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Sample records for plausible rapid time

  1. Hamiltonian formulation of time-dependent plausible inference

    CERN Document Server

    Davis, Sergio

    2014-01-01

    Maximization of the path information entropy is a clear prescription for performing time-dependent plausible inference. Here it is shown that, following this prescription under the assumption of arbitrary instantaneous constraints on position and velocity, a Lagrangian emerges which determines the most probable trajectory. Deviations from the probability maximum can be consistently described as slices in time by a Hamiltonian, according to a nonlinear Langevin equation and its associated Fokker-Planck equation. The connections unveiled between the maximization of path entropy and the Langevin/Fokker-Planck equations imply that missing information about the phase space coordinate never decreases in time, a purely information-theoretical version of the Second Law of Thermodynamics. All of these results are independent of any physical assumptions, and thus valid for any generalized coordinate as a function of time, or any other parameter. This reinforces the view that the Second Law is a fundamental property of ...

  2. A biologically plausible model of time-scale invariant interval timing.

    Science.gov (United States)

    Almeida, Rita; Ledberg, Anders

    2010-02-01

    The temporal durations between events often exert a strong influence over behavior. The details of this influence have been extensively characterized in behavioral experiments in different animal species. A remarkable feature of the data collected in these experiments is that they are often time-scale invariant. This means that response measurements obtained under intervals of different durations coincide when plotted as functions of relative time. Here we describe a biologically plausible model of an interval timing device and show that it is consistent with time-scale invariant behavior over a substantial range of interval durations. The model consists of a set of bistable units that switch from one state to the other at random times. We first use an abstract formulation of the model to derive exact expressions for some key quantities and to demonstrate time-scale invariance for any range of interval durations. We then show how the model could be implemented in the nervous system through a generic and biologically plausible mechanism. In particular, we show that any system that can display noise-driven transitions from one stable state to another can be used to implement the timing device. Our work demonstrates that a biologically plausible model can qualitatively account for a large body of data and thus provides a link between the biology and behavior of interval timing.

  3. A simple biophysically plausible model for long time constants in single neurons.

    Science.gov (United States)

    Tiganj, Zoran; Hasselmo, Michael E; Howard, Marc W

    2015-01-01

    Recent work in computational neuroscience and cognitive psychology suggests that a set of cells that decay exponentially could be used to support memory for the time at which events took place. Analytically and through simulations on a biophysical model of an individual neuron, we demonstrate that exponentially decaying firing with a range of time constants up to minutes could be implemented using a simple combination of well-known neural mechanisms. In particular, we consider firing supported by calcium-controlled cation current. When the amount of calcium leaving the cell during an interspike interval is larger than the calcium influx during a spike, the overall decay in calcium concentration can be exponential, resulting in exponential decay of the firing rate. The time constant of the decay can be several orders of magnitude larger than the time constant of calcium clearance, and it could be controlled externally via a variety of biologically plausible ways. The ability to flexibly and rapidly control time constants could enable working memory of temporal history to be generalized to other variables in computing spatial and ordinal representations.

  4. Diagnostic Plausibility of MTBDRplus and MTBDRsl Line Probe Assays for Rapid Drug Susceptibility Testing of Drug Resistant Mycobacterium tuberculosis Strains in Pakistan

    Directory of Open Access Journals (Sweden)

    Javaid

    2016-06-01

    Full Text Available Background World health organization (WHO recommends the use of line probe assays (LiPAs for rapid drug susceptibility testing (DST. However, only a limited number of studies from Pakistan have documented the performance characteristics of line probe assays in testing multi-drug resistant (MDR strains of Mycobacterium tuberculosis (MTB. Objectives The objective of this work is to evaluate the diagnostic plausibility of the LiPA tests MTBDRplus and MTBDRsl on MDR MTB isolates from Pakistan. Patients and Methods This was a cross-sectional study conducted at the Indus hospital, Karachi. LiPA testing was performed on 196 smear-positive samples using BACTEC MGIT 960 as a gold standard. Results The sensitivity of MTBDRplus for isoniazid and rifampicin was found to be 88.8% and 90.2%, respectively, while sensitivity of MTBDRsl for fluoroquinolones, amikacin/capreomycin, and ethambutol was found to be 72.9%, 81.8%, and 56.6%, respectively. Conclusions The MTBDRplus and MTBDRsl genotypic testing can serve as useful additional tools for DST in a high-burden country like Pakistan provided it is used in combination with phenotypic testing.

  5. Looking for plausibility

    CERN Document Server

    Abdullah, Wan Ahmad Tajuddin Wan

    2010-01-01

    In the interpretation of experimental data, one is actually looking for plausible explanations. We look for a measure of plausibility, with which we can compare different possible explanations, and which can be combined when there are different sets of data. This is contrasted to the conventional measure for probabilities as well as to the proposed measure of possibilities. We define what characteristics this measure of plausibility should have. In getting to the conception of this measure, we explore the relation of plausibility to abductive reasoning, and to Bayesian probabilities. We also compare with the Dempster-Schaefer theory of evidence, which also has its own definition for plausibility. Abduction can be associated with biconditionality in inference rules, and this provides a platform to relate to the Collins-Michalski theory of plausibility. Finally, using a formalism for wiring logic onto Hopfield neural networks, we ask if this is relevant in obtaining this measure.

  6. Pathways to plausibility

    DEFF Research Database (Denmark)

    Wahlberg, Ayo

    2008-01-01

    Herbal medicine has long been contrasted to modern medicine in terms of a holistic approach to healing, vitalistic theories of health and illness and an emphasis on the body’s innate self-healing capacities. At the same time, since the early 20th century, the cultivation, preparation and mass...

  7. Pathways to plausibility

    DEFF Research Database (Denmark)

    Wahlberg, Ayo

    2008-01-01

    Herbal medicine has long been contrasted to modern medicine in terms of a holistic approach to healing, vitalistic theories of health and illness and an emphasis on the body’s innate self-healing capacities. At the same time, since the early 20th century, the cultivation, preparation and mass pro...... as normalised, with herbalists, phytochemists and pharmacologists working to develop standardised production procedures as well as to identify ‘plausible’ explanations for the efficacy of these remedies....

  8. Plausible scenarios for the radiography profession in Sweden in 2025.

    Science.gov (United States)

    Björkman, B; Fridell, K; Tavakol Olofsson, P

    2017-11-01

    Radiography is a healthcare speciality with many technical challenges. Advances in engineering and information technology applications may continue to drive and be driven by radiographers. The world of diagnostic imaging is changing rapidly and radiographers must be proactive in order to survive. To ensure sustainable development, organisations have to identify future opportunities and threats in a timely manner and incorporate them into their strategic planning. Hence, the aim of this study was to analyse and describe plausible scenarios for the radiography profession in 2025. The study has a qualitative design with an inductive approach based on focus group interviews. The interviews were inspired by the Scenario-Planning method. Of the seven trends identified in a previous study, the radiographers considered two as the most uncertain scenarios that would have the greatest impact on the profession should they occur. These trends, labelled "Access to career advancement" and "A sufficient number of radiographers", were inserted into the scenario cross. The resulting four plausible future scenarios were: The happy radiographer, the specialist radiographer, the dying profession and the assembly line. It is suggested that "The dying profession" scenario could probably be turned in the opposite direction by facilitating career development opportunities for radiographers within the profession. Changing the direction would probably lead to a profession composed of "happy radiographers" who are specialists, proud of their profession and competent to carry out advanced tasks, in contrast to being solely occupied by "the assembly line". Copyright © 2017 The College of Radiographers. Published by Elsevier Ltd. All rights reserved.

  9. Diagnosing herpesvirus infections by real time amplification and rapid culture.

    NARCIS (Netherlands)

    J. Guldemeester; A.D.M.E. Osterhaus (Albert); H.G.M. Niesters (Bert); G.J.J. van Doornum (Gerard)

    2003-01-01

    textabstractProcedures using real-time technique were developed to demonstrate the presence of herpes simplex virus type 1 (HSV-1) and HSV-2, varicella zoster virus (VZV), and cytomegalovirus (CMV) in miscellaneous clinical specimens. The assays were compared to rapid culture using centrifugation fo

  10. Rapid Time Response: A solution for Manufacturing Issue

    Directory of Open Access Journals (Sweden)

    Norazlin N.

    2017-01-01

    Full Text Available Respond time in manufacturing give the major impact that able to contribute too many manufacturing issues. Based on two worst case scenario occurred where Toyota in 2009 made a massive vehicles call due to car complexity of 11 major models and over 9 million vehicles. The recalls cost at least $2 billion in cost of repair, lost deals and result in lost 5% of its market share in United State of America, while A380 was reported on missing target in new production and leads to delayed market entry due to their weak product life cycle management (PLM. These cases give a sign to all industries to possess and optimize the facilities for better traceability in shortest time period. In Industry 4.0, the traceability and time respond become the factors for high performance manufacturing and rapid time respond able to expedite the traceability process and strengthen the communication level between man, machine and management. The round trip time (RTT experiment gives variant time respond between two difference operating system for intra and inter-platform signal. If this rapid time respond is adopted in any manufacturing process, the delay in traceability on every issue that lead to losses can be successfully avoided.

  11. What can we learn from Plausible Values?

    Science.gov (United States)

    Marsman, Maarten; Maris, Gunter; Bechger, Timo; Glas, Cees

    2016-06-01

    In this paper, we show that the marginal distribution of plausible values is a consistent estimator of the true latent variable distribution, and, furthermore, that convergence is monotone in an embedding in which the number of items tends to infinity. We use this result to clarify some of the misconceptions that exist about plausible values, and also show how they can be used in the analyses of educational surveys.

  12. The Plausibility of a String Quartet Performance in Virtual Reality.

    Science.gov (United States)

    Bergstrom, Ilias; Azevedo, Sergio; Papiotis, Panos; Saldanha, Nuno; Slater, Mel

    2017-04-01

    We describe an experiment that explores the contribution of auditory and other features to the illusion of plausibility in a virtual environment that depicts the performance of a string quartet. 'Plausibility' refers to the component of presence that is the illusion that the perceived events in the virtual environment are really happening. The features studied were: Gaze (the musicians ignored the participant, the musicians sometimes looked towards and followed the participant's movements), Sound Spatialization (Mono, Stereo, Spatial), Auralization (no sound reflections, reflections corresponding to a room larger than the one perceived, reflections that exactly matched the virtual room), and Environment (no sound from outside of the room, birdsong and wind corresponding to the outside scene). We adopted the methodology based on color matching theory, where 20 participants were first able to assess their feeling of plausibility in the environment with each of the four features at their highest setting. Then five times participants started from a low setting on all features and were able to make transitions from one system configuration to another until they matched their original feeling of plausibility. From these transitions a Markov transition matrix was constructed, and also probabilities of a match conditional on feature configuration. The results show that Environment and Gaze were individually the most important factors influencing the level of plausibility. The highest probability transitions were to improve Environment and Gaze, and then Auralization and Spatialization. We present this work as both a contribution to the methodology of assessing presence without questionnaires, and showing how various aspects of a musical performance can influence plausibility.

  13. Plausibility functions and exact frequentist inference

    CERN Document Server

    Martin, Ryan

    2012-01-01

    In the frequentist program, inferential methods with exact control on error rates are a primary focus. Methods based on asymptotic distribution theory may not be suitable in a particular problem, in which case, a numerical method is needed. This paper presents a general, Monte Carlo-driven framework for the construction of frequentist procedures based on plausibility functions. It is proved that the suitably defined plausibility function-based tests and confidence regions have desired frequentist properties. Moreover, in an important special case involving likelihood ratios, conditions are given such that the plausibility function behaves asymptotically like a consistent Bayesian posterior distribution. An extension of the proposed method is also given for the case where nuisance parameters are present. A number of examples are given which illustrate the method and demonstrate its strong performance compared to other popular existing methods.

  14. Bisimulation for Single-Agent Plausibility Models

    DEFF Research Database (Denmark)

    Andersen, Mikkel Birkegaard; Bolander, Thomas; van Ditmarsch, H.;

    2013-01-01

    Epistemic plausibility models are Kripke models agents use to reason about the knowledge and beliefs of themselves and each other. Restricting ourselves to the single-agent case, we determine when such models are indistinguishable in the logical language containing conditional belief, i.e., we...... define a proper notion of bisimulation, and prove that bisimulation corresponds to logical equivalence on image-finite models. We relate our results to other epistemic notions, such as safe belief and degrees of belief. Our results imply that there are only finitely many non-bisimilar single......-agent epistemic plausibility models on a finite set of propositions. This gives decidability for single-agent epistemic plausibility planning....

  15. Biologically Plausible, Human-scale Knowledge Representation

    Science.gov (United States)

    Crawford, Eric; Gingerich, Matthew; Eliasmith, Chris

    2016-01-01

    Several approaches to implementing symbol-like representations in neurally plausible models have been proposed. These approaches include binding through synchrony (Shastri & Ajjanagadde, 1993), "mesh" binding (van der Velde & de Kamps, 2006), and conjunctive binding (Smolensky, 1990). Recent theoretical work has suggested that…

  16. Time evolution of the wave equation using rapid expansion method

    KAUST Repository

    Pestana, Reynam C.

    2010-07-01

    Forward modeling of seismic data and reverse time migration are based on the time evolution of wavefields. For the case of spatially varying velocity, we have worked on two approaches to evaluate the time evolution of seismic wavefields. An exact solution for the constant-velocity acoustic wave equation can be used to simulate the pressure response at any time. For a spatially varying velocity, a one-step method can be developed where no intermediate time responses are required. Using this approach, we have solved for the pressure response at intermediate times and have developed a recursive solution. The solution has a very high degree of accuracy and can be reduced to various finite-difference time-derivative methods, depending on the approximations used. Although the two approaches are closely related, each has advantages, depending on the problem being solved. © 2010 Society of Exploration Geophysicists.

  17. Families of Plausible Solutions to the Puzzle of Boyajian's Star

    CERN Document Server

    Wright, Jason T

    2016-01-01

    Good explanations for the unusual light curve of Boyajian's Star have been hard to find. Recent results by Montet & Simon lend strength and plausibility to the conclusion of Schaefer that in addition to short-term dimmings, the star also experiences large, secular decreases in brightness on decadal timescales. This, combined with a lack of long-wavelength excess in the star's spectral energy distribution, strongly constrains scenarios involving circumstellar material, including hypotheses invoking a spherical cloud of artifacts. We show that the timings of the deepest dimmings appear consistent with being randomly distributed, and that the star's reddening and narrow sodium absorption is consistent with the total, long-term dimming observed. Following Montet & Simon's encouragement to generate alternative hypotheses, we attempt to circumscribe the space of possible explanations with a range of plausibilities, including: a cloud in the outer solar system, structure in the ISM, natural and artificial ma...

  18. Academic Librarians' Perceptions of Teamwork and Organizational Structure in a Time of Rapid Technological Change

    Science.gov (United States)

    Strecker, Beth L.

    2010-01-01

    The purpose of this study was to explore the perceptions of academic librarians on two topics: the delivery of services to students and faculty in a time of rapid technological changes and an organizational structure appropriate for delivering services to students in a time of rapid technological changes. Several researchers agree that to…

  19. Academic Librarians' Perceptions of Teamwork and Organizational Structure in a Time of Rapid Technological Change

    Science.gov (United States)

    Strecker, Beth L.

    2010-01-01

    The purpose of this study was to explore the perceptions of academic librarians on two topics: the delivery of services to students and faculty in a time of rapid technological changes and an organizational structure appropriate for delivering services to students in a time of rapid technological changes. Several researchers agree that to…

  20. PCA Based Rapid and Real Time Face Recognition Technique

    Directory of Open Access Journals (Sweden)

    T R Chandrashekar

    2013-12-01

    Full Text Available Economical and efficient that is used in various applications is face Biometric which has been a popular form biometric system. Face recognition system is being a topic of research for last few decades. Several techniques are proposed to improve the performance of face recognition system. Accuracy is tested against intensity, distance from camera, and pose variance. Multiple face recognition is another subtopic which is under research now a day. Speed at which the technique works is a parameter under consideration to evaluate a technique. As an example a support vector machine performs really well for face recognition but the computational efficiency degrades significantly with increase in number of classes. Eigen Face technique produces quality features for face recognition but the accuracy is proved to be comparatively less to many other techniques. With increase in use of core processors in personal computers and application demanding speed in processing and multiple face detection and recognition system (for example an entry detection system in shopping mall or an industry, demand for such systems are cumulative as there is a need for automated systems worldwide. In this paper we propose a novel system of face recognition developed with C# .Net that can detect multiple faces and can recognize the faces parallel by utilizing the system resources and the core processors. The system is built around Haar Cascade based face detection and PCA based face recognition system with C#.Net. Parallel library designed for .Net is used to aide to high speed detection and recognition of the real time faces. Analysis of the performance of the proposed technique with some of the conventional techniques reveals that the proposed technique is not only accurate, but also is fast in comparison to other techniques.

  1. Critical capacity, travel time delays and travel time distribution of rapid mass transit systems

    Science.gov (United States)

    Legara, Erika Fille; Monterola, Christopher; Lee, Kee Khoon; Hung, Gih Guang

    2014-07-01

    We set up a mechanistic agent-based model of a rapid mass transit system. Using empirical data from Singapore's unidentifiable smart fare card, we validate our model by reconstructing actual travel demand and duration of travel statistics. We subsequently use this model to investigate two phenomena that are known to significantly affect the dynamics within the RTS: (1) overloading in trains and (2) overcrowding in the RTS platform. We demonstrate that by varying the loading capacity of trains, a tipping point emerges at which an exponential increase in the duration of travel time delays is observed. We also probe the impact on the rail system dynamics of three types of passenger growth distribution across stations: (i) Dirac delta, (ii) uniform and (iii) geometric, which is reminiscent of the effect of land use on transport. Under the assumption of a fixed loading capacity, we demonstrate the dependence of a given origin-destination (OD) pair on the flow volume of commuters in station platforms.

  2. Anatomically Plausible Surface Alignment and Reconstruction

    DEFF Research Database (Denmark)

    Paulsen, Rasmus R.; Larsen, Rasmus

    2010-01-01

    With the increasing clinical use of 3D surface scanners, there is a need for accurate and reliable algorithms that can produce anatomically plausible surfaces. In this paper, a combined method for surface alignment and reconstruction is proposed. It is based on an implicit surface representation...... combined with a Markov Random Field regularisation method. Conceptually, the method maintains an implicit ideal description of the sought surface. This implicit surface is iteratively updated by realigning the input point sets and Markov Random Field regularisation. The regularisation is based on a prior...... energy that has earlier proved to be particularly well suited for human surface scans. The method has been tested on full cranial scans of ten test subjects and on several scans of the outer human ear....

  3. The Role of Plausible Values in Large-Scale Surveys

    Science.gov (United States)

    Wu, Margaret

    2005-01-01

    In large-scale assessment programs such as NAEP, TIMSS and PISA, students' achievement data sets provided for secondary analysts contain so-called "plausible values." Plausible values are multiple imputations of the unobservable latent achievement for each student. In this article it has been shown how plausible values are used to: (1) address…

  4. Comprehending Conflicting Science-Related Texts: Graphs as Plausibility Cues

    Science.gov (United States)

    Isberner, Maj-Britt; Richter, Tobias; Maier, Johanna; Knuth-Herzig, Katja; Horz, Holger; Schnotz, Wolfgang

    2013-01-01

    When reading conflicting science-related texts, readers may attend to cues which allow them to assess plausibility. One such plausibility cue is the use of graphs in the texts, which are regarded as typical of "hard science." The goal of our study was to investigate the effects of the presence of graphs on the perceived plausibility and…

  5. Invariant visual object recognition: biologically plausible approaches.

    Science.gov (United States)

    Robinson, Leigh; Rolls, Edmund T

    2015-10-01

    Key properties of inferior temporal cortex neurons are described, and then, the biological plausibility of two leading approaches to invariant visual object recognition in the ventral visual system is assessed to investigate whether they account for these properties. Experiment 1 shows that VisNet performs object classification with random exemplars comparably to HMAX, except that the final layer C neurons of HMAX have a very non-sparse representation (unlike that in the brain) that provides little information in the single-neuron responses about the object class. Experiment 2 shows that VisNet forms invariant representations when trained with different views of each object, whereas HMAX performs poorly when assessed with a biologically plausible pattern association network, as HMAX has no mechanism to learn view invariance. Experiment 3 shows that VisNet neurons do not respond to scrambled images of faces, and thus encode shape information. HMAX neurons responded with similarly high rates to the unscrambled and scrambled faces, indicating that low-level features including texture may be relevant to HMAX performance. Experiment 4 shows that VisNet can learn to recognize objects even when the view provided by the object changes catastrophically as it transforms, whereas HMAX has no learning mechanism in its S-C hierarchy that provides for view-invariant learning. This highlights some requirements for the neurobiological mechanisms of high-level vision, and how some different approaches perform, in order to help understand the fundamental underlying principles of invariant visual object recognition in the ventral visual stream.

  6. An application generator for rapid prototyping of Ada real-time control software

    Science.gov (United States)

    Johnson, Jim; Biglari, Haik; Lehman, Larry

    1990-01-01

    The need to increase engineering productivity and decrease software life cycle costs in real-time system development establishes a motivation for a method of rapid prototyping. The design by iterative rapid prototyping technique is described. A tool which facilitates such a design methodology for the generation of embedded control software is described.

  7. Plausibility and evidence: the case of homeopathy.

    Science.gov (United States)

    Rutten, Lex; Mathie, Robert T; Fisher, Peter; Goossens, Maria; van Wassenhoven, Michel

    2013-08-01

    Homeopathy is controversial and hotly debated. The conclusions of systematic reviews of randomised controlled trials of homeopathy vary from 'comparable to conventional medicine' to 'no evidence of effects beyond placebo'. It is claimed that homeopathy conflicts with scientific laws and that homoeopaths reject the naturalistic outlook, but no evidence has been cited. We are homeopathic physicians and researchers who do not reject the scientific outlook; we believe that examination of the prior beliefs underlying this enduring stand-off can advance the debate. We show that interpretations of the same set of evidence--for homeopathy and for conventional medicine--can diverge. Prior disbelief in homeopathy is rooted in the perceived implausibility of any conceivable mechanism of action. Using the 'crossword analogy', we demonstrate that plausibility bias impedes assessment of the clinical evidence. Sweeping statements about the scientific impossibility of homeopathy are themselves unscientific: scientific statements must be precise and testable. There is growing evidence that homeopathic preparations can exert biological effects; due consideration of such research would reduce the influence of prior beliefs on the assessment of systematic review evidence.

  8. Rapid adaptation to time-compressed speech in young and older adults.

    Science.gov (United States)

    Simhony, Ma'ayan; Grinberg, Michal; Lavie, Limor; Banai, Karen

    2014-09-01

    The ability of human listeners to comprehend rapid speech improves quickly with experience, a process known as adaptation. Whether inefficient adaptation to rapid speech partially accounts for the marked difficulties of older listeners with rapid speech is not clear. Two conditions of adaptation to time-compressed speech were used. A baseline condition intended to test the hypothesis that adaptation is different in older and younger listeners, and an interference condition in which sentences compressed to two different rates were interleaved. Identification accuracy was compared between two time points (before and after adaptation) and between older and younger listeners. The effects of adaptation did not differ between younger and older listeners in either adaptation condition. It seems that once initial performance differences are taken into account, rapid adaptation to time-compressed speech is as effective and as immune to interference by competing speech rates in younger and older adults.

  9. RAPID: real-time analytics platform for interactive data-mining in a decision support scenario

    Science.gov (United States)

    Vanni, Michelle; Kase, Sue E.; Karunasekara, Shanika; Falzon, Lucia; Harwood, Aaron

    2017-05-01

    Real-time Analytics Platform for Interactive Data-mining (RAPID), a collaboration of University of Melbourne and Australia's Defense Science and Technology Group (DSTG), consumes data streams, performs analytics computations, and produces high-quality knowledge for analysts. RAPID takes topic seed words and autonomously identifies emerging keywords in the data. Users direct the system, setting time-windowing parameters, thresholds, update intervals and sample rates. Apache Storm and Apache Kafka permit real-time streaming while logging options support off-line processing. Decision-support scenarios feature Commander Critical Information Requirements involving comparisons over time and time-sequencing of events, capabilities particularly well-served by RAPID technology, to be demonstrated in the presentation.

  10. Analytic Models of Plausible Gravitational Lens Potentials

    Energy Technology Data Exchange (ETDEWEB)

    Baltz, Edward A.; Marshall, Phil; Oguri, Masamune

    2007-05-04

    Gravitational lenses on galaxy scales are plausibly modeled as having ellipsoidal symmetry and a universal dark matter density profile, with a Sersic profile to describe the distribution of baryonic matter. Predicting all lensing effects requires knowledge of the total lens potential: in this work we give analytic forms for that of the above hybrid model. Emphasizing that complex lens potentials can be constructed from simpler components in linear combination, we provide a recipe for attaining elliptical symmetry in either projected mass or lens potential.We also provide analytic formulae for the lens potentials of Sersic profiles for integer and half-integer index. We then present formulae describing the gravitational lensing effects due to smoothly-truncated universal density profiles in cold dark matter model. For our isolated haloes the density profile falls off as radius to the minus fifth or seventh power beyond the tidal radius, functional forms that allow all orders of lens potential derivatives to be calculated analytically, while ensuring a non-divergent total mass. We show how the observables predicted by this profile differ from that of the original infinite-mass NFW profile. Expressions for the gravitational flexion are highlighted. We show how decreasing the tidal radius allows stripped haloes to be modeled, providing a framework for a fuller investigation of dark matter substructure in galaxies and clusters. Finally we remark on the need for finite mass halo profiles when doing cosmological ray-tracing simulations, and the need for readily-calculable higher order derivatives of the lens potential when studying catastrophes in strong lenses.

  11. Resetting AUDI Algorithm Used in Rapid Time-varying MIMO System Identification

    Institute of Scientific and Technical Information of China (English)

    Xu Chao(许超); Chen Zhigang; Shao Huihe

    2004-01-01

    Augmented UD identification (AUDI) technique is derived from the traditional recursive least-squares (RLS) algorithm and has been developed rapidly during the last decade. AUDI is a cluster of identification algorithms based on matrix factorization methods (such as QR and LDL) and thus shows its stable performance in system identification applications. An AUDI algorithm with resetting strategy (RAUDI) has much ability in rapid time-varying SISO system identification. In this paper, an endeavor to expand the RAUDI in MIMO system identification is made and a comparative experiement is done to exhibit its good ability in rapidly changing parameter estimate in MIMO system.

  12. Encoding the target or the plausible preview word? The nature of the plausibility preview benefit in reading Chinese.

    Science.gov (United States)

    Yang, Jinmian; Li, Nan; Wang, Suiping; Slattery, Timothy J; Rayner, Keith

    2014-01-01

    Previous studies have shown that a plausible preview word can facilitate the processing of a target word as compared to an implausible preview word (a plausibility preview benefit effect) when reading Chinese (Yang, Wang, Tong, & Rayner, 2012; Yang, 2013). Regarding the nature of this effect, it is possible that readers processed the meaning of the plausible preview word and did not actually encode the target word (given that the parafoveal preview word lies close to the fovea). The current experiment examined this possibility with three conditions wherein readers received a preview of a target word that was either (1) identical to the target word (identical preview), (2) a plausible continuation of the pre-target text, but the post-target text in the sentence was incompatible with it (initially plausible preview), or (3) not a plausible continuation of the pre-target text, nor compatible with the post-target text (implausible preview). Gaze durations on target words were longer in the initially plausible condition than the identical condition. Overall, the results showed a typical preview benefit, but also implied that readers did not encode the initially plausible preview. Also, a plausibility preview benefit was replicated: gaze durations were longer with implausible previews than the initially plausible ones. Furthermore, late eye movement measures did not reveal differences between the initially plausible and the implausible preview conditions, which argues against the possibility of misreading the plausible preview word as the target word. In sum, these results suggest that a plausible preview word provides benefit in processing the target word as compared to an implausible preview word, and this benefit is only present in early but not late eye movement measures.

  13. Rapid antimicrobial susceptibility testing of clinical isolates by digital time-lapse microscopy

    DEFF Research Database (Denmark)

    Fredborg, M; Rosenvinge, F S; Spillum, E

    2015-01-01

    Rapid antimicrobial susceptibility testing (AST) is essential for early and appropriate therapy. Methods with short detection time enabling same-day treatment optimisation are highly favourable. In this study, we evaluated the potential of a digital time-lapse microscope system, the oCelloScope s......Rapid antimicrobial susceptibility testing (AST) is essential for early and appropriate therapy. Methods with short detection time enabling same-day treatment optimisation are highly favourable. In this study, we evaluated the potential of a digital time-lapse microscope system, the o...... (168 antimicrobial agent-organism combinations) demonstrated 3.6 % minor, no major and 1.2 % very major errors of the oCelloScope system compared to conventional susceptibility testing, as well as a rapid and correct phenotypic detection of strains with methicillin-resistant Staphylococcus aureus (MRSA...

  14. A simple channel estimator for space-time coded OFDM systems in rapid fading channels

    Institute of Scientific and Technical Information of China (English)

    单淑伟; 罗汉文; 宋文涛

    2004-01-01

    A simple channel estimator for space-time coded orthogonal frequency division multiplexing (OFDM) systems in rapid fading channels is proposed. The channels at the training bauds are estimated using the EM (expectation-maximization) algorithm, while the channels at the data bauds are estimated based on the method for modelling the time-varying channel as the linear combination of several time-invariant " Doppler channels". Computer simulations showed that this estimator outperforms the decision-directed tracking in rapid fading channels and that the performance of this method can be improved by iteration.

  15. A simple channel estimator for space-time coded OFDM systems in rapid fading channels

    Institute of Scientific and Technical Information of China (English)

    SHAN Shu-wei(单淑伟); LUO Han-wen(罗汉文); SONG Wen-tao(宋文涛)

    2004-01-01

    A simple channel estimator for space-time coded orthogonal frequency division multiplexing (OFDM) systems in rapid fading channels is proposed. The channels at the training bauds are estimated using the EM (expectation-maximization) algorithm, while the channels at the data bauds are estimated based on the method for modelling the time-varying channel as the linear combination of several time-invariant "Doppler channels". Computer simulations showed that this estimator outperforms the decision-directed tracking in rapid fading channels and that the performance of this method can be improved by iteration.

  16. Rapid detection of Salmonella in bovine lymph nodes using a commercial real-time PCR system

    Science.gov (United States)

    Rapid Salmonella detection is needed to help prevent the distribution of contaminated food products. Using traditional culture methods, Salmonella detection can take up to 3-5 days. Using an improved protocol and a commercial real-time PCR system, we have shortened the detection time to under 24 h...

  17. Reading Time Allocation Strategies and Working Memory Using Rapid Serial Visual Presentation

    Science.gov (United States)

    Busler, Jessica N.; Lazarte, Alejandro A.

    2017-01-01

    Rapid serial visual presentation (RSVP) is a useful method for controlling the timing of text presentations and studying how readers' characteristics, such as working memory (WM) and reading strategies for time allocation, influence text recall. In the current study, a modified version of RSVP (Moving Window RSVP [MW-RSVP]) was used to induce…

  18. A rapid and direct real time PCR-based method for identification of Salmonella spp

    DEFF Research Database (Denmark)

    Rodriguez-Lazaro, D.; Hernández, Marta; Esteve, T.

    2003-01-01

    The aim of this work was the validation of a rapid, real-time PCR assay based on TaqMan((R)) technology for the unequivocal identification of Salmonella spp. to be used directly on an agar-grown colony. A real-time PCR system targeting at the Salmonella spp. invA gene was optimized and validated ...

  19. Rapid and simple determination of T1 relaxation times in time-domain NMR by Continuous Wave Free Precession sequence

    Science.gov (United States)

    Moraes, Tiago Bueno; Monaretto, Tatiana; Colnago, Luiz Alberto

    2016-09-01

    Longitudinal (T1) and transverse (T2) relaxation times have been widely used in time-domain NMR (TD-NMR) to determine several physicochemical properties of petroleum, polymers, and food products. The measurement of T2 through the CPMG pulse sequence has been used in most of these applications because it denotes a rapid, robust method. On the other hand, T1 has been occasionally used in TD-NMR due to the long measurement time required to collect multiple points along the T1 relaxation curve. Recently, several rapid methods to measure T1 have been proposed. Those methods based upon single shot, known as Continuous Wave Free Precession (CWFP) pulse sequences, have been employed in the simultaneous measurement of T1 and T2 in a rapid fashion. However, these sequences can be used exclusively in instrument featuring short dead time because the magnitude of the signal at thermal equilibrium is required. In this paper, we demonstrate that a special CWFP sequence with a low flip angle can be a simple and rapid method to measure T1 regardless of instruments dead time. Experimental results confirmed that the method called CWFP-T1 may be used to measure both single T1 value and T1 distribution in heterogeneous samples. Therefore, CWFP-T1 sequence can be a feasible alternative to CPMG in the determination of physicochemical properties, particularly in processes where fast protocols are requested such as industrial applications.

  20. Rapid and real-time detection technologies for emerging viruses of biomedical importance

    Indian Academy of Sciences (India)

    M M Parida

    2008-11-01

    The development of technologies with rapid and sensitive detection capabilities and increased throughput have become crucial for responding to greater number threats posed by emerging and re-emerging viruses in the recent past. The conventional identification methods require time-consuming culturing, and/ or detection of antibodies, which are not very sensitive and specific. The recent advances in molecular biology techniques in the field of genomics and proteomics greatly facilitate the rapid identification with more accuracy. We have developed two real-time assays i.e., SYBR green I based real time reverse transcription polymerase chain reaction (RT-PCR) and RT-loop-mediated isothermal amplification (LAMP) assay for rapid detection as well as typing of some of the emerging viruses of biomedical importance viz. dengue, Japanese encephalitis, chikungunya, west Nile, severe acute respiratory syndrome virus (SARS) etc. Both these techniques are capable of detection and differentiation as well as quantifying viral load with higher sensitivity, rapidity, specificity. One of the most important advantages of LAMP is its field applicability, without requirement of any sophisticated equipments. Both these assays have been extensively evaluated and validated with clinical samples of recent epidemics from different parts of India. The establishment of these real time molecular assays will certainly facilitate the rapid detection of viruses with high degree of precision and accuracy in future.

  1. Event-based plausibility immediately influences on-line language comprehension.

    Science.gov (United States)

    Matsuki, Kazunaga; Chow, Tracy; Hare, Mary; Elman, Jeffrey L; Scheepers, Christoph; McRae, Ken

    2011-07-01

    In some theories of sentence comprehension, linguistically relevant lexical knowledge, such as selectional restrictions, is privileged in terms of the time-course of its access and influence. We examined whether event knowledge computed by combining multiple concepts can rapidly influence language understanding even in the absence of selectional restriction violations. Specifically, we investigated whether instruments can combine with actions to influence comprehension of ensuing patients of (as in Rayner, Warren, Juhuasz, & Liversedge, 2004; Warren & McConnell, 2007). Instrument-verb-patient triplets were created in a norming study designed to tap directly into event knowledge. In self-paced reading (Experiment 1), participants were faster to read patient nouns, such as hair, when they were typical of the instrument-action pair (Donna used the shampoo to wash vs. the hose to wash). Experiment 2 showed that these results were not due to direct instrument-patient relations. Experiment 3 replicated Experiment 1 using eyetracking, with effects of event typicality observed in first fixation and gaze durations on the patient noun. This research demonstrates that conceptual event-based expectations are computed and used rapidly and dynamically during on-line language comprehension. We discuss relationships among plausibility and predictability, as well as their implications. We conclude that selectional restrictions may be best considered as event-based conceptual knowledge rather than lexical-grammatical knowledge.

  2. Complex Learning in Bio-plausible Memristive Networks.

    Science.gov (United States)

    Deng, Lei; Li, Guoqi; Deng, Ning; Wang, Dong; Zhang, Ziyang; He, Wei; Li, Huanglong; Pei, Jing; Shi, Luping

    2015-06-19

    The emerging memristor-based neuromorphic engineering promises an efficient computing paradigm. However, the lack of both internal dynamics in the previous feedforward memristive networks and efficient learning algorithms in recurrent networks, fundamentally limits the learning ability of existing systems. In this work, we propose a framework to support complex learning functions by introducing dedicated learning algorithms to a bio-plausible recurrent memristive network with internal dynamics. We fabricate iron oxide memristor-based synapses, with well controllable plasticity and a wide dynamic range of excitatory/inhibitory connection weights, to build the network. To adaptively modify the synaptic weights, the comprehensive recursive least-squares (RLS) learning algorithm is introduced. Based on the proposed framework, the learning of various timing patterns and a complex spatiotemporal pattern of human motor is demonstrated. This work paves a new way to explore the brain-inspired complex learning in neuromorphic systems.

  3. Plausibility Judgments in Conceptual Change and Epistemic Cognition

    Science.gov (United States)

    Lombardi, Doug; Nussbaum, E. Michael; Sinatra, Gale M.

    2016-01-01

    Plausibility judgments rarely have been addressed empirically in conceptual change research. Recent research, however, suggests that these judgments may be pivotal to conceptual change about certain topics where a gap exists between what scientists and laypersons find plausible. Based on a philosophical and empirical foundation, this article…

  4. Source Effects and Plausibility Judgments When Reading about Climate Change

    Science.gov (United States)

    Lombardi, Doug; Seyranian, Viviane; Sinatra, Gale M.

    2014-01-01

    Gaps between what scientists and laypeople find plausible may act as a barrier to learning complex and/or controversial socioscientific concepts. For example, individuals may consider scientific explanations that human activities are causing current climate change as implausible. This plausibility judgment may be due-in part-to individuals'…

  5. Diagnosing herpesvirus infections by real-time amplification and rapid culture

    NARCIS (Netherlands)

    J. Guldemeester; H.G.M. Niesters (Bert); A.D.M.E. Osterhaus (Albert); G.J.J. van Doornum (Gerard)

    2003-01-01

    textabstractProcedures using real-time technique were developed to demonstrate the presence of herpes simplex virus type 1 (HSV-1) and HSV-2, varicella zoster virus (VZV), and cytomegalovirus (CMV) in miscellaneous clinical specimens. The assays were compared to rapid culture using centrifugation fo

  6. Efficacy of real-time polymerase chain reaction for rapid diagnosis of endobronchial tuberculosis

    Directory of Open Access Journals (Sweden)

    Gang Hou

    2014-10-01

    Conclusions: Real-time PCR detection of M. tuberculosis DNA in EBTB biopsy tissue is more sensitive than sputum smear and bronchial brush smear, including at early disease stages. This PCR method may be a useful adjunct to culture- and smear-based techniques to allow more rapid EBTB diagnosis and timelier treatment.

  7. Biologically plausible and evidence-based risk intervals in immunization safety research.

    Science.gov (United States)

    Rowhani-Rahbar, Ali; Klein, Nicola P; Dekker, Cornelia L; Edwards, Kathryn M; Marchant, Colin D; Vellozzi, Claudia; Fireman, Bruce; Sejvar, James J; Halsey, Neal A; Baxter, Roger

    2012-12-17

    In immunization safety research, individuals are considered at risk for the development of certain adverse events following immunization (AEFI) within a specific period of time referred to as the risk interval. These intervals should ideally be determined based on biologic plausibility considering features of the AEFI, presumed or known pathologic mechanism, and the vaccine. Misspecification of the length and timing of these intervals may result in introducing bias in epidemiologic and clinical studies of immunization safety. To date, little work has been done to formally assess and determine biologically plausible and evidence-based risk intervals in immunization safety research. In this report, we present a systematic process to define biologically plausible and evidence-based risk interval estimates for two specific AEFIs, febrile seizures and acute disseminated encephalomyelitis. In addition, we review methodologic issues related to the determination of risk intervals for consideration in future studies of immunization safety.

  8. Mapping land cover through time with the Rapid Land Cover Mapper—Documentation and user manual

    Science.gov (United States)

    Cotillon, Suzanne E.; Mathis, Melissa L.

    2017-02-15

    The Rapid Land Cover Mapper is an Esri ArcGIS® Desktop add-in, which was created as an alternative to automated or semiautomated mapping methods. Based on a manual photo interpretation technique, the tool facilitates mapping over large areas and through time, and produces time-series raster maps and associated statistics that characterize the changing landscapes. The Rapid Land Cover Mapper add-in can be used with any imagery source to map various themes (for instance, land cover, soils, or forest) at any chosen mapping resolution. The user manual contains all essential information for the user to make full use of the Rapid Land Cover Mapper add-in. This manual includes a description of the add-in functions and capabilities, and step-by-step procedures for using the add-in. The Rapid Land Cover Mapper add-in was successfully used by the U.S. Geological Survey West Africa Land Use Dynamics team to accurately map land use and land cover in 17 West African countries through time (1975, 2000, and 2013).

  9. Rapid Real-Time Antimicrobial Susceptibility Testing with Electrical Sensing on Plastic Microchips with Printed Electrodes.

    Science.gov (United States)

    Safavieh, Mohammadali; Pandya, Hardik J; Venkataraman, Maanasa; Thirumalaraju, Prudhvi; Kanakasabapathy, Manoj Kumar; Singh, Anupriya; Prabhakar, Devbalaji; Chug, Manjyot Kaur; Shafiee, Hadi

    2017-03-30

    Rapid antimicrobial susceptibility testing is important for efficient and timely therapeutic decision making. Due to globally spread bacterial resistance, the efficacy of antibiotics is increasingly being impeded. Conventional antibiotic tests rely on bacterial culture, which is time-consuming and can lead to potentially inappropriate antibiotic prescription and up-front broad range of antibiotic use. There is an urgent need to develop point-of-care platform technologies to rapidly detect pathogens, identify the right antibiotics, and monitor mutations to help adjust therapy. Here, we report a biosensor for rapid (microchips with printed electrodes using antibodies (30 min), and its electrical response is monitored in the presence and absence of antibiotics over an hour of incubation time. We evaluated the microchip with Escherichia coli and methicillin-resistant Staphylococcus aureus (MRSA) as clinical models with ampicillin, ciprofloxacin, erythromycin, daptomycin, gentamicin, and methicillin antibiotics. The results are compared with the current standard methods, i.e. bacteria viability and conventional antibiogram assays. The technology presented here has the potential to provide precise and rapid bacteria screening and guidance in clinical therapies by identifying the correct antibiotics for pathogens.

  10. Fuji apple storage time rapid determination method using Vis/NIR spectroscopy.

    Science.gov (United States)

    Liu, Fuqi; Tang, Xuxiang

    2015-01-01

    Fuji apple storage time rapid determination method using visible/near-infrared (Vis/NIR) spectroscopy was studied in this paper. Vis/NIR diffuse reflection spectroscopy responses to samples were measured for 6 days. Spectroscopy data were processed by stochastic resonance (SR). Principal component analysis (PCA) was utilized to analyze original spectroscopy data and SNR eigen value. Results demonstrated that PCA could not totally discriminate Fuji apples using original spectroscopy data. Signal-to-noise ratio (SNR) spectrum clearly classified all apple samples. PCA using SNR spectrum successfully discriminated apple samples. Therefore, Vis/NIR spectroscopy was effective for Fuji apple storage time rapid discrimination. The proposed method is also promising in condition safety control and management for food and environmental laboratories.

  11. Developments in time-resolved high pressure x-ray diffraction using rapid compression and decompression

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Jesse S.; Sinogeikin, Stanislav V.; Lin, Chuanlong; Rod, Eric; Bai, Ligang; Shen, Guoyin [High Pressure Collaborative Access Team, Geophysical Laboratory, Carnegie Institution of Washington, Argonne, Illinois 60439 (United States)

    2015-07-15

    Complementary advances in high pressure research apparatus and techniques make it possible to carry out time-resolved high pressure research using what would customarily be considered static high pressure apparatus. This work specifically explores time-resolved high pressure x-ray diffraction with rapid compression and/or decompression of a sample in a diamond anvil cell. Key aspects of the synchrotron beamline and ancillary equipment are presented, including source considerations, rapid (de)compression apparatus, high frequency imaging detectors, and software suitable for processing large volumes of data. A number of examples are presented, including fast equation of state measurements, compression rate dependent synthesis of metastable states in silicon and germanium, and ultrahigh compression rates using a piezoelectric driven diamond anvil cell.

  12. [Rapid diagnosis of psittacosis using a recently developed real-time PCR technique].

    Science.gov (United States)

    van der Bruggen, T; Kaan, J A; Heddema, E R; van Hannen, E J; de Jongh, B M

    2008-08-23

    A 37-year-old man was admitted with cough and fever. Three days after admission he was tested using a newly developed real-time PCR technique that detects the DNA of Chlamydophila psittaci. The result was positive; serological investigation was not positive until 14 days later. Psittacosis is a potentially life-threatening infectious disease. Laboratory diagnosis relies mainly on the assessment of paired sera, but this approach has obvious disadvantages in the acute setting. Routine use of the real-time PCR technique led to the rapid diagnosis of psittacosis in 6 other patients. All 7 patients recovered after antibiotic treatment. This PCR technique is a valuable adjuvant to serological testing for the rapid diagnosis of psittacosis.

  13. Fuji apple storage time rapid determination method using Vis/NIR spectroscopy

    Science.gov (United States)

    Liu, Fuqi; Tang, Xuxiang

    2015-01-01

    Fuji apple storage time rapid determination method using visible/near-infrared (Vis/NIR) spectroscopy was studied in this paper. Vis/NIR diffuse reflection spectroscopy responses to samples were measured for 6 days. Spectroscopy data were processed by stochastic resonance (SR). Principal component analysis (PCA) was utilized to analyze original spectroscopy data and SNR eigen value. Results demonstrated that PCA could not totally discriminate Fuji apples using original spectroscopy data. Signal-to-noise ratio (SNR) spectrum clearly classified all apple samples. PCA using SNR spectrum successfully discriminated apple samples. Therefore, Vis/NIR spectroscopy was effective for Fuji apple storage time rapid discrimination. The proposed method is also promising in condition safety control and management for food and environmental laboratories. PMID:25874818

  14. Rapid, Time-Division Multiplexed, Direct Absorption- and Wavelength Modulation-Spectroscopy

    OpenAIRE

    Alexander Klein; Oliver Witzel; Volker Ebert

    2014-01-01

    We present a tunable diode laser spectrometer with a novel, rapid time multiplexed direct absorption- and wavelength modulation-spectroscopy operation mode. The new technique allows enhancing the precision and dynamic range of a tunable diode laser absorption spectrometer without sacrificing accuracy. The spectroscopic technique combines the benefits of absolute concentration measurements using calibration-free direct tunable diode laser absorption spectroscopy (dTDLAS) with the enhanced nois...

  15. Plausible values: how to deal with their limitations.

    Science.gov (United States)

    Monseur, Christian; Adams, Raymond

    2009-01-01

    Rasch modeling and plausible values methodology were used to scale and report the results of the Organization for Economic Cooperation and Development's Programme for International Student Achievement (PISA). This article will describe the scaling approach adopted in PISA. In particular it will focus on the use of plausible values, a multiple imputation approach that is now commonly used in large-scale assessment. As with all imputation models the plausible values must be generated using models that are consistent with those used in subsequent data analysis. In the case of PISA the plausible value generation assumes a flat linear regression with all students' background variables collected through the international student questionnaire included as regressors. Further, like most linear models, homoscedasticity and normality of the conditional variance are assumed. This article will explore some of the implications of this approach. First, we will discuss the conditions under which the secondary analyses on variables not included in the model for generating the plausible values might be biased. Secondly, as plausible values were not drawn from a multi-level model, the article will explore the adequacy of the PISA procedures for estimating variance components when the data have a hierarchical structure.

  16. A biologically plausible embodied model of action discovery

    Directory of Open Access Journals (Sweden)

    Rufino eBolado-Gomez

    2013-03-01

    Full Text Available During development, animals can spontaneously discover action-outcomepairings enabling subsequent achievement of their goals. We present abiologically plausible embodied model addressing key aspects of thisprocess. The biomimetic model core comprises the basal ganglia and itsloops through cortex and thalamus. We incorporate reinforcementlearning with phasic dopamine supplying a sensory prediction error,signalling 'surprising' outcomes. Phasic dopamine is used in acorticostriatal learning rule which is consistent with recent data. Wealso hypothesised that objects associated with surprising outcomesacquire 'novelty salience' contingent on the predicability of theoutcome. To test this idea we used a simple model of predictiongoverning the dynamics of novelty salience and phasic dopamine. Thetask of the virtual robotic agent mimicked an in vivo counterpart(Gancarz et al., 2011 and involved interaction with a target objectwhich caused a light flash, or a control object which did not.Learning took place according to two schedules. In one, the phasicoutcome was delivered after interaction with the target in anunpredictable way which emulated the in vivo protocol. Without noveltysalience, the model was unable to account for the experimental data.In the other schedule, the phasic outcome was reliably delivered andthe agent showed a rapid increase in the number of interactions withthe target which then decreased over subsequent sessions. We arguethis is precisely the kind of change in behaviour required torepeatedly present representations of context, action and outcome, toneural networks responsible for learning action-outcome contingency.The model also showed corticostriatal plasticity consistent withlearning a new action in basal ganglia. We conclude that actionlearning is underpinned by a complex interplay of plasticity andstimulus salience, and that our model contains many of the elementsfor biological action discovery to take place.

  17. The MODIS Rapid Response Project: Near-Real-Time Processing for Fire Monitoring and Other Applications

    Science.gov (United States)

    Descloitres, J.; Justice, C.; Sohlberg, R.; Giglio, L.; Schmaltz, J.; Seaton, J.; Davies, D.; Anyamba, A.; Hansen, M.; Carroll, M.; Sullivan, M.

    2003-12-01

    The Moderate-resolution Imaging Spectroradiometer (MODIS) instrument on board the Terra and Aqua satellites offers an unprecedented combination of daily spatial coverage, spatial resolution, and spectral characteristics. These capabilities make MODIS ideal to observe a variety of rapid events: active fires, floods, smoke transport, dust storms, severe storms, iceberg calving, and volcanic eruptions. The MODIS Rapid Response System (http://rapidfire.sci.gsfc.nasa.gov) was developed at NASA's Goddard Space Flight Center to provide a rapid response to those events, with initial emphasis on active fire detection and 250m-resolution imagery. MODIS data for most of the Earth's land surface is processed just a few hours after data acquisition. A collaboration between NASA, the University of Maryland and the U.S.D.A. Forest Service has been developed to provide fire information derived from MODIS to federal fire managers. Active fire locations in the conterminous United States are produced by the MODIS Rapid Response System and communicated to the Forest Service within a few minutes of production. The MODIS Rapid Response processing was also adapted to Direct Broadcast to reduce the product turn-around to just minutes after data acquisition regionally. MODIS active fire locations are used by the Forest Service to generate regional fire maps over the United States, updated twice daily and provided to the fire managers to help them allocate firefighting resources. Active fire locations are also distributed in near-real-time to the Global Observation of Forest Cover (G.O.F.C.) user community through a web interface integrating MODIS active fire locations and Geographic Information System (G.I.S.) datasets. The suite of MODIS rapid fire products is currently being complemented with a Smoke Index product and a Burned Area product that will represent two new key tools available to the fire community. Finally a new collaboration with the U.S.D.A. Foreign Agricultural Service was

  18. Rapid diagnosis of sepsis with TaqMan-Based multiplex real-time PCR.

    Science.gov (United States)

    Liu, Chang-Feng; Shi, Xin-Ping; Chen, Yun; Jin, Ye; Zhang, Bing

    2017-05-17

    The survival rate of septic patients mainly depends on a rapid and reliable diagnosis. A rapid, broad range, specific and sensitive quantitative diagnostic test is the urgent need. Thus, we developed a TaqMan-Based Multiplex real-time PCR assays to identify bloodstream pathogens within a few hours. Primers and TaqMan probes were designed to be complementary to conserved regions in the 16S rDNA gene of different kinds of bacteria. To evaluate accurately, sensitively, and specifically, the known bacteria samples (Standard strains, whole blood samples) are determined by TaqMan-Based Multiplex real-time PCR. In addition, 30 blood samples taken from patients with clinical symptoms of sepsis were tested by TaqMan-Based Multiplex real-time PCR and blood culture. The mean frequency of positive for Multiplex real-time PCR was 96% at a concentration of 100 CFU/mL, and it was 100% at a concentration greater than 1000 CFU/mL. All the known blood samples and Standard strains were detected positively by TaqMan-Based Multiplex PCR, no PCR products were detected when DNAs from other bacterium were used in the multiplex assay. Among the 30 patients with clinical symptoms of sepsis, 18 patients were confirmed positive by Multiplex real-time PCR and seven patients were confirmed positive by blood culture. TaqMan-Based Multiplex real-time PCR assay with highly sensitivity, specificity and broad detection range, is a rapid and accurate method in the detection of bacterial pathogens of sepsis and should have a promising usage in the diagnosis of sepsis. © 2017 Wiley Periodicals, Inc.

  19. Rapid variability as a probe of warped space-time around accreting black holes

    Science.gov (United States)

    Axelsson, Magnus

    2016-07-01

    The geometry of the inner accretion flow of X-ray binaries is complex, with multiple regions contributing to the observed emission. Frequency-resolved spectroscopy is a powerful tool in breaking this spectral degeneracy. We have extracted the spectra of the strong low-frequency quasi-periodic oscillation (QPO) and its harmonic in GX339-4 and XTE J1550-564, and compare these to the time-averaged spectrum and the spectrum of the rapid (plaguing the time-averaged spectrum and revealing the geometry of the accretion flow close to the black hole.

  20. Rapid homogenous time-resolved fluorescence (HTRF) immunoassay for anthrax detection.

    Science.gov (United States)

    Cohen, Noam; Mechaly, Adva; Mazor, Ohad; Fisher, Morly; Zahavy, Eran

    2014-05-01

    Infection with Bacillus anthracsis spores induces an acute anthrax disease that can cause casualties and death in untreated cases. Thus rapid diagnosis of anthrax at early stage of the disease is essential to allow an effective treatment. Here we present the development of rapid and sensitive homogenous time-resolved fluorescence (HTRF) immunoassays based on the energy transfer process of europium cryptate (EuK) donor to AlexaFluor647 acceptor. The energy transfer process is limited to d bacteremia in infected hosts, using two monoclonal anti-PA antibodies that specifically recognize two different epitopes on the PA molecule. The assay was sensitive enabling detection of 2 ng/ml PA in the serum of B. anthracsis-infected rabbits in only 15 min assay. Additionally, HTRF assay was developed for the detection of bacterial spores using polyclonal anti-spore antibodies that recognize many epitopes on the bacterial surface. The assay enabled the detection of 2 × 10(6) spores/ml in 30 min assay and was specific, showing no cross reactivity with closely related non-virulent bacillus cereus strain. This study describes the use of the HTRF assay for the detection of both singled-epitope (proteins) and multi-epitope (particles) as rapid, simple and sensitive method that can be used at the time that fast results are needed to allow an effective medical care.

  1. High space-time resolution analysis of ice motion at a rapidly retreating tidewater glacier (Invited)

    Science.gov (United States)

    Oneel, S.; Joughin, I. R.; March, R. S.; Burgess, E. W.; Welty, E.; Pfeffer, W. T.; Larsen, C. F.

    2013-12-01

    Rapid changes to rates of sea level rise are forced in large part by tidewater glacier dynamics. Alaska's Columbia Glacier is an iconic example; in recent years, calving losses account for roughly 20% of the net mass loss from the entire Alaska region. In turn, the Alaska region accounts for ~20% of global new-water sea-level rise. To better understand the mechanics of rapid tidewater glacier mass loss, we present and analyze surface elevation and velocity data acquired at high time resolution since fall 2011. Strong seasonality in flow speed exists, with more than a doubling of near-terminus speed occurring between summer and winter. The imagery provides unprecedented spatial coverage, demonstrating spatial coherence in flow variability across most, but not all, tributaries. Preliminary calculations of ice flux also show strong seasonality, with variable year-to-year timing of peak discharge. Compared to previous estimates, the average flux in this most recent interval is reduced by ~30-40%. An additional overdeepening is located upstream from the present-day terminus, indicating another episode of increased flux is possible. However, total glacier volume has been reduced by ~50% during the retreat, and peak discharge from Columbia has likely already occurred. Our analysis suggests that, as the Columbia Glacier retreat comes to a conclusion, rates of mass loss from the Alaska region will decrease in the near-future, unless another tidewater glacier enters rapid retreat.

  2. A battery-powered notebook thermal cycler for rapid multiplex real-time PCR analysis.

    Science.gov (United States)

    Belgrader, P; Young, S; Yuan, B; Primeau, M; Christel, L A; Pourahmadi, F; Northrup, M A

    2001-01-15

    A compact, real-time PCR instrument was developed for rapid, multiplex analysis of nucleic acids in an inexpensive, portable format. The instrument consists of a notebook computer, two reaction modules with integrated optics for four-color fluorescence detection, batteries, and a battery-charging system. The instrument weighs 3.3 kg, measures 26 x 22 x 7.5 cm, and can run continuously on the internal batteries for 4 h. Independent control of the modules allows differing temperature profiles and detection schemes to be run simultaneously. Results are presented that demonstrate rapid (1) detection and identification of Bacillus subtilis and Bacillus thuringensis spores and (2) characterization of a single nucleotide polymorphism for the hereditary hemochromatosis gene.

  3. Finding Significant Stress Episodes in a Discontinuous Time Series of Rapidly Varying Mobile Sensor Data.

    Science.gov (United States)

    Sarker, Hillol; Tyburski, Matthew; Rahman, Md Mahbubur; Hovsepian, Karen; Sharmin, Moushumi; Epstein, David H; Preston, Kenzie L; Furr-Holden, C Debra; Milam, Adam; Nahum-Shani, Inbal; al'Absi, Mustafa; Kumar, Santosh

    2016-05-01

    Management of daily stress can be greatly improved by delivering sensor-triggered just-in-time interventions (JITIs) on mobile devices. The success of such JITIs critically depends on being able to mine the time series of noisy sensor data to find the most opportune moments. In this paper, we propose a time series pattern mining method to detect significant stress episodes in a time series of discontinuous and rapidly varying stress data. We apply our model to 4 weeks of physiological, GPS, and activity data collected from 38 users in their natural environment to discover patterns of stress in real-life. We find that the duration of a prior stress episode predicts the duration of the next stress episode and stress in mornings and evenings is lower than during the day. We then analyze the relationship between stress and objectively rated disorder in the surrounding neighborhood and develop a model to predict stressful episodes.

  4. Response time distributions in rapid chess: A large-scale decision making experiment

    Directory of Open Access Journals (Sweden)

    Mariano Sigman

    2010-10-01

    Full Text Available Rapid chess provides an unparalleled laboratory to understand decision making in a natural environment. In a chess game, players choose consecutively around 40 moves in a finite time budget. The goodness of each choice can be determined quantitatively since current chess algorithms estimate precisely the value of a position. Web-based chess produces vast amounts of data, millions of decisions per day, incommensurable with traditional psychological experiments. We generated a database of response times and position value in rapid chess games. We measured robust emergent statistical observables: 1 Response time (RT distributions are long-tailed and show qualitatively distinct forms at different stages of the game, 2 RT of successive moves are highly correlated both for intra- and inter-player moves. These findings have theoretical implications since they deny two basic assumptions of sequential decision making algorithms: RTs are not stationary and can not be generated by a state function. Our results also have practical implications. First, we characterized the capacity of blunders and score fluctuations to predict a player strength, which is yet an open problem in chess softwares. Second, we show that the winning likelihood can be reliably estimated from a weighted combination of remaining times and position evaluation.

  5. Real-time PCR assay for rapid qualitative and quantitative detection of Entamoeba histolytica.

    Science.gov (United States)

    Orosz, Erika; Perkátai, Katalin; Kapusinszky, Beatrix; Farkas, Agnes; Kucsera, István

    2012-12-01

    Simple real-time PCR assay with one set of primer and probe for rapid, sensitive qualitative and quantitative detection of Entamoeba histolytica has been used. Consensus sequences were used to amplify a species-specific region of the 16S rRNA gene, and fluorescence resonance energy transfer hybridization probes were used for detection in a LightCycler platform (Roche). The anchor probe sequence was designed to be a perfect match for the 16S rRNA gene of Entamoeba species, while the acceptor probe sequence was designed for Entamoeba histolytica, which allowed differentiation. The performed characteristics of the real-time PCR assay were compared with ELISA antigen and microscopical detection from 77 samples of individuals with suspected clinical diagnosis of imported E. histolytica infection. Stool and liver abscess pus samples were examined with analytical sensitivity of 5 parasites per PCR reaction. The melting curve means Tms (standard deviation) in clinical isolates were 54°C. The real-time assay was 100% sensitive and specific for differentiation of Entamoeba histolytica, compared with conventional ELISA or microscopy. This real-time PCR assay with melting curve analysis is rapid, and specific for the detection and differentiation of Entamoeba histolytica. The suitability for routine use of this assay in clinical diagnostic laboratories is discussed.

  6. Rapid expansion method (REM) for time‐stepping in reverse time migration (RTM)

    KAUST Repository

    Pestana, Reynam C.

    2009-01-01

    We show that the wave equation solution using a conventional finite‐difference scheme, derived commonly by the Taylor series approach, can be derived directly from the rapid expansion method (REM). After some mathematical manipulation we consider an analytical approximation for the Bessel function where we assume that the time step is sufficiently small. From this derivation we find that if we consider only the first two Chebyshev polynomials terms in the rapid expansion method we can obtain the second order time finite‐difference scheme that is frequently used in more conventional finite‐difference implementations. We then show that if we use more terms from the REM we can obtain a more accurate time integration of the wave field. Consequently, we have demonstrated that the REM is more accurate than the usual finite‐difference schemes and it provides a wave equation solution which allows us to march in large time steps without numerical dispersion and is numerically stable. We illustrate the method with post and pre stack migration results.

  7. Rapid parapatric speciation on holey adaptive landscapes

    CERN Document Server

    Gavrilets, S; Vose, M D; Gavrilets, Sergey; Li, Hai; Vose, Michael D.

    1998-01-01

    A classical view of speciation is that reproductive isolation arises as a by-product of genetic divergence. Here, individual-based simulations are used to evaluate whether the mechanisms implied by this view may result in rapid speciation if the only source of genetic divergence are mutation and random genetic drift. Distinctive features of the simulations are the consideration of the complete process of speciation (from initiation until completion), and of a large number of loci, which was only one order of magnitude smaller than that of bacteria. It is demonstrated that rapid speciation on the time scale of hundreds of generations is plausible without the need for extreme founder events, complete geographic isolation, the existence of distinct adaptive peaks or selection for local adaptation. The plausibility of speciation is enhanced by population subdivision. Simultaneous emergence of more than two new species from a subdivided population is highly probable. Numerical examples relevant to the theory of ce...

  8. Implementation of Real-time CORBA middleware based on RapidIO%基于RapidIO的实时CORBA中间件实现

    Institute of Scientific and Technical Information of China (English)

    赵蕾

    2012-01-01

    In order to resolve the uncertain delay of CORBA traditional transport protocol TCP/IP, in this paper, a solution to replace TCP/IP with RapidIO technology based on end-to-end packet exchange is proposed and the pluggable transport protocol framework of CORBA is studied.So real-time CORBA middleware based on RapidIO is implemented.The test result shows that the real- time performance of CORBA based on RapidIO is superior to that of CORBA based on TCP/IE%为了解决CORBA传统传输协议TCP/IP的时延不确定问题,提出了使用基于点对点的包交换RapidIO协议来替代TCP/IP的方法,研究了CORBA的可插拔传输协议框架,从而实现了CORBA报文在RapidIO总线上的传输。测试结果显示,基于RapidIO的CORBA实时性优于基于TCP/IP的CORBA。

  9. Duplex real-time PCR assay for rapid detection of ampicillin-resistant Enterococcus faecium.

    Science.gov (United States)

    Mohn, Stein Christian; Ulvik, Arve; Jureen, Roland; Willems, Rob J L; Top, Janetta; Leavis, Helen; Harthug, Stig; Langeland, Nina

    2004-02-01

    Rapid and accurate identification of carriers of resistant microorganisms is an important aspect of efficient infection control in hospitals. Traditional identification methods of antibiotic-resistant bacteria usually take at least 3 to 4 days after sampling. A duplex real-time PCR assay was developed for rapid detection of ampicillin-resistant Enterococcus faecium (ARE). Primers and probes that are used in this assay specifically detected the D-Ala-D-Ala ligase gene of E. faecium and the modified penicillin-binding protein 5 gene (pbp5) carrying the Glu-to-Val substitution at position 629 (Val-629) in a set of 129 tested E. faecium strains with known pbp5 sequence. Presence of the Val-629 in the strain set from 11 different countries was highly correlated with ampicillin resistance. In a screening of hospitalized patients, the real-time PCR assay yielded a sensitivity and a specificity for the detection of ARE colonization of 95% and 100%, respectively. The results were obtained 4 h after samples were harvested from overnight broth of rectal swab samples, identifying both species and the resistance marker mutation in pbp5. This novel assay reliably identifies ARE 2 to 3 days more quickly than traditional culture methods, thereby increasing laboratory throughput, making it useful for rectal screening of ARE. The assay demonstrates the advantages of real-time PCR for detection of nosocomial pathogens.

  10. Early Flood Detection for Rapid Humanitarian Response: Harnessing Near Real-Time Satellite and Twitter Signals

    Directory of Open Access Journals (Sweden)

    Brenden Jongman

    2015-10-01

    Full Text Available Humanitarian organizations have a crucial role in response and relief efforts after floods. The effectiveness of disaster response is contingent on accurate and timely information regarding the location, timing and impacts of the event. Here we show how two near-real-time data sources, satellite observations of water coverage and flood-related social media activity from Twitter, can be used to support rapid disaster response, using case-studies in the Philippines and Pakistan. For these countries we analyze information from disaster response organizations, the Global Flood Detection System (GFDS satellite flood signal, and flood-related Twitter activity analysis. The results demonstrate that these sources of near-real-time information can be used to gain a quicker understanding of the location, the timing, as well as the causes and impacts of floods. In terms of location, we produce daily impact maps based on both satellite information and social media, which can dynamically and rapidly outline the affected area during a disaster. In terms of timing, the results show that GFDS and/or Twitter signals flagging ongoing or upcoming flooding are regularly available one to several days before the event was reported to humanitarian organizations. In terms of event understanding, we show that both GFDS and social media can be used to detect and understand unexpected or controversial flood events, for example due to the sudden opening of hydropower dams or the breaching of flood protection. The performance of the GFDS and Twitter data for early detection and location mapping is mixed, depending on specific hydrological circumstances (GFDS and social media penetration (Twitter. Further research is needed to improve the interpretation of the GFDS signal in different situations, and to improve the pre-processing of social media data for operational use.

  11. Some Remarks on the Model Theory of Epistemic Plausibility Models

    CERN Document Server

    Demey, Lorenz

    2010-01-01

    Classical logics of knowledge and belief are usually interpreted on Kripke models, for which a mathematically well-developed model theory is available. However, such models are inadequate to capture dynamic phenomena. Therefore, epistemic plausibility models have been introduced. Because these are much richer structures than Kripke models, they do not straightforwardly inherit the model-theoretical results of modal logic. Therefore, while epistemic plausibility structures are well-suited for modeling purposes, an extensive investigation of their model theory has been lacking so far. The aim of the present paper is to fill exactly this gap, by initiating a systematic exploration of the model theory of epistemic plausibility models. Like in 'ordinary' modal logic, the focus will be on the notion of bisimulation. We define various notions of bisimulations (parametrized by a language L) and show that L-bisimilarity implies L-equivalence. We prove a Hennesy-Milner type result, and also two undefinability results. ...

  12. Rapid and economic DNA extraction from a single salmon egg for real-time PCR amplification.

    Science.gov (United States)

    Yang, Jing-Iong; Huang, Hsiao-Yun; Chou, Yii-Cheng; Chen, Chien-Cheng; Lee, Guo-Chi; Chang, Hsueh-Wei

    2011-01-01

    Salmon eggs are common in Japanese sushi and other seafood products; however, certain fish eggs are used as counterfeit salmon eggs which are found in foods and processed products. This study develops a simple, rapid, and cost-effective method for DNA extraction, filtration (FT) and dilution (DL) protocols from a single salmon egg with good DNA quality for real-time PCR amplification. The DNA amount, DNA quality, and real-time PCR performance for different dilutions and different lengths of PCR amplicons were evaluated and compared with the common Qiagen tissue kit (QTK) and Chelex-100-based (CX) protocols. The extracted DNA from a single salmon egg using the FT or DL protocol can be applied in phylogenic research, food authentication and post-marketing monitoring of genetically modified (GM) food products.

  13. A rapid reflectance-difference spectrometer for real-time semiconductor growth monitoring with sub-second time resolution.

    Science.gov (United States)

    Núñez-Olvera, O; Balderas-Navarro, R E; Ortega-Gallegos, J; Guevara-Macías, L E; Armenta-Franco, A; Lastras-Montaño, M A; Lastras-Martínez, L F; Lastras-Martínez, A

    2012-10-01

    We report on a rapid, 32-channel reflectance-difference (RD) spectrometer with sub-second spectra acquisition times and ΔR/R sensitivity in the upper 10(-4) range. The spectrometer is based on a 50 kHz photo-elastic modulator for light polarization modulation and on a lock-in amplifier for signal harmonic analysis. Multichannel operation is allowed by multiplexing the 32 outputs of the spectrometer into the input of the lock-in amplifier. The spectrometer spans a wavelength range of 230 nm that can be tuned to cover E(1) and E(1) + Δ(1) transitions for a number of III-V semiconductors at epitaxial growth temperatures, including GaAs, InAs, AlAs, and their alloys. We present two examples of real-time measurements to demonstrate the performance of the RD spectrometer, namely, the evolution of the RD spectrum of GaAs (001) annealed at 500 °C and the time-dependent RD spectrum during the first stages of the epitaxial growth of In(0.3)Ga(0.7)As on GaAs (001) substrates.

  14. UMTS rapid response real-time seismic networks: implementation and strategies at INGV

    Science.gov (United States)

    Govoni, Aladino; Margheriti, Lucia; Moretti, Milena; Lauciani, Valentino; Sensale, Gianpaolo; Bucci, Augusto; Criscuoli, Fabio

    2015-04-01

    The benefits of portable real-time seismic networks are several and well known. During the management of a temporary experiment from the real-time data it is possible to detect and fix rapidly problems with power supply, time synchronization, disk failures and, most important, seismic signal quality degradation due to unexpected noise sources or sensor alignment/tampering. This usually minimizes field maintenance trips and maximizes both the quantity and the quality of the acquired data. When the area of the temporary experiment is not well monitored by the local permanent network, the real-time data from the temporary experiment can be fed to the permanent network monitoring system improving greatly both the real-time hypocentral locations and the final revised bulletin. All these benefits apply also in case of seismic crises when rapid deployment stations can significantly contribute to the aftershock analysis. Nowadays data transmission using meshed radio networks or satellite systems is not a big technological problem for a permanent seismic network where each site is optimized for the device power consumption and is usually installed by properly specialized technicians that can configure transmission devices and align antennas. This is not usually practical for temporary networks and especially for rapid response networks where the installation time is the main concern. These difficulties are substantially lowered using the now widespread UMTS technology for data transmission. A small (but sometimes power hungry) properly configured device with an omnidirectional antenna must be added to the station assembly. All setups are usually configured before deployment and this allows for an easy installation also by untrained personnel. We describe here the implementation of a UMTS based portable seismic network for both temporary experiments and rapid response applications developed at INGV. The first field experimentation of this approach dates back to the 2009 L

  15. Rapid, Time-Division Multiplexed, Direct Absorption- and Wavelength Modulation-Spectroscopy

    Directory of Open Access Journals (Sweden)

    Alexander Klein

    2014-11-01

    Full Text Available We present a tunable diode laser spectrometer with a novel, rapid time multiplexed direct absorption- and wavelength modulation-spectroscopy operation mode. The new technique allows enhancing the precision and dynamic range of a tunable diode laser absorption spectrometer without sacrificing accuracy. The spectroscopic technique combines the benefits of absolute concentration measurements using calibration-free direct tunable diode laser absorption spectroscopy (dTDLAS with the enhanced noise rejection of wavelength modulation spectroscopy (WMS. In this work we demonstrate for the first time a 125 Hz time division multiplexed (TDM-dTDLAS-WMS spectroscopic scheme by alternating the modulation of a DFB-laser between a triangle-ramp (dTDLAS and an additional 20 kHz sinusoidal modulation (WMS. The absolute concentration measurement via the dTDLAS-technique allows one to simultaneously calibrate the normalized 2f/1f-signal of the WMS-technique. A dTDLAS/WMS-spectrometer at 1.37 µm for H2O detection was built for experimental validation of the multiplexing scheme over a concentration range from 50 to 3000 ppmV (0.1 MPa, 293 K. A precision of 190 ppbV was achieved with an absorption length of 12.7 cm and an averaging time of two seconds. Our results show a five-fold improvement in precision over the entire concentration range and a significantly decreased averaging time of the spectrometer.

  16. Rapid, time-division multiplexed, direct absorption- and wavelength modulation-spectroscopy.

    Science.gov (United States)

    Klein, Alexander; Witzel, Oliver; Ebert, Volker

    2014-11-14

    We present a tunable diode laser spectrometer with a novel, rapid time multiplexed direct absorption- and wavelength modulation-spectroscopy operation mode. The new technique allows enhancing the precision and dynamic range of a tunable diode laser absorption spectrometer without sacrificing accuracy. The spectroscopic technique combines the benefits of absolute concentration measurements using calibration-free direct tunable diode laser absorption spectroscopy (dTDLAS) with the enhanced noise rejection of wavelength modulation spectroscopy (WMS). In this work we demonstrate for the first time a 125 Hz time division multiplexed (TDM-dTDLAS-WMS) spectroscopic scheme by alternating the modulation of a DFB-laser between a triangle-ramp (dTDLAS) and an additional 20 kHz sinusoidal modulation (WMS). The absolute concentration measurement via the dTDLAS-technique allows one to simultaneously calibrate the normalized 2f/1f-signal of the WMS-technique. A dTDLAS/WMS-spectrometer at 1.37 µm for H2O detection was built for experimental validation of the multiplexing scheme over a concentration range from 50 to 3000 ppmV (0.1 MPa, 293 K). A precision of 190 ppbV was achieved with an absorption length of 12.7 cm and an averaging time of two seconds. Our results show a five-fold improvement in precision over the entire concentration range and a significantly decreased averaging time of the spectrometer.

  17. Rapid, Time-Division Multiplexed, Direct Absorption- and Wavelength Modulation-Spectroscopy

    Science.gov (United States)

    Klein, Alexander; Witzel, Oliver; Ebert, Volker

    2014-01-01

    We present a tunable diode laser spectrometer with a novel, rapid time multiplexed direct absorption- and wavelength modulation-spectroscopy operation mode. The new technique allows enhancing the precision and dynamic range of a tunable diode laser absorption spectrometer without sacrificing accuracy. The spectroscopic technique combines the benefits of absolute concentration measurements using calibration-free direct tunable diode laser absorption spectroscopy (dTDLAS) with the enhanced noise rejection of wavelength modulation spectroscopy (WMS). In this work we demonstrate for the first time a 125 Hz time division multiplexed (TDM-dTDLAS-WMS) spectroscopic scheme by alternating the modulation of a DFB-laser between a triangle-ramp (dTDLAS) and an additional 20 kHz sinusoidal modulation (WMS). The absolute concentration measurement via the dTDLAS-technique allows one to simultaneously calibrate the normalized 2f/1f-signal of the WMS-technique. A dTDLAS/WMS-spectrometer at 1.37 μm for H2O detection was built for experimental validation of the multiplexing scheme over a concentration range from 50 to 3000 ppmV (0.1 MPa, 293 K). A precision of 190 ppbV was achieved with an absorption length of 12.7 cm and an averaging time of two seconds. Our results show a five-fold improvement in precision over the entire concentration range and a significantly decreased averaging time of the spectrometer. PMID:25405508

  18. Does rapid HIV testing result in an early diagnosis and reduce the waiting time for patients to receive medical care?

    Science.gov (United States)

    Melo, Magaly Carvalho Vieira de; Ximenes, Ricardo Arraes de Alencar; Falcão, Ilka Veras; Miranda-Filho, Demócrito de Barros

    2017-08-01

    The implementation of rapid HIV testing in Brazil began in 2006 for specific groups, and from 2009 was extended to the Counseling and Testing Centers (CTC) in certain Brazilian capitals. The aim of this study was to compare two groups of individuals: those diagnosed with HIV infection by conventional testing and those diagnosed with rapid testing, with respect to: the waiting time before receiving medical care, the time of the first laboratory tests and the virological, immune and clinical status. This is a cross-sectional study to compare a group with individuals diagnosed by conventional testing (2006-2008) and another with those diagnosed by rapid testing (2010-2011).The median time between blood collection and diagnosis of HIV in the conventional test group was 76 days, while in the rapid test group 94.2% of the subjects received their results on the same day of blood collection (p rapid test group the time was 14 days (p rapid test group (p rapid test group (472) was higher than in the conventional test group (397) (p = 0.01). The introduction of rapid HIV testing as a diagnostic strategy has reduced the waiting times for medical care and laboratory tests and also allowed earlier diagnosis of HIV infection than with the conventional test.

  19. Development of rapid methods for relaxation time mapping and motion estimation using magnetic resonance imaging

    Energy Technology Data Exchange (ETDEWEB)

    Gilani, Syed Irtiza Ali

    2008-09-15

    Recent technological developments in the field of magnetic resonance imaging have resulted in advanced techniques that can reduce the total time to acquire images. For applications such as relaxation time mapping, which enables improved visualisation of in vivo structures, rapid imaging techniques are highly desirable. TAPIR is a Look- Locker-based sequence for high-resolution, multislice T{sub 1} relaxation time mapping. Despite the high accuracy and precision of TAPIR, an improvement in the k-space sampling trajectory is desired to acquire data in clinically acceptable times. In this thesis, a new trajectory, termed line-sharing, is introduced for TAPIR that can potentially reduce the acquisition time by 40 %. Additionally, the line-sharing method was compared with the GRAPPA parallel imaging method. These methods were employed to reconstruct time-point images from the data acquired on a 4T high-field MR research scanner. Multislice, multipoint in vivo results obtained using these methods are presented. Despite improvement in acquisition speed, through line-sharing, for example, motion remains a problem and artefact-free data cannot always be obtained. Therefore, in this thesis, a rapid technique is introduced to estimate in-plane motion. The presented technique is based on calculating the in-plane motion parameters, i.e., translation and rotation, by registering the low-resolution MR images. The rotation estimation method is based on the pseudo-polar FFT, where the Fourier domain is composed of frequencies that reside in an oversampled set of non-angularly, equispaced points. The essence of the method is that unlike other Fourier-based registration schemes, the employed approach does not require any interpolation to calculate the pseudo-polar FFT grid coordinates. Translation parameters are estimated by the phase correlation method. However, instead of two-dimensional analysis of the phase correlation matrix, a low complexity subspace identification of the phase

  20. Classification using sparse representations: a biologically plausible approach.

    Science.gov (United States)

    Spratling, M W

    2014-02-01

    Representing signals as linear combinations of basis vectors sparsely selected from an overcomplete dictionary has proven to be advantageous for many applications in pattern recognition, machine learning, signal processing, and computer vision. While this approach was originally inspired by insights into cortical information processing, biologically plausible approaches have been limited to exploring the functionality of early sensory processing in the brain, while more practical applications have employed non-biologically plausible sparse coding algorithms. Here, a biologically plausible algorithm is proposed that can be applied to practical problems. This algorithm is evaluated using standard benchmark tasks in the domain of pattern classification, and its performance is compared to a wide range of alternative algorithms that are widely used in signal and image processing. The results show that for the classification tasks performed here, the proposed method is competitive with the best of the alternative algorithms that have been evaluated. This demonstrates that classification using sparse representations can be performed in a neurally plausible manner, and hence, that this mechanism of classification might be exploited by the brain.

  1. Adjustment to Subtle Time Constraints and Power Law Learning in Rapid Serial Visual Presentation.

    Science.gov (United States)

    Shin, Jacqueline C; Chang, Seah; Cho, Yang Seok

    2015-01-01

    We investigated whether attention could be modulated through the implicit learning of temporal information in a rapid serial visual presentation (RSVP) task. Participants identified two target letters among numeral distractors. The stimulus-onset asynchrony immediately following the first target (SOA1) varied at three levels (70, 98, and 126 ms) randomly between trials or fixed within blocks of trials. Practice over 3 consecutive days resulted in a continuous improvement in the identification rate for both targets and attenuation of the attentional blink (AB), a decrement in target (T2) identification when presented 200-400 ms after another target (T1). Blocked SOA1s led to a faster rate of improvement in RSVP performance and more target order reversals relative to random SOA1s, suggesting that the implicit learning of SOA1 positively affected performance. The results also reveal "power law" learning curves for individual target identification as well as the reduction in the AB decrement. These learning curves reflect the spontaneous emergence of skill through subtle attentional modulations rather than general attentional distribution. Together, the results indicate that implicit temporal learning could improve high level and rapid cognitive processing and highlights the sensitivity and adaptability of the attentional system to subtle constraints in stimulus timing.

  2. Adjustment to subtle time constraints and power law learning in rapid serial visual presentation

    Directory of Open Access Journals (Sweden)

    Jacqueline Chakyung Shin

    2015-11-01

    Full Text Available We investigated whether attention could be modulated through the implicit learning of temporal information in a rapid serial visual presentation (RSVP task. Participants identified two target letters among numeral distractors. The stimulus-onset asynchrony immediately following the first target (SOA1 varied at three levels (70, 98, and 126 ms randomly between trials or fixed within blocks of trials. Practice over three consecutive days resulted in a continuous improvement in the identification rate for both targets and attenuation of the attentional blink (AB, a decrement in target (T2 identification when presented 200-400 ms after another target (T1. Blocked SOA1s led to a faster rate of improvement in RSVP performance and more target order reversals relative to random SOA1s, suggesting that the implicit learning of SOA1 positively affected performance. The results also reveal power law learning curves for individual target identification as well as the reduction in the AB decrement. These learning curves reflect the spontaneous emergence of skill through subtle attentional modulations rather than general attentional distribution. Together, the results indicate that implicit temporal learning could improve high level and rapid cognitive processing and highlights the sensitivity and adaptability of the attentional system to subtle constraints in stimulus timing.

  3. Assessment of the 60 km Rapid Update Cycle (RUC) with Near Real-Time Aircraft Reports

    Science.gov (United States)

    Cole, R. E.; Richard, C.; Kim, S.; Bailey, D.

    1998-01-01

    The National Aeronautics and Space Administration (NASA) is developing the Center-TRA-CON Advisory System (CTAS), a set of Air Traffic Management (ATM) Decision Support Tools (DST) for en route (Center) and terminal (TRACON) airspace designed to enable controllers to increase capacity and flight efficiency. A crucial component of the CTAS, or any ATM DST, is the computation of the time-of-flight of aircraft along flight path segments. Earlier NASA studies show that accurate knowledge of the wind through which the aircraft are flying is required to estimate time-of-flight accurately. There are current envisioned to be two sources of wind data for CTAS: The Rapid Update Cycle (RUC) for the Center airspace, a numerical model developed by the National Oceanic and Atmospheric Administration (NOAA) Forecast System Laboratory (FSL) and run operationally by the National Weather Service (NWS) National Center for Environmental Prediction (NCEP); and The Integrated Terminal Weather System (ITWS) Terminal Winds (TW) for the TRACON airspace, developed at MIT Lincoln Laboratory under funding from the Federal Aviation Administration (FAA). This study has three goals: (1) determine the errors in the baseline 60 km resolution RUC forecast wind fields relative to the needs of en route DSTs such as CTAS, (2) determine the benefit of using the TW algorithm to refine the RUC forecast wind fields with near real-time Meteorological Data Collection and Reporting System (MDCRS) reports, and (3) identify factors that influence wind errors in order to improve accuracy and estimate errors in real time.

  4. Precise orbit determination and rapid orbit recovery supported by time synchronization

    Science.gov (United States)

    Guo, Rui; Zhou, JianHua; Hu, XiaoGong; Liu, Li; Tang, Bo; Li, XiaoJie; Wu, Shan

    2015-06-01

    In order to maintain optimal signal coverage, GNSS satellites have to experience orbital maneuvers. For China's COMPASS system, precise orbit determination (POD) as well as rapid orbit recovery after maneuvers contribute to the overall Positioning, Navigation and Timing (PNT) service performance in terms of accuracy and availability. However, strong statistical correlations between clock offsets and the radial component of a satellite's positions require long data arcs for POD to converge. We propose here a new strategy which relies on time synchronization between ground tracking stations and in-orbit satellites. By fixing satellite clock offsets measured by the satellite station two-way synchronization (SSTS) systems and receiver clock offsets, POD and orbital recovery performance can be improved significantly. Using the Satellite Laser Ranging (SLR) as orbital accuracy evaluation, we find the 4-hr recovered orbit achieves about 0.71 m residual root mean square (RMS) error of fit SLR data, the recovery time is improved from 24-hr to 4-hr compared with the conventional POD without time synchronization support. In addition, SLR evaluation shows that for 1-hr prediction, about 1.47 m accuracy is achieved with the new proposed POD strategy.

  5. Empirical Assessment on Factors Affecting Travel Time of Bus Rapid Transit

    Directory of Open Access Journals (Sweden)

    Fergyanto E Gunawan

    2015-02-01

    Full Text Available Since the beginning of the century, many cities around the world adopt the bus rapid transit (BRT system to fulfill their need of mass transportation system. The system features with platform-level boarding, bus lanes in the central verge of the road, off-vehicle fare collection, and physically protected busway. So far, these criteria are considered to be the most important aspects with respect to the BRT performance. In this research, we intend to study to what extent the BRT performance may be affected by the interference of the mixed traffic during the BRT operation. We adopt an empirical approach by observing the phenomenon unfolding in the eleven TransJakarta BRT corridors. The TransJakarta BRT operates in the city of Jakarta, the capital of the Republic of Indonesia. We record the travel time data from station to station for the case where the TransJakarta bus can travel smoothly and the case where the traveling bus is interfered with the mixed traffic. For the cases, we evaluate the travel time variation. As the results, we found that the Corridor 1 of TransJakarta BRT has the best performance in term of the travel time variation. For the two directions, the corridor has the mean travel time of 34 min, the standard deviation of 3 min, and the travel time variation of 8%. On this corridor, the mixed-traffic interference is relatively negligible. On the Corridor 7, the two-direction travel times have the mean of 45 min, the standard deviation of 8 min, and the travel time variation of 16%. On the Corridor 9, the twodirection travel times have the mean of 1 hr and 25 min, the standard deviation of 11 min, and the travel time variation of 14%. On the last two corridors, the busways are heavily interfered by the mixed traffic; thus, the end-to-end travel times are significantly uncertain although only very few road segments are interfered. The research leads us to a conclusion that the interference, although only occurs on a road segment, may

  6. Development of real-time PCR method for rapid detection and quantification of Heterosigma akashiwo

    Institute of Scientific and Technical Information of China (English)

    HE Shan-ying; YU Zhi-gang; MI Tie-zhu

    2008-01-01

    To rapidly detect the harmful algae H. Akashiwo qualitatively and quantitatively, sequences of the 18S rDNA deduced from H. Akashiwo were used for designing species-specific primers, and a RFQ-PCR (Real-time Fluorescent Quantitative Polymerase Chain Reaction) method was developed for quantitative detection of H.akashiwo. Primer H. Akashiwo and TaqMan probe were designed, and the specificity of primer was checked with PCR. A calibration curve was constructed with cycle threshold value against visual counted cell number. And the value of the curve was tested with other H. Akashiwo samples, which were assayed with both the RFQ-PCR method and visual count under microscope.

  7. Rapid quality assessment of Radix Aconiti Preparata using direct analysis in real time mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Zhu Hongbin; Wang Chunyan; Qi Yao [Changchun Center of Mass Spectrometry and Chemical Biology Laboratory, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022 (China); University of Chinese Academy of Sciences, Beijing 100039 (China); Song Fengrui, E-mail: songfr@ciac.jl.cn [Changchun Center of Mass Spectrometry and Chemical Biology Laboratory, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022 (China); Liu Zhiqiang; Liu Shuying [Changchun Center of Mass Spectrometry and Chemical Biology Laboratory, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022 (China)

    2012-11-08

    Highlights: Black-Right-Pointing-Pointer DART MS combined with PCA and HCA was used to rapidly identify markers of Radix Aconiti. Black-Right-Pointing-Pointer The DART MS behavior of six aconitine-type alkaloids was investigated. Black-Right-Pointing-Pointer Chemical markers were recognized between the qualified and unqualified samples. Black-Right-Pointing-Pointer DART MS was shown to be an effective tool for quality control of Radix Aconiti Preparata. - Abstract: This study presents a novel and rapid method to identify chemical markers for the quality control of Radix Aconiti Preparata, a world widely used traditional herbal medicine. In the method, the samples with a fast extraction procedure were analyzed using direct analysis in real time mass spectrometry (DART MS) combined with multivariate data analysis. At present, the quality assessment approach of Radix Aconiti Preparata was based on the two processing methods recorded in Chinese Pharmacopoeia for the purpose of reducing the toxicity of Radix Aconiti and ensuring its clinical therapeutic efficacy. In order to ensure the safety and effectivity in clinical use, the processing degree of Radix Aconiti should be well controlled and assessed. In the paper, hierarchical cluster analysis and principal component analysis were performed to evaluate the DART MS data of Radix Aconiti Preparata samples in different processing times. The results showed that the well processed Radix Aconiti Preparata, unqualified processed and the raw Radix Aconiti could be clustered reasonably corresponding to their constituents. The loading plot shows that the main chemical markers having the most influence on the discrimination amongst the qualified and unqualified samples were mainly some monoester diterpenoid aconitines and diester diterpenoid aconitines, i.e. benzoylmesaconine, hypaconitine, mesaconitine, neoline, benzoylhypaconine, benzoylaconine, fuziline, aconitine and 10-OH-mesaconitine. The established DART MS approach in

  8. Rapid expansion and pseudo spectral implementation for reverse time migration in VTI media

    KAUST Repository

    Pestana, Reynam C

    2012-04-24

    In isotropic media, we use the scalar acoustic wave equation to perform reverse time migration (RTM) of the recorded pressure wavefield data. In anisotropic media, P- and SV-waves are coupled, and the elastic wave equation should be used for RTM. For computational efficiency, a pseudo-acoustic wave equation is often used. This may be solved using a coupled system of second-order partial differential equations. We solve these using a pseudo spectral method and the rapid expansion method (REM) for the explicit time marching. This method generates a degenerate SV-wave in addition to the P-wave arrivals of interest. To avoid this problem, the elastic wave equation for vertical transversely isotropic (VTI) media can be split into separate wave equations for P- and SV-waves. These separate wave equations are stable, and they can be effectively used to model and migrate seismic data in VTI media where |ε- δ| is small. The artifact for the SV-wave has also been removed. The independent pseudo-differential wave equations can be solved one for each mode using the pseudo spectral method for the spatial derivatives and the REM for the explicit time advance of the wavefield. We show numerically stable and high-resolution modeling and RTM results for the pure P-wave mode in VTI media. © 2012 Sinopec Geophysical Research Institute.

  9. Spectroscopic measurements and terahertz imaging of the cornea using a rapid scanning terahertz time domain spectrometer

    Science.gov (United States)

    Wen-Quan, Liu; Yuan-Fu, Lu; Guo-Hua, Jiao; Xian-Feng, Chen; Zhi-Sheng, Zhou; Rong-Bin, She; Jin-Ying, Li; Si-Hai, Chen; Yu-Ming, Dong; Jian-Cheng, Lv

    2016-06-01

    Spectroscopic measurements and terahertz imaging of the cornea are carried out by using a rapid scanning terahertz time domain spectroscopy (THz-TDS) system. A voice coil motor stage based optical delay line (VCM-ODL) is developed to provide a rather simple and robust structure with both the high scanning speed and the large delay length. The developed system is used for THz spectroscopic measurements and imaging of the corneal tissue with different amounts of water content, and the measurement results show the consistence with the reported results, in which the measurement time using VCM-ODL is a factor of 360 shorter than the traditional motorized optical delay line (MDL). With reducing the water content a monotonic decrease of the complex permittivity of the cornea is observed. The two-term Debye relaxation model is employed to explain our experimental results, revealing that the fast relaxation time of a dehydrated cornea is much larger than that of a hydrated cornea and its dielectric behavior can be affected by the presence of the biological macromolecules. These results demonstrate that our THz spectrometer may be a promising candidate for tissue hydration sensing and practical application of THz technology. Project supported by the National Natural Science Foundation of China (Grant No. 61205101), the Shenzhen Municipal Research Foundation, China (Grant Nos. GJHZ201404171134305 and JCYJ20140417113130693), and the Marie Curie Actions-International Research Staff Exchange Scheme (IRSES) (Grant No. FP7 PIRSES-2013-612267).

  10. [Rapid detection of rotavirus in water samples using immunomagnetic separation combined with real time PCR].

    Science.gov (United States)

    Yang, Wan; He, Miao; Li, Dan; Shi, Han-Chang; Liu, Li

    2009-05-15

    A quantitative and rapid detection method for rotavirus in water samples was developed, by using immunomagnetic separation combined with reverse transcription and real time polymerase chain reaction (IMS-RT-real time PCR). Magnetic beads coated with antibodies directed against group A rotavirus were used to capture and purify the virus in water samples. The experimental results showed that IMS was optimized when 1 mL samples were supplemented with 10 microL of immunomagnetic beads, 2.5 microL of Tween 20 and incubated for 2 h. The IMS method was employed in the detection of rotavirus in seeded virus eluant such as 3% beef extract successfully and thus manifested its compatibility with established virus concentration methods. The IMS-RT-real time PCR method could yield quantitative results within about 5 h with a detection limit at 1 x 10(4) copies/mL (equivalent to 3-4 PFU/mL). The method exhibited a high level correlation (R2 = 0.9816) with cell culture assay, indicating that it could perform as well as cell culture assay does in infection tests. And the method functioned satisfactorily in seeded concentrate of secondary waste water treatment plant effluent, reclaimed water, surface water and tap water.

  11. The Onset and Time Course of Semantic Priming During Rapid Recognition of Visual Words.

    Science.gov (United States)

    Hoedemaker, Renske S; Gordon, Peter C

    2017-02-23

    In 2 experiments, we assessed the effects of response latency and task-induced goals on the onset and time course of semantic priming during rapid processing of visual words as revealed by ocular response tasks. In Experiment 1 (ocular lexical decision task), participants performed a lexical decision task using eye movement responses on a sequence of 4 words. In Experiment 2, the same words were encoded for an episodic recognition memory task that did not require a metalinguistic judgment. For both tasks, survival analyses showed that the earliest observable effect (divergence point [DP]) of semantic priming on target-word reading times occurred at approximately 260 ms, and ex-Gaussian distribution fits revealed that the magnitude of the priming effect increased as a function of response time. Together, these distributional effects of semantic priming suggest that the influence of the prime increases when target processing is more effortful. This effect does not require that the task include a metalinguistic judgment; manipulation of the task goals across experiments affected the overall response speed but not the location of the DP or the overall distributional pattern of the priming effect. These results are more readily explained as the result of a retrospective, rather than a prospective, priming mechanism and are consistent with compound-cue models of semantic priming. (PsycINFO Database Record

  12. Representations of physical plausibility revealed by event-related potentials.

    Science.gov (United States)

    Roser, Matthew E; Fugelsang, Jonathan A; Handy, Todd C; Dunbar, Kevin N; Gazzaniga, Michael S

    2009-08-05

    Maintaining an accurate mental representation of the current environment is crucial to detecting change in that environment and ensuring behavioral coherence. Past experience with interactions between objects, such as collisions, has been shown to influence the perception of object interactions. To assess whether mental representations of object interactions derived from experience influence the maintenance of a mental model of the current stimulus environment, we presented physically plausible and implausible collision events while recording brain electrical activity. The parietal P300 response to 'oddball' events was found to be modulated by the physical plausibility of the stimuli, suggesting that past experience of object interactions can influence working memory processes involved in monitoring ongoing changes to the environment.

  13. Probabilistic reasoning in intelligent systems networks of plausible inference

    CERN Document Server

    Pearl, Judea

    1988-01-01

    Probabilistic Reasoning in Intelligent Systems is a complete and accessible account of the theoretical foundations and computational methods that underlie plausible reasoning under uncertainty. The author provides a coherent explication of probability as a language for reasoning with partial belief and offers a unifying perspective on other AI approaches to uncertainty, such as the Dempster-Shafer formalism, truth maintenance systems, and nonmonotonic logic. The author distinguishes syntactic and semantic approaches to uncertainty--and offers techniques, based on belief networks, that provid

  14. Complex Learning in Bio-plausible Memristive Networks

    OpenAIRE

    Deng, Lei; Li, Guoqi; Deng, Ning; Dong WANG; Zhang, Ziyang; He, Wei; Li, Huanglong; Pei, Jing; Shi, Luping

    2015-01-01

    The emerging memristor-based neuromorphic engineering promises an efficient computing paradigm. However, the lack of both internal dynamics in the previous feedforward memristive networks and efficient learning algorithms in recurrent networks, fundamentally limits the learning ability of existing systems. In this work, we propose a framework to support complex learning functions by introducing dedicated learning algorithms to a bio-plausible recurrent memristive network with internal dynamic...

  15. Biologically plausible learning in recurrent neural networks reproduces neural dynamics observed during cognitive tasks.

    Science.gov (United States)

    Miconi, Thomas

    2017-02-23

    Neural activity during cognitive tasks exhibits complex dynamics that flexibly encode task-relevant variables. Chaotic recurrent networks, which spontaneously generate rich dynamics, have been proposed as a model of cortical computation during cognitive tasks. However, existing methods for training these networks are either biologically implausible, and/or require a continuous, real-time error signal to guide learning. Here we show that a biologically plausible learning rule can train such recurrent networks, guided solely by delayed, phasic rewards at the end of each trial. Networks endowed with this learning rule can successfully learn nontrivial tasks requiring flexible (context-dependent) associations, memory maintenance, nonlinear mixed selectivities, and coordination among multiple outputs. The resulting networks replicate complex dynamics previously observed in animal cortex, such as dynamic encoding of task features and selective integration of sensory inputs. We conclude that recurrent neural networks offer a plausible model of cortical dynamics during both learning and performance of flexible behavior.

  16. Real-time PCR using mycobacteriophage DNA for rapid phenotypic drug susceptibility results for Mycobacterium tuberculosis.

    Science.gov (United States)

    Pholwat, Suporn; Ehdaie, Beeta; Foongladda, Suporn; Kelly, Kimberly; Houpt, Eric

    2012-03-01

    Managing drug-resistant Mycobacterium tuberculosis requires drug susceptibility testing, yet conventional drug susceptibility testing is slow, and molecular testing does not yield results for all antituberculous drugs. We addressed these challenges by utilizing real-time PCR of mycobacteriophage D29 DNA to evaluate the drug resistance of clinical M. tuberculosis isolates. Mycobacteriophages infect and replicate in viable bacterial cells faster than bacterial cells replicate and have been used for detection and drug resistance testing for M. tuberculosis either by using reporter cells or phages with engineered reporter constructs. Our primary protocol involved culturing M. tuberculosis isolates for 48 h with and without drugs at critical concentrations, followed by incubation with 10(3) PFU/ml of D29 mycobacteriophage for 24 h and then real-time PCR. Many drugs could be incubated instantly with M. tuberculosis and phage for 24 h alone. The change in phage DNA real-time PCR cycle threshold (C(T)) between control M. tuberculosis and M. tuberculosis treated with drugs was calculated and correlated with conventional agar proportion drug susceptibility results. Specifically, 9 susceptible clinical isolates, 22 multidrug-resistant (MDR), and 1 extensively drug-resistant (XDR) M. tuberculosis strains were used and C(T) control-C(T) drug cutoffs of between +0.3 and -6.0 yielded 422/429 (98%) accurate results for isoniazid, rifampin, streptomycin, ethambutol, amikacin, kanamycin, capreomycin, ofloxacin, moxifloxacin, ethionamide, para-aminosalicylic acid, cycloserine, and linezolid. Moreover, the ΔC(T) values correlated with isolate MIC for most agents. This D29 quantitative PCR assay offers a rapid, accurate, 1- to 3-day phenotypic drug susceptibility test for first- and second-line drugs and may suggest an approximate MIC.

  17. Phenomapping of rangelands in South Africa using time series of RapidEye data

    Science.gov (United States)

    Parplies, André; Dubovyk, Olena; Tewes, Andreas; Mund, Jan-Peter; Schellberg, Jürgen

    2016-12-01

    Phenomapping is an approach which allows the derivation of spatial patterns of vegetation phenology and rangeland productivity based on time series of vegetation indices. In our study, we propose a new spatial mapping approach which combines phenometrics derived from high resolution (HR) satellite time series with spatial logistic regression modeling to discriminate land management systems in rangelands. From the RapidEye time series for selected rangelands in South Africa, we calculated bi-weekly noise reduced Normalized Difference Vegetation Index (NDVI) images. For the growing season of 2011⿿2012, we further derived principal phenology metrics such as start, end and length of growing season and related phenological variables such as amplitude, left derivative and small integral of the NDVI curve. We then mapped these phenometrics across two different tenure systems, communal and commercial, at the very detailed spatial resolution of 5 m. The result of a binary logistic regression (BLR) has shown that the amplitude and the left derivative of the NDVI curve were statistically significant. These indicators are useful to discriminate commercial from communal rangeland systems. We conclude that phenomapping combined with spatial modeling is a powerful tool that allows efficient aggregation of phenology and productivity metrics for spatially explicit analysis of the relationships of crop phenology with site conditions and management. This approach has particular potential for disaggregated and patchy environments such as in farming systems in semi-arid South Africa, where phenology varies considerably among and within years. Further, we see a strong perspective for phenomapping to support spatially explicit modelling of vegetation.

  18. Following the rapid evolution of the central star of the Stingray Nebula in real time

    Science.gov (United States)

    Reindl, Nicole

    2014-10-01

    SAO 244567 is an unusually fast evolving star. Within twenty years only, it has turned from a B-type supergiant into the central star of the Stingray nebula. Space and ground-based observations obtained over the last decades have revealed that its spectrum changes noticeably over just a few years, showing stellar evolution in real time. Previous analysis indicates it must be a low mass star and thus the observed fast evolution is in strong contradiction with canonical post-asymptotic giant branch (AGB) evolution. A late He-shell flash is able to account for the rapid evolution. This scenario would predict an evolution back to the AGB, e.g. a decrease of the effective temperature (which is already indicated by the FUSE observations in 2006) and an increase of luminosity. With COS spectroscopy we want to follow the evolution of the surface properties of SAO 244567 to verify this thesis. The very compact nebula of SAO 244567 makes it impossible to derive these parameters from optical spectra, because most of the photospheric lines are blended by nebular emission lines thus they are not suitable for a spectral analysis. The derived surface parameters will establish constraints for late thermal pulse evolutionary calculations. With these calculations we aim not only to explain the nature of SAO 244567, but they also will provide a deeper insight in the formation process of hydrogen deficient stars, which make up 25% of the post AGB-stars and white dwarfs.

  19. Rapid testing and identification of actuator using dSPACE real-time emulator

    Science.gov (United States)

    Xie, Daocheng; Wang, Zhongwei; Zeng, Qinghua

    2011-10-01

    To solve the problem of model identification of actuator in control system design of aerocraft, testing system based on dSPACE emulator is established, sending testing signal and receiving feedback voltage are realized using dSPACE interactive cards, communication between signal generating equipment and feedback voltage acquisition equipment is synchronized. This paper introduces the hardware architecture and key technologies of the simulation system. Constructing, downloading and calculating of the testing model is finished using dSPACE emulator, D/A transfer of testing signal is realized using DS2103 card, DS2002 card transfer the feedback voltage to digital value. Filtering module is added to the signal acquisition, for reduction of noise interference in the A/D channel. Precision of time and voltage is improved by setting acquisition period 1ms. The data gathered is recorded and displayed with Controldesk tools. The response of four actuators under different frequency are tested, frequency-domain analysis is done using least square method, the model of actuator is identified, simulation data fits well with real response of the actuator. The testing system created with dSPACE emulator satisfies the rapid testing and identification of actuator.

  20. Bidirectional Control of Generalized Epilepsy Networks via Rapid Real-Time Switching of Firing Mode.

    Science.gov (United States)

    Sorokin, Jordan M; Davidson, Thomas J; Frechette, Eric; Abramian, Armen M; Deisseroth, Karl; Huguenard, John R; Paz, Jeanne T

    2017-01-04

    Thalamic relay neurons have well-characterized dual firing modes: bursting and tonic spiking. Studies in brain slices have led to a model in which rhythmic synchronized spiking (phasic firing) in a population of relay neurons leads to hyper-synchronous oscillatory cortico-thalamo-cortical rhythms that result in absence seizures. This model suggests that blocking thalamocortical phasic firing would treat absence seizures. However, recent in vivo studies in anesthetized animals have questioned this simple model. Here we resolve this issue by developing a real-time, mode-switching approach to drive thalamocortical neurons into or out of a phasic firing mode in two freely behaving genetic rodent models of absence epilepsy. Toggling between phasic and tonic firing in thalamocortical neurons launched and aborted absence seizures, respectively. Thus, a synchronous thalamocortical phasic firing state is required for absence seizures, and switching to tonic firing rapidly halts absences. This approach should be useful for modulating other networks that have mode-dependent behaviors.

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

    Science.gov (United States)

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

    2015-01-01

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

  2. RAPID REAL TIME PCR BASED DETECTION OF CELL COUNT IN CASE OF URINARY TRACT INFECTION

    Directory of Open Access Journals (Sweden)

    Poulomi Nandy

    2013-01-01

    Full Text Available Microbial identification and antimicrobial susceptibility testing methods currently used in clinical microbiology laboratories require at least two to three days because they rely on the growth and isolation of micro-organisms. This long, but necessary, delay has enormous consequences on prophylactic usage of antimicrobial drugs. This study was an attempt to reduce this detection time span. Taq Man Real Time PCR has been used as an important tool in the differentiation of Gram nature of bacteria present in UTI patients that allows detection of spiked bacterial 16S rDNA from urine samples within a short span of 5h and also gives us the corresponding cell count of both/either Gram positive and negative organisms present. A standard curve was generated which was used to determine the cell count of control as well as patient samples. Detection could be done in the range of 103 to 106 cells/mL Patient samples screened clustered either in the allele 1 or allele 2 axes, depending on majority concentration of Gram nature of the micro-organisms. The cell counts for control individuals were scattered within 0 to 102, while very few in the range of 104. The case was just reverse for patient group, where most of the points were scattered within 104 to 108. Thus the optimal selection of appropriate antimicrobials (depending on the gram nature by clinicians, will be gradually improved as an increasing number of rapid molecular diagnostic tools for the detection, identification and characterization of infectious agents become commercially available.

  3. UMTS rapid response real-time seismic networks: implementation and strategies at INGV

    Science.gov (United States)

    Govoni, A.; Margheriti, L.; Moretti, M.; Lauciani, V.; Sensale, G.; Bucci, A.; Criscuoli, F.

    2015-12-01

    Universal Mobile Telecommunications System (UMTS) and its evolutions are nowadays the most affordable and widespread data communication infrastructure available almost world wide. Moreover the always growing cellular phone market is pushing the development of new devices with higher performances and lower power consumption. All these characteristics make UMTS really useful for the implementation of an "easy to deploy" temporary real-time seismic station. Despite these remarkable features, there are many drawbacks that must be properly taken in account to effectively transmit the seismic data: Internet security, signal and service availability, power consumption. - Internet security: exposing seismological data services and seismic stations to the Internet is dangerous, attack prone and can lead to downtimes in the services, so we setup a dedicated Virtual Private Network (VPN) service to protect all the connected devices. - Signal and service availability: while for temporary experiment a carefull planning and an accurate site selection can minimize the problem, this is not always the case with rapid response networks. Moreover, as with any other leased line, the availability of the UMTS service during a seismic crisis is basically unpredictable. Nowadays in Italy during a major national emergency a Committee of the Italian Civil Defense ensures unified management and coordination of emergency activities. Inside it the telecom companies are committed to give support to the crisis management improving the standards in their communication networks. - Power consumption: it is at least of the order of that of the seismic station and, being related to data flow and signal quality is largely unpredictable. While the most secure option consists in adding a second independent solar power supply to the seismic station, this is not always a very convenient solution since it doubles the cost and doubles the equipment on site. We found that an acceptable trade-off is to add an

  4. Families of Plausible Solutions to the Puzzle of Boyajian’s Star

    Science.gov (United States)

    Wright, Jason T.; Sigurd̵sson, Steinn

    2016-09-01

    Good explanations for the unusual light curve of Boyajian's Star have been hard to find. Recent results by Montet & Simon lend strength and plausibility to the conclusion of Schaefer that in addition to short-term dimmings, the star also experiences large, secular decreases in brightness on decadal timescales. This, combined with a lack of long-wavelength excess in the star's spectral energy distribution, strongly constrains scenarios involving circumstellar material, including hypotheses invoking a spherical cloud of artifacts. We show that the timings of the deepest dimmings appear consistent with being randomly distributed, and that the star's reddening and narrow sodium absorption is consistent with the total, long-term dimming observed. Following Montet & Simon's encouragement to generate alternative hypotheses, we attempt to circumscribe the space of possible explanations with a range of plausibilities, including: a cloud in the outer solar system, structure in the interstellar medium (ISM), natural and artificial material orbiting Boyajian's Star, an intervening object with a large disk, and variations in Boyajian's Star itself. We find the ISM and intervening disk models more plausible than the other natural models.

  5. Rapidly-steered single-element ultrasound for real-time volumetric imaging and guidance

    Science.gov (United States)

    Stauber, Mark; Western, Craig; Solek, Roman; Salisbury, Kenneth; Hristov, Dmitre; Schlosser, Jeffrey

    2016-03-01

    Volumetric ultrasound (US) imaging has the potential to provide real-time anatomical imaging with high soft-tissue contrast in a variety of diagnostic and therapeutic guidance applications. However, existing volumetric US machines utilize "wobbling" linear phased array or matrix phased array transducers which are costly to manufacture and necessitate bulky external processing units. To drastically reduce cost, improve portability, and reduce footprint, we propose a rapidly-steered single-element volumetric US imaging system. In this paper we explore the feasibility of this system with a proof-of-concept single-element volumetric US imaging device. The device uses a multi-directional raster-scan technique to generate a series of two-dimensional (2D) slices that were reconstructed into three-dimensional (3D) volumes. At 15 cm depth, 90° lateral field of view (FOV), and 20° elevation FOV, the device produced 20-slice volumes at a rate of 0.8 Hz. Imaging performance was evaluated using an US phantom. Spatial resolution was 2.0 mm, 4.7 mm, and 5.0 mm in the axial, lateral, and elevational directions at 7.5 cm. Relative motion of phantom targets were automatically tracked within US volumes with a mean error of -0.3+/-0.3 mm, -0.3+/-0.3 mm, and -0.1+/-0.5 mm in the axial, lateral, and elevational directions, respectively. The device exhibited a mean spatial distortion error of 0.3+/-0.9 mm, 0.4+/-0.7 mm, and -0.3+/-1.9 in the axial, lateral, and elevational directions. With a production cost near $1000, the performance characteristics of the proposed system make it an ideal candidate for diagnostic and image-guided therapy applications where form factor and low cost are paramount.

  6. Rapid detection of blaKPC carbapenemase genes by real-time PCR.

    Science.gov (United States)

    Hindiyeh, Musa; Smollen, Gill; Grossman, Zehava; Ram, Daniela; Davidson, Yehudit; Mileguir, Fernando; Vax, Marina; Ben David, Debbie; Tal, Ilana; Rahav, Galia; Shamiss, Ari; Mendelson, Ella; Keller, Nathan

    2008-09-01

    Carbapenem resistance among Enterobacteriaceae is an emerging problem worldwide. Klebsiella pneumoniae carbapenemase (bla(KPC)) enzymes are among the most common beta-lactamases described. In this study, we report the development and validation of a real-time PCR (q-PCR) assay for the detection of bla(KPC) genes using TaqMan chemistry. The q-PCR amplification of bla(KPC) DNA was linear over 7 log dilutions (r(2) = 0.999; slope, 3.54), and the amplification efficiency was 91.6%. The q-PCR detection limit was 1 CFU, and there was no cross-reaction with DNA extracted from several multidrug-resistant bacteria. Perianal/rectal swabs (n = 187) collected in duplicate from 128 patients admitted to Sheba Medical Center surgical intensive care units were evaluated for the presence of carbapenem-resistant bacteria by culturing on MacConkey agar-plus-carbapenem disks and for bla(KPC) genes by q-PCR. Carbapenem-resistant organisms, all K. pneumoniae, were isolated from 47 (25.1%) of the 187 samples collected, while bla(KPC) genes were detected in 54 (28.9%) of the patient samples extracted by the NucliSENS easyMAG system. Of these, seven samples were positive for bla(KPC) genes by q-PCR but negative for carbapenem resistance by culture, while all samples in which no carbapenem-resistant bacteria were detected by culture also tested negative by q-PCR. Thus, the sensitivity and specificity of the q-PCR assay after extraction by the NucliSENS easyMAG system were 100% and 95%, respectively. Similar values were obtained after DNA extraction by the Roche MagNA Pure LC instrument: 97.9% sensitivity and 96.4% specificity. Overall, the bla(KPC) q-PCR assay appears to be highly sensitive and specific. The utilization of q-PCR will shorten the time to bla(KPC) detection from 24 h to 4 h and will help in rapidly isolating colonized or infected patients and assigning them to cohorts.

  7. Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences.

    Science.gov (United States)

    Derr, Julien; Manapat, Michael L; Rajamani, Sudha; Leu, Kevin; Xulvi-Brunet, Ramon; Joseph, Isaac; Nowak, Martin A; Chen, Irene A

    2012-05-01

    During the origin of life, the biological information of nucleic acid polymers must have increased to encode functional molecules (the RNA world). Ribozymes tend to be compositionally unbiased, as is the vast majority of possible sequence space. However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences. While natural selection could lead to complex sequences, molecules with some activity are required to begin this process. Was the emergence of compositionally diverse sequences a matter of chance, or could prebiotically plausible reactions counter chemical biases to increase the probability of finding a ribozyme? Our in silico simulations using a two-letter alphabet show that template-directed ligation and high concatenation rates counter compositional bias and shift the pool toward longer sequences, permitting greater exploration of sequence space and stable folding. We verified experimentally that unbiased DNA sequences are more efficient templates for ligation, thus increasing the compositional diversity of the pool. Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules. Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life.

  8. Rapid spin-lattice relaxation time mapping incorporating flip angle calibration in quantitative magnetic resonance imaging

    Institute of Scientific and Technical Information of China (English)

    Zhongliang Zu; Qi Liu; Yanming Yu; Song Gao; Shanglian Bao

    2008-01-01

    Driven equilibrium single pulse observation of T1(DESPOT1)is a rapid spin-lattice relaxation constant(T1)mapping technique in magnetic resonance imaging(MRI).However,DESPOT1 is very sensitive to flip angle(FA)inhomogeneity,resulting in T1 inaccuracy.Here,a five-point DESPOTl method is proposed to reduce the sensitivity to FA inhomogeneity through FA measurement and calibra-tion.Phantom and in vivo experiments are performed to validate the technique.As a result.a rapid and accurate T1 mapping is acquired by using the proposed five-point DESPOT1 method.

  9. Impact of time-variable vegetation on accuracy of rapid hydrologic predictions

    Science.gov (United States)

    Stec, Magdalena; Niedzielski, Tomasz

    2016-04-01

    It is crucial to identify the processes that impact errors of hydrologic forecasts. Since existence of vegetation and its ability to store precipitation is an important element of water distribution in the catchment, especially at the beginning of a rainfall event, it may be considered as one of the processes influencing skills of hydrological forecasts. The main objective of the study is to verify the hypothesis that water level predictions are controlled by vegetation dynamics in the contributing mountainous basins. The analysis is conducted for the upper Nysa Klodzka catchment with the outlet in Bardo (SW Poland). The basin includes a mid-mountain abasement covered with crops, while surrounding medium-altitude mountain ranges are mainly covered with forests. We focus on the entire year, from autumn 2013 to summer 2014. Herein, we analyze prediction errors and efficiency measures of hydrologic forecasts provided by two stochastic models - uni- and multivariate autoregressive models as well as their two-model ensemble prediction. In addition, we use the satellite-derived Leaf Area Index (LAI) images from the Moderate Resolution Imaging Spectroradiometer (MODIS). Hydrological prognoses are derived by the HydroProg real-time rapid forecasting system, built at the University of Wroclaw (Poland) in frame of the research project 2011/01/D/ST10/04171 of the National Science Centre of Poland. Correlation analysis between the plant maximum water storage capacity and prediction error/skill statistics (mean absolute error, root mean square error, Nash-Sutcliffe efficiency , index of agreement) is conducted. To cope with small sample size, the bootstrap simulation is performed. We conclude that there is a strong negative association between mean or median prediction errors and vegetation state for all meteorological seasons of a year. This result implies that basins with higher interception potential are more vulnerable to forecast inaccuracy than those with sparse natural

  10. Real-time fluorescence Loop-Mediated Isothermal Amplification (LAMP) for rapid and reliable diagnosis of pulmonary tuberculosis.

    Science.gov (United States)

    Cao, Donglin; Hu, Liangshan; Lin, Maorui; Li, Mingyou; Ye, Zebing; Sun, Hongtao; Huang, Jiwei; Yang, Huawen; Tian, Junzhang

    2015-02-01

    A reliable, simple and rapid diagnostic method that can be helpful in pulmonary tuberculosis diagnosis is urgently needed. Loop-mediated Isothermal Amplification (LAMP) allows DNA to be amplified rapidly at a constant temperature. In this study, real-time fluorescence LAMP was evaluated to rapidly detect Mycobacterium tuberculosis in sputum and was compared to the performance of real-time fluorescence quantitative PCR (Q-PCR). All the standard MTB strains were successfully detected and limit of detection (LOD) was 10(2)CFU/mL by real-time fluorescence LAMP within 20min. In light of MTB in sputum, the real-time fluorescence LAMP method yielded a sensitivity of 98.0% and a specificity of 78.3%, compared to Q-PCR assay, which yielded a sensitivity of 96.0% and a specificity of 82.6% for PTB diagnosis. There was an excellent overall agreement between LAMP and Q-PCR for PTB (κ=0.315) and non-PTB (κ=0.862). Therefore, the real-time fluorescence LAMP assay is a rapid, sensitive, and specific method to detect pulmonary tuberculosis.

  11. Rapid process development of chromatographic process using direct analysis in real time mass spectrometry as a process analytical technology tool.

    Science.gov (United States)

    Yan, Binjun; Chen, Teng; Xu, Zhilin; Qu, Haibin

    2014-06-01

    The concept of quality by design (QbD) is widely applied in the process development of pharmaceuticals. However, the additional cost and time have caused some resistance about QbD implementation. To show a possible solution, this work proposed a rapid process development method, which used direct analysis in real time mass spectrometry (DART-MS) as a process analytical technology (PAT) tool for studying the chromatographic process of Ginkgo biloba L., as an example. The breakthrough curves were fast determined by DART-MS at-line. A high correlation coefficient of 0.9520 was found between the concentrations of ginkgolide A determined by DART-MS and HPLC. Based on the PAT tool, the impacts of process parameters on the adsorption capacity were discovered rapidly, which showed a decreased adsorption capacity with the increase of the flow rate. This work has shown the feasibility and advantages of integrating PAT into QbD implementation for rapid process development.

  12. Timing is essential for rapid effects of corticosterone on synaptic potentiation in the mouse hippocampus.

    NARCIS (Netherlands)

    Wiegert, O.; Joëls, M.; Krugers, H.

    2006-01-01

    Stress facilitates memory formation, but only when the stressor is closely linked to the learning context. These effects are, at least in part, mediated by corticosteroid hormones. Here we demonstrate that corticosterone rapidly facilitates synaptic potentiation in the mouse hippocampal CA1 area

  13. Timing is Essential for Rapid Effects of Corticosterone on Synaptic Potentiation in the Mouse Hippocampus

    Science.gov (United States)

    Joels, Marian; Krugers, Harm; Wiegert, Olof

    2006-01-01

    Stress facilitates memory formation, but only when the stressor is closely linked to the learning context. These effects are, at least in part, mediated by corticosteroid hormones. Here we demonstrate that corticosterone rapidly facilitates synaptic potentiation in the mouse hippocampal CA1 area when high levels of the hormone and high-frequency…

  14. It is Time to Ban Rapid Weight Loss from Combat Sports.

    Science.gov (United States)

    Artioli, Guilherme G; Saunders, Bryan; Iglesias, Rodrigo T; Franchini, Emerson

    2016-11-01

    Most competitions in combat sports are divided into weight classes, theoretically allowing for fairer and more evenly contested disputes between athletes of similar body size, strength and agility. It has been well documented that most athletes, regardless of the combat sports discipline, reduce significant amounts of body weight in the days prior to competition to qualify for lighter weight classes. Rapid weight loss is characterised by the reduction of a significant amount of body weight (typically 2-10 %, although larger reductions are often seen) in a few days prior to weigh-in (mostly in the last 2-3 days) achieved by a combination of methods that include starvation, severe restriction of fluid intake and intentional sweating. In doing so, athletes try to gain a competitive advantage against lighter, smaller and weaker opponents. Such a drastic and rapid weight reduction is only achievable via a combination of aggressive strategies that lead to hypohydration and starvation. The negative impact of these procedures on health is well described in the literature. Although the impact of rapid weight loss on performance is debated, there remains robust evidence showing that rapid weight loss may not impair performance, and translates into an actual competitive advantage. In addition to the health and performance implications, rapid weight loss clearly breaches fair play and stands against the spirit of the sport because an athlete unwilling to compete having rapidly reduced weight would face unfair contests against opponents who are 'artificially' bigger and stronger. The World Anti-Doping Agency Code states that a prohibited method must meet at least two of the following criteria: (1) enhances performance; (2) endangers an athlete's health; and (3) violates the spirit of the sport. We herein argue that rapid weight loss clearly meets all three criteria and, therefore, should be banned from the sport. To quote the World Anti-Doping Agency Code, this would "protect

  15. Timing of HIV Seroreversion Among HIV-Exposed, Breastfed Infants in Malawi: Type of HIV Rapid Test Matters.

    Science.gov (United States)

    Smith, Emily R; Hudgens, Michael; Sheahan, Anna D; Miller, William C; Wheeler, Stephanie; Nelson, Julie A E; Dube, Queen; Van Rie, Annelies

    2017-02-01

    Introduction Rapid HIV serological tests are a cost-effective, point-of-care test among HIV exposed infants but cannot distinguish between maternal and infant antibodies. The lack of data on the timing of decay of maternal antibodies in young infants hinders the potential use of rapid tests in exposed infants. We aimed to determine the time to seroreversion for two commonly used rapid tests in a prospective cohort of HIV-exposed breastfeeding infants ages 3-18 months of life. Methods We collected data on the performance of two commonly used rapid tests (Determine and Unigold) in Malawi between 2008 and 2012 or at the University of North Carolina between 2014 and 2015. Time to seroreversion was estimated for both rapid tests using the Kaplan-Meier product limit estimator which allows for interval censored data. Results At 3 months of age, 3 % of infants had seroreverted according to Determine and 7 % had seroreverted according to Unigold. About one in four infants had achieved seroreversion by 4 months using Unigold, but only about one in twelve infants by 4 months when using Determine. More than 95 % of all infants had seroverted by 7 months according to Unigold and by 12 months according to the Determine assay. Discussion We show that the time of seroreversion depends greatly on the type of test used. Our results highlight the need for recommendations to specify the timing and type of test used in the context of infant HIV detection in resource-poor settings, and base the interpretation of test result on knowledge of time to seroreversion of the selected test.

  16. Neural networks, nativism, and the plausibility of constructivism.

    Science.gov (United States)

    Quartz, S R

    1993-09-01

    Recent interest in PDP (parallel distributed processing) models is due in part to the widely held belief that they challenge many of the assumptions of classical cognitive science. In the domain of language acquisition, for example, there has been much interest in the claim that PDP models might undermine nativism. Related arguments based on PDP learning have also been given against Fodor's anti-constructivist position--a position that has contributed to the widespread dismissal of constructivism. A limitation of many of the claims regarding PDP learning, however, is that the principles underlying this learning have not been rigorously characterized. In this paper, I examine PDP models from within the framework of Valiant's PAC (probably approximately correct) model of learning, now the dominant model in machine learning, and which applies naturally to neural network learning. From this perspective, I evaluate the implications of PDP models for nativism and Fodor's influential anti-constructivist position. In particular, I demonstrate that, contrary to a number of claims, PDP models are nativist in a robust sense. I also demonstrate that PDP models actually serve as a good illustration of Fodor's anti-constructivist position. While these results may at first suggest that neural network models in general are incapable of the sort of concept acquisition that is required to refute Fodor's anti-constructivist position, I suggest that there is an alternative form of neural network learning that demonstrates the plausibility of constructivism. This alternative form of learning is a natural interpretation of the constructivist position in terms of neural network learning, as it employs learning algorithms that incorporate the addition of structure in addition to weight modification schemes. By demonstrating that there is a natural and plausible interpretation of constructivism in terms of neural network learning, the position that nativism is the only plausible model of

  17. Rapid detection of Panton-Valentine leukocidin from clinical isolates of Staphylococcus aureus strains by real-time PCR

    NARCIS (Netherlands)

    Deurenberg, Ruud H; Vink, Cornelis; Driessen, Christel; Bes, Michèle; London, Nancy; Etienne, Jerome; Stobberingh, Ellen E

    2004-01-01

    To allow rapid identification of Panton-Valentine leukocidin (PVL)-producing Staphylococcus aureus strains, a real-time PCR assay for detection of PVL was developed. This assay is convenient, since it can be applied directly on bacterial suspensions and does not require previous DNA purification.

  18. A Novel Discovery of Growth Process for Ag Nanowires and Plausible Mechanism

    Directory of Open Access Journals (Sweden)

    Jiejun Zhu

    2016-01-01

    Full Text Available A novel growth process of silver nanowires was revealed by tracing the morphology evolution of Ag nanostructures fabricated by an improved polyol process. A mixture of Ag nanowires and nanoparticles was obtained with the usage of PVP-K25 (MW = 38,000. The products sampled at different reaction time were studied in detail using UV-visible absorption spectra and transmission electron microscopy (TEM. An interesting phenomenon unknown in the past was observed where Ag nanoparticles undergo an important dissolution-recrystallization process and Ag nanowires are formed at the expense of the preformed Ag nanoparticles. A plausible novel growth mechanism for the silver nanowires was proposed.

  19. On the biological plausibility of Wind Turbine Syndrome.

    Science.gov (United States)

    Harrison, Robert V

    2015-01-01

    An emerging environmental health issue relates to potential ill-effects of wind turbine noise. There have been numerous suggestions that the low-frequency acoustic components in wind turbine signals can cause symptoms associated with vestibular system disorders, namely vertigo, nausea, and nystagmus. This constellation of symptoms has been labeled as Wind Turbine Syndrome, and has been identified in case studies of individuals living close to wind farms. This review discusses whether it is biologically plausible for the turbine noise to stimulate the vestibular parts of the inner ear and, by extension, cause Wind Turbine Syndrome. We consider the sound levels that can activate the semicircular canals or otolith end organs in normal subjects, as well as in those with preexisting conditions known to lower vestibular threshold to sound stimulation.

  20. Alkaloids from Pandanus amaryllifolius: Isolation and Their Plausible Biosynthetic Formation.

    Science.gov (United States)

    Tsai, Yu-Chi; Yu, Meng-Lun; El-Shazly, Mohamed; Beerhues, Ludger; Cheng, Yuan-Bin; Chen, Lei-Chin; Hwang, Tsong-Long; Chen, Hui-Fen; Chung, Yu-Ming; Hou, Ming-Feng; Wu, Yang-Chang; Chang, Fang-Rong

    2015-10-23

    Pandanus amaryllifolius Roxb. (Pandanaceae) is used as a flavor and in folk medicine in Southeast Asia. The ethanolic crude extract of the aerial parts of P. amaryllifolius exhibited antioxidant, antibiofilm, and anti-inflammatory activities in previous studies. In the current investigation, the purification of the ethanolic extract yielded nine new compounds, including N-acetylnorpandamarilactonines A (1) and B (2); pandalizines A (3) and B (4); pandanmenyamine (5); pandamarilactones 2 (6) and 3 (7), and 5(E)-pandamarilactonine-32 (8); and pandalactonine (9). The isolated alkaloids, with either a γ-alkylidene-α,β-unsaturated-γ-lactone or γ-alkylidene-α,β-unsaturated-γ-lactam system, can be classified into five skeletons including norpandamarilactonine, indolizinone, pandanamine, pandamarilactone, and pandamarilactonine. A plausible biosynthetic route toward 1-5, 7, and 9 is proposed.

  1. Real-time PCR assay for rapid detection of epidemiologically and clinically significant Mycobacterium tuberculosis Beijing genotype isolates.

    Science.gov (United States)

    Mokrousov, Igor; Vyazovaya, Anna; Zhuravlev, Viacheslav; Otten, Tatiana; Millet, Julie; Jiao, Wei-Wei; Shen, A-Dong; Rastogi, Nalin; Vishnevsky, Boris; Narvskaya, Olga

    2014-05-01

    Mycobacterium tuberculosis Beijing genotype strains are rapidly disseminating, frequently hypervirulent, and multidrug resistant. Here, we describe a method for their rapid detection by real-time PCR that targets the specific IS6110 insertion in the dnaA-dnaN genome region. The method was evaluated with a geographically and genetically diverse collection representing areas in East Asia and the former Soviet Union in which the Beijing genotype is endemic and epidemic (i.e., major foci of its global propagation) and with clinical specimens.

  2. Pattern and timing of late Cenozoic rapid exhumation and uplift of the Helan Mountain,China

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The Helan Mountain, an intraplate deformation belt in the North China Craton, is located in the northern portion of the China North-South seismic belt, and at the northwestern margin of the Ordos Block. The Cenozoic deformation history of the Helan Mountain is characterized by extension along the eastern Helan Mountain fault (EHSF), resulting in the exhumation and uplift of the Helan Mountain, relative to the rifting of the adjacent Yinchuan Basin. Here we present new apatite fission track (AFT) data from several transects adjacent to the EHSF in the central and northern Helan Mountain. AFT ages from the northern Helan Mountain (Dawukou and Zhengyiguan transects) range from 10 Ma to 89 Ma, whereas AFT ages from the southern Helan Mountain (Suyukou transect) are greater than 71 Ma. The AFT data analysis reveals initiation of rapid uplift and exhumation of the Helan Mountain at 10–12 Ma. Additionally, a plot of the AFT ages versus their mean track length shows a distinctive "boomerang" pattern indicating that the Helan Mountain experienced a discrete phase of accelerated exhumation beginning at 10-12 Ma. Spatially, AFT samples systematically increase in age away from the EHSF and are consistent with late Cenozoic exhumation that was slow in the southwestern Helan Mountain and rapid in the northeastern Helan Mountain, as well more rapid adjacent to the EHSF and slower away from the EHSF. Obviously, the spatial distribution of late Cenozoic exhumation indicates that normal faulting of the EHSF is related to southwestward tilting and rapid exhumation of the Helan Mountain beginning at 10–12 Ma. The uplift and exhumation of the Helan Mountain was a response to the intensive extension of the northwestern margin of the Ordos Block in the late Cenozoic; this occurred under a regional extensional stress field oriented NW-SE along the Yinchuan-Jilantai-Hetao and the Weihe-Shanxi graben systems adjacent to the Ordos Block.

  3. Effects of oncoming target velocities on rapid force production and accuracy of force production intensity and timing.

    Science.gov (United States)

    Ohta, Yoichi

    2016-12-12

    The present study aimed to clarify the effects of oncoming target velocities on the ability of rapid force production and accuracy and variability of simultaneous control of both force production intensity and timing. Twenty male participants (age: 21.0 ± 1.4 years) performed rapid gripping with a handgrip dynamometer to coincide with the arrival of an oncoming target by using a horizontal electronic trackway. The oncoming target velocities were 4, 8, and 12 m · s(-1), which were randomly produced. The grip force required was 30% of the maximal voluntary contraction. Although the peak force (Pf) and rate of force development (RFD) increased with increasing target velocity, the value of the RFD to Pf ratio was constant across the 3 target velocities. The accuracy of both force production intensity and timing decreased at higher target velocities. Moreover, the intrapersonal variability in temporal parameters was lower in the fast target velocity condition, but constant variability in 3 target velocities was observed in force intensity parameters. These results suggest that oncoming target velocity does not intrinsically affect the ability for rapid force production. However, the oncoming target velocity affects accuracy and variability of force production intensity and timing during rapid force production.

  4. Empirical Assessment on Factors Affecting Travel Time of Bus Rapid Transit

    OpenAIRE

    Fergyanto E Gunawan

    2015-01-01

    Since the beginning of the century, many cities around the world adopt the bus rapid transit (BRT) system to fulfill their need of mass transportation system. The system features with platform-level boarding, bus lanes in the central verge of the road, off-vehicle fare collection, and physically protected busway. So far, these criteria are considered to be the most important aspects with respect to the BRT performance. In this research, we intend to study to what extent the BRT performance ma...

  5. Rapid Purification of Salmonella DNA in Minced Meat and Detection by Real-time PCR

    DEFF Research Database (Denmark)

    Jenikova, G.; Jensen, Annette Nygaard; Demnerova, K.;

    2001-01-01

    of DNeasy was found to be 6-8 CFU in just 19 end-point fluorescence (C-t) values, while this was 22 C-t for a combination of DNeasy and BactXtractor. Extraction by DNeasy resulted in C-t ...Four rapid and simple DNA purification and sample treatment protocols were evaluated for detection of Salmonella enterica in spiked minced meat, using a fluorogenic 5' nuclease (TaqMan) PCR assay in an ABI-Prism 7700 Sequence Detector. The detection limit with the single separation treatment...

  6. Higher Data Quality by Online Data-Entry and Automated Plausibility Checks

    Science.gov (United States)

    Pietragalla, Barbara; Sigg, Christian; Güsewell, Sabine; Clot, Bernard

    2014-05-01

    Long-term phenological observations are now recognized as important indicators for climate change impact studies. With the increased need for phenological data, there is also an increased need for higher data quality. Since 1951 MeteoSwiss has been operating a national phenological observation network. Currently the network consists of about 150 active stations observing up to 69 different phenophases. An important aim of a running three years project at MeteoSwiss is a further increase of the quality of the collected data. The higher data quality will be achieved by an automated procedure performing plausibility checks on the data and by online data-entry. Further measures such as intensified observer instructions and collection of more detailed metadata also contribute to a high data quality standard. The plausibility checks include the natural order of the phenophases within a species and also between different species (with regard to possible natural deviation). Additionally it will be checked if the observed date differs by less than two standard deviations from the average for this phenophase at the altitude of the station. A value outside of these limits is not necessarily a false value, since occurrences of extreme values will be beyond these limits. Therefore, within this check of the limits, the timing of the season of the respective year will also be taken into account. In case of an implausible value a comparison with other stations of the same region and sea level is proposed. A further possibility of data quality control could be to model the different phenophases statistically and to use this model for estimating the likelihood of observed values. An overall exploratory data analysis is currently performed providing a solid basis to implement the best possible methods for the plausibility checks. Important advantages of online data-entry are the near real-time availability of the data as well as the avoidance of various kinds of typical mistakes

  7. Rapid weight loss followed by recovery time does not affect judo-related performance.

    Science.gov (United States)

    Artioli, Guilherme G; Iglesias, Rodrigo T; Franchini, Emerson; Gualano, Bruno; Kashiwagura, Daniel B; Solis, Marina Y; Benatti, Fabiana B; Fuchs, Marina; Lancha Junior, Antonio H

    2010-01-01

    In this study, we investigated the effects of rapid weight loss followed by a 4-h recovery on judo-related performance. Seven weight-cycler athletes were assigned to a weight loss group (5% body weight reduction by self-selected regime) and seven non-weight-cyclers to a control group (no weight reduction). Body composition, performance, glucose, and lactate were assessed before and after weight reduction (5-7 days apart; control group kept weight stable). The weight loss group had 4 h to re-feed and rehydrate after the weigh-in. Food intake was recorded during the weight loss period and recovery after the weigh-in. Performance was evaluated through a specific judo exercise, followed by a 5-min judo combat and by three bouts of the Wingate test. Both groups significantly improved performance after the weight loss period. No interaction effects were observed. The energy and macronutrient intake of the weight loss group were significantly lower than for the control group. The weight loss group consumed large amounts of food and carbohydrate during the 4-h recovery period. No changes were observed in lactate concentration, but a significant decrease in glucose during rest was observed in the weight loss group. In conclusion, rapid weight loss did not affect judo-related performance in experienced weight-cyclers when the athletes had 4 h to recover. These results should not be extrapolated to inexperienced weight-cyclers.

  8. Rapid Increase in Neural Conduction Time in the Adult Human Auditory Brainstem Following Sudden Unilateral Deafness.

    Science.gov (United States)

    Maslin, M R D; Lloyd, S K; Rutherford, S; Freeman, S; King, A; Moore, D R; Munro, K J

    2015-10-01

    Individuals with sudden unilateral deafness offer a unique opportunity to study plasticity of the binaural auditory system in adult humans. Stimulation of the intact ear results in increased activity in the auditory cortex. However, there are no reports of changes at sub-cortical levels in humans. Therefore, the aim of the present study was to investigate changes in sub-cortical activity immediately before and after the onset of surgically induced unilateral deafness in adult humans. Click-evoked auditory brainstem responses (ABRs) to stimulation of the healthy ear were recorded from ten adults during the course of translabyrinthine surgery for the removal of a unilateral acoustic neuroma. This surgical technique always results in abrupt deafferentation of the affected ear. The results revealed a rapid (within minutes) reduction in latency of wave V (mean pre = 6.55 ms; mean post = 6.15 ms; p < 0.001). A latency reduction was also observed for wave III (mean pre = 4.40 ms; mean post = 4.13 ms; p < 0.001). These reductions in response latency are consistent with functional changes including disinhibition or/and more rapid intra-cellular signalling affecting binaurally sensitive neurons in the central auditory system. The results are highly relevant for improved understanding of putative physiological mechanisms underlying perceptual disorders such as tinnitus and hyperacusis.

  9. A real-time loop-mediated isothermal amplification assay for rapid detection of Shigella species.

    Science.gov (United States)

    Liew, P S; Teh, C S J; Lau, Y L; Thong, K L

    2014-12-01

    Shigellosis is a foodborne illness caused by the genus Shigella and is an important global health issue. The development of effective techniques for rapid detection of this pathogen is essential for breaking the chain of transmission. Therefore, we have developed a novel loop-mediated isothermal amplification (LAMP) assay targeting the invasion plasmid antigen H (ipaH) gene to rapidly detect Shigella species. This assay could be performed in 90 min at an optimal temperature of 64ºC, with endpoint results visualized directly. Notably, the method was found to be more sensitive than conventional PCR. Indeed, the detection limit for the LAMP assay on pure bacterial cultures was 5.9 x 10(5) CFU/ml, while PCR displayed a limit of 5.9 x 10(7) CFU/ml. In spiked lettuce samples, the sensitivity of the LAMP assay was 3.6 x 10(4) CFU/g, whereas PCR was 3.6 x 10(5) CFU/g. Overall, the assay accurately identified 32 Shigella spp. with one enteroinvasive Escherichia coli displaying positive reaction while the remaining 32 non-Shigella strains tested were negative.

  10. Motor vehicle injuries in Qatar: time trends in a rapidly developing Middle Eastern nation.

    Science.gov (United States)

    Mamtani, Ravinder; Al-Thani, Mohammed H; Al-Thani, Al-Anoud Mohammed; Sheikh, Javaid I; Lowenfels, Albert B

    2012-04-01

    Despite their wealth and modern road systems, traffic injury rates in Middle Eastern countries are generally higher than those in Western countries. The authors examined traffic injuries in Qatar during 2000-2010, a period of rapid population growth, focusing on the impact of speed control cameras installed in 2007 on overall injury rates and mortality. During the period 2000-2006, prior to camera installation, the mean (SD) vehicular injury death rate per 100,000 was 19.9±4.1. From 2007 to 2010, the mean (SD) vehicular death rates were significantly lower: 14.7±1.5 (p=0.028). Non-fatal severe injury rates also declined, but mild injury rates increased, perhaps because of increased traffic congestion and improved notification. It is possible that speed cameras decreased speeding enough to affect the death rate, without affecting overall injury rates. These data suggest that in a rapidly growing Middle Eastern country, photo enforcement (speed) cameras can be an important component of traffic control, but other measures will be required for maximum impact.

  11. Stopped-flow ultra-rapid-scanning Fourier transform infrared spectroscopy on the millisecond time scale.

    Science.gov (United States)

    Reback, Matthew L; Roske, Christopher W; Bitterwolf, Thomas E; Griffiths, Peter R; Manning, Christopher J

    2010-08-01

    Full-range mid-infrared spectra were measured during the reaction of CpCo(CO)(2) with nitrosyl chloride by interfacing a rapid-mixing stopped-flow device with an ultra-rapid-scanning Fourier transform infrared (FT-IR) spectrometer having a temporal resolution of 5 ms. Changes to the data acquisition hardware of this spectrometer now allow a sequence of well over 2000 spectra to be collected without interruption. Two transient species were observed spectroscopically during the first 500 ms of the reaction of CpCo(CO)(2) with nitrosyl chloride. The shortest-lived species that was observed, [CpCo(CO)(2)(NO)](+), had a half-life of approximately 20 ms at 25 degrees C and approximately 70 ms at 10 degrees C. This intermediate transformed into a longer-lived (approximately 0.5 s) intermediate, CpCo(NO)Cl. Potential intermediate species with one CO and one NO ligand, such as [CpCo(CO)(NO)](+) and CpCo(CO)(NO)Cl, were not observed, although the possibility that they exist cannot be ruled out.

  12. Time-Resolved Fluorescent Immunochromatography of Aflatoxin B1 in Soybean Sauce: A Rapid and Sensitive Quantitative Analysis

    Science.gov (United States)

    Wang, Du; Zhang, Zhaowei; Li, Peiwu; Zhang, Qi; Zhang, Wen

    2016-01-01

    Rapid and quantitative sensing of aflatoxin B1 with high sensitivity and specificity has drawn increased attention of studies investigating soybean sauce. A sensitive and rapid quantitative immunochromatographic sensing method was developed for the detection of aflatoxin B1 based on time-resolved fluorescence. It combines the advantages of time-resolved fluorescent sensing and immunochromatography. The dynamic range of a competitive and portable immunoassay was 0.3–10.0 µg·kg−1, with a limit of detection (LOD) of 0.1 µg·kg−1 and recoveries of 87.2%–114.3%, within 10 min. The results showed good correlation (R2 > 0.99) between time-resolved fluorescent immunochromatographic strip test and high performance liquid chromatography (HPLC). Soybean sauce samples analyzed using time-resolved fluorescent immunochromatographic strip test revealed that 64.2% of samples contained aflatoxin B1 at levels ranging from 0.31 to 12.5 µg·kg−1. The strip test is a rapid, sensitive, quantitative, and cost-effective on-site screening technique in food safety analysis. PMID:27428975

  13. Rapid detection of lineage IV peste des petits ruminants virus by real-time RT-PCR.

    Science.gov (United States)

    Li, Lin; Wu, Xiaodong; Liu, Fuxiao; Wang, Zhiliang; Liu, Chunju; Wang, Qinghua; Bao, Jingyue

    2016-09-01

    Peste des petits ruminants virus (PPRV) is the cause agent of peste des petitis ruminants (PPR). A novel lineage IV PPRV has reemerged in China in 2013 and 2014. Mass vaccination was implemented in most provinces in China. In order to detect lineage IV PPRV in clinical samples and to distinguish rapidly it from the other lineages PPRVs, a real-time RT-PCR assay was developed. This assay showed high sensitivity, specificity and efficiency in differentiating the lineage IV PPRV from others. The performance of this assay was evaluated by positive clinical samples of lineage IV viruses. This new real-time RT-PCR assay will facilitate epidemiological investigations and rapid differentiatial diagnosis in areas where lineage IV viruses are circulating. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Comprehensive and Rapid Real-Time PCR Analysis of 21 Foodborne Outbreaks

    Directory of Open Access Journals (Sweden)

    Hiroshi Fukushima

    2009-01-01

    Full Text Available A set of four duplex SYBR Green I PCR (SG-PCR assay combined with DNA extraction using QIAamp DNA Stool Mini kit was evaluated for the detection of foodborne bacteria from 21 foodborne outbreaks. The causative pathogens were detected in almost all cases in 2 hours or less. The first run was for the detection of 8 main foodborne pathogens in 5 stool specimens within 2 hours and the second run was for the detection of other unusual suspect pathogens within a further 45 minutes. After 2 to 4 days, the causative agents were isolated and identified. The results proved that for comprehensive and rapid molecular diagnosis in foodborne outbreaks, Duplex SG-PCR assay is not only very useful, but is also economically viable for one-step differentiation of causative pathogens in fecal specimens obtained from symptomatic patients. This then allows for effective diagnosis and management of foodborne outbreaks.

  15. Rapid Detection/pathotyping of Newcastle disease virus isolates in clinical samples using real time polymerase chain reaction assay

    OpenAIRE

    sprotocols

    2014-01-01

    Authors: Abdul Wajid, Muhammad Wasim, Tahir Yaqub, Shafqat F Rehmani, Tasra Bibi, Nadia Mukhtar, Javed Muhammad, Umar Bacha, Suliman Qadir Afridi, Muhammad Nauman Zahid, Zia u ddin, Muhammad Zubair Shabbir, Kamran Abbas & Muneer Ahmad ### Abstract In the present protocol we describe the real time reverse transcription polymerase chain reaction (rRT-PCR) assay for the rapid detection/pathotyping of Newcastle disease virus (NDV) isoaltes in clinical samples. Fusion gene and matrix ...

  16. Liderazgo preventivo para la universidad. Una experiencia plausible

    Directory of Open Access Journals (Sweden)

    Alejandro Rodríguez Rodríguez

    2015-06-01

    Full Text Available El desarrollo del liderazgo, en el ámbito educativo superior, busca soluciones de aplicación inmediata a contextos en que todo líder se desenvuelve, pero se diluye el sustento teórico-práctico en la formación del líder que posibilite entender los procesos intelectivos durante la toma de decisiones. El paradigma de convergencia entre el método antropológico lonerganiano, la comunidad de aprendizaje vygotskiana y una relectura del sistema preventivo salesiano se presentan como propuesta plausible de formación al liderazgo preventivo entre los diversos actores de una comunidad universitaria. Un estudio de caso de la Universidad Salesiana en México empleando un método mixto de investigación, facilita una relectura del liderazgo desde una óptica preventiva como posibilidad de convergencia en un diálogo interdisciplinar. Los resultados teórico-práctico propuestos y examinados se muestran como herramienta útil para evaluar, enriquecer y renovar la teoría sobre el líder y el desarrollo de liderazgo en las universidades frente a una sociedad globalizada.

  17. A perspective on SIDS pathogenesis. The hypotheses: plausibility and evidence

    Directory of Open Access Journals (Sweden)

    Goldwater Paul N

    2011-05-01

    Full Text Available Abstract Several theories of the underlying mechanisms of Sudden Infant Death Syndrome (SIDS have been proposed. These theories have born relatively narrow beach-head research programs attracting generous research funding sustained for many years at expense to the public purse. This perspective endeavors to critically examine the evidence and bases of these theories and determine their plausibility; and questions whether or not a safe and reasoned hypothesis lies at their foundation. The Opinion sets specific criteria by asking the following questions: 1. Does the hypothesis take into account the key pathological findings in SIDS? 2. Is the hypothesis congruent with the key epidemiological risk factors? 3. Does it link 1 and 2? Falling short of any one of these answers, by inference, would imply insufficient grounds for a sustainable hypothesis. Some of the hypotheses overlap, for instance, notional respiratory failure may encompass apnea, prone sleep position, and asphyxia which may be seen to be linked to co-sleeping. For the purposes of this paper, each element will be assessed on the above criteria.

  18. A plausible explanation for male dominance in typhoid ileal perforation

    Directory of Open Access Journals (Sweden)

    Khan M

    2012-11-01

    Full Text Available Mohammad KhanDepartment of Microbiology, College of Medicine, Chichiri, Blantyre, MalawiAbstract: The phenomenon of consistent male dominance in typhoid ileal perforation (TIP is not well understood. It cannot be explained on the basis of microbial virulence, Peyer's patch anatomy, ileal wall thickness, gastric acidity, host genetic factors, or sex-linked bias in hospital attendance. The cytokine response to an intestinal infection in males is predominantly proinflammatory as compared with that in females, presumably due to differences in the sex hormonal milieu. Sex hormone receptors have been detected on lymphocytes and macrophages, including on Peyer's patches, inflammation of which (probably similar to the Shwartzman reaction/Koch phenomenon is the forerunner of TIP, and is not excluded from the regulatory effects of sex hormones. Hormonal control of host-pathogen interaction may override genetic control. Environmental exposure to Salmonella typhi may be more frequent in males, presumably due to sex-linked differences in hygiene practices and dining-out behavior. A plausible explanation of male dominance in TIP could include sex-linked differences in the degree of natural exposure of Peyer's patches to S. typhi. An alternative explanation may include sexual dimorphism in host inflammatory response patterns in Peyer's patches that have been induced by S. typhi. Both hypotheses are testable.Keywords: explanation, dominance, male, perforation, ileum, typhoid

  19. A plausible explanation for male dominance in typhoid ileal perforation.

    Science.gov (United States)

    Khan, Mohammad

    2012-01-01

    The phenomenon of consistent male dominance in typhoid ileal perforation (TIP) is not well understood. It cannot be explained on the basis of microbial virulence, Peyer's patch anatomy, ileal wall thickness, gastric acidity, host genetic factors, or sex-linked bias in hospital attendance. The cytokine response to an intestinal infection in males is predominantly proinflammatory as compared with that in females, presumably due to differences in the sex hormonal milieu. Sex hormone receptors have been detected on lymphocytes and macrophages, including on Peyer's patches, inflammation of which (probably similar to the Shwartzman reaction/Koch phenomenon) is the forerunner of TIP, and is not excluded from the regulatory effects of sex hormones. Hormonal control of host-pathogen interaction may override genetic control. Environmental exposure to Salmonella typhi may be more frequent in males, presumably due to sex-linked differences in hygiene practices and dining-out behavior. A plausible explanation of male dominance in TIP could include sex-linked differences in the degree of natural exposure of Peyer's patches to S. typhi. An alternative explanation may include sexual dimorphism in host inflammatory response patterns in Peyer's patches that have been induced by S. typhi. Both hypotheses are testable.

  20. Time-gated FRET nanoassemblies for rapid and sensitive intra- and extracellular fluorescence imaging

    NARCIS (Netherlands)

    Afsari, Hamid Samareh; Cardoso Dos Santos, Marcelina; Lindén, Stina; Chen, Ting; Qiu, Xue; van Bergen En Henegouwen, Paul M P; Jennings, Travis L; Susumu, Kimihiro; Medintz, Igor L; Hildebrandt, Niko; Miller, Lawrence W

    2016-01-01

    Time-gated Förster resonance energy transfer (FRET) using the unique material combination of long-lifetime terbium complexes (Tb) and semiconductor quantum dots (QDs) provides many advantages for highly sensitive and multiplexed biosensing. Although time-gated detection can efficiently suppress samp

  1. Rapid Microcystin Determination Using a Paper Spray Ionization Method with a Time-of-Flight Mass Spectrometry System.

    Science.gov (United States)

    Zhu, Xiaoqiang; Huang, Zhengxu; Gao, Wei; Li, Xue; Li, Lei; Zhu, Hui; Mo, Ting; Huang, Bao; Zhou, Zhen

    2016-07-13

    The eutrophication of surface water sources and climate changes have resulted in an annual explosion of cyanobacterial blooms in many irrigating and drinking water resources. To decrease health risks to the public, a rapid real time method for the synchronous determination of two usually harmful microcystins (MC-RR and MC-LR) in environmental water samples was built by employing a paper spray ionization method coupled with a time-of-flight mass spectrometer system. With this approach, direct analysis of microcystin mixtures without sample preparation has been achieved. Rapid detection was performed, simulating the release process of microcystins in reservoir water samples, and the routine detection frequency was every three minutes. The identification time of microcystins was reduced from several hours to a few minutes. The limit of detection is 1 μg/L, and the limit of quantitation is 3 μg/L. This method displays the ability for carrying out rapid, direct, and high-throughput experiments for determination of microcystins, and it would be of significant interest for environmental and food safety applications.

  2. [Simple and rapid screening for psychotropic natural products using Direct Analysis in Real Time (DART)-TOFMS].

    Science.gov (United States)

    Kawamura, Maiko; Kikura-Hanajiri, Ruri; Goda, Yukihiro

    2009-06-01

    Direct Analysis in Real Time (DART) is a novel ionization technique that provides for the rapid ionization of small molecules under ambient conditions. To investigate the trend of non-controlled psychotropic plants of abuse in Japan, a rapid screening method, without sample preparation, was developed using DART-time of flight mass spectrometer (TOFMS) for plant products. The major psychotropic constituents of these products were determined using liquid chromatography-mass spectrometry (LC/MS). As a result of the DART-TOFMS analyses of 36 products, the protonated molecular ions [M+H](+), corresponding to 6 kinds of major hallucinogenic constituents (mescaline, salvinorin A, N,N-dimethyltryptamine, harmine, harmaline and lysergamide), were detected in 21 products. It was possible to estimate their accurate elemental compositions through exact mass measurements. These results were consistent with those of the LC/MS analyses and the contents of the 6 psychotropic constituents were in the range from 0.05 to 45 microg/mg. Typical controlled narcotic drugs, tetrahydrocannabinol, opioid alkaloids and psilocin were also directly detected in marijuana cigarette, opium gum and magic mushroom respectively. Although it is difficult to estimate the matrix effects caused by other plant ingredients, the DART-TOFMS could be useful as a simple and rapid screening method for the targeted psychotropic natural products, because it provides the molecular information of the target compounds without time-consuming extraction and pre-treatment steps.

  3. Development and validation of a real-time quantitative PCR assay for rapid identification of Bacillus anthracis in environmental samples.

    Science.gov (United States)

    Irenge, Léonid M; Durant, Jean-François; Tomaso, Herbert; Pilo, Paola; Olsen, Jaran S; Ramisse, Vincent; Mahillon, Jacques; Gala, Jean-Luc

    2010-11-01

    A real-time polymerase chain reaction (PCR) assay was developed for rapid identification of Bacillus anthracis in environmental samples. These samples often harbor Bacillus cereus bacteria closely related to B. anthracis, which may hinder its specific identification by resulting in false positive signals. The assay consists of two duplex real-time PCR: the first PCR allows amplification of a sequence specific of the B. cereus group (B. anthracis, B. cereus, Bacillus thuringiensis, Bacillus weihenstephanensis, Bacillus pseudomycoides, and Bacillus mycoides) within the phosphoenolpyruvate/sugar phosphotransferase system I gene and a B. anthracis specific single nucleotide polymorphism within the adenylosuccinate synthetase gene. The second real-time PCR assay targets the lethal factor gene from virulence plasmid pXO1 and the capsule synthesis gene from virulence plasmid pXO2. Specificity of the assay is enhanced by the use of minor groove binding probes and/or locked nucleic acids probes. The assay was validated on 304 bacterial strains including 37 B. anthracis, 67 B. cereus group, 54 strains of non-cereus group Bacillus, and 146 Gram-positive and Gram-negative bacteria strains. The assay was performed on various environmental samples spiked with B. anthracis or B. cereus spores. The assay allowed an accurate identification of B. anthracis in environmental samples. This study provides a rapid and reliable method for improving rapid identification of B. anthracis in field operational conditions.

  4. Three-time rapid transfer alignment method of SINS/GPS navigation system of high-speed marine missile

    Institute of Scientific and Technical Information of China (English)

    WANG Si; DENG Zheng-long; SU Ling-feng

    2008-01-01

    The transfer alignment of SINS/GPS navigation system of a high-speed marine missile was investiga-ted. With the help of the big acceleration of a high-speed missile, the transfer alignment was changed into a three-time alignment. The azimuth alignment was coarsely finished in 10s in the first time alignment, the hori-zontal alignment was accurately and rapidly finished in the second time alignment, and the azimuth alignment was accurately finished in the third time alignment. Because the second time alignment and the third time align-ment were finished by GPS after the missile was launched, the horizontal alignment and the second azimuth a-lignment got rid of the influence of the warship body flexibility deforming. The precision and rapidity of the hori-zontal alignment were prominently increased due to the vertical launch of the marine missile with the big accel-eration. Simulation verifies the effectiveness of the proposed alignment method.

  5. Rapid PCR amplification protocols decrease the turn-around time for detection of antibiotic resistance genes in Gram-negative pathogens.

    Science.gov (United States)

    Geyer, Chelsie N; Hanson, Nancy D

    2013-10-01

    A previously designed end-point multiplex PCR assay and singleplex assays used to detect β-lactamase genes were evaluated using rapid PCR amplification methodology. Amplification times were 16-18 minutes with an overall detection time of 1.5 hours. Rapid PCR amplifications could decrease the time required to identify resistance mechanisms in Gram-negative organisms.

  6. The Sarrazin effect: the presence of absurd statements in conspiracy theories makes canonical information less plausible.

    Science.gov (United States)

    Raab, Marius Hans; Auer, Nikolas; Ortlieb, Stefan A; Carbon, Claus-Christian

    2013-01-01

    Reptile prime ministers and flying Nazi saucers-extreme and sometimes off-wall conclusion are typical ingredients of conspiracy theories. While individual differences are a common research topic concerning conspiracy theories, the role of extreme statements in the process of acquiring and passing on conspiratorial stories has not been regarded in an experimental design so far. We identified six morphological components of conspiracy theories empirically. On the basis of these content categories a set of narrative elements for a 9/11 story was compiled. These elements varied systematically in terms of conspiratorial allegation, i.e., they contained official statements concerning the events of 9/11, statements alleging to a conspiracy limited in time and space as well as extreme statements indicating an all-encompassing cover-up. Using the method of narrative construction, 30 people were given a set of cards with these statements and asked to construct the course of events of 9/11 they deem most plausible. When extreme statements were present in the set, the resulting stories were more conspiratorial; the number of official statements included in the narrative dropped significantly, whereas the self-assessment of the story's plausibility did not differ between conditions. This indicates that blatant statements in a pool of information foster the synthesis of conspiracy theories on an individual level. By relating these findings to one of Germany's most successful (and controversial) non-fiction books, we refer to the real-world dangers of this effect.

  7. Rapid telomere motions in live human cells analyzed by highly time-resolved microscopy

    Directory of Open Access Journals (Sweden)

    Wang Xueying

    2008-10-01

    Full Text Available Abstract Background Telomeres cap chromosome ends and protect the genome. We studied individual telomeres in live human cancer cells. In capturing telomere motions using quantitative imaging to acquire complete high-resolution three-dimensional datasets every second for 200 seconds, telomere dynamics were systematically analyzed. Results The motility of individual telomeres within the same cancer cell nucleus was widely heterogeneous. One class of internal heterochromatic regions of chromosomes analyzed moved more uniformly and showed less motion and heterogeneity than telomeres. The single telomere analyses in cancer cells revealed that shorter telomeres showed more motion, and the more rapid telomere motions were energy dependent. Experimentally increasing bulk telomere length dampened telomere motion. In contrast, telomere uncapping, but not a DNA damaging agent, methyl methanesulfonate, significantly increased telomere motion. Conclusion New methods for seconds-scale, four-dimensional, live cell microscopic imaging and data analysis, allowing systematic tracking of individual telomeres in live cells, have defined a previously undescribed form of telomere behavior in human cells, in which the degree of telomere motion was dependent upon telomere length and functionality.

  8. [Preventive medicine in times of a rapid epidemiologic transition in Korea].

    Science.gov (United States)

    Park, Jung Han

    2006-01-01

    Ever since the foundation of the Korean Society for Preventive Medicine in 1947, members of the Society had made remarkable contributions to the public health development and national health promotion. They had played key roles in establishing national health system, improving environmental hygiene, controlling infectious and chronic diseases, promoting family planning, improving industrial and environmental health, and developing health service management. However, the Society had less actively responded to the changes in health service needs of the population that were caused by a rapid epidemiologic transition in last a few decades. Early detection and treatment of chronic diseases including cancer and cardiovascular diseases and risk reduction by the life style modification are major approaches to the contemporary national health problems and they are the core contents of preventive medicine. The author proposed to develop the clinical preventive medicine specialist who will have additional training in clinical medicine for health screening and life style modification to the current preventive medicine training program and thus will be able to provide comprehensive preventive medical services. Another area that the Society may take the initiative is training preventive medicine specialist in the disaster, including bioterrorism, preparedness and management. The Society should be more active in proposing health policy and health service program and also participate collectively in a large scale health research project of the government. These approaches may not only contribute more effectively to the national health promotion but also improve the identity of the Society.

  9. Direct observation of f-pair magnetic field effects and time-dependence of radical pair composition using rapidly switched magnetic fields and time-resolved infrared methods.

    Science.gov (United States)

    Woodward, Jonathan R; Foster, Timothy J; Salaoru, Adrian T; Vink, Claire B

    2008-07-21

    A rapidly switched (magnetic field was employed to directly observe magnetic fields from f-pair reactions of radical pairs in homogeneous solution. Geminate radical pairs from the photoabstraction reaction of benzophenone from cyclohexanol were observed directly using a pump-probe pulsed magnetic field method to determine their existence time. No magnetic field effects from geminate pairs were observed at times greater than 100 ns after initial photoexcitation. By measuring magnetic field effects for fields applied continuously only after this initial geminate period, f-pair effects could be directly observed. Measurement of the time-dependence of the field effect for the photolysis of 2-hydroxy-4-(2-hydroxyethoxy)-2-methylpropiophenone in cyclohexanol using time-resolved infrared spectroscopy revealed not only the presence of f-pair magnetic field effects but also the ability of the time dependence of the MARY spectra to observe the changing composition of the randomly encountering pairs throughout the second order reaction period.

  10. Rapid spatial frequency domain inverse problem solutions using look-up tables for real-time processing (Conference Presentation)

    Science.gov (United States)

    Angelo, Joseph P.; Bigio, Irving J.; Gioux, Sylvain

    2016-03-01

    Imaging technologies working in the spatial frequency domain are becoming increasingly popular for generating wide-field optical property maps, enabling further analysis of tissue parameters such as absorption or scattering. While acquisition methods have witnessed a very rapid growth and are now performing in real-time, processing methods are yet slow preventing information to be acquired and displayed in real-time. In this work, we present solutions for rapid inverse problem solving for optical properties by use of advanced look-up tables. In particular, we present methods and results from a dense, linearized look-up table and an analytical representation that currently run 100 times faster than the standard method and within 10% in both absorption and scattering. With the resulting computation time in the tens of milliseconds range, the proposed techniques enable video-rate feedback of real-time techniques such as snapshot of optical properties (SSOP) imaging, making full video-rate guidance in the clinic possible.

  11. Identification of time-varying dynamics of the human triceps surae stretch reflex. I. Rapid isometric contraction.

    Science.gov (United States)

    Kirsch, R F; Kearney, R E; MacNeil, J B

    1993-01-01

    We have examined the time variations of stretch reflex dynamics throughout rapid voluntary changes in the isometric contraction level of the human triceps surae muscles. This was achieved by superimposing a small stochastic displacement upon many such changing contractions and then identifying the time-varying relationship between the perturbation and the evoked electromyograms (EMGs). An "ensemble" time-varying system identification technique was used to estimate these input-output dynamics as a set of impulse response functions, one for each time before, during, and after the change in contraction level, with a temporal resolution equal to the data acquisition rate. Three main findings resulted. First, stretch reflex gain (relating joint velocity to EMG) was significantly modulated during changes in voluntary contraction level, increasing as the subject contracted the muscles and decreasing as the subject relaxed. Second, stretch reflex dynamics did not change with contraction level, even when its gain varied substantially. Third, the time course of the gain changes closely followed the level of the EMG, even though the subjects used rather different activation and deactivation patterns. These results suggest that, for the behavior studied (i.e., rapid changes in isometric contraction level), stretch reflex gain and motoneuron pool activation level were controlled by a common descending command rather than being independently specified.

  12. Quantitative muscle ultrasound measures rapid declines over time in children with SMA type 1.

    Science.gov (United States)

    Ng, Kay W; Connolly, Anne M; Zaidman, Craig M

    2015-11-15

    Muscles are small in spinal muscular atrophy (SMA). It is not known if muscle size changes over time in SMA type 1. We quantified changes over time in muscle size and echointensity during two repeated ultrasound examinations of unilateral proximal (biceps brachii/brachialis and quadriceps) and distal (anterior forearm flexors and tibialis anterior) muscles in three children with SMA type 1. We compared muscle thickness (MT) to body weight-dependent normal reference values. Children were 1, 6, and 11months old at baseline and had 2, 2 and 4 months between ultrasound examinations, respectively. At baseline, MT was normal for weight in all muscles except an atrophic quadriceps in the oldest child. MT decreased and echointensity increased (worsened) over time. At follow up, MT was below normal for weight in the quadriceps in all three children, in the biceps/brachioradialis in two, and in the anterior forearm in one. Tibialis anterior MT remained normal for weight in all three children. Muscle echointensity increased over time in all muscles and, on average, more than doubled in two children. In children with SMA type 1, muscle atrophies and becomes hyperechoic over time. Quantitative muscle ultrasound measures disease progression in SMA type 1 that warrants additional study in more children. Copyright © 2015. Published by Elsevier B.V.

  13. Integration of Simulink, MARTe and MDSplus for rapid development of real-time applications

    Energy Technology Data Exchange (ETDEWEB)

    Manduchi, G., E-mail: gabriele.manduchi@igi.cnr.it [Consorzio RFX (CNR, ENEA, INFN, Università di Padova, Acciaierie Venete SpA), Padova (Italy); Luchetta, A.; Taliercio, C. [Consorzio RFX (CNR, ENEA, INFN, Università di Padova, Acciaierie Venete SpA), Padova (Italy); Neto, A.; Sartori, F. [Fusion for Energy, Barcelona (Spain); De Tommasi, G. [Fusion for Energy, Barcelona (Spain); Consorzio CREATE/DIETI, Università degli Studi di Napoli Federico II, Via Claudio 21, 80125 Napoli (Italy)

    2015-10-15

    Highlights: • The integration of two frameworks for real-time control and data acquisition is described. • The integration may significantly fasten the development of system components. • The system includes also a code generator for the integration of code written in Simulink. • A real-time control systemcan be implemented without the need of writing any line of code. - Abstract: Simulink is a graphical data flow programming tool for modeling and simulating dynamic systems. A component of Simulink, called Simulink Coder, generates C code from Simulink diagrams. MARTe is a framework for the implementation of real-time systems, currently in use in several fusion experiments. MDSplus is a framework widely used in the fusion community for the management of data. The three systems provide a solution to different facets of the same process, that is, real-time plasma control development. Simulink diagrams will describe the algorithms used in control, which will be implemented as MARTe GAMs and which will use parameters read from and produce results written to MDSplus pulse files. The three systems have been integrated in order to provide a tool suitable to speed up the development of real-time control applications. In particular, it will be shown how from a Simulink diagram describing a given algorithm to be used in a control system, it is possible to generate in an automated way the corresponding MARTe and MDSplus components that can be assembled to implement the target system.

  14. Climate change correlates with rapid delays and advancements in reproductive timing in an amphibian community.

    Science.gov (United States)

    Todd, Brian D; Scott, David E; Pechmann, Joseph H K; Gibbons, J Whitfield

    2011-07-22

    Climate change has had a significant impact globally on the timing of ecological events such as reproduction and migration in many species. Here, we examined the phenology of reproductive migrations in 10 amphibian species at a wetland in South Carolina, USA using a 30 year dataset. We show for the first time that two autumn-breeding amphibians are breeding increasingly later in recent years, coincident with an estimated 1.2°C increase in local overnight air temperatures during the September through February pre-breeding and breeding periods. Additionally, two winter-breeding species in the same community are breeding increasingly earlier. Four of the 10 species studied have shifted their reproductive timing an estimated 15.3 to 76.4 days in the past 30 years. This has resulted in rates of phenological change that range from 5.9 to 37.2 days per decade, providing examples of some of the greatest rates of changing phenology in ecological events reported to date. Owing to the opposing direction of the shifts in reproductive timing, our results suggest an alteration in the degree of temporal niche overlap experienced by amphibian larvae in this community. Reproductive timing can drive community dynamics in larval amphibians and our results identify an important pathway by which climate change may affect amphibian communities.

  15. Time-dependent injection as a model for rapid blazar flares

    CERN Document Server

    Zacharias, Michael

    2016-01-01

    Time-dependent injection can cause non-linear cooling effects, which lead to a faster energy loss of the electrons in jets. The most obvious result is the appearance of unique breaks in the SED, which would normally be attributed to a complicated electron distribution. The knowledge of the observation time and duration is important to interpret the observed spectra, because of the non-trivial evolution of the SED. Intrinsic gamma-gamma absorption processes in the emission region are only of minor importance.

  16. Plausible rice yield losses under future climate warming.

    Science.gov (United States)

    Zhao, Chuang; Piao, Shilong; Wang, Xuhui; Huang, Yao; Ciais, Philippe; Elliott, Joshua; Huang, Mengtian; Janssens, Ivan A; Li, Tao; Lian, Xu; Liu, Yongwen; Müller, Christoph; Peng, Shushi; Wang, Tao; Zeng, Zhenzhong; Peñuelas, Josep

    2016-12-19

    Rice is the staple food for more than 50% of the world's population(1-3). Reliable prediction of changes in rice yield is thus central for maintaining global food security. This is an extraordinary challenge. Here, we compare the sensitivity of rice yield to temperature increase derived from field warming experiments and three modelling approaches: statistical models, local crop models and global gridded crop models. Field warming experiments produce a substantial rice yield loss under warming, with an average temperature sensitivity of -5.2 ± 1.4% K(-1). Local crop models give a similar sensitivity (-6.3 ± 0.4% K(-1)), but statistical and global gridded crop models both suggest less negative impacts of warming on yields (-0.8 ± 0.3% and -2.4 ± 3.7% K(-1), respectively). Using data from field warming experiments, we further propose a conditional probability approach to constrain the large range of global gridded crop model results for the future yield changes in response to warming by the end of the century (from -1.3% to -9.3% K(-1)). The constraint implies a more negative response to warming (-8.3 ± 1.4% K(-1)) and reduces the spread of the model ensemble by 33%. This yield reduction exceeds that estimated by the International Food Policy Research Institute assessment (-4.2 to -6.4% K(-1)) (ref. 4). Our study suggests that without CO2 fertilization, effective adaptation and genetic improvement, severe rice yield losses are plausible under intensive climate warming scenarios.

  17. Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae).

    Science.gov (United States)

    McKain, Michael R; McNeal, Joel R; Kellar, P Roxanne; Eguiarte, Luis E; Pires, J Chris; Leebens-Mack, Jim

    2016-10-01

    Yucca species are ideal candidates for the study of coevolution due to the obligate mutualism they form with yucca moth pollinators (genera Tegeticula and Parategeticula). Yuccas are not the only species to exhibit a mutualism with yucca moths; the genus Hesperoyucca is pollinated by the California yucca moth (Tegeticula maculata). Relationships among yuccas, Hesperoyucca, and other members of subfamily Agavoideae are necessary to understand the evolution of this unique pollination syndrome. Here, we investigate evolutionary relationships of yuccas and closely related genera looking at the timing and origin of yucca moth pollination. In this study, we sequenced the chloroplast genomes of 20 species in the subfamily Agavoideae (Asparagaceae) and three confamilial outgroup taxa to resolve intergeneric phylogenetic relationships of Agavoideae. We estimated divergence times using protein-coding genes from 67 chloroplast genomes sampled across monocots to determine the timing of the yucca moth pollination origin. We confidently resolved intergeneric relationships in Agavoideae, demonstrating the origin of the yucca-yucca moth mutualism on two distinct lineages that diverged 27 million years ago. Comparisons of Yucca and Hesperoyucca divergence time to those of yucca moths (Tegeticula and Parategeticula, Prodoxidae) indicate overlapping ages for the origin of pollinating behavior in the moths and pollination by yucca moths in the two plant lineages. Whereas pollinating yucca moths have been shown to have a single origin within the Prodoxidae, there were independent acquisitions of active pollination on lineages leading to Yucca and Hesperoyucca within the Agavoideae. © 2016 Botanical Society of America.

  18. Rapid quantification of semen hepatitis B virus DNA by real-time polymerase chain reaction

    Institute of Scientific and Technical Information of China (English)

    Wei-Ping Qian; Li-Ka Shing; Yue-Qiu Tan; Ying Chen; Ying Peng; Zhi Li; Guang-Xiu Lu; Marie C. Lin; Hsiang-Fu Kung; Ming-Ling He

    2005-01-01

    AIM: To examine the sensitivity and accuracy of real-time polymerase chain reaction (PCR) for the quantification of hepatitis B virus (HBV) DNA in semen.METHODS: Hepatitis B viral DNA was isolated from HBV carriers' semen and sera using phenol extraction method and QTAamp DNA blood mini kit (Qiagen, Germany). HBV DNA was detected by conventional PCR and quantified by TaqMan technology-based real-time PCR (quantitative polymerase chain reaction (qPCR)). The detection threshold was 200 copies of HBV DNA for conventional PCR and 10 copies of HBV DNA for real time PCR per reaction.RESULTS: Both methods of phenol extraction and QIAamp DNA blood mini kit were suitable for isolating HBV DNA from semen. The value of the detection thresholds was 500 copies of HBV DNA per mL in the semen. The viral loads were 7.5×107 and 1.67×107 copies of HBV DNA per mL in two HBV infected patients' sera, while 2.L4×105 and 3.02×105 copies of HBV DNA per mL in the semen.CONCLUSION: Real-time PCR is a more sensitive and accurate method to detect and quantify HBV DNA in the semen.

  19. Changing beliefs about implausible autobiographical events: a little plausibility goes a long way.

    Science.gov (United States)

    Mazzoni, G A; Loftus, E F; Kirsch, I

    2001-03-01

    Three experiments investigated the malleability of perceived plausibility and the subjective likelihood of occurrence of plausible and implausible events among participants who had no recollection of experiencing them. In Experiment 1, a plausibility-enhancing manipulation (reading accounts of the occurrence of events) combined with a personalized suggestion increased the perceived plausibility of the implausible event, as well as participants' ratings of the likelihood that they had experienced it. Plausibility and likelihood ratings were uncorrelated. Subsequent studies showed that the plausibility manipulation alone was sufficient to increase likelihood ratings but only if the accounts that participants read were set in a contemporary context. These data suggest that false autobiographical beliefs can be induced in clinical and forensic contexts even for initially implausible events.

  20. Rapid High-throughput Species Identification of Botanical Material Using Direct Analysis in Real Time High Resolution Mass Spectrometry.

    Science.gov (United States)

    Lesiak, Ashton D; Musah, Rabi A

    2016-10-02

    We demonstrate that direct analysis in real time-high resolution mass spectrometry can be used to produce mass spectral profiles of botanical material, and that these chemical fingerprints can be used for plant species identification. The mass spectral data can be acquired rapidly and in a high throughput manner without the need for sample extraction, derivatization or pH adjustment steps. The use of this technique bypasses challenges presented by more conventional techniques including lengthy chromatography analysis times and resource intensive methods. The high throughput capabilities of the direct analysis in real time-high resolution mass spectrometry protocol, coupled with multivariate statistical analysis processing of the data, provide not only class characterization of plants, but also yield species and varietal information. Here, the technique is demonstrated with two psychoactive plant products, Mitragyna speciosa (Kratom) and Datura (Jimsonweed), which were subjected to direct analysis in real time-high resolution mass spectrometry followed by statistical analysis processing of the mass spectral data. The application of these tools in tandem enabled the plant materials to be rapidly identified at the level of variety and species.

  1. Rapid High-throughput Species Identification of Botanical Material Using Direct Analysis in Real Time High Resolution Mass Spectrometry

    Science.gov (United States)

    Lesiak, Ashton D.; Musah, Rabi A.

    2016-01-01

    We demonstrate that direct analysis in real time-high resolution mass spectrometry can be used to produce mass spectral profiles of botanical material, and that these chemical fingerprints can be used for plant species identification. The mass spectral data can be acquired rapidly and in a high throughput manner without the need for sample extraction, derivatization or pH adjustment steps. The use of this technique bypasses challenges presented by more conventional techniques including lengthy chromatography analysis times and resource intensive methods. The high throughput capabilities of the direct analysis in real time-high resolution mass spectrometry protocol, coupled with multivariate statistical analysis processing of the data, provide not only class characterization of plants, but also yield species and varietal information. Here, the technique is demonstrated with two psychoactive plant products, Mitragyna speciosa (Kratom) and Datura (Jimsonweed), which were subjected to direct analysis in real time-high resolution mass spectrometry followed by statistical analysis processing of the mass spectral data. The application of these tools in tandem enabled the plant materials to be rapidly identified at the level of variety and species. PMID:27768072

  2. Rapid Adjustment of Circadian Clocks to Simulated Travel to Time Zones across the Globe.

    Science.gov (United States)

    Harrison, Elizabeth M; Gorman, Michael R

    2015-12-01

    Daily rhythms in mammalian physiology and behavior are generated by a central pacemaker located in the hypothalamic suprachiasmatic nuclei (SCN), the timing of which is set by light from the environment. When the ambient light-dark cycle is shifted, as occurs with travel across time zones, the SCN and its output rhythms must reset or re-entrain their phases to match the new schedule-a sluggish process requiring about 1 day per hour shift. Using a global assay of circadian resetting to 6 equidistant time-zone meridians, we document this characteristically slow and distance-dependent resetting of Syrian hamsters under typical laboratory lighting conditions, which mimic summer day lengths. The circadian pacemaker, however, is additionally entrainable with respect to its waveform (i.e., the shape of the 24-h oscillation) allowing for tracking of seasonally varying day lengths. We here demonstrate an unprecedented, light exposure-based acceleration in phase resetting following 2 manipulations of circadian waveform. Adaptation of circadian waveforms to long winter nights (8 h light, 16 h dark) doubled the shift response in the first 3 days after the shift. Moreover, a bifurcated waveform induced by exposure to a novel 24-h light-dark-light-dark cycle permitted nearly instant resetting to phase shifts from 4 to 12 h in magnitude, representing a 71% reduction in the mismatch between the activity rhythm and the new photocycle. Thus, a marked enhancement of phase shifting can be induced via nonpharmacological, noninvasive manipulation of the circadian pacemaker waveform in a model species for mammalian circadian rhythmicity. Given the evidence of conserved flexibility in the human pacemaker waveform, these findings raise the promise of flexible resetting applicable to circadian disruption in shift workers, frequent time-zone travelers, and any individual forced to adjust to challenging schedules. © 2015 The Author(s).

  3. Rapid Anomaly Detection and Tracking via Compressive Time-Spectra Measurement

    Science.gov (United States)

    2016-02-12

    includes the data, the MMD and Z -score and the combined detection metric in four separate graphs for each measurement, we have generated receiver...distributions. 4. The product of Z -score and MMD score generates our change detection score. 5. The change detection scores are also a time series... characteristic and precision recall curves. New 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND SUBTITLE 13. SUPPLEMENTARY NOTES 12. DISTRIBUTION

  4. Real-Time Cytotoxicity Assay for Rapid and Sensitive Detection of Ricin from Complex Matrices

    Science.gov (United States)

    Pauly, Diana; Worbs, Sylvia; Kirchner, Sebastian; Shatohina, Olena; Dorner, Martin B.; Dorner, Brigitte G.

    2012-01-01

    Background In the context of a potential bioterrorist attack sensitive and fast detection of functionally active toxins such as ricin from complex matrices is necessary to be able to start timely countermeasures. One of the functional detection methods currently available for ricin is the endpoint cytotoxicity assay, which suffers from a number of technical deficits. Methodology/Findings This work describes a novel online cytotoxicity assay for the detection of active ricin and Ricinus communis agglutinin, that is based on a real-time cell electronic sensing system and impedance measurement. Characteristic growth parameters of Vero cells were monitored online and used as standardized viability control. Upon incubation with toxin the cell status and the cytotoxic effect were visualized using a characteristic cell index–time profile. For ricin, tested in concentrations of 0.06 ng/mL or above, a concentration-dependent decrease of cell index correlating with cytotoxicity was recorded between 3.5 h and 60 h. For ricin, sensitive detection was determined after 24 h, with an IC50 of 0.4 ng/mL (for agglutinin, an IC50 of 30 ng/mL was observed). Using functionally blocking antibodies, the specificity for ricin and agglutinin was shown. For detection from complex matrices, ricin was spiked into several food matrices, and an IC50 ranging from 5.6 to 200 ng/mL was observed. Additionally, the assay proved to be useful in detecting active ricin in environmental sample materials, as shown for organic fertilizer containing R. communis material. Conclusions/Significance The cell-electrode impedance measurement provides a sensitive online detection method for biologically active cytotoxins such as ricin. As the cell status is monitored online, the assay can be standardized more efficiently than previous approaches based on endpoint measurement. More importantly, the real-time cytotoxicity assay provides a fast and easy tool to detect active ricin in complex sample matrices. PMID

  5. Time-gated FRET nanoassemblies for rapid and sensitive intra- and extracellular fluorescence imaging.

    Science.gov (United States)

    Afsari, Hamid Samareh; Cardoso Dos Santos, Marcelina; Lindén, Stina; Chen, Ting; Qiu, Xue; van Bergen En Henegouwen, Paul M P; Jennings, Travis L; Susumu, Kimihiro; Medintz, Igor L; Hildebrandt, Niko; Miller, Lawrence W

    2016-06-01

    Time-gated Förster resonance energy transfer (FRET) using the unique material combination of long-lifetime terbium complexes (Tb) and semiconductor quantum dots (QDs) provides many advantages for highly sensitive and multiplexed biosensing. Although time-gated detection can efficiently suppress sample autofluorescence and background fluorescence from directly excited FRET acceptors, Tb-to-QD FRET has rarely been exploited for biomolecular imaging. We demonstrate Tb-to-QD time-gated FRET nanoassemblies that can be applied for intra- and extracellular imaging. Immunostaining of different epitopes of the epidermal growth factor receptor (EGFR) with Tb- and QD-conjugated antibodies and nanobodies allowed for efficient Tb-to-QD FRET on A431 cell membranes. The broad usability of Tb-to-QD FRET was further demonstrated by intracellular Tb-to-QD FRET and Tb-to-QD-to-dye FRET using microinjection as well as cell-penetrating peptide-mediated endocytosis with HeLa cells. Effective brightness enhancement by FRET from several Tb to the same QD, the use of low nanomolar concentrations, and the quick and sensitive detection void of FRET acceptor background fluorescence are important advantages for advanced intra- and extracellular imaging of biomolecular interactions.

  6. Rapid estimation of earthquake magnitude from the arrival time of the peak high‐frequency amplitude

    Science.gov (United States)

    Noda, Shunta; Yamamoto, Shunroku; Ellsworth, William L.

    2016-01-01

    We propose a simple approach to measure earthquake magnitude M using the time difference (Top) between the body‐wave onset and the arrival time of the peak high‐frequency amplitude in an accelerogram. Measured in this manner, we find that Mw is proportional to 2logTop for earthquakes 5≤Mw≤7, which is the theoretical proportionality if Top is proportional to source dimension and stress drop is scale invariant. Using high‐frequency (>2  Hz) data, the root mean square (rms) residual between Mw and MTop(M estimated from Top) is approximately 0.5 magnitude units. The rms residuals of the high‐frequency data in passbands between 2 and 16 Hz are uniformly smaller than those obtained from the lower‐frequency data. Top depends weakly on epicentral distance, and this dependence can be ignored for distances earthquake produces a final magnitude estimate of M 9.0 at 120 s after the origin time. We conclude that Top of high‐frequency (>2  Hz) accelerograms has value in the context of earthquake early warning for extremely large events.

  7. A Bayesian Surrogate Model for Rapid Time Series Analysis and Application to Exoplanet Observations

    CERN Document Server

    Ford, Eric B; Veras, Dimitri

    2011-01-01

    We present a Bayesian surrogate model for the analysis of periodic or quasi-periodic time series data. We describe a computationally efficient implementation that enables Bayesian model comparison. We apply this model to simulated and real exoplanet observations. We discuss the results and demonstrate some of the challenges for applying our surrogate model to realistic exoplanet data sets. In particular, we find that analyses of real world data should pay careful attention to the effects of uneven spacing of observations and the choice of prior for the "jitter" parameter.

  8. Rapid detection of Van genes in rectal swabs by real time PCR in Southern Brazil

    Directory of Open Access Journals (Sweden)

    Vlademir Cantarelli

    2011-10-01

    Full Text Available INTRODUCTION: Laboratory-based surveillance is an important component in the control of vancomycin resistant enterococci (VRE. METHODS: The study aimed to evaluate real-time polymerase chain reaction (RT-PCR (genes vanA-vanB for VRE detection on 115 swabs from patients included in a surveillance program. RESULTS: Sensitivity of RT-PCR was similar to primary culture (75% and 79.5%, respectively when compared to broth enriched culture, whereas specificity was 83.1%. CONCLUSIONS: RT-PCR provides same day results, however it showed low sensitivity for VRE detection.

  9. Development of a real-time PCR method for Thalassiosira rotula rapid detection

    Institute of Scientific and Technical Information of China (English)

    HE Shanying; YU Zhigang; MI Tiezhu

    2007-01-01

    Gene specific primers and DNA probe were designed based on the sequence of 18S rDNA cloned from the red tide alga Thalassiosira rotula. A real-time fluorescent quantitative PCR (RFQ - PCR) method was developed for quantitative detection of T. rotula. The RFQ - PCR assay data showed that the results obtained with the RFQ - PCR quite good agreement with those with the light microscope (LM) counting method, which suggested that the RFQ - PCR could be a useful method for red tide alga detection.

  10. Use of TaqMan® real-time PCR for rapid detection of Salmonella enterica serovar Typhi.

    Science.gov (United States)

    Ranjbar, Reza; Naghoni, Ali; Farshad, Shohreh; Lashini, Hadi; Najafi, Ali; Sadeghifard, Nourkhoda; Mammina, Caterina

    2014-06-01

    We evaluated the performances of a newly designed real-time polymerase chain reaction (PCR) assay using TaqMan® probes to detect Salmonella Typhi. TaqMan® real-time PCR assays were performed by designed primers and probe based on the staG gene for detecting S. Typhi. The specificity of the assay was evaluated on 15 Salmonella serovars. The analytical specificity was evaluated on 20 non-Salmonella microorganisms. The analytical sensitivity was assessed using decreasing DNA quantities of S. Typhi ATCC 19430. Finally the detection capability of the TaqMan® real-time PCR assay on isolates recovered from patients with Salmonella infections was compared to the conventional PCR assay. Only S. Typhi strain had positive results when subjected to the assay using Typhi-specific real-time PCR. No amplification products were observed in real-time PCR with any of the non-Salmonella microorganisms tested. The TaqMan® real-time PCR was more sensitive than the conventional PCR. In conclusion, we found that the easy-to-use real-time PCR assays were faster than conventional PCR systems. The staG-based TaqMan® real-time PCR assay showed to be specific and sensitive method for the safe and rapid detection of the S. Typhi.

  11. A Rapid Prototyping Tool for Embedded, Real-Time Hierarchical Control Systems

    Directory of Open Access Journals (Sweden)

    Ramamoorthy Subramanian

    2008-01-01

    Full Text Available Abstract Laboratory Virtual Instrumentation and Engineering Workbench (LabVIEW is a graphical programming tool based on the dataflow language G. Recently, runtime support for a hard real-time environment has become available for LabVIEW, which makes it an option for embedded systems prototyping. Due to its characteristics, the environment presents itself as an ideal tool for both the design and implementation of embedded software. In this paper, we study the design and implementation of embedded software by using G as the specification language and the LabVIEW RT real-time platform. One of the main advantages of this approach is that the environment leads itself to a very smooth transition from design to implementation, allowing for powerful cosimulation strategies (e.g., hardware in the loop, runtime modeling. We characterize the semantics and formal model of computation of G. We compare it to other models of computation and develop design rules and algorithms to propose sound embedded design in the language. We investigate the specification and mapping of hierarchical control systems in LabVIEW and G. Finally, we describe the development of a state-of-the-art embedded motion control system using LabVIEW as the specification, simulation and implementation tool, using the proposed design principles. The solution is state-of-the-art in terms of flexibility and control performance.

  12. A Rapid Prototyping Tool for Embedded, Real-Time Hierarchical Control Systems

    Directory of Open Access Journals (Sweden)

    Hugo Andrade

    2008-12-01

    Full Text Available Laboratory Virtual Instrumentation and Engineering Workbench (LabVIEW is a graphical programming tool based on the dataflow language G. Recently, runtime support for a hard real-time environment has become available for LabVIEW, which makes it an option for embedded systems prototyping. Due to its characteristics, the environment presents itself as an ideal tool for both the design and implementation of embedded software. In this paper, we study the design and implementation of embedded software by using G as the specification language and the LabVIEW RT real-time platform. One of the main advantages of this approach is that the environment leads itself to a very smooth transition from design to implementation, allowing for powerful cosimulation strategies (e.g., hardware in the loop, runtime modeling. We characterize the semantics and formal model of computation of G. We compare it to other models of computation and develop design rules and algorithms to propose sound embedded design in the language. We investigate the specification and mapping of hierarchical control systems in LabVIEW and G. Finally, we describe the development of a state-of-the-art embedded motion control system using LabVIEW as the specification, simulation and implementation tool, using the proposed design principles. The solution is state-of-the-art in terms of flexibility and control performance.

  13. Time-resolved temperature measurements in a rapid compression machine using quantum cascade laser absorption in the intrapulse mode

    KAUST Repository

    Nasir, Ehson Fawad

    2016-07-16

    A temperature sensor based on the intrapulse absorption spectroscopy technique has been developed to measure in situ temperature time-histories in a rapid compression machine (RCM). Two quantum-cascade lasers (QCLs) emitting near 4.55μm and 4.89μm were operated in pulsed mode, causing a frequency "down-chirp" across two ro-vibrational transitions of carbon monoxide. The down-chirp phenomenon resulted in large spectral tuning (δν ∼2.8cm-1) within a single pulse of each laser at a high pulse repetition frequency (100kHz). The wide tuning range allowed the application of the two-line thermometry technique, thus making the sensor quantitative and calibration-free. The sensor was first tested in non-reactive CO-N2 gas mixtures in the RCM and then applied to cases of n-pentane oxidation. Experiments were carried out for end of compression (EOC) pressures and temperatures ranging 9.21-15.32bar and 745-827K, respectively. Measured EOC temperatures agreed with isentropic calculations within 5%. Temperature rise measured during the first-stage ignition of n-pentane is over-predicted by zero-dimensional kinetic simulations. This work presents, for the first time, highly time-resolved temperature measurements in reactive and non-reactive rapid compression machine experiments. © 2016 Elsevier Ltd.

  14. Role of real-time PCR (RT-PCR) in rapid diagnosis of tuberculous mycobacteria in different clinical samples.

    Science.gov (United States)

    2014-02-01

    The study was aimed for molecular detection of mycobacterial DNA in different clinical samples using real-time polymerase chain reaction (RT-PCR) system and rapid diagnosis of tuberculosis. A total of 508 clinical specimens (blood 343, menstrual fluid 53, endometrial tissue 43, body fluid 36, pus from lymph nodes 18, sputum 8, urine 5 and semen 2) were included in this study. We extracted DNA using QIAamp DNA Mini Kit (QIAGEN, Germany) and performed real-time assay using Rotor-Gene Q machine from Corbett Research, Australia for specific amplification of IS6110 sequence of mycobacterial genome. The RT-PCR result was also compared with bacterial culture and acid-fast bacillus staining. RT-PCR assay showed positivity in 52 cases and negative in 456 cases. Corresponding positive results in culture and acid-fast bacillus staining methods were 49 cases and 24 cases respectively. The sensitivity and specificity of detecting Mycobacterium tuberculosis by RT-PCR were 93.87% and 98.69% respectively taking positive culture results as reference standards. The overall positive and negative predictive values were 88.46% and 99.34% respectively. RT-PCR is a useful diagnostic tool for rapid and sensitive detection of mycobacteria in different clinical samples. The easy processing, fast reporting and relative lack of contamination issues make it worthy as a possible replacement to time consuming culture techniques. Moreover, it has added advantage of quantification of mycobacterial DNA, hence bacterial load.

  15. Rapid detection and typing of pathogenic nonpneumophila Legionella spp. isolates using a multiplex real-time PCR assay.

    Science.gov (United States)

    Benitez, Alvaro J; Winchell, Jonas M

    2016-04-01

    We developed a single tube multiplex real-time PCR assay that allows for the rapid detection and typing of 9 nonpneumophila Legionella spp. isolates that are clinically relevant. The multiplex assay is capable of simultaneously detecting and discriminating L. micdadei, L. bozemanii, L. dumoffii, L. longbeachae, L. feeleii, L. anisa, L. parisiensis, L. tucsonensis serogroup (sg) 1 and 3, and L. sainthelensis sg 1 and 2 isolates. Evaluation of the assay with nucleic acid from each of these species derived from both clinical and environmental isolates and typing strains demonstrated 100% sensitivity and 100% specificity when tested against 43 other Legionella spp. Typing of L. anisa, L. parisiensis, and L. tucsonensis sg 1 and 3 isolates was accomplished by developing a real-time PCR assay followed by high-resolution melt (HRM) analysis targeting the ssrA gene. Further typing of L. bozemanii, L. longbeachae, and L. feeleii isolates to the serogroup level was accomplished by developing a real-time PCR assay followed by HRM analysis targeting the mip gene. When used in conjunction with other currently available diagnostic tests, these assays may aid in rapidly identifying specific etiologies associated with Legionella outbreaks, clusters, sporadic cases, and potential environmental sources.

  16. Rapid qualitative urinary tract infection pathogen identification by SeptiFast real-time PCR.

    Directory of Open Access Journals (Sweden)

    Lutz E Lehmann

    Full Text Available BACKGROUND: Urinary tract infections (UTI are frequent in outpatients. Fast pathogen identification is mandatory for shortening the time of discomfort and preventing serious complications. Urine culture needs up to 48 hours until pathogen identification. Consequently, the initial antibiotic regimen is empirical. AIM: To evaluate the feasibility of qualitative urine pathogen identification by a commercially available real-time PCR blood pathogen test (SeptiFast® and to compare the results with dipslide and microbiological culture. DESIGN OF STUDY: Pilot study with prospectively collected urine samples. SETTING: University hospital. METHODS: 82 prospectively collected urine samples from 81 patients with suspected UTI were included. Dipslide urine culture was followed by microbiological pathogen identification in dipslide positive samples. In parallel, qualitative DNA based pathogen identification (SeptiFast® was performed in all samples. RESULTS: 61 samples were SeptiFast® positive, whereas 67 samples were dipslide culture positive. The inter-methodological concordance of positive and negative findings in the gram+, gram- and fungi sector was 371/410 (90%, 477/492 (97% and 238/246 (97%, respectively. Sensitivity and specificity of the SeptiFast® test for the detection of an infection was 0.82 and 0.60, respectively. SeptiFast® pathogen identifications were available at least 43 hours prior to culture results. CONCLUSION: The SeptiFast® platform identified bacterial DNA in urine specimens considerably faster compared to conventional culture. For UTI diagnosis sensitivity and specificity is limited by its present qualitative setup which does not allow pathogen quantification. Future quantitative assays may hold promise for PCR based UTI pathogen identification as a supplementation of conventional culture methods.

  17. Development and validation of real-time PCR for rapid detection of Mecistocirrus digitatus.

    Directory of Open Access Journals (Sweden)

    Subhra Subhadra

    Full Text Available Hematophagous activity of Mecistocirrus digitatus, which causes substantial blood and weight loss in large ruminants, is an emerging challenge due to the economic loss it brings to the livestock industry. Infected animals are treated with anthelmintic drugs, based on the identification of helminth species and the severity of infection; however, traditional methods such as microscopic identification and the counting of eggs for diagnosis and determination of level of infection are laborious, cumbersome and unreliable. To facilitate the detection of this parasite, a SYBR green-based real-time PCR was standardized and validated for the detection of M. digitatus infection in cattle and buffaloes. Oligonucleotides were designed to amplify partial Internal Transcribed Spacer (ITS-1 sequence of M. digitatus. The specificity of the primers was confirmed by non-amplification of DNA extracted from other commonly occurring gastrointestinal nematodes in ruminants. Plasmids were ligated with partial ITS-1 sequence of M. digitatus, serially diluted (hundred fold and used as standards in the real-time PCR assay. The quantification cycle (Cq values were plotted against the standard DNA concentration to produce a standard curve. The assay was sensitive enough to detect one plasmid containing the M. digitatus DNA. Clinical application of this assay was validated by testing the DNA extracted from the faeces of naturally infected cattle (n = 40 and buffaloes (n = 25. The results were compared with our standard curve to calculate the quantity of M. digitatus in each faecal sample. The Cq value of the assay depicted a strong linear relationship with faecal DNA content, with a regression coefficient of 0.984 and efficiency of 99%. This assay has noteworthy advantages over the conventional methods of diagnosis because it is more specific, sensitive and reliable.

  18. Development of a real-time SYBR Green PCR assay for the rapid detection of Dermatophilus congolensis.

    Science.gov (United States)

    García, Alfredo; Martínez, Remigio; Benitez-Medina, José Manuel; Risco, David; Garcia, Waldo Luis; Rey, Joaquín; Alonso, Juan Manuel; Hermoso de Mendoza, Javier

    2013-01-01

    Methods such as real time (RT)-PCR have not been developed for the rapid detection and diagnosis of Dermatophilus (D.) congolensis infection. In the present study, a D. congolensis-specific SYBR Green RT-PCR assay was evaluated. The detection limit of the RT-PCR assay was 1 pg of DNA per PCR reaction. No cross-reaction with nucleic acids extracted from Pseudomonas aeruginosa, Mycobacterium tuberculosis, Staphylococcus aureus, or Austwickia chelonae was observed. Finally, the RT-PCR assay was used to evaluate clinical samples collected from naturally infected animals with D. congolensis. The results showed that this assay is a fast and reliable method for diagnosing dermatophilosis.

  19. Rapid detection of Lactobacillus kefiranofaciens in kefir grain and kefir milk using newly developed real-time PCR.

    Science.gov (United States)

    Kim, Dong-Hyeon; Chon, Jung-Whan; Kim, Hong-Seok; Yim, Jin-Hyeok; Kim, Hyunsook; Seo, Kun-Ho

    2015-04-01

    Lactobacillus kefiranofaciens is an indicator microorganism for kefir and a key factor in kefir grain formation and kefiran production. We designed a novel real-time PCR primer and probe set, LKF_KU504, for the rapid detection of L. kefiranofaciens. In inclusivity and exclusivity tests, only 14 L. kefiranofaciens strains were positive among 61 microorganisms, indicating 100 % sensitivity and specificity. The LKF_KU504 set also differentiated kefir milk from 30 commercial nonkefir yogurts. The levels of L. kefiranofaciens in kefir grain and kefir milk were significantly different, indicating L. kefiranofaciens was more concentrated in kefir grain than in kefir milk.

  20. Universal Probe Library based real-time PCR for rapid detection of bacterial pathogens from positive blood culture bottles.

    Science.gov (United States)

    Zhu, Lingxiang; Shen, Ding-Xia; Zhou, Qiming; Liu, Chao-Jun; Li, Zexia; Fang, Xiangdong; Li, Quan-Zhen

    2014-03-01

    A set of real-time PCR based assays using the locked nucleic acid probes from Roche Universal ProbeLibrary were developed for rapid detection of eight bacterial species from positive blood culture bottles. Four duplex real-time PCR reactions targeting to one Gram-positive bacterium and one Gram-negative bacterium were optimized for species identification according to Gram stain results. We also included mecA-specific primers and probes in the assays to indicate the presence of methicillin resistance in the bacterial species. The analytical sensitivity was in the range of 1-10 CFU per PCR reaction mixture. The specificity and cross reactivity of the assay was validated by 28 ATCC reference strains and 77 negative blood culture specimens. No cross-reactivity was observed in these samples thus demonstrating 100 % specificity. 72 previously characterized clinical isolates were tested by the real-time PCR assay and validated the accuracy and feasibility of the real-time PCR assay. Furthermore, 55 positive blood culture samples were tested using real-time PCR and 50 (90.9 %) of them were identified as the same species as judged by biochemical analysis. In total, real-time PCR showed 98.2 % consistent to that of traditional methods. Real-time PCR can be used as a supplement for early detection of the frequently-occurred pathogens from the positive blood cultures.

  1. Time-resolved fluorescence-based assay for rapid detection of Escherichia coli.

    Science.gov (United States)

    Kulpakko, Janne; Kopra, Kari; Hänninen, Pekka

    2015-02-01

    Fast and simple detection of pathogens is of utmost importance in health care and the food industry. In this article, a novel technology for the detection of pathogenic bacteria is presented. The technology uses lytic-specific bacteriophages and a nonspecific interaction of cellular components with a luminescent lanthanide chelate. As a proof of principle, Escherichia coli-specific T4 bacteriophage was used to infect the bacteria, and the cell lysis was detected. In the absence of E. coli, luminescent Eu(3+)-chelate complex cannot be formed and low time-resolved luminescence signal is monitored. In the presence of E. coli, increased luminescence signal is observed as the cellular contents are leached to the surrounding medium. The luminescence signal is observed as a function of the number of bacteria in the sample. The homogeneous assay can detect living E. coli in bacterial cultures and simulated urine samples within 25 min with a detection limit of 1000 or 10,000 bacterial cells/ml in buffer or urine, respectively. The detection limit is at the clinically relevant level, which indicates that the method could also be applicable to clinical settings for fast detection of urine bacteria.

  2. Effect of central metal ions of analogous metal-organic frameworks on adsorption of organoarsenic compounds from water: plausible mechanism of adsorption and water purification.

    Science.gov (United States)

    Jun, Jong Won; Tong, Minman; Jung, Beom K; Hasan, Zubair; Zhong, Chongli; Jhung, Sung Hwa

    2015-01-02

    The adsorptive removal of organoarsenic compounds such as p-arsanilic acid (ASA) and roxarsone (ROX) from water using metal-organic frameworks (MOFs) has been investigated for the first time. A MOF, iron benzenetricarboxylate (also called MIL-100-Fe) exhibits a much higher adsorption capacity for ASA and ROX than activated carbon, zeolite (HY), goethite, and other MOFs. The adsorption of ASA and ROX over MIL-100-Fe is also much more rapid than that over activated carbon. Moreover, the used MIL-100-Fe can be recycled by simply washing with acidic ethanol. Therefore, it is determined that a MOF such as MIL-100-Fe can be used to remove organoarsenic compounds from contaminated water because of its high adsorption capacity, rapid adsorption, and ready regeneration. Moreover, only one of three analogous MIL-100 species (MIL-100-Fe, rather than MIL-100-Al or MIL-100-Cr) can effectively remove the organoarsenic compounds. This selective and high adsorption over MIL-100-Fe, different from other analogous MIL-100 species, can be explained (through calculations) by the facile desorption of water from MIL-100-Fe as well as the large (absolute value) replacement energy (difference between the adsorption energies of the organoarsenic compounds and water) exhibited by MIL-100-Fe. A plausible adsorption/desorption mechanism is proposed based on the surface charge of the MOFs, FTIR results, calculations, and the reactivation results with respect to the solvents used in the experiments.

  3. Signature of Plausible Accreting Supermassive Black Holes in Mrk 261/262 and Mrk 266

    Directory of Open Access Journals (Sweden)

    Gagik Ter-Kazarian

    2013-01-01

    Full Text Available We address the neutrino radiation of plausible accreting supermassive black holes closely linking to the 5 nuclear components of galaxy samples of Mrk 261/262 and Mrk 266. We predict a time delay before neutrino emission of the same scale as the age of the Universe. The ultrahigh energy neutrinos are produced in superdense protomatter medium via simple (quark or pionic reactions or modified URCA processes (G. Gamow was inspired to name the process URCA after the name of a casino in Rio de Janeiro. The resulting neutrino fluxes for quark reactions are ranging from to , where is the opening parameter. For pionic and modified URCA reactions, the fluxes are and , respectively. These fluxes are highly beamed along the plane of accretion disk, peaked at ultrahigh energies, and collimated in smaller opening angle .

  4. Slow Computing Simulation of Bio-plausible Control

    Science.gov (United States)

    2012-03-01

    following discussion have been derived using a few key assumptions: occlusions are ignored, the set of discrete luminance functions is sampled...simulation framework that was provided by the Murray group, and the Grand Unified Fly (GUF) simulation framework developed by Dr. Andrew Straw...sensor inputs, parallelizing sensor processing, and rapidly responding. Thus, the parallel nature of the processors is key to eliciting a low power

  5. Rapid increases and time-lagged declines in amphibian occupancy after wildfire

    Science.gov (United States)

    Hossack, Blake R.; Lowe, Winsor H.; Corn, Paul Stephen

    2013-01-01

    Climate change is expected to increase the frequency and severity of drought and wildfire. Aquatic and moisture-sensitive species, such as amphibians, may be particularly vulnerable to these modified disturbance regimes because large wildfires often occur during extended droughts and thus may compound environmental threats. However, understanding of the effects of wildfires on amphibians in forests with long fire-return intervals is limited. Numerous stand-replacing wildfires have occurred since 1988 in Glacier National Park (Montana, U.S.A.), where we have conducted long-term monitoring of amphibians. We measured responses of 3 amphibian species to fires of different sizes, severity, and age in a small geographic area with uniform management. We used data from wetlands associated with 6 wildfires that burned between 1988 and 2003 to evaluate whether burn extent and severity and interactions between wildfire and wetland isolation affected the distribution of breeding populations. We measured responses with models that accounted for imperfect detection to estimate occupancy during prefire (0-4 years) and different postfire recovery periods. For the long-toed salamander (Ambystoma macrodactylum) and Columbia spotted frog (Rana luteiventris), occupancy was not affected for 6 years after wildfire. But 7-21 years after wildfire, occupancy for both species decreased ≥ 25% in areas where >50% of the forest within 500 m of wetlands burned. In contrast, occupancy of the boreal toad (Anaxyrus boreas) tripled in the 3 years after low-elevation forests burned. This increase in occupancy was followed by a gradual decline. Our results show that accounting for magnitude of change and time lags is critical to understanding population dynamics of amphibians after large disturbances. Our results also inform understanding of the potential threat of increases in wildfire frequency or severity to amphibians in the region.

  6. Rapid detection of Listeria monocytogenes by real-time PCR in processed meat and dairy products.

    Science.gov (United States)

    Heo, Eun Jeong; Song, Bo Ra; Park, Hyun Jung; Kim, Young Jo; Moon, Jin San; Wee, Sung Hwan; Kim, Jin-Seok; Yoon, Yohan

    2014-03-01

    The objectives of this study were to evaluate the detection of Listeria monocytogenes in different ready-to-eat foods using real-time PCR (RT-PCR). Various concentrations (10(0) to 10(5) CFU/ml) of L. monocytogenes ATCC 19115 were inoculated into ham, sausage, ground meat, processed milk, cheese, and infant formula. L. monocytogenes ATCC 19115 in the samples was then enumerated on Oxford agar, and DNA was extracted from the samples before and after incubation at 36°C for 4 h. A set of primers and hybridization probe designed in this study was then used to detect the pathogen. The standard curve was then prepared by plotting cycle threshold values for each dilution versus L. monocytogenes cell counts (log CFU). The specificity of the set of primers and hybridization probe was appropriate. A 4-h incubation at 36°C before DNA extraction produced optimum standard curves in comparison to the results for a 0-h incubation. Thus, a 4-h incubation at 36°C was applied for monitoring L. monocytogenes in collected food samples. To monitor L. monocytogenes in foods, 533 samples (ham, 129; sausage, 226; ground meat, 72; processed cheese, 54; processed milk, 42; and infant formula, 10) were collected from retail markets and from the step before pasteurization in plants. Of all 533 samples, 4 samples (0.8%) showed positive signals in RT-PCR. Two samples from hams (1.6%) and two samples from sausages (0.9%) were determined to be positive for L. monocytogenes at processed meat and milk products.

  7. Rapid increases and time-lagged declines in amphibian occupancy after wildfire.

    Science.gov (United States)

    Hossack, Blake R; Lowe, Winsor H; Corn, Paul Stephen

    2013-02-01

    Climate change is expected to increase the frequency and severity of drought and wildfire. Aquatic and moisture-sensitive species, such as amphibians, may be particularly vulnerable to these modified disturbance regimes because large wildfires often occur during extended droughts and thus may compound environmental threats. However, understanding of the effects of wildfires on amphibians in forests with long fire-return intervals is limited. Numerous stand-replacing wildfires have occurred since 1988 in Glacier National Park (Montana, U.S.A.), where we have conducted long-term monitoring of amphibians. We measured responses of 3 amphibian species to fires of different sizes, severity, and age in a small geographic area with uniform management. We used data from wetlands associated with 6 wildfires that burned between 1988 and 2003 to evaluate whether burn extent and severity and interactions between wildfire and wetland isolation affected the distribution of breeding populations. We measured responses with models that accounted for imperfect detection to estimate occupancy during prefire (0-4 years) and different postfire recovery periods. For the long-toed salamander (Ambystoma macrodactylum) and Columbia spotted frog (Rana luteiventris), occupancy was not affected for 6 years after wildfire. But 7-21 years after wildfire, occupancy for both species decreased ≥ 25% in areas where >50% of the forest within 500 m of wetlands burned. In contrast, occupancy of the boreal toad (Anaxyrus boreas) tripled in the 3 years after low-elevation forests burned. This increase in occupancy was followed by a gradual decline. Our results show that accounting for magnitude of change and time lags is critical to understanding population dynamics of amphibians after large disturbances. Our results also inform understanding of the potential threat of increases in wildfire frequency or severity to amphibians in the region.

  8. Rapid update of odd DCT and DST for real-time signal processing

    Science.gov (United States)

    Sherlock, B. G.; Kakad, Y. P.; Shukla, A.

    2005-05-01

    When processing a signal or an image using the Discrete Cosine Transform (DCT) or Discrete Sine Transform (DST), a typical approach is to extract a portion of the signal by windowing and then form the DCT or DST of the window contents. By shifting the window point by point over the signal, the entire signal may be processed. DCTs and DSTs are defined where the denominator in the transform kernel is either an odd or an even integer, resulting in transforms known as the even DCT (EDCT), even DST (EDST), odd DCT (ODCT) and odd DST (ODST). Each is available in types I to IV, for a total of 16 different transforms. The widely used transform commonly called the "DCT" is actually the EDCT-II. In this paper we extend our previous work using the EDCT-II and EDST-II, and show that a similar approach yields algorithms for the ODCT-II and ODST-II. We develop algorithms to "update" the ODCT-II and ODST-II simultaneously to reflect the modified window contents using less computation than directly evaluating the modified transform via standard Fast Transform algorithms. These algorithms are able to handle arbitrary step sizes up to the length of the transform, i.e. the algorithm simultaneously updates the ODCT-II and ODST-II to reflect inclusion of r, where 1 <= r <= N-1, additional data points and removal of r old points from the signal. Examples of applications where this algorithm would be useful include target recognition where time constraints may not permit the immediate processing of every incoming data point, adaptive system identification, etc.

  9. Rapid and sensitive detection of Yersinia pestis using amplification of plague diagnostic bacteriophages monitored by real-time PCR.

    Directory of Open Access Journals (Sweden)

    Kirill V Sergueev

    Full Text Available BACKGROUND: Yersinia pestis, the agent of plague, has caused many millions of human deaths and still poses a serious threat to global public health. Timely and reliable detection of such a dangerous pathogen is of critical importance. Lysis by specific bacteriophages remains an essential method of Y. pestis detection and plague diagnostics. METHODOLOGY/PRINCIPAL FINDINGS: The objective of this work was to develop an alternative to conventional phage lysis tests--a rapid and highly sensitive method of indirect detection of live Y. pestis cells based on quantitative real-time PCR (qPCR monitoring of amplification of reporter Y. pestis-specific bacteriophages. Plague diagnostic phages phiA1122 and L-413C were shown to be highly effective diagnostic tools for the detection and identification of Y. pestis by using qPCR with primers specific for phage DNA. The template DNA extraction step that usually precedes qPCR was omitted. phiA1122-specific qPCR enabled the detection of an initial bacterial concentration of 10(3 CFU/ml (equivalent to as few as one Y. pestis cell per 1-microl sample in four hours. L-413C-mediated detection of Y. pestis was less sensitive (up to 100 bacteria per sample but more specific, and thus we propose parallel qPCR for the two phages as a rapid and reliable method of Y. pestis identification. Importantly, phiA1122 propagated in simulated clinical blood specimens containing EDTA and its titer rise was detected by both a standard plating test and qPCR. CONCLUSIONS/SIGNIFICANCE: Thus, we developed a novel assay for detection and identification of Y. pestis using amplification of specific phages monitored by qPCR. The method is simple, rapid, highly sensitive, and specific and allows the detection of only live bacteria.

  10. Rapid concentration and sensitive detection of hookworm ova from wastewater matrices using a real-time PCR method.

    Science.gov (United States)

    Gyawali, P; Sidhu, J P S; Ahmed, W; Jagals, P; Toze, S

    2015-12-01

    The risk of human hookworm infections from land application of wastewater matrices could be high in regions with high hookworm prevalence. A rapid, sensitive and specific hookworm detection method from wastewater matrices is required in order to assess human health risks. Currently available methods used to identify hookworm ova to the species level are time consuming and lack accuracy. In this study, a real-time PCR method was developed for the rapid, sensitive and specific detection of canine hookworm (Ancylostoma caninum) ova from wastewater matrices. A. caninum was chosen because of its morphological similarity to the human hookworm (Ancylostoma duodenale and Necator americanus). The newly developed PCR method has high detection sensitivity with the ability to detect less than one A. caninum ova from 1 L of secondary treated wastewater at the mean threshold cycle (CT) values ranging from 30.1 to 34.3. The method is also able to detect four A. caninum ova from 1 L of raw wastewater and from ∼4 g of treated sludge with mean CT values ranging from 35.6 to 39.8 and 39.8 to 39.9, respectively. The better detection sensitivity obtained for secondary treated wastewater compared to raw wastewater and sludge samples could be attributed to sample turbidity. The proposed method appears to be rapid, sensitive and specific compared to traditional methods and has potential to aid in the public health risk assessment associated with land application of wastewater matrices. Furthermore, the method can be adapted to detect other helminth ova of interest from wastewater matrices.

  11. Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times

    Directory of Open Access Journals (Sweden)

    Harrod Chris

    2010-05-01

    Full Text Available Abstract Background After a volcano erupts, a lake may form in the cooled crater and become an isolated aquatic ecosystem. This makes fishes in crater lakes informative for understanding sympatric evolution and ecological diversification in barren environments. From a geological and limnological perspective, such research offers insight about the process of crater lake ecosystem establishment and speciation. In the present study we use genetic and coalescence approaches to infer the colonization history of Midas cichlid fishes (Amphilophus cf. citrinellus that inhabit a very young crater lake in Nicaragua-the ca. 1800 year-old Lake Apoyeque. This lake holds two sympatric, endemic morphs of Midas cichlid: one with large, hypertrophied lips (~20% of the total population and another with thin lips. Here we test the associated ecological, morphological and genetic diversification of these two morphs and their potential to represent incipient speciation. Results Gene coalescence analyses [11 microsatellite loci and mitochondrial DNA (mtDNA sequences] suggest that crater lake Apoyeque was colonized in a single event from the large neighbouring great lake Managua only about 100 years ago. This founding in historic times is also reflected in the extremely low nuclear and mitochondrial genetic diversity in Apoyeque. We found that sympatric adult thin- and thick-lipped fishes occupy distinct ecological trophic niches. Diet, body shape, head width, pharyngeal jaw size and shape and stable isotope values all differ significantly between the two lip-morphs. The eco-morphological features pharyngeal jaw shape, body shape, stomach contents and stable isotopes (δ15N all show a bimodal distribution of traits, which is compatible with the expectations of an initial stage of ecological speciation under disruptive selection. Genetic differentiation between the thin- and thick-lipped population is weak at mtDNA sequence (FST = 0.018 and absent at nuclear

  12. Rapid detection and monitoring therapeutic efficacy of Mycobacterium tuberculosis complex using a novel real-time assay.

    Science.gov (United States)

    Jiang, Li Juan; Wu, Wen Juan; Wu, Hai; Ryang, Son Sik; Zhou, Jian; Wu, Wei; Li, Tao; Guo, Jian; Wang, Hong Hai; Lu, Shui Hua; Li, Yao

    2012-09-01

    We combined real-time RT-PCR and real-time PCR (R/P) assays using a hydrolysis probe to detect Mycobacterium tuberculosis complex (MTBC)-specific 16S rRNA and its rRNA gene (rDNA). The assay was applied to 28 nonrespiratory and 207 respiratory specimens from 218 patients. Total nucleic acids (including RNA and DNA) were extracted from samples, and results were considered positive if the repeat RT-PCR threshold cycle was real-time RT-PCR and real-time PCR load was > or =1.51. The results were compared with those from existing methods, including smear, culture, and real-time PCR. Following resolution of the discrepant results between R/P assay and culture, the overall sensitivity, specificity, positive predictive values (PPV), and negative predictive values (NPV) of all samples (including nonrespiratory and respiratory specimens) were 98.2%, 97.2%, 91.7%, and 99.4%, respectively, for R/P assay, and 83.9%, 89.9%, 72.3%, and 94.7%, respectively, for real-time PCR. Furthermore, the R/P assay of four patient samples showed a higher ratio before treatment than after several days of treatment. We conclude that the R/P assay is a rapid and accurate method for direct detection of MTBC, which can distinguish viable and nonviable MTBC, and thus may guide patient therapy and public health decisions.

  13. Rapid and simultaneous detection of common aneuploidies by quadruplex real-time polymerase chain reaction combined with melting curve analysis

    Science.gov (United States)

    Lou, Jiwu; Sun, Manna; Zhao, Ying; Ji, Zhisong; Liu, Fenghua; Li, Dongzhi; Xu, Wanfang; Lin, Yangyang; Liu, Yanhui

    2017-01-01

    Background During the prenatal period, the number variation of chromosomes 13, 18, 21, X and Y accounts for more than 80% of the clinically significant chromosomal abnormalities diagnosed. Rapid tests for prenatal diagnosis of these abnormalities can improve pregnancy management and alleviate parental anxiety. Here, we present a molecular alternative method for detecting common aneuploidies. Methods This method is based on co-amplification of segmental duplications located on two different chromosomes using a single pair of primers. Segmental duplications have a high degree of sequence identity, but have single-nucleotide differences in some regions. These sequence differences can be quantified using melting curve analysis of dual-labeled probes to estimate the relative dosages of different chromosomes. We designed two quadruplex real-time PCR assays to detect aneuploidies of chromosomes 13, 18, 21, X and Y. Results We examined 75 aneuploid DNA samples and 56 unaffected DNA control samples using these two assays and correctly identified all samples. Four cases of unbalanced translocation were also accurately detected. The observed averaged ratio for each chromosomal disorder was similar to the theoretically expected value. Conclusions Our real-time assay is a robust, rapid, and easy to conduct technique for prenatal diagnosis of common aneuploidies, representing a competitive alternative for use in diagnostic laboratories. PMID:28241016

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

    Directory of Open Access Journals (Sweden)

    Erin P Price

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

  15. Loop-mediated isothermal amplification: rapid visual and real-time methods for detection of genetically modified crops.

    Science.gov (United States)

    Randhawa, Gurinder Jit; Singh, Monika; Morisset, Dany; Sood, Payal; Zel, Jana

    2013-11-27

    A rapid, reliable, and sensitive loop-mediated isothermal amplification (LAMP) system was developed for screening of genetically modified organisms (GMOs). The optimized LAMP assays using designed primers target commonly employed promoters, i.e., Cauliflower Mosaic Virus 35S (P-35S) and Figwort Mosaic Virus promoter (P-FMV), and marker genes, i.e., aminoglycoside 3'-adenyltransferase (aadA), neomycin phosphotransferase II (nptII), and β-glucuronidase (uidA). The specificity and performance of the end-point and real-time LAMP assays were confirmed using eight genetically modified (GM) cotton events on four detection systems, employing two chemistries. LAMP assays on the isothermal real-time system were found to be most sensitive, detecting up to four target copies, within 35 min. The LAMP assays herein presented using alternate detection systems can be effectively utilized for rapid and cost-effective screening of the GM status of a sample, irrespective of the crop species or GM trait. These assays coupled with a fast and simple DNA extraction method may further facilitate on-site GMO screening.

  16. Clinical validation of a real-time polymerase chain reaction assay for rapid detection of Acinetobacter baumannii colonization.

    Science.gov (United States)

    Blanco-Lobo, P; González-Galán, V; García-Quintanilla, M; Valencia, R; Cazalla, A; Martín, C; Alonso, I; Pérez-Romero, P; Cisneros, J M; Aznar, J; McConnell, M J

    2016-09-01

    Real-time polymerase chain reaction (PCR)-based approaches have not been assessed in terms of their ability to detect patients colonized by Acinetobacter baumannii during active surveillance. This prospective, double-blind study demonstrated that a real-time PCR assay had high sensitivity (100%) and specificity (91.2%) compared with conventional culture for detecting A. baumannii in 397 active surveillance samples, and provided results within 3h. Receiver-operator curve analyses demonstrated that the technique has diagnostic accuracy of 97.7% (95% confidence interval 96.0-99.3%). This method could facilitate the rapid implementation of infection control measures for preventing the transmission of A. baumannii.

  17. A Novel Real-time Fluorescence Mutant-allele-specific Amplification Method for Rapid Single Nucleotide Polymorphism Analysis

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Current methods for single nucleotide polymorphism (SNP) analysis are timeconsuming and complicated. We aimed at development of one-step real-time fluorescence mutant-allele-specific amplification (MASA) method for rapid SNP analysis. The method is a marriage of two technologies: MASA primers for target DNA and a double-stranded DNA-selective fluorescent dye, SYBR Green I. Genotypes are separated according to the different threshold cycles of the wild-type and mutant primers. K-ras oncogene was used as a target to validate the feasibility of the method. The experimental results showed that the different genotypes can be clearly discriminated by the assay. The real-time fluorescence MASA method will have an enormous potential for fast and reliable SNP analysis due to its simplicity and low cost.

  18. Urey prize lecture: On the diversity of plausible planetary systems

    Science.gov (United States)

    Lissauer, J. J.

    1995-01-01

    Models of planet formation and of the orbital stability of planetary systems are used to predict the variety of planetary and satellite systems that may be present within our galaxy. A new approximate global criterion for orbital stability of planetary systems based on an extension of the local resonance overlap criterion is proposed. This criterion implies that at least some of Uranus' small inner moons are significantly less massive than predicted by estimates based on Voyager volumes and densities assumed to equal that of Miranda. Simple calculations (neglecting planetary gravity) suggest that giant planets which acrete substantial amounts of gas while their envelopes are extremely distended ultimately rotate rapidly in the prgrade direction.

  19. Multiplex real-time PCR assay for rapid detection of methicillin-resistant staphylococci directly from positive blood cultures.

    Science.gov (United States)

    Wang, Hye-Young; Kim, Sunghyun; Kim, Jungho; Park, Soon-Deok; Uh, Young; Lee, Hyeyoung

    2014-06-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is the most prevalent cause of bloodstream infections (BSIs) and is recognized as a major nosocomial pathogen. This study aimed to evaluate a newly designed multiplex real-time PCR assay capable of the simultaneous detection of mecA, S. aureus, and coagulase-negative staphylococci (CoNS) in blood culture specimens. The Real-MRSA and Real-MRCoNS multiplex real-time PCR assays (M&D, Republic of Korea) use the TaqMan probes 16S rRNA for Staphylococcus spp., the nuc gene for S. aureus, and the mecA gene for methicillin resistance. The detection limit of the multiplex real-time PCR assay was 10(3) CFU/ml per PCR for each gene target. The multiplex real-time PCR assay was evaluated using 118 clinical isolates from various specimen types and a total of 350 positive blood cultures from a continuous monitoring blood culture system. The results obtained with the multiplex real-time PCR assay for the three targets were in agreement with those of conventional identification and susceptibility testing methods except for one organism. Of 350 positive bottle cultures, the sensitivities of the multiplex real-time PCR kit were 100% (166/166 cultures), 97.2% (35/36 cultures), and 99.2% (117/118 cultures) for the 16S rRNA, nuc, and mecA genes, respectively, and the specificities for all three targets were 100%. The Real-MRSA and Real-MRCoNS multiplex real-time PCR assays are very useful for the rapid accurate diagnosis of staphylococcal BSIs. In addition, the Real-MRSA and Real-MRCoNS multiplex real-time PCR assays could have an important impact on the choice of appropriate antimicrobial therapy, based on detection of the mecA gene.

  20. A plausible mechanism of biosorption in dual symbioses by vesicular-arbuscular mycorrhizal in plants.

    Science.gov (United States)

    Azmat, Rafia; Hamid, Neelofer

    2015-03-01

    Dual symbioses of vesicular-arbuscular mycorrhizal (VAM) fungi with growth of Momordica charantia were elucidated in terms of plausible mechanism of biosorption in this article. The experiment was conducted in green house and mixed inoculum of the VAM fungi was used in the three replicates. Results demonstrated that the starch contents were the main source of C for the VAM to builds their hyphae. The increased plant height and leaves surface area were explained in relation with an increase in the photosynthetic rates to produce rapid sugar contents for the survival of plants. A decreased in protein, and amino acid contents and increased proline and protease activity in VAM plants suggested that these contents were the main bio-indicators of the plants under biotic stress. The decline in protein may be due to the degradation of these contents, which later on converted into dextrose where it can easily be absorbed by for the period of symbioses. A mechanism of C chemisorption in relation with physiology and morphology of plant was discussed.

  1. The Sarrazin effect: the presence of absurd statements in conspiracy theories makes canonical information less plausible

    Directory of Open Access Journals (Sweden)

    Marius Hans Raab

    2013-07-01

    Full Text Available Reptile prime ministers and flying Nazi saucers—extreme and sometimes off-wall conclusion are common ingredients of conspiracy theories. While individual differences are a common research topic concerning conspiracy theories, the role of extreme statements in the process of acquiring and passing on conspiratorial stories has not been regarded in an experimental design so far. We identified six morphological components of conspiracy theories empirically. On the basis of these content categories a set of narrative elements for a 9/11 story was compiled. These elements varied systematically in terms of conspiratorial allegation, i.e., they contained official statements concerning the events of 9/11, statements alleging to a conspiracy limited in time and space as well as extreme statements indicating an all-encompassing cover-up. Using the method of narrative construction, 30 people were given a set of cards with these statements and asked to construct the course of events of 9/11 they deem most plausible. When extreme statements were present in the set, the resulting stories were more conspiratorial; the number of official statements included in the narrative dropped significantly, whereas the self-assessment of the story’s plausibility did not differ between conditions. This indicates that blatant statements in a pool of information foster the synthesis of conspiracy theories on an individual level. By relating these findings to one of Germany’s most successful (and controversial non-fiction books, we refer to the real-world dangers of this effect.

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

    Science.gov (United States)

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

    2012-05-01

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

  3. [Rapid detection of novel avian influenza virus subtype H7N9 by multiplex real-time RT-PCR].

    Science.gov (United States)

    Luo, Bao-Zheng; Mo, Qiu-Hua; Li, Ru-Shu; Bo, Qing-Ru; Xu, Hai-Nie; Sha, Cai-Hua; Liao, Xiu-Yun

    2014-01-01

    In order to develop a rapid detection kit for novel avian influenza virus (AIV) subtype H7N9, two sets of specific primers and probes were designed based on the nucleotide sequences of hemagglutinin antigen (HA) and neuraminidase antigen (NA) of novel H7N9 virus (2013) available in GenBank to establish the method of TaqMan probe-based multiplex real-time RT-PCR for rapid detection of AIV subtype H7N9. The primer and probe of HA were for all H7 subtype AIVs, while the primer and probe of NA were only for novel N9 subtype AIVs. The results showed that this method had high sensitivity and specificity. This method was applicable to the testing of positive standard sample with a minimum concentration of 10 copies/microL; it not only distinguished H7 subtype from H1, H3, H5, H6, and H9 subtypes, but also distinguished novel N9 subtype from traditional N9 subtype. A total of 2700 samples from Zhuhai, China were tested by this method, and the results were as expected. For the advantages of sensitivity and specificity, the method holds promise for wide application.

  4. Rapid detection and differentiation of Clonorchis sinensis and Opisthorchis viverrini using real-time PCR and high resolution melting analysis.

    Science.gov (United States)

    Cai, Xian-Quan; Yu, Hai-Qiong; Li, Rong; Yue, Qiao-Yun; Liu, Guo-Hua; Bai, Jian-Shan; Deng, Yan; Qiu, De-Yi; Zhu, Xing-Quan

    2014-01-01

    Clonorchis sinensis and Opisthorchis viverrini are both important fish-borne pathogens, causing serious public health problem in Asia. The present study developed an assay integrating real-time PCR and high resolution melting (HRM) analysis for the specific detection and rapid identification of C. sinensis and O. viverrini. Primers targeting COX1 gene were highly specific for these liver flukes, as evidenced by the negative amplification of closely related trematodes. Assays using genomic DNA extracted from the two flukes yielded specific amplification and their identity was confirmed by sequencing, having the accuracy of 100% in reference to conventional methods. The assay was proved to be highly sensitive with a detection limit below 1 pg of purified genomic DNA, 5 EPG, or 1 metacercaria of C. sinensis. Moreover, C. sinensis and O. viverrini were able to be differentiated by their HRM profiles. The method can reduce labor of microscopic examination and the contamination of agarose electrophoresis. Moreover, it can differentiate these two flukes which are difficult to be distinguished using other methods. The established method provides an alternative tool for rapid, simple, and duplex detection of C. sinensis and O. viverrini.

  5. Rapid Detection and Differentiation of Clonorchis sinensis and Opisthorchis viverrini Using Real-Time PCR and High Resolution Melting Analysis

    Directory of Open Access Journals (Sweden)

    Xian-Quan Cai

    2014-01-01

    Full Text Available Clonorchis sinensis and Opisthorchis viverrini are both important fish-borne pathogens, causing serious public health problem in Asia. The present study developed an assay integrating real-time PCR and high resolution melting (HRM analysis for the specific detection and rapid identification of C. sinensis and O. viverrini. Primers targeting COX1 gene were highly specific for these liver flukes, as evidenced by the negative amplification of closely related trematodes. Assays using genomic DNA extracted from the two flukes yielded specific amplification and their identity was confirmed by sequencing, having the accuracy of 100% in reference to conventional methods. The assay was proved to be highly sensitive with a detection limit below 1 pg of purified genomic DNA, 5 EPG, or 1 metacercaria of C. sinensis. Moreover, C. sinensis and O. viverrini were able to be differentiated by their HRM profiles. The method can reduce labor of microscopic examination and the contamination of agarose electrophoresis. Moreover, it can differentiate these two flukes which are difficult to be distinguished using other methods. The established method provides an alternative tool for rapid, simple, and duplex detection of C. sinensis and O. viverrini.

  6. Rapid, sensitive, and specific detection of Mycobacterium tuberculosis complex by real-time PCR on paraffin-embedded human tissues.

    Science.gov (United States)

    Lee, Hye Seung; Park, Kyoung Un; Park, Jung Ok; Chang, Ho Eun; Song, Junghan; Choe, Gheeyoung

    2011-07-01

    The detection of Mycobacterium tuberculosis complex (MTB) in clinical specimens is important for diagnosing and caring for patients in whom tuberculosis is clinically suspected. We collected 129 FFPE specimens, including 56 nontuberculosis cases, 63 MTB cases, and 10 nontuberculous mycobacteria (NTM) cases determined by acid-fast bacilli (AFB) culture. We performed AFB staining; nested MTB PCR, targeting the IS6110 gene; and real-time MTB PCR, targeting the senX3-regX3 intergenic region in the 129 FFPE specimens. The sensitivity and specificity of AFB staining were 37.0% and 98.2%, respectively, using AFB culture results as the reference standard. The sensitivity and specificity of detecting MTB were 68.3% and 98.5%, respectively, by nested PCR; and 74.6% and 98.5% by real-time PCR, respectively. Among the 129 specimens, four were positive by AFB staining but negative by nested or real-time PCR. NTM grew in all four of these cases by AFB culture. AFB density in FFPE tissue sections significantly correlated with MTB DNA load. Thus, real-time PCR is a useful diagnostic tool for rapid and sensitive MTB detection in FFPE specimens, whereas NTM should be included in differential diagnoses of cases positive by AFB staining but negative by PCR.

  7. Development of a real-time SYBR Green PCR assay for the rapid detection of Dermatophilus congolensis

    Science.gov (United States)

    Martínez, Remigio; Benitez-Medina, José Manuel; Risco, David; García, Waldo Luis; Rey, Joaquín; Alonso, Juan Manuel; de Mendoza, Javier Hermoso

    2013-01-01

    Methods such as real time (RT)-PCR have not been developed for the rapid detection and diagnosis of Dermatophilus (D.) congolensis infection. In the present study, a D. congolensis-specific SYBR Green RT-PCR assay was evaluated. The detection limit of the RT-PCR assay was 1 pg of DNA per PCR reaction. No cross-reaction with nucleic acids extracted from Pseudomonas aeruginosa, Mycobacterium tuberculosis, Staphylococcus aureus, or Austwickia chelonae was observed. Finally, the RT-PCR assay was used to evaluate clinical samples collected from naturally infected animals with D. congolensis. The results showed that this assay is a fast and reliable method for diagnosing dermatophilosis. PMID:23820221

  8. Development of a real-time PCR assay for the rapid detection of Acinetobacter baumannii from whole blood samples.

    Science.gov (United States)

    De Gregorio, Eliana; Roscetto, Emanuela; Iula, Vita Dora; Martinucci, Marianna; Zarrilli, Raffaele; Di Nocera, Pier Paolo; Catania, Maria Rosaria

    2015-04-01

    Acinetobacter baumannii is a multidrug-resistant pathogen associated with severe infections in hospitalized patients, including pneumonia, urinary and bloodstream infections. Rapid detection of A. baumannii infection is crucial for timely treatment of septicemic patients. The aim of the present study was to develop a specific marker for a quantitative polymerase chain reaction (PCR) assay for the detection of A. baumannii. The target gene chosen is the biofilm-associated protein (bap) gene, encoding a cell surface protein involved in biofilm formation. The assay is specific for A. baumannii, allowing its discrimination from different species of Acinetobacter and other clinically relevant bacterial pathogens. The assay is able to detect one genomic copy of A. baumannii, corresponding to 4 fg of purified DNA, and 20 colony-forming units/ml using DNA extracted from spiked whole blood samples.

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

    Science.gov (United States)

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

    2014-06-01

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

  10. Eye exercises enhance accuracy and letter recognition, but not reaction time, in a modified rapid serial visual presentation task.

    Directory of Open Access Journals (Sweden)

    Paula Di Noto

    Full Text Available Eye exercises have been prescribed to resolve a multitude of eye-related problems. However, studies on the efficacy of eye exercises are lacking, mainly due to the absence of simple assessment tools in the clinic. Because similar regions of the brain are responsible for eye movements and visual attention, we used a modified rapid serial visual presentation (RSVP to assess any measurable effect of short-term eye exercise in improvements within these domains. In the present study, twenty subjects were equally divided into control and experimental groups, each of which performed a pre-training RSVP assessment where target letters, to which subjects were asked to respond to by pressing a spacebar, were serially and rapidly presented. Response time to target letters, accuracy of correctly responding to target letters, and correct identification of target letters in each of 12 sessions was measured. The experimental group then performed active eye exercises, while the control group performed a task that minimized eye movements for 18.5 minutes. A final post-training RSVP assessment was performed by both groups and response time, accuracy, and letter identification were compared between and within subject groups both pre- and post-training. Subjects who performed eye exercises were more accurate in responding to target letters separated by one distractor and in letter identification in the post-training RSVP assessment, while latency of responses were unchanged between and within groups. This suggests that eye exercises may prove useful in enhancing cognitive performance on tasks related to attention and memory over a very brief course of training, and RSVP may be a useful measure of this efficacy. Further research is needed on eye exercises to determine whether they are an effective treatment for patients with cognitive and eye-related disorders.

  11. Eye exercises enhance accuracy and letter recognition, but not reaction time, in a modified rapid serial visual presentation task.

    Science.gov (United States)

    Di Noto, Paula; Uta, Sorin; DeSouza, Joseph F X

    2013-01-01

    Eye exercises have been prescribed to resolve a multitude of eye-related problems. However, studies on the efficacy of eye exercises are lacking, mainly due to the absence of simple assessment tools in the clinic. Because similar regions of the brain are responsible for eye movements and visual attention, we used a modified rapid serial visual presentation (RSVP) to assess any measurable effect of short-term eye exercise in improvements within these domains. In the present study, twenty subjects were equally divided into control and experimental groups, each of which performed a pre-training RSVP assessment where target letters, to which subjects were asked to respond to by pressing a spacebar, were serially and rapidly presented. Response time to target letters, accuracy of correctly responding to target letters, and correct identification of target letters in each of 12 sessions was measured. The experimental group then performed active eye exercises, while the control group performed a task that minimized eye movements for 18.5 minutes. A final post-training RSVP assessment was performed by both groups and response time, accuracy, and letter identification were compared between and within subject groups both pre- and post-training. Subjects who performed eye exercises were more accurate in responding to target letters separated by one distractor and in letter identification in the post-training RSVP assessment, while latency of responses were unchanged between and within groups. This suggests that eye exercises may prove useful in enhancing cognitive performance on tasks related to attention and memory over a very brief course of training, and RSVP may be a useful measure of this efficacy. Further research is needed on eye exercises to determine whether they are an effective treatment for patients with cognitive and eye-related disorders.

  12. Rapid detection of Salmonella in pet food: design and evaluation of integrated methods based on real-time PCR detection.

    Science.gov (United States)

    Balachandran, Priya; Friberg, Maria; Vanlandingham, V; Kozak, K; Manolis, Amanda; Brevnov, Maxim; Crowley, Erin; Bird, Patrick; Goins, David; Furtado, Manohar R; Petrauskene, Olga V; Tebbs, Robert S; Charbonneau, Duane

    2012-02-01

    Reducing the risk of Salmonella contamination in pet food is critical for both companion animals and humans, and its importance is reflected by the substantial increase in the demand for pathogen testing. Accurate and rapid detection of foodborne pathogens improves food safety, protects the public health, and benefits food producers by assuring product quality while facilitating product release in a timely manner. Traditional culture-based methods for Salmonella screening are laborious and can take 5 to 7 days to obtain definitive results. In this study, we developed two methods for the detection of low levels of Salmonella in pet food using real-time PCR: (i) detection of Salmonella in 25 g of dried pet food in less than 14 h with an automated magnetic bead-based nucleic acid extraction method and (ii) detection of Salmonella in 375 g of composite dry pet food matrix in less than 24 h with a manual centrifugation-based nucleic acid preparation method. Both methods included a preclarification step using a novel protocol that removes food matrix-associated debris and PCR inhibitors and improves the sensitivity of detection. Validation studies revealed no significant differences between the two real-time PCR methods and the standard U.S. Food and Drug Administration Bacteriological Analytical Manual (chapter 5) culture confirmation method.

  13. Correction of dead-time and pile-up in a detector array for constant and rapidly varying counting rates

    Energy Technology Data Exchange (ETDEWEB)

    Guerrero, C. [Centro de Investigaciones Medioambientales, Energéticas y Tecnológicas (CIEMAT), Madrid (Spain); Departamento de Física Atómica, Molecular y Nuclear, Universidad de Sevilla (Spain); Cano-Ott, D.; Mendoza, E. [Centro de Investigaciones Medioambientales, Energéticas y Tecnológicas (CIEMAT), Madrid (Spain); Wright, T. [University of Manchester, Manchester (United Kingdom)

    2015-03-21

    The effect of dead-time and pile-up in counting experiments may become a significant source of uncertainty if not properly taken into account. Although analytical solutions to this problem have been proposed for simple set-ups with one or two detectors, these are limited when it comes to arrays where time correlation between the detector modules is used, and also in situations of variable counting rates. In this paper we describe the dead-time and pile-up corrections applied to the n-TOF Total Absorption Calorimeter (TAC), a 4π γ-ray detector made of 40 BaF{sub 2} modules operating at the CERN n-TOF facility. Our method is based on the simulation of the complete signal detection and event reconstruction processes and can be applied as well in the case of rapidly varying counting rates. The method is discussed in detail and then we present its successful application to the particular case of the measurement of {sup 238}U(n, γ) reactions with the TAC detector.

  14. Qualitative and quantitative analysis of Andrographis paniculata by rapid resolution liquid chromatography/time-of-flight mass spectrometry.

    Science.gov (United States)

    Song, Yong-Xi; Liu, Shi-Ping; Jin, Zhao; Qin, Jian-Fei; Jiang, Zhi-Yuan

    2013-09-30

    A rapid resolution liquid chromatography/time-of-flight tandem mass spectrometry (RRLC-TOF/MS) method was developed for qualitative and quantitative analysis of the major chemical constituents in Andrographis paniculata. Fifteen compounds, including flavonoids and diterpenoid lactones, were unambiguously or tentatively identified in 10 min by comparing their retention times and accurate masses with standards or literature data. The characteristic fragmentation patterns of flavonoids and diterpenoid lactones were summarized, and the structures of the unknown compounds were predicted. Andrographolide, dehydroandrographolide and neoandrographolide were further quantified as marker substances. It was found that the calibration curves for all analytes showed good linearity (R² > 0.9995) within the test ranges. The overall limits of detection (LODs) and limits of quantification (LOQs) were 0.02 μg/mL to 0.06 μg/mL and 0.06 μg/mL to 0.2 μg/mL, respectively. The relative standard deviations (RSDs) for intra- and inter-day precisions were below 3.3% and 4.2%, respectively. The mean recovery rates ranged from 96.7% to 104.5% with the relative standard deviations (RSDs) less than 2.72%. It is concluded that RRLC-TOF/MS is powerful and practical in qualitative and quantitative analysis of complex plant samples due to time savings, sensitivity, precision, accuracy and lowering solvent consumption.

  15. Qualitative and Quantitative Analysis of Andrographis paniculata by Rapid Resolution Liquid Chromatography/Time-of-Flight Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Jian-Fei Qin

    2013-09-01

    Full Text Available A rapid resolution liquid chromatography/time-of-flight tandem mass spectrometry (RRLC-TOF/MS method was developed for qualitative and quantitative analysis of the major chemical constituents in Andrographis paniculata. Fifteen compounds, including flavonoids and diterpenoid lactones, were unambiguously or tentatively identified in 10 min by comparing their retention times and accurate masses with standards or literature data. The characteristic fragmentation patterns of flavonoids and diterpenoid lactones were summarized, and the structures of the unknown compounds were predicted. Andrographolide, dehydroandrographolide and neoandrographolide were further quantified as marker substances. It was found that the calibration curves for all analytes showed good linearity (R2 > 0.9995 within the test ranges. The overall limits of detection (LODs and limits of quantification (LOQs were 0.02 μg/mL to 0.06 μg/mL and 0.06 μg/mL to 0.2 μg/mL, respectively. The relative standard deviations (RSDs for intra- and inter-day precisions were below 3.3% and 4.2%, respectively. The mean recovery rates ranged from 96.7% to 104.5% with the relative standard deviations (RSDs less than 2.72%. It is concluded that RRLC-TOF/MS is powerful and practical in qualitative and quantitative analysis of complex plant samples due to time savings, sensitivity, precision, accuracy and lowering solvent consumption.

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

    Science.gov (United States)

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

    2013-05-01

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

  17. Generation of Plausible Hurricane Tracks for Preparedness Exercises

    Science.gov (United States)

    2017-04-25

    emergency managers (EMs) make accurate and timely evacuation decisions for their community by providing planning, situation awareness, data analytics...provides planning, situational awareness, data analytics, and training tools to enable EMs to make accurate, timely evacu- ation decisions. MIT Lincoln...the best track data from the NHC’s post-storm analysis of actual tropical cyclones. Tables are provided for the North Atlantic Basin and the

  18. Rapid phase-correlated rescanning irradiation improves treatment time in carbon-ion scanning beam treatment under irregular breathing

    Science.gov (United States)

    Mori, Shinichiro; Furukawa, Takuji

    2016-05-01

    To shorten treatment time in pencil beam scanning irradiation, we developed rapid phase-controlled rescanning (rPCR), which irradiates two or more isoenergy layers in a single gating window. Here, we evaluated carbon-ion beam dose distribution with rapid and conventional PCR (cPCR). 4 dimensional computed tomography (4DCT) imaging was performed on 12 subjects with lung or liver tumors. To compensate for intrafractional range variation, the field-specific target volume (FTV) was calculated using 4DCT within the gating window (T20-T80). We applied an amplitude-based gating strategy, in which the beam is on when the tumor is within the gating window defined by treatment planning. Dose distributions were calculated for layered phase-controlled rescanning under an irregular respiratory pattern, although a single 4DCT data set was used. The number of rescannings was eight times. The prescribed doses were 48 Gy(RBE)/1 fr (where RBE is relative biological effectiveness) delivered via four beam ports to the FTV for the lung cases and 45 Gy(RBE)/2 fr delivered via two beam ports to the FTV for the liver cases. In the liver cases, the accumulated dose distributions showed an increased magnitude of hot/cold spots with rPCR compared with cPCR. The results of the dose assessment metrics for the cPCR and rPCR were very similar. The D 95, D max, and D min values (cPCR/rPCR) averaged over all the patients were 96.3  ±  0.9%/96.0  ±  1.2%, 107.3  ±  3.6%/107.1  ±  2.9%, and 88.8  ±  3.2%/88.1  ±  3.1%, respectively. The treatment times in cPCR and rPCR were 110.7 s and 53.5 s, respectively. rPCR preserved dose conformation under irregular respiratory motion and reduced the total treatment time compared with cPCR.

  19. Gut Microbiome and Obesity: A Plausible Explanation for Obesity

    Science.gov (United States)

    Sanmiguel, Claudia; Gupta, Arpana; Mayer, Emeran A.

    2015-01-01

    Obesity is a multifactorial disorder that results in excessive accumulation of adipose tissue. Although obesity is caused by alterations in the energy consumption/expenditure balance, the factors promoting this disequilibrium are incompletely understood. The rapid development of new technologies and analysis strategies to decode the gut microbiota composition and metabolic pathways has opened a door into the complexity of the guest-host interactions between the gut microbiota and its human host in health and in disease. Pivotal studies have demonstrated that manipulation of the gut microbiota and its metabolic pathways can affect host’s adiposity and metabolism. These observations have paved the way for further assessment of the mechanisms underlying these changes. In this review we summarize the current evidence for possible mechanisms underlying gut microbiota induced obesity. The review addresses some well-known effects of the gut microbiota on energy harvesting and changes in metabolic machinery, on metabolic and immune interactions and on possible changes in brain function and behavior. Although there is limited understanding on the symbiotic relationship between us and our gut microbiome, and how disturbances of this relationship affects our health, there is compelling evidence for an important role of the gut microbiota in the development and perpetuation of obesity. PMID:26029487

  20. A versatile DSP, FPGA structure optimized for rapid prototyping and digital real-time simulation of power electronic and electrical drive systems

    OpenAIRE

    Karipidis, Claus-Ulrich

    2001-01-01

    A Versatile DSP/ FPGA Structure optimized for Rapid Prototyping and Digital Real-Time Simulation of Power Electronic and Electrical Drive Systems This thesis is devoted to the development of a powerful digital computer equipped with flexible interfaces. It is designed to suit Rapid Prototyping and digital real-time simulation methods of power electronic and electrical drive (PE&ED) systems. This universal hardware basis unites the possibilities (benefit) to implement control equipment and com...

  1. Plausible impact of global climate change on water resources in the Tarim River Basin

    Institute of Scientific and Technical Information of China (English)

    CHEN; Yaning; XU; Zongxue

    2005-01-01

    Combining the temperature and precipitation data from 77 climatological stations and the climatic and hydrological change data from three headstreams of the Tarim River: Hotan, Yarkant, and Aksu in the study area, the plausible association between climate change and the variability of water resources in the Tarim River Basin in recent years was investigated, the long-term trend of the hydrological time series including temperature, precipitation, and streamflow was detected, and the possible association between the El Ni(n)o/Southern Oscillation (ENSO) and these three kinds of time series was tested. The results obtained in this study show that during the past years, the temperature experienced a significant monotonic increase at the speed of 5%, nearly 1℃ rise; the precipitation showed a significant decrease in the 1970s, and a significant increase in the1980s and 1990s, the average annual precipitation was increased with the magnitude of 6.8 mm per decade. A step change occurred in both temperature and precipitation time series around 1986, which may be influenced by the global climate change. Climate change resulted in the increase of the streamflow at the headwater of the Tarim River, but the anthropogenic activities such as over-depletion of the surface water resulted in the decrease of the streamflow at the lower reaches of the Tarim River. The study result also showed that there is no significant association between the ENSO and the temperature, precipitation and streamflow.

  2. Rapid identification of polymer additives by atmospheric solid analysis probe with quadrupole time-of-flight mass spectrometry.

    Science.gov (United States)

    Du, Zhenxia; Zhang, Yun; Li, Ailin; Lv, Surong

    2014-10-15

    A method using an atmospheric solid analysis probe (ASAP) combined with quadrupole time-of-flight mass spectrometry (QTOFMS) assisted by a pre-built MS library was found to be efficient in fast and direct analysis of additives for polymers. By this method, sample pretreatment could be eliminated from the additives identification process. Some crucial parameters, such as desolvation gas temperature, corona current, sample cone voltage and collision energy, should be optimized. A MS library of 100 polymer additives, including phenols (Irganox 1010, Irganox 1076), hydroxyl phenyl benzotriazole derivatives (Tinuvin 326, Tinuvin 327, Tinuvin 328), hindered amines (Tinuvin 944, Tinuvin 770) and plasticizers, was built based on the optimized conditions. To verify the application of the MS library, the ASAP-QTOFMS method was applied to identify complex additives, a simulated polypropylene (PP) sample and a real polymethylmethacrylate (PMMA) sample purchased from a local market. By searching the exact mass, and comparing the MS and MS/MS spectra of samples with standards in the MS library, complex additives such as Irganox GX 2921, as well as additives in PP and PMMA samples, could be identified quickly and easily. The determination of mass accuracy increased the confidence of peak identification as well. Moreover, the results also provided information of the characterization for PP and PMMA polymers. A rapid identification method has been developed for polymer additives by ASAP-QTOFMS. A MS library of 100 polymer additives was built by this method. Using ASAP-QTOFMS assisted by the pre-built MS library, polymer additives can be quickly identified. This method was found to be a promising tool in the rapid analysis of additives in polymers and polymer matrices. Copyright © 2014 John Wiley & Sons, Ltd.

  3. Multi-sensor time series of remote sensing data indicate rapid warming trend for lakes in California and Nevada

    Science.gov (United States)

    Schneider, P.; Hook, S. J.; Radocinski, R. R.; Corlett, G. K.; Hulley, G. C.; Schladow, S. G.; Steissberg, T. E.

    2009-12-01

    The temperature of large lakes is a potential indicator of climate change. However, its usefulness is limited by the paucity of in situ measurements and lack of long-term data records. Thermal infrared (TIR) satellite imagery can be used to obtain frequent and accurate remote observations of lake surface temperatures. The archive of TIR imagery from the Moderate Resolution Imaging Spectroradiometer (MODIS), the series of Along-Track Scanning Radiometers (ATSR/ATSR-2/AATSR) sensors, as well as from the series of Advanced Very High Resolution Radiometers (AVHRR), now spans nearly three decades and together these data sets can provide continuous time series of global lake surface temperatures. As part of an ongoing project involving the construction of 30-year time series of lake temperatures for 164 large lakes worldwide, we present the results of a case study for six lakes in California and Nevada. Seventeen years of data from the ATSR series was processed in combination with nine years of MODIS data in order to obtain time series of lake skin temperature. The accuracy of the skin temperature retrievals was tested against automated in situ measurements from buoys at the Lake Tahoe test site. The results indicate that nighttime skin temperatures can be estimated with mean errors as low as 0.2 °C. An analysis of average summer lake temperatures retrieved from the ATSR sensors shows that the six case study sites have exhibited average warming trends of 0.11 ± 0.026 °C yr-1 (p < 0.002) since 1992. The magnitude of the trend is confirmed by the shorter time series of MODIS data as well as by in situ measurements at Lake Tahoe. A comparison with air temperature observations suggests that the lake surface is warming more rapidly than the surface air temperature.

  4. Rapid diagnostic tests as a source of DNA for Plasmodium species-specific real-time PCR

    Directory of Open Access Journals (Sweden)

    Van Esbroeck Marjan

    2011-03-01

    Full Text Available Abstract Background This study describes the use of malaria rapid diagnostic tests (RDTs as a source of DNA for Plasmodium species-specific real-time PCR. Methods First, the best method to recover DNA from RDTs was investigated and then the applicability of this DNA extraction method was assessed on 12 different RDT brands. Finally, two RDT brands (OptiMAL Rapid Malaria Test and SDFK60 malaria Ag Plasmodium falciparum/Pan test were comprehensively evaluated on a panel of clinical samples submitted for routine malaria diagnosis at ITM. DNA amplification was done with the 18S rRNA real-time PCR targeting the four Plasmodium species. Results of PCR on RDT were compared to those obtained by PCR on whole blood samples. Results Best results were obtained by isolating DNA from the proximal part of the nitrocellulose component of the RDT strip with a simple DNA elution method. The PCR on RDT showed a detection limit of 0.02 asexual parasites/μl, which was identical to the same PCR on whole blood. For all 12 RDT brands tested, DNA was detected except for one brand when a low parasite density sample was applied. In RDTs with a plastic seal covering the nitrocellulose strip, DNA extraction was hampered. PCR analysis on clinical RDT samples demonstrated correct identification for single species infections for all RDT samples with asexual parasites of P. falciparum (n = 60, Plasmodium vivax (n = 10, Plasmodium ovale (n = 10 and Plasmodium malariae (n = 10. Samples with only gametocytes were detected in all OptiMAL and in 10 of the 11 SDFK60 tests. None of the negative samples (n = 20 gave a signal by PCR on RDT. With PCR on RDT, higher Ct-values were observed than with PCR on whole blood, with a mean difference of 2.68 for OptiMAL and 3.53 for SDFK60. Mixed infections were correctly identified with PCR on RDT in 4/5 OptiMAL tests and 2/5 SDFK60 tests. Conclusions RDTs are a reliable source of DNA for Plasmodium real-time PCR. This study demonstrates the

  5. Rapid and accurate identification by real-time PCR of biotoxin-producing dinoflagellates from the family gymnodiniaceae.

    Science.gov (United States)

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

    2014-03-07

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

  6. Cochrane Rapid Reviews Methods Group to play a leading role in guiding the production of informed high-quality, timely research evidence syntheses.

    Science.gov (United States)

    Garritty, Chantelle; Stevens, Adrienne; Gartlehner, Gerald; King, Valerie; Kamel, Chris

    2016-10-28

    Policymakers and healthcare stakeholders are increasingly seeking evidence to inform the policymaking process, and often use existing or commissioned systematic reviews to inform decisions. However, the methodologies that make systematic reviews authoritative take time, typically 1 to 2 years to complete. Outside the traditional SR timeline, "rapid reviews" have emerged as an efficient tool to get evidence to decision-makers more quickly. However, the use of rapid reviews does present challenges. To date, there has been limited published empirical information about this approach to compiling evidence. Thus, it remains a poorly understood and ill-defined set of diverse methodologies with various labels. In recent years, the need to further explore rapid review methods, characteristics, and their use has been recognized by a growing network of healthcare researchers, policymakers, and organizations, several with ties to Cochrane, which is recognized as representing an international gold standard for high-quality, systematic reviews. In this commentary, we introduce the newly established Cochrane Rapid Reviews Methods Group developed to play a leading role in guiding the production of rapid reviews given they are increasingly employed as a research synthesis tool to support timely evidence-informed decision-making. We discuss how the group was formed and outline the group's structure and remit. We also discuss the need to establish a more robust evidence base for rapid reviews in the published literature, and the importance of promoting registration of rapid review protocols in an effort to promote efficiency and transparency in research. As with standard systematic reviews, the core principles of evidence-based synthesis should apply to rapid reviews in order to minimize bias to the extent possible. The Cochrane Rapid Reviews Methods Group will serve to establish a network of rapid review stakeholders and provide a forum for discussion and training. By facilitating

  7. The Utility of Cognitive Plausibility in Language Acquisition Modeling: Evidence From Word Segmentation

    National Research Council Canada - National Science Library

    Phillips, Lawrence; Pearl, Lisa

    2015-01-01

    The informativity of a computational model of language acquisition is directly related to how closely it approximates the actual acquisition task, sometimes referred to as the model's cognitive plausibility...

  8. Choosing diverse sets of plausible scenarios in multidimensional exploratory futures techniques

    NARCIS (Netherlands)

    Lord, Steven; Helfgott, Ariella; Vervoort, Joost M.

    2016-01-01

    Abstract Morphological analysis allows any number of dimensions to be retained when framing future conditions, and techniques within morphological analysis determine which combinations of those dimensions represent plausible futures. However, even a relatively low number of dimensions in future cond

  9. A Retrospective Study of the Impact of Rapid Diagnostic Testing on Time to Pathogen Identification and Antibiotic Use for Children with Positive Blood Cultures.

    Science.gov (United States)

    Veesenmeyer, Angela Fimbres; Olson, Jared A; Hersh, Adam L; Stockmann, Chris; Korgenski, Kent; Thorell, Emily A; Pavia, Andrew T; Blaschke, Anne J

    2016-12-01

    Rapid identification of bloodstream pathogens provides crucial information that can improve the choice of antimicrobial therapy for children. Previous impact studies have primarily focused on adults. Our objective was to evaluate the impact of rapid testing in a children's hospital on time to organism identification and antibiotic use in the setting of an established antimicrobial stewardship program. We conducted a retrospective study over three consecutive time periods (spanning January 2013-August 2015) as our hospital sequentially introduced two rapid testing methods for positive blood cultures. An antimicrobial stewardship program was active throughout the study. In the baseline period, no rapid diagnostic methods were routinely utilized. In the second period (PNAFISH), a fluorescent in situ hybridization test was implemented for gram-positive organisms and in the third a rapid multiplex PCR (rmPCR) test was employed. For children with positive blood cultures, time to organism identification use and duration of select antimicrobial therapies were compared between periods. Positive blood cultures were analyzed. Median overall time to organism identification was 23, 11, and 0 h in the baseline, PNAFISH, and rmPCR periods, respectively (p Rapid diagnostic testing for children with positive blood cultures results in faster time to identification and can influence antibiotic prescribing in the setting of active antimicrobial stewardship particularly for gram-positive pathogens. Merck.

  10. Rapid detection of isoniazid resistance in Mycobacterium tuberculosis isolates by use of real-time-PCR-based melting curve analysis.

    Science.gov (United States)

    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], 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.

  11. Rapid gains in segmenting fluent speech when words match the rhythmic unit: evidence from infants acquiring syllable-timed languages

    Directory of Open Access Journals (Sweden)

    Laura eBosch

    2013-03-01

    Full Text Available The ability to extract word-forms from sentential contexts represents an initial step in infants’ process towards lexical acquisition. By age 6 months the ability is just emerging and evidence of it is restricted to certain testing conditions. Most research has been developed with infants acquiring stress-timed languages (English, but also German and Dutch whose rhythmic unit is not the syllable. Data from infants acquiring syllable-timed languages are still scarce and limited to French (European and Canadian, partially revealing some discrepancies with English regarding the age at which word segmentation ability emerges. Research reported here aims at broadening this cross-linguistic perspective by presenting first data on the early ability to segment monosyllabic word-forms by infants acquiring Spanish and Catalan. Three different language groups (two monolingual and one bilingual and two different age groups (8- and 6-month-old infants were tested using natural language and a modified version of the HPP with familiarization to passages and testing on words. Results revealed positive evidence of word segmentation in all groups at both ages, but critically, the pattern of preference differed by age. A novelty preference was obtained in the older groups, while the expected familiarity preference was only found at the younger age tested, suggesting more advanced segmentation ability with an increase in age. These results offer first evidence of an early ability for monosyllabic word segmentation in infants acquiring syllable-timed languages such as Spanish or Catalan, not previously described in the literature. Data show no impact of bilingual exposure in the emergence of this ability and results suggest rapid gains in early segmentation for words that match the rhythm unit of the native language.

  12. Rapid gains in segmenting fluent speech when words match the rhythmic unit: evidence from infants acquiring syllable-timed languages.

    Science.gov (United States)

    Bosch, Laura; Figueras, Melània; Teixidó, Maria; Ramon-Casas, Marta

    2013-01-01

    The ability to extract word-forms from sentential contexts represents an initial step in infants' process toward lexical acquisition. By age 6 months the ability is just emerging and evidence of it is restricted to certain testing conditions. Most research has been developed with infants acquiring stress-timed languages (English, but also German and Dutch) whose rhythmic unit is not the syllable. Data from infants acquiring syllable-timed languages are still scarce and limited to French (European and Canadian), partially revealing some discrepancies with English regarding the age at which word segmentation ability emerges. Research reported here aims at broadening this cross-linguistic perspective by presenting first data on the early ability to segment monosyllabic word-forms by infants acquiring Spanish and Catalan. Three different language groups (two monolingual and one bilingual) and two different age groups (8- and 6-month-old infants) were tested using natural language and a modified version of the HPP with familiarization to passages and testing on words. Results revealed positive evidence of word segmentation in all groups at both ages, but critically, the pattern of preference differed by age. A novelty preference was obtained in the older groups, while the expected familiarity preference was only found at the younger age tested, suggesting more advanced segmentation ability with an increase in age. These results offer first evidence of an early ability for monosyllabic word segmentation in infants acquiring syllable-timed languages such as Spanish or Catalan, not previously described in the literature. Data show no impact of bilingual exposure in the emergence of this ability and results suggest rapid gains in early segmentation for words that match the rhythm unit of the native language.

  13. Rapid gains in segmenting fluent speech when words match the rhythmic unit: evidence from infants acquiring syllable-timed languages

    Science.gov (United States)

    Bosch, Laura; Figueras, Melània; Teixidó, Maria; Ramon-Casas, Marta

    2013-01-01

    The ability to extract word-forms from sentential contexts represents an initial step in infants' process toward lexical acquisition. By age 6 months the ability is just emerging and evidence of it is restricted to certain testing conditions. Most research has been developed with infants acquiring stress-timed languages (English, but also German and Dutch) whose rhythmic unit is not the syllable. Data from infants acquiring syllable-timed languages are still scarce and limited to French (European and Canadian), partially revealing some discrepancies with English regarding the age at which word segmentation ability emerges. Research reported here aims at broadening this cross-linguistic perspective by presenting first data on the early ability to segment monosyllabic word-forms by infants acquiring Spanish and Catalan. Three different language groups (two monolingual and one bilingual) and two different age groups (8- and 6-month-old infants) were tested using natural language and a modified version of the HPP with familiarization to passages and testing on words. Results revealed positive evidence of word segmentation in all groups at both ages, but critically, the pattern of preference differed by age. A novelty preference was obtained in the older groups, while the expected familiarity preference was only found at the younger age tested, suggesting more advanced segmentation ability with an increase in age. These results offer first evidence of an early ability for monosyllabic word segmentation in infants acquiring syllable-timed languages such as Spanish or Catalan, not previously described in the literature. Data show no impact of bilingual exposure in the emergence of this ability and results suggest rapid gains in early segmentation for words that match the rhythm unit of the native language. PMID:23467921

  14. A plausible (overlooked) super-luminous supernova in the SDSS Stripe 82 data

    CERN Document Server

    Kostrzewa-Rutkowska, Zuzanna; Wyrzykowski, Lukasz; Djorgovski, S George; Glikman, Eilat; Mahabal, Ashish A

    2013-01-01

    We present the discovery of a plausible super-luminous supernova (SLSN), found in the archival data of Sloan Digital Sky Survey (SDSS) Stripe 82, called PSN 000123+000504. The supernova peaked at M_g<-21.3 mag in the second half of September 2005, but was missed by the real-time supernova hunt. The observed part of the light curve (17 epochs) showed that the rise to the maximum took over 30 days, while the decline time lasted at least 70 days (observed frame), closely resembling other SLSNe of SN2007bi type. Spectrum of the host galaxy reveals a redshift of z=0.281 and the distance modulus of \\mu=40.77 mag. Combining this information with the SDSS photometry, we found the host galaxy to be an LMC-like irregular dwarf galaxy with the absolute magnitude of M_B=-18.2+/-0.2 mag and the oxygen abundance of 12+log[O/H]=8.3+/-0.2. Our SLSN follows the relation for the most energetic/super-luminous SNe exploding in low-metallicity environments, but we found no clear evidence for SLSNe to explode in low-luminosity ...

  15. A biologically plausible learning rule for the Infomax on recurrent neural networks.

    Science.gov (United States)

    Hayakawa, Takashi; Kaneko, Takeshi; Aoyagi, Toshio

    2014-01-01

    A fundamental issue in neuroscience is to understand how neuronal circuits in the cerebral cortex play their functional roles through their characteristic firing activity. Several characteristics of spontaneous and sensory-evoked cortical activity have been reproduced by Infomax learning of neural networks in computational studies. There are, however, still few models of the underlying learning mechanisms that allow cortical circuits to maximize information and produce the characteristics of spontaneous and sensory-evoked cortical activity. In the present article, we derive a biologically plausible learning rule for the maximization of information retained through time in dynamics of simple recurrent neural networks. Applying the derived learning rule in a numerical simulation, we reproduce the characteristics of spontaneous and sensory-evoked cortical activity: cell-assembly-like repeats of precise firing sequences, neuronal avalanches, spontaneous replays of learned firing sequences and orientation selectivity observed in the primary visual cortex. We further discuss the similarity between the derived learning rule and the spike timing-dependent plasticity of cortical neurons.

  16. The Utility of Cognitive Plausibility in Language Acquisition Modeling: Evidence From Word Segmentation.

    Science.gov (United States)

    Phillips, Lawrence; Pearl, Lisa

    2015-11-01

    The informativity of a computational model of language acquisition is directly related to how closely it approximates the actual acquisition task, sometimes referred to as the model's cognitive plausibility. We suggest that though every computational model necessarily idealizes the modeled task, an informative language acquisition model can aim to be cognitively plausible in multiple ways. We discuss these cognitive plausibility checkpoints generally and then apply them to a case study in word segmentation, investigating a promising Bayesian segmentation strategy. We incorporate cognitive plausibility by using an age-appropriate unit of perceptual representation, evaluating the model output in terms of its utility, and incorporating cognitive constraints into the inference process. Our more cognitively plausible model shows a beneficial effect of cognitive constraints on segmentation performance. One interpretation of this effect is as a synergy between the naive theories of language structure that infants may have and the cognitive constraints that limit the fidelity of their inference processes, where less accurate inference approximations are better when the underlying assumptions about how words are generated are less accurate. More generally, these results highlight the utility of incorporating cognitive plausibility more fully into computational models of language acquisition.

  17. Developmental dynamics: toward a biologically plausible evolutionary psychology.

    Science.gov (United States)

    Lickliter, Robert; Honeycutt, Hunter

    2003-11-01

    There has been a conceptual revolution in the biological sciences over the past several decades. Evidence from genetics, embryology, and developmental biology has converged to offer a more epigenetic, contingent, and dynamic view of how organisms develop. Despite these advances, arguments for the heuristic value of a gene-centered, predeterministic approach to the study of human behavior and development have become increasingly evident in the psychological sciences during this time. In this article, the authors review recent advances in genetics, embryology, and developmental biology that have transformed contemporary developmental and evolutionary theory and explore how these advances challenge gene-centered explanations of human behavior that ignore the complex, highly coordinated system of regulatory dynamics involved in development and evolution.

  18. Evaluation of a rapid, quantitative real-time PCR method for enumeration of pathogenic Candida cells in water

    Science.gov (United States)

    Brinkman, Nichole E.; Haugland, Richard A.; Wymer, Larry J.; Byappanahalli, Muruleedhara N.; Whitman, Richard L.; Vesper, Stephen J.

    2003-01-01

    Quantitative PCR (QPCR) technology, incorporating fluorigenic 5′ nuclease (TaqMan) chemistry, was utilized for the specific detection and quantification of six pathogenic species of Candida (C. albicans, C. tropicalis, C. krusei, C. parapsilosis, C. glabrata and C. lusitaniae) in water. Known numbers of target cells were added to distilled and tap water samples, filtered, and disrupted directly on the membranes for recovery of DNA for QPCR analysis. The assay's sensitivities were between one and three cells per filter. The accuracy of the cell estimates was between 50 and 200% of their true value (95% confidence level). In similar tests with surface water samples, the presence of PCR inhibitory compounds necessitated further purification and/or dilution of the DNA extracts, with resultant reductions in sensitivity but generally not in quantitative accuracy. Analyses of a series of freshwater samples collected from a recreational beach showed positive correlations between the QPCR results and colony counts of the corresponding target species. Positive correlations were also seen between the cell quantities of the target Candida species detected in these analyses and colony counts of Enterococcus organisms. With a combined sample processing and analysis time of less than 4 h, this method shows great promise as a tool for rapidly assessing potential exposures to waterborne pathogenic Candida species from drinking and recreational waters and may have applications in the detection of fecal pollution.

  19. Rapid Diagnosis of Mycobacterial Infections and Quantitation of Mycobacterium tuberculosis Load by Two Real-Time Calibrated PCR Assays

    Science.gov (United States)

    Broccolo, Francesco; Scarpellini, Paolo; Locatelli, Giuseppe; Zingale, Anna; Brambilla, Anna M.; Cichero, Paola; Sechi, Leonardo A.; Lazzarin, Adriano; Lusso, Paolo; Malnati, Mauro S.

    2003-01-01

    Sensitive and specific techniques to detect and identify Mycobacterium tuberculosis directly in clinical specimens are important for the diagnosis and management of patients with tuberculosis (TB). We developed two real-time PCR assays, based on the IS6110 multicopy element and on the senX3-regX3 intergenic region, which provide a rapid method for the diagnosis of mycobacterial infections. The sensitivity and specificity of both assays were established by using purified DNA from 71 clinical isolates and 121 clinical samples collected from 83 patients, 20 of whom were affected by TB. Both assays are accurate, sensitive, and specific, showing a complementary pattern of Mycobacterium recognition: broader for the IS6110-based assay and restricted to the M. tuberculosis complex for the senX3-regX3-based assay. Moreover, the addition of a synthetic DNA calibrator prior to DNA extraction allowed us to measure the efficiency of DNA recovery and to control for the presence of PCR inhibitors. The mycobacterial burden of the clinical samples, as assessed by direct microscopy, correlates with the M. tuberculosis DNA load measured by the senX3-regX3-based assay. In addition, reduced levels of M. tuberculosis DNA load are present in those patients subjected to successful therapy, suggesting a potential use of this assay for monitoring treatment efficacy. Therefore, these assays represent a fully controlled high-throughput system for the evaluation of mycobacterial burden in clinical specimens. PMID:14532183

  20. Rapid detection of mecA and nuc genes in staphylococci by real-time multiplex polymerase chain reaction.

    Science.gov (United States)

    Costa, Anna-Maria; Kay, Ian; Palladino, Silvano

    2005-01-01

    A multiplex real-time polymerase chain reaction (RT-PCR) targeting the mecA and nuc genes was developed for the detection of methicillin resistance and identification of Staphylococcus aureus. Novel mecA and nuc primers and fluorescence resonance energy transfer hybridization probes specific for the mecA and nuc genes were evaluated. The assay was performed using the LightCycler system (Roche Molecular Biochemicals, Mannheim, Germany) and evaluated against the traditional gel-based multiplex PCR (PCR-gel) method currently used at Royal Perth Hospital. Clinical isolates (n = 222) and isolates from a culture collection library (n = 206) were tested by both assays in parallel. The RT-PCR assay was 100% sensitive and specific for the detection of methicillin resistance and for the identification of S. aureus when compared with the PCR-gel assay. Results from the RT-PCR assay showed 5 isolates with lower efficiency fluorescence curves for the nuc gene PCR fragment. DNA sequencing showed mutations within the region of the probe-binding sites compared with the reference strain. The results of the RT-PCR assay were available within 2 h. This rapid mecA/nuc RT-PCR assay is a suitable and practical tool for the routine detection of methicillin resistance and identification of S. aureus, which can be easily incorporated into the diagnostic molecular microbiology laboratory work flow.

  1. Real-time PCR assay and rapid diagnostic tests for the diagnosis of clinically suspected malaria patients in Bangladesh

    Directory of Open Access Journals (Sweden)

    Khanum Hamida

    2011-06-01

    Full Text Available Abstract Background More than 95% of total malaria cases in Bangladesh are reported from the 13 high endemic districts. Plasmodium falciparum and Plasmodium vivax are the two most abundant malaria parasites in the country. To improve the detection and management of malaria patients, the National Malaria Control Programme (NMCP has been using rapid diagnostic test (RDT in the endemic areas. A study was conducted to establish a SYBR Green-based modified real-time PCR assay as a gold standard to evaluate the performance of four commercially-available malaria RDTs, along with the classical gold standard- microscopy. Methods Blood samples were collected from 338 febrile patients referred for the diagnosis of malaria by the attending physician at Matiranga Upazila Health Complex (UHC from May 2009 to August 2010. Paracheck RDT and microscopy were performed at the UHC. The blood samples were preserved in EDTA tubes. A SYBR Green-based real-time PCR assay was performed and evaluated. The performances of the remaining three RDTs (Falcivax, Onsite Pf and Onsite Pf/Pv were also evaluated against microscopy and real-time PCR using the stored blood samples. Result In total, 338 febrile patients were enrolled in the study. Malaria parasites were detected in 189 (55.9% and 188 (55.6% patients by microscopy and real-time PCR respectively. Among the RDTs, the highest sensitivity for the detection of P. falciparum (including mixed infection was obtained by Paracheck [98.8%, 95% confidence interval (CI 95.8-99.9] and Falcivax (97.6%, 95% CI 94.1-99.4 compared to microscopy and real-time PCR respectively. Paracheck and Onsite Pf/Pv gave the highest specificity (98.8%, 95% CI 95.7-99.9 compared to microscopy and Onsite Pf/Pv (98.8, 95% CI 95.8-99.9 compared to real-time PCR respectively for the detection of P. falciparum. On the other hand Falcivax and Onsite Pf/Pv had equal sensitivity (90.5%, 95% CI 69.6-98.8 and almost 100% specificity compared to microscopy for

  2. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for rapid identification of fungal rhinosinusitis pathogens.

    Science.gov (United States)

    Huang, Yanfei; Wang, Jinglin; Zhang, Mingxin; Zhu, Min; Wang, Mei; Sun, Yufeng; Gu, Haitong; Cao, Jingjing; Li, Xue; Zhang, Shaoya; Lu, Xinxin

    2017-03-01

    Filamentous fungi are among the most important pathogens, causing fungal rhinosinusitis (FRS). Current laboratory diagnosis of FRS pathogens mainly relies on phenotypic identification by culture and microscopic examination, which is time consuming and expertise dependent. Although matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS has been employed to identify various fungi, its efficacy in the identification of FRS fungi is less clear. A total of 153 FRS isolates obtained from patients were analysed at the Clinical Laboratory at the Beijing Tongren Hospital affiliated to the Capital Medical University, between January 2014 and December 2015. They were identified by traditional phenotypic methods and Bruker MALDI-TOF MS (Bruker, Biotyper version 3.1), respectively. Discrepancies between the two methods were further validated by sequencing. Among the 153 isolates, 151 had correct species identification using MALDI-TOF MS (Bruker, Biot 3.1, score ≥2.0 or 2.3). MALDI-TOF MS enabled identification of some very closely related species that were indistinguishable by conventional phenotypic methods, including 1/10 Aspergillus versicolor, 3/20 Aspergillus flavus, 2/30 Aspergillus fumigatus and 1/20 Aspergillus terreus, which were misidentified by conventional phenotypic methods as Aspergillus nidulans, Aspergillus oryzae, Aspergillus japonicus and Aspergillus nidulans, respectively. In addition, 2/2 Rhizopus oryzae and 1/1 Rhizopus stolonifer that were identified only to the genus level by the phenotypic method were correctly identified by MALDI-TOF MS. MALDI-TOF MS is a rapid and accurate technique, and could replace the conventional phenotypic method for routine identification of FRS fungi in clinical microbiology laboratories.

  3. Rapid prototyping of SoC-based real-time vision system: application to image preprocessing and face detection

    Science.gov (United States)

    Jridi, Maher; Alfalou, Ayman

    2017-05-01

    By this paper, the major goal is to investigate the Multi-CPU/FPGA SoC (System on Chip) design flow and to transfer a know-how and skills to rapidly design embedded real-time vision system. Our aim is to show how the use of these devices can be benefit for system level integration since they make possible simultaneous hardware and software development. We take the facial detection and pretreatments as case study since they have a great potential to be used in several applications such as video surveillance, building access control and criminal identification. The designed system use the Xilinx Zedboard platform. The last is the central element of the developed vision system. The video acquisition is performed using either standard webcam connected to the Zedboard via USB interface or several camera IP devices. The visualization of video content and intermediate results are possible with HDMI interface connected to HD display. The treatments embedded in the system are as follow: (i) pre-processing such as edge detection implemented in the ARM and in the reconfigurable logic, (ii) software implementation of motion detection and face detection using either ViolaJones or LBP (Local Binary Pattern), and (iii) application layer to select processing application and to display results in a web page. One uniquely interesting feature of the proposed system is that two functions have been developed to transmit data from and to the VDMA port. With the proposed optimization, the hardware implementation of the Sobel filter takes 27 ms and 76 ms for 640x480, and 720p resolutions, respectively. Hence, with the FPGA implementation, an acceleration of 5 times is obtained which allow the processing of 37 fps and 13 fps for 640x480, and 720p resolutions, respectively.

  4. Rapid assessment of tsunami impact from real-time seismology and geographic, historical other datasets using machine learning

    Science.gov (United States)

    Michelini, Alberto; Lomax, Anthony

    2017-04-01

    The impact of an earthquake, tsunami, volcanic eruption, severe weather or other natural disaster is related to: the intensity of the hazard; the vulnerability or exposure of the population, such as housing quality, infrastructure and proximity to a coastlines; and the capacity to resist and cope with the disaster. Rapid assessment by monitoring agencies of the impact of a natural event is fundamental for early warning and response. We previously* proposed the "tsunami importance" parameter, It, for characterizing the strength of a tsunami. This parameter combines 5 descriptive indices from the NOAA/WDC Historical Tsunami Database: 4 tsunami impact measures (deaths, injuries, damage, houses destroyed), and maximum water height. Accordingly, It = 2 corresponds approximately to the JMA threshold for issuing a ''Tsunami Warning'' whereas the largest or most devastating tsunamis typically have It = 10. Here we discuss extending this simple, 5-component parameter with additional impact-related measures from relevant databases (e.g., LandScan population density, major infrastructures) and historical / archaeological information, and measures that might be obtained in near-real-time (e.g., emergency services, news, social media). We combine these measures with seismological and other real-time observations as an ensemble of features within automated procedures to estimate impact and guide decision making. We examine using modern machine learning methodologies to train and calibrate the procedures, while working with high-dimensional feature space. * Lomax, A. and A. Michelini (2011), Tsunami early warning using earthquake rupture duration and P-wave dominant period: the importance of length and depth of faulting, Geophys. J. Int., 185, 283-291, doi: 10.1111/j.1365-246X.2010.04916.x

  5. Development of an on-site rapid real-time polymerase chain reaction system and the characterization of suitable DNA polymerases for TaqMan probe technology.

    Science.gov (United States)

    Furutani, Shunsuke; Naruishi, Nahoko; Hagihara, Yoshihisa; Nagai, Hidenori

    2016-08-01

    On-site quantitative analyses of microorganisms (including viruses) by the polymerase chain reaction (PCR) system are significantly influencing medical and biological research. We have developed a remarkably rapid and portable real-time PCR system that is based on microfluidic approaches. Real-time PCR using TaqMan probes consists of a complex reaction. Therefore, in a rapid real-time PCR, the optimum DNA polymerase must be estimated by using actual real-time PCR conditions. In this study, we compared the performance of three DNA polymerases in actual PCR conditions using our rapid real-time PCR system. Although KAPA2G Fast HS DNA Polymerase has the highest enzymatic activity among them, SpeedSTAR HS DNA Polymerase exhibited better performance to rapidly increase the fluorescence signal in an actual real-time PCR using TaqMan probes. Furthermore, we achieved rapid detection of Escherichia coli in 7 min by using SpeedSTAR HS DNA Polymerase with the same sensitivity as that of a conventional thermal cycler.

  6. Ezekiel and the Northern Lights: Biblical aurora seems plausible

    Science.gov (United States)

    Siscoe, George L.; Silverman, Samuel M.; Siebert, Keith D.

    Auroral specialists have suggested that in the Bible's Old Testament book of Ezekiel, the opening vision of a "storm cloud out of the north" depicts imagery inspired by a low-latitude auroral display [Link, 1967; Eather, 1980; Silverman, 1998]. Naturally, other interpretations have been suggested, including a true epiphany, a sandstorm, a thunderstorm, a tornado, a solar halo, a hallucination, and a UFO. Biblical scholars place the site of the Ezekiel's vision about 100 km south of Babylon near Nippur, latitude ˜32°, longitude ˜45°, and the date is within a year or two of 593 B.C., or about 2600 years ago.An auroral interpretation of the vision is subject to possible refutation due to several geophysical considerations. Can auroras be seen at Ezekiel's latitude? More important, can they reach a coronal stage of development, which is what the vision requires? Was the tilt of the dipole axis favorable? Was the general level of solar activity favorable? And finally, What effect does a larger dipole moment in Ezekiel's time have on the question? All but the last question could have been answered on the basis of geophysical data a decade ago or earlier.

  7. Flood Foresight: A near-real time flood monitoring and forecasting tool for rapid and predictive flood impact assessment

    Science.gov (United States)

    Revilla-Romero, Beatriz; Shelton, Kay; Wood, Elizabeth; Berry, Robert; Bevington, John; Hankin, Barry; Lewis, Gavin; Gubbin, Andrew; Griffiths, Samuel; Barnard, Paul; Pinnell, Marc; Huyck, Charles

    2017-04-01

    The hours and days immediately after a major flood event are often chaotic and confusing, with first responders rushing to mobilise emergency responders, provide alleviation assistance and assess loss to assets of interest (e.g., population, buildings or utilities). Preparations in advance of a forthcoming event are becoming increasingly important; early warning systems have been demonstrated to be useful tools for decision markers. The extent of damage, human casualties and economic loss estimates can vary greatly during an event, and the timely availability of an accurate flood extent allows emergency response and resources to be optimised, reduces impacts, and helps prioritise recovery. In the insurance sector, for example, insurers are under pressure to respond in a proactive manner to claims rather than waiting for policyholders to report losses. Even though there is a great demand for flood inundation extents and severity information in different sectors, generating flood footprints for large areas from hydraulic models in real time remains a challenge. While such footprints can be produced in real time using remote sensing, weather conditions and sensor availability limit their ability to capture every single flood event across the globe. In this session, we will present Flood Foresight (www.floodforesight.com), an operational tool developed to meet the universal requirement for rapid geographic information, before, during and after major riverine flood events. The tool provides spatial data with which users can measure their current or predicted impact from an event - at building, basin, national or continental scales. Within Flood Foresight, the Screening component uses global rainfall predictions to provide a regional- to continental-scale view of heavy rainfall events up to a week in advance, alerting the user to potentially hazardous situations relevant to them. The Forecasting component enhances the predictive suite of tools by providing a local

  8. Using critical evaluation to reappraise plausibility judgments: A critical cognitive component of conceptual change

    Science.gov (United States)

    Lombardi, D.

    2011-12-01

    Plausibility judgments-although well represented in conceptual change theories (see, for example, Chi, 2005; diSessa, 1993; Dole & Sinatra, 1998; Posner et al., 1982)-have received little empirical attention until our recent work investigating teachers' and students' understanding of and perceptions about human-induced climate change (Lombardi & Sinatra, 2010, 2011). In our first study with undergraduate students, we found that greater plausibility perceptions of human-induced climate accounted for significantly greater understanding of weather and climate distinctions after instruction, even after accounting for students' prior knowledge (Lombardi & Sinatra, 2010). In a follow-up study with inservice science and preservice elementary teachers, we showed that anger about the topic of climate change and teaching about climate change was significantly related to implausible perceptions about human-induced climate change (Lombardi & Sinatra, 2011). Results from our recent studies helped to inform our development of a model of the role of plausibility judgments in conceptual change situations. The model applies to situations involving cognitive dissonance, where background knowledge conflicts with an incoming message. In such situations, we define plausibility as a judgment on the relative potential truthfulness of incoming information compared to one's existing mental representations (Rescher, 1976). Students may not consciously think when making plausibility judgments, expending only minimal mental effort in what is referred to as an automatic cognitive process (Stanovich, 2009). However, well-designed instruction could facilitate students' reappraisal of plausibility judgments in more effortful and conscious cognitive processing. Critical evaluation specifically may be one effective method to promote plausibility reappraisal in a classroom setting (Lombardi & Sinatra, in progress). In science education, critical evaluation involves the analysis of how evidentiary

  9. Plausible ergogenic effects of vitamin D on athletic performance and recovery.

    Science.gov (United States)

    Dahlquist, Dylan T; Dieter, Brad P; Koehle, Michael S

    2015-01-01

    The purpose of this review is to examine vitamin D in the context of sport nutrition and its potential role in optimizing athletic performance. Vitamin D receptors (VDR) and vitamin D response elements (VDREs) are located in almost every tissue within the human body including skeletal muscle. The hormonally-active form of vitamin D, 1,25-dihydroxyvitamin D, has been shown to play critical roles in the human body and regulates over 900 gene variants. Based on the literature presented, it is plausible that vitamin D levels above the normal reference range (up to 100 nmol/L) might increase skeletal muscle function, decrease recovery time from training, increase both force and power production, and increase testosterone production, each of which could potentiate athletic performance. Therefore, maintaining higher levels of vitamin D could prove beneficial for athletic performance. Despite this situation, large portions of athletic populations are vitamin D deficient. Currently, the research is inconclusive with regards to the optimal intake of vitamin D, the specific forms of vitamin D one should ingest, and the distinct nutrient-nutrient interactions of vitamin D with vitamin K that affect arterial calcification and hypervitaminosis. Furthermore, it is possible that dosages exceeding the recommendations for vitamin D (i.e. dosages up to 4000-5000 IU/day), in combination with 50 to 1000 mcg/day of vitamin K1 and K2 could aid athletic performance. This review will investigate these topics, and specifically their relevance to athletic performance.

  10. Plausible futures of a social-ecological system: Yahara watershed, Wisconsin, USA

    Directory of Open Access Journals (Sweden)

    Stephen R. Carpenter

    2015-06-01

    Full Text Available Agricultural watersheds are affected by changes in climate, land use, agricultural practices, and human demand for energy, food, and water resources. In this context, we analyzed the agricultural, urbanizing Yahara watershed (size: 1345 km², population: 372,000 to assess its responses to multiple changing drivers. We measured recent trends in land use/cover and water quality of the watershed, spatial patterns of 10 ecosystem services, and spatial patterns and nestedness of governance. We developed scenarios for the future of the Yahara watershed by integrating trends and events from the global scenarios literature, perspectives of stakeholders, and models of biophysical drivers and ecosystem services. Four qualitative scenarios were created to explore plausible trajectories to the year 2070 in the watershed's social-ecological system under different regimes: no action on environmental trends, accelerated technological development, strong intervention by government, and shifting values toward sustainability. Quantitative time-series for 2010-2070 were developed for weather and land use/cover during each scenario as inputs to model changes in ecosystem services. Ultimately, our goal is to understand how changes in the social-ecological system of the Yahara watershed, including management of land and water resources, can build or impair resilience to shifting drivers, including climate.

  11. Interactions between visual and motor areas during the recognition of plausible actions as revealed by magnetoencephalography.

    Science.gov (United States)

    Pavlidou, Anastasia; Schnitzler, Alfons; Lange, Joachim

    2014-02-01

    Several studies have shown activation of the mirror neuron system (MNS), comprising the temporal, posterior parietal, and sensorimotor areas when observing plausible actions, but far less is known on how these cortical areas interact during the recognition of a plausible action. Here, we recorded neural activity with magnetoencephalography while subjects viewed point-light displays of biologically plausible and scrambled versions of actions. We were interested in modulations of oscillatory activity and, specifically, in coupling of oscillatory activity between visual and motor areas. Both plausible and scrambled actions elicited modulations of θ (5-7 Hz), α (7-13 Hz), β (13-35 Hz), and γ (55-100 Hz) power within visual and motor areas. When comparing between the two actions, we observed sequential and spatially distinct increases of γ (∼65 Hz), β (∼25 Hz), and α (∼11 Hz) power between 0.5 and 1.3 s in parieto-occipital, sensorimotor, and left temporal areas. In addition, significant clusters of γ (∼65 Hz) and α/β (∼15 Hz) power decrease were observed in right temporal and parieto-occipital areas between 1.3 and 2.0 s. We found β-power in sensorimotor areas to be positively correlated on a trial-by-trial basis with parieto-occipital γ and left temporal α-power for the plausible but not for the scrambled condition. These results provide new insights in the neuronal oscillatory activity of the areas involved in the recognition of plausible action movements and their interaction. The power correlations between specific areas underscore the importance of interactions between visual and motor areas of the MNS during the recognition of a plausible action.

  12. Quantitative multiplex real-time PCR assay for shrimp allergen: comparison of commercial master mixes and PCR platforms in rapid cycling.

    Science.gov (United States)

    Eischeid, Anne C; Kasko, Sasha M

    2015-01-01

    Real-time PCR has been used widely in numerous fields. In food safety, it has been applied to detection of microbes and other contaminants, including food allergens. Interest in rapid (fast) cycling real-time PCR has grown because it yields results in less time than does conventional cycling. However, fast cycling can adversely affect assay performance. Here we report on tests of commercial master mixes specifically designed for fast real-time PCR using a shrimp allergen assay we previously developed and validated. The objective of this work was to determine whether specialized commercial master mixes lead to improved assay performance in rapid cycling. Real-time PCR assays were carried out using four different master mixes and two different rapid cycling protocols. Results indicated that specialized master mixes did yield quality results. In many cases, linear ranges spanned up to 7 orders of magnitude, R(2) values were at least 0.95, and reaction efficiencies were within or near the optimal range of 90 to 110%. In the faster of the two rapid cycling protocols tested, assay performance and PCR amplification were markedly better for the shorter PCR product. In conclusion, specialized commercial master mixes were effective as part of rapid cycling protocols, but conventional cycling as used in our previous work is more reliable for the shrimp assay tested.

  13. Real-time reverse transcriptase PCR for the rapid and sensitive detection of Salmonella typhimurium from pork.

    Science.gov (United States)

    Techathuvanan, Chayapa; Draughon, Frances Ann; D'Souza, Doris Helen

    2010-03-01

    Reverse transcriptase PCR (RT-PCR) detects the presence of mRNA and has a greater potential for detecting viable pathogens than do DNA-based PCR assays, with improved speed and sensitivity compared with traditional methods. Our objective was to rapidly and sensitively detect Salmonella Typhimurium from pork within two 8-h work shifts using a SYBR Green I real-time RT-PCR (rt-RT-PCR) assay. Pork chop and sausage samples (25 g) were inoculated with 10(8) to 10(0) CFU of Salmonella Typhimurium and stomached in 225 ml of tetrathionate broth. Serial dilutions were spread plated on xylose lysine Tergitol 4 agar either immediately or after 10 h of selective preenrichment or preenrichment followed by 12 h of selective enrichment (for stressed cells) at 37 degrees C for standard cultural enumeration. RNA was extracted using the TRIzol method. The rt-RT-PCR assay was carried out in a Bio-Rad iCycler using a SYBR Green I one-step RT-PCR kit and Salmonella specific invA gene primers with an internal amplification control (IAC). The PCR was followed by melting temperature (T(m)) analysis to determine specific Salmonella invA (T(m) = 87.5 degrees C) and IAC (T(m) = 82 degrees C) products. Improved Salmonella detection up to 10(1) CFU/25 g of pork and 10(0) CFU/25 g of sausages was obtained after 10 h of enrichment within approximately 24 h. Even without enrichment, Salmonella could be detected from both pork chop and sausage at 10(6) CFU/25 g within 1 day. This robust rt-RT-PCR detects and confirms Salmonella in pork within approximately 24 h and thus is significantly faster than traditional methods that take >/=1 week. This assay shows promise for routine testing and monitoring of Salmonella by the pork industry.

  14. Interlaboratory validation of a real-time PCR 24-hour rapid method for detection of Salmonella in foods.

    Science.gov (United States)

    Cheng, Chorng-Ming; Van Khanh, T; Lin, Wen; Ruby, Richard M

    2009-05-01

    The efficacy of a 24-h Salmonella real-time, or quantitative, PCR (qPCR) detection method was assessed through a collaborative effort involving eight Federal and state laboratories. Eleven foods including mashed potatoes, soft cheese, chili powder, chocolate, eggs, sprouts, apple juice, fish, shrimp, ground beef, and ground chicken were tested. For each food, seven blind samples were distributed to each participant for testing. These included six samples equivalently inoculated with 1 to 5 CFU/25 g of various serotypes of Salmonella (Gaminara, Weltevreden, Heidelberg, Senftenberg, Enteritidis, Newport, Typhimurium, and Kentucky for each food) and 10 to 50 CFU/25 g of the competitor Enterobacter cloacae. The seventh sample was inoculated with 10 to 50 CFU/25 g of the competitor, E. cloacae, only. These samples were tested for Salmonella by using four methods in parallel: (i) 24-h qPCR method detecting Salmonella from modified buffered peptone water enrichment medium; (ii) 48-h qPCR method detecting Salmonella from a secondary selective enrichment broth; (iii) modified Bacteriological Analytical Manual method; and (iv) VIDAS, an immunoassay system. The results of the statistical analysis showed there was no significant (P > or = 0.05) difference between either of the qPCR methods and the modified Bacteriological Analytical Manual method for 10 of 11 foods. For the one exception, sprouts, detection by qPCR required 48 h. Both qPCR methods showed a detection limit of 0.08 to 0.2 CFU/g. These results provide a solid basis for using this 24-h qPCR rapid screening method to detect Salmonella in foods.

  15. Rapid differential diagnosis between extrapulmonary tuberculosis and focal complications of brucellosis using a multiplex real-time PCR assay.

    Directory of Open Access Journals (Sweden)

    María Isabel Queipo-Ortuño

    Full Text Available BACKGROUND: Arduous to differ clinically, extrapulmonary tuberculosis and focal complications of brucellosis remain important causes of morbidity and mortality in many countries. We developed and applied a multiplex real-time PCR assay (M RT-PCR for the simultaneous detection of Mycobacterium tuberculosis complex and Brucella spp. METHODOLOGY: Conventional microbiological techniques and M RT-PCR for M. tuberculosis complex and Brucella spp were performed on 45 clinical specimens from patients with focal complications of brucellosis or extrapulmonary tuberculosis and 26 control samples. Fragments of 207 bp and 164 bp from the conserved region of the genes coding for an immunogenic membrane protein of 31 kDa of B. abortus (BCSP31 and the intergenic region SenX3-RegX3 were used for the identification of Brucella and M. tuberculosis complex, respectively. CONCLUSIONS: The detection limit of the M RT-PCR was 2 genomes per reaction for both pathogens and the intra- and inter-assay coefficients of variation were 0.44% and 0.93% for Brucella and 0.58% and 1.12% for Mycobacterium. M RT-PCR correctly identified 42 of the 45 samples from patients with tuberculosis or brucellosis and was negative in all the controls. Thus, the overall sensitivity, specificity, PPV and NPV values of the M RT PCR assay were 93.3%, 100%, 100% and 89.7%, respectively, with an accuracy of 95.8% (95% CI, 91.1%-100%. Since M RT-PCR is highly reproducible and more rapid and sensitive than conventional microbiological tests, this technique could be a promising and practical approach for the differential diagnosis between extrapulmonary tuberculosis and focal complications of brucellosis.

  16. Rapid cold hardening improves recovery of ion homeostasis and chill coma recovery time in the migratory locust, Locusta migratoria.

    Science.gov (United States)

    Findsen, Anders; Andersen, Jonas Lembcke; Calderon, Sofia; Overgaard, Johannes

    2013-05-01

    Chill tolerance of insects is defined as the ability to tolerate low temperature under circumstances not involving freezing of intracellular or extracellular fluids. For many insects chill tolerance is crucial for their ability to persist in cold environments and mounting evidence indicates that chill tolerance is associated with the ability to maintain ion and water homeostasis, thereby ensuring muscular function and preventing chill injury at low temperature. The present study describes the relationship between muscle and haemolymph ion homeostasis and time to regain posture following cold shock (CS, 2 h at -4°C) in the chill-susceptible locust Locusta migratoria. This relationship was examined in animals with and without a prior rapid cold-hardening treatment (RCH, 2 h at 0°C) to investigate the physiological underpinnings of RCH. CS elicited a doubling of haemolymph [K(+)] and this disturbance was greater in locusts pre-exposed to RCH. Recovery of ion homeostasis was, however, markedly faster in RCH-treated animals, which correlated well with whole-organism performance as hardened individuals regained posture faster than non-hardened individuals following CS. The present study indicates that loss and recovery of muscular function are associated with the resting membrane potential of excitable membranes as attested by the changes in the equilibrium potential for K(+) (EK) following CS. Both hardened and non-hardened animals regained movement once K(+) homeostasis had recovered to a fixed level (EK≈-41 mV). RCH is therefore not associated with altered sensitivity to ion disturbance but instead is correlated to a faster recovery of haemolymph [K(+)].

  17. Multicapillary gas chromatography coupled to inductively coupled plasma-time-of-flight mass spectrometry for rapid mercury speciation analysis

    Energy Technology Data Exchange (ETDEWEB)

    Jitaru, Petru; Goenaga Infante, Heidi; Adams, Freddy C

    2003-08-11

    A simple, rapid and accurate method on the basis of multicapillary gas chromatography (MCGC) combined with inductively coupled plasma-time-of-flight mass spectrometry (ICP-TOFMS) was developed for speciation analysis of methylmercury (MeHg{sup +}) and inorganic mercury (Hg{sup 2+}). The potential of the ICP-TOFMS for transient multi-isotope detection of very short signals (peak width of 0.4 s at half peak height) was evaluated. Two injection systems (purge-and-trap (PTI) and split (SI) injections) were compared in terms of species separation resolution and transient signal profile. Using purge-and-trap injection, after in situ derivatization of the ionic mercury species with sodium tetraethylborate, a baseline separation of MeHg{sup +} and Hg{sup 2+} was achieved within a chromatographic run of <35 s. To correct for matrix-induced ion signal variation and instrumental drift, propylmercury (PrHg{sup +}) was used as internal standard. Detection limits of 16 and 257 fg g{sup -1} for MeHg{sup +} (as Hg) and Hg{sup 2+}, respectively, were achieved. The analytical precision (R.S.D. (%)) for 10 successive injections of a standard mixture containing 10 pg MeHg{sup +} (as Hg) and Hg{sup 2+} was 1.2% for MeHg{sup +} and 4.1% for Hg{sup 2+}. The method was validated by analysis of two biological certified reference materials (CRM): a dogfish muscle (DORM-2) and a freeze-dried tuna fish (CRM 464)

  18. Evaluation of a rapid and completely automated real-time reverse transcriptase PCR assay for diagnosis of enteroviral meningitis.

    Science.gov (United States)

    Nolte, Frederick S; Rogers, Beverly B; Tang, Yi-Wei; Oberste, M Steven; Robinson, Christine C; Kehl, K Sue; Rand, Kenneth A; Rotbart, Harley A; Romero, Jose R; Nyquist, Ann-Christine; Persing, David H

    2011-02-01

    Nucleic acid amplification tests (NAATs) for enterovirus RNA in cerebrospinal fluid (CSF) have emerged as the new gold standard for diagnosis of enteroviral meningitis, and their use can improve the management and decrease the costs for caring for children with enteroviral meningitis. The Xpert EV assay (Cepheid, Sunnyvale, CA) is a rapid, fully automated real-time PCR test for the detection of enterovirus RNA that was approved by the U.S. Food and Drug Administration for in vitro diagnostic use in March 2007. In this multicenter trial we established the clinical performance characteristics of the Xpert EV assay in patients presenting with meningitis symptoms relative to clinical truth. Clinical truth for enteroviral meningitis was defined as clinical evidence of meningitis, the absence of another detectable pathogen in CSF, and detection of enterovirus in CSF either by two reference NAATs or by viral culture. A total of 199 prospectively and 235 retrospectively collected specimens were eligible for inclusion in this study. The overall prevalence of enteroviral meningitis was 26.04%. The Xpert EV assay had a sensitivity of 94.69% (90% confidence interval [CI] = 89.79 to 97.66%), specificity of 100% (90% CI = 99.07 to 100%), positive predictive value of 100%, negative predictive value of 98.17, and an accuracy of 98.62% relative to clinical truth. The Xpert EV assay demonstrated a high degree of accuracy for diagnosis of enteroviral meningitis. The simplicity and on-demand capability of the Xpert EV assay should prove to be a valuable adjunct to the evaluation of suspected meningitis cases.

  19. Stereotyping to infer group membership creates plausible deniability for prejudice-based aggression.

    Science.gov (United States)

    Cox, William T L; Devine, Patricia G

    2014-02-01

    In the present study, participants administered painful electric shocks to an unseen male opponent who was either explicitly labeled as gay or stereotypically implied to be gay. Identifying the opponent with a gay-stereotypic attribute produced a situation in which the target's group status was privately inferred but plausibly deniable to others. To test the plausible deniability hypothesis, we examined aggression levels as a function of internal (personal) and external (social) motivation to respond without prejudice. Whether plausible deniability was present or absent, participants high in internal motivation aggressed at low levels, and participants low in both internal and external motivation aggressed at high levels. The behavior of participants low in internal and high in external motivation, however, depended on experimental condition. They aggressed at low levels when observers could plausibly attribute their behavior to prejudice and aggressed at high levels when the situation granted plausible deniability. This work has implications for both obstacles to and potential avenues for prejudice-reduction efforts.

  20. Diversification of Angraecum (Orchidaceae, Vandeae) in Madagascar: Revised Phylogeny Reveals Species Accumulation through Time Rather than Rapid Radiation.

    Science.gov (United States)

    Andriananjamanantsoa, Herinandrianina N; Engberg, Shannon; Louis, Edward E; Brouillet, Luc

    Angraecum. The macroevolutionary model-based phylogeny failed to detect shifts in diversification that could be associated directly with morphological diversification. Diversification in Angraecum resulted from gradual species accumulation through time rather than from rapid radiation, a diversification pattern often encountered in tropical rain forests.

  1. Novel real-time simultaneous amplification and testing method to accurately and rapidly detect Mycobacterium tuberculosis complex.

    Science.gov (United States)

    Cui, Zhenling; Wang, Yongzhong; Fang, Liang; Zheng, Ruijuan; Huang, Xiaochen; Liu, Xiaoqin; Zhang, Gang; Rui, Dongmei; Ju, Jinliang; Hu, Zhongyi

    2012-03-01

    The aim of this study was to establish and evaluate a simultaneous amplification and testing method for detection of the Mycobacterium tuberculosis complex (SAT-TB assay) in clinical specimens by using isothermal RNA amplification and real-time fluorescence detection. In the SAT-TB assay, a 170-bp M. tuberculosis 16S rRNA fragment is reverse transcribed to DNA by use of Moloney murine leukemia virus (M-MLV) reverse transcriptase, using specific primers incorporating the T7 promoter sequence, and undergoes successive cycles of amplification using T7 RNA polymerase. Using a real-time PCR instrument, hybridization of an internal 6-carboxyfluorescein-4-[4-(dimethylamino)phenylazo] benzoic acid N-succinimidyl ester (FAM-DABCYL)-labeled fluorescent probe can be used to detect RNA amplification. The SAT-TB assay takes less than 1.5 h to perform, and the sensitivity of the assay for detection of M. tuberculosis H37Rv is 100 CFU/ml. The TB probe has no cross-reactivity with nontuberculous mycobacteria or other common respiratory tract pathogens. For 253 pulmonary tuberculosis (PTB) specimens and 134 non-TB specimens, the SAT-TB results correlated with 95.6% (370/387 specimens) of the Bactec MGIT 960 culture assay results. The sensitivity, specificity, and positive and negative predictive values of the SAT-TB test for the diagnosis of PTB were 67.6%, 100%, 100%, and 62.0%, respectively, compared to 61.7%, 100%, 100%, and 58.0% for Bactec MGIT 960 culture. For PTB diagnosis, the sensitivities of the SAT-TB and Bactec MGIT 960 culture methods were 97.6% and 95.9%, respectively, for smear-positive specimens and 39.2% and 30.2%, respectively, for smear-negative specimens. In conclusion, the SAT-TB assay is a novel, simple test with a high specificity which may enhance the detection rate of TB. It is therefore a promising tool for rapid diagnosis of M. tuberculosis infection in clinical microbiology laboratories.

  2. High-Throughput Sequencing Reveals Hypothalamic MicroRNAs as Novel Partners Involved in Timing the Rapid Development of Chicken (Gallus gallus) Gonads.

    Science.gov (United States)

    Han, Wei; Zou, Jianmin; Wang, Kehua; Su, Yijun; Zhu, Yunfen; Song, Chi; Li, Guohui; Qu, Liang; Zhang, Huiyong; Liu, Honglin

    2015-01-01

    Onset of the rapid gonad growth is a milestone in sexual development that comprises many genes and regulatory factors. The observations in model organisms and mammals including humans have shown a potential link between miRNAs and development timing. To determine whether miRNAs play roles in this process in the chicken (Gallus gallus), the Solexa deep sequencing was performed to analyze the profiles of miRNA expression in the hypothalamus of hens from two different pubertal stages, before onset of the rapid gonad development (BO) and after onset of the rapid gonad development (AO). 374 conserved and 46 novel miRNAs were identified as hypothalamus-expressed miRNAs in the chicken. 144 conserved miRNAs were showed to be differentially expressed (reads > 10, P 4.0, P rapid development of chicken gonads. Considering the characteristics of miRNA functional conservation, the results will contribute to the research on puberty onset in humans.

  3. Don't Plan for the Unexpected: Planning Based on Plausibility Models

    DEFF Research Database (Denmark)

    Andersen, Mikkel Birkegaard; Bolander, Thomas; Jensen, Martin Holm

    2015-01-01

    We present a framework for automated planning based on plausibility models, as well as algorithms for computing plans in this framework. Our plausibility models include postconditions, as ontic effects are essential for most planning purposes. The framework presented extends a previously developed...... framework based on dynamic epistemic logic (DEL), without plausibilities/beliefs. In the pure epistemic framework, one can distinguish between strong and weak epistemic plans for achieving some, possibly epistemic, goal. By taking all possible outcomes of actions into account, a strong plan guarantees...... that the agent achieves this goal. Conversely, a weak plan promises only the possibility of leading to the goal. In real-life planning scenarios where the planning agent is faced with a high degree of uncertainty and an almost endless number of possible exogenous events, strong epistemic planning...

  4. Inference and Plausible Reasoning in a Natural Language Understanding System Based on Object-Oriented Semantics

    CERN Document Server

    Ostapov, Yuriy

    2012-01-01

    Algorithms of inference in a computer system oriented to input and semantic processing of text information are presented. Such inference is necessary for logical questions when the direct comparison of objects from a question and database can not give a result. The following classes of problems are considered: a check of hypotheses for persons and non-typical actions, the determination of persons and circumstances for non-typical actions, planning actions, the determination of event cause and state of persons. To form an answer both deduction and plausible reasoning are used. As a knowledge domain under consideration is social behavior of persons, plausible reasoning is based on laws of social psychology. Proposed algorithms of inference and plausible reasoning can be realized in computer systems closely connected with text processing (criminology, operation of business, medicine, document systems).

  5. The semiosis of prayer and the creation of plausible fictional worlds

    Directory of Open Access Journals (Sweden)

    J. Peter Södergård

    1999-01-01

    Full Text Available Prayer and incantation can perhaps be said to be 'mechanisms' that promise that lack will be liquidated and that there is an unlimited signator, a father, or some other metaphysical creature, standing behind and legitimizing the discourse. A way of communicating with the Unlimited that is privileged by an interpretive community that read the prayers aloud and enacted the magical stage-scripts. These highly overlapping categories function as one of the most common subforms of religious discourse for the creation, actualization and maintenance of plausible fictional worlds. They are liminal and transitional mechanisms that manipulate an empirical reader to phase-shift from an actual world to a plausible, by being inscribed in a possible and fictional world, thus creating a model reader, that perceives and acts according to the plausible world outlined by a given interpretive community, and that hears god talking in voces magicae and in god-speaking silence.

  6. Don't Plan for the Unexpected: Planning Based on Plausibility Models

    DEFF Research Database (Denmark)

    Andersen, Mikkel Birkegaard; Bolander, Thomas; Jensen, Martin Holm

    2015-01-01

    that the agent achieves this goal. Conversely, a weak plan promises only the possibility of leading to the goal. In real-life planning scenarios where the planning agent is faced with a high degree of uncertainty and an almost endless number of possible exogenous events, strong epistemic planning......We present a framework for automated planning based on plausibility models, as well as algorithms for computing plans in this framework. Our plausibility models include postconditions, as ontic effects are essential for most planning purposes. The framework presented extends a previously developed...... framework based on dynamic epistemic logic (DEL), without plausibilities/beliefs. In the pure epistemic framework, one can distinguish between strong and weak epistemic plans for achieving some, possibly epistemic, goal. By taking all possible outcomes of actions into account, a strong plan guarantees...

  7. A plausible (overlooked) super-luminous supernova in the Sloan digital sky survey stripe 82 data

    Energy Technology Data Exchange (ETDEWEB)

    Kostrzewa-Rutkowska, Zuzanna; Kozłowski, Szymon; Wyrzykowski, Łukasz [Warsaw University Observatory, Al. Ujazdowskie 4, 00-478 Warszawa (Poland); Djorgovski, S. George; Mahabal, Ashish A. [California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125 (United States); Glikman, Eilat [Department of Physics and Yale Center for Astronomy and Astrophysics, Yale University, P.O. Box 208121, New Haven, CT 06520-8121 (United States); Koposov, Sergey, E-mail: zkostrzewa@astrouw.edu.pl, E-mail: simkoz@astrouw.edu.pl, E-mail: wyrzykow@astrouw.edu.pl [Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HA (United Kingdom)

    2013-12-01

    We present the discovery of a plausible super-luminous supernova (SLSN), found in the archival data of Sloan Digital Sky Survey (SDSS) Stripe 82, called PSN 000123+000504. The supernova (SN) peaked at m {sub g} < 19.4 mag in the second half of 2005 September, but was missed by the real-time SN hunt. The observed part of the light curve (17 epochs) showed that the rise to the maximum took over 30 days, while the decline time lasted at least 70 days (observed frame), closely resembling other SLSNe of SN 2007bi type. The spectrum of the host galaxy reveals a redshift of z = 0.281 and the distance modulus of μ = 40.77 mag. Combining this information with the SDSS photometry, we found the host galaxy to be an LMC-like irregular dwarf galaxy with an absolute magnitude of M{sub B} = –18.2 ± 0.2 mag and an oxygen abundance of 12+log [O/H]=8.3±0.2; hence, the SN peaked at M {sub g} < –21.3 mag. Our SLSN follows the relation for the most energetic/super-luminous SNe exploding in low-metallicity environments, but we found no clear evidence for SLSNe to explode in low-luminosity (dwarf) galaxies only. The available information on the PSN 000123+000504 light curve suggests the magnetar-powered model as a likely scenario of this event. This SLSN is a new addition to a quickly growing family of super-luminous SNe.

  8. Development of a Rapid Real-Time PCR Assay for Quantitation of Pneumocystis carinii f. sp. Carinii

    DEFF Research Database (Denmark)

    Larsen, Hans Henrik; Kovacs, Joseph A; Stock, Frida

    2002-01-01

    A method for reliable quantification of Pneumocystis carinii in research models of P. carinii pneumonia (PCP) that is more convenient and reproducible than microscopic enumeration of organisms would greatly facilitate investigations of this organism. We developed a rapid quantitative touchdown (QTD....... In conclusion, a rapid, sensitive, and reproducible quantitative PCR assay for P. carinii f. sp. carinii has been developed and is applicable to in vivo as well as in vitro systems. The assay should prove useful for conducting studies in which quantification of organism burden or growth assessment is critical...

  9. Real-time reverse-transcriptase polymerase chain reaction for the rapid detection of Salmonella using invA primers.

    Science.gov (United States)

    D'Souza, Doris H; Critzer, Faith J; Golden, David A

    2009-11-01

    Recent outbreaks of Salmonella linked to fresh produce emphasize the need for rapid detection methods to help control the spread of disease. Reverse-transcriptase polymerase chain reaction (RT-PCR) can detect the presence of mRNA (shorter half-life than DNA) with greater potential for detecting viable pathogens. The chromosomally located invA gene required for host invasion by Salmonella is widely used for detection of this pathogen by PCR. Detection of Salmonella was undertaken by real-time RT-PCR (rt-RT-PCR) using newly designed invA gene primers to develop a sensitive and specific assay. Salmonella serovars Typhimurium and Enteritidis were grown (7.68 log(10) CFU/mL) in Luria-Bertani broth overnight at 37 degrees C, and RNA was extracted, followed by rt-RT-PCR with and without SYBR green I and agarose gel electrophoresis. All experiments were replicated at least thrice. Detection for both serovars using traditional RT-PCR was lower ( approximately 10(5) CFU/mL) than rt-RT-PCR (10(3) CFU/mL) by gel electrophoresis. Melt curve analysis showed melt temperatures at 87.5 degrees C with Ct values from 12 to 15 for up to 10(3) CFU/mL and improved to 10(2) CFU/mL after further optimization. Further, addition of RNA internal amplification control constructed using in vitro transcription with a T7 RNA polymerase promoter, to the RT-PCR assay also gave detection limits of 10(2) CFU/mL. Cross-reactivity was not observed against a panel of 21 non-Salmonella bacteria. Heat-inactivated (autoclaved) Salmonella showed faint or no detection by rt-RT-PCR or gel electrophoresis. This method has potential to be applied for the detection of Salmonella serovars in fresh produce and the simultaneous detection of foodborne viral (RNA viruses) and bacterial pathogens in a multiplex format.

  10. Development of a Rapid Real-Time PCR Assay for Quantitation of Pneumocystis carinii f. sp. Carinii

    DEFF Research Database (Denmark)

    Larsen, Hans Henrik; Kovacs, Joseph A; Stock, Frida

    2002-01-01

    . In conclusion, a rapid, sensitive, and reproducible quantitative PCR assay for P. carinii f. sp. carinii has been developed and is applicable to in vivo as well as in vitro systems. The assay should prove useful for conducting studies in which quantification of organism burden or growth assessment is critical...

  11. A SIMPLE AND RAPID MATRIX-ASSISTED LASER DESORPTION/IONIZATION TIME OF FLIGHT MASS SPECTROMETRY METHOD TO SCREEN FISH PLASMA SAMPLES FOR ESTROGEN-RESPONSIVE BIOMARKERS

    Science.gov (United States)

    In this study, we describe and evaluate the performance of a simple and rapid mass spectral method for screening fish plasma for estrogen-responsive biomarkers using matrix assisted laster desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) couopled with a short...

  12. An evaluation of a rapid real time polymerase chain reaction assay for detection of group B streptococcus as part of a neonatal group B streptococcus prevention strategy.

    Science.gov (United States)

    Money, Deborah; Dobson, Simon; Cole, Lesley; Karacabeyli, Eda; Blondel-Hill, Edith; Milner, Ruth; Thomas, Eva

    2008-09-01

    To evaluate the sensitivity, specificity, and feasibility of a rapid real-time polymerase chain reaction (PCR) test for group B streptococcus (GBS) completed during labour, compared with the standard culture test performed at 35 to 37 weeks' gestation. Women presenting to the maternity unit for term vaginal delivery had two vaginal/rectal samples collected. One swab was tested using a rapid PCR method (IDI-Strep B, Infectio Diagnostic [IDI] Inc., Sainte-Foy QC ), and the other was cultured after enrichment (intrapartum culture). Comparisons were made between these results and those of a culture-based screen at 35 to 37 weeks' gestation. Of the 190 women enrolled, 85% had results of the standard screen at 35 to 37 weeks available for comparison. The sensitivity and specificity of the standard 35- to 37-week screen were 84.3% (95% confidence interval [CI], 71.4-93.0) and 93.2% (95% CI 86.5-97.2) respectively, whereas the sensitivity and specificity of the rapid PCR were 90.7% (95% CI 79.7-96.9) and 97.6% (95% CI 93.1-99.5), respectively. The median reporting time for the rapid PCR test was 99 minutes (range 50-255). Results were available more than four hours before delivery in 81% of cases. In this Canadian centre, a rapid PCR test done at the time of labour (IDI-Strep B) demonstrated high sensitivity and specificity, comparable to the 35- to 37-week screen. The time to reporting results was acceptably short, allowing for timely administration of intrapartum prophylactic antibiotics.

  13. The Utility of Cognitive Plausibility in Language Acquisition Modeling: Evidence from Word Segmentation

    Science.gov (United States)

    Phillips, Lawrence; Pearl, Lisa

    2015-01-01

    The informativity of a computational model of language acquisition is directly related to how closely it approximates the actual acquisition task, sometimes referred to as the model's "cognitive plausibility." We suggest that though every computational model necessarily idealizes the modeled task, an informative language acquisition…

  14. The Utility of Cognitive Plausibility in Language Acquisition Modeling: Evidence from Word Segmentation

    Science.gov (United States)

    Phillips, Lawrence; Pearl, Lisa

    2015-01-01

    The informativity of a computational model of language acquisition is directly related to how closely it approximates the actual acquisition task, sometimes referred to as the model's "cognitive plausibility." We suggest that though every computational model necessarily idealizes the modeled task, an informative language acquisition…

  15. Plausible Explanation of Quantization of Intrinsic Redshift from Hall Effect and Weyl Quantization

    Directory of Open Access Journals (Sweden)

    Smarandache F.

    2006-10-01

    Full Text Available Using phion condensate model as described by Moffat [1], we consider a plausible explanation of (Tifft intrinsic redshift quantization as described by Bell [6] as result of Hall effect in rotating frame. We also discuss another alternative to explain redshift quantization from the viewpoint of Weyl quantization, which could yield Bohr- Sommerfeld quantization.

  16. “合情推理”辨析%Analysis of Plausible Reasoning

    Institute of Scientific and Technical Information of China (English)

    连四清; 方运加

    2012-01-01

    波利亚的“合情推理”模式引进我国数学课程标准后,就成了我国数学教育研究的关键词。然而,“合情推理”的科学性尚需考证:(1)它的中文意义不明确;(2)它不满足推理模式的客观性要求,存在明显的缺陷;(3)过分强调“合情推理模式”则是过分强调归纳推理和演绎推理的区别,容易割裂它们之间的关系。%After the model of "plausible inference" being introduced into the mathematics curriculum standards, it became a key word of the research on mathematics education in China. However, there are doubts on whether it is scientific. (1) Chinese meaning of plausible inference is ambiguous. (2) The plausible inference can not meet the objective requirement of the reasoning, which has obvious defects. (3) Overemphasizing the model of plausible inference would overemphasize the difference between deductive inference and inductive inference, and would dispart them.

  17. RAPID COMMUNICATION: Formation of MgB2 at ambient temperature with an electrochemical process: a plausible mechanism

    Science.gov (United States)

    Jadhav, A. B.; Subhedar, K. M.; Hyam, R. S.; Talaptra, A.; Sen, Pintu; Bandyopadhyay, S. K.; Pawar, S. H.

    2005-06-01

    The binary intermetallic MgB2 superconductor has been synthesized by many research groups. However, the mechanism of its formation is not clearly understood. In this communication, a comprehensive mechanism of the formation of MgB2 from Le Chatelier's principle of equilibrium reaction has been explained both for solid-state reaction and electrodeposition methods.

  18. Rapid and direct quantitative detection of viable bifidobacteria in probiotic yogurt by combination of ethidium monoazide and real-time PCR using a molecular beacon approach.

    Science.gov (United States)

    Meng, X C; Pang, R; Wang, C; Wang, L Q

    2010-11-01

    The potential of ethidium monoazide (EMA) real-time PCR method based on molecular beacon probe for rapid detection of viable bifidobacteria present in probiotic yogurt was evaluated in this work. A real-time PCR with molecular beacon assay was developed to determine genus Bifidobacterium quantitatively in order to increase the sensitivity and specificity of assay. EMA was used to treat probiotic yogurt prior to DNA extraction and real-time PCR detection to allow detection of only viable bacteria. The primer set of Bif-F/Bif-R which is genus-specific for Bifid. was designed. The specificity of the probes ensures that no signal is generated by non-target amplicons. Linear regression analysis demonstrated a good correlation (R² = 0·9948) between the EMA real-time PCR results and the plate counting, and real-time quantitative PCR results correlated adequately with enumeration of bifidobacteria by culture for commercial probiotic yogurt. This culture-independent approach is promising for the direct and rapid detection of viable bifidobacteria in commercial probiotic yogurt, and the detection can be carried out within 4 h. The detection limit for this method is about 10⁴ cell/ml. In conclusion, the direct quantitative EMA real-time PCR assay based on molecular beacon described in this research is a rapid and quantitative method.

  19. Rapid Blue-Carba test: reduction in the detection time of carbapenemases performed from a 4-hour bacterial lawn.

    Science.gov (United States)

    Nastro, Marcela; Ayora, Melisa; García, Susana; Vay, Carlos; Famiglietti, Ángela; Rodriguez, Carlos Hernán

    2017-06-01

    The increase in carbapenem-resistant gram-negative bacteria is a matter of concern due to the limited therapeutic options available. In severe infections caused by these isolates, the rapid detection of the mechanisms of resistance is vital. We described a slightly modified version of the Blue-Carba test, rapid Blue-Carba test, which allows the detection of carbapenemases at 4 h of incubation from a haze of bacterial growth obtained from a positive blood culture. It was able to detect carbapenemase-producing isolates (Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii) with a sensitivity and specificity of 98.1 and 100%, respectively. It is a rapid, easy-to-perform and an inexpensive technique that can be applied to routine laboratories, together with the simultaneous identification by mass spectrometry which would help to screen non-enzymatic carbapenem resistance; this method allows the detection of clinically relevant multidrug-resistant bacteria and the early implementation of accurate therapeutic interventions.

  20. Time-dependence between upper arm muscles activity during rapid movements: observation of the proportional effects predicted by the kinematic theory.

    Science.gov (United States)

    Plamondon, Réjean; Djioua, Moussa; Mathieu, Pierre A

    2013-10-01

    Rapid human movements can be assimilated to the output of a neuromuscular system with an impulse response modeled by a Delta-Lognormal equation. In such a model, the main assumption concerns the cumulative time delays of the response as it propagates toward the effector following a command. To verify the validity of this assumption, delays between bursts in electromyographic (EMG) signals of agonist and antagonist muscles activated during a rapid hand movement were investigated. Delays were measured between the surface EMG signals of six muscles of the upper limb during single rapid handwriting strokes. From EMG envelopes, regressions were obtained between the timing of the burst of activity produced by each monitored muscle. High correlation coefficients were obtained supporting the proportionality of the cumulative time delays, the basic hypothesis of the Delta-Lognormal model. A paradigm governing the sequence of muscle activities in a rapid movement could, in the long run, be useful for applications dealing with the analysis and synthesis of human movements.

  1. From bone to plausible bipedal locomotion. Part II: Complete motion synthesis for bipedal primates.

    Science.gov (United States)

    Nicolas, Guillaume; Multon, Franck; Berillon, Gilles

    2009-05-29

    This paper addresses the problem of synthesizing plausible bipedal locomotion according to 3D anatomical reconstruction and general hypotheses on human motion control strategies. In a previous paper [Nicolas, G., Multon, F., Berillon, G., Marchal, F., 2007. From bone to plausible bipedal locomotion using inverse kinematics. Journal of Biomechanics 40 (5) 1048-1057], we have validated a method based on using inverse kinematics to obtain plausible lower-limb motions knowing the trajectory of the ankle. In this paper, we propose a more general approach that also involves computing a plausible trajectory of the ankles for a given skeleton. The inputs are the anatomical descriptions of the bipedal species, imposed footprints and a rest posture. This process is based on optimizing a reference ankle trajectory until a set of criteria is minimized. This optimization loop is based on the assumption that a plausible motion is supposed to have little internal mechanical work and should be as less jerky as possible. For each tested ankle trajectory, inverse kinematics is used to compute a lower-body motion that enables us to compute the resulting mechanical work and jerk. This method was tested on a set of modern humans (male and female, with various anthropometric properties). We show that the results obtained with this method are close to experimental data for most of the subjects. We also demonstrate that the method is not sensitive to the choice of the reference ankle trajectory; any ankle trajectory leads to very similar result. We finally apply the method to a skeleton of Pan paniscus (Bonobo), and compare the resulting motion to those described by zoologists.

  2. Direct real-time PCR with ethidium monoazide: a method for the rapid detection of viable Cronobacter sakazakii in powdered infant formula.

    Science.gov (United States)

    Minami, Jun-Ichi; Soejima, Takashi; Yaeshima, Tomoko; Iwatsuki, Keiji

    2012-09-01

    The goal of this study was to establish a rapid assay for the specific detection of viable Cronobacter sakazakii in powdered infant formula (PIF). Samples were subjected to treatment multiple times with ethidium monoazide with a concentration gradient (gEMA) prior to PCR to discriminate viable from dead C. sakazakii cells. To improve the current detection limits, we developed a new buffer for direct quantitative real-time PCR (DqPCR) without DNA isolation. Using 17 PIF samples, our rapid assay was compared with the new U.S. Food and Drug Administration (FDA) method published in the Bacteriological Analytical Manual in 2012. Although both the new FDA method and our rapid assay, which consists of DqPCR combined with gEMA (gEMA-DqPCR), produced negative results for all 17 PIF samples, 5 of the 17 PIFs were positive by DqPCR when they were not treated with EMA. Furthermore, for PIF samples artificially contaminated with viable C. sakazakii, gEMA-DqPCR successfully detected between 1 and 9 CFU of viable C. sakazakii in 300 g of PIF within 9 h, including a 6-h preincubation. Our results indicate that multiple EMA treatments are required to avoid false-positive results due to the contamination of commercial PIF with dead or injured C. sakazakii cells. Our rapid assay may also improve the sensitivity of the screening portion required by the new FDA method published in the Bacteriological Analytical Manual in 2012.

  3. A CCD-based fluorescence imaging system for real-time loop-mediated isothermal amplification-based rapid and sensitive detection of waterborne pathogens on microchips.

    Science.gov (United States)

    Ahmad, Farhan; Seyrig, Gregoire; Tourlousse, Dieter M; Stedtfeld, Robert D; Tiedje, James M; Hashsham, Syed A

    2011-10-01

    Rapid, sensitive, and low-cost pathogen diagnostic systems are needed for early disease diagnosis and treatment, especially in resource-limited settings. This study reports a low-cost charge-coupled device (CCD)-based fluorescence imaging system for rapid detection of waterborne pathogens by isothermal gene amplification in disposable microchips. Fluorescence imaging capability of this monochromatic CCD camera is evaluated by optimizing the gain, offset, and exposure time. This imaging system is validated for 12 virulence genes of major waterborne pathogens on cyclic olefin polymer (COP) microchips, using SYTO-82 dye and real time fluorescence loop-mediated isothermal amplification referred here as microRT(f)-LAMP. Signal-to-noise ratio (SNR) and threshold time (Tt) of microRT(f)-LAMP assays are compared with those from a commercial real-time polymerase chain reaction (PCR) instrument. Applying a CCD exposure of 5 s to 10(5) starting DNA copies of microRT(f)-LAMP assays increases the SNR by 8-fold and reduces the Tt by 9.8 min in comparison to a commercial real-time PCR instrument. Additionally, single copy level sensitivity for Campylobacter jejuni 0414 gene is obtained for microRT(f)-LAMP with a Tt of 19 min, which is half the time of the commercial real-time PCR instrument. Due to the control over the exposure time and the wide field imaging capability of CCD, this low-cost fluorescence imaging system has the potential for rapid and parallel detection of pathogenic microorganisms in high throughput microfluidic chips.

  4. The SAFRR Tsunami Scenario: Improving Resilience for California from a Plausible M9 Earthquake near the Alaska Peninsula

    Science.gov (United States)

    Ross, S.; Jones, L.; Wilson, R. I.; Bahng, B.; Barberopoulou, A.; Borrero, J. C.; Brosnan, D.; Bwarie, J.; Geist, E. L.; Johnson, L.; Kirby, S. H.; Knight, W.; Long, K.; Lynett, P. J.; Miller, K.; Mortensen, C. E.; Nicolsky, D.; Oglesby, D. D.; Perry, S. C.; Plumlee, G. S.; Porter, K. A.; Real, C. R.; Ryan, K. J.; Suleimani, E.; Thio, H. K.; Titov, V.; Wein, A. M.; Whitmore, P.; Wood, N. J.

    2013-12-01

    The SAFRR Tsunami Scenario models a hypothetical but plausible tsunami, created by an Mw9.1 earthquake occurring offshore from the Alaskan peninsula, and its impacts on the California coast. We present the likely inundation areas, current velocities in key ports and harbors, physical damage and repair costs, economic consequences, environmental impacts, social vulnerability, emergency management, and policy implications for California associated with the tsunami scenario. The intended users are those who must make mitigation decisions before and rapid decisions during future tsunamis. Around a half million people would be present in the scenario's inundation area in residences, businesses, public venues, parks and beaches. Evacuation would likely be ordered for the State of California's maximum mapped tsunami inundation zone, evacuating an additional quarter million people from residences and businesses. Some island and peninsula communities would face particular evacuation challenges because of limited access options and short warning time, caused by the distance between Alaska and California. Evacuations may also be a challenge for certain dependent-care populations. One third of the boats in California's marinas could be damaged or sunk, costing at least 700 million in repairs to boats and docks, and potentially much more to address serious issues due to sediment transport and environmental contamination. Fires would likely start at many sites where fuel and petrochemicals are stored in ports and marinas. Tsunami surges and bores may travel several miles inland up coastal rivers. Debris clean-up and recovery of inundated and damaged areas will take days, months, or years depending on the severity of impacts and the available resources for recovery. The Ports of Los Angeles and Long Beach (POLA/LB) would be shut down for a miniμm of two days due to strong currents. Inundation of dry land in the ports would result in 100 million damages to cargo and additional

  5. Development of a Rapid Real-Time PCR Assay for Quantitation of Pneumocystis carinii f. sp. Carinii

    DEFF Research Database (Denmark)

    Larsen, Hans Henrik; Kovacs, Joseph A; Stock, Frida

    2002-01-01

    A method for reliable quantification of Pneumocystis carinii in research models of P. carinii pneumonia (PCP) that is more convenient and reproducible than microscopic enumeration of organisms would greatly facilitate investigations of this organism. We developed a rapid quantitative touchdown (QTD...... 6 log values for standards containing > or =5 copies/tube. Application of the assay to a series of 10-fold dilutions of P. carinii organisms isolated from rat lung demonstrated that it was reproducibly quantitative over 5 log values (r = 0.99). The assay was applied to a recently reported in vitro...... axenic cultivation system for P. carinii and confirmed our microscopy findings that no organism multiplication had occurred during culture. For all cultures analyzed, QTD PCR assays showed a decrease in P. carinii DNA that exceeded the expected decrease due to dilution of the inoculum upon transfer...

  6. A Novel Reverse-Transcriptase Real-Time PCR Method for Quantification of Viable Vibrio Parahemolyticus in Raw Shrimp Based on a Rapid Construction of Standard Curve Method

    OpenAIRE

    Mengtong Jin; Haiquan Liu; Wenshuo Sun; Qin Li; Zhaohuan Zhang; Jibing Li; Yingjie Pan; Yong Zhao

    2015-01-01

    Vibrio parahemolyticus is an important pathogen that leads to food illness associated seafood. Therefore, rapid and reliable methods to detect and quantify the total viable V. parahaemolyticus in seafood are needed. In this assay, a RNA-based real-time reverse-transcriptase PCR (RT-qPCR) without an enrichment step has been developed for detection and quantification of the total viable V. parahaemolyticus in shrimp. RNA standards with the target segments were synthesized in vitro with T7 RNA p...

  7. Identifying plausible genetic models based on association and linkage results: application to type 2 diabetes.

    Science.gov (United States)

    Guan, Weihua; Boehnke, Michael; Pluzhnikov, Anna; Cox, Nancy J; Scott, Laura J

    2012-12-01

    When planning resequencing studies for complex diseases, previous association and linkage studies can constrain the range of plausible genetic models for a given locus. Here, we explore the combinations of causal risk allele frequency (RAFC ) and genotype relative risk (GRRC ) consistent with no or limited evidence for affected sibling pair (ASP) linkage and strong evidence for case-control association. We find that significant evidence for case-control association combined with no or moderate evidence for ASP linkage can define a lower bound for the plausible RAFC . Using data from large type 2 diabetes (T2D) linkage and genome-wide association study meta-analyses, we find that under reasonable model assumptions, 23 of 36 autosomal T2D risk loci are unlikely to be due to causal variants with combined RAFC < 0.005, and four of the 23 are unlikely to be due to causal variants with combined RAFC < 0.05.

  8. Acquiring Plausible Predications from MEDLINE by Clustering MeSH Annotations.

    Science.gov (United States)

    Miñarro-Giménez, Jose Antonio; Kreuzthaler, Markus; Bernhardt-Melischnig, Johannes; Martínez-Costa, Catalina; Schulz, Stefan

    2015-01-01

    The massive accumulation of biomedical knowledge is reflected by the growth of the literature database MEDLINE with over 23 million bibliographic records. All records are manually indexed by MeSH descriptors, many of them refined by MeSH subheadings. We use subheading information to cluster types of MeSH descriptor co-occurrences in MEDLINE by processing co-occurrence information provided by the UMLS. The goal is to infer plausible predicates to each resulting cluster. In an initial experiment this was done by grouping disease-pharmacologic substance co-occurrences into six clusters. Then, a domain expert manually performed the assignment of meaningful predicates to the clusters. The mean accuracy of the best ten generated biomedical facts of each cluster was 85%. This result supports the evidence of the potential of MeSH subheadings for extracting plausible medical predications from MEDLINE.

  9. Spelling in oral deaf and hearing dyslexic children: A comparison of phonologically plausible errors.

    Science.gov (United States)

    Roy, P; Shergold, Z; Kyle, F E; Herman, R

    2014-11-01

    A written single word spelling to dictation test and a single word reading test were given to 68 severe-profoundly oral deaf 10-11-year-old children and 20 hearing children with a diagnosis of dyslexia. The literacy scores of the deaf children and the hearing children with dyslexia were lower than expected for children of their age and did not differ from each other. Three quarters of the spelling errors of hearing children with dyslexia compared with just over half the errors of the oral deaf group were phonologically plausible. Expressive vocabulary and speech intelligibility predicted the percentage of phonologically plausible errors in the deaf group only. Implications of findings for the phonological decoding self-teaching model and for supporting literacy development are discussed.

  10. Of paradox and plausibility: the dynamic of change in medical law.

    Science.gov (United States)

    Harrington, John

    2014-01-01

    This article develops a model of change in medical law. Drawing on systems theory, it argues that medical law participates in a dynamic of 'deparadoxification' and 'reparadoxification' whereby the underlying contingency of the law is variously concealed through plausible argumentation, or revealed by critical challenge. Medical law is, thus, thoroughly rhetorical. An examination of the development of the law on abortion and on the sterilization of incompetent adults shows that plausibility is achieved through the deployment of substantive common sense and formal stylistic devices. It is undermined where these elements are shown to be arbitrary and constructed. In conclusion, it is argued that the politics of medical law are constituted by this antagonistic process of establishing and challenging provisionally stable normative regimes.

  11. Clinical evaluation of β-tubulin real-time PCR for rapid diagnosis of dermatophytosis, a comparison with mycological methods.

    Science.gov (United States)

    Motamedi, Marjan; Mirhendi, Hossein; Zomorodian, Kamiar; Khodadadi, Hossein; Kharazi, Mahboobeh; Ghasemi, Zeinab; Shidfar, Mohammad Reza; Makimura, Koichi

    2017-10-01

    Following our previous report on evaluation of the beta tubulin real-time PCR for detection of dermatophytosis, this study aimed to compare the real-time PCR assay with conventional methods for the clinical assessment of its diagnostic performance. Samples from a total of 853 patients with suspected dermatophyte lesions were subjected to direct examination (all samples), culture (499 samples) and real-time PCR (all samples). Fungal DNA was extracted directly from clinical samples using a conical steel bullet, followed by purification with a commercial kit and subjected to the Taq-Man probe-based real-time PCR. The study showed that among the 499 specimens for which all three methods were used, 156 (31.2%), 128 (25.6%) and 205 (41.0%) were found to be positive by direct microscopy, culture and real-time PCR respectively. Real-time PCR significantly increased the detection rate of dermatophytes compared with microscopy (288 vs 229) with 87% concordance between the two methods. The sensitivity, specificity, positive predictive value, and negative predictive value of the real-time PCR was 87.5%, 85%, 66.5% and 95.2% respectively. Although real-time PCR performed better on skin than on nail samples, it should not yet fully replace conventional diagnosis. © 2017 Blackwell Verlag GmbH.

  12. Rapid analysis of Delta-9-tetrahydrocannabinol in hair using direct analysis in real time ambient ionization orbitrap mass spectrometry

    NARCIS (Netherlands)

    Duvivier, W.F.; Beek, van T.A.; Pennings, E.J.M.; Nielen, M.W.F.

    2014-01-01

    RATIONALE - Forensic hair analysis methods are laborious, time-consuming and provide only a rough retrospective estimate of the time of drug intake. Recently, hair imaging methods using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) were reported, but these methods require

  13. Engineering aspects and time effects of rapid deterioration of sandstone in the tropical environment of Sabah, Malaysia

    NARCIS (Netherlands)

    Tating, Frederick; Hack, Robert; Jetten, Victor

    2013-01-01

    Cut slopes in rock masses start to deteriorate directly after excavation due to stress relief and weathering. The deterioration is a time dependent process that depends on the local climate and the rock mass including its history, and the environment. The amount of deterioration per time unit (‘the

  14. On the plausible association between environmental conditions and human eye damage.

    Science.gov (United States)

    Feretis, Elias; Theodorakopoulos, Panagiotis; Varotsos, Costas; Efstathiou, Maria; Tzanis, Christos; Xirou, Tzina; Alexandridou, Nancy; Aggelou, Michael

    2002-01-01

    The increase in solar ultraviolet radiation can have various direct and indirect effects on human health, like the incidence of ocular damage. Data of eye damage in residents of three suburban regions in Greece and in two groups of monks/nuns and fishermen are examined here. The statistics performed on these data provides new information about the plausible association between increased levels of solar ultraviolet radiation, air-pollution at ground level, and the development of ocular defects.

  15. Plausibility check of a redesigned rain-on-snow simulator (RASA)

    Science.gov (United States)

    Rössler, Ole; Probst, Sabine; Weingartner, Rolf

    2016-04-01

    Rain-on-snow events are fascinating but still not completely understood processes. Although, several studies and equations have been published since decades that describe past events and theoretical descriptions, empirical data of what is happening in the snow cover is far less available. A way to fill this gap of empirical data, rain-on-snow-simulators might be of help. In 2013, Juras et al. published their inspiring idea of a portable rain-on-snow simulator. The huge advantage of this devise - in contrast to other purely field-based experiments - are their fixed, and mostly standardized conditions and the possibility to measure all required data to monitor the water fluxes and melting processes at a time. Mounted in a convenient location, a large number of experiments are relatively easy conductible. We applied and further developed the original device and plausified the results of this redesigned version, called RASA. The principal design was borrowed from the original version being a frame with a sprinkler on top and a snow sample in a box at the bottom, from which the outflow is measured with a tipping gauge. We added a moving sprinkling plate to ensure a uniform distribution of raindrops on the snow, and - most importantly - we suspended the watered snow sampled on weighting cells. The latter enables to continuous measurement of the snow sample throughout the experiment and thus the indirect quantification of liquid water saturation, water holding capacity, and snowmelt amount via balance equations. As it is remains unclear if this device is capable to reproduce known processes, a hypothesis based plausibility check was accomplished. Thus, eight hypothesizes were derived from literature and tested in 28 experiments with the RASA mounted at 2000 m elevation. In general, we were able to reproduce most of the hypotheses. The RASA proved to be a very valuable device that can generate suitable results and has the potential to extend the empirical-experimental data

  16. What happened (and what didn't): Discourse constraints on encoding of plausible alternatives.

    Science.gov (United States)

    Fraundorf, Scott H; Benjamin, Aaron S; Watson, Duane G

    2013-10-01

    Three experiments investigated how font emphasis influences reading and remembering discourse. Although past work suggests that contrastive pitch contours benefit memory by promoting encoding of salient alternatives, it is unclear both whether this effect generalizes to other forms of linguistic prominence and how the set of alternatives is constrained. Participants read discourses in which some true propositions had salient alternatives (e.g., British scientists found the endangered monkey when the discourse also mentioned French scientists) and completed a recognition memory test. In Experiments 1 and 2, font emphasis in the initial presentation increased participants' ability to later reject false statements about salient alternatives but not about unmentioned items (e.g., Portuguese scientists). In Experiment 3, font emphasis helped reject false statements about plausible alternatives, but not about less plausible alternatives that were nevertheless established in the discourse. These results suggest readers encode a narrow set of only those alternatives plausible in the particular discourse. They also indicate that multiple manipulations of linguistic prominence, not just prosody, can lead to consideration of alternatives.

  17. Improved layer-based method for rapid hologram generation and real-time interactive holographic display applications.

    Science.gov (United States)

    Chen, J-S; Chu, D P

    2015-07-13

    Layer-based method has been proposed as an efficient approach to calculate holograms for holographic image display. This paper further improves its calculation speed and depth cues quality by introducing three different techniques, an improved coding scheme, a multilayer depth- fused 3D method and a fraction method. As a result the total computation time is reduced more than 4 times, and holographic images with accommodation cue are calculated in real time to interactions with the displayed image in a proof-of-concept setting of head-mounted holographic displays.

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

    Science.gov (United States)

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

    2012-11-01

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

  19. Rapid direct detection of multiple rifampin and isoniazid resistance mutations in Mycobacterium tuberculosis in respiratory samples by real-time PCR.

    Science.gov (United States)

    Marín, Mercedes; García de Viedma, Darío; Ruíz-Serrano, María Jesús; Bouza, Emilio

    2004-11-01

    Rapid detection of resistance in Mycobacterium tuberculosis can optimize the efficacy of antituberculous therapy and control the transmission of resistant M. tuberculosis strains. Real-time PCR has minimized the time required to obtain the susceptibility pattern of M. tuberculosis strains, but little effort has been made to adapt this rapid technique to the direct detection of resistance from clinical samples. In this study, we adapted and evaluated a real-time PCR design for direct detection of resistance mutations in clinical respiratory samples. The real-time PCR was evaluated with (i) 11 clinical respiratory samples harboring bacilli resistant to isoniazid (INH) and/or rifampin (RIF), (ii) 10 culture-negative sputa spiked with a set of strains encoding 14 different resistance mutations in 10 independent codons, and (iii) 16 sputa harboring susceptible strains. The results obtained with this real-time PCR design completely agreed with DNA sequencing data. In all sputa harboring resistant M. tuberculosis strains, the mutation encoding resistance was successfully detected. No mutation was detected in any of the susceptible sputa. The test was applied only to smear-positive specimens and succeeded in detecting a bacterial load equivalent to 10(3) CFU/ml in sputum samples (10 acid-fast bacilli/line). The analytical specificity of this method was proved with a set of 14 different non-M. tuberculosis bacteria. This real-time PCR design is an adequate method for the specific and rapid detection of RIF and INH resistance in smear-positive clinical respiratory samples.

  20. A method to rapidly determine the sintering process parameters of powder metallurgy by real-time resistivity monitoring

    Science.gov (United States)

    Xiao, Zhen; Liu, Huanchao; Geng, Haoran; Leng, Jinfeng

    2016-10-01

    A new method, which is called the resistivity method, is applied in this paper to explore the optimum sintering parameters of powder metallurgy (PM) since general methods are always labor-intensive and time-consuming. This method can probe the resistivity of the powder metallurgy samples in real-time during the sintering process, to quickly estimate the change of the relative density, which consequently determine the properties of the sintered item. As an example, in this paper, copper/tungsten carbide (Cu/WC) composites and pure aluminum (Al) powder compacts are experimentally considered. As a result, for the Cu/WC composites, the highest value of relative density appeared at the holding time of 50 min where the sample has the lowest resistivity. For the Al compacts, the optimum sintering temperature is 450 °C, and the longer the holding time the better.

  1. Ebola Virus Disease: Rapid Diagnosis and Timely Case Reporting are Critical to the Early Response for Outbreak Control.

    Science.gov (United States)

    Stamm, Lola V

    2015-09-01

    Ebola virus disease (EVD) is a life-threatening zoonosis caused by infection with the Ebola virus. Since the first reported EVD outbreak in the Democratic Republic of the Congo, several small outbreaks have been reported in central Africa with about 2,400 cases occurring between 1976 and 2013. The 2013-2015 EVD outbreak in west Africa is the first documented outbreak in this region and the largest ever with over 27,000 cases and more than 11,000 deaths. Although EVD transmission rates have recently decreased in west Africa, this crisis continues to threaten global health and security, particularly since infected travelers could spread EVD to other resource-limited areas of the world. Because vaccines and drugs are not yet licensed for EVD, outbreak control is dependent on the use of non-pharmaceutical interventions (e.g., infection control practices, isolation of EVD cases, contact tracing with follow-up and quarantine, sanitary burial, health education). However, delays in diagnosing and reporting EVD cases in less accessible rural areas continue to hamper control efforts. New advances in rapid diagnostics for identifying presumptive EVD cases and in mobile-based technologies for communicating critical health-related information should facilitate deployment of an early response to prevent the amplification of sporadic EVD cases into large-scale outbreaks. © The American Society of Tropical Medicine and Hygiene.

  2. Detection of malaria infection in blood transfusion: a comparative study among real-time PCR, rapid diagnostic test and microscopy: sensitivity of Malaria detection methods in blood transfusion.

    Science.gov (United States)

    Hassanpour, Gholamreza; Mohebali, Mehdi; Raeisi, Ahmad; Abolghasemi, Hassan; Zeraati, Hojjat; Alipour, Mohsen; Azizi, Ebrahim; Keshavarz, Hossein

    2011-06-01

    The transmission of malaria by blood transfusion was one of the first transfusion-transmitted infections recorded in the world. Transfusion-transmitted malaria may lead to serious problems because infection with Plasmodium falciparum may cause rapidly fatal death. This study aimed to compare real-time polymerase chain reaction (real-time PCR) with rapid diagnostic test (RDT) and light microscopy for the detection of Plasmodium spp. in blood transfusion, both in endemic and non-endemic areas of malaria disease in Iran. Two sets of 50 blood samples were randomly collected. One set was taken from blood samples donated in blood bank of Bandar Abbas, a city located in a malarious-endemic area, and the other set from Tehran, a non-endemic one. Light microscopic examination on both thin and thick smears, RDTs, and real-time PCR were performed on the blood samples and the results were compared. Thin and thick light microscopic examinations of all samples as well as RDT results were negative for Plasmodium spp. Two blood samples from endemic area were positive only with real-time PCR. It seems that real-time PCR as a highly sensitive method can be helpful for the confirmation of malaria infection in different units of blood transfusion organization especially in malaria-endemic areas where the majority of donors may be potentially infected with malaria parasites.

  3. The Application of Gas Dwell Time Control for Rapid Single Wall Carbon Nanotube Forest Synthesis to Acetylene Feedstock

    Directory of Open Access Journals (Sweden)

    Naoyuki Matsumoto

    2015-07-01

    Full Text Available One aspect of carbon nanotube (CNT synthesis that remains an obstacle to realize industrial mass production is the growth efficiency. Many approaches have been reported to improve the efficiency, either by lengthening the catalyst lifetime or by increasing the growth rate. We investigated the applicability of dwell time and carbon flux control to optimize yield, growth rate, and catalyst lifetime of water-assisted chemical vapor deposition of single-walled carbon nanotube (SWCNT forests using acetylene as a carbon feedstock. Our results show that although acetylene is a precursor to CNT synthesis and possesses a high reactivity, the SWCNT forest growth efficiency is highly sensitive to dwell time and carbon flux similar to ethylene. Through a systematic study spanning a wide range of dwell time and carbon flux levels, the relationship of the height, growth rate, and catalyst lifetime is found. Further, for the optimum conditions for 10 min growth, SWCNT forests with ~2500 μm height, ~350 μm/min initial growth rates and extended lifetimes could be achieved by increasing the dwell time to ~5 s, demonstrating the generality of dwell time control to highly reactive gases.

  4. The Application of Gas Dwell Time Control for Rapid Single Wall Carbon Nanotube Forest Synthesis to Acetylene Feedstock

    Science.gov (United States)

    Matsumoto, Naoyuki; Oshima, Azusa; Sakurai, Shunsuke; Yamada, Takeo; Yumura, Motoo; Hata, Kenji; Futaba, Don N.

    2015-01-01

    One aspect of carbon nanotube (CNT) synthesis that remains an obstacle to realize industrial mass production is the growth efficiency. Many approaches have been reported to improve the efficiency, either by lengthening the catalyst lifetime or by increasing the growth rate. We investigated the applicability of dwell time and carbon flux control to optimize yield, growth rate, and catalyst lifetime of water-assisted chemical vapor deposition of single-walled carbon nanotube (SWCNT) forests using acetylene as a carbon feedstock. Our results show that although acetylene is a precursor to CNT synthesis and possesses a high reactivity, the SWCNT forest growth efficiency is highly sensitive to dwell time and carbon flux similar to ethylene. Through a systematic study spanning a wide range of dwell time and carbon flux levels, the relationship of the height, growth rate, and catalyst lifetime is found. Further, for the optimum conditions for 10 min growth, SWCNT forests with ~2500 μm height, ~350 μm/min initial growth rates and extended lifetimes could be achieved by increasing the dwell time to ~5 s, demonstrating the generality of dwell time control to highly reactive gases.

  5. Rapid Characterization of Microalgae and Microalgae Mixtures Using Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS)

    Science.gov (United States)

    Barbano, Duane; Diaz, Regina; Zhang, Lin; Sandrin, Todd; Gerken, Henri; Dempster, Thomas

    2015-01-01

    Current molecular methods to characterize microalgae are time-intensive and expensive. Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) may represent a rapid and economical alternative approach. The objectives of this study were to determine whether MALDI-TOF MS can be used to: 1) differentiate microalgae at the species and strain levels and 2) characterize simple microalgal mixtures. A common protein extraction sample preparation method was used to facilitate rapid mass spectrometry-based analysis of 31 microalgae. Each yielded spectra containing between 6 and 56 peaks in the m/z 2,000 to 20,000 range. The taxonomic resolution of this approach appeared higher than that of 18S rDNA sequence analysis. For example, two strains of Scenedesmus acutus differed only by two 18S rDNA nucleotides, but yielded distinct MALDI-TOF mass spectra. Mixtures of two and three microalgae yielded relatively complex spectra that contained peaks associated with members of each mixture. Interestingly, though, mixture-specific peaks were observed at m/z 11,048 and 11,230. Our results suggest that MALDI-TOF MS affords rapid characterization of individual microalgae and simple microalgal mixtures. PMID:26271045

  6. Duplex real-time PCR for rapid simultaneous detection of Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans in Amphibian samples.

    Science.gov (United States)

    Blooi, M; Pasmans, F; Longcore, J E; Spitzen-van der Sluijs, A; Vercammen, F; Martel, A

    2013-12-01

    Chytridiomycosis is a lethal fungal disease contributing to declines and extinctions of amphibian species worldwide. The currently used molecular screening tests for chytridiomycosis fail to detect the recently described species Batrachochytrium salamandrivorans. In this study, we present a duplex real-time PCR that allows the simultaneous detection of B. salamandrivorans and Batrachochytrium dendrobatidis. With B. dendrobatidis- and B. salamandrivorans-specific primers and probes, detection of the two pathogens in amphibian samples is possible, with a detection limit of 0.1 genomic equivalent of zoospores of both pathogens per PCR. The developed real-time PCR shows high degrees of specificity and sensitivity, high linear correlations (r(2) > 0.995), and high amplification efficiencies (>94%) for B. dendrobatidis and B. salamandrivorans. In conclusion, the described duplex real-time PCR can be used to detect DNA of B. dendrobatidis and B. salamandrivorans with highly reproducible and reliable results.

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

    Science.gov (United States)

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

    2012-09-01

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

  8. Development of a Real-Time PCR Method (Taqman) for Rapid Identification and Quantification of Prorocentrum donghaiense

    Institute of Scientific and Technical Information of China (English)

    YUAN Jian; MI Tiezhu; ZHEN Yu; YU Zhigang

    2012-01-01

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

  9. Rapid DNA extraction protocol for detection of alpha-1 antitrypsin deficiency from dried blood spots by real-time PCR.

    Science.gov (United States)

    Struniawski, R; Szpechcinski, A; Poplawska, B; Skronski, M; Chorostowska-Wynimko, J

    2013-01-01

    The dried blood spot (DBS) specimens have been successfully employed for the large-scale diagnostics of α1-antitrypsin (AAT) deficiency as an easy to collect and transport alternative to plasma/serum. In the present study we propose a fast, efficient, and cost effective protocol of DNA extraction from dried blood spot (DBS) samples that provides sufficient quantity and quality of DNA and effectively eliminates any natural PCR inhibitors, allowing for successful AAT genotyping by real-time PCR and direct sequencing. DNA extracted from 84 DBS samples from chronic obstructive pulmonary disease patients was genotyped for AAT deficiency variants by real-time PCR. The results of DBS AAT genotyping were validated by serum IEF phenotyping and AAT concentration measurement. The proposed protocol allowed successful DNA extraction from all analyzed DBS samples. Both quantity and quality of DNA were sufficient for further real-time PCR and, if necessary, for genetic sequence analysis. A 100% concordance between AAT DBS genotypes and serum phenotypes in positive detection of two major deficiency S- and Z- alleles was achieved. Both assays, DBS AAT genotyping by real-time PCR and serum AAT phenotyping by IEF, positively identified PI*S and PI*Z allele in 8 out of the 84 (9.5%) and 16 out of 84 (19.0%) patients, respectively. In conclusion, the proposed protocol noticeably reduces the costs and the hand-on-time of DBS samples preparation providing genomic DNA of sufficient quantity and quality for further real-time PCR or genetic sequence analysis. Consequently, it is ideally suited for large-scale AAT deficiency screening programs and should be method of choice.

  10. Multiplex Real-Time PCR Assay for Rapid Detection of Methicillin-Resistant Staphylococci Directly from Positive Blood Cultures

    OpenAIRE

    Wang, Hye-young; Kim, Sunghyun; Kim, Jungho; Park, Soon-Deok; Uh, Young; Lee, Hyeyoung

    2014-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is the most prevalent cause of bloodstream infections (BSIs) and is recognized as a major nosocomial pathogen. This study aimed to evaluate a newly designed multiplex real-time PCR assay capable of the simultaneous detection of mecA, S. aureus, and coagulase-negative staphylococci (CoNS) in blood culture specimens. The Real-MRSA and Real-MRCoNS multiplex real-time PCR assays (M&D, Republic of Korea) use the TaqMan probes 16S rRNA for Staphylo...

  11. A new real-time PCR assay for rapid identification of the S. aureus/MRSA strains

    Directory of Open Access Journals (Sweden)

    Ivan Manga

    2013-01-01

    Full Text Available The Methicillin-resistant Staphylococcus aureus (MRSA with the livestock-associated MRSA (LA-MRSA are of great interest to scientists and general public. The aim of our study was to present a new more rapid and reliable diagnostic method working on the RT-PCR platform applicable for monitoring of MRSA/S. aureus. The parallel testing of the S. aureus specific nuc gene sequence and the mecA gene sequence was utilised for this purpose. A collection of ten S. aureus/MRSA reference strains, fifteen genetically related non S. aureus reference strains and fifty-six environmental samples was employed for estimation of the assay performance and parameters. The environmental samples acquired in the Czech livestock farms were represented with the livestock and human nasal mucosae or skin swabs, the slaughter meat swabs and were chosen preferentially from individuals with previously confi rmed or suspected positive MRSA/S. aureus cases. The classic selective cultivation approach with the biochemical test and agar disk diffusion test was accepted as reference diagnostic method. As there were no culture positive samples that were negative using RT-PCR, our method featured with 100% sensitivity in comparison to reference method. The limit of detection allowed to identify from tens to hundreds copies of S. aureus/MRSA genome. Further, the RT-PCR assay featured with 100% inclusivity and 95% exclusivity at Cq value below 30. These parameters suggested on powerful and reliable diagnostic method with real potential of practical utilisation. We consider our method as ideal for testing of individual suspected colonies, when the results can be acquired in less than 1.5 hour.

  12. Rapid detection of Salmonella in raw chicken breast using real-time PCR combined with immunomagnetic separation and whole genome amplification.

    Science.gov (United States)

    Hyeon, Ji-Yeon; Deng, Xiangyu

    2017-05-01

    We presented the first attempt to combine immunomagnetic separation (IMS), whole genome amplification by multiple displacement amplification (MDA) and real-time PCR for detecting a bacterial pathogen in a food sample. This method was effective in enabling real-time PCR detection of low levels of Salmonella enterica Serotype Enteritidis (SE) (∼10 CFU/g) in raw chicken breast without culture enrichment. In addition, it was able to detect refrigeration-stressed SE cells at lower concentrations (∼0.1 CFU/g) in raw chicken breast after a 4-h culture enrichment, shortening the detection process from days to hours and displaying no statistical difference in detection rate in comparison with a culture-based detection method. By substantially improving performance in SE detection over conventional real-time PCR, we demonstrated the potential of IMS-MDA real-time PCR as a rapid, sensitive and affordable method for detecting Salmonella in food.

  13. EVALUATION OF A RAPID, QUANTITATIVE REAL-TIME PCR METHOD FOR ENUMERATION OF PATHOGENIC CANDIDA CELLS IN WATER

    Science.gov (United States)

    Quantitative Real-Time PCR (QRT-PCR) technology, incorporating fluorigenic 5' nuclease (TaqMan?) chemistry, was developed for the specific detection and quantification of six pathogenic species of Candida (C. albicans, C. tropicalis, C. krusei, C. parapsilosis, C. glabrata and C....

  14. Rapid Detection of KPC, NDM, and OXA-48-Like Carbapenemases by Real-Time PCR from Rectal Swab Surveillance Samples

    Science.gov (United States)

    Lee, Tracy D.; Adie, Kathleen; McNabb, Alan; Purych, Dale; Mannan, Kulvinder; Azana, Robert; Ng, Corrinne; Tang, Patrick

    2015-01-01

    We describe a multiplex real-time PCR assay for use on the ABI 7500 Fast TaqMan platform to detect all currently described Klebsiella pneumoniae carbapenemases (KPC), New Delhi metallo-β-lactamases (NDM), and the OXA-48-like family of carbapenemases from bacterial culture lysates or sample enrichment broth lysates. PMID:26019195

  15. Time-dependent Takagi-Taupin eikonal theory of X-ray diffraction in rapidly changing crystal structures.

    Science.gov (United States)

    Adams, Bernhard W

    2004-03-01

    The Takagi-Taupin theory is extended by synthesizing it with the eikonal theory in a unified space-time approach based upon microscopic electromagnetism. The principal goal is the description of X-ray diffraction in a crystal undergoing subpicosecond and few-femtosecond changes.

  16. High time to use rapid tests to detect multidrug resistance in sputum smear-negative tuberculosis in Belarus.

    Science.gov (United States)

    Rusovich, V; Kumar, A M V; Skrahina, A; Hurevich, H; Astrauko, A; de Colombani, P; Tayler-Smith, K; Dara, M; Zachariah, R

    2014-12-21

    Contexte : Le Belarus (Europe de l'Est) est confronté à une épidémie de tuberculose multirésistante (TB-MDR). En 2012, les patients atteints de tuberculose pulmonaire (TBP) à frottis positif ont bénéficié en priorité de diagnostics moléculaires pour confirmer une TB-MDR, tandis que les patients atteints de TBP à frottis négatif (SN-PTB) ont bénéficié de méthodes conventionnelles qui retardaient souvent le diagnostic de TB-MDR de 2 à 4 mois.Objectif : Déterminer la proportion de TB-MDR parmi les patients SN-PTB enregistrés en 2012, ainsi que les facteurs cliniques et démographiques associés.Schéma : Etude de cohorte rétrospective basée sur des données émanant de tout le pays grâce au registre électronique national de la TB.Résultats : Sur 5377 cas de TB enregistrés, 2960 (55%) étaient des SN-PTB. Parmi ces derniers, 1639 (55%) avaient une culture positive, dont 768 (47%) avaient une TB-MDR : 33% (363/1084) nouveaux cas et 73% (405/555) patients déjà traités préalablement. La notion de traitement antérieur, l'âge, la région, la résidence en milieu urbain, le statut à l'égard du virus de l'immunodéficience humaine et le fait d'être retraité étaient indépendamment associés à la TB-MDR.Conclusion : Près de la moitié des patients SN-PTB à culture positive ont une TB-MDR, et dans les cas de retraitement, on arrive à plus de sept patients sur dix. La décision politique nationale d'extension des diagnostics moléculaires rapides à tous les patients TBP, y compris les patients SN-PTB, semble donc justifiée. Il est nécessaire de prendre des mesures afin d'assurer la mise en œuvre de cette priorité urgente, en raison des implications d'un diagnostic retardé à la fois pour les patients et en termes de santé publique.

  17. Rapid motion correction in MR-guided high-intensity focused ultrasound heating using real-time ultrasound echo information.

    Science.gov (United States)

    de Oliveira, Philippe Lourenço; de Senneville, Baudouin Denis; Dragonu, Iulius; Moonen, Chrit T W

    2010-11-01

    The objective of this study was to evaluate the feasibility of integrating real-time ultrasound echo guidance in MR-guided high-intensity focused ultrasound (HIFU) heating of mobile targets in order to reduce latency between displacement analysis and HIFU treatment. Experiments on a moving phantom were carried out with MRI-guided HIFU during continuous one-dimensional ultrasound echo detection using separate HIFU and ultrasound imaging transducers. Excellent correspondence was found between MR- and ultrasound-detected displacements. Real-time ultrasound echo-based target tracking during MR-guided HIFU heating is shown with the dimensions of the heated area similar to those obtained for a static target. This work demonstrates that the combination of the two modalities opens up perspectives for motion correction in MRI-guided HIFU with negligible latency.

  18. Rapid, sensitive and real-time multiplexing platform for the analysis of protein and nucleic-acid biomarkers.

    Science.gov (United States)

    Falconnet, Didier; She, Joseph; Tornay, Raphaël; Leimgruber, Elisa; Bernasconi, David; Lagopoulos, Lucienne; Renaud, Philippe; Demierre, Nicolas; van den Bogaard, Patrick

    2015-02-03

    We describe a multiplexing technology, named Evalution, based on novel digitally encoded microparticles in microfluidic channels. Quantitative multiplexing is becoming increasingly important for research and routine clinical diagnostics, but fast, easy-to-use, flexible and highly reproducible technologies are needed to leverage the advantages of multiplexing. The presented technology has been tailored to ensure (i) short assay times and high reproducibility thanks to reaction-limited binding regime, (ii) dynamic control of assay conditions and real-time binding monitoring allowing optimization of multiple parameters within a single assay run, (iii) compatibility with various immunoassay formats such as coflowing the samples and detection antibodies simultaneously and hence simplifying workflows, (iv) analyte quantification based on initial binding rates leading to increased system dynamic range and (v) high sensitivity via enhanced fluorescence collection. These key features are demonstrated with assays for proteins and nucleic acids showing the versatility of this technology.

  19. Direct Analysis in Real Time-Mass Spectrometry for the Rapid Detection of Metabolites of Aconite Alkaloids in Intestinal Bacteria

    Science.gov (United States)

    Li, Xue; Hou, Guangyue; Xing, Junpeng; Song, Fengrui; Liu, Zhiqiang; Liu, Shuying

    2014-12-01

    In the present work, direct analysis of real time ionization combined with multi-stage tandem mass spectrometry (DART-MSn) was used to investigate the metabolic profile of aconite alkaloids in rat intestinal bacteria. A total of 36 metabolites from three aconite alkaloids were identified by using DART-MSn, and the feasibility of quantitative analysis of these analytes was examined. Key parameters of the DART ion source, such as helium gas temperature and pressure, the source-to-MS distance, and the speed of the autosampler, were optimized to achieve high sensitivity, enhance reproducibility, and reduce the occurrence of fragmentation. The instrument analysis time for one sample can be less than 10 s for this method. Compared with ESI-MS and UPLC-MS, the DART-MS is more efficient for directly detecting metabolic samples, and has the advantage of being a simple, high-speed, high-throughput method.

  20. Rapid detection of hazardous chemicals in textiles by direct analysis in real-time mass spectrometry (DART-MS).

    Science.gov (United States)

    Antal, Borbála; Kuki, Ákos; Nagy, Lajos; Nagy, Tibor; Zsuga, Miklós; Kéki, Sándor

    2016-07-01

    Residues of chemicals on clothing products were examined by direct analysis in real-time (DART) mass spectrometry. Our experiments have revealed the presence of more than 40 chemicals in 15 different clothing items. The identification was confirmed by DART tandem mass spectrometry (MS/MS) experiments for 14 compounds. The most commonly detected hazardous substances were nonylphenol ethoxylates (NPEs), phthalic acid esters (phthalates), amines released by azo dyes, and quinoline derivates. DART-MS was able to detect NPEs on the skin of the person wearing the clothing item contaminated by NPE residuals. Automated data acquisition and processing method was developed and tested for the recognition of NPE residues thereby reducing the analysis time.

  1. Thin film synthesis of SbSI micro-crystals for self-powered photodetectors with rapid time response.

    Science.gov (United States)

    Gödel, Karl C; Steiner, Ullrich

    2016-09-21

    We describe a new thin film deposition method for the growth of crystalline SbSI micro-needles via the conversion of Sb2S3 using SbI3 vapour, in a facile process that takes less than 15 minutes. These films were used to construct photodetectors in a sandwich-type architecture, which are superior to previously reported SbSI photodetectors. The devices exhibit a detectivity of D* = 10(9) Jones, a signal-to-noise ratio greater than SNR = 10(3) and a responsivity of R = 10(-5) A W(-1). In time response measurements, raise and fall times of less than 8 ms and 34 ms were determined. This manufacturing method greatly simplifies the creation of fast photodetectors.

  2. Variable angle stereo imaging for rapid patient position correction in an in-house real-time position monitoring system.

    Science.gov (United States)

    Arumugam, Sankar; Sidhom, Mark; Truant, Daniel; Xing, Aitang; Udovitch, Mark; Holloway, Lois

    2017-01-01

    To develop and validate a variable angle stereo image based position correction methodology in an X-ray based in-house online position monitoring system. A stereo imaging module that enables 3D position determination and couch correction of the patient based on images acquired at any arbitrary angle and arbitrary angular separation was developed and incorporated to the in-house SeedTracker real-time position monitoring system. The accuracy of the developed system was studied by imaging an anthropomorphic phantom implanted with radiopaque markers set to known offset positions from its reference position in an Elekta linear accelerator (LA) and associated XVI imaging system. The accuracy of the system was further validated using CBCT data set from 10 prostate SBRT patients. The time gains achieved with the stereo image based position correction was compared with the manual matching of seed positions in Digitally Reconstructed Radiographs (DRRs) and kV images in the Mosaiq record and verify system. Based on phantom and patient CBCT dataset study stereo imaging module implemented in the SeedTracker shown to have an accuracy of 0.1(σ=0.5)mm in detecting the 3D position offset. The time comparison study showed that stereo image based methodology implemented in SeedTracker was a minimum of 80(4)s faster than the manual method implemented in Mosaiq R&V system with a maximum time saving of 146(6)s. The variable angle stereo image based position correction method was shown to be accurate and faster than the standard manual DRR-kV image based correction approach, leading to more efficient treatment. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  3. Development of a multiplex real-time PCR assay for the rapid diagnosis of neonatal late onset sepsis.

    Science.gov (United States)

    van den Brand, Marre; Peters, Remco P H; Catsburg, Arnold; Rubenjan, Anna; Broeke, Ferdi J; van den Dungen, Frank A M; van Weissenbruch, Mirjam M; van Furth, A Marceline; Kõressaar, Triinu; Remm, Maido; Savelkoul, Paul H M; Bos, Martine P

    2014-11-01

    The diagnosis of late onset sepsis (LOS), a severe condition with high prevalence in preterm infants, is hampered by the suboptimal sensitivity and long turnaround time of blood culture. Detection of the infecting pathogen directly in blood by PCR would provide a much more timely result. Unfortunately, PCR-based assays reported so far are labor intensive and often lack direct species identification. Therefore we developed a real-time multiplex PCR assay tailored to LOS diagnosis which is easy-to-use, is applicable on small blood volumes and provides species-specific results within 4h. Species-specific PCR assays were selected from literature or developed using bioinformatic tools for the detection of the most prevalent etiologic pathogens: Enterococcus faecalis, Staphylococcus aureus, Staphylococcus spp., Streptococcus agalactiae, Escherichia coli, Pseudomonas aeruginosa, Klebsiella spp. and Serratia marcescens. The PCR assays showed 100% specificity, full coverage of the target pathogens and a limit of detection (LOD) of ≤10CFUeq./reaction. These LOD values were maintained in the multiplex format or when bacterial DNA was isolated from blood. Clinical evaluation showed high concordance between the multiplex PCR and blood culture. In conclusion, we developed a multiplex PCR that allows the direct detection of the most important bacterial pathogens causing LOS in preterm infants.

  4. Rapid protein global fold determination using ultrasparse sampling, high-dynamic range artifact suppression, and time-shared NOESY.

    Science.gov (United States)

    Coggins, Brian E; Werner-Allen, Jonathan W; Yan, Anthony; Zhou, Pei

    2012-11-14

    In structural studies of large proteins by NMR, global fold determination plays an increasingly important role in providing a first look at a target's topology and reducing assignment ambiguity in NOESY spectra of fully protonated samples. In this work, we demonstrate the use of ultrasparse sampling, a new data processing algorithm, and a 4-D time-shared NOESY experiment (1) to collect all NOEs in (2)H/(13)C/(15)N-labeled protein samples with selectively protonated amide and ILV methyl groups at high resolution in only four days, and (2) to calculate global folds from this data using fully automated resonance assignment. The new algorithm, SCRUB, incorporates the CLEAN method for iterative artifact removal but applies an additional level of iteration, permitting real signals to be distinguished from noise and allowing nearly all artifacts generated by real signals to be eliminated. In simulations with 1.2% of the data required by Nyquist sampling, SCRUB achieves a dynamic range over 10000:1 (250× better artifact suppression than CLEAN) and completely quantitative reproduction of signal intensities, volumes, and line shapes. Applied to 4-D time-shared NOESY data, SCRUB processing dramatically reduces aliasing noise from strong diagonal signals, enabling the identification of weak NOE crosspeaks with intensities 100× less than those of diagonal signals. Nearly all of the expected peaks for interproton distances under 5 Å were observed. The practical benefit of this method is demonstrated with structure calculations for 23 kDa and 29 kDa test proteins using the automated assignment protocol of CYANA, in which unassigned 4-D time-shared NOESY peak lists produce accurate and well-converged global fold ensembles, whereas 3-D peak lists either fail to converge or produce significantly less accurate folds. The approach presented here succeeds with an order of magnitude less sampling than required by alternative methods for processing sparse 4-D data.

  5. Rapid Protein Global Fold Determination Using Ultrasparse Sampling, High-Dynamic Range Artifact Suppression, and Time-Shared NOESY

    OpenAIRE

    Coggins, Brian E.; Werner-Allen, Jonathan W.; Yan, Anthony; Zhou, Pei

    2012-01-01

    In structural studies of large proteins by NMR, global fold determination plays an increasingly important role in providing a first look at a target’s topology and reducing assignment ambiguity in NOESY spectra of fully-protonated samples. In this work, we demonstrate the use of ultrasparse sampling, a new data processing algorithm, and a 4-D time-shared NOESY experiment (1) to collect all NOEs in 2H/13C/15N-labeled protein samples with selectively-protonated amide and ILV methyl groups at hi...

  6. Understanding Karma Police: The Perceived Plausibility of Noun Compounds as Predicted by Distributional Models of Semantic Representation

    Science.gov (United States)

    Günther, Fritz; Marelli, Marco

    2016-01-01

    Noun compounds, consisting of two nouns (the head and the modifier) that are combined into a single concept, differ in terms of their plausibility: school bus is a more plausible compound than saddle olive. The present study investigates which factors influence the plausibility of attested and novel noun compounds. Distributional Semantic Models (DSMs) are used to obtain formal (vector) representations of word meanings, and compositional methods in DSMs are employed to obtain such representations for noun compounds. From these representations, different plausibility measures are computed. Three of those measures contribute in predicting the plausibility of noun compounds: The relatedness between the meaning of the head noun and the compound (Head Proximity), the relatedness between the meaning of modifier noun and the compound (Modifier Proximity), and the similarity between the head noun and the modifier noun (Constituent Similarity). We find non-linear interactions between Head Proximity and Modifier Proximity, as well as between Modifier Proximity and Constituent Similarity. Furthermore, Constituent Similarity interacts non-linearly with the familiarity with the compound. These results suggest that a compound is perceived as more plausible if it can be categorized as an instance of the category denoted by the head noun, if the contribution of the modifier to the compound meaning is clear but not redundant, and if the constituents are sufficiently similar in cases where this contribution is not clear. Furthermore, compounds are perceived to be more plausible if they are more familiar, but mostly for cases where the relation between the constituents is less clear. PMID:27732599

  7. Rapid screening and quantification of residual pesticides and illegal adulterants in red wine by direct analysis in real time mass spectrometry.

    Science.gov (United States)

    Guo, Tianyang; Fang, Pingping; Jiang, Juanjuan; Zhang, Feng; Yong, Wei; Liu, Jiahui; Dong, Yiyang

    2016-11-04

    A rapid method to screen and quantify multi-class analytic targets in red wine has been developed by direct analysis in real time (DART) coupled with triple quadruple tandem mass spectrometry (QqQ-MS). A modified QuEChERS (Quick, Easy, Cheap, Effective, Rugged, and Safe) procedure was used for increasing analytical speed and reducing matrix effect, and the multiple reaction monitoring (MRM) in DART-MS/MS ensured accurate analysis. One bottle of wine containing 50 pesticides and 12 adulterants, i.e., preservatives, antioxidant, sweeteners, and azo dyes, could be totally determined less than 12min. This method exhibited proper linearity (R(2)≥0.99) in the range of 1-1000ng/mL for pesticides and 10-5000ng/mL for adulterants. The limits of detection (LODs) were obtained in a 0.5-50ng/mL range for pesticides and 5-50ng/mL range for adulterants, and the limits of quantification (LOQs) were in a 1-100ng/mL range for pesticides and 10-250ng/mL range for adulterants. Three spiked levels for each analyte in wine were evaluated, and the recoveries were in a scope of 75-120%. The results demonstrated DART-MS/MS was a rapid and simple method, and could be applied to rapid analyze residual pesticides and illegal adulterants in a large quantities of red wine.

  8. Novel route for rapid sol-gel synthesis of hydroxyapatite, avoiding ageing and using fast drying with a 50-fold to 200-fold reduction in process time.

    Science.gov (United States)

    Ben-Arfa, Basam A E; Salvado, Isabel M Miranda; Ferreira, José M F; Pullar, Robert C

    2017-01-01

    We have developed an innovative, rapid sol-gel method of producing hydroxyapatite nanopowders that avoids the conventional lengthy ageing and drying processes (over a week), being 200 times quicker in comparison to conventional aqueous sol-gel preparation, and 50 times quicker than ethanol based sol-gel synthesis. Two different sets of experimental conditions, in terms of pH value (5.5 and 7.5), synthesis temperature (45 and 90°C), drying temperature (60 and 80°C) and calcination temperature (400 and 700°C) were explored. The products were characterised by X-ray diffraction (XRD) Fourier-transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM) and specific surface area (SSA) measurements. Pure hydroxyapatite (Ca10(PO4)6(OH)2, HAp) was obtained for the powders synthesised at pH7.5 and calcined at 400°C, while biphasic mixtures of HAp/β-tricalcium phosphate (β-Ca3(PO4)2, TCP) were produced at pH5.5 and (pH7.5 at elevated temperature). The novel rapid drying was up to 200 times faster than conventional drying, only needing 1h with no prior ageing step, and favoured the formation of smaller/finer nanopowders, while producing pure HAp or phase mixtures virtually identical to those obtained from the slow conventional drying method, despite the absence of a slow ageing process. The products of this novel rapid process were actually shown to have smaller crystallite sizes and larger SSA, which should result in increased bioactivity.

  9. A method for rapid sampling and characterization of smokeless powder using sorbent-coated wire mesh and direct analysis in real time - mass spectrometry (DART-MS).

    Science.gov (United States)

    Li, Frederick; Tice, Joseph; Musselman, Brian D; Hall, Adam B

    2016-09-01

    Improvised explosive devices (IEDs) are often used by terrorists and criminals to create public panic and destruction, necessitating rapid investigative information. However, backlogs in many forensic laboratories resulting in part from time-consuming GC-MS and LC-MS techniques prevent prompt analytical information. Direct analysis in real time - mass spectrometry (DART-MS) is a promising analytical technique that can address this challenge in the forensic science community by permitting rapid trace analysis of energetic materials. Therefore, we have designed a qualitative analytical approach that utilizes novel sorbent-coated wire mesh and dynamic headspace concentration to permit the generation of information rich chemical attribute signatures (CAS) for trace energetic materials in smokeless powder with DART-MS. Sorbent-coated wire mesh improves the overall efficiency of capturing trace energetic materials in comparison to swabbing or vacuuming. Hodgdon Lil' Gun smokeless powder was used to optimize the dynamic headspace parameters. This method was compared to traditional GC-MS methods and validated using the NIST RM 8107 smokeless powder reference standard. Additives and energetic materials, notably nitroglycerin, were rapidly and efficiently captured by the Carbopack X wire mesh, followed by detection and identification using DART-MS. This approach has demonstrated the capability of generating comparable results with significantly reduced analysis time in comparison to GC-MS. All targeted components that can be detected by GC-MS were detected by DART-MS in less than a minute. Furthermore, DART-MS offers the advantage of detecting targeted analytes that are not amenable to GC-MS. The speed and efficiency associated with both the sample collection technique and DART-MS demonstrate an attractive and viable potential alternative to conventional techniques.

  10. Rapid "breath-print" of liver cirrhosis by proton transfer reaction time-of-flight mass spectrometry. A pilot study.

    Directory of Open Access Journals (Sweden)

    Filomena Morisco

    Full Text Available UNLABELLED: The aim of the present work was to test the potential of Proton Transfer Reaction Time-of-Flight Mass Spectrometry (PTR-ToF-MS in the diagnosis of liver cirrhosis and the assessment of disease severity by direct analysis of exhaled breath. Twenty-six volunteers have been enrolled in this study: 12 patients (M/F 8/4, mean age 70.5 years, min-max 42-80 years with liver cirrhosis of different etiologies and at different severity of disease and 14 healthy subjects (M/F 5/9, mean age 52.3 years, min-max 35-77 years. Real time breath analysis was performed on fasting subjects using a buffered end-tidal on-line sampler directly coupled to a PTR-ToF-MS. Twelve volatile organic compounds (VOCs resulted significantly differently in cirrhotic patients (CP compared to healthy controls (CTRL: four ketones (2-butanone, 2- or 3- pentanone, C8-ketone, C9-ketone, two terpenes (monoterpene, monoterpene related, four sulphur or nitrogen compounds (sulfoxide-compound, S-compound, NS-compound, N-compound and two alcohols (heptadienol, methanol. Seven VOCs (2-butanone, C8-ketone, a monoterpene, 2,4-heptadienol and three compounds containing N, S or NS resulted significantly differently in compensate cirrhotic patients (Child-Pugh A; CP-A and decompensated cirrhotic subjects (Child-Pugh B+C; CP-B+C. ROC (Receiver Operating Characteristic analysis was performed considering three contrast groups: CP vs CTRL, CP-A vs CTRL and CP-A vs CP-B+C. In these comparisons monoterpene and N-compound showed the best diagnostic performance. CONCLUSIONS: Breath analysis by PTR-ToF-MS was able to distinguish cirrhotic patients from healthy subjects and to discriminate those with well compensated liver disease from those at more advanced severity stage. A breath-print of liver cirrhosis was assessed for the first time.

  11. Grassland habitat mapping by intra-annual time series analysis - Comparison of RapidEye and TerraSAR-X satellite data

    Science.gov (United States)

    Schuster, Christian; Schmidt, Tobias; Conrad, Christopher; Kleinschmit, Birgit; Förster, Michael

    2015-02-01

    Remote sensing concepts are needed to monitor open landscape habitats for environmental change and biodiversity loss. However, existing operational approaches are limited to the monitoring of European dry heaths only. They need to be extended to further habitats. Thus far, reported studies lack the exploitation of intra-annual time series of high spatial resolution data to take advantage of the vegetations' phenological differences. In this study, we investigated the usefulness of such data to classify grassland habitats in a nature reserve area in northeastern Germany. Intra-annual time series of 21 observations were used, acquired by a multi-spectral (RapidEye) and a synthetic aperture radar (TerraSAR-X) satellite system, to differentiate seven grassland classes using a Support Vector Machine classifier. The classification accuracy was evaluated and compared with respect to the sensor type - multi-spectral or radar - and the number of acquisitions needed. Our results showed that very dense time series allowed for very high accuracy classifications (>90%) of small scale vegetation types. The classification for TerraSAR-X obtained similar accuracy as compared to RapidEye although distinctly more acquisitions were needed. This study introduces a new approach to enable the monitoring of small-scale grassland habitats and gives an estimate of the amount of data required for operational surveys.

  12. Rapid detection of foot-and-mouth disease virus, influenza A virus and classical swine fever virus by high-speed real-time RT-PCR.

    Science.gov (United States)

    Wernike, Kerstin; Beer, Martin; Hoffmann, Bernd

    2013-10-01

    High sensitivity, minor risk of cross-contamination and in particular the rapid reaction time make quantitative real-time polymerase chain reaction (qPCR) assays well suited for outbreak investigations as well as for monitoring epidemics of pathogens. In this study qPCR assays for three highly contagious animal diseases, namely foot-and-mouth-disease (FMD), influenza A (IA) and classical swine fever (CSF) have been developed. Furthermore, an amplification control targeting 18S ribosomal RNA was included. Each assay was validated with samples from infected animals using three different standard qPCR-machines in two thermal profiles: one standard and one high-speed approach, respectively. The high-speed PCR assays allowed the reliable diagnosis of FMD, influenza A and CSF in less than 28 min with an analytical sensitivity of at least 200 genome copies/μl in every case, with slight differences regarding reaction time and sensitivity for the individual PCR-cycler instruments. Therefore, the newly established rapid RT-PCR systems will be a valuable method for the monitoring and control of these three important viruses and will be a robust option for the development of novel molecular pen-side tests. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

  13. Time-resolved photoluminescence of Ga(NAsP) multiple quantum wells grown on Si substrate: Effects of rapid thermal annealing

    Energy Technology Data Exchange (ETDEWEB)

    Woscholski, R., E-mail: ronja.woscholski@physik.uni-marburg.de; Shakfa, M.K.; Gies, S.; Wiemer, M.; Rahimi-Iman, A.; Zimprich, M.; Reinhard, S.; Jandieri, K.; Baranovskii, S.D.; Heimbrodt, W.; Volz, K.; Stolz, W.; Koch, M.

    2016-08-31

    Time-resolved photoluminescence (TR-PL) spectroscopy has been used to study the impact of rapid thermal annealing (RTA) on the optical properties and carrier dynamics in Ga(NAsP) multiple quantum well heterostructures (MQWHs) grown on silicon substrates. TR-PL measurements reveal an enhancement in the PL efficiency when the RTA temperature is increased up to 925 °C. Then, the PL intensity dramatically decreases with the annealing temperature. This behavior is explained by the variation of the disorder degree in the studied structures. The analysis of the low-temperature emission-energy-dependent PL decay time enables us to characterize the disorder in the Ga(NAsP) MQWHs. The theoretically extracted energy-scales of disorder confirm the experimental observations. - Highlights: • Ga(NAsP) multiple quantum well heterostructures (MQWHs) grown on silicon substrates • Impact of rapid thermal annealing on the optical properties and carrier dynamics • Time resolved photoluminescence spectroscopy was applied. • PL transients became continuously faster with increasing annealing temperature. • Enhancement in the PL efficiency with increasing annealing temperature up to 925 °C.

  14. Urinary metabonomics of stomach cancer assessed by rapid resolution liquid chromatography/time-of-flight mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yan; REN Hui; JIANG Yang; GAO Yu-fei; LIU Shu-ying

    2013-01-01

    Background Stomach cancer is among the most commonly occurring malignancies worldwide.It would be beneficial to develop a urine-based assay whereby patients with undiagnosed stomach cancer could be screened and their cancer detected in the earliest stages.Methods A urinary metabonomics method based on ultra-performance liquid chromatography combined with quadruple time-of-flight mass spectrometry was used to analyze urine samples from patients with stomach cancer and healthy controls.Results Statistical analysis revealed a clear separation of patients and healthy controls using the aforementioned methodology.Some significantly changed metabolites were identified.Conclusions Use of the metabonomics method in patients with stomach cancer could effectively detect distinct changes in urinary metabolites and had the capacity to detect cancer; therefore,it may be a valuable tool in earlier diagnosis.Furthermore,the detection and identification of altered metabolites in the current study may help elucidate possible mechanisms involved in stomach cancer.

  15. Rapid quantitative detection of, Listeria monocytogenes in salmon products: evaluation of pre-real-time PCR strategies.

    Science.gov (United States)

    Rodríguez-Lázaro, David; Jofré, Anna; Aymerich, Teresa; Garriga, Margarita; Pla, Maria

    2005-07-01

    The spread and persistence of Listeria monocytogenes in smoked fish products and seafood processing factories are big concerns. Thus, the corresponding quality assurance programs must include adequate microbiological control measures. We evaluated eight different pre-PCR sample processing strategies to be coupled with a previously developed real-time PCR assay for the quantitative detection of L. monocytogenes in salmon products. The optimal pre-PCR procedure involved filtration and DNA purification with the use of a commercial kit. This strategy could detect 10 CFU of L. monocytogenes per g of smoked salmon and could quantify 1,000 CFU/g with excellent accuracy compared with the standard plate count method. Thus, this method could be a promising alternative for the quantitative detection of L. monocytogenes in smoked fish products and processing factories. This method could also detect the bacterium in raw salmon.

  16. MGB probe assay for rapid detection of mtDNA11778 mutation in the Chinese LHON patients by real-time PCR

    Institute of Scientific and Technical Information of China (English)

    Jian-yong WANG; Yang-shun GU; Jing WANG; Yi TONG; Ying WANG; Jun-bing SHAO; Ming QI

    2008-01-01

    Objective:Leber's hereditary optic neuropathY (LHON)is a maternally inherited degeneration of the optic nerve caused by point mutations of mitochondrial DNA(mtDNA).Many unsolved questions regarding the penetrance and pathophysiological mechanism of LHON demand efficient and reliable mutation testing.This study aims to develop a minor groove binder(MGB) probe assay for rapid detection of mtDNA11778 mutation and heteroplasmy in Chinese LHON patients by real-time polymerase chain reaction(PCR).Methods:Forty-eight patients suspected of having LHON and their maternal relatives underwent a molecular genetic evaluation,with 20 normal individuals as a control group at the same time.A real-time PCR involving two MGB probes was used to detect the mtDNA 11778 mutation and heteroplasmy.A linear standard curve was obtained by pUCmLHONG and pUCmLHONA clones.Results:All 48 LHON patients and their matemal relatives were positive for mtDNA 11778 mutation in our assay,27 heteroplasmic and 21 homoplasmic.Eighteen cases did not show an occurrence of the disease,while 9 developed the disease among the 27 heteroplasmic mutation cases.Eleven did not show an occurrence of the disease,while 10 cases developed the disease among 21 homoplasmic mutation cases.There was a significant difierence in the incidence between the heteroplasmic and the homoplasmic mutation types.The time needed for running a real-time PCR assay was only 80 min.Conclusion:This real-time PCR assay is a rapid,reliable method for mtDNA mutation detection as well as heteroplasmy quantification.Detecting this ratio is very important for predicting phenotypic expression of unaffected carriers.

  17. ‘One of the Challenges that Can Plausibly Be Raised Against Them’?

    DEFF Research Database (Denmark)

    Holtermann, Jakob v. H.

    2017-01-01

    International criminal tribunals (ICTs) are epistemic engines in the sense that they find (or claim to find) factual truths about such past events that qualify as genocide, crimes against humanity and war crimes. The value of this kind of knowledge would seem to be beyond dispute. Yet, in general...... in law is intimately connected to ordinary truth. Truth-finding capacity therefore does belong in legitimacy debates as a challenge that can plausibly be raised against them. This, in turn makes it relevant, in future research, to map, analyse and interrelate the various critiques that have been launched...

  18. A biological plausible Generalized Leaky Integrate-and-Fire neuron model.

    Science.gov (United States)

    Wang, Zhenzhong; Guo, Lilin; Adjouadi, Malek

    2014-01-01

    This study introduces a new Generalized Leaky Integrate-and-Fire (GLIF) neuron model. Unlike Normal Leaky Integrate-and-Fire (NLIF) models, the leaking resistor in the GLIF model equation is assumed to be variable, and an additional term would have the bias current added to the model equation in order to improve the accuracy. Adjusting the parameters defined for the leaking resistor and bias current, a GLIF model could be accurately matched to any Hodgkin-Huxley (HH) model and be able to reproduce plausible biological neuron behaviors.

  19. Exploring discrepancies between quantitative validation results and the geomorphic plausibility of statistical landslide susceptibility maps

    Science.gov (United States)

    Steger, Stefan; Brenning, Alexander; Bell, Rainer; Petschko, Helene; Glade, Thomas

    2016-06-01

    Empirical models are frequently applied to produce landslide susceptibility maps for large areas. Subsequent quantitative validation results are routinely used as the primary criteria to infer the validity and applicability of the final maps or to select one of several models. This study hypothesizes that such direct deductions can be misleading. The main objective was to explore discrepancies between the predictive performance of a landslide susceptibility model and the geomorphic plausibility of subsequent landslide susceptibility maps while a particular emphasis was placed on the influence of incomplete landslide inventories on modelling and validation results. The study was conducted within the Flysch Zone of Lower Austria (1,354 km2) which is known to be highly susceptible to landslides of the slide-type movement. Sixteen susceptibility models were generated by applying two statistical classifiers (logistic regression and generalized additive model) and two machine learning techniques (random forest and support vector machine) separately for two landslide inventories of differing completeness and two predictor sets. The results were validated quantitatively by estimating the area under the receiver operating characteristic curve (AUROC) with single holdout and spatial cross-validation technique. The heuristic evaluation of the geomorphic plausibility of the final results was supported by findings of an exploratory data analysis, an estimation of odds ratios and an evaluation of the spatial structure of the final maps. The results showed that maps generated by different inventories, classifiers and predictors appeared differently while holdout validation revealed similar high predictive performances. Spatial cross-validation proved useful to expose spatially varying inconsistencies of the modelling results while additionally providing evidence for slightly overfitted machine learning-based models. However, the highest predictive performances were obtained for

  20. A biologically plausible transform for visual recognition that is invariant to translation, scale and rotation

    Directory of Open Access Journals (Sweden)

    Pavel eSountsov

    2011-11-01

    Full Text Available Visual object recognition occurs easily despite differences in position, size, and rotation of the object, but the neural mechanisms responsible for this invariance are not known. We have found a set of transforms that achieve invariance in a neurally plausible way. We find that a transform based on local spatial frequency analysis of oriented segments and on logarithmic mapping, when applied twice in an iterative fashion, produces an output image that is unique to the object and that remains constant as the input image is shifted, scaled or rotated.

  1. Real-Time Earthquake Risk Mitigation Of Infrastructures Using Istanbul Earthquake Early Warning and Rapid Response Network

    Science.gov (United States)

    Zulfikar, Can; Pinar, Ali; Tunc, Suleyman; Erdik, Mustafa

    2014-05-01

    The Istanbul EEW network consisting of 10 inland and 5 OBS strong motion stations located close to the Main Marmara Fault zone is operated by KOERI. Data transmission between the remote stations and the base station at KOERI is provided both with satellite and fiber optic cable systems. The continuous on-line data from these stations is used to provide real time warning for emerging potentially disastrous earthquakes. The data transmission time from the remote stations to the KOERI data center is a few milliseconds through fiber optic lines and less than a second via satellites. The early warning signal (consisting three alarm levels) is communicated to the appropriate servo shut-down systems of the receipent facilities, that automatically decide proper action based on the alarm level. Istanbul Gas Distribution Corporation (IGDAS) is one of the end users of the EEW signal. IGDAS, the primary natural gas provider in Istanbul, operates an extensive system 9,867 km of gas lines with 550 district regulators and 474,000 service boxes. State of-the-art protection systems automatically cut natural gas flow when breaks in the pipelines are detected. Since 2005, buildings in Istanbul using natural gas are required to install seismometers that automatically cut natural gas flow when certain thresholds are exceeded. IGDAS uses a sophisticated SCADA (supervisory control and data acquisition) system to monitor the state-of-health of its pipeline network. This system provides real-time information about quantities related to pipeline monitoring, including input-output pressure, drawing information, positions of station and RTU (remote terminal unit) gates, slum shut mechanism status at 581 district regulator sites. The SCADA system of IGDAŞ receives the EEW signal from KOERI and decide the proper actions according to the previously specified ground acceleration levels. Presently, KOERI sends EEW signal to the SCADA system of IGDAS Natural Gas Network of Istanbul. The EEW signal

  2. Specialist Individuals, Generalist Populations, and Gentoo Penguin Foraging Ecology Across the Scotia Arc During a Time of Rapid Environmental Change

    Science.gov (United States)

    Herman, R.; Polito, M. J.

    2016-02-01

    Populations of Gentoo penguins (Pygoscelis papua), have increased in the Scotia arc in the last four decades, while sister species such as Chinstrap (P. antarctics) and Adélie penguins (P. adeliae) have experienced substantial declines in numbers. Previous dietary analyses suggest Gentoo penguins have a generalist foraging niche, which may help buffer them from recent climate-driven declines in key prey species, such as Antarctic krill (Euphausia superba). Ecological theory indicates that generalist populations fall under two different categories: Type A generalist populations exhibit large variation within individuals, and little variation between individuals, where Type B generalist populations are comprised of individual specialists, with large variation between individuals. It is important to identify which type of generalist population Gentoo penguins fall under, as these strategies impart differing ecological and evolutionary ramifications under times of environmental change. We conducted stable isotope analysis using tail feathers from Gentoo penguins at four breeding sites across the Scotia arc, including the Falkland Islands, South Georgia, the South Shetland Islands, and the Western Antarctic Peninsula, to assess individual variation in winter diets and determine the type of generalist strategies that Gentoo penguins utilize. Preliminary analysis indicates the presence of individual specialization within the four geographically distinct breeding colonies, suggesting that individual resilience to further shifts in food availability may vary within Gentoo penguin populations.

  3. Drug Retention Times

    Energy Technology Data Exchange (ETDEWEB)

    Center for Human Reliability Studies

    2007-05-01

    The purpose of this monograph is to provide information on drug retention times in the human body. The information provided is based on plausible illegal drug use activities that might be engaged in by a recreational drug user.

  4. Drug Retention Times

    Energy Technology Data Exchange (ETDEWEB)

    Center for Human Reliability Studies

    2007-05-01

    The purpose of this monograph is to provide information on drug retention times in the human body. The information provided is based on plausible illegal drug use activities that might be engaged in by a recreational drug user

  5. Effective Teacher Practice on the Plausibility of Human-Induced Climate Change

    Science.gov (United States)

    Niepold, F.; Sinatra, G. M.; Lombardi, D.

    2013-12-01

    Climate change education programs in the United States seek to promote a deeper understanding of the science of climate change, behavior change and stewardship, and support informed decision making by individuals, organizations, and institutions--all of which are summarized under the term 'climate literacy.' The ultimate goal of climate literacy is to enable actors to address climate change, both in terms of stabilizing and reducing emissions of greenhouse gases, but also an increased capacity to prepare for the consequences and opportunities of climate change. However, the long-term nature of climate change and the required societal response involve the changing students' ideas about controversial scientific issues which presents unique challenges for educators (Lombardi & Sinatra, 2010; Sinatra & Mason, 2008). This session will explore how the United States educational efforts focus on three distinct, but related, areas: the science of climate change, the human-climate interaction, and using climate education to promote informed decision making. Each of these approaches are represented in the Atlas of Science Literacy (American Association for the Advancement of Science, 2007) and in the conceptual framework for science education developed at the National Research Council (NRC) in 2012. Instruction to develop these fundamental thinking skills (e.g., critical evaluation and plausibility reappraisal) has been called for by the Next Generation Science Standards (NGSS) (Achieve, 2013), an innovative and research based way to address climate change education within the decentralized U.S. education system. However, the promise of the NGSS is that students will have more time to build mastery on the subjects, but the form of that instructional practice has been show to be critical. Research has show that effective instructional activities that promote evaluation of evidence improve students' understanding and acceptance toward the scientifically accepted model of human

  6. Rapid Analysis of Components in Coptis chinensis Franch by Ultra-Performance Liquid Chromatography with Quadrupole Time-of-Flight Mass Spectrometry

    Science.gov (United States)

    Tian, Peng-peng; Zhang, Xiao-xu; Wang, Hong-ping; Li, Pu-ling; Liu, Yu-xin; Li, Shao-jing

    2017-01-01

    Background: Coptis chinensis Franch is a traditional Chinese medical herb. Objective: In this article, ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry was used to rapidly, qualitatively, and comprehensively identify the components in Coptis chinensis Franch. Materials and Methods: Chromatographic separation was achieved on an Agilent Zorbax RRHD Eclipse Plus C18 column. The mobile phase consisted of 0.1% formic acid water (A) and 0.1% formic acid acetonitrile (B) with a gradient program. Qualitative analysis was performed on an Agilent 6540 quadrupole time-of-flight mass spectrometer, which was equipped with a Dual AJS ESI source operating in negative mode. Results: A total of 30 alkaloid and non-alkaloid components of Coptis chinensis Franch were identified in only 14 min. Conclusion: This study helped to provide a basis for the quality control of Coptis chinensis Franch. SUMMARY Qualitative analysis method of chlorogenic alkaloids and non-alkaloids in Coptis chinensis Franch is developed by Ultra-performance liquid chromatography with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS/MS) method.Established UPLC-Q-TOF-MS/MS analysis method is validated with rapidness and accuracy.The developed method was successfully applied for qualitative analysis of Coptis chinensis Franch sample collected from cultivation place in China. Abbreviations used: Q-TOF-MS: quadrupole time-of-flight mass spectrometry, UPLC: ultra-performance liquid chromatography, pos: positive, neg: negative. Q-TOF-MS: quadrupole time-of-flight mass spectrometry, UPLC: ultra-performance liquid chromatography, pos: positive, neg: negative. UPLC: ultra-performance liquid chromatography, pos: positive, neg: negative. pos: positive, neg: negative. neg: negative. PMID:28216903

  7. Rapid Prenatal Diagnosis of Trisomy 21 by Real-time Quantitative Polymerase Chain Reaction with Amplification of Small Tandem Repeats and S100B in Chromosome 21

    Science.gov (United States)

    Nam, Mi Suk; Yang, Eun Suk

    2005-01-01

    Trisomy 21 (Down syndrome) is the most common congenital anomaly, and it occurs in one out of 700-1000 births. Current techniques such as amniocentesis and chorionic villi sampling (CVS) require lengthy laboratory culture procedures and high costs. This study was undertaken to establish a rapid prenatal diagnosis of trisomy 21 using real-time quantitative polymerase chain reaction (PCR) of fetal DNA from amniotic fluid. Real-time quantitative PCR was performed with DNA templates obtained from 14 normal blood samples, 10 normal amniotic fluid samples, 14 Down syndrome blood samples, and 7 Down syndrome amniotic fluid samples. Primers for D21S167 and S100B of chromosome 21 were used. Primers that direct the amplification of the 165-bp fragment of the insulin-like growth factor (IGF)-1 gene on chromosome 12 using a PCR primer were included to generate an internal standard for quantitation. The relative levels of D21S167 and S100B were 2.6 and 2.4 times higher in the blood of Down syndrome patients than those in the control group. The differences between these two groups were statistically significant (p-values were 0.0012 and 0.0016, respectively). The relative levels of D21S167 and S100B were 2.1 and 2.7 times higher in the amniotic fluid of Down syndrome fetuses than those in the control group. The difference between these two groups was statistically significant (p-values were 0.0379 and 0.0379, respectively). Prenatal diagnosis of trisomy 21 by real-time quantitative PCR using STR (small tandem repeats) amplification of D21S167 and S100B is a useful, accurate and rapid diagnostic method. Furthermore, it may also be useful for prenatal diagnosis with fetal DNA from maternal blood, and for preimplantation genetic diagnosis and prenatal counseling. PMID:15861490

  8. A Biomass-based Model to Estimate the Plausibility of Exoplanet Biosignature Gases

    CERN Document Server

    Seager, S; Hu, R

    2013-01-01

    Biosignature gas detection is one of the ultimate future goals for exoplanet atmosphere studies. We have created a framework for linking biosignature gas detectability to biomass estimates, including atmospheric photochemistry and biological thermodynamics. The new framework is intended to liberate predictive atmosphere models from requiring fixed, Earth-like biosignature gas source fluxes. New biosignature gases can be considered with a check that the biomass estimate is physically plausible. We have validated the models on terrestrial production of NO, H2S, CH4, CH3Cl, and DMS. We have applied the models to propose NH3 as a biosignature gas on a "cold Haber World," a planet with a N2-H2 atmosphere, and to demonstrate why gases such as CH3Cl must have too large of a biomass to be a plausible biosignature gas on planets with Earth or early-Earth-like atmospheres orbiting a Sun-like star. To construct the biomass models, we developed a functional classification of biosignature gases, and found that gases (such...

  9. Self-assembly of phosphate amphiphiles in mixtures of prebiotically plausible surfactants.

    Science.gov (United States)

    Albertsen, A N; Duffy, C D; Sutherland, J D; Monnard, P-A

    2014-06-01

    The spontaneous formation of closed bilayer structures from prebiotically plausible amphiphiles is an essential requirement for the emergence of early cells on prebiotic Earth. The sources of amphiphiles could have been both endo- and exogenous (accretion of meteorite carbonaceous material or interstellar dust particles). Among all prebiotic possible amphiphile candidates, those containing phosphate are the least investigated species because their self-assembly occurs in a seemingly too narrow range of conditions. The self-assembly of simple phosphate amphiphiles should, however, be of great interest, as contemporary membranes predominantly contain phospholipids. In contrast to common expectations, we show that these amphiphiles can be easily synthesized under prebiotically plausible environmental conditions and can efficiently form bilayer structures in the presence of various co-surfactants across a large range of pH values. Vesiculation was even observed in crude reaction mixtures that contained 1-decanol as the amphiphile precursor. The two best co-surfactants promoted vesicle formation over the entire pH range in aqueous solutions. Expanding the pH range where bilayer membranes self-assemble and remain intact is a prerequisite for the emergence of early cell-like compartments and their preservation under fluctuating environmental conditions. These mixed bilayers also retained small charged solutes, such as dyes. These results demonstrate that alkyl phosphate amphiphiles might have played a significant role as early compartment building blocks.

  10. A swarm intelligence framework for reconstructing gene networks: searching for biologically plausible architectures.

    Science.gov (United States)

    Kentzoglanakis, Kyriakos; Poole, Matthew

    2012-01-01

    In this paper, we investigate the problem of reverse engineering the topology of gene regulatory networks from temporal gene expression data. We adopt a computational intelligence approach comprising swarm intelligence techniques, namely particle swarm optimization (PSO) and ant colony optimization (ACO). In addition, the recurrent neural network (RNN) formalism is employed for modeling the dynamical behavior of gene regulatory systems. More specifically, ACO is used for searching the discrete space of network architectures and PSO for searching the corresponding continuous space of RNN model parameters. We propose a novel solution construction process in the context of ACO for generating biologically plausible candidate architectures. The objective is to concentrate the search effort into areas of the structure space that contain architectures which are feasible in terms of their topological resemblance to real-world networks. The proposed framework is initially applied to the reconstruction of a small artificial network that has previously been studied in the context of gene network reverse engineering. Subsequently, we consider an artificial data set with added noise for reconstructing a subnetwork of the genetic interaction network of S. cerevisiae (yeast). Finally, the framework is applied to a real-world data set for reverse engineering the SOS response system of the bacterium Escherichia coli. Results demonstrate the relative advantage of utilizing problem-specific knowledge regarding biologically plausible structural properties of gene networks over conducting a problem-agnostic search in the vast space of network architectures.

  11. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for the rapid identification of yeasts causing bloodstream infections.

    Science.gov (United States)

    Ghosh, A K; Paul, S; Sood, P; Rudramurthy, S M; Rajbanshi, A; Jillwin, T J; Chakrabarti, A

    2015-04-01

    Few studies have systematically standardised and evaluated matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identification of yeasts from bloodstream infections. This is rapidly becoming pertinent for early identification of yeasts and appropriate antifungal therapy. We used 354 yeast strains identified by polymerase chain reaction (PCR) sequencing for standardisation and 367 blind clinical strains for validation of our MALDI-TOF MS protocols. We also evaluated different sample preparation methods and found the on-plate formic acid extraction method as most cost- and time-efficient. The MALDI-TOF assay correctly identified 98.9% of PCR-sequenced yeasts. Novel main spectrum projections (MSP) were developed for Candida auris, C. viswanathii and Kodamaea ohmeri, which were missing from the Bruker MALDI-TOF MS database. Spectral cut-offs computed by receiver operating characteristics (ROC) analysis showed 99.4% to 100% accuracy at a log score of ≥ 1.70 for C. tropicalis, C. parapsilosis, C. pelliculosa, C. orthopsilosis, C. albicans, C. rugosa, C. guilliermondii, C. lipolytica, C. metapsilosis, C. nivariensis. The differences in the species-specific scores of our standardisation and blind validation strains were not statistically significant, implying the optimal performance of our test protocol. The MSPs of the three new species also were validated. We conclude that MALDI-TOF MS is a rapid, accurate and reliable tool for identification of bloodstream yeasts. With proper standardisation, validation and regular database expansion, its efficiency can be further enhanced.

  12. Multiplexed real-time PCR amplification of tlh, tdh and trh genes in Vibrio parahaemolyticus and its rapid detection in shellfish and Gulf of Mexico water.

    Science.gov (United States)

    Rizvi, Amy V; Bej, Asim K

    2010-10-01

    In this study, we have developed a SYBR Green I-based real-time multiplexed PCR assay for the detection of Vibrio parahaemolyticus in Gulf of Mexico water (gulf water), artificially seeded and natural oysters targeting three hemolysin genes, tlh, tdh and trh in a single reaction. Post-amplification melt-temperature analysis confirmed the amplification of all three targeted genes with high specificity. The detection sensitivity was 10 cfu (initial inoculum) in 1 ml of gulf water or oyster tissue homogenate, following 5 h enrichment. The results showed 58% of the oysters to be positive for tlh, indicating the presence of V. parahaemolyticus; of which 21% were positive for tdh; and 0.7% for trh, signifying the presence of pathogenic strains. The C(t) values showed that oyster tissue matrix had some level of inhibition, whereas the gulf water had negligible effect on PCR amplification. The assay was rapid (approximately 8 h), specific and sensitive, meeting the ISSC guidelines. Rapid detection using real-time multiplexed PCR will help reduce V. parahaemolyticus-related disease outbreaks, thereby increasing consumer confidence and economic success of the seafood industry.

  13. Real-Time Detection and Rapid Multiwavelength Follow-up Observations of a Highly Subluminous Type II-P Supernova from the Palomar Transient Factory Survey

    CERN Document Server

    Gal-Yam, Avishay; Arcavi, Iair; Green, Yoav; Yaron, Ofer; Ben-Ami, Sagi; Xu, Dong; Sternberg, Assaf; Quimby, Robert M; Kulkarni, Shrinivas R; Ofek, Eran O; Walters, Richard; Nugent, Peter E; Poznanski, Dovi; Bloom, Joshua S; Cenko, S Bradley; Filippenko, Alexei V; Li, Weidong; Silverman, J; Walker, Emma S; Sullivan, Mark; Maguire, K; Howell, D Andrew; Mazzali, Paolo A; Frail, Dale A; Bersier, David; James, Phil A; Akerlof, C W; Yuan, Fang; Fox, Derek B; Law, Nicholas; Gehrels, Neil

    2011-01-01

    The Palomar Transient Factory (PTF) is an optical wide-field variability survey carried out using a camera with a 7.8 square degree field of view mounted on the 48-in Oschin Schmidt telescope at Palomar Observatory. One of the key goals of this survey is to conduct high-cadence monitoring of the sky in order to detect optical transient sources shortly after they occur. Here, we describe the real-time capabilities of the PTF and our related rapid multiwavelength follow-up programs, extending from the radio to the gamma-ray bands. We present as a case study observations of the optical transient PTF10vdl (SN 2010id), revealed to be a very young core-collapse (Type II-P) supernova having a remarkably low luminosity. Our results demonstrate that the PTF now provides for optical transients the real-time discovery and rapid-response follow-up capabilities previously reserved only for high-energy transients like gamma-ray bursts.

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

    Science.gov (United States)

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

    2013-12-01

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

  15. Evaluation of a Semiquantitative Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Method for Rapid Antimicrobial Susceptibility Testing of Positive Blood Cultures.

    Science.gov (United States)

    Jung, Jette S; Hamacher, Christina; Gross, Birgit; Sparbier, Katrin; Lange, Christoph; Kostrzewa, Markus; Schubert, Sören

    2016-11-01

    With the increasing prevalence of multidrug-resistant Gram-negative bacteria, rapid identification of the pathogen and its individual antibiotic resistance is crucial to ensure adequate antiinfective treatment at the earliest time point. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry for the identification of bacteria directly from the blood culture bottle has been widely established; however, there is still an urgent need for new methods that permit rapid resistance testing. Recently, a semiquantitative MALDI-TOF mass spectrometry-based method for the prediction of antibiotic resistance was described. We evaluated this method for detecting nonsusceptibility against two β-lactam and two non-β-lactam antibiotics. A collection of 30 spiked blood cultures was tested for nonsusceptibility against gentamicin and ciprofloxacin. Furthermore, 99 patient-derived blood cultures were tested for nonsusceptibility against cefotaxime, piperacillin-tazobactam, and ciprofloxacin in parallel with MALDI-TOF mass spectrometry identification from the blood culture fluid. The assay correctly classified all isolates tested for nonsusceptibility against gentamicin and cefotaxime. One misclassification for ciprofloxacin nonsusceptibility and five misclassifications for piperacillin-tazobactam nonsusceptibility occurred. Identification of the bacterium and prediction of nonsusceptibility was possible within approximately 4 h.

  16. Development of a rapid detection method to detect tdh gene in Vibrio parahaemolyticus using 2-step ultrarapid real-time polymerase chain reaction.

    Science.gov (United States)

    Kang, Min-Hee; Kim, Il-Wook; Lee, Dong-Woo; Yoo, Mi-Sun; Han, Sang-Hoon; Yoon, Byoung-Su

    2011-01-01

    Thermostable direct hemolysin encoded by tdh gene has been considered an important virulence factor in pathogenic Vibrio parahaemolyticus. Two-step ultrarapid real-time polymerase chain reaction (URRT PCR) with a microchip was devised to detect V. parahaemolyticus carrying tdh gene. This novel method has a 6-μL reaction volume and extremely reduces running time since one cycle can be completed in 10 s or less. Consequently, 35 cycles of URRT PCR was successfully able to detect up to 100 fg (18 copies) of genomic DNA from pathogenic V. parahaemolyticus carrying tdh gene in 6 min. These results indicate that this method is at present the most rapid detection method for tdh gene and pathogenic V. parahaemolyticus.

  17. A temperature control method for shortening thermal cycling time to achieve rapid polymerase chain reaction (PCR) in a disposable polymer microfluidic device

    Science.gov (United States)

    Bu, Minqiang; Perch-Nielsen, Ivan R.; Sørensen, Karen S.; Skov, Julia; Sun, Yi; Duong Bang, Dang; Pedersen, Michael E.; Hansen, Mikkel F.; Wolff, Anders

    2013-07-01

    We present a temperature control method capable of effectively shortening the thermal cycling time of polymerase chain reaction (PCR) in a disposable polymer microfluidic device with an external heater and a temperature sensor. The method employs optimized temperature overshooting and undershooting steps to achieve a rapid ramping between the temperature steps for DNA denaturation, annealing and extension. The temperature dynamics within the microfluidic PCR chamber was characterized and the overshooting and undershooting parameters were optimized using the temperature-dependent fluorescence signal from Rhodamine B. The method was validated with the PCR amplification of mecA gene (162 bp) from methicillin-resistant Staphylococcus aureus bacterium (MRSA), where the time for 30 cycles was reduced from 50 min (without over- and undershooting) to 20 min.

  18. A flowing liquid test system for assessing the linearity and time-response of rapid fibre optic oxygen partial pressure sensors.

    Science.gov (United States)

    Chen, R; Hahn, C E W; Farmery, A D

    2012-08-15

    The development of a methodology for testing the time response, linearity and performance characteristics of ultra fast fibre optic oxygen sensors in the liquid phase is presented. Two standard medical paediatric oxygenators are arranged to provide two independent extracorporeal circuits. Flow from either circuit can be diverted over the sensor under test by means of a system of rapid cross-over solenoid valves exposing the sensor to an abrupt change in oxygen partial pressure, P O2. The system is also capable of testing the oxygen sensor responses to changes in temperature, carbon dioxide partial pressure P CO2 and pH in situ. Results are presented for a miniature fibre optic oxygen sensor constructed in-house with a response time ≈ 50 ms and a commercial fibre optic sensor (Ocean Optics Foxy), when tested in flowing saline and stored blood.

  19. Evaluation of real-time loop-mediated isothermal amplification (RealAmp) for rapid detection of Mycobacterium tuberculosis from sputum samples.

    Science.gov (United States)

    Li, Yiming; Shi, Lei; Pan, Anqi; Cao, Weiwei; Chen, Xun; Meng, Hecheng; Yan, He; Miyoshi, Shin-ichi; Ye, Lei

    2014-09-01

    Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB) leads to serious health problems as a chronic respiratory infectious disease. Here we established a real-time fluorescence loop-mediated isothermal amplification assay (RealAmp) using a portable ESE Quant tube scanner as a convenient rapid detection method for MTB. The method efficacy from sputum samples was further investigated, and the reaction time was only 20min with the detection limit low to 10(2)CFU/ml concentration of MTB. We assessed a total of 1067 samples by the RealAmp assay, comparing the results with smear microscopy and conventional culture methods. To examine whether the failure to detect TB by culturing is due to low sensitivity or true absence, we examined the culture negative samples by commercial real time PCR MTB detection kit, and the results were compared with RealAmp. The data showed that RealAmp assay had a higher positive rate than that of sputum smear and culture methods. RealAmp had a sensitivity of 96.70% and a specificity of 91.55% when compared with culture. In addition, its sensitivity and specificity were 95.29% and 86.88% respectively compared with examination of smear samples using light microscopy. The sensitivity of RealAmp in comparison to real time PCR was 98.25% and specificity was 99.11% in validation of culture negative samples. The present study revealed the newly established RealAmp assay as a convenient, efficient, sensitive and specific method that could be an alternative for rapid detection of MTB and a tool to validate culture and smear negative samples. Furthermore, the portability of the ESE Quant tube scanner also contributed to the promising application for grassroots and field detection of MTB.

  20. Skull reconstruction after resection of bone tumors in a single surgical time by the association of the techniques of rapid prototyping and surgical navigation.

    Science.gov (United States)

    Anchieta, M V M; Salles, F A; Cassaro, B D; Quaresma, M M; Santos, B F O

    2016-10-01

    Presentation of a new cranioplasty technique employing a combination of two technologies: rapid prototyping and surgical navigation. This technique allows the reconstruction of the skull cap after the resection of a bone tumor in a single surgical time. The neurosurgeon plans the craniotomy previously on the EximiusMed software, compatible with the Eximius Surgical Navigator, both from the company Artis Tecnologia (Brazil). The navigator imports the planning and guides the surgeon during the craniotomy. The simulation of the bone fault allows the virtual reconstruction of the skull cap and the production of a personalized modelling mold using the Magics-Materialise (Belgium)-software. The mold and a replica of the bone fault are made by rapid prototyping by the company Artis Tecnologia (Brazil) and shipped under sterile conditions to the surgical center. The PMMA prosthesis is produced during the surgical act with the help of a hand press. The total time necessary for the planning and production of the modelling mold is four days. The precision of the mold is submillimetric and accurately reproduces the virtual reconstruction of the prosthesis. The production of the prosthesis during surgery takes until twenty minutes depending on the type of PMMA used. The modelling mold avoids contraction and dissipates the heat generated by the material's exothermic reaction in the polymerization phase. The craniectomy is performed with precision over the drawing made with the help of the Eximius Surgical Navigator, according to the planned measurements. The replica of the bone fault serves to evaluate the adaptation of the prosthesis as a support for the perforations and the placement of screws and fixation plates, as per the surgeon's discretion. This technique allows the adequate oncologic treatment associated with a satisfactory aesthetic result, with precision, in a single surgical time, reducing time and costs.

  1. Combination of monoclonal antibodies and DPP-IV inhibitors in the treatment of type 1 diabetes: a plausible treatment modality?

    Science.gov (United States)

    Dubala, Anil; Gupta, Ankur; Samanta, Malay K

    2014-07-01

    Regulatory T cells (Tregs) are crucial for the maintenance of immunological tolerance. Type 1 diabetes (T1D) occurs when the immune-regulatory mechanism fails. In fact, T1D is reversed by islet transplantation but is associated with hostile effects of persistent immune suppression. T1D is believed to be dependent on the activation of type-1 helper T (Th1) cells. Immune tolerance is liable for the activation of the Th1 cells. The important role of Th1 cells in pathology of T1D entails the depletion of CD4(+) T cells, which initiated the use of monoclonal antibodies (mAbs) against CD4(+) T cells to interfere with induction of T1D. Prevention of autoimmunity is not only a step forward for the treatment of T1D, but could also restore the β-cell mass. Glucagon-like peptide (GLP)-1 stimulates β-cell proliferation and also has anti-apoptotic effects on them. However, the potential use of GLP-1 as a possible method to restore pancreatic β-cells is limited due to rapid degradation by dipeptidyl peptidase (DPP)-IV. We hypothesize that treatment with combination of CD4 mAbs and DPP-IV inhibitors could prevent/reverse T1D. CD4 mAbs have the ability to induce immune tolerance, thereby arresting further progression of T1D; DPP-IV inhibitors have the capability to regenerate the β-cell mass. Consequently, the combination of CD4 mAbs and DPP-IV inhibitor could avoid or at least minimize the constraints of intensive subcutaneous insulin therapy. We presume that if this hypothesis proves correct, it may become one of the plausible therapeutic options for T1D.

  2. A locked nucleic acid (LNA-based real-time PCR assay for the rapid detection of multiple bacterial antibiotic resistance genes directly from positive blood culture.

    Directory of Open Access Journals (Sweden)

    Lingxiang Zhu

    Full Text Available Bacterial strains resistant to various antibiotic drugs are frequently encountered in clinical infections, and the rapid identification of drug-resistant strains is highly essential for clinical treatment. We developed a locked nucleic acid (LNA-based quantitative real-time PCR (LNA-qPCR method for the rapid detection of 13 antibiotic resistance genes and successfully used it to distinguish drug-resistant bacterial strains from positive blood culture samples. A sequence-specific primer-probe set was designed, and the specificity of the assays was assessed using 27 ATCC bacterial strains and 77 negative blood culture samples. No cross-reaction was identified among bacterial strains and in negative samples, indicating 100% specificity. The sensitivity of the assays was determined by spiking each bacterial strain into negative blood samples, and the detection limit was 1-10 colony forming units (CFU per reaction. The LNA-qPCR assays were first applied to 72 clinical bacterial isolates for the identification of known drug resistance genes, and the results were verified by the direct sequencing of PCR products. Finally, the LNA-qPCR assays were used for the detection in 47 positive blood culture samples, 19 of which (40.4% were positive for antibiotic resistance genes, showing 91.5% consistency with phenotypic susceptibility results. In conclusion, LNA-qPCR is a reliable method for the rapid detection of bacterial antibiotic resistance genes and can be used as a supplement to phenotypic susceptibility testing for the early detection of antimicrobial resistance to allow the selection of appropriate antimicrobial treatment and to prevent the spread of resistant isolates.

  3. Development of a rapid and simplified protocol for direct bacterial identification from positive blood cultures by using matrix assisted laser desorption ionization time-of- flight mass spectrometry.

    Science.gov (United States)

    Jakovljev, Aleksandra; Bergh, Kåre

    2015-11-06

    Bloodstream infections represent serious conditions carrying a high mortality and morbidity rate. Rapid identification of microorganisms and prompt institution of adequate antimicrobial therapy is of utmost importance for a successful outcome. Aiming at the development of a rapid, simplified and efficient protocol, we developed and compared two in-house preparatory methods for the direct identification of bacteria from positive blood culture flasks (BD BACTEC FX system) by using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF MS). Both methods employed saponin and distilled water for erythrocyte lysis. In method A the cellular pellet was overlaid with formic acid on the MALDI TOF target plate for protein extraction, whereas in method B the pellet was exposed to formic acid followed by acetonitrile prior to placing on the target plate. Best results were obtained by method A. Direct identification was achieved for 81.9 % and 65.8 % (50.3 % and 26.2 % with scores >2.0) of organisms by method A and method B, respectively. Overall concordance with final identification was 100 % to genus and 97.9 % to species level. By applying a lower cut-off score value, the levels of identification obtained by method A and method B increased to 89.3 % and 77.8 % of organisms (81.9 % and 65.8 % identified with scores >1.7), respectively. Using the lowered score criteria, concordance with final results was obtained for 99.3 % of genus and 96.6 % of species identifications. The reliability of results, rapid performance (approximately 25 min) and applicability of in-house method A have contributed to implementation of this robust and cost-effective method in our laboratory.

  4. Rapid identification of Bacillus anthracis spores in suspicious powder samples by using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS).

    Science.gov (United States)

    Dybwad, Marius; van der Laaken, Anton L; Blatny, Janet Martha; Paauw, Armand

    2013-09-01

    Rapid and reliable identification of Bacillus anthracis spores in suspicious powders is important to mitigate the safety risks and economic burdens associated with such incidents. The aim of this study was to develop and validate a rapid and reliable laboratory-based matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis method for identifying B. anthracis spores in suspicious powder samples. A reference library containing 22 different Bacillus sp. strains or hoax materials was constructed and coupled with a novel classification algorithm and standardized processing protocol for various powder samples. The method's limit of B. anthracis detection was determined to be 2.5 × 10(6) spores, equivalent to a 55-μg sample size of the crudest B. anthracis-containing powder discovered during the 2001 Amerithrax incidents. The end-to-end analysis method was able to successfully discriminate among samples containing B. anthracis spores, closely related Bacillus sp. spores, and commonly encountered hoax materials. No false-positive or -negative classifications of B. anthracis spores were observed, even when the analysis method was challenged with a wide range of other bacterial agents. The robustness of the method was demonstrated by analyzing samples (i) at an external facility using a different MALDI-TOF MS instrument, (ii) using an untrained operator, and (iii) using mixtures of Bacillus sp. spores and hoax materials. Taken together, the observed performance of the analysis method developed demonstrates its potential applicability as a rapid, specific, sensitive, robust, and cost-effective laboratory-based analysis tool for resolving incidents involving suspicious powders in less than 30 min.

  5. Rapid quantification of viable Campylobacter bacteria on chicken carcasses, using real-time PCR and propidium monoazide treatment, as a tool for quantitative risk assessment.

    Science.gov (United States)

    Josefsen, M H; Löfström, C; Hansen, T B; Christensen, L S; Olsen, J E; Hoorfar, J

    2010-08-01

    A number of intervention strategies against Campylobacter-contaminated poultry focus on postslaughter reduction of the number of cells, emphasizing the need for rapid and reliable quantitative detection of only viable Campylobacter bacteria. We present a new and rapid quantitative approach to the enumeration of food-borne Campylobacter bacteria that combines real-time quantitative PCR (Q-PCR) with simple propidium monoazide (PMA) sample treatment. In less than 3 h, this method generates a signal from only viable and viable but nonculturable (VBNC) Campylobacter bacteria with an intact membrane. The method's performance was evaluated by assessing the contributions to variability by individual chicken carcass rinse matrices, species of Campylobacter, and differences in efficiency of DNA extraction with differing cell inputs. The method was compared with culture-based enumeration on 50 naturally infected chickens. The cell contents correlated with cycle threshold (C(T)) values (R(2) = 0.993), with a quantification range of 1 x 10(2) to 1 x 10(7) CFU/ml. The correlation between the Campylobacter counts obtained by PMA-PCR and culture on naturally contaminated chickens was high (R(2) = 0.844). The amplification efficiency of the Q-PCR method was not affected by the chicken rinse matrix or by the species of Campylobacter. No Q-PCR signals were obtained from artificially inoculated chicken rinse when PMA sample treatment was applied. In conclusion, this study presents a rapid tool for producing reliable quantitative data on viable Campylobacter bacteria in chicken carcass rinse. The proposed method does not detect DNA from dead Campylobacter bacteria but recognizes the infectious potential of the VBNC state and is thereby able to assess the effect of control strategies and provide trustworthy data for risk assessment.

  6. Rapid Identification of microbes in positive blood cultures by use of the vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system.

    Science.gov (United States)

    Foster, Arnold G W

    2013-11-01

    Sepsis is a major cause of death worldwide among nonhospitalized people and hospitalized patients. A wide range of pathogens are involved, and the correct identification and correct antimicrobial therapy are critical to ensure optimal clinical outcomes. With the recent introduction of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), rapid identification of bacteria and fungi is now possible. The purpose of this study was to develop a rapid technique for identifying organisms in positive blood cultures using the Vitek MS system (bioMérieux). This technique is a lysis centrifugation method which involves a four-step washing and centrifugation procedure. A total of 253 positive monomicrobial blood cultures (Bactec Plus aerobic, anaerobic, and pediatric bottles) were tested using the Vitek MS system (KnowledgeBase version 2.0), with 92.1% and 88.1% of organisms overall being identified to the genus level and the species level, respectively. Of 161 Gram-positive bacterial isolates, 95.7% and 90.1% were identified to the genus level and the species level, respectively; of 92 Gram-negative bacterial isolates, 84.7% and 83.7% were identified to the genus level and the species level, respectively. The results obtained using this method demonstrate that the Vitek MS system can be used for rapid and effective identification of bacteria from positive blood cultures within 30 to 45 min after the positive signal has been provided by the Bactec FX blood culture system (Becton, Dickinson). This will lead to faster administration of the appropriate antimicrobial therapy and increase the chances for optimal clinical outcomes for patients.

  7. Optimization of rapid Salmonella enterica detection in liquid whole eggs by SYBR green I-based real-time reverse transcriptase-polymerase chain reaction.

    Science.gov (United States)

    Techathuvanan, Chayapa; D'Souza, Doris Helen

    2011-04-01

    Eggs and egg products have a high risk of Salmonella enterica serovar Enteritidis contamination leading to gastroenteritis outbreaks in humans. Thus, a rapid screening tool for viable Salmonella Enteritidis cells in the egg industry is needed. Our objective was to rapidly and sensitively detect viable Salmonella Enteritidis from spiked liquid whole eggs (LWEs) within 24 h using SYBR green I-based real-time reverse transcriptase-polymerase chain reaction (PCR) targeting the Salmonella specific invA gene along with an internal amplification control in a Bio-Rad iCycler. LWE was inoculated with Salmonella Enteritidis and mixed with tetrathionate broth, and 100 μL of serially diluted portions in phosphate-buffered saline was plated on Xylose Lysine Tergitol 4 agar or 5 mL were used for RNA extraction by the TRIzol method immediately or after enrichment of 6, 12, or 16 h at 37 °C. The real-time reverse transcriptase-PCR assay was carried out using previously described Salmonella invA gene primers. Melt temperature analysis of the PCR product was included to determine specific invA amplification. Without enrichment, the assay detection limit was 10(7) colony forming units (CFU)/25 mL LWE. After enrichment for 6 and 12 h, Salmonella Enteritidis could be detected from LWE up to 10(4) and 10(2) CFU/25 mL, respectively. Improved Salmonella Enteritidis detection up to 10(0) CFU/25 mL was obtained after 16-h enrichment. Even with 16-h enrichment, the results could be still be obtained within 24 h, which is much faster than by traditional cultural detection that takes several days. Therefore, this assay appears suitable for routine detection of Salmonella enterica contamination by the egg industry to help prevent the transmission of egg-associated Salmonella outbreaks and timely recall of contaminated products.

  8. Rapid detection by direct analysis in real time-mass spectrometry (DART-MS) of psychoactive plant drugs of abuse: the case of Mitragyna speciosa aka "Kratom".

    Science.gov (United States)

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

    2014-09-01

    Mitragyna speciosa, also known commonly as "Kratom" or "Ketum", is a plant with psychoactive properties that have been attributed to the presence of various indole alkaloids such as mitragynine and 7-hydroxymitragynine. M. speciosa use is gaining popularity internationally as a natural and legal alternative to narcotics. As a drug of abuse, its detection and identification are not straightforward, since M. speciosa plant material is not particularly distinctive. Here, we show that direct analysis in real time-mass spectrometry (DART-MS) can be used not only to rapidly identify M. speciosa plant material and distinguish it from other plants, but also to distinguish between M. speciosa plant varieties, based on differences between their chemical profiles. The method is rapid and the analysis expeditious. Plant material such as that found at a crime scene can be analyzed directly with no sample pre-preparation steps. Furthermore, we show that the basis set of principal components that permit characterization of the plant material can be used to positively identify M. speciosa.

  9. Establishment of one-step SYBR green-based real time-PCR assay for rapid detection and quantification of chikungunya virus infection.

    Science.gov (United States)

    Ho, Phui San; Ng, Mary Mah Lee; Chu, Justin Jang Hann

    2010-01-21

    Chikungunya virus (CHIKV) is a mosquito-borne alphavirus and one of the prevalent re-emerging arbovirus in tropical and subtropical regions of Asia, Africa, and Central and South America. It produces a spectrum of illness ranging from inapparent infection to moderate febrile illness as well as severe arthralgia or arthritis affecting multiple joints. In this study, a quantitative, one-step real-time SYBR Green-based RT-PCR system for the non-structural protein 2 (nsP2) of CHIKV that can quantify a wide range of viral RNA concentrations was developed. Comparisons between the conventional semi-quantitative RT-PCR assay, immunofluorescence detection method and the one-step SYBR Green-based RT-PCR assay in the detection of CHIKV infection revealed much rapid and increase sensitivity of the latter method. Furthermore, this newly developed assay was validated by in vitro experiments in which ribavirin, a well-known RNA virus inhibitor, showed a dose-dependent inhibition of virus replication on cells that was assessed by viral infectivity and viral RNA production. Our results demonstrate the potential of this newly developed one-step SYBR Green I-based RT-PCR assay may be a useful tool in rapid detection of CHIKV and monitoring the extent of viral replication possibly in patients' samples.

  10. Rapid detection of Mycobacterium tuberculosis complex by real-time PCR in sputum samples and its use in the routine diagnosis in a reference laboratory.

    Science.gov (United States)

    Watanabe Pinhata, Juliana Maira; Cergole-Novella, Maria Cecilia; Moreira dos Santos Carmo, Andreia; Ruivo Ferro e Silva, Regina; Ferrazoli, Lucilaine; Tavares Sacchi, Claudio; Siqueira de Oliveira, Rosangela

    2015-09-01

    Tuberculosis (TB) is an infectious disease of global distribution, constituting a serious public health problem in Brazil. São Paulo State, located in the south-east of Brazil, notified 16,580 new TB cases in 2013. The Instituto Adolfo Lutz is a public health reference laboratory for TB diagnosis for all the State. Considering that rapid and accurate diagnosis is essential for TB control, the aim of this study was to evaluate the use of an in-house real-time (RT)-PCR assay targeting the mpt64 gene in the routine diagnosis of TB, and to compare this technique with smear microscopy and culture. From August 2012 to October 2013, 715 sputum samples from 657 patients were included in the study. Smear microscopy, culture, phenotypic and PRA-hsp65 identification of mycobacteria, and mpt64 RT-PCR were performed. With respect to confirmed TB cases (n = 62/657; 9.4%), smear microscopy had a sensitivity of 82.3%. Culture and RT-PCR showed the same sensitivity, i.e. 90.3%. Specificity was 99.7, 99.4 and 98.6% for smear microscopy, culture and RT-PCR, respectively. mpt64 RT-PCR showed high sensitivity and specificity for the detection of Mycobacterium tuberculosis complex in sputum samples. This technique can be deployed in laboratories that do not have a rapid test for TB available, enabling the performance of TB diagnosis in up to 5 h.

  11. Rapid screening for the adulterants of Berberis aristata using direct analysis in real-time mass spectrometry and principal component analysis for discrimination.

    Science.gov (United States)

    Bajpai, Vikas; Singh, Awantika; Arya, Kamal Ram; Srivastava, Mukesh; Kumar, Brijesh

    2015-01-01

    Adulteration or substitution of commercial Berberis aristata and its herbal products with inferior-quality substituents is very common. Metabolic profiling of B. aristata, along with its common adulterants/contaminants/substituents such as B. asiatica, Mahonia borealis and Coscinium fenestratum, was rapidly carried out using direct analysis in real-time mass spectrometry (DART MS) to generate the chemical fingerprints for the differentiation of these species. Phytochemical analysis showed the presence of mainly alkaloids. The identified alkaloids were berberrubine, berberine, jatrorrhizine, ketoberberine, palmatine, dihydropalmatine or 7,8-dihydro-8-hydroxyberberine, berbamine and pakistanamine. Berberine, which was mainly reported from the root and stem bark of B. aristata, was also identified in the leaf along with chlorogenic acid. The DART MS data have been subjected to principal component analysis (PCA). The resulting score plots showed clustering and clear differentiation of the species and plant parts. It is thus apparent that the technique of DART MS followed by PCA is a quick and reliable method for the direct profiling of B. aristata and its adulterant plants and plant parts. The study reports the rapid analytical method to identify the possibility of illegal adulteration/contamination/substitution in potential plant materials and herbal extracts.

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

    Science.gov (United States)

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

    2009-12-01

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

  13. Establishment of one-step SYBR green-based real time-PCR assay for rapid detection and quantification of chikungunya virus infection

    Directory of Open Access Journals (Sweden)

    Chu Justin

    2010-01-01

    Full Text Available Abstract Chikungunya virus (CHIKV is a mosquito-borne alphavirus and one of the prevalent re-emerging arbovirus in tropical and subtropical regions of Asia, Africa, and Central and South America. It produces a spectrum of illness ranging from inapparent infection to moderate febrile illness as well as severe arthralgia or arthritis affecting multiple joints. In this study, a quantitative, one-step real-time SYBR Green-based RT-PCR system for the non-structural protein 2 (nsP2 of CHIKV that can quantify a wide range of viral RNA concentrations was developed. Comparisons between the conventional semi-quantitative RT-PCR assay, immunofluorescence detection method and the one-step SYBR Green-based RT-PCR assay in the detection of CHIKV infection revealed much rapid and increase sensitivity of the latter method. Furthermore, this newly developed assay was validated by in vitro experiments in which ribavirin, a well-known RNA virus inhibitor, showed a dose-dependent inhibition of virus replication on cells that was assessed by viral infectivity and viral RNA production. Our results demonstrate the potential of this newly developed one-step SYBR Green I-based RT-PCR assay may be a useful tool in rapid detection of CHIKV and monitoring the extent of viral replication possibly in patients' samples.

  14. Application of Whole-Cell Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Rapid Identification and Clustering Analysis of Pantoea Species ▿ †

    Science.gov (United States)

    Rezzonico, Fabio; Vogel, Guido; Duffy, Brion; Tonolla, Mauro

    2010-01-01

    Pantoea agglomerans is an ecologically diverse taxon that includes commercially important plant-beneficial strains and opportunistic clinical isolates. Standard biochemical identification methods in diagnostic laboratories were repeatedly shown to run into false-positive identifications of P. agglomerans, a fact which is also reflected by the high number of 16S rRNA gene sequences in public databases that are incorrectly assigned to this species. More reliable methods for rapid identification are required to ascertain the prevalence of this species in clinical samples and to evaluate the biosafety of beneficial isolates. Whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) methods and reference spectra (SuperSpectrum) were developed for accurate identification of P. agglomerans and related bacteria and used to detect differences in the protein profile within variants of the same strain, including a ribosomal point mutation conferring streptomycin resistance. MALDI-TOF MS-based clustering was shown to generally agree with classification based on gyrB sequencing, allowing rapid and reliable identification at the species level. PMID:20453125

  15. Rapid identification and typing of Yersinia pestis and other Yersinia species by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry.

    Science.gov (United States)

    Ayyadurai, Saravanan; Flaudrops, Christophe; Raoult, Didier; Drancourt, Michel

    2010-11-12

    Accurate identification is necessary to discriminate harmless environmental Yersinia species from the food-borne pathogens Yersinia enterocolitica and Yersinia pseudotuberculosis and from the group A bioterrorism plague agent Yersinia pestis. In order to circumvent the limitations of current phenotypic and PCR-based identification methods, we aimed to assess the usefulness of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) protein profiling for accurate and rapid identification of Yersinia species. As a first step, we built a database of 39 different Yersinia strains representing 12 different Yersinia species, including 13 Y. pestis isolates representative of the Antiqua, Medievalis and Orientalis biotypes. The organisms were deposited on the MALDI-TOF plate after appropriate ethanol-based inactivation, and a protein profile was obtained within 6 minutes for each of the Yersinia species. When compared with a 3,025-profile database, every Yersinia species yielded a unique protein profile and was unambiguously identified. In the second step of analysis, environmental and clinical isolates of Y. pestis (n = 2) and Y. enterocolitica (n = 11) were compared to the database and correctly identified. In particular, Y. pestis was unambiguously identified at the species level, and MALDI-TOF was able to successfully differentiate the three biotypes. These data indicate that MALDI-TOF can be used as a rapid and accurate first-line method for the identification of Yersinia isolates.

  16. Non-invasive rapid harvest time determination of oil-producing microalgae cultivations for bio-diesel production by using Chlorophyll fluorescence

    Directory of Open Access Journals (Sweden)

    Yaqin eQiao

    2015-10-01

    Full Text Available For the large-scale cultivation of microalgae for biodiesel production, one of the key problems is the determination of the optimum time for algal harvest when algae cells are saturated with neutral lipids. In this study, a method to determine the optimum harvest time in oil-producing microalgal cultivations by measuring the maximum photochemical efficiency of photosystem II (PSII, also called Fv/Fm, was established. When oil-producing Chlorella strains were cultivated and then treated with nitrogen starvation, it not only stimulated neutral lipid accumulation, but also affected the photosynthesis system, with the neutral lipid contents in all four algae strains – Chlorella sorokiniana C1, Chlorella sp. C2, C. sorokiniana C3, C. sorokiniana C7 – correlating negatively with the Fv/Fm values. Thus, for the given oil-producing algae, in which a significant relationship between the neutral lipid content and Fv/Fm value under nutrient stress can be established, the optimum harvest time can be determined by measuring the value of Fv/Fm. It is hoped that this method can provide an efficient way to determine the harvest time rapidly and expediently in large-scale oil-producing microalgae cultivations for biodiesel production.

  17. Evaluation of peptide nucleic acid-mediated multiplex real-time PCR kits for rapid detection of carbapenemase genes in gram-negative clinical isolates.

    Science.gov (United States)

    Jeong, Seri; Kim, Jung Ok; Jeong, Seok Hoon; Bae, Il Kwon; Song, Wonkeun

    2015-06-01

    The emergence of clinical isolates of carbapenemase-producing microbes confers multidrug-resistance to these bacteria and renders them difficult to treat. This study was performed to evaluate peptide nucleic acid (PNA) probe-based multiplex real-time PCR kits used to detect carbapenemase genes. In total, 324 carbapenemase genes, collected from 318 gram-negative clinical isolates in 36 different hospital laboratories, were assayed to evaluate multiplex real-time PCR kits (PANAGENE; Daejeon, Korea). The nine most prevalent carbapenemase genes (KPC, OXA-48, GES, IMP, VIM, NDM, ISAba1-OXA-51, OXA-23, and OXA-58) were included in this study. The sensitivity and specificity of the multiplex real-time PCR assay to all of the carbapenemase genes were above 99.0%, except for ISAba1-OXA-51. The detection limit of the assay was 100 target copies per 25 μL of reaction volume for all of the nine genetic types of carbapenemases, and the genes were all detected in a single three-hour PCR. The assay also showed considerable efficiency (above 80.0%), stable reproducibility (coefficient of variation, below 5.0%) and a long shelf-life (more than eight months) with no cross reactivity. The developed PNA-mediated multiplex real-time PCR assay was useful for the rapid, accurate and simultaneous identification of nine carbapenemase genes in gram-negative clinical isolates, suggesting its potential to help choose the appropriate antibiotics and aid the control of carbapenemase genes.

  18. Générateur de timing local pour l'acquisition des transformateurs rapides (LEIR, LINAC 3, LINAC 2, Ligne d'injection PSB)

    CERN Document Server

    Schnell, J D

    2006-01-01

    Dans le cadre des acquisitions des transformateurs rapides des deux LINACS, de la ligne d'injection PSB et de la machine LEIR, un nouveau hardware a été mis en opération [1]. Celui-ci assure la digitalisation des signaux analogiques et aussi de certains signaux de timing devant cadrer la mesure. Pour ce faire des ADC SIS3300 (SIS3320) et des DPRAM 80408 sont mis en service. Ces unités nécéssitent pour leur fonctionnement des horloges et des timings qui normalement sont intégralement fournis par l'équipement standard CO, notamment des CTRV et autres TG8. Suite à des problèmes d'approvisionnement, il existe des cas où l'on ne dispose pas (du moins pour le court terme) de suffisemment de ressources standard pour pourvoir au timing mentionné plus haut. Le tiroir qui fait l'objet de la présente description assure, avec certaines limitations, la génération des timings et autres horloges utilisées par les DPRAM 80408 et les ADC SIS3300.

  19. Relatively Selective Production of the Simplest Criegee Intermediate in a CH4/O2 Electric Discharge: Kinetic Analysis of a Plausible Mechanism.

    Science.gov (United States)

    Nguyen, Thanh Lam; McCarthy, Michael C; Stanton, John F

    2015-07-16

    High -accuracy coupled cluster methods in combination with microcanonical semiclassical transition state theory are used to investigate a plausible formation mechanism of the simplest Criegee intermediate in a CH4/O2 discharge experiment. Our results suggest that the Criegee intermediate is produced in a three-step process: (i) production of methyl radical by cleavage of a C-H bond of CH4; (ii) association of methyl radical with molecular oxygen to form a vibrationally excited methyl peroxy, which is in a rapid microequilibrium with the reactants; and finally, (iii) H-abstraction of CH3OO by O2, which results in the formation of cool CH2OO, which has insufficient internal energy to rearrange to dioxirane.

  20. A neurophysiologically plausible population code model for feature integration explains visual crowding.

    Directory of Open Access Journals (Sweden)

    Ronald van den Berg

    2010-01-01

    Full Text Available An object in the peripheral visual field is more difficult to recognize when surrounded by other objects. This phenomenon is called "crowding". Crowding places a fundamental constraint on human vision that limits performance on numerous tasks. It has been suggested that crowding results from spatial feature integration necessary for object recognition. However, in the absence of convincing models, this theory has remained controversial. Here, we present a quantitative and physiologically plausible model for spatial integration of orientation signals, based on the principles of population coding. Using simulations, we demonstrate that this model coherently accounts for fundamental properties of crowding, including critical spacing, "compulsory averaging", and a foveal-peripheral anisotropy. Moreover, we show that the model predicts increased responses to correlated visual stimuli. Altogether, these results suggest that crowding has little immediate bearing on object recognition but is a by-product of a general, elementary integration mechanism in early vision aimed at improving signal quality.

  1. A neurophysiologically plausible population code model for feature integration explains visual crowding.

    Science.gov (United States)

    van den Berg, Ronald; Roerdink, Jos B T M; Cornelissen, Frans W

    2010-01-22

    An object in the peripheral visual field is more difficult to recognize when surrounded by other objects. This phenomenon is called "crowding". Crowding places a fundamental constraint on human vision that limits performance on numerous tasks. It has been suggested that crowding results from spatial feature integration necessary for object recognition. However, in the absence of convincing models, this theory has remained controversial. Here, we present a quantitative and physiologically plausible model for spatial integration of orientation signals, based on the principles of population coding. Using simulations, we demonstrate that this model coherently accounts for fundamental properties of crowding, including critical spacing, "compulsory averaging", and a foveal-peripheral anisotropy. Moreover, we show that the model predicts increased responses to correlated visual stimuli. Altogether, these results suggest that crowding has little immediate bearing on object recognition but is a by-product of a general, elementary integration mechanism in early vision aimed at improving signal quality.

  2. Quantum theory as plausible reasoning applied to data obtained by robust experiments.

    Science.gov (United States)

    De Raedt, H; Katsnelson, M I; Michielsen, K

    2016-05-28

    We review recent work that employs the framework of logical inference to establish a bridge between data gathered through experiments and their objective description in terms of human-made concepts. It is shown that logical inference applied to experiments for which the observed events are independent and for which the frequency distribution of these events is robust with respect to small changes of the conditions under which the experiments are carried out yields, without introducing any concept of quantum theory, the quantum theoretical description in terms of the Schrödinger or the Pauli equation, the Stern-Gerlach or Einstein-Podolsky-Rosen-Bohm experiments. The extraordinary descriptive power of quantum theory then follows from the fact that it is plausible reasoning, that is common sense, applied to reproducible and robust experimental data.

  3. Plausible families of compact objects with a Non Local Equation of State

    CERN Document Server

    Hernández, H

    2012-01-01

    We investigate the plausibility of some models emerging from an algorithm devised to generate a one-parameter family of interior solutions for the Einstein equations. It is explored how their physical variables change as the family-parameter varies. The models studied correspond to anisotropic spherical matter configurations having a non local equation of state. This particular type of equation of state with no causality problems provides, at a given point, the radial pressure not only as a function of the density but as a functional of the enclosed matter distribution. We have found that there are several model-independent tendencies as the parameter increases: the equation of state tends to be stiffer and the total mass becomes half of its external radius. Profiting from the concept of cracking of materials in General Relativity, we obtain that those models become more stable as the family parameter increases.

  4. Plausible role of nanoparticle contamination in the synthesis and properties of organic electronic materials

    Science.gov (United States)

    Ananikov, Valentine P.

    2016-12-01

    Traceless transition metal catalysis (Pd, Ni, Cu, etc.) is very difficult to achieve. Metal contamination in the synthesized products is unavoidable and the most important questions are: How to control metal impurities? What amount of metal impurities can be tolerated? What is the influence of metal impurities? In this brief review, the plausible origins of nanoparticle contamination are discussed in the framework of catalytic synthesis of organic electronic materials. Key factors responsible for increasing the probability of contamination are considered from the point of view of catalytic reaction mechanisms. The purity of the catalyst may greatly affect the molecular weight of a polymer, reaction yield, selectivity and several other parameters. Metal contamination in the final polymeric products may induce some changes in the electric conductivity, charge transport properties, photovoltaic performance and other important parameters.

  5. Spontaneous formation and base pairing of plausible prebiotic nucleotides in water.

    Science.gov (United States)

    Cafferty, Brian J; Fialho, David M; Khanam, Jaheda; Krishnamurthy, Ramanarayanan; Hud, Nicholas V

    2016-04-25

    The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life.

  6. Complex adaptive HIV/AIDS risk reduction: Plausible implications from findings in Limpopo Province, South Africa.

    Science.gov (United States)

    Burman, Chris J; Aphane, Marota A

    2016-05-16

    This article emphasises that when working with complex adaptive systems it is possible to stimulate new social practices and/or cognitive perspectives that contribute to risk reduction, associated with reducing aggregate community viral loads. The process of achieving this is highly participatory and is methodologically possible because evidence of 'attractors' that influence the social practices can be identified using qualitative research techniques. Using findings from Limpopo Province, South Africa, we argue that working with 'wellness attractors' and increasing their presence within the HIV/AIDS landscape could influence aggregate community viral loads. While the analysis that is presented is unconventional, it is plausible that this perspective may hold potential to develop a biosocial response - which the Joint United Nations Programme on HIV and AIDS (UNAIDS) has called for - that reinforces the biomedical opportunities that are now available to achieve the ambition of ending AIDS by 2030.

  7. Reciprocity-based reasons for benefiting research participants: most fail, the most plausible is problematic.

    Science.gov (United States)

    Sofaer, Neema

    2014-11-01

    A common reason for giving research participants post-trial access (PTA) to the trial intervention appeals to reciprocity, the principle, stated most generally, that if one person benefits a second, the second should reciprocate: benefit the first in return. Many authors consider it obvious that reciprocity supports PTA. Yet their reciprocity principles differ, with many authors apparently unaware of alternative versions. This article is the first to gather the range of reciprocity principles. It finds that: (1) most are false. (2) The most plausible principle, which is also problematic, applies only when participants experience significant net risks or burdens. (3) Seldom does reciprocity support PTA for participants or give researchers stronger reason to benefit participants than equally needy non-participants. (4) Reciprocity fails to explain the common view that it is bad when participants in a successful trial have benefited from the trial intervention but lack PTA to it.

  8. Oxidation of cefazolin by potassium permanganate: Transformation products and plausible pathways.

    Science.gov (United States)

    Li, Liping; Wei, Dongbin; Wei, Guohua; Du, Yuguo

    2016-04-01

    Cefazolin was demonstrated to exert high reactivity toward permanganate (Mn(VII)), a common oxidant in water pre-oxidation treatment. In this study, five transformation products were found to be classified into three categories according to the contained characteristic functional groups: three (di-)sulfoxide products, one sulfone product and one di-ketone product. Products analyses showed that two kinds of reactions including oxidation of thioether and the cleavage of unsaturated CC double bond occurred during transformation of cefazolin by Mn(VII). Subsequently, the plausible transformation pathways under different pH conditions were proposed based on the identified products and chemical reaction principles. More importantly, the simulation with real surface water matrix indicated that the proposed transformation pathways of cefazolin could be replayed in real water treatment practices.

  9. Plausible authentication of manuka honey and related products by measuring leptosperin with methyl syringate.

    Science.gov (United States)

    Kato, Yoji; Fujinaka, Rie; Ishisaka, Akari; Nitta, Yoko; Kitamoto, Noritoshi; Takimoto, Yosuke

    2014-07-01

    Manuka honey, obtained from Leptospermum scoparium flowers in New Zealand, has strong antibacterial properties. In this study, plausible authentication of the manuka honey was inspected by measuring leptosperin, methyl syringate 4-O-β-D-gentiobiose, along with methyl syringate. Despite a gradual decrease in methyl syringate content over 30 days at 50 °C, even at moderate 37 °C, leptosperin remained stable. A considerable correlation between nonperoxide antibacterial activity and leptosperin content was observed in 20 certified manuka honey samples. Leptosperin and methyl syringate in manuka honey and related products were analyzed using HPLC connected with mass spectrometry. One noncertified brand displayed significant variations in the leptosperin and methyl syringate contents between two samples obtained from different regions. Therefore, certification is clearly required to protect consumers from disguised and/or low-quality honey. Because leptosperin is stable during storage and specific to manuka honey, its measurement may be applicable for manuka honey authentication.

  10. A plausible simultaneous synthesis of amino acids and simple peptides on the primordial Earth.

    Science.gov (United States)

    Parker, Eric T; Zhou, Manshui; Burton, Aaron S; Glavin, Daniel P; Dworkin, Jason P; Krishnamurthy, Ramanarayanan; Fernández, Facundo M; Bada, Jeffrey L

    2014-07-28

    Following his seminal work in 1953, Stanley Miller conducted an experiment in 1958 to study the polymerization of amino acids under simulated early Earth conditions. In the experiment, Miller sparked a gas mixture of CH4, NH3, and H2O, while intermittently adding the plausible prebiotic condensing reagent cyanamide. For unknown reasons, an analysis of the samples was not reported. We analyzed the archived samples for amino acids, dipeptides, and diketopiperazines by liquid chromatography, ion mobility spectrometry, and mass spectrometry. A dozen amino acids, 10 glycine-containing dipeptides, and 3 glycine-containing diketopiperazines were detected. Miller's experiment was repeated and similar polymerization products were observed. Aqueous heating experiments indicate that Strecker synthesis intermediates play a key role in facilitating polymerization. These results highlight the potential importance of condensing reagents in generating diversity within the prebiotic chemical inventory.

  11. Evaluation and integration of cancer gene classifiers: identification and ranking of plausible drivers.

    Science.gov (United States)

    Liu, Yang; Tian, Feng; Hu, Zhenjun; DeLisi, Charles

    2015-05-11

    The number of mutated genes in cancer cells is far larger than the number of mutations that drive cancer. The difficulty this creates for identifying relevant alterations has stimulated the development of various computational approaches to distinguishing drivers from bystanders. We develop and apply an ensemble classifier (EC) machine learning method, which integrates 10 classifiers that are publically available, and apply it to breast and ovarian cancer. In particular we find the following: (1) Using both standard and non-standard metrics, EC almost always outperforms single method classifiers, often by wide margins. (2) Of the 50 highest ranked genes for breast (ovarian) cancer, 34 (30) are associated with other cancers in either the OMIM, CGC or NCG database (P plausible. Biological implications are briefly discussed. Source codes and detailed results are available at http://www.visantnet.org/misi/driver_integration.zip.

  12. Probability, plausibility, and adequacy evaluations of the Oriente Study demonstrate that supplementation improved child growth.

    Science.gov (United States)

    Habicht, Jean-Pierre; Martorell, Reynaldo

    2010-02-01

    This article presents evidence that the high-nutrient supplement in the Oriente study (Atole) improved child growth. The evidence is presented at 4 levels. There was a causal effect of the intervention on child length, as assessed by probability analyses of the randomized, controlled trial (P < 0.05). The plausibility analyses, which included an examination of wasting, showed that the nutritional impact was due to the Atole, especially in those who were <3 y old and who suffered from diarrhea. The adequacy analyses revealed excellent biological efficacy of the Atole at the individual level. At the level of the whole population, the efficacy of impact was much less, because many children did not participate fully in the supplementation program. The external validity of the biological impact is likely to be good for populations with similar diets and medical care.

  13. Time-series Doppler images and surface differential rotation of the effectively-single rapidly-rotating K-giant KU Pegasi

    CERN Document Server

    Kővári, Zs; Strassmeier, K G; Carroll, T A; Weber, M; Kriskovics, L; Oláh, K; Vida, K; Granzer, T

    2016-01-01

    According to most stellar dynamo theories, differential rotation (DR) plays a crucial role for the generation of toroidal magnetic fields. Numerical models predict surface differential rotation to be anti-solar for rapidly-rotating giant stars, i.e., their surface angular velocity could increase with stellar latitude. However, surface differential rotation has been derived only for a handful of individual giant stars to date. The spotted surface of the K-giant KU Pegasi is investigated in order to detect its time evolution and quantify surface differential rotation. We present altogether 11 Doppler images from spectroscopic data collected with the robotic telescope STELLA between 2006--2011. All maps are obtained with the surface reconstruction code iMap. Differential rotation is extracted from these images by detecting systematic (latitude-dependent) spot displacements. We apply a cross-correlation technique to find the best differential rotation law. The surface of KU Peg shows cool spots at all latitudes a...

  14. Direct Quantification of Campylobacter jejuni in Chicken Fecal Samples Using Real-Time PCR: Evaluation of Six Rapid DNA Extraction Methods

    DEFF Research Database (Denmark)

    Garcia Clavero, Ana Belén; Kamara, Judy N.; Vigre, Håkan

    2013-01-01

    Direct and accurate quantification of Campylobacter in poultry is crucial for the assessment of public health risks and the evaluation of the effectiveness of control measures against Campylobacter in poultry. The aim of this study was to assess several rapid DNA extraction methods...... DNA extraction methods were compared based on their limit of detection, efficiency, reproducibility, and precision. Standard curves were designed for all the methods tested in order to assess their performance on the direct quantification of C. jejuni in chicken fecal samples. As a result...... efficiency was not optimal (AE = 139.5 %). DNA extraction methods Easy-DNA Invitrogen, MiniMAG® and NucleoSpin® Tissue produced good real-time PCR reproducibility generating standard deviations from 0.3 to 0.8 between replicates....

  15. Real-time quantitative PCR assay with Taqman® probe for rapid detection of MCR-1 plasmid-mediated colistin resistance

    Directory of Open Access Journals (Sweden)

    S. Chabou

    2016-09-01

    Full Text Available Here we report the development of two rapid real-time quantitative PCR assays with TaqMan® probes to detect the MCR-1 plasmid-mediated colistin resistance gene from bacterial isolates and faecal samples from chickens. Specificity and sensitivity of the assay were 100% on bacterial isolates including 18 colistin-resistant isolates carrying the mcr-1 gene (six Klebsiella pneumoniae and 12 Escherichia coli with a calibration curve that was linear from 101 to 108 DNA copies. Five out of 833 faecal samples from chickens from Algeria were positive, from which three E. coli strains were isolated and confirmed to harbour the mcr-1 gene by standard PCR and sequencing.

  16. Exploitation of rapid acidification phenomena of food waste in reducing the hydraulic retention time (HRT) of high rate anaerobic digester without conceding on biogas yield.

    Science.gov (United States)

    Kuruti, Kranti; Begum, Sameena; Ahuja, Shruti; Anupoju, Gangagni Rao; Juntupally, Sudharshan; Gandu, Bharath; Ahuja, Devender Kumar

    2017-02-01

    The aim of the present work was to study and infer a full scale experience on co-digestion of 1000kg of FW (400kg cooked food waste and 600kg uncooked food waste) and 2000L of rice gruel (RG) on daily basis based on a high rate biomethanation technology called "Anaerobic gas lift reactor" (AGR). The pH of raw substrate was low (5.2-5.5) that resulted in rapid acidification phenomena with in 12h in the feed preparation tank that facilitated to obtain a lower hydraulic residence time (HRT) of 10days. At full load, AGR was fed with 245kg of total solids, 205kg of volatile solids (167kg of organic matter in terms of chemical oxygen demand) which resulted in the generation of biogas and bio manure of 140m(3)/day and 110kg/day respectively. The produced biogas replaced 60-70kg of LPG per day.

  17. Rapid and quantitative detection of Fusarium oxysporum f. sp. cubense race 4 in soil by real-time fluorescence loop-mediated isothermal amplification.

    Science.gov (United States)

    Peng, Jun; Zhang, He; Chen, Fengping; Zhang, Xin; Xie, Yixian; Hou, Xianwen; Li, Guangyi; Pu, Jinji

    2014-12-01

    In this study, a real-time fluorescence loop-mediated isothermal amplification (RealAmp) was developed and evaluated for the rapid and quantitative detection of Fusarium oxysporum f. sp. cubense race 4 (R4) in soil. The LAMP primer set was designed based on previously verified RAPD marker sequences, and the RealAmp assay could specifically detect and distinguish R4 isolates from other related species. The detection sensitivity of the RealAmp assay was approx. 3·82 × 10(3) copies of plasmid DNA or 10(3) of spores per gram in artificially infested soil, indicating that the method is highly tolerant to inhibitor substances in soil compared to real-time PCR. Combining previously published TR4-specific detection methods with the newly established R4-specific RealAmp assay, an indirect approach to detect and differentiate ST4 isolates was achieved by comparing the detection results of R4 and TR4 simultaneously. The existence of ST4 isolates in China was subsequently confirmed through the developed approach. The developed RealAmp assay has been confirmed to be a simple, rapid and effective method to detect R4 in soil, which facilitates to further identify and distinguish ST4 isolates through the comparative analysis of detection results between TR4 and R4 simultaneously. The technique is an alternative quantitative detection method, which will be used for a routine detection service for the soil-borne pathogen in China. © 2014 The Society for Applied Microbiology.

  18. Rapid and accurate identification of species belonging to the Candida parapsilosis complex by real-time PCR and melting curve analysis.

    Science.gov (United States)

    Hays, Constantin; Duhamel, Chantal; Cattoir, Vincent; Bonhomme, Julie

    2011-04-01

    Candida parapsilosis is the second most frequent Candida species isolated from blood cultures. Since 2005, C. parapsilosis has been divided into three distinct species based on genetic traits: Candida parapsilosis, Candida metapsilosis and Candida orthopsilosis. The aim of this study was to develop a rapid real-time PCR assay able to distinguish these closely related species via a melting curve analysis. This identification method was optimized by using reference strains and well-characterized clinical isolates of Candida species. A single set of consensus primers was designed to amplify a 184 bp portion of the SADH gene in order to identify species based on the unique melt profile resulting from DNA sequence variations from each species of the complex. PCR products were detected with SYBR Green fluorescent dye and identification was established by melting curve analysis. For validation of the technique, a total of 116 clinical isolates, phenotypically identified as C. parapsilosis, were tested by real-time PCR and results were further compared with PCR-RFLP patterns of the SADH gene, used as the reference method. The melting curve analysis of amplified DNA could differentiate between C. parapsilosis (83.5 °C), C. metapsilosis (82.9 °C) and C. orthopsilosis (82.1 °C), with a sensitivity and specificity comparable to those of the reference method. One hundred and fourteen C. parapsilosis and two C. orthopsilosis isolates were identified among the clinical isolates. This method provides a simple, rapid and reliable identification of species belonging to the C. parapsilosis complex. This novel approach could be helpful for clinical and epidemiological investigations.

  19. Rapid detection of enterobacteriaceae producing extended spectrum beta-lactamases directly from positive blood cultures by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

    Science.gov (United States)

    Oviaño, M; Fernández, B; Fernández, A; Barba, M J; Mouriño, C; Bou, G

    2014-11-01

    Bacteria that produce extended-spectrum β-lactamases (ESBLs) are an increasing healthcare problem and their rapid detection is a challenge that must be overcome in order to optimize antimicrobial treatment and patient care. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has been used to determine resistance to β-lactams, including carbapenems in Enterobacteriaceae, but the methodology has not been fully validated as it remains time-consuming. We aimed to assess whether MALDI-TOF can be used to detect ESBL-producing Enterobacteriaceae from positive blood culture bottles in clinical practice. In the assay, 141 blood cultures were tested, 13 of them were real bacteraemias and 128 corresponded to blood culture bottles seeded with bacterial clinical isolates. Bacteraemias were analysed by MALDI-TOF after a positive growth result and the 128 remaining blood cultures 24 h after the bacterial seeding. β-lactamase activity was determined through the profile of peaks associated with the antibiotics cefotaxime and ceftazidime and its hydrolyzed forms. Clavulanic acid was added to rule out the presence of non-ESBL mechanisms. Overall data show a 99% (103 out of 104) sensitivity in detecting ESBL in positive blood cultures. Data were obtained in 90 min (maximum 150 min). The proposed methodology has a great impact on the early detection of ESBL-producing Enterobacteriaceae from positive blood cultures, being a rapid and efficient method and allowing early administration of an appropriate antibiotic therapy.

  20. Simultaneous observations of a pair of kilohertz QPOs and a plausible 1860 Hz QPO from an accreting neutron star system

    CERN Document Server

    Bhattacharyya, Sudip

    2009-01-01

    We report an indication (3.22 sigma) of ~ 1860 Hz quasi-periodic oscillations from a neutron star low-mass X-ray binary 4U 1636-536. If confirmed, this will be by far the highest frequency feature observed from an accreting neutron star system, and hence could be very useful to understand such systems. This plausible timing feature was observed simultaneously with lower (~ 585 Hz) and upper (~ 904 Hz) kilohertz quasi-periodic oscillations. The two kilohertz quasi-periodic oscillation frequencies had the ratio of ~ 1.5, and the frequency of the alleged ~ 1860 Hz feature was close to the triple and the double of these frequencies. This can be useful to constrain the models of all the three features. In particular, the ~ 1860 Hz feature could be (1) from a new and heretofore unknown class of quasi-periodic oscillations, or (2) the first observed overtone of lower or upper kilohertz quasi-periodic oscillations. Finally we note that, although the relatively low significance of the ~ 1860 Hz feature argues for caut...

  1. Rapid and specific detection of Salmonella in water samples using real-time PCR and High Resolution Melt (HRM) curve analysis.

    Science.gov (United States)

    van Blerk, G N; Leibach, L; Mabunda, A; Chapman, A; Louw, D

    2011-01-01

    A real-time PCR assay combined with a pre-enrichment step for the specific and rapid detection of Salmonella in water samples is described. Following amplification of the invA gene target, High Resolution Melt (HRM) curve analysis was used to discriminate between products formed and to positively identify invA amplification. The real-time PCR assay was evaluated for specificity and sensitivity. The assay displayed 100% specificity for Salmonella and combined with a 16-18 h non-selective pre-enrichment step, the assay proved to be highly sensitive with a detection limit of 1.0 CFU/ml for surface water samples. The detection assay also demonstrated a high intra-run and inter-run repeatability with very little variation in invA amplicon melting temperature. When applied to water samples received routinely by the laboratory, the assay showed the presence of Salmonella in particularly surface water and treated effluent samples. Using the HRM based assay, the time required for Salmonella detection was drastically shortened to less than 24 h compared to several days when using standard culturing methods. This assay provides a useful tool for routine water quality monitoring as well as for quick screening during disease outbreaks.

  2. Rapid diagnosis of acute hemorrhagic conjunctivitis due to coxsackievirus A24 variant by real-time one-step RT-PCR.

    Science.gov (United States)

    Lévêque, Nicolas; Lahlou Amine, Idriss; Tcheng, Remy; Falcon, Delphine; Rivat, Nathalie; Dussart, Philippe; Muyembe, Jean-Jacques; Chomel, Jean-Jacques; Norder, Helene; Eugene, Maxime; Lina, Bruno

    2007-06-01

    Coxsackievirus A24 variant is, together with enterovirus 70 and adenoviruses, the major etiological agent involved in acute hemorrhagic conjunctivitis outbreaks worldwide. However, the standard virus isolation method followed by serotyping or VP1 region sequencing is time-consuming. A rapid method for the detection of coxsackievirus A24 variant from conjunctival swab specimens would be useful in the context of explosive and extensive outbreaks. A one-step real-time RT-PCR assay based on TaqMan technology was thus developed and assessed on 36 conjunctival swabs from outbreaks of conjunctivitis in Morocco in 2004 due to a coxsackievirus A24 variant and in Corsica in 2006 due to adenovirus type 3, and 83 virus strains including 41 coxsackievirus A24 variant collected in French Guiana and Guadeloupe in 2003, in the Democratic Republic of the Congo in 2003, in Morocco in 2004 and 42 other virus species genetically close or known to be responsible for conjunctivitis. All the conjunctival swabs from coxsackievirus A24 variant related outbreak and the 41 coxsackievirus A24 variant strains were tested positive by the RT-PCR assay within 4h. This novel single-tube real-time RT-PCR assay is sensitive and specific, and consists in a reliable and faster alternative to the viral culture for recent and future acute hemorrhagic conjunctivitis outbreaks caused by coxsackievirus A24 variant.

  3. Rapid genome detection of Schmallenberg virus and bovine viral diarrhea virus by use of isothermal amplification methods and high-speed real-time reverse transcriptase PCR.

    Science.gov (United States)

    Aebischer, Andrea; Wernike, Kerstin; Hoffmann, Bernd; Beer, Martin

    2014-06-01

    Over the past few years, there has been an increasing demand for rapid and simple diagnostic tools that can be applied outside centralized laboratories by using transportable devices. In veterinary medicine, such mobile test systems would circumvent barriers associated with the transportation of samples and significantly reduce the time to diagnose important infectious animal diseases. Among a wide range of available technologies, high-speed real-time reverse transcriptase quantitative PCR (RT-qPCR) and the two isothermal amplification techniques loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) represent three promising candidates for integration into mobile pen-side tests. The aim of this study was to investigate the performance of these amplification strategies and to evaluate their suitability for field application. In order to enable a valid comparison, novel pathogen-specific assays have been developed for the detection of Schmallenberg virus and bovine viral diarrhea virus. The newly developed assays were evaluated in comparison with established standard RT-qPCR using samples from experimentally or field-infected animals. Even though all assays allowed detection of the target virus in less than 30 min, major differences were revealed concerning sensitivity, specificity, robustness, testing time, and complexity of assay design. These findings indicated that the success of an assay will depend on the integrated amplification technology. Therefore, the application-specific pros and cons of each method that were identified during this study provide very valuable insights for future development and optimization of pen-side tests.

  4. Rapid differentiation of Dirofilaria immitis and Dirofilaria repens in canine peripheral blood by real-time PCR coupled to high resolution melting analysis.

    Science.gov (United States)

    Albonico, Francesca; Loiacono, Monica; Gioia, Gloria; Genchi, Claudio; Genchi, Marco; Mortarino, Michele

    2014-02-24

    Dirofilaria immitis and D. repens are the principal causative agents of canine filariosis and, although the number of dogs subjected to specific prevention is increasing, the prevalence of these parasites remains high in many areas of the world. The discrimination between the two Dirofilaria species using the classical diagnostic methods can be difficult and may lead to misdiagnosis especially on samples from areas where both Dirofilaria are present. Over the last years, several molecular methods with higher sensitivity and specificity compared to classical microscopy and ELISA assays were designed. Nevertheless, a need for simple, rapid, and cost-effective molecular protocols to accurately discriminate between D. immitis and D. repens still remains. High resolution melting analysis coupled to real-time PCR (real-time PCR-HRMA) is a widely used technique to target sequence polymorphisms of the same gene in different species without the need to perform DNA sequencing or to use species-specific probes. In this work, a fast and cost-effective real-time PCR-HRMA protocol to detect and differentiate simultaneously and unequivocally D. immitis and D. repens microfilarial DNA extracted from peripheral dog blood samples is described. The present method is simpler to use than most other DNA-based methods and provides comparable discrimination between the two sibling species.

  5. A rapid inversion technique for the measurement of longitudinal relaxation times of brain metabolites: application to lactate in high-grade gliomas at 3 T.

    Science.gov (United States)

    Landheer, Karl; Sahgal, Arjun; Myrehaug, Sten; Chen, Albert P; Cunningham, Charles H; Graham, Simon J

    2016-10-01

    The aim of this study was to develop a time-efficient inversion technique to measure the T1 relaxation time of the methyl group of lactate (Lac) in the presence of contaminating lipids and to measure T1 at 3 T in a cohort of primary high-grade gliomas. Three numerically optimized inversion times (TIs) were chosen to minimize the expected error in T1 estimates for a given input total scan duration (set to be 30 min). A two-cycle spectral editing scheme was used to suppress contaminating lipids. The T1 values were then estimated from least-squares fitting of signal measurements versus TI. Lac T1 was estimated as 2000 ± 280 ms. After correcting for T1 (and T2 from literature values), the mean absolute Lac concentration was estimated as 4.3 ± 2.6 mm. The technique developed agrees with the results obtained by standard inversion recovery and can be used to provide rapid T1 estimates of other spectral components as required. Lac T1 exhibits similar variations to other major metabolites observable by MRS in high-grade gliomas. The T1 estimate provided here will be useful for future MRS studies wishing to report relaxation-corrected estimates of Lac concentration as an objective tumor biomarker. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  6. Rapid and accurate detection of Arcobacter contamination in commercial chicken products and wastewater samples by real-time polymerase chain reaction.

    Science.gov (United States)

    González, Ana; Suski, Jan; Ferrús, Maria A

    2010-03-01

    An SYBR Green real-time polymerase chain reaction (PCR) assay was developed for Arcobacter detection in food and wastewater samples. The assay was applied to 36 chicken and 33 wastewater samples, and the results were compared with those obtained for conventional PCR, multiplex PCR, and culture isolation. Isolates were identified by multiplex PCR and restriction fragment length polymorphism analysis of PCR-amplified DNA fragment, and typed by randomly amplified polymorphic DNA. Arcobacter sp. was detected in 25 of the 26 chicken carcasses (96%) and in 4 of the 10 liver samples (40%) by real-time PCR. Twenty-five chicken samples were positive also by conventional PCR, but in most of them the detection was only possible after 48-h enrichment. Arcobacter butzleri was the most frequently detected species. Twenty-four Arcobacter isolates were obtained from chicken samples, where A. butzleri is the only identified species. All the wastewater samples (100%) were positive for Arcobacter sp. by real-time PCR without enrichment. A. butzleri and Arcobacter cryaerophilus were detected by multiplex PCR. Fifteen samples were found to be positive by culture. Thirty-six isolates were obtained; all of them were identified as A. butzleri by multiplex PCR. However, by PCR-restriction fragment length polymorphism, 34 were identified as A. butzleri, 1 as A. cryaerophilus, and another 1 as Arcobacter skirrowii. A great genetic heterogeneity was observed by randomly amplified polymorphic DNA-PCR profiling. The real-time PCR assay developed in this work showed better detection levels than conventional PCR, together with shorter times of testing samples. Therefore, it could be used as a rapid and accurate instrument for monitoring Arcobacter contamination levels in food and water samples.

  7. Time-dependent effects of the flame retardant tris(1,3-dichloro-2-propyl) phosphate (TDCPP) on mRNA expression, in vitro and in ovo, reveal optimal sampling times for rapidly metabolized compounds.

    Science.gov (United States)

    Farhat, Amani; Crump, Doug; Porter, Emily; Chiu, Suzanne; Letcher, Robert J; Su, Guanyong; Kennedy, Sean W

    2014-12-01

    The flame retardant, tris(1,3-dichloro-2-propyl) phosphate (TDCPP), was previously shown to affect chicken embryo growth, gallbladder size, and lipid homeostasis. A microarray study, however, revealed only modest transcriptional alterations in liver tissue of pipping embryos (days 20-21), which was attributed to the rapid metabolism of TDCPP throughout incubation. To identify the most appropriate sampling time for rapidly metabolized compounds, the present study assessed the time-dependent effects of TDCPP on 27 genes, in ovo (50 µg [116 nmol] TDCPP/g egg) and in vitro (10 µM), using a chicken ToxChip polymerase chain reaction array. The greatest magnitude in dysregulation (up to 362-fold) occurred on day 8 of incubation (in ovo) with alterations of genes involved in phase I, II, and III metabolism, among others. Gallbladder hypotrophy was observed by embryonic day 12, corroborating the finding in pipping embryos from our previous study. From days 12 to 19, genes involved in lipid homeostasis, steroid hormone metabolism, and oxidative stress were affected. In chicken embryonic hepatoctyes (CEHs), TDCPP was completely metabolized to bis(1,3-dichloro-2-propyl) phosphate (BDCPP) within 36 h, but transcriptional changes remained significant up to 36 h. These changes were not attributed to BDCPP exposure as it only altered 1 gene (CYP1A4). An 18-h exposure in CEHs altered the greatest number of genes, making it an appropriate time point for high-throughput chemical screening; however, depending on the biological pathways of interest, shorter or longer incubation times may be more informative. Overall, TDCPP elicits the transcriptional and phenotypic alterations observed in vitro and in ovo, whereas its major metabolite, BDCPP, is far less biologically active.

  8. Rapid genotyping of cytomegalovirus in dried blood spots by multiplex real-time PCR assays targeting the envelope glycoprotein gB and gH genes.

    Science.gov (United States)

    de Vries, Jutte J C; Wessels, Els; Korver, Anna M H; van der Eijk, Annemiek A; Rusman, Lisette G; Kroes, Aloys C M; Vossen, Ann C T M

    2012-02-01

    Genotyping of cytomegalovirus (CMV) is useful to examine potential differences in the pathogenicity of strains and to demonstrate coinfection with multiple strains involved in CMV disease in adults and congenitally infected newborns. Studies on genotyping of CMV in dried blood spots (DBS) are rare and have been hampered by the small amount of dried blood available. In this study, two multiplex real-time PCR assays for rapid gB and gH genotyping of CMV in DBS were developed. Validation of the assays with 39 CMV-positive plasma samples of transplant recipients and 21 urine specimens of congenitally infected newborns was successful in genotyping 100% of the samples, with gB1 and gB3 being the most prevalent genotypes. Multiple gB and gH genotypes were detected in 36% and 33% of the plasma samples, respectively. One urine sample from a newborn with symptomatic congenital CMV was positive for gB1 and gB2. DBS of congenitally infected newborns (n = 41) were tested using 9 μl of dried blood, and genotypes were detected in 81% (gB) and 73% (gH) of the samples, with gB3 being the most prevalent genotype. No clear association of specific genotypes with clinical outcome was observed. In conclusion, the CMV gB and gH PCR assays were found to be rapid, sensitive for detecting mixed infections, and suitable for direct usage on DBS. These assays are efficient tools for genotyping of CMV in DBS of congenitally infected newborns.

  9. Performance of a new gelled nested PCR test for the diagnosis of imported malaria: comparison with microscopy, rapid diagnostic test, and real-time PCR.

    Science.gov (United States)

    Iglesias, Nuria; Subirats, Mercedes; Trevisi, Patricia; Ramírez-Olivencia, Germán; Castán, Pablo; Puente, Sabino; Toro, Carlos

    2014-07-01

    Microscopy and rapid diagnostic tests (RDTs) are the techniques commonly used for malaria diagnosis but they are usually insensitive at very low levels of parasitemia. Nested PCR is commonly used as a reference technique in the diagnosis of malaria due to its high sensitivity and specificity. However, it is a cumbersome assay only available in reference centers. We evaluated a new nested PCR-based assay, BIOMALAR kit (Biotools B&M Labs, Madrid, Spain) which employs ready-to-use gelled reagents and allows the identification of the main four species of Plasmodium. Blood samples were obtained from patients with clinical suspicion of malaria. A total of 94 subjects were studied. Fifty-two (55.3%) of them were malaria-infected subjects corresponding to 48 cases of Plasmodium falciparum, 1 Plasmodium malariae, 2 Plasmodium vivax, and 1 Plasmodium ovale. The performance of the BIOMALAR test was compared with microscopy, rapid diagnostic test (RDT) (BinaxNOW® Malaria) and real-time quantitative PCR (qPCR). The BIOMALAR test showed a sensitivity of 98.1% (95% confidence interval [CI], 89.7-100), superior to microscopy (82.7% [95% CI, 69.7-91.8]) and RDT (94.2% [95% CI, 84.1-98.8]) and similar to qPCR (100% [95% CI, 93.2-100]). In terms of specificity, the BIOMALAR assay showed the same value as microscopy and qPCR (100% [95% CI, 93.2-100]). Nine subjects were submicroscopic carriers of malaria. The BIOMALAR test identified almost all of them (8/9) in comparison with RDT (6/9) and microscopy (0/9). In conclusion, the BIOMALAR is a PCR-based assay easy to use with an excellent performance and especially useful for diagnosis submicroscopic malaria.

  10. Minimizing the extra-oral time in autogeneous tooth transplantation: use of computer-aided rapid prototyping (CARP as a duplicate model tooth

    Directory of Open Access Journals (Sweden)

    Seung-Jong Lee

    2012-08-01

    Full Text Available Objectives The maintenance of the healthy periodontal ligament cells of the root surface of donor tooth and intimate surface contact between the donor tooth and the recipient bone are the key factors for successful tooth transplantation. In order to achieve these purposes, a duplicated donor tooth model can be utilized to reduce the extra-oral time using the computer-aided rapid prototyping (CARP technique. Materials and Methods Briefly, a three-dimensional digital imaging and communication in medicine (DICOM image with the real dimensions of the donor tooth was obtained from a computed tomography (CT, and a life-sized resin tooth model was fabricated. Dimensional errors between real tooth, 3D CT image model and CARP model were calculated. And extra-oral time was recorded during the autotransplantation of the teeth. Results The average extra-oral time was 7 min 25 sec with the range of immediate to 25 min in cases which extra-oral root canal treatments were not performed while it was 9 min 15 sec when extra-oral root canal treatments were performed. The average radiographic distance between the root surface and the alveolar bone was 1.17 mm and 1.35 mm at mesial cervix and apex; they were 0.98 mm and 1.26 mm at the distal cervix and apex. When the dimensional errors between real tooth, 3D CT image model and CARP model were measured in cadavers, the average of absolute error was 0.291 mm between real teeth and CARP model. Conclusions These data indicate that CARP may be of value in minimizing the extra-oral time and the gap between the donor tooth and the recipient alveolar bone in tooth transplantation.

  11. Performance of the new automated Abbott RealTime MTB assay for rapid detection of Mycobacterium tuberculosis complex in respiratory specimens.

    Science.gov (United States)

    Chen, J H K; She, K K K; Kwong, T-C; Wong, O-Y; Siu, G K H; Leung, C-C; Chang, K-C; Tam, C-M; Ho, P-L; Cheng, V C C; Yuen, K-Y; Yam, W-C

    2015-09-01

    The automated high-throughput Abbott RealTime MTB real-time PCR assay has been recently launched for Mycobacterium tuberculosis complex (MTBC) clinical diagnosis. This study would like to evaluate its performance. We first compared its diagnostic performance with the Roche Cobas TaqMan MTB assay on 214 clinical respiratory specimens. Prospective analysis of a total 520 specimens was then performed to further evaluate the Abbott assay. The Abbott assay showed a lower limit of detection at 22.5 AFB/ml, which was more sensitive than the Cobas assay (167.5 AFB/ml). The two assays demonstrated a significant difference in diagnostic performance (McNemar's test; P = 0.0034), in which the Abbott assay presented significantly higher area under curve (AUC) than the Cobas assay (1.000 vs 0.880; P = 0.0002). The Abbott assay demonstrated extremely low PCR inhibition on clinical respiratory specimens. The automated Abbott assay required only very short manual handling time (0.5 h), which could help to improve the laboratory management. In the prospective analysis, the overall estimates for sensitivity and specificity of the Abbott assay were both 100 % among smear-positive specimens, whereas the smear-negative specimens were 96.7 and 96.1 %, respectively. No cross-reactivity with non-tuberculosis mycobacterial species was observed. The superiority in sensitivity of the Abbott assay for detecting MTBC in smear-negative specimens could further minimize the risk in MTBC false-negative detection. The new Abbott RealTime MTB assay has good diagnostic performance which can be a useful diagnostic tool for rapid MTBC detection in clinical laboratories.

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

    Science.gov (United States)

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

    2015-07-01

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

  13. Rapid detection of Opisthorchis viverrini and Strongyloides stercoralis in human fecal samples using a duplex real-time PCR and melting curve analysis.

    Science.gov (United States)

    Janwan, Penchom; Intapan, Pewpan M; Thanchomnang, Tongjit; Lulitanond, Viraphong; Anamnart, Witthaya; Maleewong, Wanchai

    2011-12-01

    Human opisthorchiasis caused by the liver fluke Opisthorchis viverrini is an endemic disease in Southeast Asian countries including the Lao People's Democratic Republic, Cambodia, Vietnam, and Thailand. Infection with the soil-transmitted roundworm Strongyloides stercoralis is an important problem worldwide. In some areas, both parasitic infections are reported as co-infections. A duplex real-time fluorescence resonance energy transfer (FRET) PCR merged with melting curve analysis was developed for the rapid detection of O. viverrini and S. stercoralis in human fecal samples. Duplex real-time FRET PCR is based on fluorescence melting curve analysis of a hybrid of amplicons generated from two genera of DNA elements: the 162 bp pOV-A6 DNA sequence specific to O. viverrini and the 244 bp 18S rRNA sequence specific to S. stercoralis, and two pairs of specific fluorophore-labeled probes. Both O. viverrini and S. stercoralis can be differentially detected in infected human fecal samples by this process through their different fluorescence channels and melting temperatures. Detection limit of the method was as little as two O. viverrini eggs and four S. stercoralis larvae in 100 mg of fecal sample. The assay could distinguish the DNA of both parasites from the DNA of negative fecal samples and fecal samples with other parasite materials, as well as from the DNA of human leukocytes and other control parasites. The technique showed 100% sensitivity and specificity. The introduced duplex real-time FRET PCR can reduce labor time and reagent costs and is not prone to carry over contamination. The method is important for simultaneous detection especially in areas where both parasites overlap incidence and is useful as the screening tool in the returning travelers and immigrants to industrialized countries where number of samples in the diagnostic units will become increasing.

  14. Comparison of plan quality and delivery time between volumetric arc therapy (RapidArc) and Gamma Knife radiosurgery for multiple cranial metastases.

    Science.gov (United States)

    Thomas, Evan M; Popple, Richard A; Wu, Xingen; Clark, Grant M; Markert, James M; Guthrie, Barton L; Yuan, Yu; Dobelbower, Michael C; Spencer, Sharon A; Fiveash, John B

    2014-10-01

    Volumetric modulated arc therapy (VMAT) has been shown to be feasible for radiosurgical treatment of multiple cranial lesions with a single isocenter. To investigate whether equivalent radiosurgical plan quality and reduced delivery time could be achieved in VMAT for patients with multiple intracranial targets previously treated with Gamma Knife (GK) radiosurgery. We identified 28 GK treatments of multiple metastases. These were replanned for multiarc and single-arc, single-isocenter VMAT (RapidArc) in Eclipse. The prescription for all targets was standardized to 18 Gy. Each plan was normalized for 100% prescription dose to 99% to 100% of target volume. Plan quality was analyzed by target conformity (Radiation Therapy Oncology Group and Paddick conformity indices [CIs]), dose falloff (area under the dose-volume histogram curve), as well as the V4.5, V9, V12, and V18 isodose volumes. Other end points included beam-on and treatment time. Compared with GK, multiarc VMAT improved median plan conformity (CIVMAT = 1.14, CIGK = 1.65; P < .001) with no significant difference in median dose falloff (P = .269), 12 Gy isodose volume (P = .500), or low isodose spill (P = .49). Multiarc VMAT plans were associated with markedly reduced treatment time. A predictive model of the 12 Gy isodose volume as a function of tumor number and volume was also developed. For multiple target stereotactic radiosurgery, 4-arc VMAT produced clinically equivalent conformity, dose falloff, 12 Gy isodose volume, and low isodose spill, and reduced treatment time compared with GK. Because of its similar plan quality and increased delivery efficiency, single-isocenter VMAT radiosurgery may constitute an attractive alternative to multi-isocenter radiosurgery for some patients.

  15. Rapid quantification of hepatitis B virus DNA by real-time PCR using efficient TaqMan probe and extraction of virus DNA

    Institute of Scientific and Technical Information of China (English)

    Yan-Qin Lu; Jin-Xiang Han; Peng Qi; Wei Xu; Yan-Hui Zu; Bo Zhu

    2006-01-01

    AIM: To rapidly quantify hepatitis B virus (HBV) DNA by real-time PCR using efficient TaqMan probe and extraction methods of virus DNA.METHODS: Three standards were prepared by cloning PCR products which targeted S, C and X region of HBV genome into pGEM-T vector respectively. A pair of primers and matched TaqMan probe were selected by comparing the copy number and the Ct values of HBV serum samples derived from the three different standard curves using certain serum DNA. Then the efficiency of six HBV DNA extraction methods including guanidinium isothiocyanate, proteinase K, NaI, NaOH lysis, alkaline lysis and simple boiling was analyzed in sample A, B and C by real-time PCR. Meanwhile, 8 clinical HBV serum samples were quantified.RESULTS: The copy number of the same HBV serum sample originated from the standard curve of S, C and Xregions was 5.7 x 104/mL, 6.3 x 102/mL and 1.6 x 103/mL respectively. The relative Ct value was 26.6, 31.8 and 29.5 respectively. Therefore, primers and matched probe from S region were chosen for further optimization of six extraction methods. The copy number of HBV serum samples A, B and C was 3.49 x 109/mL, 2.08 x 106/mL and 4.40 x 107/mL respectively, the relative Ct value was 19.9, 30 and 26.2 in the method of NaOH lysis,which was the efficientest among six methods. Simple boiling showed a slightly lower efficiency than NaOH lysis. Guanidinium isothiocyanate, proteinase K and NaI displayed that the copy number of HBV serum sample A,B and C was around 105/mL, meanwhile the Ct value was about 30. Alkaline failed to quantify the copy number of three HBV serum samples. Standard deviation (SD) and coefficient variation (CV) were very low in all 8 clinical HBV serum samples, showing that quantification of HBV DNA in triplicate was reliable and accurate.CONCLUSION: Real-time PCR based on optimized primers and TaqMan probe from S region in combination with NaOH lysis is a simple, rapid and accurate method for quantification of HBV serum DNA.

  16. Accuracy of a rapid real-time polymerase chain reaction assay for diagnosis of group B Streptococcus colonization in a cohort of HIV-infected pregnant women.

    Science.gov (United States)

    Gouvea, Maria Isabel S; Joao, Esau C; Teixeira, Maria de Lourdes B; Read, Jennifer S; Fracalanzza, Sergio E L; Souza, Claudia T V; Souza, Maria José de; Torres Filho, Helio M; Leite, Cassiana C F; do Brasil, Pedro E A A

    2017-05-01

    There are limited data regarding Xpert performance to detect Group B Streptococcus (GBS) in HIV-infected pregnant women. We evaluated the accuracy of a rapid real-time polymerase chain reaction (PCR) test in a cohort of HIV-infected women. At 35-37 weeks of pregnancy, a pair of combined rectovaginal swabs were collected for two GBS assays in a cohort of sequentially included HIV-infected women in Rio de Janeiro: (1) culture; and (2) real-time PCR assay [GeneXpert GBS (Cepheid, Sunnyvale, CA)]. Using culture as the reference, sensitivity, specificity, positive and negative-likelihood ratios were estimated. From June 2012 to February 2015, 337 pregnant women met inclusion criteria. One woman was later excluded, due to failure to obtain a result in the index test; 336 were included in the analyses. The GBS colonization rate was 19.04%. Sensitivity and specificity of the GeneXpert GBS assay were 85.94% (95% CI: 75.38-92.42) and 94.85% (95% CI: 91.55-96.91), respectively. Positive and negative predictive values were 79.71% (95% CI: 68.78-87.51) and 96.63% (95% CI: 93.72-98.22), respectively. GeneXpert GBS is an acceptable test for the identification of GBS colonization in HIV-infected pregnant women and represents a reasonable option to detect GBS colonization in settings where culture is not feasible.

  17. Direct analysis in real time-mass spectrometry (DART-MS) for rapid qualitative screening of toxic glycols in glycerin-containing products.

    Science.gov (United States)

    Self, Randy L

    2013-06-01

    In 2007, the United States Food and Drug Administration released guidance recommending testing of glycerin used in regulated consumer products, such as cough syrup preparations, toothpaste, and other pharmaceutical and food products, for the toxic compounds ethylene glycol and diethylene glycol. Regulatory laboratories routinely test glycerin, and products containing glycerin or related compounds for these toxic glycols, using an official gas chromatographic method, to ensure the safety of these products. The current work describes a companion technique to compliment this GC-FID method utilizing Orbitrap mass spectrometry with direct analysis in real time ionization to rapidly screen these samples qualitatively, with results in as little as five seconds, with no sample preparation required. This allows the more time and resource intensive method to be reserved for those rare cases when these compounds are detected, potentially greatly improving laboratory efficiency. The technique was evaluated for qualitative sensitivity and repeatability, and compared against the GC-FID method. The method appears to perform well against these metrics.

  18. Development of a rapid method to quantify Salmonella Typhimurium using a combination of MPN with qPCR and a shortened time incubation.

    Science.gov (United States)

    Kim, Sun Ae; Park, Si Hong; Lee, Sang In; Ricke, Steven C

    2017-08-01

    A novel method was developed for the specific quantification of S. Typhimurium using a most-probable-number (MPN) combined with qPCR and a shortened incubation time (MPN-qPCR-SIT). For S. Typhimurium enumeration, dilutions of samples were transferred into three wells on a microtiter plate and the plate was incubated for 4 h. The S. Typhimurium presence in the wells was identified using a qPCR and populations were determined based on an MPN calculation. The R(2) between the MPN-qPCR-SIT and conventional MPN exhibited a high level of correlation (0.9335-0.9752), suggesting that the MPN-qPCR-SIT offers a reliable alternative method for S. Typhimurium quantification. Although plating and qPCR were limited in their ability to detect low levels of S. Typhimurium (e.g. 0.18 log MPN/ml), these levels could be successfully detected with the MPN-qPCR-SIT. Chicken breast samples inoculated with S. Typhimurium were incubated at 0, 4, and 24 h and incubated samples were subjected to microbiome analysis. Levels of Salmonella and Enterobacteriaceae increased significantly with incubation time. The obvious benefits of the MPN-qPCR-SIT are: 1) a further confirmation step is not required, 2) the detection limit is as low as conventional MPN, but 3) is more rapid, requiring approximately 7 h to simultaneously complete quantification. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Rapid identification of erythrocyte phospholipids in Sprague-Dawley rats by ultra high performance liquid chromatography with electrospray ionization quadrupole time-of-flight tandem mass spectrometry.

    Science.gov (United States)

    Pi, Juanjuan; Wu, Xia; Yang, Shitian; Zeng, Pingyan; Feng, Yifan

    2015-03-01

    A rapid, sensitive, and reliable approach for analyzing five kinds of erythrocyte phospholipids in Sprague-Dawley rats was provided by ultra high performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry with MassLynx(TM) MassFragment. Improving conventional high performance liquid chromatography techniques, ultra high performance liquid chromatography integrated with quadrupole time-of-flight tandem mass spectrometry offers high sensitivity and increased analytical speed by using columns packed with sub-2 μm particles (1.7 μm), which allows a faster separation to be achieved. Through this method, 83 phospholipids were tentatively characterized based on their mass spectra and tandem mass spectra, as well as by matching the in-house formula database within a mass error of 5 ppm, including 40 phosphatidylcholines, 24 phosphatidyl ethanolamines, three phosphatidylinositols, six phosphatidylserines, and ten sphingomyelins. Our present results proved that the established method could be used to qualitatively analyze complex erythrocyte phospholipids in Sprague-Dawley rats and provide a useful data base for pharmacology and phospholipidomics to seek potential biomarkers of disease prediction.

  20. A Simple, Rapid and Reliable Method to Determine Imipramine and Desipramine in Mouse Serum Using Ultra-High-Performance Liquid Chromatography-Quadrupole-Time-of-Flight Mass Spectrometry.

    Science.gov (United States)

    Zhao, Jing; Shin, Yujin; Chun, Kwang-Hoon; Yoon, Hye-Ran; Lee, Jeongmi

    2016-04-01

    A rapid and sensitive ultra-high-performance liquid chromatography-quadrupole-time-of-flight mass spectrometric (UHPLC-Q-TOF-MS) method was developed for quantification of imipramine, one of the most widely used tricyclic antidepressants, and desipramine, an active metabolite of imipramine, in mouse serum. The developed method included a simple protein precipitation with acetonitrile in 50 μL of serum and analyte separation on an Acquity UPLC BEH C18 column using a gradient elution of acetonitrile with 0.1% formic acid and 20 mM ammonium formate. As a result, the entire analysis time was imipramine and desipramine, and calibration curves were linear over the concentration range of 5.0-1,000.0 and 5.0-250.0 ng mL(-1) for imipramine and desipramine, respectively. Intraday precisions at three levels were 2.2-3.6 and 1.7-4.2% for imipramine and desipramine, respectively, whereas interday precisions were 2.6-5.0 and 2.0-8.4% for imipramine and desipramine, respectively. Accuracy ranged between 93.6 and 106.6% for imipramine and 94.1 and 106.4% for desipramine. Absolute recovery was 96.0-97.6% for imipramine and 87.0-99.5% for desipramine. Finally, the described method was applied to mice administered with imipramine, demonstrating the suitability for quantification of imipramine and desipramine for therapeutic drug monitoring or bioequivalence studies.

  1. Time resolved long-wave infrared laser-induced breakdown spectroscopy of inorganic energetic materials by a rapid mercury-cadmium-telluride linear array detection system.

    Science.gov (United States)

    Yang, Clayton S-C; Jin, Feng; Trivedi, Sudhir; Brown, Eiei; Hommerich, Uwe; Khurgin, Jacob B; Samuels, Alan C

    2016-11-10

    A mercury-cadmium-telluride linear array detection system that is capable of rapidly capturing (∼1-5 s) a broad spectrum of atomic and molecular laser-induced breakdown spectroscopy (LIBS) emissions in the long-wave infrared region (LWIR, ∼5.6-10 μm) was recently developed. Similar to the conventional ultraviolet-visible LIBS, a broadband emission spectrum of condensed phase samples covering a 5.6-10 μm spectral region could be acquired from just a single laser-induced micro-plasma. Intense and distinct atomic and molecular LWIR emission signatures of various solid inorganic energetic materials were readily observed and identified. Time resolved emissions of inorganic energetic materials were studied to assess the lifetimes of LWIR atomic and molecular emissions. The LWIR atomic emissions generally decayed fast on the scale of tens of microseconds, while the molecular signature emissions from target molecules excited by the laser-induced plasma appeared to be very long lived (∼millisecond). The time dependence of emission intensities and peak wavelengths of these signature emissions gave an insight into the origin and the environment of the emitting target species. Moreover, observed lifetimes of these LWIR emissions can be utilized for further optimization of the signal quality and detection limits of this technique.

  2. Virtual neurorobotics (VNR to accelerate development of plausible neuromorphic brain architectures

    Directory of Open Access Journals (Sweden)

    Philip H Goodman

    2007-11-01

    Full Text Available Traditional research in artificial intelligence and machine learning has viewed the brain as a specially adapted information-processing system. More recently the field of social robotics has been advanced to capture the important dynamics of human cognition and interaction. An overarching societal goal of this research is to incorporate the resultant knowledge about intelligence into technology for prosthetic, assistive, security, and decision support applications. However, despite many decades of investment in learning and classification systems, this paradigm has yet to yield truly “intelligent” systems. For this reason, many investigators are now attempting to incorporate more realistic neuromorphic properties into machine learning systems, encouraged by over two decades of neuroscience research that has provided parameters that characterize the brain’s interdependent genomic, proteomic, metabolomic, anatomic, and electrophysiological networks. Given the complexity of neural systems, developing tenable models to capture the essence of natural intelligence for real-time application requires that we discriminate features underlying information processing and intrinsic motivation from those reflecting biological constraints (such as maintaining structural integrity and transporting metabolic products. We propose herein a conceptual framework and an iterative method of virtual neurorobotics (VNR intended to rapidly forward-engineer and test progressively more complex putative neuromorphic brain prototypes for their ability to support intrinsically intelligent, intentional interaction with humans. The VNR system is based on the viewpoint that a truly intelligent system must be driven by emotion rather than programmed tasking, incorporating intrinsic motivation and intentionality. We report pilot results of a closed-loop, real-time interactive VNR system with a spiking neural brain, and provide a video demonstration as online supplemental

  3. Virtual Neurorobotics (VNR) to Accelerate Development of Plausible Neuromorphic Brain Architectures.

    Science.gov (United States)

    Goodman, Philip H; Buntha, Sermsak; Zou, Quan; Dascalu, Sergiu-Mihai

    2007-01-01

    Traditional research in artificial intelligence and machine learning has viewed the brain as a specially adapted information-processing system. More recently the field of social robotics has been advanced to capture the important dynamics of human cognition and interaction. An overarching societal goal of this research is to incorporate the resultant knowledge about intelligence into technology for prosthetic, assistive, security, and decision support applications. However, despite many decades of investment in learning and classification systems, this paradigm has yet to yield truly "intelligent" systems. For this reason, many investigators are now attempting to incorporate more realistic neuromorphic properties into machine learning systems, encouraged by over two decades of neuroscience research that has provided parameters that characterize the brain's interdependent genomic, proteomic, metabolomic, anatomic, and electrophysiological networks. Given the complexity of neural systems, developing tenable models to capture the essence of natural intelligence for real-time application requires that we discriminate features underlying information processing and intrinsic motivation from those reflecting biological constraints (such as maintaining structural integrity and transporting metabolic products). We propose herein a conceptual framework and an iterative method of virtual neurorobotics (VNR) intended to rapidly forward-engineer and test progressively more complex putative neuromorphic brain prototypes for their ability to support intrinsically intelligent, intentional interaction with humans. The VNR system is based on the viewpoint that a truly intelligent system must be driven by emotion rather than programmed tasking, incorporating intrinsic motivation and intentionality. We report pilot results of a closed-loop, real-time interactive VNR system with a spiking neural brain, and provide a video demonstration as online supplemental material.

  4. Rapid identification and quantification of Campylobacter coli and Campylobacter jejuni by real-time PCR in pure cultures and in complex samples

    Science.gov (United States)

    2011-01-01

    Background Campylobacter spp., especially Campylobacter jejuni (C. jejuni) and Campylobacter coli (C. coli), are recognized as the leading human foodborne pathogens in developed countries. Livestock animals carrying Campylobacter pose an important risk for human contamination. Pigs are known to be frequently colonized with Campylobacter, especially C. coli, and to excrete high numbers of this pathogen in their faeces. Molecular tools, notably real-time PCR, provide an effective, rapid, and sensitive alternative to culture-based methods for the detection of C. coli and C. jejuni in various substrates. In order to serve as a diagnostic tool supporting Campylobacter epidemiology, we developed a quantitative real-time PCR method for species-specific detection and quantification of C. coli and C. jejuni directly in faecal, feed, and environmental samples. Results With a sensitivity of 10 genome copies and a linear range of seven to eight orders of magnitude, the C. coli and C. jejuni real-time PCR assays allowed a precise quantification of purified DNA from C. coli and C. jejuni. The assays were highly specific and showed a 6-log-linear dynamic range of quantification with a quantitative detection limit of approximately 2.5 × 102 CFU/g of faeces, 1.3 × 102 CFU/g of feed, and 1.0 × 103 CFU/m2 for the environmental samples. Compared to the results obtained by culture, both C. coli and C. jejuni real-time PCR assays exhibited a specificity of 96.2% with a kappa of 0.94 and 0.89 respectively. For faecal samples of experimentally infected pigs, the coefficients of correlation between the C. coli or C. jejuni real-time PCR assay and culture enumeration were R2 = 0.90 and R2 = 0.93 respectively. Conclusion The C. coli and C. jejuni real-time quantitative PCR assays developed in this study provide a method capable of directly detecting and quantifying C. coli and C. jejuni in faeces, feed, and environmental samples. These assays represent a new diagnostic tool for studying

  5. 基孔肯雅病毒荧光定量PCR检测方法的建立%Real-time PCR method for rapid detection of Chikungunya virus

    Institute of Scientific and Technical Information of China (English)

    杨宇; 白琳; 胡健萍; 姚李四; 魏莲; 杨志红; 王静

    2012-01-01

    Objective To establish a rapid, sensitive and specific detection method for detecting Chikungunya virus(CHIKV) using Real-time fluorescence quantitative PCR. Methods With specifically designed primers and a TaqMan probe on the highly conserved sequence of CHIKV through alignment, the sensitivity of the Real - time fluorescence quantitative PCR assay was optimized by evaluating different concentrations of primers and probes. Results A specific Real - time PCR method was developed with the sensitivity of 21 copies/μl for CHIKV, a synthetic CHIKV genome DNA as a positive control; Japanese encephalitis virus, Yellow fever virus, Dengue virus were using to examine the specificity. Conclusion Promising prospects of this assay could be expected for Chikungunya fever prevention and control.%目的 建立一种快速、敏感、特异的实时荧光定量PCR方法,检测基孔肯雅病毒.方法 通过序列比对挑选出基孔肯雅病毒基因组中高度保守的序列,在此序列上设计引物及TaqMan探针,建立实时荧光定量PCR反应体系.结果 经优化的荧光定量PCR方法有较好的灵敏度和特异性,对阳性对照质粒标准品的灵敏度可达21拷贝/μl,通过检测与传播媒介相似的流行性乙型脑炎病毒、黄热病毒、登革热病毒无交叉反应.结论 该方法的建立在基孔肯雅热的疾病防控方面有较好的应用前景.

  6. Locked Nucleic Acid Probe-Based Real-Time PCR Assay for the Rapid Detection of Rifampin-Resistant Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Yong Zhao

    Full Text Available Drug-resistant Mycobacterium tuberculosis can be rapidly diagnosed through nucleic acid amplification techniques by analyzing the variations in the associated gene sequences. In the present study, a locked nucleic acid (LNA probe-based real-time PCR assay was developed to identify the mutations in the rpoB gene associated with rifampin (RFP resistance in M. tuberculosis. Six LNA probes with the discrimination capability of one-base mismatch were designed to monitor the 23 most frequent rpoB mutations. The target mutations were identified using the probes in a "probe dropout" manner (quantification cycle = 0; thus, the proposed technique exhibited superiority in mutation detection. The LNA probe-based real-time PCR assay was developed in a two-tube format with three LNA probes and one internal amplification control probe in each tube. The assay showed excellent specificity to M. tuberculosis with or without RFP resistance by evaluating 12 strains of common non-tuberculosis mycobacteria. The limit of detection of M. tuberculosis was 10 genomic equivalents (GE/reaction by further introducing a nested PCR method. In a blind validation of 154 clinical mycobacterium isolates, 142/142 (100% were correctly detected through the assay. Of these isolates, 88/88 (100% were determined as RFP susceptible and 52/54 (96.3% were characterized as RFP resistant. Two unrecognized RFP-resistant strains were sequenced and were found to contain mutations outside the range of the 23 mutation targets. In conclusion, this study established a sensitive, accurate, and low-cost LNA probe-based assay suitable for a four-multiplexing real-time PCR instrument. The proposed method can be used to diagnose RFP-resistant tuberculosis in clinical laboratories.

  7. Locked Nucleic Acid Probe-Based Real-Time PCR Assay for the Rapid Detection of Rifampin-Resistant Mycobacterium tuberculosis.

    Science.gov (United States)

    Zhao, Yong; Li, Guilian; Sun, Chongyun; Li, Chao; Wang, Xiaochen; Liu, Haican; Zhang, Pingping; Zhao, Xiuqin; Wang, Xinrui; Jiang, Yi; Yang, Ruifu; Wan, Kanglin; Zhou, Lei

    2015-01-01

    Drug-resistant Mycobacterium tuberculosis can be rapidly diagnosed through nucleic acid amplification techniques by analyzing the variations in the associated gene sequences. In the present study, a locked nucleic acid (LNA) probe-based real-time PCR assay was developed to identify the mutations in the rpoB gene associated with rifampin (RFP) resistance in M. tuberculosis. Six LNA probes with the discrimination capability of one-base mismatch were designed to monitor the 23 most frequent rpoB mutations. The target mutations were identified using the probes in a "probe dropout" manner (quantification cycle = 0); thus, the proposed technique exhibited superiority in mutation detection. The LNA probe-based real-time PCR assay was developed in a two-tube format with three LNA probes and one internal amplification control probe in each tube. The assay showed excellent specificity to M. tuberculosis with or without RFP resistance by evaluating 12 strains of common non-tuberculosis mycobacteria. The limit of detection of M. tuberculosis was 10 genomic equivalents (GE)/reaction by further introducing a nested PCR method. In a blind validation of 154 clinical mycobacterium isolates, 142/142 (100%) were correctly detected through the assay. Of these isolates, 88/88 (100%) were determined as RFP susceptible and 52/54 (96.3%) were characterized as RFP resistant. Two unrecognized RFP-resistant strains were sequenced and were found to contain mutations outside the range of the 23 mutation targets. In conclusion, this study established a sensitive, accurate, and low-cost LNA probe-based assay suitable for a four-multiplexing real-time PCR instrument. The proposed method can be used to diagnose RFP-resistant tuberculosis in clinical laboratories.

  8. Multiplex, rapid and sensitive isothermal detection of nucleic-acid sequence by endonuclease restriction-mediated real-time multiple cross displacement amplification

    Directory of Open Access Journals (Sweden)

    Yi eWang

    2016-05-01

    Full Text Available We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA, which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5’ end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labelled at the 5’ end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5’ end short sequences and their complementary sequences, which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 minutes, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.

  9. Semantics-based plausible reasoning to extend the knowledge coverage of medical knowledge bases for improved clinical decision support.

    Science.gov (United States)

    Mohammadhassanzadeh, Hossein; Van Woensel, William; Abidi, Samina Raza; Abidi, Syed Sibte Raza

    2017-01-01

    Capturing complete medical knowledge is challenging-often due to incomplete patient Electronic Health Records (EHR), but also because of valuable, tacit medical knowledge hidden away in physicians' experiences. To extend the coverage of incomplete medical knowledge-based systems beyond their deductive closure, and thus enhance their decision-support capabilities, we argue that innovative, multi-strategy reasoning approaches should be applied. In particular, plausible reasoning mechanisms apply patterns from human thought processes, such as generalization, similarity and interpolation, based on attributional, hierarchical, and relational knowledge. Plausible reasoning mechanisms include inductive reasoning, which generalizes the commonalities among the data to induce new rules, and analogical reasoning, which is guided by data similarities to infer new facts. By further leveraging rich, biomedical Semantic Web ontologies to represent medical knowledge, both known and tentative, we increase the accuracy and expressivity of plausible reasoning, and cope with issues such as data heterogeneity, inconsistency and interoperability. In this paper, we present a Semantic Web-based, multi-strategy reasoning approach, which integrates deductive and plausible reasoning and exploits Semantic Web technology to solve complex clinical decision support queries. We evaluated our system using a real-world medical dataset of patients with hepatitis, from which we randomly removed different percentages of data (5%, 10%, 15%, and 20%) to reflect scenarios with increasing amounts of incomplete medical knowledge. To increase the reliability of the results, we generated 5 independent datasets for each percentage of missing values, which resulted in 20 experimental datasets (in addition to the original dataset). The results show that plausibly inferred knowledge extends the coverage of the knowledge base by, on average, 2%, 7%, 12%, and 16% for datasets with, respectively, 5%, 10%, 15%, and

  10. Biologic plausibility, cellular effects, and molecular mechanisms of eicosapentaenoic acid (EPA) in atherosclerosis.

    Science.gov (United States)

    Borow, Kenneth M; Nelson, John R; Mason, R Preston

    2015-09-01

    Residual cardiovascular (CV) risk remains in dyslipidemic patients despite intensive statin therapy, underscoring the need for additional intervention. Eicosapentaenoic acid (EPA), an omega-3 polyunsaturated fatty acid, is incorporated into membrane phospholipids and atherosclerotic plaques and exerts beneficial effects on the pathophysiologic cascade from onset of plaque formation through rupture. Specific salutary actions have been reported relating to endothelial function, oxidative stress, foam cell formation, inflammation, plaque formation/progression, platelet aggregation, thrombus formation, and plaque rupture. EPA also improves atherogenic dyslipidemia characterized by reduction of triglycerides without raising low-density lipoprotein cholesterol. Other beneficial effects of EPA include vasodilation, resulting in blood pressure reductions, as well as improved membrane fluidity. EPA's effects are at least additive to those of statins when given as adjunctive therapy. In this review, we present data supporting the biologic plausibility of EPA as an anti-atherosclerotic agent with potential clinical benefit for prevention of CV events, as well as its cellular effects and molecular mechanisms of action. REDUCE-IT is an ongoing, randomized, controlled study evaluating whether the high-purity ethyl ester of EPA (icosapent ethyl) at 4 g/day combined with statin therapy is superior to statin therapy alone for reducing CV events in high-risk patients with mixed dyslipidemia. The results from this study are expected to clarify the role of EPA as adjunctive therapy to a statin for reduction of residual CV risk.

  11. Mindfulness and Cardiovascular Disease Risk: State of the Evidence, Plausible Mechanisms, and Theoretical Framework.

    Science.gov (United States)

    Loucks, Eric B; Schuman-Olivier, Zev; Britton, Willoughby B; Fresco, David M; Desbordes, Gaelle; Brewer, Judson A; Fulwiler, Carl

    2015-12-01

    The purpose of this review is to provide (1) a synopsis on relations of mindfulness with cardiovascular disease (CVD) and major CVD risk factors, and (2) an initial consensus-based overview of mechanisms and theoretical framework by which mindfulness might influence CVD. Initial evidence, often of limited methodological quality, suggests possible impacts of mindfulness on CVD risk factors including physical activity, smoking, diet, obesity, blood pressure, and diabetes regulation. Plausible mechanisms include (1) improved attention control (e.g., ability to hold attention on experiences related to CVD risk, such as smoking, diet, physical activity, and medication adherence), (2) emotion regulation (e.g., improved stress response, self-efficacy, and skills to manage craving for cigarettes, palatable foods, and sedentary activities), and (3) self-awareness (e.g., self-referential processing and awareness of physical sensations due to CVD risk factors). Understanding mechanisms and theoretical framework should improve etiologic knowledge, providing customized mindfulness intervention targets that could enable greater mindfulness intervention efficacy.

  12. From ether to acid: A plausible degradation pathway of glycerol dialkyl glycerol tetraethers

    Science.gov (United States)

    Liu, Xiao-Lei; Birgel, Daniel; Elling, Felix J.; Sutton, Paul A.; Lipp, Julius S.; Zhu, Rong; Zhang, Chuanlun; Könneke, Martin; Peckmann, Jörn; Rowland, Steven J.; Summons, Roger E.; Hinrichs, Kai-Uwe

    2016-06-01

    Glycerol dialkyl glycerol tetraethers (GDGTs) are ubiquitous microbial lipids with extensive demonstrated and potential roles as paleoenvironmental proxies. Despite the great attention they receive, comparatively little is known regarding their diagenetic fate. Putative degradation products of GDGTs, identified as hydroxyl and carboxyl derivatives, were detected in lipid extracts of marine sediment, seep carbonate, hot spring sediment and cells of the marine thaumarchaeon Nitrosopumilus maritimus. The distribution of GDGT degradation products in environmental samples suggests that both biotic and abiotic processes act as sinks for GDGTs. More than a hundred newly recognized degradation products afford a view of the stepwise degradation of GDGT via (1) ether bond hydrolysis yielding hydroxyl isoprenoids, namely, GDGTol (glycerol dialkyl glycerol triether alcohol), GMGD (glycerol monobiphytanyl glycerol diether), GDD (glycerol dibiphytanol diether), GMM (glycerol monobiphytanol monoether) and bpdiol (biphytanic diol); (2) oxidation of isoprenoidal alcohols into corresponding carboxyl derivatives and (3) chain shortening to yield C39 and smaller isoprenoids. This plausible GDGT degradation pathway from glycerol ethers to isoprenoidal fatty acids provides the link to commonly detected head-to-head linked long chain isoprenoidal hydrocarbons in petroleum and sediment samples. The problematic C80 to C82 tetraacids that cause naphthenate deposits in some oil production facilities can be generated from H-shaped glycerol monoalkyl glycerol tetraethers (GMGTs) following the same process, as indicated by the distribution of related derivatives in hydrothermally influenced sediments.

  13. Plausible molecular and crystal structures of chitosan/HI type II salt.

    Science.gov (United States)

    Lertworasirikul, Amornrat; Noguchi, Keiichi; Ogawa, Kozo; Okuyama, Kenji

    2004-03-15

    Chitosan/HI type II salt prepared from crab tendon was investigated by X-ray fiber diffraction. Two polymer chains and 16 iodide ions (I(-)) crystallized in a tetragonal unit cell with lattice parameters of a = b = 10.68(3), c (fiber axis) = 40.77(13) A, and a space group P4(1). Chitosan forms a fourfold helix with a 40.77 A fiber period having a disaccharide as the helical asymmetric unit. One of the O-3... O-5 intramolecular hydrogen bonds at the glycosidic linkage is weakened by interacting with iodide ions, which seems to cause the polymer to take the 4/1-helical symmetry rather than the extended 2/1-helix. The plausible orientations of two O-6 atoms in the helical asymmetric unit were found to be gt and gg. Two chains are running through at the corner and the center of the unit cell along the c-axis. They are linked by hydrogen bonds between N-21 and O-61 atoms. Two out of four independent iodide ions are packed between the corner chains while the other two are packed between the corner and center chains when viewing through the ab-plane. The crystal structure of the salt is stabilized by hydrogen bonds between these iodide ions and N-21, N-22, O-32, O-61, O-62 of the polymer chains.

  14. Solvent effects on the photochemistry of 4-aminoimidazole-5-carbonitrile, a prebiotically plausible precursor of purines.

    Science.gov (United States)

    Szabla, Rafał; Sponer, Judit E; Sponer, Jiří; Sobolewski, Andrzej L; Góra, Robert W

    2014-09-01

    4-Aminoimidazole-5-carbonitrile (AICN) was suggested as a prebiotically plausible precursor of purine nucleobases and nucleotides. Although it can be formed in a sequence of photoreactions, AICN is immune to further irradiation with UV-light. We present state-of-the-art multi-reference quantum-chemical calculations of potential energy surface cuts and conical intersection optimizations to explain the molecular mechanisms underlying the photostability of this compound. We have identified the N-H bond stretching and ring-puckering mechanisms that should be responsible for the photochemistry of AICN in the gas phase. We have further considered the photochemistry of AICN-water clusters, while including up to six explicit water molecules. The calculations reveal charge transfer to solvent followed by formation of an H3O(+) cation, both of which occur on the (1)πσ* hypersurface. Interestingly, a second proton transfer to an adjacent water molecule leads to a (1)πσ*/S0 conical intersection. We suggest that this electron-driven proton relay might be characteristic of low-lying (1)πσ* states in chromophore-water clusters. Owing to its nature, this mechanism might also be responsible for the photostability of analogous organic molecules in bulk water.

  15. Vitamin D in primary biliary cirrhosis, a plausible marker of advanced disease.

    Science.gov (United States)

    Agmon-Levin, Nancy; Kopilov, Ron; Selmi, Carlo; Nussinovitch, Udi; Sánchez-Castañón, María; López-Hoyos, Marcos; Amital, Howie; Kivity, Shaye; Gershwin, Eric M; Shoenfeld, Yehuda

    2015-02-01

    Vitamin D immune-modulating effects were extensively studied, and low levels have been linked with autoimmune diseases. The associations of vitamin D with autoimmune diseases of the liver, and particularly primary biliary cirrhosis (PBC), are yet to be defined. Hence, in this study, serum levels of vitamin D were determined in 79 patients with PBC and 70 age- and sex-matched controls by the LIAISON chemiluminescent immunoassays (DiaSorin-Italy). Clinical and serological parameters of patients were analyzed with respect to vitamin D status. Mean levels of vitamin D were significantly lower among patients with PBC compared with controls (16.8 ± 9 vs. 22.1 ± 9 ng/ml; p = 0.029), and vitamin D deficiency (≤10 ng/ml) was documented in 33% of patients with PBC versus 7% of controls (p plausible roles of vitamin D as a prognostic marker of PBC severity, and as a potential player in this disease pathogenesis. While further studies are awaited, monitoring vitamin D in patients with PBC and use of supplements may be advisable.

  16. Is the de Broglie-Bohm interpretation of quantum mechanics really plausible?

    Science.gov (United States)

    Jung, Kurt

    2013-06-01

    Bohmian mechanics also known as de Broglie-Bohm theory is the most popular alternative approach to quantum mechanics. Whereas the standard interpretation of quantum mechanics is based on the complementarity principle Bohmian mechanics assumes that both particle and wave are concrete physical objects. In 1993 Peter Holland has written an ardent account on the plausibility of the de Broglie-Bohm theory. He proved that it fully reproduces quantum mechanics if the initial particle distribution is consistent with a solution of the Schrödinger equation. Which may be the reasons that Bohmian mechanics has not yet found global acceptance? In this article it will be shown that predicted properties of atoms and molecules are in conflict with experimental findings. Moreover it will be demonstrated that repeatedly published ensembles of trajectories illustrating double slit diffraction processes do not agree with quantum mechanics. The credibility of a theory is undermined when recognizably wrong data presented frequently over years are finally not declared obsolete.

  17. Rapid identification of bacillus anthracis spores in suspicious powder samples by using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)

    NARCIS (Netherlands)

    Dybwad, M.; Laaken, A.L. van der; Blatny, J.M.; Paauw, A.

    2013-01-01

    Rapid and reliable identification of Bacillus anthracis spores in suspicious powders is important to mitigate the safety risks and economic burdens associated with such incidents. The aim of this study was to develop and validate a rapid and reliable laboratory- based matrix-assisted laser desorptio

  18. A Real Time Quality Monitoring System for the Lighting Industry: A Practical and Rapid Approach Using Computer Vision and Image Processing (CVIP Tools

    Directory of Open Access Journals (Sweden)

    C.K. Ng

    2011-11-01

    Full Text Available In China, the manufacturing of lighting products is very labour intensive. The approach used to check quality and control production relies on operators who test using various types of fixtures. In order to increase the competitiveness of the manufacturer and the efficiency of production, the authors propose an integrated system. This system has two major elements: a computer vision system (CVS and a real‐time monitoring system (RTMS. This model focuses not only on the rapid and practical application of modern technology to a traditional industry, but also represents a process innovation in the lighting industry. This paper describes the design and development of the prototyped lighting inspection system based on a practical and fast approach using computer vision and imaging processing (CVIP tools. LabVIEW with IMAQ Vision Builder is the chosen tool for building the CVS. Experimental results show that this system produces a lower error rate than humans produce in the quality checking process. The whole integrated manufacturing strategy, aimed at achieving a better performance, is most suitable for a China and other labour intensive environments such as India.

  19. Rapid detection and simultaneous genotyping of Cronobacter spp. (formerly Enterobacter sakazakii in powdered infant formula using real-time PCR and high resolution melting (HRM analysis.

    Directory of Open Access Journals (Sweden)

    Xian-Quan Cai

    Full Text Available Cronobacter spp. is an emerging pathogen that causes meningitis, sepsis, bacteremia, and necrotizing enterocolitis in neonates and children. The present study developed an assay integrating real-time PCR and high resolution melting (HRM analysis targeting the OmpA gene for the specific detection and rapid identification of Cronobacter spp. (formerly Enterobacter sakazakii in powdered infant formula. Eleven Cronobacter field isolates and 25 reference strains were examined using one pair of primers, having the accuracy of 100% in reference to conventional methods. The assay was proved to be highly sensitive with a detection limit of 10(2 CFU/ml without pre-enrichment, and highly concordant (100% when compared with ISO-IDF 22964 in 89 actual samples. The method performed for Cronobacter spp. detection was less than 24 h, drastically shortened, compared to several days using standard culturing method, it is probe-free and reduces a risk of PCR carryover. Moreover, all Cronobacter strains examined in this study were genotyped into two species according to their HRM profiles. The established method should provide a molecular tool for direct detection and simultaneous genotyping of Cronobacter spp. in powdered infant formula.

  20. Detecting quinoxaline-2-carboxylic acid in animal tissues by using sensitive rapid enzyme-linked immunosorbent assay and time-resolved fluoroimmunoassay.

    Science.gov (United States)

    Le, Tao; Yu, Huan; Niu, Xiaodong

    2015-05-15

    An indirect competitive enzyme-linked immunosorbent assay (ic-ELISA) and time-resolved fluoroimmunoassay (TR-FIA) based on an anti-N-butylquinoxaline-2-carboxamide (BQCA) monoclonal antibody were standardized and validated for quinoxaline-2-carboxylic acid (QCA) screening in animal tissues and its performance were compared to HPLC. The sensitivities obtained for edible tissue extracts were 1.62 and 1.12 ng ml(-1) for ic-ELISA and TR-FIA detection, respectively. Two samples were spiked with QCA and analyzed by both methods. The recovery values ranged from 92.6% to 112.2% and the coefficients of variation were less than 15% for QCA spiking into swine tissue samples at concentrations of 2.5-50.0 μg kg(-1). Excellent correlations (r(2)=0.987-0.996) of the ic-ELISA/HPLC and TR-FIA/HPLC data were observed for processed samples. The results demonstrated that the ic-ELISA and TR-FIA methods were rapid and accurate for the residue detection of QCA in animal tissues.

  1. Rapid Detection of the GSTM3 A/B Polymorphism Using Real-time PCR with TaqMan(®) Probes.

    Science.gov (United States)

    Martínez-Treviño, Denisse A; Moreno-Treviño, María G; Salinas-Santander, Mauricio; Wohn, Luisa; Herrera-González, Sarahí; Aguirre-Garza, Marcelino; Rojas, O Carolina; León-Cachón, Rafael B R

    2016-02-01

    Glutathione S-transferases (GSTs) are a group of phase II detoxification enzymes, which catalyze the conjugation of glutathione (GSH) with carcinogens, among other xenobiotics. The GSTM3 gene is part of the GSTs gene family, and its polymorphism A/B has been associated with risk and protective effects of several cancers. This genetic variant is a deletion of 3 bp (AGG) in intron 6. Previous association studies have performed genotyping using techniques such as polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). In this study, we took advantage of the TaqMan(®) probes features and developed a reliable, faster, more simple and economic method to identify the 3-bp deletion. Our allelic discrimination method was able to distinguish between homozygous A/A, heterozygous A/B and homozygous B/B samples, as shown by TaqMan(®) based real-time PCR. Results were validated by Sanger Sequencing. In conclusion, we developed a specific and rapid method to detect the 3-bp deletion from the GSTM3 A/B polymorphism.

  2. Development of a Taqman real-time PCR assay for rapid detection and quantification of Vibrio tapetis in extrapallial fluids of clams

    Directory of Open Access Journals (Sweden)

    Adeline Bidault

    2015-12-01

    Full Text Available The Gram-negative bacterium Vibrio tapetis is known as the causative agent of Brown Ring Disease (BRD in the Manila clam Venerupis (=Ruditapes philippinarum. This bivalve is the second most important species produced in aquaculture and has a high commercial value. In spite of the development of several molecular methods, no survey has been yet achieved to rapidly quantify the bacterium in the clam. In this study, we developed a Taqman real-time PCR assay targeting virB4 gene for accurate and quantitative identification of V. tapetis strains pathogenic to clams. Sensitivity and reproducibility of the method were assessed using either filtered sea water or extrapallial fluids of clam injected with the CECT4600T V. tapetis strain. Quantification curves of V. tapetis strain seeded in filtered seawater (FSW or extrapallial fluids (EF samples were equivalent showing reliable qPCR efficacies. With this protocol, we were able to specifically detect V. tapetis strains down to 1.125 101 bacteria per mL of EF or FSW, taking into account the dilution factor used for appropriate template DNA preparation. This qPCR assay allowed us to monitor V. tapetis load both experimentally or naturally infected Manila clams. This technique will be particularly useful for monitoring the kinetics of massive infections by V. tapetis and for designing appropriate control measures for aquaculture purposes.

  3. Rapid and nondestructive analysis of phthalic acid esters in toys made of poly(vinyl chloride) by direct analysis in real time single-quadrupole mass spectrometry.

    Science.gov (United States)

    Rothenbacher, Thorsten; Schwack, Wolfgang

    2009-09-01

    In the European Community, selected phthalic acid esters (PAE) are restricted in their use for the manufacture of toys and childcare articles to a content of 0.1% by weight. As PAE are mainly used as plasticisers for poly(vinyl chloride) (PVC), a rapid screening method for PVC samples with direct analysis in real time ionisation and single-quadrupole mass spectrometry (DART-MS) was developed. Using the ions for the protonated molecules, a limit of detection (LOD) of 0.05% was obtained for benzyl butyl phthalate, bis(2-ethylhexyl) phthalate and diisononyl phthalate, while for dibutyl phthalate, di-n-octyl phthalate and diisodecyl phthalate the LOD was 0.1%. Validation of identification by the presence of ammonium adducts and characteristic fragment ions was possible to a content of >or=1% for all PAE, except for benzyl butyl phthalate (>or=5%). Based on the fragment ions, bis(2-ethylhexyl) phthalate could clearly be distinguished from di-n-octyl phthalate, if the concentrations were >r=5% and >or=1% at measured DART helium temperatures of 130 and 310 degrees C, respectively. The complete analysis of one sample only took about 8 min. At the generally used gas temperature of 130 degrees C, most toy and childcare samples did not sustain damage if their shape fitted into the DART source. Copyright (c) 2009 John Wiley & Sons, Ltd.

  4. Rapid detection and characterization of surface CO2 leakage through the real-time measurement of δ13C signatures in CO2 flux from the ground

    Science.gov (United States)

    Krevor, Samuel; Benson, Sally; Rella, Chris; Perrin, Jean-Christophe; Esposito, Ariel; Crosson, Eric

    2010-05-01

    The surface monitoring of CO2 over geologic sequestration sites will be an essential tool in the monitoring and verification of sequestration projects. Surface monitoring is the only tool that currently provides the opportunity to detect and quantify leakages on the order of 1000 tons/year CO2. Near-surface detection and quantification can be made complicated, however, due to large temporal and spatial variations in natural background CO2 fluxes from biological processes. In addition, current surface monitoring technologies, such as the use of IR spectroscopy in eddy covariance towers and aerial surveys, radioactive or noble gas isotopic tracers, and flux chamber gas measurements can generally accomplish one or two of the necessary tasks of leak detection, identification, and quantification, at both large spatial scales and high spatial resolution. It would be useful, however, to combine the utility of these technologies so that a much simplified surface monitoring program can be deployed. Carbon isotopes of CO2 provide an opportunity to distinguish between natural biogenic CO2 fluxes from the ground and CO2 leaking from a sequestration reservoir that has ultimate origins in a process giving it a distinct isotopic signature such as natural gas processing. Until recently, measuring isotopic compositions of gases was a time-consuming and expensive process utilizing mass-spectrometry, not practical for deployment in a high-resolution survey of a potential leakage site at the surface. Recent developments in commercially available instruments utilizing wavelength scanned cavity ringdown spectroscopy (WS-CRDS) and Fourier transform infrared spectroscopy (FT-IR) have made it possible to rapidly measure the isotopic composition of gases including the 13C and 12C isotopic composition of CO2 in a field setting. A portable stable carbon isotope ratio analyzer for carbon dioxide, based on wavelength scanned cavity ringdown spectroscopy, has been used to rapidly detect and

  5. Rapid detection of multidrug-resistant Mycobacterium tuberculosis by use of real-time PCR and high-resolution melt analysis.

    Science.gov (United States)

    Ramirez, Melissa V; Cowart, Kelley C; Campbell, Patricia J; Morlock, Glenn P; Sikes, David; Winchell, Jonas M; Posey, James E

    2010-11-01

    The current study describes the development of a unique real-time PCR assay for the detection of mutations conferring drug resistance in Mycobacterium tuberculosis. The rifampicin resistance determinant region (RRDR) of rpoB and specific regions of katG and the inhA promoter were targeted for the detection of rifampin (RIF) and isoniazid (INH) resistance, respectively. Additionally, this assay was multiplexed to discriminate Mycobacterium tuberculosis complex (MTC) strains from nontuberculous Mycobacteria (NTM) strains by targeting the IS6110 insertion element. High-resolution melting (HRM) analysis following real-time PCR was used to identify M. tuberculosis strains containing mutations at the targeted loci, and locked nucleic acid (LNA) probes were used to enhance the detection of strains containing specific single-nucleotide polymorphism (SNP) transversion mutations. This method was used to screen 252 M. tuberculosis clinical isolates, including 154 RIF-resistant strains and 174 INH-resistant strains based on the agar proportion method of drug susceptibility testing (DST). Of the 154 RIF-resistant strains, 148 were also resistant to INH and therefore classified as multidrug resistant (MDR). The assay demonstrated sensitivity and specificity of 91% and 98%, respectively, for the detection of RIF resistance and 87% and 100% for the detection of INH resistance. Overall, this assay showed a sensitivity of 85% and a specificity of 98% for the detection of MDR strains. This method provides a rapid, robust, and inexpensive way to detect the dominant mutations known to confer MDR in M. tuberculosis strains and offers several advantages over current molecular and culture-based techniques.

  6. Rapid detection of carbapenem resistance in Acinetobacter baumannii using matrix-assisted laser desorption ionization-time of flight mass spectrometry.

    Directory of Open Access Journals (Sweden)

    Marie Kempf

    Full Text Available Rapid detection of carbapenem-resistant Acinetobacter baumannii strains is critical and will benefit patient care by optimizing antibiotic therapies and preventing outbreaks. Herein we describe the development and successful application of a mass spectrometry profile generated by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF that utilized the imipenem antibiotic for the detection of carbapenem resistance in a large series of A. baumannii clinical isolates from France and Algeria. A total of 106 A. baumannii strains including 63 well-characterized carbapenemase-producing and 43 non-carbapenemase-producing strains, as well as 43 control strains (7 carbapenem-resistant and 36 carbapenem-sensitive strains were studied. After an incubation of bacteria with imipenem for up to 4 h, the mixture was centrifuged and the supernatant analyzed by MALDI-TOF MS. The presence and absence of peaks representing imipenem and its natural metabolite was analyzed. The result was interpreted as positive for carbapenemase production if the specific peak for imipenem at 300.0 m/z disappeared during the incubation time and if the peak of the natural metabolite at 254.0 m/z increased as measured by the area under the curves leading to a ratio between the peak for imipenem and its metabolite being <0.5. This assay, which was applied to the large series of A. baumannii clinical isolates, showed a sensitivity of 100.0% and a specificity of 100.0%. Our study is the first to demonstrate that this quick and simple assay can be used as a routine tool as a point-of-care method for the identification of A. baumannii carbapenemase-producers in an effort to prevent outbreaks and the spread of uncontrollable superbugs.

  7. Rapid Detection of Carbapenem Resistance in Acinetobacter baumannii Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

    Science.gov (United States)

    Flaudrops, Christophe; Berrazeg, Meryem; Brunel, Jean-Michel; Drissi, Mourad; Mesli, Esma; Touati, Abdelaziz; Rolain, Jean-Marc

    2012-01-01

    Rapid detection of carbapenem-resistant Acinetobacter baumannii strains is critical and will benefit patient care by optimizing antibiotic therapies and preventing outbreaks. Herein we describe the development and successful application of a mass spectrometry profile generated by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) that utilized the imipenem antibiotic for the detection of carbapenem resistance in a large series of A. baumannii clinical isolates from France and Algeria. A total of 106 A. baumannii strains including 63 well-characterized carbapenemase-producing and 43 non-carbapenemase-producing strains, as well as 43 control strains (7 carbapenem-resistant and 36 carbapenem-sensitive strains) were studied. After an incubation of bacteria with imipenem for up to 4 h, the mixture was centrifuged and the supernatant analyzed by MALDI-TOF MS. The presence and absence of peaks representing imipenem and its natural metabolite was analyzed. The result was interpreted as positive for carbapenemase production if the specific peak for imipenem at 300.0 m/z disappeared during the incubation time and if the peak of the natural metabolite at 254.0 m/z increased as measured by the area under the curves leading to a ratio between the peak for imipenem and its metabolite being <0.5. This assay, which was applied to the large series of A. baumannii clinical isolates, showed a sensitivity of 100.0% and a specificity of 100.0%. Our study is the first to demonstrate that this quick and simple assay can be used as a routine tool as a point-of-care method for the identification of A. baumannii carbapenemase-producers in an effort to prevent outbreaks and the spread of uncontrollable superbugs. PMID:22359616

  8. Developing spatially explicit footprints of plausible land-use scenarios in the Santa Cruz Watershed, Arizona and Sonora

    Science.gov (United States)

    Norman, Laura M.; Feller, Mark; Villarreal, Miguel L.

    2012-01-01

    The SLEUTH urban growth model is applied to a binational dryland watershed to envision and evaluate plausible future scenarios of land use change into the year 2050. Our objective was to create a suite of geospatial footprints portraying potential land use change that can be used to aid binational decision-makers in assessing the impacts relative to sustainability of natural resources and potential socio-ecological consequences of proposed land-use management. Three alternatives are designed to simulate different conditions: (i) a Current Trends Scenario of unmanaged exponential growth, (ii) a Conservation Scenario with managed growth to protect the environment, and (iii) a Megalopolis Scenario in which growth is accentuated around a defined international trade corridor. The model was calibrated with historical data extracted from a time series of satellite images. Model materials, methodology, and results are presented. Our Current Trends Scenario predicts the footprint of urban growth to approximately triple from 2009 to 2050, which is corroborated by local population estimates. The Conservation Scenario results in protecting 46% more of the Evergreen class (more than 150,000 acres) than the Current Trends Scenario and approximately 95,000 acres of Barren Land, Crops, Deciduous Forest (Mesquite Bosque), Grassland/Herbaceous, Urban/Recreational Grasses, and Wetlands classes combined. The Megalopolis Scenario results also depict the preservation of some of these land-use classes compared to the Current Trends Scenario, most notably in the environmentally important headwaters region. Connectivity and areal extent of land cover types that provide wildlife habitat were preserved under the alternative scenarios when compared to Current Trends.

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

    Science.gov (United States)

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

    2010-04-01

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

  10. Cultural group selection is plausible, but the predictions of its hypotheses should be tested with real-world data.

    Science.gov (United States)

    Turchin, Peter; Currie, Thomas E

    2016-01-01

    The evidence compiled in the target article demonstrates that the assumptions of cultural group selection (CGS) theory are often met, and it is therefore a useful framework for generating plausible hypotheses. However, more can be said about how we can test the predictions of CGS hypotheses against competing explanations using historical, archaeological, and anthropological data.

  11. Flux-based transport enhancement as a plausible unifying mechanism for auxin transport in meristem development.

    Directory of Open Access Journals (Sweden)

    Szymon Stoma

    2008-10-01

    Full Text Available Plants continuously generate new organs through the activity of populations of stem cells called meristems. The shoot apical meristem initiates leaves, flowers, and lateral meristems in highly ordered, spiralled, or whorled patterns via a process called phyllotaxis. It is commonly accepted that the active transport of the plant hormone auxin plays a major role in this process. Current hypotheses propose that cellular hormone transporters of the PIN family would create local auxin maxima at precise positions, which in turn would lead to organ initiation. To explain how auxin transporters could create hormone fluxes to distinct regions within the plant, different concepts have been proposed. A major hypothesis, canalization, proposes that the auxin transporters act by amplifying and stabilizing existing fluxes, which could be initiated, for example, by local diffusion. This convincingly explains the organised auxin fluxes during vein formation, but for the shoot apical meristem a second hypothesis was proposed, where the hormone would be systematically transported towards the areas with the highest concentrations. This implies the coexistence of two radically different mechanisms for PIN allocation in the membrane, one based on flux sensing and the other on local concentration sensing. Because these patterning processes require the interaction of hundreds of cells, it is impossible to estimate on a purely intuitive basis if a particular scenario is plausible or not. Therefore, computational modelling provides a powerful means to test this type of complex hypothesis. Here, using a dedicated computer simulation tool, we show that a flux-based polarization hypothesis is able to explain auxin transport at the shoot meristem as well, thus providing a unifying concept for the control of auxin distribution in the plant. Further experiments are now required to distinguish between flux-based polarization and other hypotheses.

  12. Identifying and reducing potentially wrong immunoassay results even when plausible and "not-unreasonable".

    Science.gov (United States)

    Ismail, Adel A A

    2014-01-01

    The primary role of the clinical laboratory is to report accurate results for diagnosis of disease and management of illnesses. This goal has, to a large extent been achieved for routine biochemical tests, but not for immunoassays which remained susceptible to interference from endogenous immunoglobulin antibodies, causing false, and clinically misleading results. Clinicians regard all abnormal results including false ones as "pathological" necessitating further investigations, or concluding iniquitous diagnosis. Even more seriously, "false-negative" results may wrongly exclude pathology, thus denying patients' necessary treatment. Analytical error rate in immunoassays is relatively high, ranging from 0.4% to 4.0%. Because analytical interference from endogenous antibodies is confined to individuals' sera, it can be inconspicuous, pernicious, sporadic, and insidious because it cannot be detected by internal or external quality assessment procedures. An approach based on Bayesian reasoning can enhance the robustness of clinical validation in highlighting potentially erroneous immunoassay results. When this rational clinical/statistical approach is followed by analytical affirmative follow-up tests, it can help identifying inaccurate and clinically misleading immunoassay data even when they appear plausible and "not-unreasonable." This chapter is largely based on peer reviewed articles associated with and related to this approach. The first section underlines (without mathematical equations) the dominance and misuse of conventional statistics and the underuse of Bayesian paradigm and shows that laboratorians are intuitively (albeit unwittingly) practicing Bayesians. Secondly, because interference from endogenous antibodies is method's dependent (with numerous formats and different reagents), it is almost impossible to accurately assess its incidence in all differently formulated immunoassays and for each analytes/biomarkers. However, reiterating the basic concepts

  13. Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation

    KAUST Repository

    Abdellah, Marwan

    2017-02-15

    Background We present a visualization pipeline capable of accurate rendering of highly scattering fluorescent neocortical neuronal models. The pipeline is mainly developed to serve the computational neurobiology community. It allows the scientists to visualize the results of their virtual experiments that are performed in computer simulations, or in silico. The impact of the presented pipeline opens novel avenues for assisting the neuroscientists to build biologically accurate models of the brain. These models result from computer simulations of physical experiments that use fluorescence imaging to understand the structural and functional aspects of the brain. Due to the limited capabilities of the current visualization workflows to handle fluorescent volumetric datasets, we propose a physically-based optical model that can accurately simulate light interaction with fluorescent-tagged scattering media based on the basic principles of geometric optics and Monte Carlo path tracing. We also develop an automated and efficient framework for generating dense fluorescent tissue blocks from a neocortical column model that is composed of approximately 31000 neurons. Results Our pipeline is used to visualize a virtual fluorescent tissue block of 50 μm3 that is reconstructed from the somatosensory cortex of juvenile rat. The fluorescence optical model is qualitatively analyzed and validated against experimental emission spectra of different fluorescent dyes from the Alexa Fluor family. Conclusion We discussed a scientific visualization pipeline for creating images of synthetic neocortical neuronal models that are tagged virtually with fluorescent labels on a physically-plausible basis. The pipeline is applied to analyze and validate simulation data generated from neuroscientific in silico experiments.

  14. On The Plausibility of The Gravitational Collapse As Driving Mechanism For Tectonic Extension

    Science.gov (United States)

    Viti, M.; Mantovani, E.; Albarello, D.

    The possibility that gravitational collapse of a thickened zone induces tensional failure in the lithosphere has quantitatively been investigated by comparing driving forces and lithospheric strength. The force induced by a lateral variation of crustal thickness has been estimated by the difference of gravitational potential energy stored in unit-area lithospheric columns, set in the thickened and reference domains. This force quadrati- cally depends on the thickness ratio and on the thickness of the reference lithosphere. The tensional strength of the thickened belt is obtained by its strength envelope, ten- tatively reconstructed by taking into account the gross petrological composition, the thermal state and the mechanical properties of the crust-mantle system. The effects of normal and hot geotherms (corresponding to a superficial heat flow density of 55 and 70 mW m-2, respectively) have also been investigated. Thickening of both oceanic and continental crust is considered. In the case of oceanic crust, the spreading force, obtained by increasing the crustal thickness up to 4 times the 5-km reference value, is considerably lower than the lithospheric strength, even when the tensional resis- tance is reduced by thermal weakening. Thus, the gravitational collapse of thickened oceanic zones appears to be unlikely. For continental domains, the effect of crustal thickening, up to 60 km, has been investigated. In this kind of structures, lithospheric strength rapidly decreases with the increase of crustal thickness. By assuming a nor- mal geotherm, the spreading force of a thickened (h>40 km) chain facing a 40 km thick foreland is always lower than the lithospheric strength. When a hot geotherm is assumed, the same orogenic belt may collapse when the thickness difference between the chain and the foreland exceeds 10 km. The collapse of an orogenic zone (h>20 km) surrounded by a 20 km-thick foreland occurs when the thickness difference is greater than 30 km, with a

  15. Rapid detection of KPC type carbapenemase gene with real time PCR%KPC型碳青霉烯酶基因荧光定量PCR快速鉴定

    Institute of Scientific and Technical Information of China (English)

    罗芸; 金大智; 叶菊莲; 张政; 沈伟伟; 陈慧红

    2013-01-01

    Objective To develop a rapid, specific assay for detection of Klebsiella pneumoniae carbapenemase (KPC) type carbapenemase gene. Methods The sequences of KPC type carbapenemase gene from 11 kinds of genotypes were aligned, and then the primer pair and probe from conserved sequences were designed. The suitable PCR condition was obtained through systematical optimization of PCR reaction and thereafter the specificity, sensitivity and repro-ducibility were evaluated. Meanwhile,the assay was applied to detect the isolates from the clinical specimens,and then the validity of the assay was verified through direct sequencing and drug resistance experiment. Results The KPC type carbapenemase gene was identified by real time PCR accurately and quickly. Furthermore, when other strains not containing KPC type carbapenemase gene were detected, no positive results appeared. Consequently, the detection limit for control plasmid,pure culture,and mocked specimen of Klebsiella pneumoniae producing KPC type carbapenemase gene was 10 copies/μL, 10 colony forming unit(CFU)/mL,and 102 CFU/mL,respectively. When the assay was applied directly to identify the 489 isolates,the results showed that 7 were positive to Klebsiella pneumoniae, 11 positive to Escherichia coli and one positive to Citrobacter. The results were the same to the results obtained from direct sequencing assay. Conclusion Real time PCR is a rapid, reliable and easy-to-perform assay for the detection of KPC type carbapenemase gene, and could be applied to clinical diagnosis and investigation of epidemic disease. Meanwhile, the results of direct sequencing indicate that the strains carrying KPC type carbapenemase-2 gene are the main bacteria in Zhejiang region.%目的 建立一种准确地鉴定肺炎克雷伯菌碳青霉烯酶(KPC)基因的方法.方法 比对11种KPC型碳青霉烯酶基因,在保守区设计引物和探针,优化PCR反应体系,评价特异性、灵敏度和重复性,对样本分离株进行检测,通

  16. Performances of the Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system for rapid identification of bacteria in routine clinical microbiology.

    Science.gov (United States)

    Dubois, Damien; Grare, Marion; Prere, Marie-Françoise; Segonds, Christine; Marty, Nicole; Oswald, Eric

    2012-08-01

    Rapid and cost-effective matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based systems will replace conventional phenotypic methods for routine identification of bacteria. We report here the first evaluation of the new MALDI-TOF MS-based Vitek MS system in a large clinical microbiology laboratory. This system uses an original spectrum classifier algorithm and a specific database designed for the identification of clinically relevant species. We have tested 767 routine clinical isolates representative of 50 genera and 124 species. Vitek MS-based identifications were performed by means of a single deposit on a MALDI disposable target without any prior extraction step and compared with reference identifications obtained mainly with the VITEK2 phenotypic system; if the identifications were discordant, molecular techniques provided reference identifications. The Vitek MS system provided 96.2% correct identifications to the species level (86.7%), to the genus level (8.2%), or within a range of species belonging to different genera (1.3%). Conversely, 1.3% of isolates were misidentified and 2.5% were unidentified, partly because the species was not included in the database; a second deposit provided a successful identification for 0.8% of isolates unidentified with the first deposit. The Vitek MS system is a simple, convenient, and accurate method for routine bacterial identification with a single deposit, considering the high bacterial diversity studied and as evidenced by the low prevalence of species without correct identification. In addition to a second deposit in uncommon cases, expanding the spectral database is expected to further enhance performances.

  17. Rapid detection and grouping of porcine bocaviruses by an EvaGreen(®) based multiplex real-time PCR assay using melting curve analysis.

    Science.gov (United States)

    Zheng, Xiaowen; Liu, Gaopeng; Opriessnig, Tanja; Wang, Zining; Yang, Zongqi; Jiang, Yonghou

    2016-08-01

    Several novel porcine bocaviruses (PBoVs) have been identified in pigs in recent years and association of these viruses with respiratory signs or diarrhea has been suggested. In this study, an EvaGreen(®)-based multiplex real-time PCR (EG-mPCR) with melting curve analysis was developed for simultaneous detection and grouping of novel PBoVs into the same genogroups G1, G2 and G3. Each target produced a specific amplicon with a melting peak of 81.3 ± 0.34 °C for PBoV G1, 78.2 ± 0.37 °C for PBoV G2, and 85.0 ± 0.29 °C for PBoV G3. Non-specific reactions were not observed when other pig viruses were used to assess the EG-mPCR assay. The sensitivity of the EG-mPCR assay using purified plasmid constructs containing the specific viral target fragments was 100 copies for PBoV G1, 50 for PBoV G2 and 100 for PBoV G3. The assay is able to detect and distinguish three PBoV groups with intra-assay and inter-assay variations ranging from 0.13 to 1.59%. The newly established EG-mPCR assay was validated with 227 field samples from pigs. PBoV G1, G2 and G3 was detected in 15.0%, 25.1% and 41.9% of the investigated samples and coinfections of two or three PBoV groups were also detected in 25.1% of the cases, indicating that all PBoV groups are prevalent in Chinese pigs. The agreement of the EG-mPCR assay with an EvaGreen-based singleplex real-time PCR (EG-sPCR) assay was 99.1%. This EG-mPCR will serve as a rapid, sensitive, reliable and cost effective alternative for routine surveillance testing of multiple PBoVs in pigs and will enhance our understanding of the epidemiological features and possible also pathogenetic changes associated with these viruses in pigs.

  18. Plausible antioxidant biomechanics and anticonvulsant pharmacological activity of brain-targeted β-carotene nanoparticles.

    Science.gov (United States)

    Yusuf, Mohammad; Khan, Riaz A; Khan, Maria; Ahmed, Bahar

    2012-01-01

    increased in P-80-BCNP to 231.0 ± 16.30 seconds, as compared to PTZ (120.10 ± 4.50 seconds) and placebo control (120.30 ± 7.4 seconds). The results of this study demonstrate a plausible novel anticonvulsant activity of β-carotene at a low dose of 2 mg/kg, with brain-targeted nanodelivery, thus increasing its bioavailability and stability.

  19. Exploring apposite therapeutic target for apoptosis in filarial parasite: a plausible hypothesis.

    Science.gov (United States)

    Hande, Sneha; Goswami, Kalyan; Jena, Lingaraj; Reddy, Maryada Venkata Rami

    2014-03-01

    Human lymphatic filariasis is a parasitic disease with profound socioeconomic encumbrance owing to its associated disability, affecting predominantly but not limited to the developing nations of tropics and subtropics. There are several technical issues like poor therapeutic and preventive repertoire as well as administrative and infrastructural limitations which jeopardize the salvage measures and further complicate the plight. Therefore, considering the gravity of the problem, WHO has mandated (under tropical disease research scheme) for placing emphasis on validation of novel therapeutic targets against this disease with the unfortunate tag of 'neglected tropical disease'. However, dearth of knowledge of parasite biology viciously coupled with difficulty of access to parasitic material from suitable animal model along with growing cost burden of high end research poses formidable challenge. Based on the recent research evidences, here we propose a premise with targeted apoptotic impact as a novel rationale to be exploited towards anti-parasitic drug development. The new era of bioinformatics ushers in new optimism with a wide range of genomic and proteomic database in public domain. Such platform might offer wonders for drug research, but needs highly selective criterion specificity. In order to test our hypothesis presumptively, we deployed a scheme for identification of target proteins from filarial parasitic origin through wide database search with precise criteria of non-homology against the host along with functional essentiality for the parasite. Further screening for proteins with growth potential from such list of essential non-homologous proteins was undertaken to mine out suitable representative target for ensuing apoptotic impact though effective inhibitors. A unique protein enzyme, RNA dependent RNA polymerase, which besides its vital role in RNA virus is believed to have regulatory role in gene expression, emerged as a plausible target. This protein

  20. Lead-induced SCC of alloy 600 in plausible steam generator crevice environments

    Energy Technology Data Exchange (ETDEWEB)

    Wright, M.D. [Atomic Energy of Canada Limited, Chalk River, Ontario (Canada); Manolescu, A. [Ontario Hydro Technologies, Toronto, Ontario (Canada); Mirzai, M. [Ontario Hydro, Toronto, Ontario (Canada)

    1998-07-01

    Laboratory stress corrosion cracking (SCC) test environments developed to simulate representative BNGS-A steam generator (SG) crevice chemistries have been used to determine the susceptibility of Alloy 600 to lead-induced SCC under plausible SG conditions. Test environments were based on plant SG hideout return data and analysis of removed tubes and deposits. Deviations from the normal near neutral crevice pH environment were considered to simulate possible faulted excursion crevice chemistry and to bound the postulated crevice pH range of 3-9 (at temperature). The effect of lead contamination up to 1000 ppm, but with an emphasis on the 100 to 500 ppm range, was determined. SCC susceptibility was investigated using constant extension rate tensile (CERT) tests and encapsulated C-ring tests. CERT tests were performed at 305 degrees C on tubing representative of BNGS-A SG U-bends. The C-ring test method allowed a wider test matrix covering three temperatures (280, 304 and 315 degrees C), three strain levels (0.2%, 2% and 4%) and tubing representative of U-bends plus tubing given a simulated stress relief to represent material at the tubesheet. The results of this test program confirmed that in the absence of lead contamination, cracking does not occur in these concentrated, 3.3 to 8.9 pH range, crevice environments. Also, it appears that the concentrated crevice environments suppress lead-induced cracking relative to that seen in all-volatile-treatment (AVT) water. For the (static) C-ring tests, lead-induced SCC was only produced in the near-neutral crevice environment and was more severe at 500 ppm than 100 ppm PbO. This trend was also observed in CERT tests but some cracking/grain boundary attack occurred in acidic (pH 3.3) and alkaline (pH 8.9) environments. The C-ring tests indicated that a certain amount of resistance to cracking was imparted by simulated stress relief of the tubing. This heat treatment, confirmed to have resulted in sensitization, promoted

  1. Lead-induced stress-corrosion cracking of alloy 600 in plausible steam generator crevice environments

    Energy Technology Data Exchange (ETDEWEB)

    Wright, M.D. [Atomic Energy of Canada Limited, Chalk River, Ontario (Canada); Manolescu, A. [Ontario Hydro Technologies, Toronto, Ontario (Canada); Mirzai, M. [Ontario Hydro, Toronto, Ontario (Canada)

    1999-03-01

    Laboratory stress-corrosion cracking (SCC) test environments were developed to simulate crevice chemistries representative of Bruce Nuclear Generating Station A (BNPD A) steam generators (SGs); these test environments were used to determine the susceptibility of Alloy 600 to lead-induced SCC under plausible SG conditions. Test environments were based on plant SG hideout return data and analysis of removed tubes and deposits. Deviations from the normal near-neutral crevice pH environment were considered to simulate possible faulted excursion crevice chemistry and to bound the postulated crevice pH range of 3 to 9 (at temperature). The effect of lead contamination up to 1000 ppm, but with an emphasis on the 100- to 500-ppm range, was determined. SCC susceptibility was investigated using constant extension rate tensile (CERT) tests and encapsulated C-ring tests. CERT tests were performed at 305 degrees C on tubing representative of BNPD A SG U-bends. The C-ring test method allowed a wider test matrix, covering 3 temperatures (280 degrees C, 304 degrees C and 315 degrees C), 3 strain levels (0.2%, 2% and 4%), and tubing representative of U-bends plus tubing given a simulated stress relief to represent material at the tube sheet. The results of this test program confirmed that in the absence of lead contamination, cracking does not occur in these concentrated, 3.3 to 8.9 pH range, crevice environments. Also, it appears that the concentrated crevice environments suppress lead-induced cracking relative to that seen in all-volatile-treatment (AVT) water. For the (static) C-ring tests, lead-induced SCC was only produced in the near-neutral crevice environment and was more severe at 500 ppm than at 100 ppm PbO. This trend was also observed in CERT tests, but some cracking-grain boundary attack occurred in acidic (pH 3.3) and alkaline (pH 8.9) environments. The C-ring tests indicated that a certain amount of resistance to cracking was imparted by simulated stress relief of

  2. Rapid detection of Streptococcus pneumoniae by real-time fluorescence quantitation PCR%实时荧光定量PCR快速诊断肺炎链球菌

    Institute of Scientific and Technical Information of China (English)

    颜善活; 孙雷; 符可鹏; 卓永光; 杨善业; 樊祖茜; 黄永霞

    2013-01-01

    -positive (the positive rate was 8%). Conclusions Real-time fluorescence quantitation PCR is a rapid, sensitive and specific assay for the detection of Streptococcus pneumoniae. It can be used for the diagnosis and epidemiological studies.

  3. Rapid Prototyping Reconsidered

    Science.gov (United States)

    Desrosier, James

    2011-01-01

    Continuing educators need additional strategies for developing new programming that can both reduce the time to market and lower the cost of development. Rapid prototyping, a time-compression technique adapted from the high technology industry, represents one such strategy that merits renewed evaluation. Although in higher education rapid…

  4. Changes in the Distribution of Lesser Adjutant Storks (Leptoptilos javanicus in South and Southeast Asia: A Plausible Evidence of Global Climate and Land-use Change Effect

    Directory of Open Access Journals (Sweden)

    Kapil K. Khadka

    2014-01-01

    Full Text Available Species distribution Models (SDMs illustrate the relation between species and environmental variables. In an attempt to model the historical and current distribution of Lesser Adjutant Stork (Leptoptilos javanicus and gain qualitative insight into range shift, maxEnt modeling approach was applied. The model was projected into maps to illustrate the variation in spatial distribution of the species in South and Southeast Asia over time. A distributional shift was observed towards the north accompanied by range contraction to the south and expansion to the north. Besides, annual precipitation and temperature of the coldest period of a year appeared to be the major climatic determinants of species distribution. It provides plausible evidence of global climate and land-use change effect on the bird’s distribution and suggests avenues for further research.

  5. Gram-stain plus MALDI-TOF MS (Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for a rapid diagnosis of urinary tract infection.

    Directory of Open Access Journals (Sweden)

    Almudena Burillo

    Full Text Available Microbiological confirmation of a urinary tract infection (UTI takes 24-48 h. In the meantime, patients are usually given empirical antibiotics, sometimes inappropriately. We assessed the feasibility of sequentially performing a Gram stain and MALDI-TOF MS mass spectrometry (MS on urine samples to anticipate clinically useful information. In May-June 2012, we randomly selected 1000 urine samples from patients with suspected UTI. All were Gram stained and those yielding bacteria of a single morphotype were processed for MALDI-TOF MS. Our sequential algorithm was correlated with the standard semiquantitative urine culture result as follows: Match, the information provided was anticipative of culture result; Minor error, the information provided was partially anticipative of culture result; Major error, the information provided was incorrect, potentially leading to inappropriate changes in antimicrobial therapy. A positive culture was obtained in 242/1000 samples. The Gram stain revealed a single morphotype in 207 samples, which were subjected to MALDI-TOF MS. The diagnostic performance of the Gram stain was: sensitivity (Se 81.3%, specificity (Sp 93.2%, positive predictive value (PPV 81.3%, negative predictive value (NPV 93.2%, positive likelihood ratio (+LR 11.91, negative likelihood ratio (-LR 0.20 and accuracy 90.0% while that of MALDI-TOF MS was: Se 79.2%, Sp 73.5, +LR 2.99, -LR 0.28 and accuracy 78.3%. The use of both techniques provided information anticipative of the culture result in 82.7% of cases, information with minor errors in 13.4% and information with major errors in 3.9%. Results were available within 1 h. Our serial algorithm provided information that was consistent or showed minor errors for 96.1% of urine samples from patients with suspected UTI. The clinical impacts of this rapid UTI diagnosis strategy need to be assessed through indicators of adequacy of treatment such as a reduced time to appropriate empirical treatment or

  6. Multiplex real-time quantitative PCR, microscopy and rapid diagnostic immuno-chromatographic tests for the detection of Plasmodium spp: performance, limit of detection analysis and quality assurance

    Directory of Open Access Journals (Sweden)

    Ralevski Filip

    2009-12-01

    Full Text Available Abstract Background Accurate laboratory diagnosis of malaria species in returning travelers is paramount in the treatment of this potentially fatal infectious disease. Materials and methods A total of 466 blood specimens from returning travelers to Africa, Asia, and South/Central America with suspected malaria infection were collected between 2007 and 2009 at the reference public health laboratory. These specimens were assessed by reference microscopy, multipex real-time quantitative polymerase chain reaction (QPCR, and two rapid diagnostic immuno-chromatographic tests (ICT in a blinded manner. Key clinical laboratory parameters such as limit of detection (LOD analysis on clinical specimens by parasite stage, inter-reader variability of ICTs, staffing implications, quality assurance and cost analysis were evaluated. Results QPCR is the most analytically sensitive method (sensitivity 99.41%, followed by CARESTART (sensitivity 88.24%, and BINAXNOW (sensitivity 86.47% for the diagnosis of malaria in returning travelers when compared to reference microscopy. However, microscopy was unable to specifically identify Plasmodia spp. in 18 out of 170 positive samples by QPCR. Moreover, the 17 samples that were negative by microscopy and positive by QPCR were also positive by ICTs. Quality assurance was achieved for QPCR by exchanging a blinded proficiency panel with another reference laboratory. The Kappa value of inter-reader variability among three readers for BINAXNOW and CARESTART was calculated to be 0.872 and 0.898 respectively. Serial dilution studies demonstrated that the QPCR cycle threshold correlates linearly with parasitemia (R2 = 0.9746 in a clinically relevant dynamic range and retains a LOD of 11 rDNA copies/μl for P. falciparum, which was several log lower than reference microscopy and ICTs. LOD for QPCR is affected not only by parasitemia but the parasite stage distribution of each clinical specimen. QPCR was approximately 6-fold more

  7. A novel high performance stopped-flow apparatus equipped with a special constructed mixing chamber containing a plunger under inert condition with a very short dead-time to investigate very rapid reactions

    Directory of Open Access Journals (Sweden)

    Sayyed Mostafa Habibi Khorassani

    2015-11-01

    Full Text Available The present work set out to establish a novel stopped-flow instrument equipped with a special constructed mixing chamber containing a plunger to enable a kinetic study of the very rapid reactions under a dry inert atmosphere glove bag, in particular, for the reactions are sensitive to moisture or air. A stopped-flow spectrophotometer is essentially a conventional spectrophotometer with the addition of a system for rapid mixing of solutions. The purpose of this work is to describe the fabrication and evaluation of specially constructed and in-expensive stopped-flow system. The evaluation includes determination of the dead-time, relative mixing efficiency, and the measurement of known rate constants. Herein, a dead-time of about 3.4 ms was determined in the final modified construction of the stopped-flow apparatus in order to investigate the rapid initial during which some form of reaction intermediate is presented to be formed.

  8. Is air pollution a plausible candidate for prenatal exposure in autism spectrum disorder (ASD)? : a systematic review / y Dhanashree Vernekar

    OpenAIRE

    Vernekar, Dhanashree

    2013-01-01

    Objective: To present a systematic review of existing literature that investigates biological plausibility of prenatal hazardous air pollutants’ (HAPs) exposure, in the etiology of autism spectrum disorder (ASD) and related outcomes. Method: Electronic databases Pubmed, Biomed Central and National Database for Autism Research, and grey literature pertaining to air pollution association with ASD and related outcomes were searched using specific keywords. The search included 190 HAPs as defi...

  9. Rapid genotyping of the OATP1B1 polymorphisms A388G and T521C with real-time PCR FRET assays

    NARCIS (Netherlands)

    op den Buijsch, R.A.; Wijnen, P.A.H.M.; van Dieijen-Visser, M.P.; de Vries, J.E.; Bekers, O.

    2005-01-01

    The polymorphisms (OATP)1B1 A388G and T521C of the solute carrier organic anion-transporter family member 1B1 gene (SLCO1B1), previously known as OATP-C, have potential impacts on drug metabolism. In order to establish a fast and consistent assay for these polymorphisms, rapid speed polymerase chain

  10. Plausible antioxidant biomechanics and anticonvulsant pharmacological activity of brain-targeted β-carotene nanoparticles

    Directory of Open Access Journals (Sweden)

    Yusuf M

    2012-08-01

    general tonic–clonic seizures reduced significantly to 2.90 ± 0.98 seconds by the use of BCNP and was further reduced on P-80-BCNP to 1.20 ± 0.20 seconds as compared to PTZ control and PTZ-placebo control (8.09 ± 0.26 seconds. General tonic–clonic seizures latency was increased significantly to 191.0 ± 9.80 seconds in BCNP and was further increased in P-80-BCNP to 231.0 ± 16.30 seconds, as compared to PTZ (120.10 ± 4.50 seconds and placebo control (120.30 ± 7.4 seconds. The results of this study demonstrate a plausible novel anticonvulsant activity of β-carotene at a low dose of 2 mg/kg, with brain-targeted nanodelivery, thus increasing its bioavailability and stability.Keywords: anticonvulsant, blood–brain barrier (BBB, targeted brain delivery, polysorbate-80-coated β-carotene nanoparticles (P-80-BCNP, maximal electroshock seizure (MES, pentylenetetrazole (PTZ

  11. Vulnerabilities to agricultural production shocks: An extreme, plausible scenario for assessment of risk for the insurance sector

    Directory of Open Access Journals (Sweden)

    Tobias Lunt

    2016-01-01

    Full Text Available Climate risks pose a threat to the function of the global food system and therefore also a hazard to the global financial sector, the stability of governments, and the food security and health of the world’s population. This paper presents a method to assess plausible impacts of an agricultural production shock and potential materiality for global insurers. A hypothetical, near-term, plausible, extreme scenario was developed based upon modules of historical agricultural production shocks, linked under a warm phase El Niño-Southern Oscillation (ENSO meteorological framework. The scenario included teleconnected floods and droughts in disparate agricultural production regions around the world, as well as plausible, extreme biotic shocks. In this scenario, global crop yield declines of 10% for maize, 11% for soy, 7% for wheat and 7% for rice result in quadrupled commodity prices and commodity stock fluctuations, civil unrest, significant negative humanitarian consequences and major financial losses worldwide. This work illustrates a need for the scientific community to partner across sectors and industries towards better-integrated global data, modeling and analytical capacities, to better respond to and prepare for concurrent agricultural failure. Governments, humanitarian organizations and the private sector collectively may recognize significant benefits from more systematic assessment of exposure to agricultural climate risk.

  12. Development and bench validation of real time RT-PCR protocols for rapid detection of the subtypes H6, H9 and H11 of avian influenza viruses in experimental samples

    Science.gov (United States)

    Real time RT-PCR (RRT-PCR) is commonly used for the rapid detection of avian influenza viruses (AIV) from clinical samples. Samples are typically screened for type A influenza by targeting the matrix gene, and then positive samples are further tested for hemagglutinin (HA) and neuraminidase (NA) su...

  13. Preliminary Study on Plausible Reasoning in Chemistry Teaching of Senior Middle School%高中化学合情推理教学的初步研究

    Institute of Scientific and Technical Information of China (English)

    杨健; 吴俊明; 骆红山

    2009-01-01

    合情推理(Plausible reasoning)对科学教育具重要意义.通过科学哲学、逻辑学讨论以及历史实例说明科学发现离不开合情推理,科学教育必须重视合情推理能力的培养,并对高中化学合情推理教学的可能性、对象和内容等问题进行了讨论.%Plausible reasoning is significant to science education. Scientific philosophy, logic and historical examples prove that plausible reasoning is indispensable to scientific discoveries,so science education must pay attention to the development of plausible reasoning ability of students. Moreover, it discusses the possibility, object and content of plausible reasoning teaching in chemistry of senior middle school.

  14. Real-time PCR assay for rapid detection of Listeria monocytogenes in simulated milk specimens%奶液模拟标本中单增李斯特菌real-time PCR检测方法的建立

    Institute of Scientific and Technical Information of China (English)

    王娉; 袁飞; 杨海荣; 赵勇胜; 胡玥; 赵贵明; 陈颖

    2011-01-01

    Objective To establish a real-time PCR assay for the rapid detection of Listeria monocytogenes in simulated milk specimens. Methods Based on part fragments of hlyO gene, a pair of primers and Taq-Man probe were designed for quantitative detection of L. Monocytogenes. The specificity of the primers and probe were tested by using different L monocytogenes strains and other common pathogenic bacteria. Results L. Monocytogenes strains were positive in the detection and other tested strains were negative. The sensitivity of assay was 9 copies per PCR reaction. Conclusion The specificity and sensitivity of Taq Man real-time PCR technology for detecting L. Monocytogenes in simulated dairy specimens were high, and the assay could be completed within 1. 5 h. This method could be used to detect other food samples contaminated by L. Monocytogenes and identify the cause of food-borne Listeriosis outbreaks.%目的 建立了基于TaqMan探针的real-time PCR技术针对奶液模拟标本中单增李斯特菌的快速检测方法.方法 用单增李斯特菌hlyO基因的部分片段作为靶基因,制作标准曲线,定量检测奶液中的单增李斯特菌.结果 通过对不同李斯特菌及一些较为常见的致病菌的DNA进行扩增,只有单增李斯特菌能够产生扩增曲线,其余菌株均不产生扩增曲线.单增孛斯特菌的检测灵敏度可以达到9copies/反应体系.结论 该方法特异性好,灵敏度高,整个实验可在1.5h内完成,可用于食品中单增李斯特菌的快速检测和疫情暴发时的相关病原调查.

  15. Sensitivity of Five Rapid HIV Tests on Oral Fluid or Finger-Stick Whole Blood: A Real-Time Comparison in a Healthcare Setting

    Science.gov (United States)

    Pavie, Juliette; Rachline, Anne; Loze, Bénédicte; Niedbalski, Laurence; Delaugerre, Constance; Laforgerie, Eric; Plantier, Jean-Christophe; Rozenbaum, Willy; Chevret, Sylvie; Molina, Jean-Michel; Simon, François

    2010-01-01

    Background Health authorities in several countries recently recommended the expansion of human immunodeficiency virus (HIV) antibody testing, including the use of rapid tests. Several HIV rapid tests are now licensed in Europe but their sensitivity on total blood and/or oral fluid in routine healthcare settings is not known. Methods and Findings 200 adults with documented HIV-1 (n = 194) or HIV-2 infection (n = 6) were prospectively screened with five HIV rapid tests using either oral fluid (OF) or finger-stick whole blood (FSB). The OraQuick Advance rapid HIV1/2® was first applied to OF and then to FSB, while the other tests were applied to FSB, in the following order: Vikia HIV 1/2®, Determine HIV 1–2®, Determine® HIV-1/2 Ag/Ab Combo® and INSTI HIV-1/HIV-2®. Tests negative on FSB were repeated on paired serum samples. Twenty randomly selected HIV-seronegative subjects served as controls, and the results were read blindly. Most patients had HIV-1 subtype B infection (63.3%) and most were on antiretroviral therapy (68.5%). Sensitivity was 86.5%, 94.5%, 98.5%, 94.9%, 95.8% and 99% respectively, with OraQuick OF, OraQuick FSB, Vikia, Determine, Determine Ag/Ab Combo and INSTI (poral fluid than on finger-stick whole blood and less sensitive on finger-stick whole blood than on serum. PMID:20657834

  16. Evaluation of the Implementation of a Rapid Response Treatment Protocol for Patients with Acute Onset Stroke: Can We Increase the Number of Patients Treated and Shorten the Time Needed

    Directory of Open Access Journals (Sweden)

    Rajiv Advani

    2014-06-01

    Full Text Available Aims: This study aims to evaluate the implementation of a rapid response treatment protocol for patients presenting with acute onset ischemic stroke. Improvements of routines surrounding the admission and treatment of patients with intravenous thrombolysis (IVT, such as door-to-needle (DTN times, and increasing the numbers of patients treated are discussed. Methods: We conducted a retrospective analysis of all patients (n = 320 treated with IVT for acute onset ischemic stroke at the Stavanger University Hospital, Norway, between 2003 and 2012. In 2009, a succession of changes to pre- and intra-hospital routines were made as well as an improvement in the education of primary health care physicians, nurses and paramedics involved in the treatment of acute onset stroke patients (rapid response treatment protocol. Analyses of DTN times, onset-to-needle times and the number of patients treated per year were carried out to ascertain the effect of the changes made. The primary aim was to analyze DTN times to look for any changes, and the secondary aim was to analyze changes in the number of patients treated per year. Results: In the years after the implementation of the rapid treatment protocol, we saw an improvement in the median DTN time with a decrease from 73 to 50 min in the first year (p = 0.03, a decrease of 45 min in the second year (p = 0.01 and a decrease of 31 min in the third year (p Conclusions: The implementation of the rapid treatment protocol for acute onset ischemic stroke patients led to a significant decrease in the DTN time at our center. These improvements also produced an increase in the number of patients treated per year. The extension of the therapeutic window from 3 to 4.5 h for the use of intravenous recombinant tissue plasminogen activator also played a role in the increased treatment numbers.

  17. Rapid detection of Mycobacterium tuberculosis complex and rifampin resistance in smear-negative clinical samples by use of an integrated real-time PCR method.

    Science.gov (United States)

    Moure, Raquel; Muñoz, Laura; Torres, Miriam; Santin, Miguel; Martín, Rogelio; Alcaide, Fernando

    2011-03-01

    Sixty-four of 85 (75.3%) smear-negative respiratory (n = 78) and nonrespiratory (n = 7) samples with positive cultures of Mycobacterium tuberculosis complex (MTC) were detected by the GeneXpert system using the Xpert MTB/RIF assay (GX). In addition, GX found rpoB mutations in all six of the rifampin-resistant strains detected. The test was negative in 20 culture-negative and 20 nontuberculous culture-positive samples (100% specificity). GX offers high potential for the diagnosis of tuberculosis due to its capacity for direct detection of MTC, its rapidity, and its simplicity.

  18. Development and implementation of real-time nucleic acid amplification for the detection of enterovirus infections in comparison to rapid culture of various clinical specimens

    NARCIS (Netherlands)

    van Doornum, G J J; Schutten, Martin; Voermans, J; Guldemeester, G J J; Niesters, H G M

    2007-01-01

    Several real-time PCR and nucleic acid sequence-based amplification (NASBA) primer pairs and a modified real-time PCR primer pair for the detection of enteroviruses were compared. The modified real-time PCR primer pair was evaluated on clinical samples in comparison with cell culture using the Magna

  19. Rapid optical and X-ray timing observations of GX 339-4: flux correlations at the onset of a low/hard state

    CERN Document Server

    Gandhi, P; Durant, M; Fabian, A C; Dhillon, V S; Marsh, T R; Miller, J M; Shahbaz, T; Spruit, H C

    2008-01-01

    We present the discovery of optical/X-ray flux correlations on rapid timescales in the low/hard state of the Galactic black hole GX 339-4. The source had recently emerged from outburst and was associated with a relatively-faint counterpart with mag V~17. The optical (VLT/ULTRACAM) and X-ray (RXTE/PCA) data show a clear positive cross-correlation function (CCF) signal, with the optical peak lagging X-rays by ~ 150 ms, preceded by a shallow rise and followed by a steep decline along with broad anti-correlation dips. Examination of the light curves shows that the main CCF features are reproduced in superpositions of flares and dips. The CCF peak is narrow and the X-ray auto-correlation function (ACF) is broader than the optical ACF, arguing against reprocessing as the origin for the rapid optical emission. X-ray flaring is associated with spectral hardening, but no corresponding changes are detected around optical peaks and dips. The variability may be explained in the context of synchrotron emission with intera...

  20. Rapid detection and quantification of Ebola Zaire virus by one-step real-time quantitative reverse transcription-polymerase chain reaction.

    Science.gov (United States)

    Ro, Young-Tae; Ticer, Anysha; Carrion, Ricardo; Patterson, Jean L

    2017-04-01

    Given that Ebola virus causes severe hemorrhagic fever in humans with mortality rates as high as 90%, rapid and accurate detection of this virus is essential both for controlling infection and preventing further transmission. Here, a one-step qRT-PCR assay for rapid and quantitative detection of an Ebola Zaire strain using GP, VP24 or VP40 genes as a target is introduced. Routine assay conditions for hydrolysis probe detection were established from the manufacturer's protocol used in the assays. The analytical specificity and sensitivity of each assay was evaluated using in vitro synthesized viral RNA transcripts. The assays were highly specific for the RNA transcripts, no cross-reactivity being observed among them. The limits of detection of the assays ranged from 10(2) to 10(3) copies per reaction. The assays were also evaluated using viral RNAs extracted from cell culture-propagated viruses (Ebola Zaire, Sudan and Reston strains), confirming that they are gene- and strain-specific. The RT-PCR assays detected viral RNAs in blood samples from virus-infected animal, suggesting that they can be also a useful method for identifying Ebola virus in clinical samples. © 2017 The Societies and John Wiley & Sons Australia, Ltd.

  1. How plausible are the proposed formation scenarios of CEMP-r/s stars?

    CERN Document Server

    Abate, Carlo; Liu, Zheng-Wei

    2016-01-01

    CEMP-$r/s$ stars are metal-poor stars with enhanced abundances of carbon and heavy elements associated with the slow ($s$-) and rapid ($r$-) neutron-capture process. It is believed that carbon and $s$-elements were accreted from the wind of an AGB primary star, a scenario that is generally accepted to explain the formation of CEMP stars that are only enhanced in $s$-elements (CEMP-$s$ stars). The origin of $r$-element-enrichment in CEMP-$r/s$ stars is debated and many formation scenarios have been put forward. We aim to determine the likelihood of the scenarios proposed to explain the formation of CEMP-$r/s$ stars. We calculate the frequency of CEMP-$r/s$ stars among CEMP-$s$ stars for a variety of scenarios, and we compare it with that determined from an observed sample of CEMP-$r/s$ stars collected from the literature. The theoretical frequency of CEMP-$r/s$ stars predicted in most scenarios underestimates the observed ratio by at least a factor of 5. If the enrichments in $s$- and $r$-elements are independ...

  2. Sex ratio meiotic drive as a plausible evolutionary mechanism for hybrid male sterility.

    Directory of Open Access Journals (Sweden)

    Linbin Zhang

    2015-03-01

    Full Text Available Biological diversity on Earth depends on the multiplication of species or speciation, which is the evolution of reproductive isolation such as hybrid sterility between two new species. An unsolved puzzle is the exact mechanism(s that causes two genomes to diverge from their common ancestor so that some divergent genes no longer function properly in the hybrids. Here we report genetic analyses of divergent genes controlling male fertility and sex ratio in two very young fruitfly species, Drosophila albomicans and D. nasuta. A majority of the genetic divergence for both traits is mapped to the same regions by quantitative trait loci mappings. With introgressions, six major loci are found to contribute to both traits. This genetic colocalization implicates that genes for hybrid male sterility have evolved primarily for controlling sex ratio. We propose that genetic conflicts over sex ratio may operate as a perpetual dynamo for genome divergence. This particular evolutionary mechanism may largely contribute to the rapid evolution of hybrid male sterility and the disproportionate enrichment of its underlying genes on the X chromosome--two patterns widely observed across animals.

  3. Sex ratio meiotic drive as a plausible evolutionary mechanism for hybrid male sterility.

    Science.gov (United States)

    Zhang, Linbin; Sun, Tianai; Woldesellassie, Fitsum; Xiao, Hailian; Tao, Yun

    2015-03-01

    Biological diversity on Earth depends on the multiplication of species or speciation, which is the evolution of reproductive isolation such as hybrid sterility between two new species. An unsolved puzzle is the exact mechanism(s) that causes two genomes to diverge from their common ancestor so that some divergent genes no longer function properly in the hybrids. Here we report genetic analyses of divergent genes controlling male fertility and sex ratio in two very young fruitfly species, Drosophila albomicans and D. nasuta. A majority of the genetic divergence for both traits is mapped to the same regions by quantitative trait loci mappings. With introgressions, six major loci are found to contribute to both traits. This genetic colocalization implicates that genes for hybrid male sterility have evolved primarily for controlling sex ratio. We propose that genetic conflicts over sex ratio may operate as a perpetual dynamo for genome divergence. This particular evolutionary mechanism may largely contribute to the rapid evolution of hybrid male sterility and the disproportionate enrichment of its underlying genes on the X chromosome--two patterns widely observed across animals.

  4. A Note on Unified Statistics Including Fermi-Dirac, Bose-Einstein, and Tsallis Statistics, and Plausible Extension to Anisotropic Effect

    Directory of Open Access Journals (Sweden)

    Christianto V.

    2007-04-01

    Full Text Available In the light of some recent hypotheses suggesting plausible unification of thermostatistics where Fermi-Dirac, Bose-Einstein and Tsallis statistics become its special subsets, we consider further plausible extension to include non-integer Hausdorff dimension, which becomes realization of fractal entropy concept. In the subsequent section, we also discuss plausible extension of this unified statistics to include anisotropic effect by using quaternion oscillator, which may be observed in the context of Cosmic Microwave Background Radiation. Further observation is of course recommended in order to refute or verify this proposition.

  5. Variable density sampling based on physically plausible gradient waveform. Application to 3D MRI angiography

    CERN Document Server

    Chauffert, Nicolas; Boucher, Marianne; Mériaux, Sébastien; CIUCIU, Philippe

    2015-01-01

    Performing k-space variable density sampling is a popular way of reducing scanning time in Magnetic Resonance Imaging (MRI). Unfortunately, given a sampling trajectory, it is not clear how to traverse it using gradient waveforms. In this paper, we actually show that existing methods [1, 2] can yield large traversal time if the trajectory contains high curvature areas. Therefore, we consider here a new method for gradient waveform design which is based on the projection of unrealistic initial trajectory onto the set of hardware constraints. Next, we show on realistic simulations that this algorithm allows implementing variable density trajectories resulting from the piecewise linear solution of the Travelling Salesman Problem in a reasonable time. Finally, we demonstrate the application of this approach to 2D MRI reconstruction and 3D angiography in the mouse brain.

  6. Rapid screening and identification of lycodine-type alkaloids in Lycopodiaceae and Huperziaceae plants by ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry.

    Science.gov (United States)

    Shan, Si-Ming; Luo, Jian-Guang; Pan, Ke; Zou, Hong-Yan; Kong, Ling-Yi

    2016-11-01

    Lycodine-type alkaloids have gained significant interest owing to their unique skeletal characteristics and acetylcholinesterase activity. This study established a rapid and reliable method using ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UPLC-ESI-Q/TOF-MS/MS) for comprehensive characterization of lycodine-type alkaloids for the first time. The lycodine-type alkaloids were detected successfully from Lycopodiastrum casuarinoides, Huperzia serrata and Phlegmarirus carinatus in seven plants of the Lycopodiaceae and Huperziaceae families, based on the established characteristic MS fragmentation of five known alkaloids. Furthermore, a total of 13 lycodine-type alkaloids were identified, of which three pairs of isomers were structurally characterized and differentiated. This study further improves mass analysis of lycodine-type alkaloids and demonstrates the superiority of UPLC with a high-resolution mass spectrometer for the rapid and sensitive structural elucidation of other trace active compounds. Copyright © 2016 John Wiley & Sons, Ltd.

  7. Development of a Rapid and Accurate Identification Method for Citrobacter Species Isolated from Pork Products Using a Matrix-Assisted Laser-Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS).

    Science.gov (United States)

    Kwak, Hye-Lim; Han, Sun-Kyung; Park, Sunghoon; Park, Si Hong; Shim, Jae-Yong; Oh, Mihwa; Ricke, Steven C; Kim, Hae-Yeong

    2015-09-01

    Previous detection methods for Citrobacter are considered time consuming and laborious. In this study, we have developed a rapid and accurate detection method for Citrobacter species in pork products, using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). A total of 35 Citrobacter strains were isolated from 30 pork products and identified by both MALDI-TOF MS and 16S rRNA gene sequencing approaches. All isolates were identified to the species level by the MALDI-TOF MS, while 16S rRNA gene sequencing results could not discriminate them clearly. These results confirmed that MALDI-TOF MS is a more accurate and rapid detection method for the identification of Citrobacter species.

  8. Bipolar-pulses observed by the LRS/WFC-L onboard KAGUYA - Plausible evidence of lunar dust impact -

    Science.gov (United States)

    Kasahara, Yoshiya; Horie, Hiroki; Hashimoto, Kozo; Omura, Yoshiharu; Goto, Yoshitaka; Kumamoto, Atsushi; Ono, Takayuki; Tsunakawa, Hideo; Lrs/Wfc Team; Map/Lmag Team

    2010-05-01

    Introduction: The waveform capture (WFC) [1] is one of the subsystems of the Lunar Radar Sounder (LRS) [2] on board the KAGUYA spacecraft. By taking advantage of a moon orbiter, the WFC measures plasma waves and radio emis-sions around the moon. The WFC measures two components of electric wave signals detected by the two orthogonal 30 m tip-to-tip antennas from 100Hz to 1MHz. The WFC consists of the WFC-L which meas-ures electric waveform from 100Hz to 100kHz, and the WFC-H which is a fast sweep frequency analyz-er covering from 1kHz up to 1MHz. The WFC-L has two operation modes: DIFF and MONO. In DIFF mode, signals from two pairs of 30m tip-to-tip dipole antennas are obtained. MONO mode is namely an interferometry mode and we separately measure the signals from a pair of monopole antennas. This mode is dedicated to measure the phase velocities and wave numbers of plasma waves. Bipolar-pulses with their time scales of a few ms upto several tens ms were often observed by the WFC-L. Some of them are classified into elec-trostatic solitary waves (ESW) [3], while another type of bipolar pulses which are supposed to be caused by lunar dust impacts are also observed. In the present paper, we introduce the latter type of bipolar-pulses. Observation: In general, ESWs are caused by electron-holes in the nonlinear evolution of electron beam instability. Therefore waveform of ESW is basically symmetric and its propagation direction is parallel to the am-bient magnetic field. On the other hand, another type of bipolar pulses are characterized by their asymmetric waveforms, that is, the latter half of pulse is longer than the first half. It is also noted that detection probability of such asymmetric bipolar pulses in MONO mode is much higher than that in DIFF mode. This is because bipolar pulses detected by a pair of monopole antennas in MONO mode are almost identical (pulses are simultaneously detected with both monopole anten-nas and the polarities of these pulses are also

  9. Evaluation of the Xpert Methicillin-Resistant Staphylococcus aureus (MRSA) Assay Using the GeneXpert Real-Time PCR Platform for Rapid Detection of MRSA from Screening Specimens ▿

    OpenAIRE

    Rossney, Angela S.; Herra, Celine M, Dr; Brennan, Gráinne I.; Morgan, Pamela M.; O'Connell, Brian

    2008-01-01

    The need for rapid methods to accurately detect methicillin-resistant Staphylococcus aureus (MRSA) is widely acknowledged, and a number of molecular assays are commercially available. This study evaluated the Xpert MRSA assay, which is run on the GeneXpert real-time PCR platform (Cepheid) for use in a clinical laboratory. The following parameters were investigated: (i) the limits of detection (LoDs) for four MRSA strains; (ii) the ability to detect isolates of MRSA from a collection represent...

  10. Rapid Identification of Bacteria Directly from Positive Blood Cultures by Use of a Serum Separator Tube, Smudge Plate Preparation, and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

    Science.gov (United States)

    Chen, Yan; Porter, Vanessa; Mubareka, Samira; Kotowich, Leona; Simor, Andrew E

    2015-10-01

    We analyzed the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) of smudge plate growth for bacterial identification from 400 blood cultures. Ninety-seven percent of Gram-negative bacilli and 85% of Gram-positive organisms were correctly identified within 4 h; only eight isolates (2.0%) were misidentified. This method provided rapid and accurate microbial identification from positive blood cultures.

  11. Assessment of Node Trustworthiness in VANETs Using Data Plausibility Checks with Particle Filters