and isolation (FDI) architecture for spacecraft and applies it to the attitude determination and control system (ADCS) of a satellite. A system is decomposed into functional subsystems. The architecture is composed of local diagnosers for subsystems which work with local models. Fault ambiguities due to interactions between subsystems are resolved at a higher level by a supervisor, which combines the partial view of the local diagnosers and performs isolation on request. The architecture is hierarchically scalable. The structure of the ADCS is modeled as constraints and variables and used to demonstrate the decentralized architecture.

  6. Isolation and detection of ingested DNA from the immature stages of Calliphora dubia (diptera: Calliphoridae) : A forensically important blowfly.

    PubMed

    Carvalho, Filipa; Dadour, Ian R; Groth, David M; Harvey, Michelle L

    2005-12-01

    The forensic entomologist frequently bases time since death (TSD) estimation on fly larvae. In some cases, the food source on which these larvae have completed their development may be questionable, and requires verification to ensure the accuracy of the TSD estimation. Ingested DNA may be isolated from the alimentary canal of immature insects. Previous studies have confirmed the ability to extract ingested DNA from the alimentary tract of third instar blowfly larvae. This study considers the potential to detect ingested DNA from immature stages of the blue-bodied blowfly Calliphora dubia (Macquart) that had fed on sheep liver. Individuals from early first instar larvae through day 3 pupae were surface decontaminated, followed by DNA isolation and detection by amplifying the sheep satellite I region. Fragments of 197 basepairs (bp) and 87 bp were successfully isolated and detected in all stages of immatures until 2-day-old pupae, with detection at this stage being unsuccessful on 3-day-old pupae. This study presents a suitable protocol for the isolation and detection of ingested DNA from immature stages of C. dubia.

  7. Limb Preservation With Isolated Limb Infusion for Locally Advanced Nonmelanoma Cutaneous and Soft-Tissue Malignant Neoplasms

    PubMed Central

    Turaga, Kiran K.; Beasley, Georgia M.; Kane, John M.; Delman, Keith A.; Grobmyer, Stephen R.; Gonzalez, Ricardo J.; Letson, G. Douglas; Cheong, David; Tyler, Douglas S.; Zager, Jonathan S.

    2015-01-01

    Objective To demonstrate the efficacy of isolated limb infusion (ILI) in limb preservation for patients with locally advanced soft-tissue sarcomas and nonmelanoma cutaneous malignant neoplasms. Background Locally advanced nonmelanoma cutaneous and soft-tissue malignant neoplasms, including soft-tissue sarcomas of the extremities, can pose significant treatment challenges. We report our experience, including responses and limb preservation rates, using ILI in cutaneous and soft-tissue malignant neoplasms. Methods We identified 22 patients with cutaneous and soft-tissue malignant neoplasms who underwent 26 ILIs with melphalan and actinomycin from January 1, 2004, through December 31, 2009, from 5 institutions. Outcome measures included limb preservation and in-field response rates. Toxicity was measured using the Wieberdink scale and serum creatinine phosphokinase levels. Results The median age was 70 years (range, 19-92 years), and 12 patients (55%) were women. Fourteen patients (64%) had sarcomas, 7 (32%) had Merkel cell carcinoma, and 1 (5%) had squamous cell carcinoma. The median length of stay was 5.5 days (interquartile range, 4-8 days). Twenty-five of the 26 ILIs (96%) resulted in Wieberdink grade III or less toxicity, and 1 patient (4%) developed grade IV toxicity. The median serum creatinine phosphokinase level was 127 U/L for upper extremity ILIs and 93 U/L for lower extremity ILIs. Nineteen of 22 patients (86%) underwent successful limb preservation. The 3-month in-field response rate was 79% (21% complete and 58% partial), and the median follow-up was 8.6 months (range, 1-63 months). Five patients underwent resection of disease after an ILI, of whom 80% are disease free at a median of 8.6 months. Conclusions Isolated limb infusion provides an attractive alternative therapy for regional disease control and limb preservation in patients with limb-threatening cutaneous and soft-tissue malignant neoplasms. Short-term response rates appear encouraging, yet

  8. Advanced Oil Spill Detection Algorithms For Satellite Based Maritime Environment Monitoring

    NASA Astrophysics Data System (ADS)

    Radius, Andrea; Azevedo, Rui; Sapage, Tania; Carmo, Paulo

    2013-12-01

    During the last years, the increasing pollution occurrence and the alarming deterioration of the environmental health conditions of the sea, lead to the need of global monitoring capabilities, namely for marine environment management in terms of oil spill detection and indication of the suspected polluter. The sensitivity of Synthetic Aperture Radar (SAR) to the different phenomena on the sea, especially for oil spill and vessel detection, makes it a key instrument for global pollution monitoring. The SAR performances in maritime pollution monitoring are being operationally explored by a set of service providers on behalf of the European Maritime Safety Agency (EMSA), which has launched in 2007 the CleanSeaNet (CSN) project - a pan-European satellite based oil monitoring service. EDISOFT, which is from the beginning a service provider for CSN, is continuously investing in R&D activities that will ultimately lead to better algorithms and better performance on oil spill detection from SAR imagery. This strategy is being pursued through EDISOFT participation in the FP7 EC Sea-U project and in the Automatic Oil Spill Detection (AOSD) ESA project. The Sea-U project has the aim to improve the current state of oil spill detection algorithms, through the informative content maximization obtained with data fusion, the exploitation of different type of data/ sensors and the development of advanced image processing, segmentation and classification techniques. The AOSD project is closely related to the operational segment, because it is focused on the automation of the oil spill detection processing chain, integrating auxiliary data, like wind information, together with image and geometry analysis techniques. The synergy between these different objectives (R&D versus operational) allowed EDISOFT to develop oil spill detection software, that combines the operational automatic aspect, obtained through dedicated integration of the processing chain in the existing open source NEST

  9. A novel isolation curtain to reduce turbine ingress heating and an advanced model for honeycomb labyrinth seals

    NASA Astrophysics Data System (ADS)

    Choi, Dong Chun

    A combination of 3-D and 2-D computational fluid dynamics (CFD) modeling as well as experimental testing of the labyrinth seal with hexagonal honeycomb cells on the stator wall was performed. For the 3-D and 2-D CFD models, the hexagonal honeycomb structure was modeled using the concept of the baffle (zero-thickness wall) and the simplified 2-D fin, respectively. The 3-D model showed that even a small axial change of the tooth (or honeycomb wall) location, or a small circumferential change of the honeycomb wall location significantly affected the flow patterns and leakage characteristics especially for small tooth tip clearance. Also, the local details of the flow field were investigated. The seven basic procedural steps to develop a 2-D axisymmetric honeycomb labyrinth seal leakage model were shown. Clearly demonstrated for varying test conditions was the 2-D model capability to predict the 3-D honeycomb labyrinth flow that had been measured at different operating conditions from that used in developing the 2-D model. Specifically, the 2-D model showed very close agreement with measurements. In addition, the 2-D model greatly reduced the computer resource requirement needed to obtain a solution of the 3-D honeycomb labyrinth seal leakage. The novel and advanced strategy to reduce the turbine ingress heating, and thus the coolant requirement, by injecting a "coolant isolation curtain" was developed numerically using a 3-D CFD model. The coolant isolation curtain was applied under the nozzle guide vane platform for the forward cavity of a turbine stage. Specifically, the isolation curtain serves to isolate the hot mainstream gas from the turbine outer region. The effect of the geometry change, the outer cavity axial gap clearance, the circumferential location of the injection curtain slot and the injection fluid angle on the ingress heating was investigated. Adding the chamfer to the baseline design gave a similar or higher maximum temperature T*max than did the

  10. Detection of Achromobacter xylosoxidans in Hospital, Domestic, and Outdoor Environmental Samples and Comparison with Human Clinical Isolates

    PubMed Central

    Amoureux, Lucie; Bador, Julien; Fardeheb, Sakina; Mabille, Cédric; Couchot, Charlyne; Massip, Clémence; Salignon, Anne-Lise; Berlie, Guillaume; Varin, Véronique

    2013-01-01

    Achromobacter xylosoxidans is an aerobic nonfermentative Gram-negative rod considered an important emerging pathogen among cystic fibrosis (CF) patients worldwide and among immunocompromised patients. This increased prevalence remains unexplained, and to date no environmental reservoir has been identified. The aim of this study was to identify potential reservoirs of A. xylosoxidans in hospital, domestic, and outdoor environments and to compare the isolates with clinical ones. From 2011 to 2012, 339 samples were collected in Dijon's university hospital, in healthy volunteers' homes in the Dijon area, and in the outdoor environment in Burgundy (soil, water, mud, and plants). We designed a protocol to detect A. xylosoxidans in environmental samples based on a selective medium: MCXVAA (MacConkey agar supplemented with xylose, vancomycin, aztreonam, and amphotericin B). Susceptibility testing, genotypic analysis by pulsed-field gel electrophoresis, and blaOXA-114 sequencing were performed on the isolates. A total of 50 strains of A. xylosoxidans were detected in hospital (33 isolates), domestic (9 isolates), and outdoor (8 isolates) samples, mainly in hand washing sinks, showers, and water. Most of them were resistant to ciprofloxacin (49 strains). Genotypic analysis and blaOXA-114 sequencing revealed a wide diversity among the isolates, with 35 pulsotypes and 18 variants of oxacillinases. Interestingly, 10 isolates from hospital environment were clonally related to clinical isolates previously recovered from hospitalized patients, and one domestic isolate was identical to one recovered from a CF patient. These results indicate that A. xylosoxidans is commonly distributed in various environments and therefore that CF patients or immunocompromised patients are surrounded by these reservoirs. PMID:24038696

  11. Detection of extended-spectrum beta-lactamases in clinical isolates of Enterobacter cloacae and Enterobacter aerogenes.

    PubMed

    Tzelepi, E; Giakkoupi, P; Sofianou, D; Loukova, V; Kemeroglou, A; Tsakris, A

    2000-02-01

    The aim of the present study was to investigate the frequency of extended-spectrum beta-lactamases (ESBLs) in a consecutive collection of clinical isolates of Enterobacter spp. The abilities of various screening methods to detect ESBLs in enterobacters were simultaneously tested. Among the 68 consecutive isolates (56 Enterobacter cloacae and 12 Enterobacter aerogenes isolates) that were analyzed for beta-lactamase content, 21 (25 and 58%, respectively) possessed transferable ESBLs with pIs of 8.2 and phenotypic characteristics of SHV-type enzymes, 8 (14.3%) of the E. cloacae isolates produced a previously nondescribed, clavulanate-susceptible ESBL that exhibited a pI of 6.9 and that conferred a ceftazidime resistance phenotype on Escherichia coli transconjugants, and 2 E. cloacae isolates produced both of these enzymes. Among the total of 31 isolates that were considered ESBL producers, the Vitek ESBL detection test was positive for 2 (6.5%) strains, and the conventional double-disk synergy test (DDST) with amoxicillin-clavulanate and with expanded-spectrum cephalosporins and aztreonam was positive for 5 (16%) strains. Modifications of the DDST consisting of closer application of the disks (at 20 instead of 30 mm), the use of cefepime, and the use of both modifications increased the sensitivity of this test to 71, 61, and 90%, respectively. Of the 37 isolates for which isoelectric focusing failed to determine ESBLs, the Vitek test was false positive for 1 isolate and the various forms of DDSTs were false-positive for 3 isolates.

  12. Lessons Learned on Implementing Fault Detection, Isolation, and Recovery (FDIR) in a Ground Launch Environment

    NASA Technical Reports Server (NTRS)

    Ferrell, Bob A.; Lewis, Mark E.; Perotti, Jose M.; Brown, Barbara L.; Oostdyk, Rebecca L.; Goetz, Jesse W.

    2010-01-01

    This paper's main purpose is to detail issues and lessons learned regarding designing, integrating, and implementing Fault Detection Isolation and Recovery (FDIR) for Constellation Exploration Program (CxP) Ground Operations at Kennedy Space Center (KSC). Part of the0 overall implementation of National Aeronautics and Space Administration's (NASA's) CxP, FDIR is being implemented in three main components of the program (Ares, Orion, and Ground Operations/Processing). While not initially part of the design baseline for the CxP Ground Operations, NASA felt that FDIR is important enough to develop, that NASA's Exploration Systems Mission Directorate's (ESMD's) Exploration Technology Development Program (ETDP) initiated a task for it under their Integrated System Health Management (ISHM) research area. This task, referred to as the FDIIR project, is a multi-year multi-center effort. The primary purpose of the FDIR project is to develop a prototype and pathway upon which Fault Detection and Isolation (FDI) may be transitioned into the Ground Operations baseline. Currently, Qualtech Systems Inc (QSI) Commercial Off The Shelf (COTS) software products Testability Engineering and Maintenance System (TEAMS) Designer and TEAMS RDS/RT are being utilized in the implementation of FDI within the FDIR project. The TEAMS Designer COTS software product is being utilized to model the system with Functional Fault Models (FFMs). A limited set of systems in Ground Operations are being modeled by the FDIR project, and the entire Ares Launch Vehicle is being modeled under the Functional Fault Analysis (FFA) project at Marshall Space Flight Center (MSFC). Integration of the Ares FFMs and the Ground Processing FFMs is being done under the FDIR project also utilizing the TEAMS Designer COTS software product. One of the most significant challenges related to integration is to ensure that FFMs developed by different organizations can be integrated easily and without errors. Software Interface

  13. Detection of the glmM Gene in Helicobacter pylori Isolates with a Novel Primer by PCR▿

    PubMed Central

    Córdova Espinoza, Maria Guadalupe; González Vazquez, Rosa; Morales Mendez, Iyari; Ruelas Vargas, Consuelo; Giono Cerezo, Silvia

    2011-01-01

    A novel reverse primer (GLM MR1) was designed for detection of the glmM gene in Helicobacter pylori by PCR. The percentage of amplification in clinical isolates using GLM MR1 was 100% for detection of the glmM gene and 86.36% for the ureA gene. The primer designed is useful for the identification of H. pylori. PMID:21289140

  14. Detection of CC17 Enterococcus faecium in dogs and a comparison with human isolates.

    PubMed

    Kwon, K H; Moon, B Y; Hwang, S Y; Park, Y H

    2012-09-01

    Enterococcus faecium strains of clonal complex (CC) 17 were isolated from domestic dogs. The strains were more prevalent in infectious isolates than in colonized isolates, suggesting that strains of the CC17 lineage may have an advantage in causing infections in dogs. The pulsed field gel electrophoresis patterns of some dog and human isolates were over 90% similar. However, antimicrobial resistance patterns and virulence factors were not identical, which might reflect different use of antimicrobials in veterinary medicine or in host specificity.

  15. Phenotypic Detection of Metallo-Beta-Lactamases in Carbapenem Resistant Acinetobacter baumannii Isolated from Pediatric Patients in Pakistan

    PubMed Central

    Anwar, Muneeza; Ejaz, Hassan; Zafar, Aizza; Hamid, Hamdan

    2016-01-01

    Multidrug resistant A. baumannii has emerged as an important and problematic human pathogen as it is the causative agent of several types of infections especially in neonates and immunocompromised patients because they have least capacity to fight against infections. Carbapenems are used as last resort antibiotics for treating these infections but currently resistance against carbapenems due to MBL production is on the rise. The objective of this study was to determine the frequency of antibiotic resistance in A. baumannii and also to compare the efficacy of combined disk test and double disk synergy test for detection of metallo-beta-lactamases. A total of 112 A. baumannii were identified from various clinical samples and antibiotic susceptibility profile was determined by Kirby-Bauer Disk Diffusion method. Out of 112, 66 (58.9%) isolates were resistant to both imipenem and meropenem (OXOID). These resistant isolates were tested for carbapenemase production, and 55 (83.3%) were carbapenemase producers by Modified Hodge Test. These isolates were further tested for MBL production by combined disk test and double disk synergy test. Out of 66, 49 isolates were positive by both methods, CDT and DDST, and only one isolate was detected as negative (with kappa value = 0.038). All MBL producing strains showed remarkable resistance to cephalosporins, fluoroquinolones, aminoglycosides, and piperacillin/tazobactam (OXOID). The antibiotic resistance was very high in A. baumannii which were isolated from children in Pakistan specially attending a nephrology unit. PMID:27123345

  16. Favorable lifestyle before diagnosis associated with lower risk of screen-detected advanced colorectal neoplasia

    PubMed Central

    Knudsen, Markus D; de Lange, Thomas; Botteri, Edoardo; Nguyen, Dung-Hong; Evensen, Helge; Steen, Chloé B; Hoff, Geir; Bernklev, Tomm; Hjartåker, Anette; Berstad, Paula

    2016-01-01

    AIM: To investigate the association between adherence to health recommendations and detection of advanced colorectal neoplasia (ACN) in colorectal cancer (CRC) screening. METHODS: A total of 14832 women and men were invited to CRC screening, 6959 in the fecal immunochemical test arm and 7873 in the flexible sigmoidoscopy arm. These were also sent a self-reported lifestyle questionnaire to be completed prior to their first CRC screening. A lifestyle score was created to reflect current adherence to healthy behaviors in regard to smoking, body mass index, physical activity, alcohol consumption and food consumption, and ranged from zero (poorest) to six (best). Odds ratios (ORs) and 95%CIs were calculated using multivariable logistic regression to evaluate the association between the single lifestyle variables and the lifestyle score and the probability of detecting ACN. RESULTS: In all 6315 women and men completed the lifestyle questionnaire, 3323 (53%) in the FIT arm and 2992 (47%) in the FS arm. This was 89% of those who participated in screening. ACN was diagnosed in 311 (5%) participants of which 25 (8%) were diagnosed with CRC. For individuals with a lifestyle score of two, three, four, and five-six, the ORs (95%CI) for the probability of ACN detection were 0.82 (0.45-1.16), 0.43 (0.28-0.73), 0.41 (0.23-0.64), and 0.41 (0.22-0.73), respectively compared to individuals with a lifestyle score of zero-one. Of the single lifestyle factors, adherence to non-smoking and moderate alcohol intake were associated with a decreased probability of ACN detection compared to being a smoker or having a high alcohol intake 0.53 (0.42-0.68) and 0.63 (0.43-0.93) respectively. CONCLUSION: Adopted healthy behaviors were inversely associated with the probability of ACN detection. Lifestyle assessment might be useful for risk stratification in CRC screening. PMID:27468217

  17. Evaluation of crystal violet decolorization assay for minimal inhibitory concentration detection of primary antituberculosis drugs against Mycobacterium tuberculosis isolates*

    PubMed Central

    Coban, Ahmet Yilmaz; Akbal, Ahmet Ugur; Uzun, Meltem; Cayci, Yeliz Tanriverdi; Birinci, Asuman; Durupinar, Belma

    2016-01-01

    In this study we evaluated the crystal violet decolorization assay (CVDA) for detection of minimum inhibitory concentration (MIC) of antituberculosis drugs. 53 isolates were tested in this study and 13 of them were multidrug resistant (MDR) isolates. The antibiotics concentrations were 2-0.06 mg/L for isoniazid (INH) and rifampicin (RIF) and were 16-0.25 mg/L for streptomycin (STM) and ethambutol (EMB). Crystal violet (CV-25 mg/L) was added into the microwells on the seventh day of incubation and incubation was continued until decolorization. Decolorization of CV was the predictor of bacterial growth. Overall agreements for four drugs were detected as 98.1%, and the average time was detected as 9.5 ± 0.89 day after inoculation. One isolate for INH and two isolates for STM were determined resistant in the reference method, but susceptible by the CVDA. One isolate was susceptible to EMB by the reference method, but resistant by the CVDA. All results were concordant for RIF. This study shows that CVDA is a rapid, reliable and suitable for determination of MIC values of Mycobacterium tuberculosis. And it can be used easily especially in countries with limited-sources. PMID:27304025

  18. Evaluation of crystal violet decolorization assay for minimal inhibitory concentration detection of primary antituberculosis drugs against Mycobacterium tuberculosis isolates.

    PubMed

    Coban, Ahmet Yilmaz; Akbal, Ahmet Ugur; Uzun, Meltem; Cayci, Yeliz Tanriverdi; Birinci, Asuman; Durupinar, Belma

    2016-06-10

    In this study we evaluated the crystal violet decolorization assay (CVDA) for detection of minimum inhibitory concentration (MIC) of antituberculosis drugs. 53 isolates were tested in this study and 13 of them were multidrug resistant (MDR) isolates. The antibiotics concentrations were 2-0.06 mg/L for isoniazid (INH) and rifampicin (RIF) and were 16-0.25 mg/L for streptomycin (STM) and ethambutol (EMB). Crystal violet (CV-25 mg/L) was added into the microwells on the seventh day of incubation and incubation was continued until decolorization. Decolorization of CV was the predictor of bacterial growth. Overall agreements for four drugs were detected as 98.1%, and the average time was detected as 9.5 ± 0.89 day after inoculation. One isolate for INH and two isolates for STM were determined resistant in the reference method, but susceptible by the CVDA. One isolate was susceptible to EMB by the reference method, but resistant by the CVDA. All results were concordant for RIF. This study shows that CVDA is a rapid, reliable and suitable for determination of MIC values of Mycobacterium tuberculosis. And it can be used easily especially in countries with limited-sources. PMID:27304025

  19. Advances in Adipose-Derived Stem Cells Isolation, Characterization, and Application in Regenerative Tissue Engineering

    PubMed Central

    Wankhade, Umesh D.; Shen, Michael; Kolhe, Ravindra; Fulzele, Sadanand

    2016-01-01

    Obesity is a complex, multifactorial disease that has been extensively researched in recent times. Obesity is characterized by excess deposition of adipose tissue in response to surplus energy. Despite the negative connotations of adipose tissue (AT), it serves as a critical endocrine organ. Adipose tissue is a source of several adipokines and cytokines which have been deemed important for both normal metabolic function and disease formation. The discoveries of metabolically active brown AT in adult humans and adipose tissue derived stem cells (ADSC) have been key findings in the past decade with potential therapeutic implications. ADSCs represent an enticing pool of multipotent adult stem cells because of their noncontroversial nature, relative abundance, ease of isolation, and expandability. A decade and a half since the discovery of ADSCs, the scientific community is still working to uncover their therapeutic potential in a wide range of diseases. In this review, we provide an overview of the recent developments in the field of ADSCs and examine their potential use in transplantation and cell-based therapies for the regeneration of diseased organs and systems. We also hope to provide perspective on how to best utilize this readily available, powerful pool of stem cells in the future. PMID:26981130

  20. Isolated growth hormone deficiency (GHD) in childhood and adolescence: recent advances.

    PubMed

    Alatzoglou, Kyriaki S; Webb, Emma Alice; Le Tissier, Paul; Dattani, Mehul T

    2014-06-01

    The diagnosis of GH deficiency (GHD) in childhood is a multistep process involving clinical history, examination with detailed auxology, biochemical testing, and pituitary imaging, with an increasing contribution from genetics in patients with congenital GHD. Our increasing understanding of the factors involved in the development of somatotropes and the dynamic function of the somatotrope network may explain, at least in part, the development and progression of childhood GHD in different age groups. With respect to the genetic etiology of isolated GHD (IGHD), mutations in known genes such as those encoding GH (GH1), GHRH receptor (GHRHR), or transcription factors involved in pituitary development, are identified in a relatively small percentage of patients suggesting the involvement of other, yet unidentified, factors. Genome-wide association studies point toward an increasing number of genes involved in the control of growth, but their role in the etiology of IGHD remains unknown. Despite the many years of research in the area of GHD, there are still controversies on the etiology, diagnosis, and management of IGHD in children. Recent data suggest that childhood IGHD may have a wider impact on the health and neurodevelopment of children, but it is yet unknown to what extent treatment with recombinant human GH can reverse this effect. Finally, the safety of recombinant human GH is currently the subject of much debate and research, and it is clear that long-term controlled studies are needed to clarify the consequences of childhood IGHD and the long-term safety of its treatment.

  1. Advances in Adipose-Derived Stem Cells Isolation, Characterization, and Application in Regenerative Tissue Engineering.

    PubMed

    Wankhade, Umesh D; Shen, Michael; Kolhe, Ravindra; Fulzele, Sadanand

    2016-01-01

    Obesity is a complex, multifactorial disease that has been extensively researched in recent times. Obesity is characterized by excess deposition of adipose tissue in response to surplus energy. Despite the negative connotations of adipose tissue (AT), it serves as a critical endocrine organ. Adipose tissue is a source of several adipokines and cytokines which have been deemed important for both normal metabolic function and disease formation. The discoveries of metabolically active brown AT in adult humans and adipose tissue derived stem cells (ADSC) have been key findings in the past decade with potential therapeutic implications. ADSCs represent an enticing pool of multipotent adult stem cells because of their noncontroversial nature, relative abundance, ease of isolation, and expandability. A decade and a half since the discovery of ADSCs, the scientific community is still working to uncover their therapeutic potential in a wide range of diseases. In this review, we provide an overview of the recent developments in the field of ADSCs and examine their potential use in transplantation and cell-based therapies for the regeneration of diseased organs and systems. We also hope to provide perspective on how to best utilize this readily available, powerful pool of stem cells in the future.

  2. Detecting method of subjects' 3D positions and experimental advanced camera control system

    NASA Astrophysics Data System (ADS)

    Kato, Daiichiro; Abe, Kazuo; Ishikawa, Akio; Yamada, Mitsuho; Suzuki, Takahito; Kuwashima, Shigesumi

    1997-04-01

    Steady progress is being made in the development of an intelligent robot camera capable of automatically shooting pictures with a powerful sense of reality or tracking objects whose shooting requires advanced techniques. Currently, only experienced broadcasting cameramen can provide these pictures.TO develop an intelligent robot camera with these abilities, we need to clearly understand how a broadcasting cameraman assesses his shooting situation and how his camera is moved during shooting. We use a real- time analyzer to study a cameraman's work and his gaze movements at studios and during sports broadcasts. This time, we have developed a detecting method of subjects' 3D positions and an experimental camera control system to help us further understand the movements required for an intelligent robot camera. The features are as follows: (1) Two sensor cameras shoot a moving subject and detect colors, producing its 3D coordinates. (2) Capable of driving a camera based on camera movement data obtained by a real-time analyzer. 'Moving shoot' is the name we have given to the object position detection technology on which this system is based. We used it in a soccer game, producing computer graphics showing how players moved. These results will also be reported.

  3. Possibilities and Challenges of Detecting Exomoons for Colonization and for Advanced Terraforming

    NASA Astrophysics Data System (ADS)

    Ganapathy, Rohan M.

    Since the dawn of time, mankind has been in search of a way to control nature and a way to reach the stars. Nowadays, with various advancements in space technology, the possibility of colonizing our solar system and beyond looks more and more plausible everyday. Naturally, the final destination would be outside the solar system for the ultimate expansion of mankind. The search for life outside of the Solar System should not be restricted to exclusively planetary bodies; large moons of Extrasolar planets may also be common habitable environments throughout the Galaxy. Extrasolar moons, or Exomoons, may be detected through transit timing effects induced onto the host planet as a result of mutual gravitational interaction. In particular, transit timing variations (TTV) and transit duration variations (TDV) are predicted to produce a unique exomoon signature, which is not only easily distinguished from other gravitational perturbations, but also provides both the period and mass of an exomoon. Using these timing effects, photometry greater or equal to that of the Kepler Mission is readily able to detect habitable-zone exomoons down to 0.2 M and could survey up to 25,000 stars for Earth-mass satellites. We discuss future possibilities for spectral retrieval of such bodies and show that transmission spectroscopy with James Webb Space Telescope should be able to detect molecular species with 30 transit events, in the best cases. Furthermore, the paper will briefly touch the possibilities and the challenges involved in reaching these destinations as well.

  4. Recent advances in epigenomics in NSCLC: real-time detection and therapeutic implications.

    PubMed

    Di Paolo, Antonello; Del Re, Marzia; Petrini, Iacopo; Altavilla, Giuseppe; Danesi, Romano

    2016-08-01

    NSCLC is an aggressive disease with one of the poorer prognosis among cancers. The disappointing response to chemotherapy drives the search for genetic biomarkers aimed at both attaining an earlier diagnosis and choosing the most appropriate chemotherapy. In this scenario, epigenomic markers, such as DNA methylation, histone acetylation and the expression of noncoding RNAs, have been demonstrated to be reliable for the stratification of NSCLC patients. Newest techniques with increased sensitivity and the isolation of nucleic acids from plasma may allow an early diagnosis and then monitoring the efficacy over time. However, prospective confirmatory studies are still lacking. This article presents an overview of the epigenetic markers evaluated in NSCLC and discusses the role of their real-time detection in the clinical management of the disease. PMID:27479016

  5. Recent advances in epigenomics in NSCLC: real-time detection and therapeutic implications.

    PubMed

    Di Paolo, Antonello; Del Re, Marzia; Petrini, Iacopo; Altavilla, Giuseppe; Danesi, Romano

    2016-08-01

    NSCLC is an aggressive disease with one of the poorer prognosis among cancers. The disappointing response to chemotherapy drives the search for genetic biomarkers aimed at both attaining an earlier diagnosis and choosing the most appropriate chemotherapy. In this scenario, epigenomic markers, such as DNA methylation, histone acetylation and the expression of noncoding RNAs, have been demonstrated to be reliable for the stratification of NSCLC patients. Newest techniques with increased sensitivity and the isolation of nucleic acids from plasma may allow an early diagnosis and then monitoring the efficacy over time. However, prospective confirmatory studies are still lacking. This article presents an overview of the epigenetic markers evaluated in NSCLC and discusses the role of their real-time detection in the clinical management of the disease.

  6. Detection of inducible and constitutive clindamycin resistance among Staphylococcus aureus isolates in a tertiary care hospital, Eastern India

    PubMed Central

    Majhi, Subasini; Dash, Muktikesh; Mohapatra, Dharitri; Mohapatra, Ashoka; Chayani, Nirupama

    2016-01-01

    Introduction: Clindamycin is an excellent drug for skin and soft tissue Staphylococcus aureus infections, but resistance mediated by inducible macrolide-lincosamide-streptogramin B (iMLSB) phenotype leads to in vivo therapeutic failure even though they may be in vitro susceptible in Kirby–Bauer disk diffusion method. Objective: The study was aimed to detect the prevalence of iMLSB phenotype among S. aureus isolates by double disk approximation test (D-test) in a tertiary care hospital, Eastern India. Materials and Methods: A total of 209 consecutive S. aureus isolates were identified by conventional methods and subjected to antimicrobial susceptibility testing by Kirby–Bauer disk diffusion method. Erythromycin-resistant isolates were tested for D-test. Results: From 1282 clinical specimens, 209 nonrepeated S. aureus isolates were obtained. Majority of isolates 129 (61.7%) were methicillin-resistant S. aureus (MRSA). There was statistically significant difference between outpatients 60.1% and inpatients 39.9% (P < 0.0001). From 209 S. aureus isolates, 46 (22%) were D-test positive (iMLSB phenotype), 41 (19.6%) were D-test negative (methicillin sensitive [MS] phenotype), and 37 (17.7%) were constitutively resistant (constitutive macrolide-lincosamide-streptogramin B phenotype). The incidence of inducible, constitutive, and MS phenotype was higher in MRSA isolates compared to MS S. aureus (MSSA). The constitutive clindamycin resistance difference between MSSA and MRSA isolates were found to be statistically significant (P = 0.0086). Conclusion: The study revealed 22% of S. aureus isolates were inducible clindamycin resistant, which could be easily misidentified as clindamycin susceptible in Kirby–Bauer disk diffusion method. Therefore, clinical microbiology laboratory should routinely perform D-test in all clinically isolated S. aureus to guide clinicians for the appropriate use of clindamycin. PMID:27390669

  7. Fault detection, isolation, and diagnosis of status self-validating gas sensor arrays

    NASA Astrophysics Data System (ADS)

    Chen, Yin-sheng; Xu, Yong-hui; Yang, Jing-li; Shi, Zhen; Jiang, Shou-da; Wang, Qi

    2016-04-01

    The traditional gas sensor array has been viewed as a simple apparatus for information acquisition in chemosensory systems. Gas sensor arrays frequently undergo impairments in the form of sensor failures that cause significant deterioration of the performance of previously trained pattern recognition models. Reliability monitoring of gas sensor arrays is a challenging and critical issue in the chemosensory system. Because of its importance, we design and implement a status self-validating gas sensor array prototype to enhance the reliability of its measurements. A novel fault detection, isolation, and diagnosis (FDID) strategy is presented in this paper. The principal component analysis-based multivariate statistical process monitoring model can effectively perform fault detection by using the squared prediction error statistic and can locate the faulty sensor in the gas sensor array by using the variables contribution plot. The signal features of gas sensor arrays for different fault modes are extracted by using ensemble empirical mode decomposition (EEMD) coupled with sample entropy (SampEn). The EEMD is applied to adaptively decompose the original gas sensor signals into a finite number of intrinsic mode functions (IMFs) and a residual. The SampEn values of each IMF and the residual are calculated to reveal the multi-scale intrinsic characteristics of the faulty sensor signals. Sparse representation-based classification is introduced to identify the sensor fault type for the purpose of diagnosing deterioration in the gas sensor array. The performance of the proposed strategy is compared with other different diagnostic approaches, and it is fully evaluated in a real status self-validating gas sensor array experimental system. The experimental results demonstrate that the proposed strategy provides an excellent solution to the FDID of status self-validating gas sensor arrays.

  8. Fault detection, isolation, and diagnosis of status self-validating gas sensor arrays.

    PubMed

    Chen, Yin-Sheng; Xu, Yong-Hui; Yang, Jing-Li; Shi, Zhen; Jiang, Shou-da; Wang, Qi

    2016-04-01

    The traditional gas sensor array has been viewed as a simple apparatus for information acquisition in chemosensory systems. Gas sensor arrays frequently undergo impairments in the form of sensor failures that cause significant deterioration of the performance of previously trained pattern recognition models. Reliability monitoring of gas sensor arrays is a challenging and critical issue in the chemosensory system. Because of its importance, we design and implement a status self-validating gas sensor array prototype to enhance the reliability of its measurements. A novel fault detection, isolation, and diagnosis (FDID) strategy is presented in this paper. The principal component analysis-based multivariate statistical process monitoring model can effectively perform fault detection by using the squared prediction error statistic and can locate the faulty sensor in the gas sensor array by using the variables contribution plot. The signal features of gas sensor arrays for different fault modes are extracted by using ensemble empirical mode decomposition (EEMD) coupled with sample entropy (SampEn). The EEMD is applied to adaptively decompose the original gas sensor signals into a finite number of intrinsic mode functions (IMFs) and a residual. The SampEn values of each IMF and the residual are calculated to reveal the multi-scale intrinsic characteristics of the faulty sensor signals. Sparse representation-based classification is introduced to identify the sensor fault type for the purpose of diagnosing deterioration in the gas sensor array. The performance of the proposed strategy is compared with other different diagnostic approaches, and it is fully evaluated in a real status self-validating gas sensor array experimental system. The experimental results demonstrate that the proposed strategy provides an excellent solution to the FDID of status self-validating gas sensor arrays.

  9. Microfluidic devices for nucleic acid (NA) isolation, isothermal NA amplification, and real-time detection.

    PubMed

    Mauk, Michael G; Liu, Changchun; Sadik, Mohamed; Bau, Haim H

    2015-01-01

    Molecular (nucleic acid)-based diagnostics tests have many advantages over immunoassays, particularly with regard to sensitivity and specificity. Most on-site diagnostic tests, however, are immunoassay-based because conventional nucleic acid-based tests (NATs) require extensive sample processing, trained operators, and specialized equipment. To make NATs more convenient, especially for point-of-care diagnostics and on-site testing, a simple plastic microfluidic cassette ("chip") has been developed for nucleic acid-based testing of blood, other clinical specimens, food, water, and environmental samples. The chip combines nucleic acid isolation by solid-phase extraction; isothermal enzymatic amplification such as LAMP (Loop-mediated AMPlification), NASBA (Nucleic Acid Sequence Based Amplification), and RPA (Recombinase Polymerase Amplification); and real-time optical detection of DNA or RNA analytes. The microfluidic cassette incorporates an embedded nucleic acid binding membrane in the amplification reaction chamber. Target nucleic acids extracted from a lysate are captured on the membrane and amplified at a constant incubation temperature. The amplification product, labeled with a fluorophore reporter, is excited with a LED light source and monitored in situ in real time with a photodiode or a CCD detector (such as available in a smartphone). For blood analysis, a companion filtration device that separates plasma from whole blood to provide cell-free samples for virus and bacterial lysis and nucleic acid testing in the microfluidic chip has also been developed. For HIV virus detection in blood, the microfluidic NAT chip achieves a sensitivity and specificity that are nearly comparable to conventional benchtop protocols using spin columns and thermal cyclers.

  10. Molecular Detection of Genomic Islands Associated With Class 1 and 2 Integron in Haemophilus influenzae Isolated in Iran

    PubMed Central

    Boroumand, Mojgan; Irani, Shiva; Siadat, Seyed Davar; Bouzari, Saied

    2015-01-01

    Background: High levels of multidrug resistance are usually associated with mobile genetic elements that encode specific resistance genes. Integrons are important genetic elements involved in spreading antibiotic multi-resistance. In special cases, large exogenous segments in bacterial genomes form genomic islands, and one of the functions of these genomic islands is antibiotic resistance. Due to geographical heterogeneity in antibiotic resistance pattern, it is mandatory to determine resistance patterns that are region-specific rather than generalized. Objectives: The objective of this study was to detect class 1 and 2 integrons in clinical isolates of Haemophilus influenzae. Patients and Methods: Antibiogram tests were carried out for twenty clinical isolates collected from different patients admitted to the Milad hospital. The PCR reactions were performed using universal primers specified for Int1 and Int2 genes attributed to class 1 and 2 integrons. Also amplification of integrase genes related to genomic islands was investigated by designing specific primers. Results: Of the twenty isolates, all (100%) were resistant to clindamycin, chloramphenicol and tetracycline, 95% to amoxicillin, 50% to ceftriaxone, 45% to ciprofloxacin and 5% to azithromycin. Also, all isolates (100%) were sensitive to trimethoprim/sulfamethoxazole. Class 1 and 2 integrons were not detected in any of the isolates; however the integrase gene attributed to genomic islands was identified in twelve isolates. Conclusions: Antibiotic resistance gene cassettes may be carried on integron or other genetic elements. The purpose of this study was to detect integron or genomic islands involved in antibiotic resistance profile of the isolates of H. influenzae collected in this study. PMID:26034545

  11. Nanostructure embedded microchips for detection, isolation, and characterization of circulating tumor cells.

    PubMed

    Lin, Millicent; Chen, Jie-Fu; Lu, Yi-Tsung; Zhang, Yang; Song, Jinzhao; Hou, Shuang; Ke, Zunfu; Tseng, Hsian-Rong

    2014-10-21

    Circulating tumor cells (CTCs) are cancer cells that break away from either a primary tumor or a metastatic site and circulate in the peripheral blood as the cellular origin of metastasis. With their role as a "tumor liquid biopsy", CTCs provide convenient access to all disease sites, including that of the primary tumor and the site of fatal metastases. It is conceivable that detecting and analyzing CTCs will provide insightful information in assessing the disease status without the flaws and limitations encountered in performing conventional tumor biopsies. However, identifying CTCs in patient blood samples is technically challenging due to the extremely low abundance of CTCs among a large number of hematologic cells. To address this unmet need, there have been significant research endeavors, especially in the fields of chemistry, materials science, and bioengineering, devoted to developing CTC detection, isolation, and characterization technologies. Inspired by the nanoscale interactions observed in the tissue microenvironment, our research team at UCLA pioneered a unique concept of "NanoVelcro" cell-affinity substrates, in which CTC capture agent-coated nanostructured substrates were utilized to immobilize CTCs with high efficiency. The working mechanism of NanoVelcro cell-affinity substrates mimics that of Velcro: when the two fabric strips of a Velcro fastener are pressed together, tangling between the hairy surfaces on two strips leads to strong binding. Through continuous evolution, three generations (gens) of NanoVelcro CTC chips have been established to achieve different clinical utilities. The first-gen NanoVelcro chip, composed of a silicon nanowire substrate (SiNS) and an overlaid microfluidic chaotic mixer, was created for CTC enumeration. Side-by-side analytical validation studies using clinical blood samples suggested that the sensitivity of first-gen NanoVelcro chip outperforms that of FDA-approved CellSearch. In conjunction with the use of the

  12. Motion-Based System Identification and Fault Detection and Isolation Technologies for Thruster Controlled Spacecraft

    NASA Technical Reports Server (NTRS)

    Wilson, Edward; Sutter, David W.; Berkovitz, Dustin; Betts, Bradley J.; Kong, Edmund; delMundo, Rommel; Lages, Christopher R.; Mah, Robert W.; Papasin, Richard

    2003-01-01

    By analyzing the motions of a thruster-controlled spacecraft, it is possible to provide on-line (1) thruster fault detection and isolation (FDI), and (2) vehicle mass- and thruster-property identification (ID). Technologies developed recently at NASA Ames have significantly improved the speed and accuracy of these ID and FDI capabilities, making them feasible for application to a broad class of spacecraft. Since these technologies use existing sensors, the improved system robustness and performance that comes with the thruster fault tolerance and system ID can be achieved through a software-only implementation. This contrasts with the added cost, mass, and hardware complexity commonly required by FDI. Originally developed in partnership with NASA - Johnson Space Center to provide thruster FDI capability for the X-38 during re-entry, these technologies are most recently being applied to the MIT SPHERES experimental spacecraft to fly on the International Space Station in 2004. The model-based FDI uses a maximum-likelihood calculation at its core, while the ID is based upon recursive least squares estimation. Flight test results from the SPHERES implementation, as flown aboard the NASA KC-1 35A 0-g simulator aircraft in November 2003 are presented.

  13. Residual generation for fault detection and isolation in a class of uncertain nonlinear systems

    NASA Astrophysics Data System (ADS)

    Ma, Hong-Jun; Yang, Guang-Hong

    2013-02-01

    This article studies the problem of fault detection and isolation (FDI) for a class of uncertain nonlinear systems via a residual signal generated by a novel nonlinear adaptive observer. The considered faults are modelled by a set of time-varying vectors, in which a prescribed subset of faults are specially monitored and thus separable from the other faults. In the presence of Lipschitz-like nonlinearities and modelling uncertainties, the sensitivity of the residual signal to the monitored faults and its insensitivity to the other faults are rigorously analysed. Under a persistent excitation condition, the performances of the proposed fault diagnosis scheme, including the robustness to uncertainties, the quickness of estimation, the accuracy of estimation, the sensitivity to the monitored faults and the insensitivity to the complement faults, are quantified by a series of explicit design functions relevant to the observer parameters. It turns out that the number of faults which can be completely diagnosed is independent of the number of output sensors. A simulation example is given to illustrate the effectiveness of the proposed FDI method.

  14. Detection and some properties of cowpea mild mottle virus isolated from soybean in Iran.

    PubMed

    Tavassoli, M; Shahraeen, N; Ghorbani, S

    2008-12-01

    During 2006-2007 growing seasons, survey were carried to identify a virus disease causing mosaic of soybean in the field in Southern region (Khozestan Province) of Iran. To detect the viral infection, diseased leaf samples showing mild mosaic and leaf malformation were collected from soybean fields in Dezful, located in Khozestan Province. Infected samples were carried to the lab in a proper condition on ice packages. TPIA and DAS-ELISA serological tests were applied to identify the viral agent. To investigate the host-range, several indicator plants were mechanically inoculated under green-house condition. Seed transmission of CPMMV was examined using the seeds obtained from infected plants. The virus isolate was not found to be seed-borne in Clark variety of soybean. Different steps of ultracentrifugation including sucrose density gradient (10-40%) were carried out in order to obtain partial purified virus. On the basis of biological, serological and EM results, CPMMV-Carla virus was identified in the infected soybean samples. This is the first report of CPMMV infection of soybean in Iran.

  15. Functional Fault Modeling of a Cryogenic System for Real-Time Fault Detection and Isolation

    NASA Technical Reports Server (NTRS)

    Ferrell, Bob; Lewis, Mark; Oostdyk, Rebecca; Perotti, Jose

    2009-01-01

    When setting out to model and/or simulate a complex mechanical or electrical system, a modeler is faced with a vast array of tools, software, equations, algorithms and techniques that may individually or in concert aid in the development of the model. Mature requirements and a well understood purpose for the model may considerably shrink the field of possible tools and algorithms that will suit the modeling solution. Is the model intended to be used in an offline fashion or in real-time? On what platform does it need to execute? How long will the model be allowed to run before it outputs the desired parameters? What resolution is desired? Do the parameters need to be qualitative or quantitative? Is it more important to capture the physics or the function of the system in the model? Does the model need to produce simulated data? All these questions and more will drive the selection of the appropriate tools and algorithms, but the modeler must be diligent to bear in mind the final application throughout the modeling process to ensure the model meets its requirements without needless iterations of the design. The purpose of this paper is to describe the considerations and techniques used in the process of creating a functional fault model of a liquid hydrogen (LH2) system that will be used in a real-time environment to automatically detect and isolate failures.

  16. Detection, isolation and characterisation of cyclolinopeptides J and K in ageing flax.

    PubMed

    Jadhav, Pramodkumar D; Okinyo-Owiti, Denis P; Ahiahonu, Pearson W K; Reaney, Martin J T

    2013-06-01

    Methionine sulfone containing peptides CLs J (11) and K (12) may be produced from their reduced forms by oxidation but it is not known if these compounds occur in foods that contain flax. These compounds have been reported to possess greater immunosuppressive activity than their reduced methionine sulfoxide peptide forms 4 and 6, respectively. Since 11 and 12 have not been detected in commercial flax oil and milled flax seed, we tested for their presence in flax food products. Here we report that 11 and 12 accumulate in ground flaxseed that is exposed to air and heat (100°C) for more than 4h. Standards of 11 and 12 were prepared, isolated and extensively characterised using HPLC-MS/MS, 1D and 2D NMR methods. We also report the excellent thermal and oxidative stability of these peptides. Due to the harsh conditions required to produce 11 and 12, it is expected that their levels in flax based foods would be low and therefore their presence could serve as an indicative measure of severe oxidation of a food product.

  17. Recent advances in chemical imaging technology for the detection of contaminants for food safety and security

    NASA Astrophysics Data System (ADS)

    Priore, Ryan J.; Olkhovyk, Oksana; Drauch, Amy; Treado, Patrick; Kim, Moon; Chao, Kaunglin

    2009-05-01

    The need for routine, non-destructive chemical screening of agricultural products is increasing due to the health hazards to animals and humans associated with intentional and unintentional contamination of foods. Melamine, an industrial additive used to increase flame retardation in the resin industry, has recently been used to increase the apparent protein content of animal feed, of infant formula, as well as powdered and liquid milk in the dairy industry. Such contaminants, even at regulated levels, pose serious health risks. Chemical imaging technology provides the ability to evaluate large volumes of agricultural products before reaching the consumer. In this presentation, recent advances in chemical imaging technology that exploit Raman, fluorescence and near-infrared (NIR) are presented for the detection of contaminants in agricultural products.

  18. Satellite Detection in AdvancedCamera for Surveys/Wide Field Channel Images

    NASA Astrophysics Data System (ADS)

    Borncamp, D.; Lim, Pey-Lian

    2016-01-01

    This document explains the process by which satellite trails can be found within individual chips of an Advanced Camera for Surveys (ACS) Wide Field Channel (WFC) image. Since satellites are transient and sporadic events, we used the Hubble Frontier Fields (HFF) dataset which is manually checked for satellite trails has been used as a truth set to verify that the method in this document does a complete job without a high false positive rate. This document also details the process of producing a mask that will update data quality information to inform users where the trail traverses the image and properly account for the affected pixels. Along with this document, the Python source code used to detect and mask satellite trails will be released to users with as a stand-alone product within the STSDAS acstools package.

  19. Single virus detection by means of atomic force microscopy in combination with advanced image analysis.

    PubMed

    Bocklitz, Thomas; Kämmer, Evelyn; Stöckel, Stephan; Cialla-May, Dana; Weber, Karina; Zell, Roland; Deckert, Volker; Popp, Jürgen

    2014-10-01

    In the present contribution virions of five different virus species, namely Varicella-zoster virus, Porcine teschovirus, Tobacco mosaic virus, Coliphage M13 and Enterobacteria phage PsP3, are investigated using atomic force microscopy (AFM). From the resulting height images quantitative features like maximal height, area and volume of the viruses could be extracted and compared to reference values. Subsequently, these features were accompanied by image moments, which quantify the morphology of the virions. Both types of features could be utilized for an automatic discrimination of the five virus species. The accuracy of this classification model was 96.8%. Thus, a virus detection on a single-particle level using AFM images is possible. Due to the application of advanced image analysis the morphology could be quantified and used for further analysis. Here, an automatic recognition by means of a classification model could be achieved in a reliable and objective manner. PMID:25196422

  20. Advanced protocol for the detection of irradiated food by electron spin resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Shimoyama, Yuhei; Ukai, Mitsuko; Nakamura, Hideo

    2007-11-01

    Using ESR (electron spin resonance) spectroscopy, we found various free radicals in a pepper before and after irradiation. The representative ESR spectrum of the pepper composed of a sextet centered at g=2.0, a singlet at the same g-value and a singlet at g=4.0. This reflects the evidence of three independent radicals in the pepper before irradiation. Upon gamma ray irradiation, a new pair of signals appeared. The progressive saturation behavior (PSB) at various microwave power levels indicates quite different relaxation behaviors of those signals. For the evaluation of radiation-induced radicals and irradiation effects we propose a new protocol using the PSB method. This would call for an advanced protocol for the detection of irradiated foods.

  1. Advances in Resistive Pulse Sensors: Devices bridging the void between molecular and microscopic detection

    PubMed Central

    Kozak, Darby; Anderson, Will; Vogel, Robert; Trau, Matt

    2011-01-01

    Since the first reported use of a biological ion channel to detect differences in single stranded genomic base pairs in 1996, a renaissance in nanoscale resistive pulse sensors has ensued. This resurgence of a technique originally outlined and commercialized over fifty years ago has largely been driven by advances in nanoscaled fabrication, and ultimately, the prospect of a rapid and inexpensive means for genomic sequencing as well as other macromolecular characterization. In this pursuit, the potential application of these devices to characterize additional properties such as the size, shape, charge, and concentration of nanoscaled materials (10 – 900 nm) has been largely overlooked. Advances in nanotechnology and biotechnology are driving the need for simple yet sensitive individual object readout devices such as resistive pulse sensors. This review will examine the recent progress in pore-based sensing in the nanoscale range. A detailed analysis of three new types of pore sensors – in-series, parallel, and size-tunable pores – has been included. These pores offer improved measurement sensitivity over a wider particle size range. The fundamental physical chemistry of these techniques, which is still evolving, will be reviewed. PMID:22034585

  2. Detection and Genotyping of Arcobacter and Campylobacter Isolates from Retail Chicken Samples by Use of DNA Oligonucleotide Arrays▿ †

    PubMed Central

    Quiñones, Beatriz; Parker, Craig T.; Janda, John M.; Miller, William G.; Mandrell, Robert E.

    2007-01-01

    To explore the use of DNA microarrays for pathogen detection in food, we produced DNA oligonucleotide arrays to simultaneously determine the presence of Arcobacter and the presence of Campylobacter in retail chicken samples. Probes were selected that target housekeeping and virulence-associated genes in both Arcobacter butzleri and thermotolerant Campylobacter jejuni and Campylobacter coli. These microarrays showed a high level of probe specificity; the signal intensities detected for A. butzleri, C. coli, or C. jejuni probes were at least 10-fold higher than the background levels. Specific identification of A. butzleri, C. coli, and C. jejuni was achieved without the need for a PCR amplification step. By adapting an isolation method that employed membrane filtration and selective media, C. jejuni isolates were recovered from package liquid from whole chicken carcasses prior to enrichment. Increasing the time of enrichment resulted in the isolation of A. butzleri and increased the recovery of C. jejuni. C. jejuni isolates were further classified by using an additional subset of probes targeting the lipooligosaccharide (LOS) biosynthesis locus. Our results demonstrated that most of the C. jejuni isolates likely possess class B, C, or H LOS. Validation experiments demonstrated that the DNA microarray had a detection sensitivity threshold of approximately 10,000 C. jejuni cells. Interestingly, the use of C. jejuni sequence-specific primers to label genomic DNA improved the sensitivity of this DNA microarray for detection of C. jejuni in whole chicken carcass samples. C. jejuni was efficiently detected directly both in package liquid from whole chicken carcasses and in enrichment broths. PMID:17416693

  3. Detection and genotyping of Arcobacter and Campylobacter isolates from retail chicken samples by use of DNA oligonucleotide arrays.

    PubMed

    Quiñones, Beatriz; Parker, Craig T; Janda, John M; Miller, William G; Mandrell, Robert E

    2007-06-01

    To explore the use of DNA microarrays for pathogen detection in food, we produced DNA oligonucleotide arrays to simultaneously determine the presence of Arcobacter and the presence of Campylobacter in retail chicken samples. Probes were selected that target housekeeping and virulence-associated genes in both Arcobacter butzleri and thermotolerant Campylobacter jejuni and Campylobacter coli. These microarrays showed a high level of probe specificity; the signal intensities detected for A. butzleri, C. coli, or C. jejuni probes were at least 10-fold higher than the background levels. Specific identification of A. butzleri, C. coli, and C. jejuni was achieved without the need for a PCR amplification step. By adapting an isolation method that employed membrane filtration and selective media, C. jejuni isolates were recovered from package liquid from whole chicken carcasses prior to enrichment. Increasing the time of enrichment resulted in the isolation of A. butzleri and increased the recovery of C. jejuni. C. jejuni isolates were further classified by using an additional subset of probes targeting the lipooligosaccharide (LOS) biosynthesis locus. Our results demonstrated that most of the C. jejuni isolates likely possess class B, C, or H LOS. Validation experiments demonstrated that the DNA microarray had a detection sensitivity threshold of approximately 10,000 C. jejuni cells. Interestingly, the use of C. jejuni sequence-specific primers to label genomic DNA improved the sensitivity of this DNA microarray for detection of C. jejuni in whole chicken carcass samples. C. jejuni was efficiently detected directly both in package liquid from whole chicken carcasses and in enrichment broths.

  4. Earthquake Detection and Location Capabilities of the Advanced National Seismic Network

    NASA Astrophysics Data System (ADS)

    McNamara, D. E.; Buland, R. P.; Benz, H. M.; Leith, W.

    2004-12-01

    We have computed minimum earthquake moment magnitude, Mw, detection thresholds for a 1x1 degree grid across the US using the existing backbone stations of the Advanced National Seismic System (ANSS). For every grid point we compute the minimum Mw for which the P phase should be detectable by at least five ANSS stations. Detection is declared at a station when body wave power levels produced for a given Mw are above the frequency dependent 80th percentile noise level for the station. Noise levels were determined in a previous study from probability density functions of noise spectra computed for each ANSS backbone station (McNamara and Buland, 2004). To model event power levels, earthquake moment, Mo, is computed as a function of apparent corner frequency using the source scaling formulas of Brune (1970, 1971). The apparent corner frequency is the frequency at which body wave spectral amplitudes are maximum as a result of attenuation and short period filters applied during NEIC phase picking. The corresponding moment magnitude, Mw, is computed after Kanamori (1977). Body wave amplitudes are then computed for each station depending on the distance and attenuation along each raypath. Amplitude is then converted to power (dB) and compared to station noise levels. The fifth lowest power, above station noise levels then corresponds to the minimum earthquake magnitude for that particular grid point. Our theoretical minimum Mw threshold compares favorably to magnitude thresholds determined from USGS PDE catalogs. We also model the regional variation in event location improvement with the installation of planned ANSS backbone stations. Results from this study are useful for characterizing the performance of existing ANSS broadband stations, for detecting operational problems, and should be relevant to the future siting of ANSS backbone stations. Results from this analysis are also used to optimize the distribution of ANSS regional network stations.

  5. Detection of intermediately vancomycin-susceptible and heterogeneous Staphylococcus aureus isolates: comparison of Etest and Agar screening methods.

    PubMed

    Riederer, K; Shemes, S; Chase, P; Musta, A; Mar, A; Khatib, R

    2011-06-01

    Detection of Staphylococcus aureus isolates with intermediate vancomycin susceptibility (VISA) and heteroresistance (hVISA) remains problematic. The population analysis profile/area under the curve (PAP/AUC) is the gold standard but is cumbersome. We compared the performance of two Etest screening methods (macromethod [MAC] and glycopeptide resistance detection [GRD]) plus brain heart infusion (BHI) agars supplemented with 3 (BHI-V3) or 4 (BHI-V4) mg/liter vancomycin in detecting hVISA and/or VISA phenotypes. Etest hVISA screenings were done in parallel for 485 saved methicillin-resistant S. aureus (MRSA) blood isolates according to the manufacturer's instructions. The PAP/AUC was measured for all isolates according to the modified method. PAP/AUC test isolate/Mu3 ratios of <0.9, 0.9 to 1.3, and >1.3 were considered positive for susceptible MRSA (S-MRSA), hVISA, and VISA, respectively. PAP/AUC revealed seven VISA and 33 hVISA phenotypes. MAC screening was positive for 30 (75.0%) hVISA/VISA and 49 (11.0%) S-MRSA isolates. GRD screening was positive for 28 (70.0%) hVISA/VISA and 63 (14.2%) S-MRSA isolates. Growth on BHI-V3 was noted in all hVISA/VISA and 24 (5.4%) S-MRSA isolates. Growth on BHI-V4 was noted in all VISA and four (12.1%) hVISA isolates. None of the S-MRSA isolates grew on BHI-V4 agar. The sensitivity, specificity, and positive (PPV) and negative (NPV) predictive values were 75.0%, 89.0%, 38.0%, and 97.5% for MAC; 70.0%, 85.8%, 30.8%, and 97.0% for GRD; 100%, 94.6%, 62.5%, and 100% for BHI-V3; and 100, 99.2%, 63.6%, and 100% for BHI-V4 (for detecting VISA). These findings suggest that both Etest screening methods have excellent NPV, but positive results require confirmation. BHI-V3 and BHI-V4 agars provide more precise identification of hVISA and VISA, respectively; they may be reasonable alternatives to PAP/AUC.

  6. Specific Magnetic Isolation of E6 HPV16 Modified Magnetizable Particles Coupled with PCR and Electrochemical Detection

    PubMed Central

    Jimenez Jimenez, Ana Maria; Ruttkay-Nedecky, Branislav; Dostalova, Simona; Krejcova, Ludmila; Michalek, Petr; Richtera, Lukas; Adam, Vojtech

    2016-01-01

    The majority of carcinomas that were developed due to the infection with human papillomavirus (HPV) are caused by high-risk HPV types, HPV16 and HPV18. These HPV types contain the E6 and E7 oncogenes, so the fast detection of these oncogenes is an important point to avoid the development of cancer. Many different HPV tests are available to detect the presence of HPV in biological samples. The aim of this study was to design a fast and low cost method for HPV identification employing magnetic isolation, polymerase chain reaction (PCR) and electrochemical detection. These assays were developed to detect the interactions between E6-HPV16 oncogene and magnetizable particles (MPs) using commercial Dynabeads M-280 Streptavidin particles and laboratory-synthesized “homemade” particles called MANs (MAN-37, MAN-127 and MAN-164). The yields of PCR amplification of E6-HPV16 oncogene bound on the particles and after the elution from the particles were compared. A highest yield of E6-HPV16 DNA isolation was obtained with both MPs particles commercial M-280 Streptavidin and MAN-37 due to reducing of the interferents compared with the standard PCR method. A biosensor employing the isolation of E6-HPV16 oncogene with MPs particles followed by its electrochemical detection can be a very effective technique for HPV identification, providing simple, sensitive and cost-effective analysis. PMID:27164078

  7. Specific Magnetic Isolation of E6 HPV16 Modified Magnetizable Particles Coupled with PCR and Electrochemical Detection.

    PubMed

    Jimenez Jimenez, Ana Maria; Ruttkay-Nedecky, Branislav; Dostalova, Simona; Krejcova, Ludmila; Michalek, Petr; Richtera, Lukas; Adam, Vojtech

    2016-05-05

    The majority of carcinomas that were developed due to the infection with human papillomavirus (HPV) are caused by high-risk HPV types, HPV16 and HPV18. These HPV types contain the E6 and E7 oncogenes, so the fast detection of these oncogenes is an important point to avoid the development of cancer. Many different HPV tests are available to detect the presence of HPV in biological samples. The aim of this study was to design a fast and low cost method for HPV identification employing magnetic isolation, polymerase chain reaction (PCR) and electrochemical detection. These assays were developed to detect the interactions between E6-HPV16 oncogene and magnetizable particles (MPs) using commercial Dynabeads M-280 Streptavidin particles and laboratory-synthesized "homemade" particles called MANs (MAN-37, MAN-127 and MAN-164). The yields of PCR amplification of E6-HPV16 oncogene bound on the particles and after the elution from the particles were compared. A highest yield of E6-HPV16 DNA isolation was obtained with both MPs particles commercial M-280 Streptavidin and MAN-37 due to reducing of the interferents compared with the standard PCR method. A biosensor employing the isolation of E6-HPV16 oncogene with MPs particles followed by its electrochemical detection can be a very effective technique for HPV identification, providing simple, sensitive and cost-effective analysis.

  8. Detection and identification of Trichophyton tonsurans from clinical isolates and hairbrush samples by loop-mediated isothermal amplification system.

    PubMed

    Yo, Ayaka; Yamamoto, Mikachi; Nakayama, Takako; Ishikawa, Jun; Makimura, Koichi

    2016-09-01

    Since the 1990s, there have been reports of the spread of dermatophytosis caused by Trichophyton tonsurans among contact sports athletes in several countries, including Japan. This study was performed to develop a loop-mediated isothermal amplification (LAMP) system for rapid and accurate detection and identification of T. tonsurans from clinical isolates or hairbrush samples for diagnosis and to prevent the spread of infection. A specific primer set was prepared by comparing the whole genome sequence of T. tonsurans with those of six other closely related dermatophytes. After confirming the sensitivity and specificity of this system, LAMP assay was performed using 37 clinical samples obtained from three healthy volunteers and 24 judo athletes. A total of 155 fungal isolates (56 strains of various standard fungi, 96 identified T. tonsurans isolates, three hairbrush-cultured isolates from judo athletes) and 37 hairbrush samples (34 samples from 24 judo athletes, and three samples from three healthy volunteers) were used for culture and LAMP assay, respectively. The assay showed no cross-reactivity to standard strains other than T. tonsurans. The detection limit was 100 copies of DNA template per tube. All of the 96 T. tonsurans isolates were amplified, and all samples from healthy volunteers showed negative results. Four of the 34 hairbrush samples obtained from judo athletes showed positive results in LAMP assay, and two of the four were positive in both culture and LAMP assay. We developed a rapid LAMP system with high specificity and sensitivity for diagnosis of T. tonsurans infection.

  9. Detection and identification of Trichophyton tonsurans from clinical isolates and hairbrush samples by loop-mediated isothermal amplification system.

    PubMed

    Yo, Ayaka; Yamamoto, Mikachi; Nakayama, Takako; Ishikawa, Jun; Makimura, Koichi

    2016-09-01

    Since the 1990s, there have been reports of the spread of dermatophytosis caused by Trichophyton tonsurans among contact sports athletes in several countries, including Japan. This study was performed to develop a loop-mediated isothermal amplification (LAMP) system for rapid and accurate detection and identification of T. tonsurans from clinical isolates or hairbrush samples for diagnosis and to prevent the spread of infection. A specific primer set was prepared by comparing the whole genome sequence of T. tonsurans with those of six other closely related dermatophytes. After confirming the sensitivity and specificity of this system, LAMP assay was performed using 37 clinical samples obtained from three healthy volunteers and 24 judo athletes. A total of 155 fungal isolates (56 strains of various standard fungi, 96 identified T. tonsurans isolates, three hairbrush-cultured isolates from judo athletes) and 37 hairbrush samples (34 samples from 24 judo athletes, and three samples from three healthy volunteers) were used for culture and LAMP assay, respectively. The assay showed no cross-reactivity to standard strains other than T. tonsurans. The detection limit was 100 copies of DNA template per tube. All of the 96 T. tonsurans isolates were amplified, and all samples from healthy volunteers showed negative results. Four of the 34 hairbrush samples obtained from judo athletes showed positive results in LAMP assay, and two of the four were positive in both culture and LAMP assay. We developed a rapid LAMP system with high specificity and sensitivity for diagnosis of T. tonsurans infection. PMID:26892741

  10. An autonomous fault detection, isolation, and recovery system for a 20-kHz electric power distribution test bed

    NASA Technical Reports Server (NTRS)

    Quinn, Todd M.; Walters, Jerry L.

    1991-01-01

    Future space explorations will require long term human presence in space. Space environments that provide working and living quarters for manned missions are becoming increasingly larger and more sophisticated. Monitor and control of the space environment subsystems by expert system software, which emulate human reasoning processes, could maintain the health of the subsystems and help reduce the human workload. The autonomous power expert (APEX) system was developed to emulate a human expert's reasoning processes used to diagnose fault conditions in the domain of space power distribution. APEX is a fault detection, isolation, and recovery (FDIR) system, capable of autonomous monitoring and control of the power distribution system. APEX consists of a knowledge base, a data base, an inference engine, and various support and interface software. APEX provides the user with an easy-to-use interactive interface. When a fault is detected, APEX will inform the user of the detection. The user can direct APEX to isolate the probable cause of the fault. Once a fault has been isolated, the user can ask APEX to justify its fault isolation and to recommend actions to correct the fault. APEX implementation and capabilities are discussed.

  11. Active fault detection and isolation of discrete-time linear time-varying systems: a set-membership approach

    NASA Astrophysics Data System (ADS)

    Mojtaba Tabatabaeipour, Seyed

    2015-08-01

    Active fault detection and isolation (AFDI) is used for detection and isolation of faults that are hidden in the normal operation because of a low excitation signal or due to the regulatory actions of the controller. In this paper, a new AFDI method based on set-membership approaches is proposed. In set-membership approaches, instead of a point-wise estimation of the states, a set-valued estimation of them is computed. If this set becomes empty the given model of the system is not consistent with the measurements. Therefore, the model is falsified. When more than one model of the system remains un-falsified, the AFDI method is used to generate an auxiliary signal that is injected into the system for detection and isolation of faults that remain otherwise hidden or non-isolated using passive FDI (PFDI) methods. Having the set-valued estimation of the states for each model, the proposed AFDI method finds an optimal input signal that guarantees FDI in a finite time horizon. The input signal is updated at each iteration in a decreasing receding horizon manner based on the set-valued estimation of the current states and un-falsified models at the current sample time. The problem is solved by a number of linear and quadratic programming problems, which result in a computationally efficient algorithm. The method is tested on a numerical example as well as on the pitch actuator of a benchmark wind turbine.

  12. MOLECULAR DETECTION OF ANTIBIOTIC-RESISTANCE DETERMINANTS IN ESCHERICHIA COLI ISOLATED FROM THE ENDANGERED AUSTRALIAN SEA LION (NEOPHOCA CINEREA).

    PubMed

    Delport, Tiffany C; Harcourt, Robert G; Beaumont, Linda J; Webster, Koa N; Power, Michelle L

    2015-07-01

    Greater interaction between humans and wildlife populations poses significant risks of anthropogenic impact to natural ecosystems, especially in the marine environment. Understanding the spread of microorganisms at the marine interface is therefore important if we are to mitigate adverse effects on marine wildlife. We investigated the establishment of Escherichia coli in the endangered Australian sea lion (Neophoca cinerea) by comparing fecal isolation from wild and captive sea lion populations. Fecal samples were collected from wild colonies March 2009-September 2010 and from captive individuals March 2011-May 2013. Using molecular screening, we assigned a phylotype to E. coli isolates and determined the presence of integrons, mobile genetic elements that capture gene cassettes conferring resistance to antimicrobial agents common in fecal coliforms. Group B2 was the most abundant phylotype in all E. coli isolates (n = 37), with groups A, B1, and D also identified. Integrons were not observed in E. coli (n = 21) isolated from wild sea lions, but were identified in E. coli from captive animals (n = 16), from which class I integrases were detected in eight isolates. Sequencing of gene cassette arrays identified genes conferring resistance to streptomycin-spectinomycin (aadA1) and trimethoprim (dfrA17, dfrB4). Class II integrases were not detected in the E. coli isolates. The frequent detection in captive sea lions of E. coli with resistance genes commonly identified in human clinical cases suggests that conditions experienced in captivity may contribute to establishment. Identification of antibiotic resistance in the microbiota of Australian sea lions provides crucial information for disease management. Our data will inform conservation management strategies and provide a mechanism to monitor microorganism dissemination to sensitive pinniped populations. PMID:25919463

  13. MOLECULAR DETECTION OF ANTIBIOTIC-RESISTANCE DETERMINANTS IN ESCHERICHIA COLI ISOLATED FROM THE ENDANGERED AUSTRALIAN SEA LION (NEOPHOCA CINEREA).

    PubMed

    Delport, Tiffany C; Harcourt, Robert G; Beaumont, Linda J; Webster, Koa N; Power, Michelle L

    2015-07-01

    Greater interaction between humans and wildlife populations poses significant risks of anthropogenic impact to natural ecosystems, especially in the marine environment. Understanding the spread of microorganisms at the marine interface is therefore important if we are to mitigate adverse effects on marine wildlife. We investigated the establishment of Escherichia coli in the endangered Australian sea lion (Neophoca cinerea) by comparing fecal isolation from wild and captive sea lion populations. Fecal samples were collected from wild colonies March 2009-September 2010 and from captive individuals March 2011-May 2013. Using molecular screening, we assigned a phylotype to E. coli isolates and determined the presence of integrons, mobile genetic elements that capture gene cassettes conferring resistance to antimicrobial agents common in fecal coliforms. Group B2 was the most abundant phylotype in all E. coli isolates (n = 37), with groups A, B1, and D also identified. Integrons were not observed in E. coli (n = 21) isolated from wild sea lions, but were identified in E. coli from captive animals (n = 16), from which class I integrases were detected in eight isolates. Sequencing of gene cassette arrays identified genes conferring resistance to streptomycin-spectinomycin (aadA1) and trimethoprim (dfrA17, dfrB4). Class II integrases were not detected in the E. coli isolates. The frequent detection in captive sea lions of E. coli with resistance genes commonly identified in human clinical cases suggests that conditions experienced in captivity may contribute to establishment. Identification of antibiotic resistance in the microbiota of Australian sea lions provides crucial information for disease management. Our data will inform conservation management strategies and provide a mechanism to monitor microorganism dissemination to sensitive pinniped populations.

  14. Subsurface detection and characterization of Hertzian cracks in advanced ceramic materials using optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Bashkansky, Mark; Reintjes, John F.

    2002-06-01

    Optical Coherence Tomography (OCT) is an active optical imaging technique that is capable of three-dimensional resolution better than 10 microns in all dimensions. OCT was originally developed as a non-invasive technique in biomedical field. It also found uses in the NDE of various materials including ceramics, plastics and composites. In various ceramics OCT can be used to detect microscopic, subsurface defects at depths approaching hundreds of microns. The depth of penetration depends on the material and on the wavelength of light. Here we demonstrate an application of OCT to the subsurface imaging in various materials and, in particular, to the detection of a surface-penetrating Hertzian crack in a Si3N4 ceramic ball. We present measured subsurface trajectory of the crack and compare it to theoretical predictions. These cracks represent one of the most important failure mechanisms in advanced ceramic materials. The ability to map subsurface trajectories of cracks is a valuable tool in the evaluation of different existing theories. Better theoretical understanding of various properties of crack initiation and propagation can lead to engineering of improved ceramic materials.

  15. Advance in multi-hit detection and quantization in atom probe tomography

    NASA Astrophysics Data System (ADS)

    Costa, G. Da; Wang, H.; Duguay, S.; Bostel, A.; Blavette, D.; Deconihout, B.

    2012-12-01

    The preferential retention of high evaporation field chemical species at the sample surface in atom-probe tomography (e.g., boron in silicon or in metallic alloys) leads to correlated field evaporation and pronounced pile-up effects on the detector. The latter severely affects the reliability of concentration measurements of current 3D atom probes leading to an under-estimation of the concentrations of the high-field species. The multi-hit capabilities of the position-sensitive time-resolved detector is shown to play a key role. An innovative method based on Fourier space signal processing of signals supplied by an advance delay-line position-sensitive detector is shown to drastically improve the time resolving power of the detector and consequently its capability to detect multiple events. Results show that up to 30 ions on the same evaporation pulse can be detected and properly positioned. The major impact of this new method on the quantization of chemical composition in materials, particularly in highly-doped Si(B) samples is highlighted.

  16. Advances in associated-particle sealed-tube neutron probe diagnostics for substance detection

    SciTech Connect

    Rhodes, E.; Dickerman, C.E.; Frey, M.

    1995-07-01

    The development and investigation of a small associated-particle sealed-tube neutron generator (APSTNG) shows potential to allow the associated-particle diagnostic method to be moved out of the laboratory into field applications. The APSTNG interrogates the inspected object with 14-MeV neutrons generated from the deuterium-tritium reaction and detects the alpha-particle associated with each neutron inside a cone encompassing the region of interest. Gamma-ray spectra of resulting neutron reactions identify many nuclides. Flight-times determined from detection times of the gamma-rays and alpha-particles can yield a separate coarse tomographic image of each identified nuclide, from a single orientation. Chemical substances are identified by comparing relative spectral line intensities with ratios of elements in reference compounds. The high-energy neutrons and gamma-rays penetrate large objects and dense materials. Generally no collimators or radiation shielding are needed. Proof-of-concept laboratory experiments have been successfully performed for simulated nuclear, chemical warfare, and conventional munitions. Most recently, inspection applications have been investigated for radioactive waste characterization, presence of cocaine in propane tanks, and uranium and plutonium smuggling. Based on lessons learned with the present APSTNG system, an advanced APSTNG tube (along with improved high voltage supply and control units) is being designed and fabricated that will be transportable and rugged, yield a substantial neutron output increase, and provide sufficiently improved lifetime to allow operation at more than an order of magnitude increase in neutron flux.

  17. Advance in multi-hit detection and quantization in atom probe tomography.

    PubMed

    Da Costa, G; Wang, H; Duguay, S; Bostel, A; Blavette, D; Deconihout, B

    2012-12-01

    The preferential retention of high evaporation field chemical species at the sample surface in atom-probe tomography (e.g., boron in silicon or in metallic alloys) leads to correlated field evaporation and pronounced pile-up effects on the detector. The latter severely affects the reliability of concentration measurements of current 3D atom probes leading to an under-estimation of the concentrations of the high-field species. The multi-hit capabilities of the position-sensitive time-resolved detector is shown to play a key role. An innovative method based on Fourier space signal processing of signals supplied by an advance delay-line position-sensitive detector is shown to drastically improve the time resolving power of the detector and consequently its capability to detect multiple events. Results show that up to 30 ions on the same evaporation pulse can be detected and properly positioned. The major impact of this new method on the quantization of chemical composition in materials, particularly in highly-doped Si(B) samples is highlighted.

  18. The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae

    PubMed Central

    Diaz, Maureen H.; Winchell, Jonas M.

    2016-01-01

    Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen. PMID:27014191

  19. On Advanced Estimation Techniques for Exoplanet Detection and Characterization using Ground-Based Coronagraphs

    NASA Technical Reports Server (NTRS)

    Lawson, Peter R.; Frazin, Richard; Barrett, Harrison; Caucci, Luca; Devaney, Nicholas; Furenlid, Lars; Gladysz, Szymon; Guyon, Olivier; Krist, John; Maire, Jerome; Marois, Christian; Mawet, Dimitri; Mouillet, David; Mugnier, Laurent; Perrin, Marshall; Poyneer, Lisa; Pueyo, Laurent; Savransky, Dmitry; Soummer, Remi

    2012-01-01

    The direct imaging of planets around nearby stars is exceedingly difficult. Only about 14 exoplanets have been imaged to date that have masses less than 13 times that of Jupiter. The next generation of planet-finding coronagraphs, including VLT-SPHERE, the Gemini Planet Imager, Palomar P1640, and Subaru HiCIAO have predicted contrast performance of roughly a thousand times less than would be needed to detect Earth-like planets. In this paper we review the state of the art in exoplanet imaging, most notably the method of Locally Optimized Combination of Images (LOCI), and we investigate the potential of improving the detectability of faint exoplanets through the use of advanced statistical methods based on the concepts of the ideal observer and the Hotelling observer. We provide a formal comparison of techniques through a blind data challenge and evaluate performance using the Receiver Operating Characteristic (ROC) and Localization ROC (LROC) curves. We place particular emphasis on the understanding and modeling of realistic sources of measurement noise in ground-based AO-corrected coronagraphs. The work reported in this paper is the result of interactions between the co-authors during a week-long workshop on exoplanet imaging that was held in Squaw Valley, California, in March of 2012.

  20. On Advanced Estimation Techniques for Exoplanet Detection and Characterization using Ground-based Coronagraphs

    NASA Technical Reports Server (NTRS)

    Lawson, Peter; Frazin, Richard

    2012-01-01

    The direct imaging of planets around nearby stars is exceedingly difficult. Only about 14 exoplanets have been imaged to date that have masses less than 13 times that of Jupiter. The next generation of planet-finding coronagraphs, including VLT-SPHERE, the Gemini Planet Imager, Palomar P1640, and Subaru HiCIAO have predicted contrast performance of roughly a thousand times less than would be needed to detect Earth-like planets. In this paper we review the state of the art in exoplanet imaging, most notably the method of Locally Optimized Combination of Images (LOCI), and we investigate the potential of improving the detectability of faint exoplanets through the use of advanced statistical methods based on the concepts of the ideal observer and the Hotelling observer. We propose a formal comparison of techniques using a blind data challenge with an evaluation of performance using the Receiver Operating Characteristic (ROC) and Localization ROC (LROC) curves. We place particular emphasis on the understanding and modeling of realistic sources of measurement noise in ground-based AO-corrected coronagraphs. The work reported in this paper is the result of interactions between the co-authors during a week-long workshop on exoplanet imaging that was held in Squaw Valley, California, in March of 2012

  1. Development of an advanced digital detection system for multidrug resistant tuberculosis screening

    NASA Astrophysics Data System (ADS)

    Simkulet, Michelle D.; Beckstead, Jeffrey A.; Gilman, Brian C.; Bardarov, Savco; Castracane, James; Jacobs, William R., Jr.

    2000-04-01

    Tuberculosis (TB) remains the leading cause of death in the world from a single infectious disease and the threat is becoming more critical with the emergence and spread of multi-drug resistant tuberculosis (MDR-TB). Existing methods for detection of various strains of mycobacterium tuberculosis are complex, time consuming and expensive, and therefore, not suitable for use in developing countries where the spread of the disease is most rampant. Currently, a digital detection system based on advanced digital imaging technology, including CMOS and image intensification technology, is being developed by InterScience, Inc. for use with the luciferase reporter mycobacteriophages technique as developed at the Albert Einstein College of Medicine. This compact, low cost and high sensitivity system for rapid diagnosis and drug susceptibility testing for TB will have an immediate impact for both research and clinical applications. It is envisioned that the instrument will be suitable for use as a portable tool for rapid screening of MDR-TB in both developed and developing countries. The development of the system, recent results and a comparison to competing technologies will be presented.

  2. Advanced inspection methodologies for detection and classification of killer substrate defects

    NASA Astrophysics Data System (ADS)

    Chen, Aris; Huang, Victor; Chen, Sophie; Tsai, C. J.; Wu, Kenneth; Zhang, Haiping; Sun, Kevin; Saito, Jason; Chen, Henry; Hu, Debbie; Li, Ming; Shen, William; Mahajan, Uday

    2008-11-01

    The impact of embedded substrate defects on end-of-line die yield has become significant for advanced process technology nodes. Quality control and grading of wafers intended for leading-edge devices thus require effective detection and identification of embedded defects. In this paper, we present the results of a study on incoming prime-grade wafers using a new defect inspection system capable of dark field scattering and bright field differential interference contrast inspection. The wafers were scanned on a KLA-Tencor Surfscan SP2XP inspection tool, and the combined scan signal were real time analyzed to classify the defects of interest from particles. Inspection of the wafers both before and after a resist-coat process showed that all air pockets detected on the bare substrates resulted in coating defects. In the second part of the study, a set of epitaxial (epi) wafers was inspected using oblique- and normal- incidence dark field scattering as well as bright field differential interference contrast. The defects were classified by rules-based binning, and found to contain a large number of killer defects including epi stacking faults and bumps. Classification results were confirmed by SEM review, and showed that this multi-channel methodology successfully identified the killer defects with >95% accuracy and purity.

  3. On Advanced Estimation Techniques for Exoplanet Detection and Characterization Using Ground-based Coronagraphs

    PubMed Central

    Lawson, Peter R.; Poyneer, Lisa; Barrett, Harrison; Frazin, Richard; Caucci, Luca; Devaney, Nicholas; Furenlid, Lars; Gładysz, Szymon; Guyon, Olivier; Krist, John; Maire, Jérôme; Marois, Christian; Mawet, Dimitri; Mouillet, David; Mugnier, Laurent; Pearson, Iain; Perrin, Marshall; Pueyo, Laurent; Savransky, Dmitry

    2015-01-01

    The direct imaging of planets around nearby stars is exceedingly difficult. Only about 14 exoplanets have been imaged to date that have masses less than 13 times that of Jupiter. The next generation of planet-finding coronagraphs, including VLT-SPHERE, the Gemini Planet Imager, Palomar P1640, and Subaru HiCIAO have predicted contrast performance of roughly a thousand times less than would be needed to detect Earth-like planets. In this paper we review the state of the art in exoplanet imaging, most notably the method of Locally Optimized Combination of Images (LOCI), and we investigate the potential of improving the detectability of faint exoplanets through the use of advanced statistical methods based on the concepts of the ideal observer and the Hotelling observer. We propose a formal comparison of techniques using a blind data challenge with an evaluation of performance using the Receiver Operating Characteristic (ROC) and Localization ROC (LROC) curves. We place particular emphasis on the understanding and modeling of realistic sources of measurement noise in ground-based AO-corrected coronagraphs. The work reported in this paper is the result of interactions between the co-authors during a week-long workshop on exoplanet imaging that was held in Squaw Valley, California, in March of 2012. PMID:26347393

  4. Advances in methods for detection of anaerobic ammonium oxidizing (anammox) bacteria.

    PubMed

    Li, Meng; Gu, Ji-Dong

    2011-05-01

    Anaerobic ammonium oxidation (anammox), the biochemical process oxidizing ammonium into dinitrogen gas using nitrite as an electron acceptor, has only been recognized for its significant role in the global nitrogen cycle not long ago, and its ubiquitous distribution in a wide range of environments has changed our knowledge about the contributors to the global nitrogen cycle. Currently, several groups of methods are used in detection of anammox bacteria based on their physiological and biochemical characteristics, cellular chemical composition, and both 16S rRNA gene and selective functional genes as biomarkers, including hydrazine oxidoreductase and nitrite reductase encoding genes hzo and nirS, respectively. Results from these methods coupling with advances in quantitative PCR, reverse transcription of mRNA genes and stable isotope labeling have improved our understanding on the distribution, diversity, and activity of anammox bacteria in different environments both natural and engineered ones. In this review, we summarize these methods used in detection of anammox bacteria from various environments, highlight the strengths and weakness of these methods, and also discuss the new development potentials on the existing and new techniques in the future.

  5. Experimental Results of the First Two Stages of an Advanced Transonic Core Compressor Under Isolated and Multi-Stage Conditions

    NASA Technical Reports Server (NTRS)

    Prahst, Patricia S.; Kulkarni, Sameer; Sohn, Ki H.

    2015-01-01

    NASA's Environmentally Responsible Aviation (ERA) Program calls for investigation of the technology barriers associated with improved fuel efficiency of large gas turbine engines. Under ERA the task for a High Pressure Ratio Core Technology program calls for a higher overall pressure ratio of 60 to 70. This mean that the HPC would have to almost double in pressure ratio and keep its high level of efficiency. The challenge is how to match the corrected mass flow rate of the front two supersonic high reaction and high corrected tip speed stages with a total pressure ratio of 3.5. NASA and GE teamed to address this challenge by using the initial geometry of an advanced GE compressor design to meet the requirements of the first 2 stages of the very high pressure ratio core compressor. The rig was configured to run as a 2 stage machine, with Strut and IGV, Rotor 1 and Stator 1 run as independent tests which were then followed by adding the second stage. The goal is to fully understand the stage performances under isolated and multi-stage conditions and fully understand any differences and provide a detailed aerodynamic data set for CFD validation. Full use was made of steady and unsteady measurement methods to isolate fluid dynamics loss source mechanisms due to interaction and endwalls. The paper will present the description of the compressor test article, its predicted performance and operability, and the experimental results for both the single stage and two stage configurations. We focus the detailed measurements on 97 and 100 of design speed at 3 vane setting angles.

  6. Characterization of advanced shallow trench isolation (STI) CMP processes and consumables

    NASA Astrophysics Data System (ADS)

    Burkhard, Craig D.

    The main objectives of this thesis work were to elucidate the correlation between key characteristics of Chemical Mechanical Planarization (CMP) slurry and their polishing performance in shallow trench isolation (STI) applications. More specifically, a range of physical and chemical properties of STI slurries such as particle type, particle size, slurry pH, polymer additives, zeta potential were characterized. Their influences on CMP performance were examined based on their removal rate, selectivity, and response to processing parameters. Furthermore, the dependence of these performance metrics on polishing platform were also investigated. The slurry properties play a vital role in the polishing performance. The particle type influences the surface interaction and removal rate, particle size is significant in the removal rate of the film being planarized, the interaction between the abrasive particle and film surface is influenced by both the slurry pH and zeta potential and the polymer additives affect the oxide:nitride selectivity. These properties are typically studied in order to obtain a further understanding of their roles in the polishing performance. It is believed that the slurry pH, zeta potential and polymer additives are the most critical in the polishing performance for a more mechanical process. For the three slurries the abrasive particle is ceria and the particle size is similar. However, the slurry pH, zeta potential and polymer additives are not similar for each slurry. Each slurry behaves differently in terms of the polishing performance with these varying slurry properties. The removal rate is influenced by the polishing pressure, platen/carrier speeds and polishing time. The oxide:nitride selectivity is important to the polishing of patterned wafers because if the selectivity is poor than the possibility of feature dishing and erosion is greater. It is important to study the removal rate as a function of varying process parameters in order to

  7. Detection of vitamin D binding protein on the surface of cytotrophoblasts isolated from human placentae

    SciTech Connect

    Nestler, J.E.; McLeod, J.F.; Kowalski, M.A.; Strauss, J.F. 3d.; Haddad, J.G. Jr.

    1987-05-01

    Vitamin D binding protein (DBP), a Mr 56,000-58,000 alpha 2-glycoprotein, is the major serum protein involved in the transport of vitamin D sterols. Recently it has been suggested that DBP may also be involved in immunoglobulin G binding to cells. Because the trophoblast is involved in the transport of molecules such as vitamin D and immunoglobulin G to the fetus, we asked whether DBP could be detected on the surface of human placental trophoblast cells. Cytotrophoblasts purified from human term placentae were fixed and made permeant with Triton X-100 and examined by indirect immunofluorescence after incubation with a monoclonal antibody to DBP. Greater than 90% of these cells stained positively, whereas no staining was observed with nonimmune antiserum. The presence of DBP on/in the surface of cytotrophoblasts could also be demonstrated by fluorescent cytometry. When cell surface-associated proteins of cytotrophoblasts were radioiodinated, a Mr 57,000 radiolabeled protein could be immunoisolated from the cell lysate with a purified monospecific polyclonal antibody to DBP. Immunoisolation of this radiolabeled protein was prevented by the addition of excess unlabeled human DBP to the cell lysate before incubation with antibody. This Mr 57,000 radiolabeled protein could also be isolated by affinity chromatography selecting for proteins that bind to globular actin. When cytotrophoblasts were incubated with (/sup 35/S)methionine for 3 or 18 h, active synthesis of DBP could not be demonstrated by immunoisolation techniques. These studies demonstrate the presence of DBP on the surface of well washed, human cytotrophoblasts. This DBP may be maternally derived, since active synthesis of DBP could not be demonstrated.

  8. Detection of Virulence Genes and Growth Potential in Listeria monocytogenes Strains Isolated from Ricotta Salata Cheese.

    PubMed

    Coroneo, Valentina; Carraro, Valentina; Aissani, Nadhem; Sanna, Adriana; Ruggeri, Alessandra; Succa, Sara; Meloni, Barbara; Pinna, Antonella; Sanna, Clara

    2016-01-01

    Ricotta Salata is a traditional ripened and salted whey cheese made in Sardinia (Italy) from sheep's milk. This product is catalogued as ready-to-eat food (RTE) since it is not submitted to any further treatment before consumption. Thus, foodborne pathogens, such as Listeria monocytogenes, can represent a health risk for consumers. In September 2012, the FDA ordered the recall of several batches of Ricotta Salata imported from Italy linked to 22 cases of Listeriosis in the United States. This study was aimed at evaluating the presence and virulence properties of L. monocytogenes in 87 samples of Ricotta Salata produced in Sardinia. The ability of this product to support its growth under foreseen packing and storing conditions was also evaluated in 252 samples. Of the 87 samples 17.2% were positive for the presence of L. monocytogenes with an average concentration of 2.2 log10 cfu/g. All virulence-associated genes (prfA, rrn, hlyA, actA, inlA, inlB, iap, plcA, and plcB) were detected in only one isolated strain. The Ricotta Salata samples were artificially inoculated and growth potential (δ) was assessed over a period of 3 mo. The value of the growth potential was always >0.5 log10 cfu/g under foreseen packing and storing conditions. This study indicates that Ricotta Salata supports the L. monocytogenes growth to levels that may present a serious risk to public health, even while stored at refrigeration temperatures. PMID:26666835

  9. Detection of Virulence Genes and Growth Potential in Listeria monocytogenes Strains Isolated from Ricotta Salata Cheese.

    PubMed

    Coroneo, Valentina; Carraro, Valentina; Aissani, Nadhem; Sanna, Adriana; Ruggeri, Alessandra; Succa, Sara; Meloni, Barbara; Pinna, Antonella; Sanna, Clara

    2016-01-01

    Ricotta Salata is a traditional ripened and salted whey cheese made in Sardinia (Italy) from sheep's milk. This product is catalogued as ready-to-eat food (RTE) since it is not submitted to any further treatment before consumption. Thus, foodborne pathogens, such as Listeria monocytogenes, can represent a health risk for consumers. In September 2012, the FDA ordered the recall of several batches of Ricotta Salata imported from Italy linked to 22 cases of Listeriosis in the United States. This study was aimed at evaluating the presence and virulence properties of L. monocytogenes in 87 samples of Ricotta Salata produced in Sardinia. The ability of this product to support its growth under foreseen packing and storing conditions was also evaluated in 252 samples. Of the 87 samples 17.2% were positive for the presence of L. monocytogenes with an average concentration of 2.2 log10 cfu/g. All virulence-associated genes (prfA, rrn, hlyA, actA, inlA, inlB, iap, plcA, and plcB) were detected in only one isolated strain. The Ricotta Salata samples were artificially inoculated and growth potential (δ) was assessed over a period of 3 mo. The value of the growth potential was always >0.5 log10 cfu/g under foreseen packing and storing conditions. This study indicates that Ricotta Salata supports the L. monocytogenes growth to levels that may present a serious risk to public health, even while stored at refrigeration temperatures.

  10. Calcium transients in isolated amphibian skeletal muscle fibres: detection with aequorin.

    PubMed Central

    Blinks, J R; Rüdel, R; Taylor, S R

    1978-01-01

    1. Single twitch muscle fibres isolated from frogs and toads were microinjected with the Ca2+-sensitive bioluminescent protein aequorin. The fibres contracted normally and emitted flashes of light (aequorin responses) in response to stimulation for many hours thereafter. 2. No luminescence was detected from healthy fibres at rest. 3. The aequorin diffused from the site of injection at a rate consistent with a diffusion coefficient of 5 x 10(-8) cm2/sec. 4. During trains of isometric contractions there was a progressive reduction in both the amplitude and the rate of decline of the aequorin response, an observation consistent with the theory that Ca is redistributed from sites of release to sites of sequestration under such circumstances. 5. In isometric tetani light emission continued to rise long after the plateau of force had been achieved. This and the fact that the amplitude of the tetanic aequorin response increased steeply with increasing stimulus frequency suggest that in tetani the sarcoplasmic [Ca2+] may normally be above the level required to saturate the contractile apparatus. 6. Both in twitches and in tetani the amplitude of the aequorin response increased slightly and then decreased substantially as the fibre was stretched progressively beyond slack length. 7. In potassium contractures the luminescent and mechanical responses first became detectable at about the same [K+], but for equivalent force luminescence was less intense than in twitches. The aequorin response was biphasic in solutions of high [K+]. 8. Exposure of the fibre to Ca2+-free solutions had no influence on either the mechanical or the luminescent responses in twitches. In Ca2+-free solutions tetanic aequorin responses tended not to be maintained as well as normally, suggesting that intracellular Ca stores do become somewhat depleted. 9. In twitches the amplitude of the aequorin response probably reflects the amount of Ca2+ liberated into the cytoplasm rather than a [Ca2+] in

  11. Phenotypic Variation of Helicobacter pylori Isolates from Geographically Distinct Regions Detected by Lectin Typing

    PubMed Central

    Hynes, Sean O.; Broutet, Nathalie; Wadström, Torkel; Mikelsaar, Marika; O’Toole, Paul W.; Telford, John; Engstrand, Lars; Kamiya, Shigeru; Mentis, Andreas F.; Moran, Anthony P.

    2002-01-01

    A total of 309 Helicobacter pylori isolates from 18 different countries were analyzed with a previously developed lectin typing system. The system was developed by using a proteolytic pretreatment to enhance the carbohydrate fraction of the sample. Four lectins from Ulex europaeus, Lotus tetragonolobus, Erythrina cristigali, and Triticum vulgaris were used to type the strains. The lectins were chosen for their specificities for sugars commonly encountered in the lipopolysaccharide of H. pylori. The isolates were received from their parent institutions as pellets of biomass and were typed at one of three centers (in Ireland, Sweden, and Estonia). All 16 possible lectin reaction patterns were observed in the study, with the isolates with the predominant pattern exhibiting reactions with all the lectins in the panel. For European patients suffering from gastritis, an association was noted between lectin reaction pattern MH4 and atrophic chronic gastritis; isolates with lectin reaction pattern MH4 were isolated from patients with atrophic chronic gastritis, whereas isolates with this pattern were not isolated from patients with chronic gastritis (P = 0.0006). In addition, statistically significant relationships were noted between the lectin reaction pattern and the associated pathology of isolates from the Swedish population. Isolates with patterns MH13 and MH16, which had low lectin reactivities, correlated with nonulcer disease (P = 0.0025 and P = 0.0002, respectively), and all four isolates from adenocarcinoma patients were characterized as possessing reaction pattern MH16. In contrast, isolates with lectin reaction patterns MH1 and MH10, which had high lectin reactivities, were associated with ulcer disease (P = 0.046 and P = 0.0022, respectively). PMID:11773120

  12. Detection of CMY-2, CTX-M-14, and SHV-12 beta-lactamases in Escherichia coli fecal-sample isolates from healthy chickens.

    PubMed

    Briñas, Laura; Moreno, Miguel Angel; Zarazaga, Myriam; Porrero, Concepción; Sáenz, Yolanda; García, María; Dominguez, Lucas; Torres, Carmen

    2003-06-01

    Genes encoding the CMY-2, CTX-M-14, and SHV-12 beta-lactamases were detected in three of five Escherichia coli isolates from fecal samples from healthy chickens which showed resistance or diminished susceptibility to extended-spectrum cephalosporins. A -42 mutation at the promoter region of the ampC gene was detected in the other two isolates.

  13. Detection of CMY-2, CTX-M-14, and SHV-12 β-Lactamases in Escherichia coli Fecal-Sample Isolates from Healthy Chickens

    PubMed Central

    Briñas, Laura; Moreno, Miguel Angel; Zarazaga, Myriam; Porrero, Concepción; Sáenz, Yolanda; García, María; Dominguez, Lucas; Torres, Carmen

    2003-01-01

    Genes encoding the CMY-2, CTX-M-14, and SHV-12 β-lactamases were detected in three of five Escherichia coli isolates from fecal samples from healthy chickens which showed resistance or diminished susceptibility to extended-spectrum cephalosporins. A −42 mutation at the promoter region of the ampC gene was detected in the other two isolates. PMID:12760899

  14. Evaluation of the GenoType MTBDR assay for detection of rifampicin and isoniazid resistance in Mycobacterium tuberculosis complex isolates.

    PubMed

    Saglik, I; Oz, Y; Kiraz, N

    2014-01-01

    Detection of drug resistance plays a critical role in tuberculosis treatment. The aim of this study was to evaluate the performance of GenoType Mycobacteria Drug Resistance (MTBDR) assay (Hain Lifescience, Germany) and to compare it with radiometric BACTEC 460 TB system (Becton Dickinson, USA) for the detection of rifampicin (RIF) and isoniazid (INH) resistance in 84 Mycobacterium tuberculosis complex (MTBC) isolates. RIF resistance was identified in 6 of 7 (85.7%) isolates and INH resistance was identified in 8 of 14 (57.1%) isolates by the GenoType MTBDR assay. Compared with BACTEC system, the sensitivity, specificity, positive predictive value and negative predictive values were 85.7%, 98.7%, 85.7% and 98.7% for RIF resistance; and 57.1%, 100%, 100% and 92.1% for INH resistance, respectively. GenoType MTBDR assay is reliable when tested specimen is resistant to the tested drugs. Although test was more successful in the detection of RIF resistance, it exhibited low sensitivity for the detection of INH resistance. PMID:25008829

  15. Detecting the frequency of aminoglycoside modifying enzyme encoding genes among clinical isolates of methicillin-resistant Staphylococcus aureus

    PubMed Central

    Shokravi, Zahra; Mehrad, Laleh; Ramazani, Ali

    2015-01-01

    Introduction: Methicillin-resistant Staphylococcus aureus (MRSA) plays an important role in causing many serious nosocomial infections. In this study, the antimicrobial susceptibility and the frequency of aminoglycoside modifying enzyme encoding genes among clinical isolates of methicillin-resistant Staphylococcus aureus was investigated from two university hospitals of Zanjan province of Iran. Methods: In this study, the antimicrobial susceptibility of MRSA isolates to various antibiotics was investigated by the disk diffusion method. Multiplex PCR assays were used for the determination of aminoglycoside modifying enzyme (AME) genes and staphylococcal cassette chromosome mec (SCCmec) types in MRSA strains. Results: All 58 MRSA isolates were sensitive to vancomycin. Resistance to penicillin G, oxacilin, gentamicin, erythromycin, clindamycin, kanamycin, and tobramycin was found in 96.4%, 98.3%, 51.7%, 53.4%, 55.2%, 62% and 58.6% of the isolates, respectively. The most prevalent AME genes were aac(6′)/aph(2′′) (48.3 %) followed by ant(4)-Ia (24%). The aph(3′)-Ia gene was the least frequent AME gene among MRSA isolates (19%). Of the 58 tested MRSA isolates, 5 (8.6%) were harboured SCCmec type I, 11 (19%) SCCmec type II, 20 (34.5%) SCCmec type III, 17 (29.3%) SCCmec type IVa, 1 (1.7%) SCCmec type IVb, 2 (3.4%) SCCmec type IVc, 11 (19%) SCCmec type IVd, and, 18 (31%) SCCmec type V. Nineteen isolates were not typeable. Conclusion: In conclusion, the aac (6′)/aph (2′′) was the most common aminoglycoside modifying enzyme gene and SCCmec type II and V were the most frequent types detected in hospital isolates, respectively. PMID:26191502

  16. Detection of strobilurin-resistant isolates of Mycosphaerella graminicola in Morocco.

    PubMed

    Elbekali, A Y; Ramdani, A; Siah, A; Tisserant, B; Deweer, C; Hafidi, M; Reignault, P; Halama, P

    2011-01-01

    Septoria tritici blotch caused by Mycosphaerella graminicola (anamorph: Septoria tritici) is nowadays one of the most frequently occurring diseases on both bread and durum wheat crops. Two hundred and thirty isolates of the fungus were sampled from six distinct wheat-producing regions of Morocco in order to investigate the resistance of M. graminicola to strobilurins in this country, where this fungicide class is increasingly used in wheat-pest management. A subset of 134 isolates was first collected in 2008 from Meknes-Tafilalet, Tadla-Azilal, Gharb and Chaouia. Furthermore, 96 additional isolates were sampled in 2010 from the fourth regions investigated in 2008 plus Fes-Boulmane and Doukkala-Abda. Sensitivity or resistance within the isolates were determined by screening the G143A cytochrome b substitution conferring resistance. We used a mismatch amplification mutation assay allowing the amplification of either G143 (sensitive) or A143 (resistant) allele. All the 2008 isolates were found to be sensitive since they carry the wild-type allele G143. However, 9 (9%) out of the 2010 isolates were found to contain the resistant allele A143 and therefore to be resistant. Four of them were from Gharb and five from Fes-Boulmane. This study highlighted for the first time the occurrence of strobilurin-resistant isolates of M. graminicola in Morocco. Further genetic investigations should determine if the resistant isolates emerged independently in Morocco or traveled by wind-migration from Europe. PMID:22702191

  17. Genetic Detection and Isolation of Crimean-Congo hemorrhagic fever virus, Kosovo, Yugoslavia

    PubMed Central

    Boźović, Bojana; Pavlidou, Vassiliki; Papadimitriou, Evangelia; Pelemis, Mijomir; Antoniadis, Aantonis

    2002-01-01

    Crimean-Congo hemorrhagic fever virus (C-CHFV) strains were isolated from a fatal case and the attending physician in Kosovo, Yugoslavia. Early, rapid diagnosis of the disease was achieved by reverse transcription-polymerase chain reaction. The physician was successfully treated with oral ribavirin. These cases yielded the first genetically studied C-CHFV human isolates in the Balkans. PMID:12141973

  18. Performance of various testing methodologies for detection of heteroresistant vancomycin-intermediate Staphylococcus aureus in bloodstream isolates.

    PubMed

    van Hal, Sebastian J; Wehrhahn, Michael C; Barbagiannakos, Thelma; Mercer, Joanne; Chen, Dehua; Paterson, David L; Gosbell, Iain B

    2011-04-01

    The best screening method for detecting heteroresistant vancomycin-intermediate Staphylococcus aureus (hVISA) remains unclear. Using population analysis profiling utilizing the area under the concentration-time curve (PAP-AUC) as the gold standard, we screened 458 consecutive methicillin-resistant S. aureus (MRSA) bloodstream isolates to determine the most accurate and cost-effective testing strategy to detect the presence of heteroresistance. All isolates were also tested using the macromethod Etest (MET) and glycopeptide resistance detection (GRD) Etest. The MIC was determined by several methods, including standard vancomycin Etest, vancomycin broth microdilution (BMD), and Vitek2 testing. Fifty-five (12%) hVISA and 4 (1%) VISA isolates were detected by PAP-AUC. Compared to PAP-AUC, the sensitivities and specificities of MET, GRD Etest, BMD (using a MIC cutoff of ≥ 2 mg/liter), and standard vancomycin Etest (using a MIC cutoff of ≥ 2 mg/liter) were 89 and 55%, 71 and 94%, 82 and 97%, and 71 and 94%, respectively. Combination testing increased the overall testing accuracy by reducing the number of false-positive results. Cost was determined predominately by the number of PAP-AUC runs required following a screening assay. The most cost-effective strategy was BMD (using a MIC cutoff of ≥ 2 μg/ml) as a standalone assay or in combination with PAP-AUC, provided that BMD testing was batched. GRD Etest remained an alternative, with 71% of hVISA isolates detected. Prevalence influenced both cost and test accuracy, with results remaining unchanged for hVISA prevalences of up to 25%. Implementation of any testing strategy would therefore be dependent on balancing cost with accuracy in a given population and clinical context.

  19. Comparison of RNA isolation and associated methods for extracellular RNA detection by high-throughput quantitative polymerase chain reaction.

    PubMed

    Tanriverdi, Kahraman; Kucukural, Alper; Mikhalev, Ekaterina; Tanriverdi, Selim E; Lee, Rosalind; Ambros, Victor R; Freedman, Jane E

    2016-05-15

    MicroRNAs (miRNAs) are small noncoding RNA molecules that function in RNA silencing and posttranscriptional regulation of gene expression. miRNAs in biofluids are being used for clinical diagnosis as well as disease prediction. Efficient and reproducible isolation methods are crucial for extracellular RNA detection. To determine the best methodologies for miRNA detection from plasma, the performance of four RNA extraction kits, including an in-house kit, were determined with miScript miRNA assay technology; all were measured using a high-throughput quantitative polymerase chain reaction (qPCR) platform (BioMark System) with 90 human miRNA assays. In addition, the performances of complementary DNA (cDNA) and preamplification kits for TaqMan miRNA assays and miScript miRNA assays were compared using the same 90 miRNAs on the BioMark System. There were significant quantification cycle (Cq) value differences for the detection of miRNA targets between isolation kits. cDNA, preamplification, and qPCR performances were also varied. In summary, this study demonstrates differences among RNA isolation methods as measured by reverse transcription (RT)-qPCR. Importantly, differences were also noted in cDNA and preamplification performance using TaqMan and miScript. The in-house kit performed better than the other three kits. These findings demonstrate significant variability between isolation and detection methods for low-abundant miRNA detection from biofluids. PMID:26969789

  20. Microfluidic cell sorting: a review of the advances in the separation of cells from debulking to rare cell isolation.

    PubMed

    Shields, C Wyatt; Reyes, Catherine D; López, Gabriel P

    2015-03-01

    Accurate and high throughput cell sorting is a critical enabling technology in molecular and cellular biology, biotechnology, and medicine. While conventional methods can provide high efficiency sorting in short timescales, advances in microfluidics have enabled the realization of miniaturized devices offering similar capabilities that exploit a variety of physical principles. We classify these technologies as either active or passive. Active systems generally use external fields (e.g., acoustic, electric, magnetic, and optical) to impose forces to displace cells for sorting, whereas passive systems use inertial forces, filters, and adhesion mechanisms to purify cell populations. Cell sorting on microchips provides numerous advantages over conventional methods by reducing the size of necessary equipment, eliminating potentially biohazardous aerosols, and simplifying the complex protocols commonly associated with cell sorting. Additionally, microchip devices are well suited for parallelization, enabling complete lab-on-a-chip devices for cellular isolation, analysis, and experimental processing. In this review, we examine the breadth of microfluidic cell sorting technologies, while focusing on those that offer the greatest potential for translation into clinical and industrial practice and that offer multiple, useful functions. We organize these sorting technologies by the type of cell preparation required (i.e., fluorescent label-based sorting, bead-based sorting, and label-free sorting) as well as by the physical principles underlying each sorting mechanism. PMID:25598308

  1. Microfluidic Cell Sorting: A Review of the Advances in the Separation of Cells from Debulking to Rare Cell Isolation

    PubMed Central

    Shields, C. Wyatt; Reyes, Catherine D.; López, Gabriel P.

    2015-01-01

    Accurate and high throughput cell sorting is a critical enabling technology in molecular and cellular biology, biotechnology, and medicine. While conventional methods can provide high efficiency sorting in short timescales, advances in microfluidics have enabled the realization of miniaturized devices offering similar capabilities that exploit a variety of physical principles. We classify these technologies as either active or passive. Active systems generally use external fields (e.g., acoustic, electric, magnetic, and optical) to impose forces to displace cells for sorting, whereas passive systems use inertial forces, filters, and adhesion mechanisms to purify cell populations. Cell sorting on microchips provides numerous advantages over conventional methods by reducing the size of necessary equipment, eliminating potentially biohazardous aerosols, and simplifying the complex protocols commonly associated with cell sorting. Additionally, microchip devices are well suited for parallelization, enabling complete lab-on-a-chip devices for cellular isolation, analysis, and experimental processing. In this review, we examine the breadth of microfluidic cell sorting technologies, while focusing on those that offer the greatest potential for translation into clinical and industrial practice and that offer multiple, useful functions. We organize these sorting technologies by the type of cell preparation required (i.e., fluorescent label-based sorting, bead-based sorting, and label-free sorting) as well as by the physical principles underlying each sorting mechanism. PMID:25598308

  2. Assessment of Crack Detection in Cast Austenitic Piping Components Using Advanced Ultrasonic Methods.

    SciTech Connect

    Anderson, Michael T.; Crawford, Susan L.; Cumblidge, Stephen E.; Diaz, Aaron A.; Doctor, Steven R.

    2007-01-01

    Studies conducted at the Pacific N¬orthwest National Laboratory (PNNL) in Richland, Washington, have focused on developing and evaluating the reliability of nondestructive examination (NDE) approaches for inspecting coarse-grained, cast stainless steel reactor components. The objective of this work is to provide information to the United States Nuclear Regulatory Commission (NRC) on the utility, effec¬tiveness and limitations of ultrasonic testing (UT) inspection techniques as related to the in-service inspec¬tion of primary system piping components in pressurized water reactors (PWRs). Cast stainless steel pipe specimens were examined that contain thermal and mechanical fatigue cracks located close to the weld roots and have inside/outside surface geometrical conditions that simulate several PWR primary piping configurations. In addition, segments of vintage centrifugally cast piping were also examined to understand inherent acoustic noise and scattering due to grain structures and determine consistency of UT responses from different locations. The advanced UT methods were applied from the outside surface of these specimens using automated scanning devices and water coupling. The low-frequency ultrasonic method employed a zone-focused, multi-incident angle inspection protocol (operating at 250-450 kHz) coupled with a synthetic aperture focusing technique (SAFT) for improved signal-to-noise and advanced imaging capabilities. The phased array approach was implemented with a modified instrument operating at 500 kHz and composite volumetric images of the specimens were generated. Re¬sults from laboratory studies for assessing detection, localization and sizing effectiveness are discussed in this paper.

  3. Type C oncornavirus isolation studies in systemic lupus erythematosus. II. Attempted detection by viral RNA-dependent DNA polymerase assay.

    PubMed Central

    Phillips, P E; Hargrave-Granda, R

    1978-01-01

    Isolation of type C oncornavirus was attempted from 20 tissues and cell cultures of patients with systemic lupus erythematosus. Chemical inducers, cocultivation and fusion with cells from multiple other species, prolonged subculturing, and the RNA-dependent DNA polymerase assay for virus detection were used. A type C virus was isolated, but was shown to be the endogenous rat virus. Thus the methods, although generally appropriate, were not specifically permissive for replication of a human type C virus. This agrees with the failure of other investigators to isolate a virus of undisputed human origin. Combining available evidence, a fundamental role for type C viruses in lupus erythematosus remains an attractive hypothesis. Images PMID:80159

  4. A high-fidelity airbus benchmark for system fault detection and isolation and flight control law clearance

    NASA Astrophysics Data System (ADS)

    Goupil, Ph.; Puyou, G.

    2013-12-01

    This paper presents a high-fidelity generic twin engine civil aircraft model developed by Airbus for advanced flight control system research. The main features of this benchmark are described to make the reader aware of the model complexity and representativeness. It is a complete representation including the nonlinear rigid-body aircraft model with a full set of control surfaces, actuator models, sensor models, flight control laws (FCL), and pilot inputs. Two applications of this benchmark in the framework of European projects are presented: FCL clearance using optimization and advanced fault detection and diagnosis (FDD).

  5. Study of the effects of cyclodextrins on the fluorescence detection of zearalenone

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Successful applications of inclusion complexes to improve isolation and detection of small molecules have made cyclodextrins increasingly popular components in methods of detection. Studies of the effects of cyclodextrins on aflatoxins have advanced mycotoxin detection research. Recently, a capill...

  6. Molecular detection and analysis of Sheeppox and Orf viruses isolated from sheep from Qalubia, Egypt.

    PubMed

    Selim, Abdelfattah; Elhaig, Mahmoud; Höche, Jennifer; Gaede, Wolfgang

    2016-01-01

    In this study an outbreak with Sheeppox virus (SPPV) and Orf virus (ORFV) in one sheep herd in the Qalubia province, Egypt, was investigated. Both, SPPV and ORFV caused clinically manifest infections among sheep. The affected sheep showed skin lesions around the mouth or all over the body. Therefore, reliable diagnosis should confirm the aetiology of the infection and then reduce spread of the diseases in the affected areas. Clinical samples were investigated by virus isolation, PCR and real-time PCR assays. Furthermore, PCR-products of SPPV and ORFV isolates were sequenced and alignment to reference isolates was performed for phylogenetic analyses. The laboratory diagnosis showed that real-time PCR assay was more accurate and sensitive than conventional PCR and virus isolation. In phylogenetic analysis of the A29L gene genetic differences between SPPV field strains were not observed and the strains showed 100% homology with two SPPV isolates from Kazakhstan and one isolate from Turkey. The ORFV field strains are in the P55 gene genetically distinct from another and from other published isolates from Egypt 2006 and 2009. PMID:27529993

  7. Dynamic Neural Network-Based Pulsed Plasma Thruster (PPT) Fault Detection and Isolation for Formation Flying of Satellites

    NASA Astrophysics Data System (ADS)

    Valdes, A.; Khorasani, K.

    The main objective of this paper is to develop a dynamic neural network-based fault detection and isolation (FDI) scheme for the Pulsed Plasma Thrusters (PPTs) that are used in the Attitude Control Subsystem (ACS) of satellites that are tasked to perform a formation flying mission. By using data collected from the relative attitudes of the formation flying satellites our proposed "High Level" FDI scheme can detect the pair of thrusters which is faulty, however fault isolation cannot be accomplished. Based on the "High Level" FDI scheme and the DNN-based "Low Level" FDI scheme developed earlier by the authors, an "Integrated" DNN-based FDI scheme is then proposed. To demonstrate the FDI capabilities of the proposed schemes various fault scenarios are simulated.

  8. Biological and chemical detection of fumonisins produced on agar medium by Fusarium verticillioides isolates collected from corn in Sohag, Egypt.

    PubMed

    Aboul-Nasr, M B; Obied-Allah, M R A

    2013-08-01

    Fusarium verticillioides (Sacc.) Nirenberg is among the most common Fusarium species corn pathogens worldwide, and has been recognized as a fumonisin B1 (FB1) and fumonisin B2 (FB2) producer. In the present work, extracts of 58 F. verticillioides isolates from corn samples collected from Sohag Governorate, Egypt, were tested for their biotoxicity and production of fumonisin toxins. Forty-four Fusarium verticillioides isolates out of 58 tested produced FB1 or FB1 and FB2 (15 and 29 isolates, respectively) on potato-sucrose agar medium, detected by TLC, whereas the other 14 isolates did not produce fumonisin toxins. HPLC crude extract analysis confirmed the results from TLC plates. Brine shrimp larvae as well as the Gram-negative bacteria Pseudomonas aeuroginosa showed low bio-sensitivity towards the F. verticillioides crude extract toxicity, whereas the Gram-positive bacteria Bacillus cereus and Bacillus subtilis, especially B. subtilis, showed higher sensitivity towards the tested Fusarium crude extracts. These results enabled us to bio-evaluate and chemically detect fumonisin mycotoxins using a simple agar medium technique. PMID:23760819

  9. Biological and chemical detection of fumonisins produced on agar medium by Fusarium verticillioides isolates collected from corn in Sohag, Egypt.

    PubMed

    Aboul-Nasr, M B; Obied-Allah, M R A

    2013-08-01

    Fusarium verticillioides (Sacc.) Nirenberg is among the most common Fusarium species corn pathogens worldwide, and has been recognized as a fumonisin B1 (FB1) and fumonisin B2 (FB2) producer. In the present work, extracts of 58 F. verticillioides isolates from corn samples collected from Sohag Governorate, Egypt, were tested for their biotoxicity and production of fumonisin toxins. Forty-four Fusarium verticillioides isolates out of 58 tested produced FB1 or FB1 and FB2 (15 and 29 isolates, respectively) on potato-sucrose agar medium, detected by TLC, whereas the other 14 isolates did not produce fumonisin toxins. HPLC crude extract analysis confirmed the results from TLC plates. Brine shrimp larvae as well as the Gram-negative bacteria Pseudomonas aeuroginosa showed low bio-sensitivity towards the F. verticillioides crude extract toxicity, whereas the Gram-positive bacteria Bacillus cereus and Bacillus subtilis, especially B. subtilis, showed higher sensitivity towards the tested Fusarium crude extracts. These results enabled us to bio-evaluate and chemically detect fumonisin mycotoxins using a simple agar medium technique.

  10. Visual detection technique for efficient screening and isolation of Salmonella based on a novel enrichment assay using chromatography membrane.

    PubMed

    Tang, F; Xiong, Y; Zhang, H; Wu, K; Xiang, Y; Shao, J-B; Ai, H-W; Xiang, Y-P; Zheng, X-L; Lv, J-R; Sun, H; Bao, L-S; Zhang, Z; Hu, H-B; Zhang, J-Y; Chen, L; Lu, J; Liu, W-Y; Mei, H; Ma, Y; Xu, C-F; Fang, A-Y; Gu, M; Xu, C-Y; Chen, Y; Chen, Z; Sun, Z-Y

    2016-03-01

    To detect Salmonella more efficiently and isolate strains more easily, a novel and simple detection method that uses an enrichment assay and two chromogenic reactions on a chromatography membrane was developed. Grade 3 chromatography paper is used as functionalized solid phase support (SPS), which contains specially optimized medium. One reaction for screening is based on the sulfate-reducing capacity of Salmonella. Hydrogen sulfide (H2S) generated by Salmonella reacts with ammonium ferric citrate to produce black colored ferrous sulfide. Another reaction is based on Salmonella C8 esterase that is unique for Enterobacteriaceae except Serratia and interacts with 4-methylumbelliferyl caprylate (MUCAP) to produce fluorescent umbelliferone, which is visible under ultraviolet light. A very low detection limit (10(1) CFU ml(-1)) for Salmonella was achieved on the background of 10(5) CFU ml(-1) Escherichia coli. More importantly, testing with more than 1,000 anal samples indicated that our method has a high positive detection rate and is relatively low cost, compared with the traditional culture-based method. It took only 1 day for the preliminary screening and 2 days to efficiently isolate the Salmonella cells, indicating that the new assay is specific, rapid, and simple for Salmonella detection. In contrast to the traditional culture-based method, this method can be easily used to screen and isolate targeted strains with the naked eye. The results of quantitative and comparative experiments showed that the visual detection technique is an efficient alternative method for the screening of Salmonella spp. in many applications of large-sized samples related to public health surveillance. PMID:26796551

  11. Visual detection technique for efficient screening and isolation of Salmonella based on a novel enrichment assay using chromatography membrane.

    PubMed

    Tang, F; Xiong, Y; Zhang, H; Wu, K; Xiang, Y; Shao, J-B; Ai, H-W; Xiang, Y-P; Zheng, X-L; Lv, J-R; Sun, H; Bao, L-S; Zhang, Z; Hu, H-B; Zhang, J-Y; Chen, L; Lu, J; Liu, W-Y; Mei, H; Ma, Y; Xu, C-F; Fang, A-Y; Gu, M; Xu, C-Y; Chen, Y; Chen, Z; Sun, Z-Y

    2016-03-01

    To detect Salmonella more efficiently and isolate strains more easily, a novel and simple detection method that uses an enrichment assay and two chromogenic reactions on a chromatography membrane was developed. Grade 3 chromatography paper is used as functionalized solid phase support (SPS), which contains specially optimized medium. One reaction for screening is based on the sulfate-reducing capacity of Salmonella. Hydrogen sulfide (H2S) generated by Salmonella reacts with ammonium ferric citrate to produce black colored ferrous sulfide. Another reaction is based on Salmonella C8 esterase that is unique for Enterobacteriaceae except Serratia and interacts with 4-methylumbelliferyl caprylate (MUCAP) to produce fluorescent umbelliferone, which is visible under ultraviolet light. A very low detection limit (10(1) CFU ml(-1)) for Salmonella was achieved on the background of 10(5) CFU ml(-1) Escherichia coli. More importantly, testing with more than 1,000 anal samples indicated that our method has a high positive detection rate and is relatively low cost, compared with the traditional culture-based method. It took only 1 day for the preliminary screening and 2 days to efficiently isolate the Salmonella cells, indicating that the new assay is specific, rapid, and simple for Salmonella detection. In contrast to the traditional culture-based method, this method can be easily used to screen and isolate targeted strains with the naked eye. The results of quantitative and comparative experiments showed that the visual detection technique is an efficient alternative method for the screening of Salmonella spp. in many applications of large-sized samples related to public health surveillance.

  12. Increased sensitivity of RT-PCR for Potato virus Y detection using RNA isolated by a procedure with differential centrifugation.

    PubMed

    Zhang, Jianhua; Nie, Xianzhou; Boquel, Sébastien; Al-Daoud, Fadi; Pelletier, Yvan

    2015-12-01

    The sensitivity of reverse transcription-polymerase chain reaction (RT-PCR) for virus detection is influenced by many factors such as specificity of primers and quality of templates. These factors become extremely important for successful detection when virus concentration is low. Total RNA isolated from Potato virus Y (PVY)-infected potato plants using the sodium sulfite RNA isolation method or RNeasy plant mini kit contains a high proportion of host RNA and may also contain trace amount of phenolic and polysaccharide residues, which may inhibit RT-PCR. The goal of this study was to enhance the sensitivity of PVY detection by reducing host RNA in the extract by differential centrifugation followed by extraction using an RNeasy mini kit (DCR method). One-step RT-PCR had relatively low amplification efficiency for PVY RNA when a high proportion of plant RNA was present. SYBR Green-based real time RT-PCR showed that the RNA isolated by the DCR method had a higher cycle threshold value (Ct) for the elongation factor 1-α mRNA (Ef1α) of potato than the Ct value of the RNA extracted using the RNeasy plant mini kit, indicating that the DCR method significantly reduced the proportion of potato RNA in the extract. The detectable amount of RNA extracted using the DCR method was <0.001ng when plant sap from 10 PVY-infected and PVY-free potato leaflets in a 1.5:100 fresh weight ratio was extracted, compared with 0.01 and 0.02ng of RNA using the RNeasy plant mini kit and sodium sulfite RNA isolation methods, respectively. PMID:26210699

  13. DETECTION OF THE VELOCITY SHEAR EFFECT ON THE SPATIAL DISTRIBUTIONS OF THE GALACTIC SATELLITES IN ISOLATED SYSTEMS

    SciTech Connect

    Lee, Jounghun; Choi, Yun-Young E-mail: yy.choi@khu.ac.kr

    2015-02-01

    We report a detection of the effect of the large-scale velocity shear on the spatial distributions of the galactic satellites around the isolated hosts. Identifying the isolated galactic systems, each of which consists of a single host galaxy and its satellites, from the Seventh Data Release of the Sloan Digital Sky Survey and reconstructing linearly the velocity shear field in the local universe, we measure the alignments between the relative positions of the satellites from their isolated hosts and the principal axes of the local velocity shear tensors projected onto the plane of sky. We find a clear signal that the galactic satellites in isolated systems are located preferentially along the directions of the minor principal axes of the large-scale velocity shear field. Those galactic satellites that are spirals, are brighter, are located at distances larger than the projected virial radii of the hosts, and belong to the spiral hosts yield stronger alignment signals, which implies that the alignment strength depends on the formation and accretion epochs of the galactic satellites. It is also shown that the alignment strength is quite insensitive to the cosmic web environment, as well as the size and luminosity of the isolated hosts. Although this result is consistent with the numerical finding of Libeskind et al. based on an N-body experiment, owing to the very low significance of the observed signals, it remains inconclusive whether or not the velocity shear effect on the satellite distribution is truly universal.

  14. The first detection and full-length genome sequence of porcine deltacoronavirus isolated in Lao PDR.

    PubMed

    Lorsirigool, Athip; Saeng-Chuto, Kepalee; Temeeyasen, Gun; Madapong, Adthakorn; Tripipat, Thitima; Wegner, Matthew; Tuntituvanont, Angkana; Intrakamhaeng, Manakant; Nilubol, Dachrit

    2016-10-01

    Porcine deltacoronavirus (PDCoV) has been reported in many countries, including Hong Kong, the United States, South Korea, China and Thailand. In January 2016, clinical diarrhea similar to that of porcine epidemic diarrhea virus (PEDV) with a lower mortality rate was reported on a swine farm in Lao PDR. Intestine samples were collected from 3-day-old pigs with clinical diarrhea and assayed for the presence of swine enteric coronaviruses. The PCR results were positive for PDCoV but negative for PEDV and TGEV. A phylogenetic tree demonstrated that PDCoV from Lao PDR was grouped separately from PDCoV isolates from China and the USA, but was more closely related to the Chinese isolates than to the US isolates. The full-length genome sequence of the novel PDCoV isolate P1_16_BTL_0116 was determined. PMID:27424024

  15. Back Translation: An Emerging Sophisticated Cyber Strategy to Subvert Advances in "Digital Age" Plagiarism Detection and Prevention

    ERIC Educational Resources Information Center

    Jones, Michael; Sheridan, Lynnaire

    2015-01-01

    Advances have been made in detecting and deterring the student plagiarism that has accompanied the uptake and development of the internet. Many authors from the late 1990s onwards grappled with plagiarism in the digital age, presenting articles that were provoking and established the foundation for strategies to address cyber plagiarism, including…

  16. Deployment of an Advanced Electrocardiographic Analysis (A-ECG) to Detect Cardiovascular Risk in Career Firefighters

    NASA Technical Reports Server (NTRS)

    Dolezal, B. A.; Storer, T. W.; Abrazado, M.; Watne, R.; Schlegel, T. T.; Batalin, M.; Kaiser, W.; Smith, D. L.; Cooper, C. B.

    2011-01-01

    INTRODUCTION Sudden cardiac death is the leading cause of line of duty death among firefighters, accounting for approximately 45% of fatalities annually. Firefighters perform strenuous muscular work while wearing heavy, encapsulating personal protective equipment in high ambient temperatures, under chaotic and emotionally stressful conditions. These factors can precipitate sudden cardiac events like myocardial infarction, serious dysrhythmias, or cerebrovascular accidents in firefighters with underlying cardiovascular disease. Screening for cardiovascular risk factors is recommended but not always followed in this population. PHASER is a project charged with identifying and prioritizing risk factors in emergency responders. We have deployed an advanced ECG (A-ECG) system developed at NASA for improved sensitivity and specificity in the detection of cardiac risk. METHODS Forty-four professional firefighters were recruited to perform comprehensive baseline assessments including tests of aerobic performance and laboratory tests for fasting lipid profiles and glucose. Heart rate and conventional 12-lead ECG were obtained at rest and during incremental treadmill exercise testing (XT). In addition, a 5-min resting 12-lead A-ECG was obtained in a subset of firefighters (n=18) and transmitted over a secure networked system to a physician collaborator at NASA for advanced-ECG analysis. This A-ECG system has been proven, using myocardial perfusion and other imaging, to accurately identify a number of cardiac pathologies including coronary artery disease (CAD), left ventricular hypertrophy, hypertrophic cardiomyopathy, non-ischemic cardiomyopathy, and ischemic cardiomyopathy. RESULTS Subjects mean (SD) age was 43 (8) years, weight 91 (13) kg, and BMI of 28 (3) kg/square meter. Maximum oxygen uptake (VO2max) was 39 (9) ml/kg/min. This compares with the 45th %ile in healthy reference values and a recommended standard of 42 ml/kg/min for firefighters. The metabolic threshold (VO

  17. Fusion of Optimized Indicators from Advanced Driver Assistance Systems (ADAS) for Driver Drowsiness Detection

    PubMed Central

    Daza, Iván G.; Bergasa, Luis M.; Bronte, Sebastián; Yebes, J. Javier; Almazán, Javier; Arroyo, Roberto

    2014-01-01

    This paper presents a non-intrusive approach for monitoring driver drowsiness using the fusion of several optimized indicators based on driver physical and driving performance measures, obtained from ADAS (Advanced Driver Assistant Systems) in simulated conditions. The paper is focused on real-time drowsiness detection technology rather than on long-term sleep/awake regulation prediction technology. We have developed our own vision system in order to obtain robust and optimized driver indicators able to be used in simulators and future real environments. These indicators are principally based on driver physical and driving performance skills. The fusion of several indicators, proposed in the literature, is evaluated using a neural network and a stochastic optimization method to obtain the best combination. We propose a new method for ground-truth generation based on a supervised Karolinska Sleepiness Scale (KSS). An extensive evaluation of indicators, derived from trials over a third generation simulator with several test subjects during different driving sessions, was performed. The main conclusions about the performance of single indicators and the best combinations of them are included, as well as the future works derived from this study. PMID:24412904

  18. Fusion of optimized indicators from Advanced Driver Assistance Systems (ADAS) for driver drowsiness detection.

    PubMed

    Daza, Iván García; Bergasa, Luis Miguel; Bronte, Sebastián; Yebes, Jose Javier; Almazán, Javier; Arroyo, Roberto

    2014-01-09

    This paper presents a non-intrusive approach for monitoring driver drowsiness using the fusion of several optimized indicators based on driver physical and driving performance measures, obtained from ADAS (Advanced Driver Assistant Systems) in simulated conditions. The paper is focused on real-time drowsiness detection technology rather than on long-term sleep/awake regulation prediction technology. We have developed our own vision system in order to obtain robust and optimized driver indicators able to be used in simulators and future real environments. These indicators are principally based on driver physical and driving performance skills. The fusion of several indicators, proposed in the literature, is evaluated using a neural network and a stochastic optimization method to obtain the best combination. We propose a new method for ground-truth generation based on a supervised Karolinska Sleepiness Scale (KSS). An extensive evaluation of indicators, derived from trials over a third generation simulator with several test subjects during different driving sessions, was performed. The main conclusions about the performance of single indicators and the best combinations of them are included, as well as the future works derived from this study.

  19. Advances in acute kidney injury associated with cardiac surgery: the unfolding revolution in early detection.

    PubMed

    Wyckoff, Tygh; Augoustides, John G T

    2012-04-01

    Cardiac surgery-associated acute kidney injury (CSA-AKI) is important because it remains common and serious. A major limitation in the management of CSA-AKI has been ongoing delayed diagnosis by standard clinical approaches, including serum creatinine and calculated glomerular filtration rate. Recent advances in the understanding of CSA-AKI have highlighted the utility of novel biomarkers that diagnose CSA-AKI within the first 24 hours. The biomarkers that have been evaluated in clinical trials include neutrophil gelatinase-associated lipocalin (NGAL), cystatin C, kidney injury molecule 1 and interleukin-18. The biomarker with the greatest clinical promise is NGAL. Although it has multiple advantages over serum creatinine, it is still not the ideal biomarker for CSA-AKI. It is likely that a panel of early biomarkers will be developed to facilitate rapid and reliable detection of CSA-AKI, combining their different characteristics to optimize patient management. Future clinical trials likely will focus on whether these biomarkers predict adverse outcomes independent of serum creatinine fluctuations and whether therapies guided by biomarker profiles improve renal salvage and overall clinical outcomes. Given their clinical utility, these novel biomarkers have been evaluated beyond cardiac surgery for AKI in multiple clinical environments, including the emergency department, the operating room, the cardiac catheterization laboratory, and the intensive care unit. Their integration into clinical practice seems likely in the near future.

  20. Successful Resection of Isolated Para-Aortic Lymph Node Recurrence from Advanced Sigmoid Colon Cancer following 156 Courses of FOLFIRI Regimen

    PubMed Central

    Yamafuji, Kazuo; Asami, Atsunori; Baba, Hideo; Okamoto, Nobuhiko; Takahashi, Hidena; Takagi, Chisato; Kubochi, Kiyoshi

    2016-01-01

    Isolated para-aortic lymph node (PLN) recurrence from colorectal cancer (CRC) is rare, with no currently validated treatments. Few reports have described the successful resection of isolated PLN involvement from CRC following chemotherapy. We report the case of a 63-year-old man who underwent sigmoidectomy for sigmoid colon cancer at our hospital. Pathological examination demonstrated advanced sigmoid colon cancer with metastatic involvement in both of the tested PLNs. Palliative chemotherapy was initiated four weeks after surgical resection, with administration of the FOLFIRI regimen. Four years after the operation, computed tomography (CT) revealed an enlarged PLN below the left renal vein. As PLN enlarged to 15 mm in the minor axis on a CT scan in 2014 after receiving a total of 156 courses of the FOLFIRI regimen, we considered the enlarged PLN to represent an isolated metastasis. Accordingly, lymph node resection was performed with microscopically negative margins. The patient maintained a good quality of life without any side effects throughout the whole course of his treatment and remains disease-free at 24 months without chemotherapy after resection of the isolated PLN. Curative resection following chemotherapy may improve survival of carefully selected advanced CRC patients with locoregional recurrence, such as isolated PLN involvement. PMID:27648336

  1. Successful Resection of Isolated Para-Aortic Lymph Node Recurrence from Advanced Sigmoid Colon Cancer following 156 Courses of FOLFIRI Regimen.

    PubMed

    Takeshima, Kaoru; Yamafuji, Kazuo; Asami, Atsunori; Baba, Hideo; Okamoto, Nobuhiko; Takahashi, Hidena; Takagi, Chisato; Kubochi, Kiyoshi

    2016-01-01

    Isolated para-aortic lymph node (PLN) recurrence from colorectal cancer (CRC) is rare, with no currently validated treatments. Few reports have described the successful resection of isolated PLN involvement from CRC following chemotherapy. We report the case of a 63-year-old man who underwent sigmoidectomy for sigmoid colon cancer at our hospital. Pathological examination demonstrated advanced sigmoid colon cancer with metastatic involvement in both of the tested PLNs. Palliative chemotherapy was initiated four weeks after surgical resection, with administration of the FOLFIRI regimen. Four years after the operation, computed tomography (CT) revealed an enlarged PLN below the left renal vein. As PLN enlarged to 15 mm in the minor axis on a CT scan in 2014 after receiving a total of 156 courses of the FOLFIRI regimen, we considered the enlarged PLN to represent an isolated metastasis. Accordingly, lymph node resection was performed with microscopically negative margins. The patient maintained a good quality of life without any side effects throughout the whole course of his treatment and remains disease-free at 24 months without chemotherapy after resection of the isolated PLN. Curative resection following chemotherapy may improve survival of carefully selected advanced CRC patients with locoregional recurrence, such as isolated PLN involvement. PMID:27648336

  2. Molecular detection of antimicrobial resistance in local isolates of Staphylococcus epidermidis from urinary tract infections in Faisalabad region of Pakistan

    PubMed Central

    Farid, Anam; Naz, Iram; Ashraf, Asma; Ali, Aamir; Rehman, Asad-ur; Sarwar, Yasra; Haque, Abdul

    2015-01-01

    Staphylococci are one of the foremost causes of urinary tract infections (UTIs) in humans. The emergence of multiple drug resistance (MDR) among Staphylococci poses serious challenges in antimicrobial therapy for UTIs. Most work has been done on S. aureus while coagulase negative Staphylococci (mainly S. epidermidis) are often neglected. This study was conducted to establish a baseline profile of drug resistance in local S. epidermidis isolates from UTIs. Eighty urine samples were collected from suspected UTIs cases and screened for S. epidermidis. Twenty isolates were suspected as S. epidermidis based on colony morphology and Gram staining. Molecular detection by polymerase chain reaction (PCR) confirmed 13 isolates as S. epidermidis. Using disc diffusion method, phenotypic drug resistance of the isolates was observed towards erythromycin (100 %), gentamycin, azithromycin and tetracycline (92.3 %), ampicillin and oxytetracyclin (84.6 %), amikacin and srteptomycin (76.9 %), methicillin (69.2 %), cephradine, cefaclor and cefazolin (53.8 %) and vancomycin (15.3 %). Eighteen most commonly reported genes responsible for conferring resistance towards these drugs were targeted by PCR: among these tetM gene was found most prevalent (46.1 %) followed by tetK (30.7 %), aac(6')/aph(2”) (30.7 %), aacA-aphD (23 %), ermA (23 %), blaZ (23 %), mecA (23 %) blaTEM-1 (23 %), MeccA (23 %) and mecA (15.3 %). No gene fragment for vancomycin resistance was detected. The salient finding was that all S. epidermidis isolates were multiple drugs resistant as they showed resistance against at least three structurally different antimicrobial agents. It is concluded that in addition to the mostly used antimicrobial agent vancomycin, the cephalosporins including cephradine, cefaclor and cefazolin are also the drugs of choice against UTIs caused by S. epidermidis. PMID:26648821

  3. Detection and Measurement of Staphylococcal Enterotoxin-Like K (SEl-K) Secretion by Staphylococcus aureus Clinical Isolates

    PubMed Central

    Aguilar, Jorge L.; Varshney, Avanish K.; Wang, Xiaobo; Stanford, Lindsay; Scharff, Matthew

    2014-01-01

    Staphylococcal enterotoxin-like K (SEl-K) is a potent mitogen that elicits T-cell proliferation and cytokine production at very low concentrations. However, unlike the classical enterotoxins SEB and toxic shock syndrome toxin 1 (TSST-1), the gene for SEl-K is commonly present in more than half of all Staphylococcus aureus clinical isolates and is present in almost all USA300 community-acquired methicillin-resistant S. aureus (CA-MRSA) isolates. Sequencing of the sel-k gene in over 20 clinical isolates and comparative analysis with all 14 published sel-k sequences indicate that there are at least 6 variants of the sel-k gene, including one that is conserved among all examined USA300 strains. Additionally, we have developed a highly sensitive enzyme-linked immunosorbent assay (ELISA) that specifically detects and measures SEl-K protein in culture supernatants and biological fluids. Quantification of in vitro SEl-K secretion by various S. aureus isolates using this novel capture ELISA revealed detectable amounts of SEl-K secretion by all isolates, with the highest secretion levels being exhibited by MRSA strains that coexpress SEB. In vivo secretion was measured in a murine thigh abscess model, where similar levels of SEl-K accumulation were noted regardless of whether the infecting strain exhibited high or low secretion of SEl-K in vitro. We conclude that SEl-K is commonly expressed in the setting of staphylococcal infection, in significant amounts. SEl-K should be further explored as a target for passive immunotherapy against complicated S. aureus infection. PMID:24808237

  4. Molecular detection of antimicrobial resistance in local isolates of Staphylococcus epidermidis from urinary tract infections in Faisalabad region of Pakistan.

    PubMed

    Farid, Anam; Naz, Iram; Ashraf, Asma; Ali, Aamir; Rehman, Asad-Ur; Sarwar, Yasra; Haque, Abdul

    2015-01-01

    Staphylococci are one of the foremost causes of urinary tract infections (UTIs) in humans. The emergence of multiple drug resistance (MDR) among Staphylococci poses serious challenges in antimicrobial therapy for UTIs. Most work has been done on S. aureus while coagulase negative Staphylococci (mainly S. epidermidis) are often neglected. This study was conducted to establish a baseline profile of drug resistance in local S. epidermidis isolates from UTIs. Eighty urine samples were collected from suspected UTIs cases and screened for S. epidermidis. Twenty isolates were suspected as S. epidermidis based on colony morphology and Gram staining. Molecular detection by polymerase chain reaction (PCR) confirmed 13 isolates as S. epidermidis. Using disc diffusion method, phenotypic drug resistance of the isolates was observed towards erythromycin (100 %), gentamycin, azithromycin and tetracycline (92.3 %), ampicillin and oxytetracyclin (84.6 %), amikacin and srteptomycin (76.9 %), methicillin (69.2 %), cephradine, cefaclor and cefazolin (53.8 %) and vancomycin (15.3 %). Eighteen most commonly reported genes responsible for conferring resistance towards these drugs were targeted by PCR: among these tetM gene was found most prevalent (46.1 %) followed by tetK (30.7 %), aac(6')/aph(2") (30.7 %), aacA-aphD (23 %), ermA (23 %), blaZ (23 %), mecA (23 %) blaTEM-1 (23 %), MeccA (23 %) and mecA (15.3 %). No gene fragment for vancomycin resistance was detected. The salient finding was that all S. epidermidis isolates were multiple drugs resistant as they showed resistance against at least three structurally different antimicrobial agents. It is concluded that in addition to the mostly used antimicrobial agent vancomycin, the cephalosporins including cephradine, cefaclor and cefazolin are also the drugs of choice against UTIs caused by S. epidermidis.

  5. Molecular detection of antimicrobial resistance in local isolates of Staphylococcus epidermidis from urinary tract infections in Faisalabad region of Pakistan.

    PubMed

    Farid, Anam; Naz, Iram; Ashraf, Asma; Ali, Aamir; Rehman, Asad-Ur; Sarwar, Yasra; Haque, Abdul

    2015-01-01

    Staphylococci are one of the foremost causes of urinary tract infections (UTIs) in humans. The emergence of multiple drug resistance (MDR) among Staphylococci poses serious challenges in antimicrobial therapy for UTIs. Most work has been done on S. aureus while coagulase negative Staphylococci (mainly S. epidermidis) are often neglected. This study was conducted to establish a baseline profile of drug resistance in local S. epidermidis isolates from UTIs. Eighty urine samples were collected from suspected UTIs cases and screened for S. epidermidis. Twenty isolates were suspected as S. epidermidis based on colony morphology and Gram staining. Molecular detection by polymerase chain reaction (PCR) confirmed 13 isolates as S. epidermidis. Using disc diffusion method, phenotypic drug resistance of the isolates was observed towards erythromycin (100 %), gentamycin, azithromycin and tetracycline (92.3 %), ampicillin and oxytetracyclin (84.6 %), amikacin and srteptomycin (76.9 %), methicillin (69.2 %), cephradine, cefaclor and cefazolin (53.8 %) and vancomycin (15.3 %). Eighteen most commonly reported genes responsible for conferring resistance towards these drugs were targeted by PCR: among these tetM gene was found most prevalent (46.1 %) followed by tetK (30.7 %), aac(6')/aph(2") (30.7 %), aacA-aphD (23 %), ermA (23 %), blaZ (23 %), mecA (23 %) blaTEM-1 (23 %), MeccA (23 %) and mecA (15.3 %). No gene fragment for vancomycin resistance was detected. The salient finding was that all S. epidermidis isolates were multiple drugs resistant as they showed resistance against at least three structurally different antimicrobial agents. It is concluded that in addition to the mostly used antimicrobial agent vancomycin, the cephalosporins including cephradine, cefaclor and cefazolin are also the drugs of choice against UTIs caused by S. epidermidis. PMID:26648821

  6. Advanced solid-state NMR characterization of marine dissolved organic matter isolated using the coupled reverse osmosis/electrodialysis method.

    PubMed

    Mao, Jingdong; Kong, Xueqian; Schmidt-Rohr, Klaus; Pignatello, Joseph J; Perdue, E Michael

    2012-06-01

    Advanced (13)C solid-state techniques were employed to investigate the major structural characteristics of two surface-seawater dissolved organic matter (DOM) samples isolated using the novel coupled reverse osmosis/electrodialysis method. The NMR techniques included quantitative (13)C direct polarization/magic angle spinning (DP/MAS) and DP/MAS with recoupled dipolar dephasing, (13)C cross-polarization/total sideband suppression (CP/TOSS), (13)C chemical shift anisotropy filter, CH, CH(2), and CH(n) selection, two-dimensional (1)H-(13)C heteronuclear correlation NMR (2D HETCOR), 2D HETCOR combined with dipolar dephasing, and (15)N cross-polarization/magic angle spinning (CP/MAS). The two samples (Coastal and Marine DOM) were collected at the mouth of the Ogeechee River and in the Gulf Stream, respectively. The NMR results indicated that they were structurally distinct. Coastal DOM contained significantly more aromatic and carbonyl carbons whereas Marine DOM was markedly enriched in alkoxy carbon (e.g., carbohydrate-like moieties). Both samples contained significant amide N, but Coastal DOM had nitrogen bonded to aromatic carbons. Our dipolar-dephased spectra indicated that a large fraction of alkoxy carbons were not protonated. For Coastal DOM, our NMR results were consistent with the presence of the major structural units of (1) carbohydrate-like moieties, (2) lignin residues, (3) peptides or amino sugars, and (4) COO-bonded alkyls. For Marine DOM, they were (1) carbohydrate-like moieties, (2) peptides or amino sugars, and (3) COO-bonded alkyls. In addition, both samples contained significant amounts of nonpolar alkyl groups. The potential sources of the major structural units of DOM were discussed in detail. Nonprotonated O-alkyl carbon content was proposed as a possible index of humification. PMID:22553962

  7. Exprimental Results of the First Two Stages of an Advanced Transonic Core Compressor Under Isolated and Multi-Stage Conditions.

    NASA Technical Reports Server (NTRS)

    Prahst, Patricia S.; Kulkarni, Sameer; Sohn, Ki H.

    2015-01-01

    NASA's Environmentally Responsible Aviation (ERA) Program calls for investigation of the technology barriers associated with improved fuel efficiency for large gas turbine engines. Under ERA, the highly loaded core compressor technology program attempts to realize the fuel burn reduction goal by increasing overall pressure ratio of the compressor to increase thermal efficiency of the engine. Study engines with overall pressure ratio of 60 to 70 are now being investigated. This means that the high pressure compressor would have to almost double in pressure ratio while keeping a high level of efficiency. NASA and GE teamed to address this challenge by testing the first two stages of an advanced GE compressor designed to meet the requirements of a very high pressure ratio core compressor. Previous test experience of a compressor which included these front two stages indicated a performance deficit relative to design intent. Therefore, the current rig was designed to run in 1-stage and 2-stage configurations in two separate tests to assess whether the bow shock of the second rotor interacting with the upstream stage contributed to the unpredicted performance deficit, or if the culprit was due to interaction of rotor 1 and stator 1. Thus, the goal was to fully understand the stage 1 performance under isolated and multi-stage conditions, and additionally to provide a detailed aerodynamic data set for CFD validation. Full use was made of steady and unsteady measurement methods to understand fluid dynamics loss source mechanisms due to rotor shock interaction and endwall losses. This paper will present the description of the compressor test article and its measured performance and operability, for both the single stage and two stage configurations. We focus the paper on measurements at 97% corrected speed with design intent vane setting angles.

  8. [Detection of the first QnrS gene positivity in aquatic Aeromonas spp. isolates in Turkey].

    PubMed

    Onuk, Ertan Emek; Tanrıverdi Çaycı, Yeliz; Çoban, Ahmet Yılmaz; Çiftci, Alper; Balta, Fikri; Didinen, Behire Işıl; Pekmezci, Gökmen Zafer; Altun, Soner; Söğüt Ünlü, Mehtap; Deveci, Aydın

    2015-01-01

    Aeromonas spp. are oxidase positive, gram-negative, facultative anaerobic bacilli that are widely distributed in aquatic environments. A.hydrophila, A.sobria and A.bestiarum may cause severe infections in both human and cold-blooded animals. Environmental persistance of quinolones that are widely used in both human and veterinary medicine plays an important role in the selection of resistant mutants. Plasmid-mediated resistance is one of the main mechanisms involved in quinolone resistance, and qnr, qepA, aac(6')-Ib-cr, oqxAB genes are identified as resistance determinants. Determination of various types of qnr gene in different bacteria mainly in Enterobacteriaceae, suggests that they are widely distributed in nature. Recently, plasmid-mediated quinolone resistance was defined among Aeromonas species isolated from water. The aim of this study was to investigate the presence of qnr genes among aquatic Aeromonas spp. in Turkey. A total of 45 Aeromonas strains isolated from water and fishes collected from three different geographical regions (Aegean, Mediterranean and Blacksea) in Turkey, were included in the study. The isolates were identified at species level by the use of 16S rDNA-RFLP (Restriction fragment length polymorphism) analysis and multiplex polymerase chain reaction (M-PCR). Among the isolates, 20 were identified as A.sobria, 10 as A.hydrophila, nine as A.salmonicida, four as A.bestiarum and two as A.veronii. The plasmid-mediated quinolone resistance determinants, qnrA, qnrB, qnrC and qnrS genes, were investigated by M-PCR, and sequence analysis was performed for nine qnr-positive isolates. According to the sequence analysis of the genes, qnr genes were characterized in six A.sobria, in two A.bestiarum and in one A.hydrophila isolate (9/45; 20%). When the sequence was compared with GenBank database, this gene was found as qnrS2. All qnrS-positive Aeromonas spp. isolates were ciprofloxacin-susceptible, while five of them were resistant to nalidixic acid

  9. An analytical approach for detecting isolated periodic solution branches in weakly nonlinear structures

    NASA Astrophysics Data System (ADS)

    Hill, T. L.; Neild, S. A.; Cammarano, A.

    2016-09-01

    This paper considers isolated responses in nonlinear systems; both in terms of isolas in the forced responses, and isolated backbone curves (i.e. the unforced, undamped responses). As isolated responses are disconnected from other response branches, reliably predicting their existence poses a significant challenge. Firstly, it is shown that breaking the symmetry of a two-mass nonlinear oscillator can lead to the breaking of a bifurcation on the backbone curves, generating an isolated backbone. It is then shown how an energy-based, analytical method may be used to compute the points at which the forced responses cross the backbone curves at resonance, and how this may be used as a tool for finding isolas in the forced responses. This is firstly demonstrated for a symmetric system, where an isola envelops the secondary backbone curves, which emerge from a bifurcation. Next, an asymmetric configuration of the system is considered and it is shown how isolas may envelop a primary backbone curve, i.e. one that is connected directly to the zero-amplitude solution, as well as the isolated backbone curve. This is achieved by using the energy-based method to determine the relationship between the external forcing amplitude and the positions of the crossing points of the forced response. Along with predicting the existence of the isolas, this technique also reveals the nature of the responses, thus simplifying the process of finding isolas using numerical continuation.

  10. Detection and isolation of Toxoplasma gondii from fresh semen of naturally infected dogs in Southern Brazil.

    PubMed

    Koch, M O; Weiss, R R; Cruz, A A; Soccol, V T; Gonçalves, K A; Bertol, Maf; Beltrame, O C; Dittrich, R L

    2016-08-01

    The aim of this study was to isolate Toxoplasma gondii and determine the viability of the parasite in fresh semen samples of clinically healthy adult dogs naturally infected. Eleven seropositive dogs with T. gondii IgG antibodies from southern Brazil were selected to confirm the presence and viability of T. gondii in fresh semen samples using in vitro isolation in Vero cell culture, polymerase chain reaction (PCR) and sequencing analysis. The presence of viable T. gondii was confirmed by in vitro isolation and PCR in five semen samples. The ITS1 region of the isolated protozoa (TG S4) was amplified and sequenced. The nucleotide sequence obtained was 99% compatible with the T. gondii DNA sequences stored in the GenBank. It has been shown that T. gondii tachyzoites may be isolated in vitro from fresh semen samples of clinically healthy dogs seropositive for T. gondii.

  11. Detection and isolation of Toxoplasma gondii from fresh semen of naturally infected dogs in Southern Brazil.

    PubMed

    Koch, M O; Weiss, R R; Cruz, A A; Soccol, V T; Gonçalves, K A; Bertol, Maf; Beltrame, O C; Dittrich, R L

    2016-08-01

    The aim of this study was to isolate Toxoplasma gondii and determine the viability of the parasite in fresh semen samples of clinically healthy adult dogs naturally infected. Eleven seropositive dogs with T. gondii IgG antibodies from southern Brazil were selected to confirm the presence and viability of T. gondii in fresh semen samples using in vitro isolation in Vero cell culture, polymerase chain reaction (PCR) and sequencing analysis. The presence of viable T. gondii was confirmed by in vitro isolation and PCR in five semen samples. The ITS1 region of the isolated protozoa (TG S4) was amplified and sequenced. The nucleotide sequence obtained was 99% compatible with the T. gondii DNA sequences stored in the GenBank. It has been shown that T. gondii tachyzoites may be isolated in vitro from fresh semen samples of clinically healthy dogs seropositive for T. gondii. PMID:27287987

  12. Comparative study of fluorogenic and chromogenic media for specific detection of environmental isolates of thermotolerant Escherichia coli.

    PubMed

    Ramteke, Pramod W; Tewari, Suman

    2002-10-01

    In a field study 78 water samples were analysed employing Fluorocult Brilla Broth (BB) and its performance was compared with standard MPN procedure. Out of 78 water samples analysed 56 (71.7%) samples yielded positive reactions in BB whereas, 50 (64.1%) samples were positive by standard fecal coliform test. A comparative study of fluorogenic and chromogenic media containing substrate beta-D glucuronide for specific detection of environmental isolates of 313 thermotolerant E. coli has been undertaken. Five fluorogenic media were used: Fluorocult MacConkey agar (MCA), Fluorocult ECD agar (ECD), Fluorocult VRB agar (VRB), Fluorocult E. coli 0157:H7 agar (ECH7) and Fluorocult Brilla Broth (BB) and Chromogenic Chromocult agar (CCA). BB and CCA were found to be highly specific and sensitive media to detect E. coli as all E. coli yielded positive reaction on them. On ECH7 and ECD agar 67.5 and 64.9 of E. coli isolates gave positive reaction, respectively. Low sensitivity was observed in case of MCA and VRB agar in detecting E. coli. The performance of BB appears to be better when compared with standard MPN procedure employing MacConkey broth/Brilliant green bile broth in detecting E. coli in drinking water.

  13. Meta-Analysis of the Effect of Bowel Preparation on Adenoma Detection: Early Adenomas Affected Stronger than Advanced Adenomas

    PubMed Central

    Prakash, Meher; Manser, Christine N.; Heinrich, Henriette; Misselwitz, Benjamin

    2016-01-01

    Background and Aims Low-quality bowel preparation reduces efficacy of colonoscopy. We aimed to summarize effects of bowel preparation on detection of adenomas, advanced adenomas and colorectal cancer. Methods A systematic literature search was performed regarding detection of colonic lesions after normal and low-quality bowel preparation. Reported bowel preparation quality was transformed to the Aronchick scale with its qualities “excellent”, “good”, “fair”, “poor”, and “insufficient” or “optimal” (good/excellent), “suboptimal” (fair/poor/insufficient), “adequate” (good/excellent/fair) and “inadequate” (poor/insufficient). We identified two types of studies: i) Comparative studies, directly comparing lesion detection according to bowel preparation quality, and ii) repeat colonoscopy studies, reporting results of a second colonoscopy after previous low-quality preparation. Results The detection of early adenomas was reduced with inadequate vs. adequate bowel preparation (Odds Ratio (OR) 0.53, CI: 0.46–0.62, p<0.001). The advanced adenomas were affected less in comparison (0.74, CI: 0.62–0.87, p<0.001). The large number of subjects considered in the present meta-analysis resulted in smaller confidence intervals compared to earlier studies. Classifying the bowel-preparation quality as suboptimal vs. optimal led to the same qualitative conclusion (OR: 0.81, CI: 0.74–0.89, p<0.001 for early adenomas, OR: 0.94, CI: 0.87–1.01, n.s. for advanced adenomas). Bowel preparation was equally important for right-sided/ flat/ serrated vs. other lesions in most observational studies but more relevant in some repeat colonoscopy studies; data regarding carcinoma detection were insufficient. Conclusion Inadequate bowel preparation affects detection of early colonic lesions stronger than advanced lesions. PMID:27257916

  14. Detection of the intercellular adhesion gene cluster (ica) and phase variation in Staphylococcus epidermidis blood culture strains and mucosal isolates.

    PubMed Central

    Ziebuhr, W; Heilmann, C; Götz, F; Meyer, P; Wilms, K; Straube, E; Hacker, J

    1997-01-01

    Staphylococcus epidermidis is a common cause of catheter-associated infections and septicemia in immunocompromised patients. To answer the question whether S. epidermidis skin isolates differ from isolates causing septicemic diseases, 51 strains obtained from blood cultures, 1 strain from shunt-associated meningitis, and 36 saprophytic isolates were characterized. The study demonstrates that most of the blood culture strains formed a multilayered biofilm on plastic material, whereas skin and mucosal isolates did not. Moreover, biofilm-producing strains were found to generate large bacterial autoaggregates in liquid culture. Autoaggregation and biofilm formation on polymer surfaces was associated with the presence of a DNA sequence encoding an intercellular adhesion gene cluster (ica) that mediates the production of a polysaccharide intercellular adhesin. The presence of the intercellular adhesion genes in blood culture isolates was also found to be correlated with the exhibition of black colonies on Congo red agar, whereas the adhesin-negative strains formed red colonies. Upon subcultivation on Congo red agar, the black colony forms of the blood culture strains exhibited red colony variants which were biofilm and autoaggregation negative and occurred at a frequency of 10(-5). The DNA analysis of these S. epidermidis variants by pulsed-field gel electrophoresis and Southern hybridization with an ica-specific gene probe revealed no detectable difference between the black and red colony types. Moreover, after repeated passage, the phenotype of the parent strain could be restored. Therefore, these colony forms were regarded as phase variants. This phenotypic change was observed exclusively in adhesin-positive clinical isolates and not in adhesin-negative saprophytic strains of S. epidermidis. PMID:9038293

  15. Detection of Leptomonas sp. parasites in clinical isolates of Kala-azar patients from India

    PubMed Central

    Srivastava, Pankaj; Prajapati, Vijay Kumar; Vanaerschot, Manu; Van der Auwera, Gert; Dujardin, Jean Claude; Sundar, Shyam

    2010-01-01

    We report here nine unusual cases of Kala-azar, of which parasites were isolated and found by 18S rRNA gene sequencing to be most similar to Leptomonas species. One of these isolates was used to inoculate Balb/c mice; organs were collected and directly submitted to a genus-specific rDNA-ITS1 PCR analysis: this revealed the presence of both Leptomonas sp. and Leishmania donovani. Therefore, we conclude that there was a mixed infection of Leptomonas sp. and L. donovani in this isolate. We consider that mixed infection may be present in the patients themselves, Leptomonas persisting in them because of the immuno-suppression associated with Kala-azar. PMID:20633704

  16. First X-Ray Detection of AN Isolated Blackhole Candidate MACHO-96-BLG-5

    NASA Astrophysics Data System (ADS)

    Kobayashi, Yoshihito

    2002-09-01

    All previously known stellar blackholes have been found as close binaries. The MACHO team recently reported two microlensing events with exceptionally long duration, lasting several hundred days, suggesting that the lensing objects are isolated black holes with ˜6 M_{⊙} each. We thus propose a 10 ksec observation of the MACHO-96-BLG-5 lens in X-ray wavelength. By using the superior spacial resolution of Chandra, we search the X-ray counterpart of the lens. By testing the hardness ratio, we can test whether MACHO-96-BLG-5 is undoubtly due to a microlensing by an isolated blackhole or not. This observation may thus reveal that a Chandra observation of the long duration MACHO events is aunique and powerful tool to address isolated blackhole searches.

  17. An integrated microfluidic chip for immunomagnetic detection and isolation of rare prostate cancer cells from blood.

    PubMed

    Esmaeilsabzali, Hadi; Beischlag, Timothy V; Cox, Michael E; Dechev, Nikolai; Parameswaran, Ash M; Park, Edward J

    2016-02-01

    The quantitative and qualitative analysis of circulating tumor cells (CTCs) has the potential to improve the clinical management of several cancers, including prostate cancer. As such, there is much interest in the isolation of CTCs from the peripheral blood of cancer patients. We report the design, fabrication, and proof-of-principle testing of an integrated permalloy-based microfluidic chip for immunomagnetic isolation of blood-borne prostate cancer cells using an antibody targeting prostate surface membrane antigen (PSMA). The preliminary results using spiked blood samples indicate that the proposed device is consistently capable of isolating prostate cancer cells with high sensitivity (up to 98 %) at clinically relevant low concentrations (down to 20 cells/mL) and an acceptable throughput (100 μL/min). PMID:26876965

  18. Rapid detection of isoniazid resistance in Mycobacterium tuberculosis isolates by use of real-time-PCR-based melting curve analysis.

    PubMed

    Hu, Siyu; Li, Guoli; Li, Hui; Liu, Xiaoli; Niu, Jianjun; Quan, Shengmao; Wang, Feng; Wen, Huixin; Xu, Ye; Li, Qingge

    2014-05-01

    The MeltPro TB/INH assay, recently approved by the Chinese Food and Drug Administration, is a closed-tube, dual-color, melting curve analysis-based, real-time PCR test specially designed to detect 30 isoniazid (INH) resistance mutations in katG position 315 (katG 315), the inhA promoter (positions -17 to -8), inhA position 94, and the ahpC promoter (positions -44 to -30 and -15 to 3) of Mycobacterium tuberculosis. Here we evaluated both the analytical performance and clinical performance of this assay. Analytical studies with corresponding panels demonstrated that the accuracy for detection of different mutation types (10 wild-type samples and 12 mutant type samples), the limit of detection (2×10(3) to 2×10(4) bacilli/ml), reproducibility (standard deviation [SD], <0.4°C), and the lowest heteroresistance level (40%) all met the parameters preset by the kit. The assay could be run on five types of real-time PCR machines, with the shortest running time (105 min) obtained with the LightCycler 480 II. Clinical studies enrolled 1,096 clinical isolates collected from three geographically different tuberculosis centers, including 437 INH-resistant isolates and 659 INH-susceptible isolates characterized by traditional drug susceptibility testing on Löwenstein-Jensen solid medium. The clinical sensitivity and specificity of the MeltPro TB/INH assay were 90.8% and 96.4%, respectively. DNA sequencing analysis showed that, except for the 5 mutants outside the detection range of the MeltPro assay, a concordance rate between the two methods of 99.1% (457/461) was obtained. Among the 26 mutation types detected, katG S315T (AGC→ACC), inhA -15C→T, katG S315N (AGC→AAC), and ahpC promoter -10C→T accounted for more than 90%. Overall, the MeltPro TB/INH assay represents a reliable and rapid tool for the detection of INH resistance in clinical isolates.

  19. Detection of Class I Integrons in Staphyloacoccus aurous Isolated From Clinical Samples

    PubMed Central

    Yahaghi, Emad; Imani Fooladi, Abbas Ali; Amin, Mohsen; Mirnejad, Reza; Nezamzade, Reza; Amani, Jafar

    2014-01-01

    Background: Staphylococcus aurous is a major pathogen, causing variety of diseases and death in Iran and in the world. Despite the use of a spectrum of new antibiotics, this organism has caused severe infections in burns as well as in different parts of the body, due to acquired drug resistance. Widespread inappropriate use of antibiotics in treating bacterial infections has led to the selection and circulation of resistant strains and the growing risk of transferring resistant genes to sensitive bacteria. One of the causes of antibiotic resistance in S. aurous strains is the gain of resistance genes including integrase and qac/sul1. Objectives: The purpose of this study was to investigate the presence of class 1 integron in S. aurous strains isolated from clinical samples for the first time in Iran. Materials and Methods: This descriptive study was performed on 200 strains of S. aurous isolated from patients admitted to Baqiyatallah Hospital in Tehran in 2013. These strains were confirmed using biochemical and serological tests and the presence of class 1 integron was determined by polymerase chain reaction (PCR). Results: Among the 200 samples, 1% of the strains (two isolates) contained the class 1 integron gene. The results of this study showed that the highest frequency of the obtained samples belonged to males and the isolates occurred mostly in individuals aged 51-60 years old. The highest number of strains was found in wound samples. The strains were most frequently isolated from the emergency ward and the intensive care unit (ICU). Conclusions: Findings of this study showed that integron can have a limited frequency in S. aurous isolated from clinical sample in Tehran. PMID:25763211

  20. Rifoligotyping assay: an alternative method for rapid detection of rifampicin resistance in Mycobacterium tuberculosis isolates from Morocco

    PubMed Central

    Chaoui, Imane; Atalhi, Naima; Sabouni, Radia; Akrim, Mohammed; Abid, Mohammed; Amzazi, Saaid; ElMzibri, Mohammed

    2014-01-01

    One of the greatest threats to global tuberculosis (TB) control is the growing prevalence of drug resistant strains. In the past decades, considerable efforts have been made upon the development of new molecular technologies and methodologies for detection of drug resistance in Mycobacterium tuberculosis (MTB). A sensitive, specific reverse line blot assay, called rifoligotyping (RIFO), for the detection of genotypic resistance to rifampicin (RIF), was designed and evaluated. RIFO includes oligonucleotide probes specific for wild-type and mutant sequences, allowing specific and sensitive detection of both genotypes in a single assay. The RIFO was applied on 500 MTB isolates from Morocco. The results of the RIFO showed a good sensitivity (90.9%) and high specificity (100%); the positive and negative predictive values were 100% and 96.1%, respectively. This rapid, simple, economical assay provides a practical alternative for RIF genotyping, especially in low-income countries, to improve TB control and management. PMID:26740783

  1. Landslide detection and long-term monitoring in urban area by means of advanced interferometric techniques

    NASA Astrophysics Data System (ADS)

    Cigna, Francesca; Del Ventisette, Chiara; Liguori, Vincenzo; Casagli, Nicola

    2010-05-01

    This work aims at illustrating the potential of advanced interferometric techniques for detection and long-term monitoring of landslide ground deformations at local scale. Space-born InSAR (Synthetic Aperture Radar Interferometry) has been successfully exploited in recent years to measure ground deformations associated to processes with slow kinematics, such as landslides, tectonic motions, subsidence or volcanic activity, thanks to both the standard single-interferogram approach (centimeter accuracy) and advanced time-series analyses of long temporal radar satellite data stacks (millimeter accuracy), such as Persistent Scatterers Interferometry (PSI) techniques. In order to get a complete overview and an in-depth knowledge of an investigated landslide, InSAR satellite measures can support conventional in situ data. This methodology allows studying the spatial pattern and the temporal evolution of ground deformations, improving the spatial coverage and overcoming issues related to installation of ground-based instrumentation and data acquisition in unstable areas. Here we describe the application of the above-mentioned methodology on the test area of Agrigento, Sicily (Italy), affected by hydrogeological risk. The town is located in Southern Sicily, at edge of the Apennine-Maghrebian thrust belt, on the Plio-Pleistocene and Miocene sediments of the Gela Nappe. Ground instabilities affect the urban area and involve the infrastructures of its NW side, such as the Cathedral, the Seminary and many private buildings. An integration between InSAR analyses and conventional field investigations (e.g. structural damages and fractures surveys) was therefore carried out, to support Regional Civil Protection authorities for emergency management and risk mitigation. The results of InSAR analysis highlighted a general stability of the whole urban area between 1992 and 2007. However, very high deformation rates (up to 10-12 mm/y) were identified in 1992-2000 in the W slope of the

  2. Probabilistic approach to cloud and snow detection on Advanced Very High Resolution Radiometer (AVHRR) imagery

    NASA Astrophysics Data System (ADS)

    Musial, J. P.; Hüsler, F.; Sütterlin, M.; Neuhaus, C.; Wunderle, S.

    2014-03-01

    Derivation of probability estimates complementary to geophysical data sets has gained special attention over the last years. Information about a confidence level of provided physical quantities is required to construct an error budget of higher-level products and to correctly interpret final results of a particular analysis. Regarding the generation of products based on satellite data a common input consists of a cloud mask which allows discrimination between surface and cloud signals. Further the surface information is divided between snow and snow-free components. At any step of this discrimination process a misclassification in a cloud/snow mask propagates to higher-level products and may alter their usability. Within this scope a novel probabilistic cloud mask (PCM) algorithm suited for the 1 km × 1 km Advanced Very High Resolution Radiometer (AVHRR) data is proposed which provides three types of probability estimates between: cloudy/clear-sky, cloudy/snow and clear-sky/snow conditions. As opposed to the majority of available techniques which are usually based on the decision-tree approach in the PCM algorithm all spectral, angular and ancillary information is used in a single step to retrieve probability estimates from the precomputed look-up tables (LUTs). Moreover, the issue of derivation of a single threshold value for a spectral test was overcome by the concept of multidimensional information space which is divided into small bins by an extensive set of intervals. The discrimination between snow and ice clouds and detection of broken, thin clouds was enhanced by means of the invariant coordinate system (ICS) transformation. The study area covers a wide range of environmental conditions spanning from Iceland through central Europe to northern parts of Africa which exhibit diverse difficulties for cloud/snow masking algorithms. The retrieved PCM cloud classification was compared to the Polar Platform System (PPS) version 2012 and Moderate Resolution Imaging

  3. Method Comparison for Enhanced Recovery, Isolation and Qualitative Detection of C. jejuni and C. coli from Wastewater Effluent Samples

    PubMed Central

    Ugarte-Ruiz, María; Florez-Cuadrado, Diego; Wassenaar, Trudy M.; Porrero, María Concepción; Domínguez, Lucas

    2015-01-01

    Seeking a sensitive protocol, culture-dependent methods were compared to detect thermophilic Campylobacter species in untreated urban effluents. We evaluated various combinations of selective media, with and without an enrichment steps, as well as an extra filtration step. Culture-independent real-time quantitative PCR was also included and all detected isolates underwent antimicrobial susceptibility testing. All tested water samples contained Campylobacter DNA, but only 64% were positive after culture. Although enrichment using Preston broth resulted in better recovery of potentially stressed Campylobacter than Bolton or Campyfood broth (CFB), there was no significant increase in efficiency compared to direct plating. The type of selective agar media used, on the other hand, had a significant effect, with CASA plates performing better than mCCDA or CFA ones. Inclusion of an enrichment step increased the ratio of C. coli vs. C. jejuni being isolated. Resistances against all antimicrobials tested were observed in C. coli, but fewer instances of resistance were found in C. jejuni isolates. Whether this difference was the result of selection during the enrichment step could not be determined. The presence of Campylobacter in urban effluents can be considered as a valuable proxy for Campylobacter populations present in urban environments. PMID:25739008

  4. Method comparison for enhanced recovery, isolation and qualitative detection of C. jejuni and C. coli from wastewater effluent samples.

    PubMed

    Ugarte-Ruiz, María; Florez-Cuadrado, Diego; Wassenaar, Trudy M; Porrero, María Concepción; Domínguez, Lucas

    2015-03-02

    Seeking a sensitive protocol, culture-dependent methods were compared to detect thermophilic Campylobacter species in untreated urban effluents. We evaluated various combinations of selective media, with and without an enrichment steps, as well as an extra filtration step. Culture-independent real-time quantitative PCR was also included and all detected isolates underwent antimicrobial susceptibility testing. All tested water samples contained Campylobacter DNA, but only 64% were positive after culture. Although enrichment using Preston broth resulted in better recovery of potentially stressed Campylobacter than Bolton or Campyfood broth (CFB), there was no significant increase in efficiency compared to direct plating. The type of selective agar media used, on the other hand, had a significant effect, with CASA plates performing better than mCCDA or CFA ones. Inclusion of an enrichment step increased the ratio of C. coli vs. C. jejuni being isolated. Resistances against all antimicrobials tested were observed in C. coli, but fewer instances of resistance were found in C. jejuni isolates. Whether this difference was the result of selection during the enrichment step could not be determined. The presence of Campylobacter in urban effluents can be considered as a valuable proxy for Campylobacter populations present in urban environments.

  5. Detection of advanced glycation end products (AGEs) on human skin by in vivo confocal Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Martin, A. A.; Pereira, L.; Ali, S. M.; Pizzol, C. D.; Tellez, C. A.; Favero, P. P.; Santos, L.; da Silva, V. V.; Praes, C. E. O.

    2016-03-01

    The aging process involves the reduction in the production of the major components of skin tissue. During intrinsic aging and photoaging processes, in dermis of human skin, fibroblasts become senescent and have decreased activity, which produce low levels of collagen. Moreover, there is accumulation of advanced glycation end products (AGEs). AGEs have incidence in the progression of age-related diseases, principally in diabetes mellitus and in Alzheimer's diseases. AGEs causes intracellular damage and/or apoptosis leading to an increase of the free radicals, generating a crosslink with skin proteins and oxidative stress. The aim of this study is to detect AGEs markers on human skin by in vivo Confocal Raman spectroscopy. Spectra were obtained by using a Rivers Diagnostic System, 785 nm laser excitation and a CCD detector from the skin surface down to 120 μm depth. We analyzed the confocal Raman spectra of the skin dermis of 30 women volunteers divided into 3 groups: 10 volunteers with diabetes mellitus type II, 65-80 years old (DEW); 10 young healthy women, 20-33 years old (HYW); and 10 elderly healthy women, 65-80 years old (HEW). Pentosidine and glucosepane were the principally identified AGEs in the hydroxyproline and proline Raman spectral region (1000-800 cm-1), in the 1.260-1.320 cm-1 region assignable to alpha-helical amide III modes, and in the Amide I region. Pentosidine and glucosepane calculated vibrational spectra were performed through Density Functional Theory using the B3LYP functional with 3-21G basis set. Difference between the Raman spectra of diabetic elderly women and healthy young women, and between healthy elderly women and healthy young women were also obtained with the purpose of identifying AGEs Raman bands markers. AGEs peaks and collagen changes have been identified and used to quantify the glycation process in human skin.

  6. Astrobiology Sample Analysis Program (ASAP) for Advanced Life Detection Instrumentation Development and Calibration

    NASA Technical Reports Server (NTRS)

    Glavin, Daniel; Brinkerhoff, Will; Dworkin, Jason; Eigenbrode, Jennifer; Franz, Heather; Mahaffy, Paul; Stern, Jen; Blake, Daid; Sandford, Scott; Fries, marc; Steele, Andrew; Amashukeli, Xenia; Fisher, Anita; Grunthaner, Frank; Aubrey, Andrew; Bada, Jeff; Chiesl, Tom; Stockton, Amanda; Mathies, Rich

    2008-01-01

    Scientific ground-truth measurements for near-term Mars missions, such as the 2009 Mars Science Laboratory (MSL) mission, are essential for validating current in situ flight instrumentation and for the development of advanced instrumentation technologies for life-detection missions over the next decade. The NASA Astrobiology Institute (NAI) has recently funded a consortium of researchers called the Astrobiology Sample Analysis Program (ASAP) to analyze an identical set of homogenized martian analog materials in a "round-robin" style using both state-of-the-art laboratory techniques as well as in-situ flight instrumentation including the SAM gas chromatograph mass spectrometer and CHEMIN X-ray diffraction/fluorescence instruments on MSL and the Urey and MOMA organic analyzer instruments under development for the 2013 ExoMars missions. The analog samples studied included an Atacama Desert soil from Chile, the Murchison meteorite, a gypsum sample from the 2007 AMASE Mars analog site, jarosite from Panoche Valley, CA, a hydrothermal sample from Rio Tinto, Spain, and a "blind" sample collected during the 2007 MSL slow-motion field test in New Mexico. Each sample was distributed to the team for analysis to: (1) determine the nature and inventory of organic compounds, (2) measure the bulk carbon and nitrogen isotopic composition, (3) investigate elemental abundances, mineralogy and matrix, and (4) search for biological activity. The experimental results obtained from the ASAP Mars analog research consortium will be used to build a framework for understanding the biogeochemistry of martian analogs, help calibrate current spaceflight instrumentation, and enhance the scientific return from upcoming missions.

  7. Evaluation of four colourimetric susceptibility tests for the rapid detection of multidrug-resistant Mycobacterium tuberculosis isolates.

    PubMed

    Coban, Ahmet Yilmaz; Akbal, Ahmet Ugur; Uzun, Meltem; Durupinar, Belma

    2015-08-01

    The purpose of this study is to evaluate four rapid colourimetric methods, including the resazurin microtitre assay (REMA), malachite green decolourisation assay (MGDA), microplate nitrate reductase assay (MNRA) and crystal violet decolourisation assay (CVDA), for the rapid detection of multidrug-resistant (MDR) tuberculosis. Fifty Mycobacterium tuberculosis isolates were used in this study. Eighteen isolates were MDR, two isolates were only resistant to isoniazid (INH) and the remaining isolates were susceptible to both INH and rifampicin (RIF). INH and RIF were tested in 0.25 µg/mL and 0.5 µg/mL, respectively. The agar proportion method was used as a reference method. MNRA and REMA were performed with some modifications. MGDA and CVDA were performed as defined in the literature. The agreements of the MNRA for INH and RIF were 96% and 94%, respectively, while the agreement of the other assays for INH and RIF were 98%. In this study, while the specificities of the REMA, MGDA and CVDA were 100%, the specificity of the MNRA was lower than the others (93.3% for INH and 90.9% for RIF). In addition, while the sensitivity of the MNRA was 100%, the sensitivities of the others were lower than that of the MNRA (from 94.1-95%). The results were reported on the seventh-10th day of the incubation. All methods are reliable, easy to perform, inexpensive and easy to evaluate and do not require special equipment.

  8. Evaluation of four colourimetric susceptibility tests for the rapid detection of multidrug-resistant Mycobacterium tuberculosis isolates.

    PubMed

    Coban, Ahmet Yilmaz; Akbal, Ahmet Ugur; Uzun, Meltem; Durupinar, Belma

    2015-08-01

    The purpose of this study is to evaluate four rapid colourimetric methods, including the resazurin microtitre assay (REMA), malachite green decolourisation assay (MGDA), microplate nitrate reductase assay (MNRA) and crystal violet decolourisation assay (CVDA), for the rapid detection of multidrug-resistant (MDR) tuberculosis. Fifty Mycobacterium tuberculosis isolates were used in this study. Eighteen isolates were MDR, two isolates were only resistant to isoniazid (INH) and the remaining isolates were susceptible to both INH and rifampicin (RIF). INH and RIF were tested in 0.25 µg/mL and 0.5 µg/mL, respectively. The agar proportion method was used as a reference method. MNRA and REMA were performed with some modifications. MGDA and CVDA were performed as defined in the literature. The agreements of the MNRA for INH and RIF were 96% and 94%, respectively, while the agreement of the other assays for INH and RIF were 98%. In this study, while the specificities of the REMA, MGDA and CVDA were 100%, the specificity of the MNRA was lower than the others (93.3% for INH and 90.9% for RIF). In addition, while the sensitivity of the MNRA was 100%, the sensitivities of the others were lower than that of the MNRA (from 94.1-95%). The results were reported on the seventh-10th day of the incubation. All methods are reliable, easy to perform, inexpensive and easy to evaluate and do not require special equipment. PMID:26222021

  9. Influence of enrichment and isolation media on the detection of Campylobacter spp. in naturally contaminated chicken samples.

    PubMed

    Repérant, E; Laisney, M J; Nagard, B; Quesne, S; Rouxel, S; Le Gall, F; Chemaly, M; Denis, M

    2016-09-01

    Investigating Campylobacter epidemiology requires adequate technique and media to ensure optimal culturing and accurate detection and isolation of Campylobacter strains. In the present study, we investigated the performances of three enrichment durations in Bolton broth (0, 24 and 48h) and compared four isolation media (mCCDA, Karmali, Butzler no. 2 and CampyFood agar (CFA)) for the detection of Campylobacter positive samples and the identification of Campylobacter species, from naturally contaminated broiler chicken samples (caeca, neck skin from carcasses, and skin from thighs). We compared our local results to those we obtained with samples from a European survey (caeca and neck skin) and a national survey (neck skin, thigh skin, and breast). Direct plating favored the detection of positive samples highly contaminated by Campylobacter (caeca and neck skin from carcasses) whatever the media. A longer enrichment reduced the rates of Campylobacter recovery except when using Butzler no. 2, more particularly for neck skin which background microflora was less important than in caeca. As a matter of fact, enrichment allowed a higher detection rate of positive samples with low Campylobacter contamination levels (breast, thigh skin), this detection being enhanced when using Butzler no. 2. When comparing the 3 other selective media, CFA was the 2nd most efficient media prior to mCCDA and Karmali. Interestingly, enrichment promoted the growth of Campylobacter coli but this promotion was least with Butzler no. 2 agar. Our study has confirmed the need to adapt the method to the types of samples for improving the detection of Campylobacter and that the method may affect the prevalence of the species.

  10. Identification and detection of the isolated sinus venosus from the Asian toad.

    PubMed

    Deng, Xin; Guan, Chao; Wang, Yang; Zhang, Bing; Li, Sen; Sun, Guiyuan; Hao, Liying; Li, Gensong

    2013-12-01

    The pacemaker activity of mammalian sinoatrial node (SAN) of the heart plays a fundamental role in the integration of vital functions. Studying factors such as drugs that influence pacemaker activity of SAN has its significance. In this study, we isolated sinus venosus, SAN from toads (Bufo gargarizans), and analysed its electronic signal, histological characteristics and the influence of acetylcholine (ACh) and ivabradine on its pacemaker activity using PowerLab® and Chart® 5.0 software. We found that when isolated sinus venosus was treated with ACh, its histological distribution was disorganized and inter-beat (RR) interval was also broadened. The high frequency normalized unit (HFnu) and Poincaré plot of heart rate variability (HRV) of the isolated sinus venosus was also altered upon ACh treatment in a time-dependent and dose-dependent manner. When treated with ivabradine, these parameters of HRV such as square root of the mean of the squared differences between adjacent NN intervals (RMSSD) and HFnu were in the upward tendency, but low frequency normalized unit and low frequency/high frequency were in the opposite tendency. Taken together, we have developed a new model for studying the influences of drugs on autorhythmicity using isolated sinus venosus of the toad. With this model, we showed that ACh and ivabradine may affect the pacemaker activity by stimulating muscarinic receptor or inhibiting If current, respectively.

  11. A high density FinFET one-time programmable cell with new intra-fin cell isolation for advanced system on chip applications

    NASA Astrophysics Data System (ADS)

    Chen, Yu-Zheng; Yuan, Jo En; Peng, Ping Chun; Hsiao, Woan Yun; King, Ya-Chin; Lin, Chrong Jung

    2016-04-01

    A fully CMOS compatible one-time programmable (OTP) cell with a novel intra-fin cell isolation (IFCI) structure on a FinFET CMOS process has been proposed. The IFCI OTP cell utilizes the field-enhanced dielectric breakdown at fin corners to perform a fast and low-voltage program operation. Moreover, an ultrasmall intra-fin cell-to-cell isolation is firstly introduced to markedly shrink the cell size by eliminating the area-consuming spacing of fin-to-fin isolation. The IFCI FinFET OTP with fast program speed, excellent read disturb immunity, and reliable data retention is a promising solution for logic nonvolatile memory (NVM) technology in advanced CMOS nodes.

  12. Analytic Confusion Matrix Bounds for Fault Detection and Isolation Using a Sum-of-Squared- Residuals Approach

    NASA Technical Reports Server (NTRS)

    Simon, Dan; Simon, Donald L.

    2009-01-01

    Given a system which can fail in 1 or n different ways, a fault detection and isolation (FDI) algorithm uses sensor data in order to determine which fault is the most likely to have occurred. The effectiveness of an FDI algorithm can be quantified by a confusion matrix, which i ndicates the probability that each fault is isolated given that each fault has occurred. Confusion matrices are often generated with simulation data, particularly for complex systems. In this paper we perform FDI using sums of squares of sensor residuals (SSRs). We assume that the sensor residuals are Gaussian, which gives the SSRs a chi-squared distribution. We then generate analytic lower and upper bounds on the confusion matrix elements. This allows for the generation of optimal sensor sets without numerical simulations. The confusion matrix bound s are verified with simulated aircraft engine data.

  13. Isolation and immunological detection of Mycoplasma ovipneumoniae in sheep with atypical pneumonia, and lack of a role for Mycoplasma arginini.

    PubMed

    Lin, Y-C; Miles, R J; Nicholas, R A J; Kelly, D P; Wood, A P

    2008-06-01

    Mycoplasma ovipneumoniae NCTC 10151(T) and four new isolates from UK sheep flocks were compared. Only glucose and pyruvate were used as energy sources by the five strains: glucose was the best energy source for the type strain, pyruvate supported better growth of the new strains. Whole cell protein patterns and antigenic profiles showed high similarity between all five strains. The new isolates fell into two groups in ELISA tests. Serum samples from 30 pneumonic sheep were assessed for M. ovipneumoniae infection and Mycoplasma arginini co-infection. Fourteen (out of 30) serum samples were positive for M. ovipneumoniae both by ELISA and immunoblotting. Twelve antigenic proteins of M. ovipneumoniae were detected in infected serum samples: the antigen patterns were unique, with between one and at least seven occurring in any one sample. All serum samples were designated as negative for M. arginini antibodies by both ELISA and immunoblotting.

  14. Identify-Isolate-Inform: A Tool for Initial Detection and Management of Measles Patients in the Emergency Department

    PubMed Central

    Koenig, Kristi L.; Alassaf, Wajdan; Burns, Michael J.

    2015-01-01

    Measles (rubeola) is a highly contagious airborne disease that was declared eliminated in the U.S. in the year 2000. Only sporadic U.S. cases and minor outbreaks occurred until the larger outbreak beginning in 2014 that has become a public health emergency. The “Identify-Isolate-Inform” tool will assist emergency physicians to be better prepared to detect and manage measles patients presenting to the emergency department. Measles typically presents with a prodrome of high fever, and cough/coryza/conjunctivitis, sometimes accompanied by the pathognomonic Koplik spots. Two to four days later, an erythematous maculopapular rash begins on the face and spreads down the body. Suspect patients must be immediately isolated with airborne precautions while awaiting laboratory confirmation of disease. Emergency physicians must rapidly inform the local public health department and hospital infection control personnel of suspected measles cases. PMID:25834659

  15. Ascochyta blight: isolation, characterization, and development of a rapid method to detect inhibitors of the chickpea fungal pathogen Ascochyta rabiei.

    PubMed

    Bahr, Luciana; Castelli, María Victoria; Barolo, Melisa Isabel; Ruiz Mostacero, Nathalie; Tosello, María Elena; López, Silvia Noelí

    2016-03-01

    Ascochyta blight is the major disease attacking chickpea (Cicer arietinum) around the world. Since its first time report of isolation in Argentina in 2012, the pathogen has caused severe economic losses and has acquired a great importance. We report here the isolation of Ascochyta rabiei from infected chickpea beans cultivated in Santa Fe, Argentina; its identification by morphological analysis and molecular biology techniques based on internal transcribed spacer (ITS) sequence alignment, its biochemical characterization regarding the capacity to produce proteinase and phospholipase enzymes, and its antifungal susceptibility to common used antifungal agents. In order to detect new inhibitors for A. rabiei from natural sources, a bioautographic method was developed. From the screening method developed, we found that extracts from cultures of Aspergillus parasiticus are active against A. rabiei. PMID:26895871

  16. An improved method of DNA isolation suitable for PCR-based detection of begomoviruses from jute and other mucilaginous plants.

    PubMed

    Ghosh, Raju; Paul, Sujay; Ghosh, Subrata Kumar; Roy, Anirban

    2009-07-01

    A relatively quick and inexpensive modified cetyl trimethylammonium bromide method for extraction of DNA from leaf materials containing large quantities of mucilage is described. The modification including use of more volume of extraction buffer and dissolving crude nucleic acid pellet in 1 M NaCl, reduced markedly the viscosity of the mucilage and thus in the final purification step yielded a larger quantity of mucilage-free DNA suitable for subsequent PCR-based detection of begomoviruses. The method was standardized with jute samples with yellow mosaic disease and validated with different other mucilaginous-hosts with low titre of begomoviruses. DNA isolated using this method showed consistency in yield and compatibility with PCR for detection of begomoviruses from different mucilaginous plant species. The method was compared for efficacy with other reported methods and it was found to be superior over the existing methods described for isolation of DNA from mucilaginous hosts. Thus the method described could be used on a wider scale for reliable and consistent detection of begomoviruses from mucilaginous hosts for characterization and variability study.

  17. A real-time engineering software system for failure detection and isolation of self-repairing flight control system

    NASA Astrophysics Data System (ADS)

    Deng, Juan; Ai, Jianliang; Gao, Min; Luo, Changhang

    2006-11-01

    This paper introduces a real-time Failure Detection and Isolation (FDI) software system of Self-Repairing Flight Control System (SRFCS) that is developed by Institute of Vehicle Design of Fudan University. An algorithm of adopting the method of parity space to get residual sequences and the theory of residual vector data fusion is applied to detecting and isolating the abrupt change failures of SRFCS, especially the actuators' failures, single control surface's failures and multiple failures. The system follows the theory of object-oriented software design by adopting the design idea of modularization and uses Dynamic Link Library (DLL) widely so that it is easy to replant new modules and extend its ability freely. The interface of this system is friendly and the operation on it is convenient. In this paper, the system is applied to the flight control system of some type of fighter of Chinese Air Force and the results show that this software system can detect single control surface's failures within 0.125 seconds (10 sampling periods) and actuators' failures within 0.0625 seconds (5 sampling periods) under strong noise circumstances. The test results based on the simulated data prove the validity of the theory, the robust and real time property of the developed software.

  18. An improved method of DNA isolation suitable for PCR-based detection of begomoviruses from jute and other mucilaginous plants.

    PubMed

    Ghosh, Raju; Paul, Sujay; Ghosh, Subrata Kumar; Roy, Anirban

    2009-07-01

    A relatively quick and inexpensive modified cetyl trimethylammonium bromide method for extraction of DNA from leaf materials containing large quantities of mucilage is described. The modification including use of more volume of extraction buffer and dissolving crude nucleic acid pellet in 1 M NaCl, reduced markedly the viscosity of the mucilage and thus in the final purification step yielded a larger quantity of mucilage-free DNA suitable for subsequent PCR-based detection of begomoviruses. The method was standardized with jute samples with yellow mosaic disease and validated with different other mucilaginous-hosts with low titre of begomoviruses. DNA isolated using this method showed consistency in yield and compatibility with PCR for detection of begomoviruses from different mucilaginous plant species. The method was compared for efficacy with other reported methods and it was found to be superior over the existing methods described for isolation of DNA from mucilaginous hosts. Thus the method described could be used on a wider scale for reliable and consistent detection of begomoviruses from mucilaginous hosts for characterization and variability study. PMID:19442842

  19. [Comparison of the modified Hodge test and the Carba NP test for detection of carbapenemases in Enterobacteriaceae isolates].

    PubMed

    Bayramoğlu, Gülçin; Uluçam, Gülşen; Gençoğlu Özgür, Çiğdem; Kılıç, Ali Osman; Aydın, Faruk

    2016-01-01

    A rapid, practical, and accurate identification of carbapenemase-producing Enterobacteriaceae isolates is crucial for the implementation of appropriate infection control measures and proper treatment of the infections. For this purpose, a large number of phenotypic test methods have been developed, although none has 100% sensitivity and specificity. Variations in sensitivity and specificity of these tests based on the type of beta-lactamase enzymes carried by that isolates might result in differences between regions and countries. The aim of this study was to compare the performances of widely used modified Hodge test (MHT) and Carbapenemase Nordmann-Poirel (Carba NP) test in the detection of carbapenemases in Enterobacteriaceae family members. A total of 65 Enterobacteriaceae isolates (43 bla(OXA-48), 10 bla(VIM), 9 bla(IMP), 1 bla(NDM-1), 1 bla(KPC-2) and 1 bla(OXA-48)+bla(VIM) carrying strains) that showed decreased sensitivity to at least one carbapenem (ertapenem, imipenem or meropenem), and carriage of carbapenemase gene confirmed by polymerase chain reaction (PCR), were included in the study. Seventy-eight isolates showing decreased susceptibility to carbapenems but lacking carbapenemase genes were used as controls. All isolates were identified by using conventional methods as well as automated BD Phoenix System (Becton Dickinson, USA). The antimicrobial susceptibility testing was performed using the same automated system, and was confirmed by disk diffusion method. Results were evaluated according to the CLSI criteria. MHT was performed in accordance with the CLSI guideline, and Carba NP test was carried out by a modified protocol. Instead of imipenem monohydrate, which was used in the original protocol, 6 mg/ml imipenem/cilastatin was used in the modified protocol. In the study, MHT identified 90.8% (59/65) of carbapenemase-producing isolates, while 93.9% (61/65) of the isolates were identified by Carba NP test. With MHT, four Klebsiella pneumoniae

  20. Detection of Oxacillin Resistance in Staphylococcus aureus Isolated from the Neonatal and Pediatric Units of a Brazilian Teaching Hospital

    PubMed Central

    Pereira, Valéria Cataneli; Martins, André; de Souza Rugolo, Lígia Maria Suppo; de Lourdes Ribeiro de Souza da Cunha, Maria

    2009-01-01

    Objective: To determine, by phenotypic and genotypic methods, oxacillin susceptibility in Staphylococcus aureus strains isolated from pediatric and neonatal intensive care unit patients seen at the University Hospital of the Botucatu School of Medicine. Methods: A total of 100 S. aureus strains isolated from the following materials were studied: 25 blood cultures, 21 secretions, 12 catheters, 3 cannulae and one chest drain from 62 patients in the neonatal unit, and 36 blood cultures, one pleural fluid sample and one peritoneal fluid sample from 38 patients in the pediatric unit. Resistance of the S. aureus isolates to oxacillin was evaluated by the disk diffusion method with oxacillin (1 μg) and cefoxitin (30 μg), agar screening test using Mueller-Hinton agar supplemented with 6 μg/ml oxacillin and 4% NaCl, and detection of the mecA gene by PCR. In addition, the isolates were tested for β-lactamase production using disks impregnated with Nitrocefin and hyperproduction of β-lactamase using amoxicillin (20 μg) and clavulanic acid (10 μg) disks. Results: Among the 100 S. aureus strains included in the study, 18.0% were resistant to oxacillin, with 16.1% MRSA being detected in the neonatal unit and 21.0% in the pediatric unit. The oxacillin (1 μg) and cefoxitin (30 μg) disk diffusion methods presented 94.4% and 100% sensitivity, respectively, and 98.8% specificity. The screening test showed 100% sensitivity and 98.8% specificity. All isolates produced β-lactamase and one of these strains was considered to be a hyperproducer. Conclusions: The 30 μg cefoxitin disk diffusion method presented the best result when compared to the 1 μg oxacillin disk. The sensitivity of the agar screening test was similar to that of the cefoxitin disk diffusion method and higher than that of the oxacillin disk diffusion method. We observed variations in the percentage of oxacillin-resistant isolates during the study period, with a decline over the last years which might be

  1. Detection of Multidrug Resistant (MDR) and Extremely Drug Resistant (XDR) P. Aeruginosa Isolated from Patients in Tehran, Iran

    PubMed Central

    Saderi, Horieh; Owlia, Parviz

    2015-01-01

    Background: This study was done to detect multidrug resistant (MDR) and extremely drug resistant (XDR) of Pseudomonas aeruginosa among strains isolated from patients in Tehran, Iran, due to importance of these phenotypes in treatment of human infections. Methods: Eighty eight P. aeruginosa were isolated from patients in Tehran, Iran, and identified by routine methods and PCR for oprL gene. Their antimicrobial susceptibility to 16 antimicrobial agents from 7 antimicrobial categories (aminoglycosides, carbapenems, cephalosporins, fluoroquinolones, penicillins/ß-lactamase inhibitors, monobactams, polymyxins) were determined by disk diffusion method, according to recommendation of Clinical and Laboratory Standards Institute. Characterization of P. aeruginosa isolates as MDR and XDR was done according to standardized international terminology presented by European Centre for Disease Prevention and Control as well as the Centers for Disease Control and Prevention in 2011. MDR was defined as acquired non-susceptibility to at least one agent in ≥3 antimicrobial categories and XDR was defined as non-susceptibility to at least one agent in ≥6 antimicrobial categories. Results: The rates of susceptibility to antimicrobials were as follows: gentamicin 27.3%, tobramycin 54.5%, amikacin 56.8%, netilmicin 36.4%, imipenem 55.7%, meropenem 55.7%, doripenem 60.2%, ceftazidime 63.6%, cefepime 56.8%, ciprofloxacin 59.1%, levofloxacin 60.2%, ticarcillin-clavulanic acid 37.5%, piperacillin-tazobactam 63.6%, aztreonam 43.2%, colistin 90.9%, polymyxin 95.5%. Altogether, 48 (54.5%) and 29 (33%) isolates were characterized as MDR and XDR, respectively. Discussion: The high frequency of antibiotic resistance in clinical isolates of P. aeruginosa in Iran makes epidemiological surveillance of susceptibility of this bacterium more essential for the best selection of empirical antibiotics. PMID:26351496

  2. Detoxification of Atrazine by Endophytic Streptomyces sp. Isolated from Sugarcane and Detection of Nontoxic Metabolite.

    PubMed

    Mesquini, Josiane A; Sawaya, Alexandra C H F; López, Begonã G C; Oliveira, Valéria M; Miyasaka, Natalia R S

    2015-12-01

    Atrazine is still one of the most used agricultural pesticides worldwide and it has been recognized as a major contaminant of surface and ground water. The aims of this research were to isolate an endophytic microorganism from leaves of sugarcane, evaluate its ability to degrade atrazine, and investigate the formation of metabolites. By sequencing of the 16S rRNA gene, the endophytic isolate atz2 was identified as Streptomyces sp. The reduction in atrazine concentration by Streptomyces sp. atz2 was 98 % and UHPLC-MS/MS analyses showed the appearance of an unknown metabolite observed as m/z 311. Ecotoxicity tests with an aquatic organism, Daphnia similis, confirmed that this metabolite was nontoxic. This mechanism of detoxification of atrazine is different from the ones of other free-living microorganisms that inhabit the soil or rhizosphere. The results show new aspects of atrazine detoxification, highlighting a new role of endophytic bacteria in plants. PMID:26467569

  3. Isolation of Escherichia coli to detect faecal contamination of infants and their mothers in West Bengal.

    PubMed

    Dutta, S; Mondal, S K; Saha, M R; Sengupta, P G; Gupta, D N; Ghosh, S; Sircar, B K

    1997-09-01

    The present study was undertaken to gain insight into the sources of faecal contamination of infants in rural Bengal. It was carried out in three villages near Calcutta, India, from June 1993 to August 1995 among 148 infants and their mothers. Escherichia coli was used as an indicator of faecal pollution. A total of 725 samples, including hand rinsings of children and mothers, feeding utensils and leftover food were examined. The total isolation rate of faecal E. coli was 30%. The isolation rates from hands of children and mothers were 17% and 40% respectively. The germs from 30% of utensils and 59% of leftover food and drinks were recovered further. The study highlights the precarious hygiene in rural Bengal. PMID:9473882

  4. Detoxification of Atrazine by Endophytic Streptomyces sp. Isolated from Sugarcane and Detection of Nontoxic Metabolite.

    PubMed

    Mesquini, Josiane A; Sawaya, Alexandra C H F; López, Begonã G C; Oliveira, Valéria M; Miyasaka, Natalia R S

    2015-12-01

    Atrazine is still one of the most used agricultural pesticides worldwide and it has been recognized as a major contaminant of surface and ground water. The aims of this research were to isolate an endophytic microorganism from leaves of sugarcane, evaluate its ability to degrade atrazine, and investigate the formation of metabolites. By sequencing of the 16S rRNA gene, the endophytic isolate atz2 was identified as Streptomyces sp. The reduction in atrazine concentration by Streptomyces sp. atz2 was 98 % and UHPLC-MS/MS analyses showed the appearance of an unknown metabolite observed as m/z 311. Ecotoxicity tests with an aquatic organism, Daphnia similis, confirmed that this metabolite was nontoxic. This mechanism of detoxification of atrazine is different from the ones of other free-living microorganisms that inhabit the soil or rhizosphere. The results show new aspects of atrazine detoxification, highlighting a new role of endophytic bacteria in plants.

  5. First detection of OKP-A β-lactamase in two Serratia marcescens isolates in China.

    PubMed

    Zou, Likou; Pan, Xin; Wu, Qi; Luo, Yan; Liu, Shuliang; Lin, Cheng; Li, Bei; Wang, Xuxi; Long, Mei; Guo, Fang

    2011-10-01

    Two strains of Enterobacteriaceae producing prodigiosin were isolated from meat in the Sichuan province of China in 2010. The strains were identified by Vitek system, 16S rDNA, rpoB, pfs and luxS genes. Minimum inhibitory concentrations were determined using the broth microdilution method. The two strains were screened for the presence of β-lactamase genes (blaTEM, blaSHV, blaOKP, and blaCTX-M genes). Based on PCR amplification and 16S rDNA sequencing the analysed strains were identified as Serratia marcescens. In addition, morphological and biochemical identification showed that the two stains were definitely S. marcesens. Antimicrobial susceptibility test showed that both strains were resistant to ampicillin and first-generation cephalosporins while being susceptible to cefotaxime, ceftiofur, ceftriaxone, imipenem and aztreonam. It was found that blaOKP had been identified first from the two S. marcescens strains, ch1 and ch2. The isolates were closely related as shown by pulsed-field gel electrophoresis (PFGE). The narrow-spectrum OKP-A β-lactamase gene blaOKP-A-13 was found to be chromosomally located in S. marcescens. The isolates produced a β-lactamase with a pI of approximately 8.2, which corresponds to the OKPA family. Findings indicate that OKP enzymes are not Klebsiella pneumoniae-specific chromosomal ?-lactamases, and the first isolation of S. marcescens producing OKP-A ?-lactamase suggests that the blaOKP gene may be disseminated between different species.

  6. Detection of infectious bursal disease virus isolates with unknown antigenic properties by reverse genetics.

    PubMed

    Icard, Alan H; Sellers, Holly S; Mundt, Egbert

    2008-12-01

    Infectious bursal disease virus (IBDV) serotype 1 is the causative agent of a highly contagious immunosuppressive disease of young chickens. In the past, a number of antigenic, as well as pathogenic, subtypes have been described. The determination of the antigenic makeup of circulating strains is of vital interest to the poultry industry because changes in the antigenicity of circulating field strains have an impact on the use of vaccines. To obtain a more comprehensive overview of the relationship between the nucleotide and amino acid sequence and the antigenic makeup of field isolates, a system based on reverse genetics of IBDV was established. Using this approach, a database for field isolates from three different states in the United States (Georgia, Alabama, and Louisiana), consisting of nucleotide sequence, amino acid sequence, and a reaction pattern based on a panel of monoclonal antibodies, was established. The obtained results showed that phylogenic analysis, which is based on the similarity of sequences, would lead to false conclusions regarding a possible antigenic makeup of the particular isolate. Sequences of field samples were divided into three groups: 1) those that grouped with variant strain E/Del sequences but were antigenically different, 2) those that did not group with sequences of E/Del but were similar in their antigenic makeup, and 3) those that did not group with E/Del sequences and were antigenically different. In addition, using the reverse-genetics approach, a number of field isolates showed no reactivity with any of the used monoclonal antibodies, indicating that an unknown, antigenic subtype of IBDV serotype 1 is circulating in the field. PMID:19166049

  7. Low-density lipoprotein mimics blood plasma-derived exosomes and microvesicles during isolation and detection.

    PubMed

    Sódar, Barbara W; Kittel, Ágnes; Pálóczi, Krisztina; Vukman, Krisztina V; Osteikoetxea, Xabier; Szabó-Taylor, Katalin; Németh, Andrea; Sperlágh, Beáta; Baranyai, Tamás; Giricz, Zoltán; Wiener, Zoltán; Turiák, Lilla; Drahos, László; Pállinger, Éva; Vékey, Károly; Ferdinandy, Péter; Falus, András; Buzás, Edit Irén

    2016-01-01

    Circulating extracellular vesicles have emerged as potential new biomarkers in a wide variety of diseases. Despite the increasing interest, their isolation and purification from body fluids remains challenging. Here we studied human pre-prandial and 4 hours postprandial platelet-free blood plasma samples as well as human platelet concentrates. Using flow cytometry, we found that the majority of circulating particles within the size range of extracellular vesicles lacked common vesicular markers. We identified most of these particles as lipoproteins (predominantly low-density lipoprotein, LDL) which mimicked the characteristics of extracellular vesicles and also co-purified with them. Based on biophysical properties of LDL this finding was highly unexpected. Current state-of-the-art extracellular vesicle isolation and purification methods did not result in lipoprotein-free vesicle preparations from blood plasma or from platelet concentrates. Furthermore, transmission electron microscopy showed an association of LDL with isolated vesicles upon in vitro mixing. This is the first study to show co-purification and in vitro association of LDL with extracellular vesicles and its interference with vesicle analysis. Our data point to the importance of careful study design and data interpretation in studies using blood-derived extracellular vesicles with special focus on potentially co-purified LDL. PMID:27087061

  8. Detection of Anthropogenic Particles in Fish Stomachs: An Isolation Method Adapted to Identification by Raman Spectroscopy.

    PubMed

    Collard, France; Gilbert, Bernard; Eppe, Gauthier; Parmentier, Eric; Das, Krishna

    2015-10-01

    Microplastic particles (MP) contaminate oceans and affect marine organisms in several ways. Ingestion combined with food intake is generally reported. However, data interpretation often is circumvented by the difficulty to separate MP from bulk samples. Visual examination often is used as one or the only step to sort these particles. However, color, size, and shape are insufficient and often unreliable criteria. We present an extraction method based on hypochlorite digestion and isolation of MP from the membrane by sonication. The protocol is especially well adapted to a subsequent analysis by Raman spectroscopy. The method avoids fluorescence problems, allowing better identification of anthropogenic particles (AP) from stomach contents of fish by Raman spectroscopy. It was developed with commercial samples of microplastics and cotton along with stomach contents from three different Clupeiformes fishes: Clupea harengus, Sardina pilchardus, and Engraulis encrasicolus. The optimized digestion and isolation protocol showed no visible impact on microplastics and cotton particles while the Raman spectroscopic spectrum allowed the precise identification of microplastics and textile fibers. Thirty-five particles were isolated from nine fish stomach contents. Raman analysis has confirmed 11 microplastics and 13 fibers mainly made of cellulose or lignin. Some particles were not completely identified but contained artificial dyes. The novel approach developed in this manuscript should help to assess the presence, quantity, and composition of AP in planktivorous fish stomachs. PMID:26289815

  9. Low-density lipoprotein mimics blood plasma-derived exosomes and microvesicles during isolation and detection

    PubMed Central

    Sódar, Barbara W; Kittel, Ágnes; Pálóczi, Krisztina; Vukman, Krisztina V; Osteikoetxea, Xabier; Szabó-Taylor, Katalin; Németh, Andrea; Sperlágh, Beáta; Baranyai, Tamás; Giricz, Zoltán; Wiener, Zoltán; Turiák, Lilla; Drahos, László; Pállinger, Éva; Vékey, Károly; Ferdinandy, Péter; Falus, András; Buzás, Edit Irén

    2016-01-01

    Circulating extracellular vesicles have emerged as potential new biomarkers in a wide variety of diseases. Despite the increasing interest, their isolation and purification from body fluids remains challenging. Here we studied human pre-prandial and 4 hours postprandial platelet-free blood plasma samples as well as human platelet concentrates. Using flow cytometry, we found that the majority of circulating particles within the size range of extracellular vesicles lacked common vesicular markers. We identified most of these particles as lipoproteins (predominantly low-density lipoprotein, LDL) which mimicked the characteristics of extracellular vesicles and also co-purified with them. Based on biophysical properties of LDL this finding was highly unexpected. Current state-of-the-art extracellular vesicle isolation and purification methods did not result in lipoprotein-free vesicle preparations from blood plasma or from platelet concentrates. Furthermore, transmission electron microscopy showed an association of LDL with isolated vesicles upon in vitro mixing. This is the first study to show co-purification and in vitro association of LDL with extracellular vesicles and its interference with vesicle analysis. Our data point to the importance of careful study design and data interpretation in studies using blood-derived extracellular vesicles with special focus on potentially co-purified LDL. PMID:27087061

  10. Low-density lipoprotein mimics blood plasma-derived exosomes and microvesicles during isolation and detection.

    PubMed

    Sódar, Barbara W; Kittel, Ágnes; Pálóczi, Krisztina; Vukman, Krisztina V; Osteikoetxea, Xabier; Szabó-Taylor, Katalin; Németh, Andrea; Sperlágh, Beáta; Baranyai, Tamás; Giricz, Zoltán; Wiener, Zoltán; Turiák, Lilla; Drahos, László; Pállinger, Éva; Vékey, Károly; Ferdinandy, Péter; Falus, András; Buzás, Edit Irén

    2016-04-18

    Circulating extracellular vesicles have emerged as potential new biomarkers in a wide variety of diseases. Despite the increasing interest, their isolation and purification from body fluids remains challenging. Here we studied human pre-prandial and 4 hours postprandial platelet-free blood plasma samples as well as human platelet concentrates. Using flow cytometry, we found that the majority of circulating particles within the size range of extracellular vesicles lacked common vesicular markers. We identified most of these particles as lipoproteins (predominantly low-density lipoprotein, LDL) which mimicked the characteristics of extracellular vesicles and also co-purified with them. Based on biophysical properties of LDL this finding was highly unexpected. Current state-of-the-art extracellular vesicle isolation and purification methods did not result in lipoprotein-free vesicle preparations from blood plasma or from platelet concentrates. Furthermore, transmission electron microscopy showed an association of LDL with isolated vesicles upon in vitro mixing. This is the first study to show co-purification and in vitro association of LDL with extracellular vesicles and its interference with vesicle analysis. Our data point to the importance of careful study design and data interpretation in studies using blood-derived extracellular vesicles with special focus on potentially co-purified LDL.

  11. The potential of advanced ground-based gravitational wave detectors to detect generic deviations from general relativity

    NASA Astrophysics Data System (ADS)

    Narikawa, Tatsuya; Tagoshi, Hideyuki

    2016-09-01

    We discuss the potential of advanced ground-based gravitational wave detectors such as LIGO, Virgo, and KAGRA to detect generic deviations of gravitational waveforms from the predictions of general relativity. We use the parameterized post-Einsteinian formalism to characterize the deviations, and assess what magnitude of deviations are detectable by using an approximate decision scheme based on Bayesian statistics. We find that there exist detectable regions of the parameterized post-Einsteinian parameters for different binary masses from the observation of a single gravitational wave event. The regions are not excluded by currently existing binary pulsar observations for the parameterized post-Einsteinian parameters at higher post-Newtonian order. We also find that neglect of orbital eccentricity or tidal deformation effects do not cause a significant bias on the detectable region of generic deviations from general relativity.

  12. Robust detection of sea mines in side-scan sonar imagery based on advanced gray-scale morphological filters

    NASA Astrophysics Data System (ADS)

    Lange, Holger

    2000-03-01

    Computing Devices Canada, a General Dynamics company, undertakes research in image processing focusing on the automatic recognition of sea mines. This paper presents the use of advanced gray-scale morphological filters for the detection of sea mines in side-scan sonar imagery. Sea mines in side-scan sonar imagery can be characterized by a mine-body and a mine shadow. Mine-bodies consist of bright regions, relative to the background, with a specific shape and size. Mine-shadows consist of dark regions, relative to the background, with a specific shape and size. The shapes and sizes of these regions depend on the mine type, the orientation of the mine, the physical acquisition process of the sonar imagery, and the environment in which the mine is located. Advanced gray-scale morphological filters provide very powerful and robust tools to extract bright and dark regions with low signal to noise ratio in very noisy imagery using geometric constraints such as shape, size and total surface area. For the detection of sea mines we use these morphological filters with the minimum and maximum geometric constraints for the mine-bodies and mine-shadows. The independent detection of mine-bodies and mine-shadows allows the detection of bottom, moored and drifting mines with the same detection algorithm. Consistent mine-body and mine-shadow combinations are resolved into mine like objects.

  13. An isothermal amplification reactor with an integrated isolation membrane for point-of-care detection of infectious diseases

    PubMed Central

    Liu, Changchun; Geva, Eran; Mauk, Michael; Qiu, Xianbo; Abrams, William R.; Malamud, Daniel; Curtis, Kelly; Owen, S. Michele; Bau, Haim H.

    2015-01-01

    A simple, point of care, inexpensive, disposable cassette for the detection of nucleic acids extracted from pathogens was designed, constructed, and tested. The cassette utilizes a single reaction chamber for isothermal amplification of nucleic acids. The chamber is equipped with an integrated, flow-through, Flinders Technology Associates (Whatman FTA®) membrane for the isolation, concentration, and purification of DNA and/or RNA. The nucleic acids captured by the membrane are used directly as templates for amplification without elution, thus simplifying the cassette’s flow control. The FTA membrane also serves another critical role—enabling the removal of inhibitors that dramatically reduce detection sensitivity. Thermal control is provided with a thin film heater external to the cassette. The amplification process was monitored in real time with a portable, compact fluorescent reader. The utility of the integrated, single-chamber cassette was demonstrated by detecting the presence of HIV-1 in oral fluids. The HIV RNA was reverse transcribed and subjected to loop-mediated, isothermal amplification (LAMP). A detection limit of less than 10 HIV particles was demonstrated. The cassette is particularly suitable for resource poor regions, where funds and trained personnel are in short supply. The cassette can be readily modified to detect nucleic acids associated with other pathogens borne in saliva, urine, and other body fluids as well as in water and food. PMID:21455542

  14. Santorini mutation detection meeting 2011: rapid advance in sequencing technology poses challenges for interpretation of genetic variations.

    PubMed

    Stavrou, Eleana F; Goriely, Anne

    2012-10-01

    The 11th International Symposium on Mutations in the Genome was held on 6-10 June, 2011, in Santorini, Greece. Meeting participants described novel detection technologies, rapid advances in whole genome and whole-exome sequencing, but also highlighted the urgent need for the development of sequence variation databases and the clinical interpretation of the genomic data. This report summarizes some of the major themes presented during the meeting.

  15. Use of a Passive Reaction Wheel Jitter Isolation System to Meet the Advanced X-Ray Astrophysics Facility Imaging Performance Requirements

    NASA Technical Reports Server (NTRS)

    Pendergast, Karl J.; Schauwecker, Christopher J.

    1998-01-01

    Third in the series of NASA great observatories, the Advanced X-Ray Astrophysics Facility (AXAF) is scheduled for launch from the Space Shuttle in November of 1998. Following in the path of the Hubble Space Telescope and the Compton Gamma Ray Observatory, this observatory will image light at X-ray wavelengths, facilitating the detailed study of such phenomena as supernovae and quasars. The AXAF project is sponsored by the Marshall Space Flight Center in Huntsville, Alabama. Because of exacting requirements on the performance of the AXAF optical system, it was necessary to reduce the transmission of reaction wheel jitter disturbances to the observatory. This reduction was accomplished via use of a passive mechanical isolation system to interface the reaction wheels with the spacecraft central structure. In addition to presenting a description of the spacecraft, the isolation system, and the key image quality requirement flowdown, this paper details the analyses performed in support of system-level imaging performance requirement verification. These analyses include the identification of system-level requirement suballocations, quantification of imaging and pointing performance, and formulation of unit-level isolation system transmissibility requirements. Given in comparison to the non-isolated system imaging performance, the results of these analyses clearly illustrate the effectiveness of an innovative reaction wheel passive isolation system.

  16. Fault isolation detection expert (FIDEX). Part 1: Expert system diagnostics for a 30/20 Gigahertz satellite transponder

    NASA Technical Reports Server (NTRS)

    Durkin, John; Schlegelmilch, Richard; Tallo, Donald

    1992-01-01

    LeRC has recently completed the design of a Ka-band satellite transponder system, as part of the Advanced Communication Technology Satellite (ACTS) System. To enhance the reliability of this satellite, NASA funded the University of Akron to explore the application of an expert system to provide the transponder with an autonomous diagnosis capability. The results of this research was the development of a prototype diagnosis expert system called FIDEX (fault-isolation and diagnosis expert). FIDEX is a frame-based expert system that was developed in the NEXPERT Object development environment by Neuron Data, Inc. It is a MicroSoft Windows version 3.0 application, and was designed to operate on an Intel i80386 based personal computer system.

  17. Detection and isolation of nucleic acid sequences using competitive hybridization probes

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    1997-01-01

    A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided.

  18. Detection and isolation of nucleic acid sequences using competitive hybridization probes

    DOEpatents

    Lucas, J.N.; Straume, T.; Bogen, K.T.

    1997-04-01

    A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided. 7 figs.

  19. Detection of reduced RNA synthesis in UV-irradiated Cockayne syndrome group B cells using an isolated nuclear system.

    PubMed

    Yamada, Ayumi; Masutani, Chikahide; Hanaoka, Fumio

    2002-10-21

    Cockayne syndrome (CS) is a human hereditary disorder characterized by UV sensitivity, developmental abnormalities and premature aging. CS cells display a selective deficiency in transcription-coupled repair (TCR), a subpathway of nucleotide excision repair (NER) that preferentially removes lesions from transcribed strands. Following UV irradiation, the recovery of RNA synthesis is abnormally delayed in CS cells in conjunction with TCR deficiency. To date, TCR has been detected in cultured cells, but not in cell-free systems. In this study, we constructed an assay system using isolated nuclei. RNA synthesis catalyzed by RNA polymerases (pol I and II) was measured in nuclei prepared from UV-irradiated cells. In nuclei isolated from HeLa and xeroderma pigmentosum (XP) group C cells, RNA synthesis was relatively resistant to UV irradiation. In contrast, RNA synthesis by pol I and, in particular, pol II in CS-B nuclei was significantly inhibited upon UV irradiation. Our data support the utility of this assay system for the in vitro detection of the recovery of RNA synthesis in cultured cells. PMID:12379475

  20. Detection of integrons and Staphylococcal Cassette Chromosome (SCCmec) types in Staphylococcus aureus isolated from burn and non-burn patients

    PubMed Central

    Namvar, Amirmorteza Ebrahimzadeh; Khodaei, Farzaneh; Bijari, Aslan; Lari, Abdolaziz Rastegar

    2015-01-01

    Background Methicillin Resistant Staphylococcus aureus (MRSA) strains have been recognized as an important reason of infections in health care units. Integrons role in antibiotic resistance box gene transfer has been well recognized which are found in Gram positive bacteria. Objective The aim of this study was analyzed of SCCmec typing and determine of integron classes in burn and non-burn specimens. Methodology A total of 110 S. aureus strains were isolated from burn and non-burn patients. Antimicrobial susceptibility testing, detection of mecA gene, various SCCmec types and integrons classes were analyzed. Results In antimicrobial susceptibility test in burn patients, resistant to both gentamicin and oxacilin and in non-burn patients resistance to oxacilin and cefepime showed the highest ratio In PCR molecular test (80%) and (52.7%) of strains harbored the mecA gene. Therefore five different SCCmec types were recognized among our studied strains. Subsequently, integron class I was evaluated as (94.5%) in burn and (12.7%) in non-burn isolates by the multiplex PCR method. Conclusion Albeit MRSA strains have the hospital reservoir so may cause serious treats for hospitalized and non-hospitalized patients, hence clinical decision for prevention and treatment may develop due to, mecA gene, SCCmec elements and integrons detection in health care units. PMID:26715924

  1. Application of a DNA Hybridization–Hydrophobic-Grid Membrane Filter Method for Detection and Isolation of Verotoxigenic Escherichia coli

    PubMed Central

    Todd, E. C. D.; Szabo, R. A.; MacKenzie, J. M.; Martin, A.; Rahn, K.; Gyles, C.; Gao, A.; Alves, D.; Yee, A. J.

    1999-01-01

    Verotoxigenic Escherichia coli (VTEC) strains were isolated from food and animal fecal samples by using PCR to screen for the presence of VTEC after broth enrichment and then filtering VTEC-positive cultures through hydrophobic-grid membrane filters (HGMFs) which were incubated on MacConkey agar. The filters were probed with a digoxigenin-labeled PCR product generated by amplification of a conserved verotoxin gene sequence. Replication of the growth on filters allowed probe-positive colonies to be picked. When ground beef samples were inoculated with VTEC strains, 100% of the strains were recovered, and the detection limit was 0.1 CFU per g. Similar results were obtained with seven types of artificially contaminated vegetables. A survey of 32 packages of vegetables and 23 samples of apple cider obtained at the retail level did not reveal the presence of VTEC. However, the intestinal fecal contents of a moose, 1 of 35 wild mammals and birds examined, contained E. coli O157:H7. The DNA hybridization-HGMF method was also used in a prevalence survey of 327 raw and 744 ready-to-eat products; VTEC strains were recovered from 4.9% of the raw products and 0.7% of the ready-to-eat products. No serotype O157:H7 strains were detected. This method is particularly suited for surveys in which low numbers of VTEC-positive samples are expected and isolates are required. PMID:10543785

  2. Magnetic nanowires for rapid and ultrasensitive isolation of DNA from cervical specimens for the detection of multiple human papillomaviruses genotypes.

    PubMed

    Lee, HyungJae; Hwang, Na Rae; Hwang, Sang-Hyun; Cho, Youngnam

    2016-12-15

    Detecting human papillomavirus (HPV) is central in diagnosing and monitoring HPV-related disease. However, limited sensitivity and the wide variability of the HPV genome pose challenges in the identification of HPV genes, particularly high-risk types. This study reports the development of polyethyleneimine-conjugated magnetic nanowires (PEI-MNWs) and their use in the isolation, identification, and analysis of multiple genotypes of HPV DNA from cervical cancer specimens. The nanowires are electrochemically doped with a high density of magnetic nanoparticles and biotin moieties during potentiostatic deposition, thereby allowing conjugating cationic branched polymers to direct the attachment of negatively charged DNA molecules with strong magnetic response. For proof of concept, the rapid and ultrasensitive isolation of HPV DNA is performed at concentrations as low as 10pg/mL with an efficiency of >95%. For clinical optimization, the analytical and clinical sensitivity of PEI-MNWs is compared with that of the Roche Cobas 4800 HPV Test and demonstrates excellent correlation for multiple HPV DNA genotypes with superior threshold cycle values. The high sensitivity, specificity, and good reproducibility of PEI-MNWs are particularly well suited for the recovery of DNA and provide significant and clinically meaningful evidence for the early detection and treatment of HPV-associated cancers.

  3. Magnetic nanowires for rapid and ultrasensitive isolation of DNA from cervical specimens for the detection of multiple human papillomaviruses genotypes.

    PubMed

    Lee, HyungJae; Hwang, Na Rae; Hwang, Sang-Hyun; Cho, Youngnam

    2016-12-15

    Detecting human papillomavirus (HPV) is central in diagnosing and monitoring HPV-related disease. However, limited sensitivity and the wide variability of the HPV genome pose challenges in the identification of HPV genes, particularly high-risk types. This study reports the development of polyethyleneimine-conjugated magnetic nanowires (PEI-MNWs) and their use in the isolation, identification, and analysis of multiple genotypes of HPV DNA from cervical cancer specimens. The nanowires are electrochemically doped with a high density of magnetic nanoparticles and biotin moieties during potentiostatic deposition, thereby allowing conjugating cationic branched polymers to direct the attachment of negatively charged DNA molecules with strong magnetic response. For proof of concept, the rapid and ultrasensitive isolation of HPV DNA is performed at concentrations as low as 10pg/mL with an efficiency of >95%. For clinical optimization, the analytical and clinical sensitivity of PEI-MNWs is compared with that of the Roche Cobas 4800 HPV Test and demonstrates excellent correlation for multiple HPV DNA genotypes with superior threshold cycle values. The high sensitivity, specificity, and good reproducibility of PEI-MNWs are particularly well suited for the recovery of DNA and provide significant and clinically meaningful evidence for the early detection and treatment of HPV-associated cancers. PMID:27494810

  4. Alicyclobacillus spp. in the fruit juice industry: history, characteristics, and current isolation/detection procedures.

    PubMed

    Chang, Su-Sen; Kang, Dong-Hyun

    2004-01-01

    The first Alicyclobacillus spp. was isolated in 1982, and was originally thought to be strictly limited to thermophilic and acidic environments. Two years later, another Alicyclobacillus sp., A. acidoterrestris, was identified as the causative agent in spoilage of commercially pasteurized apple juice. Subsequent studies soon found that Alicyclobacillus spp. are soilborne bacteria, and do not strictly require thermophilic and acidic environments. Alicyclobacillus spp. posess several distinct characteristics; the major one is their ability to survive commercial pasteurization processes and produce off-flavors in fruit juices. The fruit juice industry has acknowledged Alicyclobacillus spp. as a major quality control target microorganism. Guaiacol and halophenols were identified as the offensive smelling agent in many Alicyclobacillus spp. related spoilage. Though the exact formation pathway of these off-flavors by Alicyclobacillus spp. are not yet identified, studies report that the presence of Alicyclobacillus spp. in the medium may be a major contributor to the formation of these off-flavors. Many identification methods and isolation media were developed in the last two decades. However, most of these methods were developed specifically for A. acidoterrestris, which was the first identified off-flavor producing Alicyclobacillus. However, recent studies indicate that other species of Alicyclobacillus may also produce guaiacol or the halophenols. In this respect, all Alicyclobacillus spp. should be monitored as potential spoilage bacteria in fruit juices. This article includes an overall review of the history of Alicyclobacillus spp., characteristics, suggested off-flavor production pathways, and commonly used identification methods for the currently identified Alicyclobacillus spp.

  5. Detection of genes involved in biofilm formation in Staphylococcus aureus isolates

    PubMed Central

    Nourbakhsh, Fahimeh; Namvar, Amirmorteza Ebrahimzadeh

    2016-01-01

    Staphylococcus aureus is one of the Gram-positive pathogens causing a wide range of nosocomial infections. The present study investigates genotypic and phenotypic aspects involved in biofilm formation in methicillin-resistant Staphylococcus aureus strains isolated from nosocomial infections in Isfahan. A total of 110 S. aureus strains were collected from three major hospitals in Isfahan, the center of Iran. The antibiotic resistance pattern, phenotypes, and biofilm formation genes were studied using Congo red agar (CRA) and multiplex PCR (M-PCR). We found that 103 out of 110 samples (93.6%) were MRSA. The highest frequency of resistance was found to penicillin (89%), ciprofloxacin (87.4%), and erythromycin (86.1%). Phenotypic results showed that 53.5% were high biofilm producers, while 33.3% and 13.2% were intermediate and low biofilm producers, respectively. icaC (69.3%) had the highest frequency in comparison to other intercellular adhesion (ica) genes, icaD (54.8%) was second most common. The results show that the adherence or attachment ability and biofilm production are important for enhancing virulence factors among isolates of S. aureus strains. PMID:27303652

  6. Detection of aac(6’)-Ib-cr in Avian Pathogenic Escherichia coli Isolates in Japan

    PubMed Central

    KAWANISHI, Michiko; OZAWA, Manao; HIKI, Mototaka; ABO, Hitoshi; KOJIMA, Akemi; ASAI, Tetsuo

    2013-01-01

    ABSTRACT We investigated the prevalence of plasmid-mediated quinolone resistance (PMQR) genes in avian pathogenic Escherichia coli (APEC) strains in Japan. A total of 117 APEC strains collected between 2004 and 2007 were examined for PMQR genes (qnrA, qnrB, qnrC, qnrD, qnrS, aac(6’)-Ib-cr, qepA and oqxAB) by polymerase chain reaction. None of the APEC strains carried qnrA, qnrB, qnrC, qnrD, qnrS, qepA or oqxAB, but one of the isolates was identified as an AAC (6’)-Ib-cr producer. Phylogenetic grouping, multi-locus sequence typing and serotyping showed that this isolate belonged to phylogenetic group A, sequence type 167 and untypable serogroup. To our knowledge, this is the first report of the aac (6’)-Ib-cr gene in bacteria from food-producing animals in Japan. PMID:23856759

  7. Detection of ureolytic activity of bacterial strains isolated from entomopathogenic nematodes using infrared spectroscopy.

    PubMed

    Lechowicz, Lukasz; Chrapek, Magdalena; Czerwonka, Grzegorz; Korzeniowska-Kowal, Agnieszka; Tobiasz, Anna; Urbaniak, Mariusz; Matuska-Lyzwa, Joanna; Kaca, Wieslaw

    2016-08-01

    The pathogenicity of entomopathogenic nematodes (EPNs) depends directly on the presence of bacteria in the nematode digestive tracts. Based on 16S rRNA and MALDI-TOF analyses 20 isolated bacteria were assigned to 10 species with 10 isolates classified as Pseudomonas ssp. Six strains (30%) show ureolytic activity on Christensen medium. Spectroscopic analysis of the strains showed that the ureolytic activity is strongly correlated with the following wavenumbers: 935 cm(-1) in window W4, which carries information about the bacterial cell wall construction and 1158 cm(-1) in window W3 which corresponds to proteins in bacterial cell. A logistic regression model designed on the basis of the selected wavenumbers differentiates ureolytic from non-ureolytic bacterial strains with an accuracy of 100%. Spectroscopic studies and mathematical analyses made it possible to differentiate EPN-associated Pseudomonas sp. strains from clinical Pseudomonas aeruginosa PAO1. These results suggest, that infrared spectra of EPN-associated Pseudomonas sp. strains may reflect its adaptation to the host. PMID:26972384

  8. Isolation and detection of single molecules on paramagnetic beads using sequential fluid flows in microfabricated polymer array assemblies.

    PubMed

    Kan, Cheuk W; Rivnak, Andrew J; Campbell, Todd G; Piech, Tomasz; Rissin, David M; Mösl, Matthias; Peterça, Andrej; Niederberger, Hans-Peter; Minnehan, Kaitlin A; Patel, Purvish P; Ferrell, Evan P; Meyer, Raymond E; Chang, Lei; Wilson, David H; Fournier, David R; Duffy, David C

    2012-03-01

    We report a method for isolating individual paramagnetic beads in arrays of femtolitre-sized wells and detecting single enzyme-labeled proteins on these beads using sequential fluid flows in microfabricated polymer array assemblies. Arrays of femtolitre-sized wells were fabricated in cyclic olefin polymer (COP) using injection moulding based on DVD manufacturing. These arrays were bonded to a complementary fluidic structure that was also moulded in COP to create an enclosed device to allow delivery of liquids to the arrays. Enzyme-associated, paramagnetic beads suspended in aqueous solutions of enzyme substrate were delivered fluidically to the array such that one bead per well was loaded by gravity. A fluorocarbon oil was then flowed into the device to remove excess beads from the surface of the array, and to seal and isolate the femtolitre-sized wells containing beads and enzyme substrate. The device was then imaged using standard fluorescence imaging to determine which wells contained single enzyme molecules. The analytical performance of this device as the detector for digital ELISA compared favourably to the standard method, i.e., glass arrays mechanically sealed against a silicone gasket; prostate specific antigen (PSA) could be detected from 0.011 pg mL(-1) up to 100 pg mL(-1). The use of an enclosed fluidic device to isolate beads in single-molecule arrays offers a multitude of advantages for low-cost manufacturing, ease of automation, and instrument development to enable applications in biomarker validation and medical diagnosis. PMID:22179487

  9. Characterization of blaKPC-containing Klebsiella pneumoniae isolates detected in different institutions in the Eastern USA

    PubMed Central

    Endimiani, Andrea; Hujer, Andrea M.; Perez, Federico; Bethel, Christopher R.; Hujer, Kristine M.; Kroeger, Jennifer; Oethinger, Margret; Paterson, David L.; Adams, Mark D.; Jacobs, Michael R.; Diekema, Daniel J.; Hall, Gerri S.; Jenkins, Stephen G.; Rice, Louis B.; Tenover, Fred C.; Bonomo, Robert A.

    2009-01-01

    Background The emergence of blaKPC-containing Klebsiella pneumoniae (KPC-Kp) isolates is attracting significant attention. Outbreaks in the Eastern USA have created serious treatment and infection control problems. A comparative multi-institutional analysis of these strains has not yet been performed. Methods We analysed 42 KPC-Kp recovered during 2006–07 from five institutions located in the Eastern USA. Antimicrobial susceptibility tests, analytical isoelectric focusing (aIEF), PCR and sequencing of bla genes, PFGE and rep-PCR were performed. Results By in vitro testing, KPC-Kp isolates were highly resistant to all non-carbapenem β-lactams (MIC90s ≥ 128 mg/L). Among carbapenems, MIC50/90s were 4/64 mg/L for imipenem and meropenem, 4/32 mg/L for doripenem and 8/128 for ertapenem. Combinations of clavulanate or tazobactam with a carbapenem or cefepime did not significantly lower the MIC values. Genetic analysis revealed that the isolates possessed the following bla genes: blaKPC-2 (59.5%), blaKPC-3 (40.5%), blaTEM-1 (90.5%), blaSHV-11 (95.2%) and blaSHV-12 (50.0%). aIEF of crude β-lactamase extracts from these strains supported our findings, showing β-lactamases at pIs of 5.4, 7.6 and 8.2. The mean number of β-lactamases was 3.5 (range 3–5). PFGE demonstrated that 32 (76.2%) isolates were clonally related (type A). Type A KPC-Kp isolates (20 blaKPC-2 and 12 blaKPC-3) were detected in each of the five institutions. rep-PCR showed patterns consistent with PFGE. Conclusions We demonstrated the complex β-lactamase background of KPC-Kp isolates that are emerging in multiple centres in the Eastern USA. The prevalence of a single dominant clone suggests that interstate transmission has occurred. PMID:19155227

  10. Advanced gray-scale morphological filters for the detection of sea mines in side-scan sonar imagery

    NASA Astrophysics Data System (ADS)

    Lange, Holger; Vincent, Luc M.

    2000-08-01

    Computing Devices Canada, a General Dynamics company, undertakes research in image processing with focus on the automatic recognition of sea mines. This paper present the use of advanced gray-scale morphological filters for this function as applied to side scan sonar imagery. Sea mines in side scan sonar imagery can be characterized by a mine-body and a mine-shadow. Mine-bodies consist of bright regions, relative to the background, with a specific shape and size. Mine-shadows consist of dark regions, relative to the background, with a specific shape and sizes. The shapes and sizes of these regions depend on the mine type, the orientation of the mine, the physical acquisition process of the sonar imagery, and the environment in which the mine is located. Advanced gray-scale morphological filters provide very powerful and robust tools to extract bright and dark regions with low signal to noise ratio in very noisy imagery using geometric constraints such as shape, size and total surface area. For the detection of sea mines we use these morphological filters with the minimum and maximum geometric constraints for the mine-bodies and mine-shadows. The independent detection of mine-bodies and mine-shadows allows the detection of bottom, moored and drifting mines with the same detection algorithm. Consistent mine-body and mine- shadow combinations are resolved into mine like objects.

  11. On-line two-dimensional capillary electrophoresis with mass spectrometric detection using a fully electric isolated mechanical valve.

    PubMed

    Kohl, Felix J; Montealegre, Cristina; Neusüß, Christian

    2016-04-01

    CE is becoming more and more important in many fields of bioanalytical chemistry. Besides optical detection, hyphenation to ESI-MS detection is increasingly applied for sensitive identification purposes. Unfortunately, many CE techniques and methods established in research and industry are not compatible to ESI-MS since essential components of the background electrolyte interfere in ES ionization. In order to identify unknown peaks in established CE methods, here, a heart-cut 2D-CE separation system is introduced using a fully isolated mechanical valve with an internal loop of only 20 nL. In this system, the sample is separated using potentially any non-ESI compatible method in the first separation dimension. Subsequently, the portion of interest is cut by the internal sample loop of the valve and reintroduced to the second dimension where the interfering compounds are removed, followed by ESI-MS detection. When comparing the separation efficiency of the system with the valve to a system using a continuous capillary only a slight increase in peak width is observed. Ultraviolet/visible detection is integrated in the first dimension for switching time determination, enabling reproducible cutting of peaks of interest. The feasibility of the system is successfully demonstrated by a 2D analysis of a BSA tryptic digest sample using a nonvolatile (phosphate based) background electrolyte in the first dimension.

  12. High Latitude Ionospheric Scintillation: Detection and Isolation From Oscillator Phase Noise as Applied to GNSS

    NASA Astrophysics Data System (ADS)

    Morrison, Aiden

    This thesis investigates the detection of high latitude ionospheric scintillation effects using data collected by the author during two field exercises into the Canadian low arctic and high arctic regions during March and October--November 2008 respectively. The effect of ionospheric phase scintillation in these regions is studied through the observation of the influence it has on both the L1CA and L2C modernized GPS signals simultaneously. A pulsation detection method is proposed and investigated which identifies, and in turn exploits an apparent high level of correlation between the phase effects present on the L1 and L2 GPS carriers during low arctic pulsation events. Using this data, the level of correlated activity between the civil GPS signals during both polar and auroral scintillation events is related to the physical scale sizes of detectable ionospheric features. As a further novel contribution the presentation of a method for estimating the epoch to epoch phase change in the local oscillator over millisecond time scales is presented. This method is potentially capable of providing apparent phase stability commensurate with the use of an ovenized quartz oscillator within equipment actually utilizing an inexpensive (e.g. TCXO) oscillator, thereby allowing phase scintillation detection while using very low cost user equipment. An appendix detailing the design and development of a multi channel multi GNSS wide bandwidth research front-end for use in future investigations is included.

  13. Quantitative detection of a marine fish iridovirus isolated from large yellow croaker, Pseudosciaena crocea, using a molecular beacon.

    PubMed

    Wang, Xiao-Wen; Ao, Jing-Qun; Li, Qing-Ge; Chen, Xin-Hua

    2006-04-01

    A real-time polymerase chain reaction (PCR) assay utilizing a molecular beacon for the quantitative detection of a marine fish iridovirus isolated from large yellow croaker, Pseudosciaena crocea (LYCIV), was developed, which involved the amplification of a 122bp DNA fragment from a conserved region of LYCIV ATPase gene. The specific probe consisting of two short arm and a central loop sequences complementary to the target amplicon was characterized with respect to its efficiency of quenching (E(ff)), and signal to background ratio by spectrofluorometric analysis of its hybridization with the complementary oligonucleotide target. The positive control plasmid pFHT-ATPase containing the target sequence was quantified to make the standard curve for sample detection after serial 10-fold dilution. Linear coefficient correlations between cycle threshold (C(T)) value and logarithmic positive plasmid concentration were close to one (r(2)=0.998) and the detection limit of the assay was 70 copies of positive plasmid/assay. The specificity of this real-time PCR was also demonstrated by using the genomic DNA templates from the healthy fish, white spot syndrome baculovirus (WSSV), and epizootic heamatopietic necrosis virus (EHNV), respectively. The coefficient of variation (CV) of the assay ranged from 1.16 to 4.42%, depending on the concentration of the positive plasmid. The quantitative detection of different tissues from LYCIV-infected fish showed that the spleen and kidney contained the largest number of viral particles (6.86 x 10(6) and 4.62 x 10(6) viral genome copies/mg tissue, respectively) while no viral DNA was detected in the muscular tissue. These results suggested that the real-time PCR assay reported here could be used for rapid, sensitive, and quantitative detection of LYCIV infection.

  14. Advancing the detection of maternal haematopoietic microchimeric cells in fetal immune organs in mice by flow cytometry

    PubMed Central

    Solano, Maria Emilia; Thiele, Kristin; Stelzer, Ina Annelies; Mittrücker, Hans-Willi; Arck, Petra Clara

    2014-01-01

    Maternal microchimerism, which occurs naturally during gestation in hemochorial placental mammals upon transplacental migration of maternal cells into the fetus, is suggested to significantly influence the fetal immune system. In our previous publication, we explored the sensitivity of quantitative polymerase chain reaction and flow cytometry to detect cellular microchimerism. With that purpose, we created mixed cells suspensions in vitro containing reciprocal frequencies of wild type cells and cells positive for enhanced green fluorescent protein or CD45.1+, respectively. Here, we now introduce the H-2 complex, which defines the major histocompatibility complex in mice and is homologous to HLA in human, as an additional target to detect maternal microchimerism among fetal haploidentical cells. We envision that this advanced approach to detect maternal microchimeric cells by flow cytometry facilitates the pursuit of phenotypic, gene expression and functional analysis of microchimeric cells in future studies. PMID:25483743

  15. Delta-doped hybrid advanced detector for low energy particle detection

    NASA Technical Reports Server (NTRS)

    Cunningham, Thomas J. (Inventor); Fossum, Eric R. (Inventor); Nikzad, Shouleh (Inventor); Pain, Bedabrata (Inventor); Soli, George A. (Inventor)

    2000-01-01

    A delta-doped hybrid advanced detector (HAD) is provided which combines at least four types of technologies to create a detector for energetic particles ranging in energy from hundreds of electron volts (eV) to beyond several million eV. The detector is sensitive to photons from visible light to X-rays. The detector is highly energy-sensitive from approximately 10 keV down to hundreds of eV. The detector operates with milliwatt power dissipation, and allows non-sequential readout of the array, enabling various advanced readout schemes.

  16. Delta-doped hybrid advanced detector for low energy particle detection

    NASA Technical Reports Server (NTRS)

    Cunningham, Thomas J. (Inventor); Fossum, Eric R. (Inventor); Nikzad, Shouleh (Inventor); Pain, Bedabrata (Inventor); Soli, George A. (Inventor)

    2002-01-01

    A delta-doped hybrid advanced detector (HAD) is provided which combines at least four types of technologies to create a detector for energetic particles ranging in energy from hundreds of electron volts (eV) to beyond several million eV. The detector is sensitive to photons from visible light to X-rays. The detector is highly energy-sensitive from approximately 10 keV down to hundreds of eV. The detector operates with milliwatt power dissipation, and allows non-sequential readout of the array, enabling various advanced readout schemes.

  17. Well differentiated follicular thyroid neoplasia: impact of molecular and technological advances on detection, monitoring and treatment.

    PubMed

    Gianoukakis, Andrew G; Giannelli, Silvana M; Salameh, Wael A; McPhaul, Laron W

    2011-01-30

    Our understanding of the molecular mechanisms responsible for follicular thyroid cell oncogenesis has been advanced significantly in recent years. Specific genetic alterations and the molecular pathways they affect have been associated with particular histologic subtypes of well-differentiated thyroid cancer and are now being evaluated for their utility as clinical tools with diagnostic, prognostic and even therapeutic relevance. This paper focuses on the most common and clinically relevant genetic alterations shown to be consistently associated with well-differentiated thyroid carcinoma. We review the impact of recent molecular and technological advances on thyroid cancer standard of care and the practice of clinical medicine.

  18. Identification and Antimicrobial Activity Detection of Lactic Acid Bacteria Isolated from Corn Stover Silage

    PubMed Central

    Li, Dongxia; Ni, Kuikui; Pang, Huili; Wang, Yanping; Cai, Yimin; Jin, Qingsheng

    2015-01-01

    A total of 59 lactic acid bacteria (LAB) strains were isolated from corn stover silage. According to phenotypic and chemotaxonomic characteristics, 16S ribosomal DNA (rDNA) sequences and recA gene polymerase chain reaction amplification, these LAB isolates were identified as five species: Lactobacillus (L.) plantarum subsp. plantarum, Pediococcus pentosaceus, Enterococcus mundtii, Weissella cibaria and Leuconostoc pseudomesenteroides, respectively. Those strains were also screened for antimicrobial activity using a dual-culture agar plate assay. Based on excluding the effects of organic acids and hydrogen peroxide, two L. plantarum subsp. plantarum strains ZZU 203 and 204, which strongly inhibited Salmonella enterica ATCC 43971T, Micrococcus luteus ATCC 4698T and Escherichia coli ATCC 11775T were selected for further research on sensitivity of the antimicrobial substance to heat, pH and protease. Cell-free culture supernatants of the two strains exhibited strong heat stability (60 min at 100°C), but the antimicrobial activity was eliminated after treatment at 121°C for 15 min. The antimicrobial substance remained active under acidic condition (pH 2.0 to 6.0), but became inactive under neutral and alkaline condition (pH 7.0 to 9.0). In addition, the antimicrobial activities of these two strains decreased remarkably after digestion by protease K. These results preliminarily suggest that the desirable antimicrobial activity of strains ZZU 203 and 204 is the result of the production of a bacteriocin-like substance, and these two strains with antimicrobial activity could be used as silage additives to inhibit proliferation of unwanted microorganism during ensiling and preserve nutrients of silage. The nature of the antimicrobial substances is being investigated in our laboratory. PMID:25924957

  19. Identification and antimicrobial activity detection of lactic Acid bacteria isolated from corn stover silage.

    PubMed

    Li, Dongxia; Ni, Kuikui; Pang, Huili; Wang, Yanping; Cai, Yimin; Jin, Qingsheng

    2015-05-01

    A total of 59 lactic acid bacteria (LAB) strains were isolated from corn stover silage. According to phenotypic and chemotaxonomic characteristics, 16S ribosomal DNA (rDNA) sequences and recA gene polymerase chain reaction amplification, these LAB isolates were identified as five species: Lactobacillus (L.) plantarum subsp. plantarum, Pediococcus pentosaceus, Enterococcus mundtii, Weissella cibaria and Leuconostoc pseudomesenteroides, respectively. Those strains were also screened for antimicrobial activity using a dual-culture agar plate assay. Based on excluding the effects of organic acids and hydrogen peroxide, two L. plantarum subsp. plantarum strains ZZU 203 and 204, which strongly inhibited Salmonella enterica ATCC 43971(T), Micrococcus luteus ATCC 4698(T) and Escherichia coli ATCC 11775(T) were selected for further research on sensitivity of the antimicrobial substance to heat, pH and protease. Cell-free culture supernatants of the two strains exhibited strong heat stability (60 min at 100°C), but the antimicrobial activity was eliminated after treatment at 121°C for 15 min. The antimicrobial substance remained active under acidic condition (pH 2.0 to 6.0), but became inactive under neutral and alkaline condition (pH 7.0 to 9.0). In addition, the antimicrobial activities of these two strains decreased remarkably after digestion by protease K. These results preliminarily suggest that the desirable antimicrobial activity of strains ZZU 203 and 204 is the result of the production of a bacteriocin-like substance, and these two strains with antimicrobial activity could be used as silage additives to inhibit proliferation of unwanted microorganism during ensiling and preserve nutrients of silage. The nature of the antimicrobial substances is being investigated in our laboratory.

  20. Multicenter Evaluation of Clinical Diagnostic Methods for Detection and Isolation of Campylobacter spp. from Stool.

    PubMed

    Fitzgerald, Collette; Patrick, Mary; Gonzalez, Anthony; Akin, Joshua; Polage, Christopher R; Wymore, Kate; Gillim-Ross, Laura; Xavier, Karen; Sadlowski, Jennifer; Monahan, Jan; Hurd, Sharon; Dahlberg, Suzanne; Jerris, Robert; Watson, Renee; Santovenia, Monica; Mitchell, David; Harrison, Cassandra; Tobin-D'Angelo, Melissa; DeMartino, Mary; Pentella, Michael; Razeq, Jafar; Leonard, Celere; Jung, Carrianne; Achong-Bowe, Ria; Evans, Yaaqobah; Jain, Damini; Juni, Billie; Leano, Fe; Robinson, Trisha; Smith, Kirk; Gittelman, Rachel M; Garrigan, Charles; Nachamkin, Irving

    2016-05-01

    The use of culture-independent diagnostic tests (CIDTs), such as stool antigen tests, as standalone tests for the detection of Campylobacter in stool is increasing. We conducted a prospective, multicenter study to evaluate the performance of stool antigen CIDTs compared to culture and PCR for Campylobacter detection. Between July and October 2010, we tested 2,767 stool specimens from patients with gastrointestinal illness with the following methods: four types of Campylobacter selective media, four commercial stool antigen assays, and a commercial PCR assay. Illnesses from which specimens were positive by one or more culture media or at least one CIDT and PCR were designated "cases." A total of 95 specimens (3.4%) met the case definition. The stool antigen CIDTs ranged from 79.6% to 87.6% in sensitivity, 95.9 to 99.5% in specificity, and 41.3 to 84.3% in positive predictive value. Culture alone detected 80/89 (89.9% sensitivity) Campylobacter jejuni/Campylobacter coli-positive cases. Of the 209 noncases that were positive by at least one CIDT, only one (0.48%) was positive by all four stool antigen tests, and 73% were positive by just one stool antigen test. The questionable relevance of unconfirmed positive stool antigen CIDT results was supported by the finding that noncases were less likely than cases to have gastrointestinal symptoms. Thus, while the tests were convenient to use, the sensitivity, specificity, and positive predictive value of Campylobacter stool antigen tests were highly variable. Given the relatively low incidence of Campylobacter disease and the generally poor diagnostic test characteristics, this study calls into question the use of commercially available stool antigen CIDTs as standalone tests for direct detection of Campylobacter in stool.

  1. Direct Detection and Quantification of Bacterial Genes Associated with Inflammation in DNA Isolated from Stool

    PubMed Central

    Gómez-Moreno, Ramón; Robledo, Iraida E.; Baerga-Ortiz, Abel

    2014-01-01

    Although predominantly associated with health benefits, the gut microbiota has also been shown to harbor genes that promote inflammation. In this work, we report a method for the direct detection and quantification of these pro-inflammatory bacterial genes by PCR and qPCR in DNA extracted from human stool samples. PCR reactions were performed to detect (i) the pks island genes, (ii) tcpC, which is present in some strains of Escherichia coli and (iii) gelE presented in some strains of Enterococcus faecalis. Additionally, we screened for the presence of the following genes encoding cyclomodulins that disrupted mammalian cell division: (iv) cdt (which encodes the cytolethal distending toxin) and (v) cnf-1 (which encodes the cytotoxic necrotizing factor-1). Our results show that 20% of the samples (N = 41) tested positive for detectable amounts of pks island genes, whereas 10% of individuals were positive for tcpC or gelE and only one individual was found to harbor the cnf-1 gene. Of the 13 individuals that were positive for at least one of the pro-inflammatory genes, 5 were found to harbor more than one. A quantitative version of the assay, which used real-time PCR, revealed the pro-inflammatory genes to be in high copy numbers: up to 1.3 million copies per mg of feces for the pks island genes. Direct detection of specific genes in stool could prove useful toward screening for the presence of pro-inflammatory bacterial genes in individuals with inflammatory bowel diseases or colorectal cancer. PMID:25635239

  2. Multicenter Evaluation of Clinical Diagnostic Methods for Detection and Isolation of Campylobacter spp. from Stool.

    PubMed

    Fitzgerald, Collette; Patrick, Mary; Gonzalez, Anthony; Akin, Joshua; Polage, Christopher R; Wymore, Kate; Gillim-Ross, Laura; Xavier, Karen; Sadlowski, Jennifer; Monahan, Jan; Hurd, Sharon; Dahlberg, Suzanne; Jerris, Robert; Watson, Renee; Santovenia, Monica; Mitchell, David; Harrison, Cassandra; Tobin-D'Angelo, Melissa; DeMartino, Mary; Pentella, Michael; Razeq, Jafar; Leonard, Celere; Jung, Carrianne; Achong-Bowe, Ria; Evans, Yaaqobah; Jain, Damini; Juni, Billie; Leano, Fe; Robinson, Trisha; Smith, Kirk; Gittelman, Rachel M; Garrigan, Charles; Nachamkin, Irving

    2016-05-01

    The use of culture-independent diagnostic tests (CIDTs), such as stool antigen tests, as standalone tests for the detection of Campylobacter in stool is increasing. We conducted a prospective, multicenter study to evaluate the performance of stool antigen CIDTs compared to culture and PCR for Campylobacter detection. Between July and October 2010, we tested 2,767 stool specimens from patients with gastrointestinal illness with the following methods: four types of Campylobacter selective media, four commercial stool antigen assays, and a commercial PCR assay. Illnesses from which specimens were positive by one or more culture media or at least one CIDT and PCR were designated "cases." A total of 95 specimens (3.4%) met the case definition. The stool antigen CIDTs ranged from 79.6% to 87.6% in sensitivity, 95.9 to 99.5% in specificity, and 41.3 to 84.3% in positive predictive value. Culture alone detected 80/89 (89.9% sensitivity) Campylobacter jejuni/Campylobacter coli-positive cases. Of the 209 noncases that were positive by at least one CIDT, only one (0.48%) was positive by all four stool antigen tests, and 73% were positive by just one stool antigen test. The questionable relevance of unconfirmed positive stool antigen CIDT results was supported by the finding that noncases were less likely than cases to have gastrointestinal symptoms. Thus, while the tests were convenient to use, the sensitivity, specificity, and positive predictive value of Campylobacter stool antigen tests were highly variable. Given the relatively low incidence of Campylobacter disease and the generally poor diagnostic test characteristics, this study calls into question the use of commercially available stool antigen CIDTs as standalone tests for direct detection of Campylobacter in stool. PMID:26962088

  3. One-PCR-tube approach for in situ DNA isolation and detection.

    PubMed

    Huang, Xin; Hou, Lihua; Xu, Xiaohe; Chen, Hongjun; Ji, Haifeng; Zhu, Shuifang

    2011-10-21

    Traditional real-time polymerase chain reaction (PCR) requires a purified DNA sample for PCR amplification and detection. This requires PCR tests be conducted in clean laboratories, and limits its applications for field tests. This work developed a method that can carry out DNA purification, amplification and detection in a single PCR tube. The polypropylene PCR tube was first treated with chromic acid and peptide nucleic acids (PNA) as DNA-capturer were immobilized on the internal surface of the tube. Cauliflower mosaic virus 35S (CaMV-35S) promoter in the crude extract was hybridized with the PNA on the tube surface, and the inhibitors, interfering agents and irrelevant DNA in the crude extract were effectively removed by rinsing with buffer solutions. The tube that has captured the target DNA can be used for the following real-time PCR (RT-PCR). By using this approach, the detection of less than 2500 copies of 35S plasmids in a complex sample could be completed within 3 hours. Chocolate samples were tested for real sample analysis, and 35S plasmids in genetically modified chocolate samples have been successfully identified with this method in situ. The novel One-PCR-tube method is competitive for commercial kits with the same time and simpler operation procedure. This method may be widely used for identifying food that contains modified DNA and specific pathogens in the field. PMID:21879029

  4. PCR detection and microbiological isolation of Salmonella spp. from fresh beef and cantaloupes.

    PubMed

    Gallegos-Robles, M A; Morales-Loredo, A; Alvarez-Ojeda, G; Osuna-García, J A; Martínez, I O; Morales-Ramos, L H; Fratamico, P

    2009-01-01

    Species belonging to the genus Salmonella are an important cause of enteric fevers, gastroenteritis, and septicemia, and the pathogens are commonly transmitted through contaminated food. In this study, polymerase chain reaction (PCR) amplification of a 287-bp region of the invA gene was compared to a microbiological technique to determine the presence of Salmonella in retail beef and in cantaloupe rinse samples. Both methods showed the same level of sensitivity, detecting 1 CFU/25 g of meat after enrichment for 24 h at 42 degrees C. The presence of Salmonella was determined in 50 commercial top sirloin beef samples that were not artificially inoculated. Three samples were positive by the microbiological method, and these samples and an additional sample were positive by the PCR. Both methods were also used to test surface rinses of cantaloupes collected from 4 farms in Nayarit, Mexico. Salmonella was detected by the microbiological method in 9 of 20 samples (45%), whereas the pathogen was detected by the PCR in 11 samples (55%). This study demonstrates the utility of the PCR targeting the invA gene to determine the presence of Salmonella spp. in beef and cantaloupe samples.

  5. Detection of Candida dubliniensis in Oropharyngeal Samples from Human Immunodeficiency Virus-Infected Patients in North America by Primary CHROMagar Candida Screening and Susceptibility Testing of Isolates

    PubMed Central

    Kirkpatrick, William R.; Revankar, Sanjay G.; Mcatee, Robert K.; Lopez-Ribot, Jose L.; Fothergill, Annette W.; McCarthy, Dora I.; Sanche, Stephen E.; Cantu, Rebecca A.; Rinaldi, Michael G.; Patterson, Thomas F.

    1998-01-01

    Candida dubliniensis has been associated with oropharyngeal candidiasis in patients infected with human immunodeficiency virus (HIV). C. dubliniensis isolates may have been improperly characterized as atypical Candida albicans due to the phenotypic similarity between the two species. Prospective screening of oral rinses from 63 HIV-infected patients detected atypical dark green isolates on CHROMagar Candida compared to typical C. albicans isolates, which are light green. Forty-eight atypical isolates and three control strains were characterized by germ tube formation, differential growth at 37, 42, and 45°C, identification by API 20C, fluorescence, chlamydoconidium production, and fingerprinting by Ca3 probe DNA hybridization patterns. All isolates were germ tube positive. Very poor or no growth occurred at 42°C with 22 of 51 isolates. All 22 poorly growing isolates at 42°C and one isolate with growth at 42°C showed weak hybridization of the Ca3 probe with genomic DNA, consistent with C. dubliniensis identification. No C. dubliniensis isolate but only 18 of 28 C. albicans isolates grew at 45°C. Other phenotypic or morphologic tests were less reliable in differentiating C. dubliniensis from C. albicans. Antifungal susceptibility testing showed fluconazole MICs ranging from ≤0.125 to 64 μg/ml. Two isolates were resistant to fluconazole (MIC, 64 μg/ml) and one strain was dose dependent susceptible (MIC, 16 μg/ml). MICs of other azoles, including voriconazole, itraconazole, and SCH 56592, for these isolates were lower. C. dubliniensis was identified in 11 of 63 (17%) serially evaluated patients. Variability in phenotypic characteristics dictates the use of molecular and biochemical techniques to identify C. dubliniensis. This study identifies C. dubliniensis in HIV-infected patients from San Antonio, Tex., and shows that C. dubliniensis is frequently detected in those patients by using a primary CHROMagar screen. PMID:9738058

  6. Molecular epidemiology of coagulase-negative bloodstream isolates: detection of Staphylococcus epidermidis ST2, ST7 and linezolid-resistant ST23.

    PubMed

    Martínez-Meléndez, Adrián; Morfín-Otero, Rayo; Villarreal-Treviño, Licet; Camacho-Ortíz, Adrián; González-González, Gloria; Llaca-Díaz, Jorge; Rodríguez-Noriega, Eduardo; Garza-González, Elvira

    2016-01-01

    The mechanisms contributing to persistence of coagulase-negative staphylococci are diverse; to better understanding of their dynamics, the characterization of nosocomial isolates is needed. Our aim was to characterize phenotypic and molecular characteristics of Staphylococcus epidermidis and Staphylococcus haemolyticus human blood isolates from two tertiary care hospitals in Mexico, the Hospital Universitario in Monterrey and the Hospital Civil in Guadalajara. Antimicrobial susceptibility was determined. Biofilm formation was assessed by crystal violet staining. Detection of the ica operon and Staphylococcal Cassette Chromosome mec typing were performed by PCR. Clonal relatedness was determined by Pulsed-fiel gel electrophoresis and Multi locus sequence typing. Methicillin-resistance was 85.5% and 93.2% for S. epidermidis and S. haemolyticus, respectively. Both species showed resistance >70% to norfloxacin, clindamycin, levofloxacin, trimethoprim/sulfamethoxazole, and erythromycin. Three S. epidermidis and two S. haemolyticus isolates were linezolid-resistant (one isolate of each species was cfr+). Most isolates of both species were strong biofilm producers (92.8% of S. epidermidis and 72.9% of S. haemolyticus). The ica operon was amplified in 36 (43.4%) S. epidermidis isolates. SCCmec type IV was found in 47.2% of the S. epidermidis isolates and SCCmec type V in 14.5% of S. haemolyticus isolates. No clonal relatedness was found in either species. Resistance to clindamycin, levofloxacin, erythromycin, oxacillin, and cefoxitin was associated with biofilm production for both species (p<0.05). A G2576T mutation in 23S rRNA gene was detected in an S. haemolyticus linezolid-resistant isolate. All linezolid-resistant S. epidermidis isolates belonged to ST23; isolate with SCCmec type IV belonged to ST7, and isolate with SCCmec type III belonged to ST2. This is the first report of ST7 in Mexico. There was a high genetic diversity in both species, though both species shared

  7. Molecular epidemiology of coagulase-negative bloodstream isolates: detection of Staphylococcus epidermidis ST2, ST7 and linezolid-resistant ST23.

    PubMed

    Martínez-Meléndez, Adrián; Morfín-Otero, Rayo; Villarreal-Treviño, Licet; Camacho-Ortíz, Adrián; González-González, Gloria; Llaca-Díaz, Jorge; Rodríguez-Noriega, Eduardo; Garza-González, Elvira

    2016-01-01

    The mechanisms contributing to persistence of coagulase-negative staphylococci are diverse; to better understanding of their dynamics, the characterization of nosocomial isolates is needed. Our aim was to characterize phenotypic and molecular characteristics of Staphylococcus epidermidis and Staphylococcus haemolyticus human blood isolates from two tertiary care hospitals in Mexico, the Hospital Universitario in Monterrey and the Hospital Civil in Guadalajara. Antimicrobial susceptibility was determined. Biofilm formation was assessed by crystal violet staining. Detection of the ica operon and Staphylococcal Cassette Chromosome mec typing were performed by PCR. Clonal relatedness was determined by Pulsed-fiel gel electrophoresis and Multi locus sequence typing. Methicillin-resistance was 85.5% and 93.2% for S. epidermidis and S. haemolyticus, respectively. Both species showed resistance >70% to norfloxacin, clindamycin, levofloxacin, trimethoprim/sulfamethoxazole, and erythromycin. Three S. epidermidis and two S. haemolyticus isolates were linezolid-resistant (one isolate of each species was cfr+). Most isolates of both species were strong biofilm producers (92.8% of S. epidermidis and 72.9% of S. haemolyticus). The ica operon was amplified in 36 (43.4%) S. epidermidis isolates. SCCmec type IV was found in 47.2% of the S. epidermidis isolates and SCCmec type V in 14.5% of S. haemolyticus isolates. No clonal relatedness was found in either species. Resistance to clindamycin, levofloxacin, erythromycin, oxacillin, and cefoxitin was associated with biofilm production for both species (p<0.05). A G2576T mutation in 23S rRNA gene was detected in an S. haemolyticus linezolid-resistant isolate. All linezolid-resistant S. epidermidis isolates belonged to ST23; isolate with SCCmec type IV belonged to ST7, and isolate with SCCmec type III belonged to ST2. This is the first report of ST7 in Mexico. There was a high genetic diversity in both species, though both species shared

  8. 78 FR 16513 - Application of Advances in Nucleic Acid and Protein Based Detection Methods to Multiplex...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-15

    ... Detection Methods to Multiplex Detection of Transfusion-Transmissible Agents and Blood Cell Antigens in...- Transmissible Agents and Blood Cell Antigens in Blood Donations.'' The purpose of this public workshop is to... and blood cell antigen typing. The public workshop has been planned in partnership with the...

  9. Evaluation of molecular markers for Phytophthora ramorum detection and identification: testing for specificity using a standardized library of isolates.

    PubMed

    Martin, F N; Coffey, M D; Zeller, K; Hamelin, R C; Tooley, P; Garbelotto, M; Hughes, K J D; Kubisiak, T; Bilodeau, G J; Levy, L; Blomquist, C; Berger, P H

    2009-04-01

    Given the importance of Phytophthora ramorum from a regulatory standpoint, it is imperative that molecular markers for pathogen detection are fully tested to evaluate their specificity in detection of the pathogen. In an effort to evaluate 11 reported diagnostic techniques, we assembled a standardized DNA library using accessions from the World Phytophthora Genetic Resource Collection for 315 isolates representing 60 described Phytophthora spp. as well as 11 taxonomically unclassified isolates. These were sent blind to collaborators in seven laboratories to evaluate published diagnostic procedures using conventional (based on internal transcribed spacer [ITS] and cytochrome oxidase gene [cox]1 and 2 spacer regions) and real-time polymerase chain reaction (based on ITS and cox1 and 2 spacer regions as well as beta-tubulin and elicitin genes). Single-strand conformation polymorphism (SSCP) analysis using an automated sequencer for data collection was also evaluated for identification of all species tested. In general, the procedures worked well, with varying levels of specificity observed among the different techniques. With few exceptions, all assays correctly identified all isolates of P. ramorum and low levels of false positives were observed for the mitochondrial cox spacer markers and most of the real-time assays based on nuclear markers (diagnostic specificity between 96.9 and 100%). The highest level of false positives was obtained with the conventional nested ITS procedure; however, this technique is not stand-alone and is used in conjunction with two other assays for diagnostic purposes. The results indicated that using multiple assays improved the accuracy of the results compared with looking at a single assay alone, in particular when the markers represented different genetic loci. The SSCP procedure accurately identified P. ramorum and was helpful in classification of a number of isolates to a species level. With one exception, all procedures accurately

  10. Advances in the study of the structures and bioactivities of metabolites isolated from mangrove-derived fungi in the South China Sea.

    PubMed

    Wang, Xin; Mao, Zhi-Gang; Song, Bing-Bing; Chen, Chun-Hua; Xiao, Wei-Wei; Hu, Bin; Wang, Ji-Wen; Jiang, Xiao-Bing; Zhu, Yong-Hong; Wang, Hai-Jun

    2013-09-30

    Many metabolites with novel structures and biological activities have been isolated from the mangrove fungi in the South China Sea, such as anthracenediones, xyloketals, sesquiterpenoids, chromones, lactones, coumarins and isocoumarin derivatives, xanthones, and peroxides. Some compounds have anticancer, antibacterial, antifungal and antiviral properties, but the biosynthesis of these compounds is still limited. This review summarizes the advances in the study of secondary metabolites from the mangrove-derived fungi in the South China Sea, and their biological activities reported between 2008 and mid-2013.

  11. Microbead-based immunoassay for simultaneous detection of Shiga toxins and isolation of Escherichia coli O157 in foods.

    PubMed

    Clotilde, Laurie M; Bernard, Clay; Hartman, Gary L; Lau, David K; Carter, J Mark

    2011-03-01

    Shiga toxin-producing Escherichia coli (STEC) is a significant foodborne pathogen with great economic consequences. There has been an increased food safety concern with this organism since outbreaks of human illnesses caused by this pathogen were first reported in 1982. Therefore, developing a reliable, sensitive, and rapid assay capable of detecting E. coli O157 and the main toxins produced by STEC (i.e., Shiga toxins 1 [Stx(1)] and 2 [Stx(2)]) will directly benefit regulatory agencies by minimizing analysis time. Here, we use Luminex technology to detect multiple analytes in a single 50-ml sample. Using commercially available monoclonal antibodies coupled to carboxylated magnetic microbeads, we developed an immunoassay capable of simultaneously serotyping E. coli O157 and detecting Stx(1) and/or Stx(2). The specificity and sensitivity of this immunoassay was tested against a collection of 34 E. coli isolates belonging to various O serogroups phenotypically different for Stx. The results were compared with microplate sandwich enzyme-linked immunosorbent assay (ELISA), and no cross-reactivity was observed for any of the monoclonal antibodies used. An increased sensitivity up to 1,000 times was observed in the microbead-based immunoassay when compared with the microplate sandwich ELISA. The results indicate that Luminex technology has the potential to simultaneously detect multiple targets without loss of specificity and/or sensitivity. A blind experiment was conducted with 48 samples of ground beef, lettuce, and milk spiked with ≤2 CFU/g E. coli. All the samples were correctly identified, with no false positives or false negatives. This microbead-based immunoassay could be extended to simultaneously detect additional foodborne pathogens and their toxic markers.

  12. Synthesis and electrochemical detection of a thiazolyl-indole natural product isolated from the nosocomial pathogen Pseudomonas aeruginosa.

    PubMed

    Buzid, Alyah; Muimhneacháin, Eoin Ó; Reen, F Jerry; Hayes, Phyllis E; Pardo, Leticia M; Shang, Fengjun; O'Gara, Fergal; Sperry, Jonathan; Luong, John H T; Glennon, Jeremy D; McGlacken, Gerard P

    2016-09-01

    Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen, capable of surviving in a broad range of natural environments and quickly acquiring resistance. It is associated with hospital-acquired infections, particularly in patients with compromised immunity, and is the primary cause of morbidity and mortality in cystic fibrosis (CF) patients. P. aeruginosa is also of nosocomial importance on dairy farms and veterinary hospitals, where it is a key morbidity factor in bovine mastitis. P. aeruginosa uses a cell-cell communication system consisting of signalling molecules to coordinate bacterial secondary metabolites, biofilm formation, and virulence. Simple and sensitive methods for the detection of biomolecules as indicators of P. aeruginosa infection would be of great clinical importance. Here, we report the synthesis of the P. aeruginosa natural product, barakacin, which was recently isolated from the bovine ruminal strain ZIO. A simple and sensitive electrochemical method was used for barakacin detection using a boron-doped diamond (BDD) and glassy carbon (GC) electrodes, based on cyclic voltammetry (CV) and differential pulse voltammetry (DPV). The influence of electrolyte pH on the peak potential and peak currents was also investigated. At pH 2.0, the peak current was linearly dependent on barakacin concentration (in the range used, 1-10 μM), with correlation coefficients greater than 0.98 on both electrodes. The detection limit (S/N = 3) on the BDD electrode was 100-fold lower than that obtained on the GC electrode. The optimized method using the BDD electrode was extended to bovine (cow feces) and human (sputum of a CF patient) samples. Spiked barakacin was easily detected in these matrices at a limit of 0.5 and 0.05 μM, respectively. Graphical abstract Electrochemical detection of barakacin. PMID:27473426

  13. New Sensors for In-Pile Temperature Detection at the Advanced Test Reactor National Scientific User Facility

    SciTech Connect

    J. L. Rempe; D. L. Knudson; J. E. Daw; K. G. Condie; S. Curtis Wilkins

    2009-09-01

    The Department of Energy (DOE) designated the Advanced Test Reactor (ATR) as a National Scientific User Facility (NSUF) in April 2007 to support U.S. leadership in nuclear science and technology. As a user facility, the ATR is supporting new users from universities, laboratories, and industry, as they conduct basic and applied nuclear research and development to advance the nation’s energy security needs. A key component of the ATR NSUF effort is to develop and evaluate new in-pile instrumentation techniques that are capable of providing measurements of key parameters during irradiation. This paper describes the strategy for determining what instrumentation is needed and the program for developing new or enhanced sensors that can address these needs. Accomplishments from this program are illustrated by describing new sensors now available and under development for in-pile detection of temperature at various irradiation locations in the ATR.

  14. Advanced technology for the improvement of adenoma and polyp detection during colonoscopy.

    PubMed

    Moriyama, Tomohiko; Uraoka, Toshio; Esaki, Motohiro; Matsumoto, Takayuki

    2015-04-01

    Early detection and removal of adenomatous polyps reduces colorectal cancer death. However, many studies have reported that up to 20% of adenomas can be missed during colonoscopy. To improve visualization and reduce the blind spot of the colonic mucosa for an increase in the adenoma detection rate, many endoscopic techniques and technologies have been developed. The benefit of the high-definition endoscope for improving adenoma and polyp detection is marginal. Wide-angle colonoscope has failed to improve adenoma detection compared to standard colonoscopy. Although the cap-assisted colonoscope can reduce cecal intubation times, it does not seem to improve adenoma and polyp detection. The diagnostic accuracy of the colon capsule endoscope is low compared to the conventional colonoscope. Third Eye(®) retroscope(®) , which provides additional retrograde viewing, has revealed significant improvement in adenoma and polyp detection compared to standard colonoscopy. However, this device increases procedural times. Recently developed full-spectrum endoscopy colonoscope and extra-wide-angle-view colonoscope have demonstrated a significantly lower miss rate of polyps. However, clinical trials are mandatory to determine the efficacy of these novel technologies for cancer screening. In addition, education and training for these novel techniques and technologies should seriously be considered to improve adenoma and polyp detection. PMID:25556542

  15. Recent advances in bacteriophage based biosensors for food-borne pathogen detection.

    PubMed

    Singh, Amit; Poshtiban, Somayyeh; Evoy, Stephane

    2013-01-30

    Foodborne diseases are a major health concern that can have severe impact on society and can add tremendous financial burden to our health care systems. Rapid early detection of food contamination is therefore relevant for the containment of food-borne pathogens. Conventional pathogen detection methods, such as microbiological and biochemical identification are time-consuming and laborious, while immunological or nucleic acid-based techniques require extensive sample preparation and are not amenable to miniaturization for on-site detection. Biosensors have shown tremendous promise to overcome these limitations and are being aggressively studied to provide rapid, reliable and sensitive detection platforms for such applications. Novel biological recognition elements are studied to improve the selectivity and facilitate integration on the transduction platform for sensitive detection. Bacteriophages are one such unique biological entity that show excellent host selectivity and have been actively used as recognition probes for pathogen detection. This review summarizes the extensive literature search on the application of bacteriophages (and recently their receptor binding proteins) as probes for sensitive and selective detection of foodborne pathogens, and critically outlines their advantages and disadvantages over other recognition elements.

  16. Recent Advances in Bacteriophage Based Biosensors for Food-Borne Pathogen Detection

    PubMed Central

    Singh, Amit; Poshtiban, Somayyeh; Evoy, Stephane

    2013-01-01

    Foodborne diseases are a major health concern that can have severe impact on society and can add tremendous financial burden to our health care systems. Rapid early detection of food contamination is therefore relevant for the containment of food-borne pathogens. Conventional pathogen detection methods, such as microbiological and biochemical identification are time-consuming and laborious, while immunological or nucleic acid-based techniques require extensive sample preparation and are not amenable to miniaturization for on-site detection. Biosensors have shown tremendous promise to overcome these limitations and are being aggressively studied to provide rapid, reliable and sensitive detection platforms for such applications. Novel biological recognition elements are studied to improve the selectivity and facilitate integration on the transduction platform for sensitive detection. Bacteriophages are one such unique biological entity that show excellent host selectivity and have been actively used as recognition probes for pathogen detection. This review summarizes the extensive literature search on the application of bacteriophages (and recently their receptor binding proteins) as probes for sensitive and selective detection of foodborne pathogens, and critically outlines their advantages and disadvantages over other recognition elements. PMID:23364199

  17. Large Variation in Detection of Histidine-Rich Protein 2 in Plasmodium falciparum Isolates from Colombia

    PubMed Central

    Pava, Zuleima; Echeverry, Diego F.; Díaz, Gustavo; Murillo, Claribel

    2010-01-01

    Most rapid diagnostic tests (RDTs) available use histidine-rich protein 2 (HRP2) as a target. However, it has been reported that sequence variations of this protein affects its sensitivity. Currently, there is insufficient evidence for HRP2 variability in Plasmodium falciparum isolates from Colombia and its relationship with RDT performance. To determine possible geographic differences and their effects on the performance of RDTs, 22 blood samples from patients with P. falciparum malaria from Tumaco and Buenaventura, Colombia were assessed by measurement of HRP2 concentration by an HRP2 enzyme-linked immunosorbent assay, RDTs, and thick blood smear. Statistical analysis showed an association between RDT performance and HRP2 concentrations. No significant difference was found between locations. A large variation of antigen concentration in samples was found at same parasitemia. In contrast to previously reports, there was no correlation between initial parasitemia and HRP2 concentration. Our results indicate that antigen quantity should be studied more carefully because the sensitivity of the RDT is affected more by antigen concentration than by parasitemia. PMID:20889875

  18. Virus isolation vs RT-PCR: which method is more successful in detecting VHSV and IHNV in fish tissue sampled under field conditions?

    PubMed

    Knüsel, R; Bergmann, S M; Einer-Jensen, K; Casey, J; Segner, H; Wahli, T

    2007-09-01

    This study compared the results of reverse transcription-polymerase chain reaction (RT-PCR) and traditional virus isolation on cell culture in detection of viral haemorrhagic septicaemia virus (VHSV) and infectious haematopoietic necrosis virus (IHNV). RT-PCR was used for 172 tissue sample pools (total of 859 fish) originating from a field survey on the occurrence of VHSV and IHNV in farmed and wild salmonids in Switzerland. These samples represented all sites with fish that were either identified as virus-positive by means of virus isolation (three sites, four positive tissue sample pools) and/or demonstrated positive anti-VHSV-antibody titres (83 sites, 121 positive blood samples) in a serum plaque neutralization test (SPNT). The RT-PCR technique confirmed the four VHSV-positive tissue sample pools detected by virus isolation and additionally identified one VHSV-positive sample that showed positive anti-VHSV-AB titres, but was negative in virus isolation. With IHNV, RT-PCR detected two positive samples not identified by virus isolation while in these fish the SPNT result had been questionable. One of the IHNV-positive samples represents the first detection of IHNV-RNA in wild brown trout in Switzerland. Compared to SPNT, the RT-PCR method detected, as with virus isolation, a much lower number of positive cases; reasons for this discrepancy are discussed. Our results indicate that RT-PCR can not only be successfully applied in field surveys, but may also be slightly more sensitive than virus isolation. However, in a titration experiment under laboratory conditions, the sensitivity of RT-PCR was not significantly higher when compared with virus isolation.

  19. Detection of Enterotoxigenic Potential and Determination of Clonal Profile in Staphylococcus aureus and Coagulase-Negative Staphylococci Isolated from Bovine Subclinical Mastitis in Different Brazilian States

    PubMed Central

    Mello, Priscila Luiza; Moraes Riboli, Danilo Flávio; Pinheiro, Luiza; de Almeida Martins, Lisiane; Vasconcelos Paiva Brito, Maria Aparecida; Ribeiro de Souza da Cunha, Maria de Lourdes

    2016-01-01

    Epidemiological studies have identified Staphylococcus aureus as the most common agent involved in food poisoning. However, current research highlights the importance of toxigenic coagulase-negative staphylococci (CoNS) isolated from food. The aim of this study was to characterize Staphylococcus spp. isolated from cows with bovine subclinical mastitis regarding the presence of genes responsible for the production of staphylococcal enterotoxins and of the tst-1 gene encoding toxic shock syndrome toxin 1, and to determine the clonal profile of the isolates carrying any of the genes studied. A total of 181 strains isolated in different Brazilian states, including the South, Southeast, and Northeast regions, were analyzed. The sea gene was the most frequent, which was detected in 18.2% of the isolates, followed by seb in 7.7%, sec in 14.9%, sed in 0.5%, see in 8.2%, seg in 1.6%, seh in 25.4%, sei in 6.6%, and ser in 1.6%. The sej, ses, set, and tst-1 genes were not detected in any of the isolates. The typing of the isolates by pulsed-field gel electrophoresis revealed important S. aureus and S. epidermidis clusters in different areas and the presence of enterotoxin genes in lineages isolated from animals that belong to herds located geographically close to each other. PMID:27092525

  20. Development of cost effective fenceline monitoring methods to support advanced leak detection and repair strategies

    EPA Science Inventory

    Improved mitigation of fugitive emissions of hazardous air pollutants (HAPs), volatile organic compounds (VOCs), and greenhouse gas (GHG) emissions is an important emerging topic in many industrial sectors. Efficacious leak detection and repair (LDAR) programs of the future yiel...

  1. Rapid Detection and Isolation of Escherichia coli O104:H4 from Milk Using Monoclonal Antibody-coated Magnetic Beads.

    PubMed

    Luciani, Mirella; Di Febo, Tiziana; Zilli, Katiuscia; Di Giannatale, Elisabetta; Armillotta, Gisella; Manna, Laura; Minelli, Fabio; Tittarelli, Manuela; Caprioli, Alfredo

    2016-01-01

    Monoclonal antibodies (MAbs) specific for the lipopolysaccharide (LPS) of Escherichia coli O104:H4 were produced by fusion of Sp2/O-Ag-14 mouse myeloma cells with spleen cells of Balb/c mice, immunized with heat-inactivated and sonicated E. coli O104:H4 bacterial cells. Four MAbs specific for the E. coli O104:H4 LPS (1E6G6, 1F4C9, 3G6G7, and 4G10D2) were characterized and evaluated for the use in a method for the detection of E. coli O104:H4 in milk samples that involves antibody conjugation to magnetic microbeads to reduce time and increase the efficiency of isolation. MAb 1E6G6 was selected and coupled to microbeads, then used for immuno-magnetic separation (IMS); the efficiency of the IMS method for E. coli O104:H4 isolation from milk was evaluated and compared to that of the EU RL VTEC conventional culture-based isolation procedure. Milk suspensions also containing other pathogenic bacteria that could potentially be found in milk (Campylobacter jejuni, Listeria monocytogenes, and Staphylococcus aureus) were also tested to evaluate the specificity of MAb-coated beads. Beads coated with MAb 1E6G6 showed a good ability to capture the E. coli O104:H4, even in milk samples contaminated with other bacteria, with a higher number of E. coli O104:H4 CFU reisolated in comparison with the official method (121 and 41 CFU, respectively, at 10(3) E. coli O104:H4 initial load; 19 and 6 CFU, respectively, at 10(2) E. coli O104:H4 initial load; 1 and 0 CFU, respectively, at 10(1) E. coli O104:H4 initial load). The specificity was 100%.

  2. Detection of extended spectrum β-lactamase in Pseudomonas spp. isolated from two tertiary care hospitals in Bangladesh

    PubMed Central

    2013-01-01

    Background Extended spectrum ß-lactamases (ESBLs) represent a major group of lactamases responsible for resistance, mostly produced by gram-negative bacteria, to newer generations of ß-lactam drugs currently being identified in large numbers worldwide. The present study was undertaken to see the frequency of ESBL producing Pseudomonas spp. isolated from six hundred clinical specimens (wound, pus, aural, urine, sputum, throat and other swabs) collected over a period of three years from two tertiary care hospitals in Bangladesh. Findings Aerobic bacterial culture was performed on aseptically collected swabs and only growth of Pseudomonas was considered for further species identification and ESBL production along with serotyping of Pseudomonas aeruginosa. Antimicrobial susceptibility testing was carried out using the Kirby-Bauer agar diffusion method and ESBL production was detected on Mueller Hinton agar by double-disk synergy technique using Amoxicillin-Clavulanic acid with Ceftazidime, Cefotaxime, Ceftriaxone and Aztreonam. Culture yielded 120 Pseudomonas spp. and 82 of them were biochemically characterized for species. Pseudomonas aeruginosa was found to be the predominant (90.2%) species. Of 82 isolates tested for ESBL, 31 (37.8%) were ESBL positive with 29 (93.5%) as Pseudomonas aeruginosa, the remaining 2 (6.5%) were Stenotrophomonas maltophilia and Ralstonia pickettii. Antibiogram revealed Imipenem as the most effective drug (93.3%) among all antimicrobials used against Pseudomonas spp. followed by Aminoglycosides (63.7%). Conclusion ESBL producing Pseudomonas spp. was found to be a frequent isolate from two tertiary care hospitals in Bangladesh, showing limited susceptibility to antimicrobials and decreased susceptibility to Imipenem in particular, which is a matter of great concern. PMID:23289861

  3. Rapid Detection and Isolation of Escherichia coli O104:H4 from Milk Using Monoclonal Antibody-coated Magnetic Beads

    PubMed Central

    Luciani, Mirella; Di Febo, Tiziana; Zilli, Katiuscia; Di Giannatale, Elisabetta; Armillotta, Gisella; Manna, Laura; Minelli, Fabio; Tittarelli, Manuela; Caprioli, Alfredo

    2016-01-01

    Monoclonal antibodies (MAbs) specific for the lipopolysaccharide (LPS) of Escherichia coli O104:H4 were produced by fusion of Sp2/O-Ag-14 mouse myeloma cells with spleen cells of Balb/c mice, immunized with heat-inactivated and sonicated E. coli O104:H4 bacterial cells. Four MAbs specific for the E. coli O104:H4 LPS (1E6G6, 1F4C9, 3G6G7, and 4G10D2) were characterized and evaluated for the use in a method for the detection of E. coli O104:H4 in milk samples that involves antibody conjugation to magnetic microbeads to reduce time and increase the efficiency of isolation. MAb 1E6G6 was selected and coupled to microbeads, then used for immuno-magnetic separation (IMS); the efficiency of the IMS method for E. coli O104:H4 isolation from milk was evaluated and compared to that of the EU RL VTEC conventional culture-based isolation procedure. Milk suspensions also containing other pathogenic bacteria that could potentially be found in milk (Campylobacter jejuni, Listeria monocytogenes, and Staphylococcus aureus) were also tested to evaluate the specificity of MAb-coated beads. Beads coated with MAb 1E6G6 showed a good ability to capture the E. coli O104:H4, even in milk samples contaminated with other bacteria, with a higher number of E. coli O104:H4 CFU reisolated in comparison with the official method (121 and 41 CFU, respectively, at 103 E. coli O104:H4 initial load; 19 and 6 CFU, respectively, at 102 E. coli O104:H4 initial load; 1 and 0 CFU, respectively, at 101 E. coli O104:H4 initial load). The specificity was 100%. PMID:27379071

  4. Rapid Detection and Isolation of Escherichia coli O104:H4 from Milk Using Monoclonal Antibody-coated Magnetic Beads.

    PubMed

    Luciani, Mirella; Di Febo, Tiziana; Zilli, Katiuscia; Di Giannatale, Elisabetta; Armillotta, Gisella; Manna, Laura; Minelli, Fabio; Tittarelli, Manuela; Caprioli, Alfredo

    2016-01-01

    Monoclonal antibodies (MAbs) specific for the lipopolysaccharide (LPS) of Escherichia coli O104:H4 were produced by fusion of Sp2/O-Ag-14 mouse myeloma cells with spleen cells of Balb/c mice, immunized with heat-inactivated and sonicated E. coli O104:H4 bacterial cells. Four MAbs specific for the E. coli O104:H4 LPS (1E6G6, 1F4C9, 3G6G7, and 4G10D2) were characterized and evaluated for the use in a method for the detection of E. coli O104:H4 in milk samples that involves antibody conjugation to magnetic microbeads to reduce time and increase the efficiency of isolation. MAb 1E6G6 was selected and coupled to microbeads, then used for immuno-magnetic separation (IMS); the efficiency of the IMS method for E. coli O104:H4 isolation from milk was evaluated and compared to that of the EU RL VTEC conventional culture-based isolation procedure. Milk suspensions also containing other pathogenic bacteria that could potentially be found in milk (Campylobacter jejuni, Listeria monocytogenes, and Staphylococcus aureus) were also tested to evaluate the specificity of MAb-coated beads. Beads coated with MAb 1E6G6 showed a good ability to capture the E. coli O104:H4, even in milk samples contaminated with other bacteria, with a higher number of E. coli O104:H4 CFU reisolated in comparison with the official method (121 and 41 CFU, respectively, at 10(3) E. coli O104:H4 initial load; 19 and 6 CFU, respectively, at 10(2) E. coli O104:H4 initial load; 1 and 0 CFU, respectively, at 10(1) E. coli O104:H4 initial load). The specificity was 100%. PMID:27379071

  5. (1)H NMR Spectroscopy of Fecal Extracts Enables Detection of Advanced Colorectal Neoplasia.

    PubMed

    Amiot, Aurelien; Dona, Anthony C; Wijeyesekera, Anisha; Tournigand, Christophe; Baumgaertner, Isabelle; Lebaleur, Yann; Sobhani, Iradj; Holmes, Elaine

    2015-09-01

    Colorectal cancer (CRC) is a growing cause of mortality in developing countries, warranting investigation into its etiopathogenesis and earlier diagnosis. Here, we investigated the fecal metabolic phenotype of patients with advanced colorectal neoplasia and controls using (1)H-nuclear magnetic resonance (NMR) spectroscopy and multivariate modeling. The fecal microbiota composition was assessed by quantitative real-time PCR as well as Wif-1 methylation levels in stools, serum, and urine and correlated to the metabolic profile of each patient. The predictivity of the model was 0.507 (Q(2)Y), and the explained variance was 0.755 (R(2)Y). Patients with advanced colorectal neoplasia demonstrated increased fecal concentrations of four short-chain fatty acids (valerate, acetate, propionate, and butyrate) and decreased signals relating to β-glucose, glutamine, and glutamate. The predictive accuracy of the multivariate (1)H NMR model was higher than that of th