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Sample records for efficient chirped-pulse amplification

  1. Next generation Chirped Pulse Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Nees, J.; Biswal, S.; Mourou, G. [Univ. Michigan, Center for Ultrafast Optical Science, Ann Arbor, MI (United States); Nishimura, Akihiko; Takuma, Hiroshi

    1998-03-01

    The limiting factors of Chirped Pulse Amplification (CPA) are discussed and experimental results of CPA in Yb:glass regenerative amplifier are given. Scaling of Yb:glass to the petawatt level is briefly discussed. (author)

  2. Pulse Distortion in Saturated Fiber Optical Parametric Chirped Pulse Amplification

    DEFF Research Database (Denmark)

    Lali-Dastjerdi, Zohreh; Da Ros, Francesco; Rottwitt, Karsten

    2012-01-01

    Fiber optical parametric chirped pulse amplification is experimentally compared for different chirped pulses in the picosecond regime. The amplified chirped pulses show distortion appearing as pedestals after recompression when the amplifier is operated in saturation....

  3. Efficient chirped-pulse amplification of sub-20 fs laser pulses

    Energy Technology Data Exchange (ETDEWEB)

    Matsuoka, Shinichi; Yamakawa, Koichi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1998-03-01

    We have developed a model for ultrabroadband and ultrashort pulse amplification including the effects of a pulse shaper for regenerative pulse shaping, gain narrowing and gain saturation in the amplifiers. Thin solid etalons are used to control both gain narrowing and gain saturation during amplification. This model has been used to design an optimized Ti:sapphire amplifier system for producing efficiently pulses of < 20-fs duration with approaching peak and average powers of 100 TW and 20 W. (author)

  4. Performance scaling via passive pulse shaping in cavity-enhanced optical parametric chirped-pulse amplification.

    Science.gov (United States)

    Siddiqui, Aleem M; Moses, Jeffrey; Hong, Kyung-Han; Lai, Chien-Jen; Kärtner, Franz X

    2010-06-15

    We show that an enhancement cavity seeded at the full repetition rate of the pump laser can automatically reshape small-signal gain across the interacting pulses in an optical parametric chirped-pulse amplifier for close-to-optimal operation, significantly increasing both the gain bandwidth and the conversion efficiency, in addition to boosting gain for high-repetition-rate amplification. Applied to a degenerate amplifier, the technique can provide an octave-spanning gain bandwidth.

  5. Fiber Optical Parametric Chirped Pulse Amplification of Sub-Picosecond Pulses

    DEFF Research Database (Denmark)

    Cristofori, Valentina; Lali-Dastjerdi, Zohreh; Da Ros, Francesco

    2013-01-01

    We demonstrate experimentally, for the first time to our knowledge, fiber optical parametric chirped pulse amplification of 400-fs pulses. The 400-fs signal is stretched, amplified by 26 dB and compressed back to 500 fs.......We demonstrate experimentally, for the first time to our knowledge, fiber optical parametric chirped pulse amplification of 400-fs pulses. The 400-fs signal is stretched, amplified by 26 dB and compressed back to 500 fs....

  6. Flashlamp pumped Ti-sapphire laser for ytterbium glass chirped pulse amplification

    Energy Technology Data Exchange (ETDEWEB)

    Nishimura, Akihiko; Ohzu, Akira; Sugiyama, Akira [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment] [and others

    1998-03-01

    A flashlamp pumped Ti:sapphire laser is designed for ytterbium glass chirped pulse amplification. A high quality Ti:sapphire rod and a high energy long pulse discharging power supply are key components. The primary step is to produce the output power of 10 J per pulse at 920 nm. (author)

  7. X-ray Chirped Pulse Amplification: towards GW Soft X-ray Lasers

    Directory of Open Access Journals (Sweden)

    Marta Fajardo

    2013-07-01

    Full Text Available Extensive modeling of the seeding of plasma-based soft X-ray lasers is reported in this article. Seminal experiments on amplification in plasmas created from solids have been studied in detail and explained. Using a transient collisional excitation scheme, we show that a 18 µJ, 80 fs fully coherent pulse is achievable by using plasmas pumped by a compact 10 Hz laser. We demonstrate that direct seeding of plasmas created by nanosecond lasers is not efficient. Therefore, we propose and fully study the transposition to soft X-rays of the Chirped Pulse Amplification (CPA technique. Soft X-ray pulses with energy of 6 mJ and 200 fs duration are reachable by seeding plasmas pumped by compact 100 J, sub-ns, 1 shot/min lasers. These soft X-ray lasers would reach GW power, corresponding to an increase of 100 times as compared to the highest peak power achievable nowadays in the soft X-ray region (30 eV–1 keV. X-ray CPA is opening new horizon for soft x-ray ultra-intense sources.

  8. All-Fiber, Directly Chirped Laser Source for Chirped-Pulse-Amplification

    Science.gov (United States)

    Xin, Ran

    Chirped-pulse-amplification (CPA) technology is widely used to produce ultra-short optical pulses (sub picosecond to femtoseconds) with high pulse energy. A chirped pulse laser source with flexible dispersion control is highly desirable as a CPA seed. This thesis presents an all-fiber, directly chirped laser source (DCLS) that produces nanosecond, linearly-chirped laser pulses at 1053 nm for seeding high energy CPA systems. DCLS produces a frequency chirp on an optical pulse through direct temporal phase modulation. DCLS provides programmable control for the temporal phase of the pulse, high pulse energy and diffraction-limited beam performance, which are beneficial for CPA systems. The DCLS concept is first described. Its key enabling technologies are identified and their experimental demonstration is presented. These include high-precision temporal phase control using an arbitrary waveform generator, multi-pass phase modulation to achieve high modulation depth, regenerative amplification in a fiber ring cavity and a negative feedback system that controls the amplifier cavity dynamics. A few technical challenges that arise from the multi-pass architecture are described and their solutions are presented, such as polarization management and gain-spectrum engineering in the DCLS fiber cavity. A DCLS has been built and its integration into a high energy OPCPA system is demonstrated. DCLS produces a 1-ns chirped pulse with a 3-nm bandwidth. The temporal phase and group delay dispersion on the DCLS output pulse is measured using temporal interferometry. The measured temporal phase has an ˜1000 rad amplitude and is close to a quadratic shape. The chirped pulse is amplified from 0.9 nJ to 76 mJ in an OPCPA system. The amplified pulse is compressed to close to its Fourier transform limit, producing an intensity autocorrelation trace with a 1.5-ps width. Direct compressed-pulse duration control by adjusting the phase modulation drive amplitude is demonstrated. Limitation

  9. Numerical investigations of signal-spectrum shaping based on conformal profile theory in optical parametric chirped pulse amplification

    Science.gov (United States)

    Li, Wenqi; Yu, Lianghong; Peng, Chun; Liang, Xiaoyan

    2017-11-01

    We proposed a theoretical description and numerical model of signal-spectrum shaping based on conformal profile theory and the three-dimensional coupling wave equations for improving the performance of optical parametric chirped pulse amplification (OPCPA). Using our model, we executed quantitative simulations of signal-spectrum shaping and compared the differences of spatiotemporal amplification characteristics between a shaped signal-spectrum and Gaussian signal-spectrum of an OPCPA based on LiB3O5 near 800 nm. By comparison, we found that the conversion efficiency from pump to signal can be dramatically boosted via signal-spectrum shaping. Meanwhile the amplified-spectrum profile, as well as the Fourier-limited pulse, can be improved significantly. We also found that the spatial spot profiles, for injecting a shaped signal or a Gaussian signal in OPCPA, are nearly the same before the saturation regime and at the maximum conversion efficiency or output energy.

  10. Spectral Phase Modulation and chirped pulse amplification in High Gain Harmonic Generation

    CERN Document Server

    Wu, Zilu; Krinsky, Sam; Loos, Henrik; Murphy, James; Shaftan, Timur; Sheehy, Brian; Shen, Yuzhen; Wang, Xijie; Yu Li Hua

    2004-01-01

    High Gain Harmonic Generation (HGHG), because it produces longitudinally coherent pulses derived from a coherent seed, presents remarkable possibilities for manipulating FEL pulses. If spectral phase modulation imposed on the seed modulates the spectral phase of the HGHG in a deterministic fashion, then chirped pulse amplification, pulse shaping, and coherent control experiments at short wavelengths become possible. In addition, the details of the transfer function will likely depend on electron beam and radiator dynamics and so prove to be a useful tool for studying these. Using the DUVFEL at the National Synchrotron Light Source at Brookhaven National Laboratory, we present spectral phase analyses of both coherent HGHG and incoherent SASE ultraviolet FEL radiation, applying Spectral Interferometry for Direct Electric Field Reconstruction (SPIDER), and assess the potential for employing compression and shaping techniques.

  11. Target diagnostics for commissioning the AWE HELEN Laser Facility 100 TW chirped pulse amplification beam

    Science.gov (United States)

    Eagleton, R. T.; Clark, E. L.; Davies, H. M.; Edwards, R. D.; Gales, S.; Girling, M. T.; Hoarty, D. J.; Hopps, N. W.; James, S. F.; Kopec, M. F.; Nolan, J. R.; Ryder, K.

    2006-10-01

    The capability of the HELEN laser at the Atomic Weapons Establishment Aldermaston has been enhanced by the addition of a short-pulse laser beam to augment the twin opposing nanosecond time scale beams. The short-pulse beam utilizes the chirped pulse amplification (CPA) technique and is capable of delivering up to 60J on target in a 500fs pulse, around 100TW, at the fundamental laser wavelength of 1.054μm. During the commissioning phase a number of diagnostic systems have been fielded, these include: x-ray pinhole imaging of the laser heated spot, charged particle time of flight, thermoluminescent dosimeter array, calibrated radiochromic film, and CR39 nuclear track detector. These diagnostic systems have been used to verify the performance of the CPA beam to achieve a focused intensity of around 1019Wcm-2 and to underwrite the facility radiological safety system.

  12. Dynamic Characterization of Fiber Optical Chirped Pulse Amplification for Sub-ps Pulses

    DEFF Research Database (Denmark)

    Cristofori, Valentina; Lali-Dastjerdi, Zohreh; Rishøj, Lars Søgaard

    2013-01-01

    We investigate experimentally the propagation of sub-picosecond pulses in fiber optical parametric chirped pulse amplifiers, showing a significant broadening of the pulses from 450 fs up to 720 fs due to dispersion and self-phase modulation.......We investigate experimentally the propagation of sub-picosecond pulses in fiber optical parametric chirped pulse amplifiers, showing a significant broadening of the pulses from 450 fs up to 720 fs due to dispersion and self-phase modulation....

  13. 200 TW 45 fs laser based on optical parametric chirped pulse amplification.

    Science.gov (United States)

    Lozhkarev, V V; Freidman, G I; Ginzburg, V N; Katin, E V; Khazanov, E A; Kirsanov, A V; Luchinin, G A; Mal'shakov, A N; Martyanov, M A; Palashov, O V; Poteomkin, A K; Sergeev, A M; Shaykin, A A; Yakovlev, I V; Garanin, S G; Sukharev, S A; Rukavishnikov, N N; Charukhchev, A V; Gerke, R R; Yashin, V E

    2006-01-09

    200 TW peak power has been achieved experimentally using a Cr:forsterite master oscillator at 1250 nm, a stretcher, three optical parametrical amplifiers based on KD*P (DKDP) crystals providing 14.5 J energy in the chirped pulse at 910 nm central wavelength, and a vacuum compressor. The final parametrical amplifier and the compressor are described in detail. Scaling of such architecture to multipetawatt power is discussed.

  14. Carrier-envelope-phase stable, high-contrast, double chirped-pulse-amplification laser system.

    Science.gov (United States)

    Jullien, Aurélie; Ricci, Aurélien; Böhle, Frederik; Rousseau, Jean-Philippe; Grabielle, Stéphanie; Forget, Nicolas; Jacqmin, Hermance; Mercier, Brigitte; Lopez-Martens, Rodrigo

    2014-07-01

    We present the first carrier-envelope-phase stable chirped-pulse amplifier (CPA) featuring high temporal contrast for relativistic intensity laser-plasma interactions at 1 kHz repetition rate. The laser is based on a double-CPA architecture including cross-polarized wave (XPW) filtering technique and a high-energy grism-based compressor. The 8 mJ, 22 fs pulses feature 10⁻¹¹ temporal contrast at -20  ps and a carrier-envelope-phase drift of 240 mrad root mean square.

  15. Optimal design of a grism-pair for simultaneous second-, third-, and fourth-order dispersion compensating in chirped-pulse amplification

    Science.gov (United States)

    Rahimi, L.; Abedi, M.; Askari, A. A.; Saghafifar, H.

    2017-06-01

    Residual high-order dispersions of chirped-pulse and optical parametric chirped-pulse amplifiers are extreme limitations for the amplification of ultra-short pulses. In this paper, we investigate the possibility of using a properly designed grism-pair compressor for simultaneously canceling the remaining second-, third-, and fourth-order dispersion of a chirped-pulse amplifier. The analytical phase shift expression of a grism-pair is used to introduce the general components for finding the optimal design of a grism-pair compressor. Particle swarm optimization algorithm is then, employed, and as an example, a tilted grism-pair compressor is designed to compensate the dispersion of a typical stretcher and amplifier. Simulation results show the possibility of complete compensation for second-, third-, and fourth-order dispersion by using an optimally aligned grism-pair compressor.

  16. Thermal properties of borate crystals for high power optical parametric chirped-pulse amplification.

    Science.gov (United States)

    Riedel, R; Rothhardt, J; Beil, K; Gronloh, B; Klenke, A; Höppner, H; Schulz, M; Teubner, U; Kränkel, C; Limpert, J; Tünnermann, A; Prandolini, M J; Tavella, F

    2014-07-28

    The potential of borate crystals, BBO, LBO and BiBO, for high average power scaling of optical parametric chirped-pulse amplifiers is investigated. Up-to-date measurements of the absorption coefficients at 515 nm and the thermal conductivities are presented. The measured absorption coefficients are a factor of 10-100 lower than reported by the literature for BBO and LBO. For BBO, a large variation of the absorption coefficients was found between crystals from different manufacturers. The linear and nonlinear absorption coefficients at 515 nm as well as thermal conductivities were determined for the first time for BiBO. Further, different crystal cooling methods are presented. In addition, the limits to power scaling of OPCPAs are discussed.

  17. Scattering-initiated parametric noise in optical parametric chirped-pulse amplification.

    Science.gov (United States)

    Wang, Jing; Ma, Jingui; Yuan, Peng; Tang, Daolong; Zhou, Binjie; Xie, Guoqiang; Qian, Liejia

    2015-07-15

    We experimentally study a new kind of parametric noise that is initiated from signal scattering and enhanced through optical parametric amplification. Such scattering-initiated parametric noise behaves similarly to parametric super-fluorescence in the spatial domain, yet is typically much stronger. In the time domain it inherits the chirp of signal pulses and can be well compressed. We demonstrate that scattering-initiated parametric noise has little influence on the pulse contrast but can degrade the energy conversion efficiency substantially.

  18. Dynamic characterization and amplification of sub-picosecond pulses in fiber optical parametric chirped pulse amplifiers

    DEFF Research Database (Denmark)

    Cristofori, Valentina; Lali-Dastjerdi, Zohreh; Rishøj, Lars Søgaard

    2013-01-01

    We show a first-time demonstration of amplification of 400 fs pulses in a fiber optical parametric amplifier. The 400 fs signal is stretched in time, amplified by 26 dB and compressed back to 500 fs. A significant broadening of the pulses is experimentally shown due to dispersion and limited gain...... bandwidth both in saturated and unsaturated gain regimes....

  19. XCAN — A coherent amplification network of femtosecond fiber chirped-pulse amplifiers

    Science.gov (United States)

    Daniault, L.; Bellanger, S.; Le Dortz, J.; Bourderionnet, J.; Lallier, É.; Larat, C.; Antier-Murgey, M.; Chanteloup, J.-C.; Brignon, A.; Simon-Boisson, C.; Mourou, G.

    2015-10-01

    The XCAN collaboration program between the Ecole Polytechnique and Thales aims at developing a laser system based on the coherent combination of several tens of laser beams produced through a network of amplifying optical fibers [1]. As a first step this project aspires to demonstrate the scalability of a combining architecture in the femtosecond regime providing high peak power with high repetition rate and high efficiency. The initial system will include 61 individual phased beams aimed to provide 10 mJ, 350 fs pulses at 50 kHz.

  20. Generation of high-contrast millijoule pulses by optical parametric chirped-pulse amplification in periodically poled KTiOPO4.

    Science.gov (United States)

    Jovanovic, Igor; Brown, Curtis G; Ebbers, Christopher A; Barty, C P J; Forget, Nicolas; Le Blanc, Catherine

    2005-05-01

    A new high-contrast, high-gain optical parametric chirped-pulse amplifier (OPCPA) architecture is demonstrated in periodically poled KTiOPO4 (PPKTP). This architecture overcomes parametric fluorescence contrast limitations of the OPCPA in periodically poled materials. The scheme is based on two passes of a single relay-imaged pump pulse and a free-propagating signal pulse through a 1.5 mm x 5 mm x 7.5 mm PPKTP crystal. The output energy of 1.2 mJ is generated at a center wavelength of 1053 nm by 24 mJ of pump energy. A prepulse contrast level of > 3 x 10(7) was measured with > 10(6) saturated gain in the amplifier. Amplified pulses were compressed to 200 fs. This simple and versatile concept requires only a modest pump energy from a commercial pump laser and represents a possible high-contrast front end for high-energy Nd:glass-based petawatt-class lasers.

  1. Power scaling of supercontinuum seeded megahertz-repetition rate optical parametric chirped pulse amplifiers.

    Science.gov (United States)

    Riedel, R; Stephanides, A; Prandolini, M J; Gronloh, B; Jungbluth, B; Mans, T; Tavella, F

    2014-03-15

    Optical parametric chirped-pulse amplifiers with high average power are possible with novel high-power Yb:YAG amplifiers with kW-level output powers. We demonstrate a compact wavelength-tunable sub-30-fs amplifier with 11.4 W average power with 20.7% pump-to-signal conversion efficiency. For parametric amplification, a beta-barium borate crystal is pumped by a 140 W, 1 ps Yb:YAG InnoSlab amplifier at 3.25 MHz repetition rate. The broadband seed is generated via supercontinuum generation in a YAG crystal.

  2. Chirped Pulse Microwave Spectroscopy on Methyl Butanoate

    Science.gov (United States)

    Hernandez-Castillo, Alicia O.; Hays, Brian M.; Abeysekera, Chamara; Zwier, Timothy S.

    2016-06-01

    The microwave spectrum of methyl butanoate has been taken from 8-18 GHz using a chirped pulse spectrometer. This molecule is a model biofuel, and its thermal decomposition products are of interest due to its many dissociation channels. As a preliminary step before such pyrolysis studies, we have examined the jet cooled spectrum of methyl butanoate in a chirped pulse spectrometer, which shows a very rich spectrum. Several conformers have been identified, each with tunneling splittings in the methyl ester group due to internal rotation. These spectra have been fit to obtain rotational constants, relative populations, and methyl rotor barriers for each conformational isomer. The results of these studies are compared to high level calculations.

  3. Chirped Pulse Spectrometer Operating at 200 GHz

    Science.gov (United States)

    Hindle, Francis; Bray, Cédric; Hickson, Kevin; Fontanari, Daniele; Mouelhi, Meriem; Cuisset, Arnaud; Mouret, Gaël; Bocquet, Robin

    2017-10-01

    The combination of electronic sources operating at high frequencies and modern microwave instrumentation has enabled the recent development of chirped pulse spectrometers for the millimetre and THz bands. This type of instrument can operate at high resolution which is particularly suited to gas-phase rotational spectroscopy. The construction of a chirped pulse spectrometer operating at 200 GHz is described in detail while attention is paid to the phase stability and the data accumulation over many cycles. Validation using carbonyl sulphide has allowed the detection limit of the instrument to be established as function of the accumulation. A large number of OCS transitions were identified using a 10-GHz chirped pulse and include the six most abundant isotopologues, the weakest line corresponding to the fundamental R(17) transition of 16O13C33S with a line strength of 4.3 × 10-26 cm-1/(molecule cm-2). The linearity of the system response for different degrees of data accumulation and transition line strength was confirmed over four orders of magnitudes. A simple analysis of the time-domain data was demonstrated to provide the line-broadening coefficient without the need for conversion by a Fourier transform. Finally, the pulse duration is discussed and optimal values are given for both Doppler-limited and collisional regimes.

  4. Highly stable ultrabroadband mid-IR optical parametric chirped-pulse amplifier optimized for superfluorescence suppression.

    Science.gov (United States)

    Moses, J; Huang, S-W; Hong, K-H; Mücke, O D; Falcão-Filho, E L; Benedick, A; Ilday, F O; Dergachev, A; Bolger, J A; Eggleton, B J; Kärtner, F X

    2009-06-01

    We present a 9 GW peak power, three-cycle, 2.2 microm optical parametric chirped-pulse amplification source with 1.5% rms energy and 150 mrad carrier envelope phase fluctuations. These characteristics, in addition to excellent beam, wavefront, and pulse quality, make the source suitable for long-wavelength-driven high-harmonic generation. High stability is achieved by careful optimization of superfluorescence suppression, enabling energy scaling.

  5. Final Technical Report "Study of Efficiency of Raman Backscattering Amplification in Plasma"

    Energy Technology Data Exchange (ETDEWEB)

    Suckewer, Szymon

    2014-03-31

    General : Our major scientific achievements in Raman Backscattering (RBS) amplification and compression of short laser pulses in plasma. The laser system based on RBS steps in where the current technology of chirped pulse amplification (CPA) (extremely successful in developing ultra-short and ultra-intense laser pulses in last 2 decades) becomes difficult and very expensive to apply. Good base for such RBS laser was created by our recent experiments, which were supported by GPS grants. The main objective of the present grant was: improvement efficiency of energy transfer from pump to seed. The results surpassed our expectations; we improved the efficiency of energy transfer from pump to seed by a factor of 6 compared to the best of our previous results and amplified seed pulse compressed down to about 50 fsec.

  6. Development of optical parametric chirped-pulse amplifiers and their applications

    Energy Technology Data Exchange (ETDEWEB)

    Ishii, Nobuhisa

    2006-11-21

    In this work, optical pulse amplification by parametric chirped-pulse amplification (OPCPA) has been applied to the generation of high-energy, few-cycle optical pulses in the near-infrared (NIR) and infrared (IR) spectral regions. Amplification of such pulses is ordinarily difficult to achieve by existing techniques of pulse amplification based on standard laser gain media followed by external compression. Potential applications of few-cycle pulses in the IR have also been demonstrated. The NIR OPCPA system produces 0.5-terawatt (10 fs,5 mJ) pulses by use of noncollinearly phase-matched optical parametric amplification and a down-chirping stretcher and up-chirping compressor pair. An IR OPCPA system was also developed which produces 20-gigawatt (20 fs,350 {mu}J) pulses at 2.1 {mu}m. The IR seed pulse is generated by optical rectification of a broadband pulse and therefore it exhibits a self-stabilized carrier-envelope phase (CEP). In the IR OPCPA a common laser source is used to generate the pump and seed resulting in an inherent sub-picosecond optical synchronization between the two pulses. This was achieved by use of a custom-built Nd:YLF picosecond pump pulse amplifier that is directly seeded with optical pulses from a custom-built ultrabroadband Ti:sapphire oscillator. Synchronization between the pump and seed pulses is critical for efficient and stable amplification. Two spectroscopic applications which utilize these unique sources have been demonstrated. First, the visible supercontinuum was generated in a solid-state media by the infrared optical pulses and through which the carrier-envelope phase (CEP) of the driving pulse was measured with an f-to-3f interferometer. This measurement confirms the self-stabilization mechanism of the CEP in a difference frequency generation process and the preservation of the CEP during optical parametric amplification. Second, high-order harmonics with energies extending beyond 200 eV were generated with the few

  7. Dispersion management for a sub-10-fs, 10 TW optical parametric chirped-pulse amplifier.

    Science.gov (United States)

    Tavella, Franz; Nomura, Yutaka; Veisz, Laszlo; Pervak, Vladimir; Marcinkevicius, Andrius; Krausz, Ferenc

    2007-08-01

    We report the amplification of three-cycle, 8.5 fs optical pulses in a near-infrared noncollinear optical parametric chirped-pulse amplifier (OPCPA) up to energies of 80 mJ. Improved dispersion management in the amplifier by means of a combination of reflection grisms and a chirped-mirror stretcher allowed us to recompress the amplified pulses to within 6% of their Fourier limit. The novel ultrabroad, ultraprecise dispersion control technology presented in this work opens the way to scaling multiterawatt technology to even shorter pulses by optimizing the OPCPA bandwidth.

  8. Double-passed, high-energy quasi-phase-matched optical parametric chirped-pulse amplifier

    Energy Technology Data Exchange (ETDEWEB)

    Jovanovic, I; Forget, N; Brown, C G; Ebbers, C A; Blanc, C L; Barty, C J

    2005-09-19

    Quasi-phase-matched (QPM) optical parametric chirped-pulse amplification (OPCPA) in periodically poled materials such as periodically poled LiNbO{sub 3} (PPLN) and periodically poled KTiOPO{sub 4} (PPKTP) has been shown to exhibit advantages over the OPCPA in bulk nonlinear crystals. [GHH98, RPN02] The use of the maximum material nonlinear coefficient results in ultra-high gain with low pump peak power. Furthermore, propagation of signal, pump, and idler beams along one of the crystal principal axes eliminates the birefringent walk-off, reduces angular sensitivity, and improves beam quality. Relatively high level of parasitic parametric fluorescence (PF) in QPM OPCPA represents an impediment for simple, single-stage, high-gain amplification of optical pulses from nJ to mJ energies. PF in QPM is increased when compared to PF in critical phase matching in bulk crystals as a result of broader angular acceptance of the nonlinear conversion process. PF reduces prepulse contrast and conversion efficiency by competition with the signal pulse for pump pulse energy. Previous experiments with QPM OPCPA have thus resulted in pulse energies limited to tens of {mu}J. [JSE03] Optical parametric amplification of a narrowband signal pulse in PPKTP utilizing two pump beams has been demonstrated at a mJ-level, [FPK03] but the conversion efficiency has been limited by low energy extraction of pump pulse in the first pass of amplification. Additionally, narrow spectral bandwidth was the result of operation far from signal-idler degeneracy. Here we present a novel double-pass, broad-bandwidth QPM OPCPA. 1.2 mJ of amplified signal energy is produced in a single PPKTP crystal utilizing a single 24-mJ pump pulse from a commercial pump laser. [JFE05] To our knowledge, this is the highest energy demonstrated in QPM OPCPA. Double-passed QPM OPCPA exhibits high gain (> 3 x 10{sup 6}), high prepulse contrast (> 3 x 10{sup 7}), high energy stability (3% rms), and excellent beam quality. We

  9. Chirped-pulse interferometry with finite frequency correlations

    Science.gov (United States)

    Resch, K. J.; Kaltenbaek, R.; Lavoie, J.; Biggerstaff, D. N.

    2009-08-01

    Chirped-pulse interferometry is a new interferometric technique encapsulating the advantages of the quantum Hong-Ou-Mandel interferometer without the drawbacks of using entangled photons. Both interferometers can exhibit even-order dispersion cancellation which allows high resolution optical delay measurements even in thick optical samples. In the present work, we show that finite frequency correlations in chirped-pulse interferometry and Hong-Ou-Mandel interferometry limit the degree of dispersion cancellation. Our results are important considerations in designing practical devices based on these technologies.

  10. Cr{sup 4+} : YAG chirped-pulse oscillator

    Energy Technology Data Exchange (ETDEWEB)

    Sorokin, Evgeni; Kalashnikov, Vladimir L [Institut fuer Photonik, TU Wien, Gusshausstr. 27/387, A-1040 Vienna (Austria); Mandon, Julien; Guelachvili, Guy; Picque, Nathalie [Laboratoire de Photophysique Moleculaire, CNRS, Universite Paris-Sud, Batiment 350, 91405 Orsay Cedex (France); Sorokina, Irina T [Department of Physics, Norwegian University of Science and Technology, N-7491 Trondheim (Norway)], E-mail: evgeni.sorokin@tuwien.ac.at

    2008-08-15

    We demonstrate chirped-pulse operation of a Cr : YAG passively mode-locked laser. Different operation regimes of the laser are extensively investigated in the vicinity of zero dispersion both experimentally and numerically. It is shown that for a given laser configuration, transition to the positive dispersion regime allows a 5-fold increase in the output pulse energy, which is otherwise limited by the onset of the multipulsing or 'chaotic' mode-locking. The output pulses have 1.4 ps duration and are compressible down to 120 fs in a 3 m piece of silica fiber, enabling supercontinuum generation in a nonlinear fiber. The spectrum shape and operation stability of the chirped-pulse regime depend strongly on the amount and shape of the intracavity dispersion. The numerical model predicts the existence of the minimum amount of the positive dispersion, above which the chirped-pulse regime can be realized. Once located, the chirped-pulse regime can be reliably reproduced and is sufficiently stable for applications.

  11. FY07 LDRD Final Report Precision, Split Beam, Chirped-Pulse, Seed Laser Technology

    Energy Technology Data Exchange (ETDEWEB)

    Dawson, J W; Messerly, M J; Phan, H H; Crane, J K; Beach, R J; Siders, C W; Barty, C J

    2009-11-12

    The goal of this LDRD ER was to develop a robust and reliable technology to seed high-energy laser systems with chirped pulses that can be amplified to kilo-Joule energies and recompressed to sub-picosecond pulse widths creating extremely high peak powers suitable for petawatt class physics experiments. This LDRD project focused on the development of optical fiber laser technologies compatible with the current long pulse National Ignition Facility (NIF) seed laser. New technologies developed under this project include, high stability mode-locked fiber lasers, fiber based techniques for reduction of compressed pulse pedestals and prepulses, new compact stretchers based on chirped fiber Bragg gratings (CFBGs), new techniques for manipulation of chirped pulses prior to amplification and new high-energy fiber amplifiers. This project was highly successful and met virtually all of its goals. The National Ignition Campaign has found the results of this work to be very helpful. The LDRD developed system is being employed in experiments to engineer the Advanced Radiographic Capability (ARC) front end and the fully engineered version of the ARC Front End will employ much of the technology and techniques developed here.

  12. Efficient audio power amplification - challenges

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, Michael A.E.

    2005-07-01

    For more than a decade efficient audio power amplification has evolved and today switch-mode audio power amplification in various forms are the state-of-the-art. The technical steps that lead to this evolution are described and in addition many of the challenges still to be faced and where extensive research and development are needed is covered. (au)

  13. Efficient Audio Power Amplification - Challenges

    DEFF Research Database (Denmark)

    Andersen, Michael Andreas E.

    2005-01-01

    For more than a decade efficient audio power amplification has evolved and today switch-mode audio power amplification in various forms are the state-of-the-art. The technical steps that lead to this evolution are described and in addition many of the challenges still to be faced and where...... extensive research and development are needed is covered....

  14. 1-MHz high power femtosecond Yb-doped fiber chirped-pulse amplifier

    Science.gov (United States)

    Hu, Zhong-Qi; Yang, Pei-Long; Teng, Hao; Zhu, Jiang-Feng; Wei, Zhi-Yi

    2018-01-01

    A practical femtosecond polarization-maintaining Yb-doped fiber amplifier enabling 153 fs transform-limited pulse duration with 32 μJ pulse energy at 1 MHz repetition rate corresponding to a peak power of 0.21 GW is demonstrated. The laser system based on chirped-pulse amplification (CPA) technique is seeded by a dispersion managed, nonlinear polarization evolution (NPE) mode-locked oscillator with spectrum bandwidth of 31 nm at 1040 nm and amplified by three fiber pre-amplifying stages and a rod type fiber main amplifying stage. The laser works with beam quality of M2 of 1.3 and power stability of 0.63% (root mean square, RMS) over 24 hours will be stable sources for industrial micromachining, medical therapy and scientific research.

  15. Optimal control of quantum systems by chirped pulses

    DEFF Research Database (Denmark)

    Amstrup, Bjarne; Doll, J. D.; Sauerbrey, R. A.

    1993-01-01

    Research on optimal control of quantum systems has been severely restricted by the lack of experimentally feasible control pulses. Here, to overcome this obstacle, optimal control is considered with the help of chirped pulses. Simulated annealing is used as the optimizing procedure. The examples...... treated are pulsed population inversion between electronic levels, and optimization of vibronic excitation in the presence of another electronic level. In the problem of population inversion effective potentials of displaced harmonic oscillators are used. For optimizing vibronic excitation the CsI model...

  16. Chirped-pulse programming of optical coherent transient true-time delays.

    Science.gov (United States)

    Merkel, K D; Babbitt, W R

    1998-04-01

    Programming an optical coherent transient true-time delay device with two frequency-chirped pulses provides a novel means of performing broadband (> >GHz) true-time delay with a wide dynamic range of delays with fine temporal resolution. We have demonstrated true-time delays exceeding 2micros with sub-100-ps resolution. Chirped-pulse programming has the advantages over the previously proposed brief pulse programming [Opt. Lett. 21 1102 (1996)] of reduced instantaneous power requirements and the ability to control the true-time delay by frequency shifting the programming pulses.

  17. Numerical simulation of extremely chirped pulse formation with an optical fiber

    Energy Technology Data Exchange (ETDEWEB)

    Itoh, Tamitake; Nishimura, Akihiko; Tei, Kazuyoku; Matoba, Tohru; Takuma, Hiroshi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Yamashita, Mikio; Morita, Ryuji

    1998-03-01

    A nonlinear propagation code which used a symmetric split-step Fourier method as an algorithm was improved to simulate a propagation behavior of extremely chirped pulse in a long fiber. The performances of pulse propagation in noble gases cored hollow fibers and a pulse stretcher using a nonlinear and normal silicate fibers have been simulated by the code. The calculation results in the case of the hollow fiber are consistent with their experimental results. We estimated that this pulse stretcher could give a extremely chirped pulse whose spectral width was 84.2 nm and temporal duration was 1.5 ns. (author)

  18. Combined Yb/Nd driver for optical parametric chirped pulse amplifiers.

    Science.gov (United States)

    Michailovas, Kirilas; Baltuska, Andrius; Pugzlys, Audrius; Smilgevicius, Valerijus; Michailovas, Andrejus; Zaukevicius, Audrius; Danilevicius, Rokas; Frankinas, Saulius; Rusteika, Nerijus

    2016-09-19

    We report on the developed front-end/pump system for optical parametric chirped pulse amplifiers. The system is based on a dual output fiber oscillator/power amplifier which seeds and assures all-optical synchronization of femtosecond Yb and picosecond Nd laser amplifiers operating at a central wavelength of 1030 nm and 1064 nm, respectively. At the central wavelength of 1030 nm, the fiber oscillator generates partially stretched 4 ps pulses with the spectrum supporting a scaling currently is prevented by limited dimensions of the diffraction gratings, which, because of the fast progress in MLD grating manufacturing technologies is only a temporary obstacle.

  19. Controlling laser-ion acceleration with chirped pulses

    Science.gov (United States)

    Mackenroth, Felix; Gonoskov, Arkady; Marklund, Mattias

    2017-10-01

    The recently proposed novel laser-ion acceleration scheme Chirped-standing-wave acceleration (CSWA) makes use of chirped high-intensity laser pulses to gain enhanced control over the accelerated ions' phase space distribution. The first proof-of-principle analysis of this scheme promised favorable scaling properties of ion energies and densities while simultaneously offering unprecedented spatial and temporal control over the ion beam itself. In this talk we provide an extended analysis of the schemes' further capabilities accessible through, e.g., customized laser chirps and targets. We provide quantitative estimates for existing and upcoming experimental facilities to highlight the scheme's versatility. Furthermore, we benchmark the newly proposed scheme against conventional laser-ion acceleration schemes. To this end we use the accelerated ions' flux as a measure for the conversion efficiency of laser energy into ion kinetic energy and provide a systematic comparison of the theoretically achievable performances of the most common laser-ion acceleration schemes. We find CSWA to be highly competitive in terms of reachable ion energies and fluxes.

  20. Time-Resolved Kinetic Chirped-Pulse Rotational Spectroscopy in a Room-Temperature Flow Reactor.

    Science.gov (United States)

    Zaleski, Daniel P; Harding, Lawrence B; Klippenstein, Stephen J; Ruscic, Branko; Prozument, Kirill

    2017-12-11

    Chirped-pulse Fourier transform millimeter-wave spectroscopy is a potentially powerful tool for studying chemical reaction dynamics and kinetics. Branching ratios of multiple reaction products and intermediates can be measured with unprecedented chemical specificity; molecular isomers, conformers, and vibrational states have distinct rotational spectra. Here we demonstrate chirped-pulse spectroscopy of vinyl cyanide photoproducts in a flow tube reactor at ambient temperature of 295 K and pressures of 1-10 μbar. This in situ and time-resolved experiment illustrates the utility of this novel approach to investigating chemical reaction dynamics and kinetics. Following 193 nm photodissociation of CH2CHCN, we observe rotational relaxation of energized HCN, HNC, and HCCCN photoproducts with 10 μs time resolution and sample the vibrational population distribution of HCCCN. The experimental branching ratio HCN/HCCCN is compared with a model based on RRKM theory using high-level ab initio calculations, which were in turn validated by comparisons to Active Thermochemical Tables enthalpies.

  1. Sub-10 fs deep-ultraviolet pulses generated by chirped-pulse four-wave mixing.

    Science.gov (United States)

    Kida, Yuichiro; Liu, Jun; Teramoto, Takahiro; Kobayashi, Takayoshi

    2010-06-01

    We propose and demonstrate experimentally a novel way of generating sub-10fs deep-UV pulses. The technique is based on chirped-pulse four-wave mixing induced by a broadband near-IR (NIR) pulse and a near-UV pulse. The broadband IR pulse is prepared by preliminarily broadening the spectral width of an NIR pulse by self-phase modulation. The positively chirped broadband IR pulse is suitable for generating a negatively chirped deep-UV pulse, which can be compressed by normal group-velocity dispersion in a transparent medium. Self-compression of the generated deep-UV pulse in air has been demonstrated to produce sub-10fs deep-UV pulses with excellent temporal and spectral profiles for ultrafast spectroscopy in the deep UV.

  2. Chirped-Pulse millimeter-Wave spectroscopy for dynamics and kinetics studies of pyrolysis reactions.

    Science.gov (United States)

    Prozument, Kirill; Barratt Park, G; Shaver, Rachel G; Vasiliou, AnGayle K; Oldham, James M; David, Donald E; Muenter, John S; Stanton, John F; Suits, Arthur G; Barney Ellison, G; Field, Robert W

    2014-08-14

    A Chirped-Pulse millimeter-Wave (CPmmW) spectrometer is applied to the study of chemical reaction products that result from pyrolysis in a Chen nozzle heated to 1000-1800 K. Millimeter-wave rotational spectroscopy unambiguously determines, for each polar reaction product, the species, the conformers, relative concentrations, conversion percentage from precursor to each product, and, in some cases, vibrational state population distributions. A chirped-pulse spectrometer can, within the frequency range of a single chirp, sample spectral regions of up to ∼10 GHz and simultaneously detect many reaction products. Here we introduce a modification to the CPmmW technique in which multiple chirps of different spectral content are applied to a molecular beam pulse that contains the pyrolysis reaction products. This technique allows for controlled allocation of its sensitivity to specific molecular transitions and effectively doubles the bandwidth of the spectrometer. As an example, the pyrolysis reaction of ethyl nitrite, CH3CH2ONO, is studied, and CH3CHO, H2CO, and HNO products are simultaneously observed and quantified, exploiting the multi-chirp CPmmW technique. Rotational and vibrational temperatures of some product molecules are determined. Subsequent to supersonic expansion from the heated nozzle, acetaldehyde molecules display a rotational temperature of 4 ± 1 K. Vibrational temperatures are found to be controlled by the collisional cooling in the expansion, and to be both species- and vibrational mode-dependent. Rotational transitions of vibrationally excited formaldehyde in levels ν4, 2ν4, 3ν4, ν2, ν3, and ν6 are observed and effective vibrational temperatures for modes 2, 3, 4, and 6 are determined and discussed.

  3. Fiber-Optical Parametric Amplification of Sub-Picosecond Pulses for High-Speed Optical Communications

    DEFF Research Database (Denmark)

    Lali-Dastjerdi, Zohreh; Cristofori, Valentina; Rottwitt, Karsten

    2015-01-01

    This article reviews recent results of amplification of short optical pulses using fiber-optical parametric amplifiers. This includes chirped-pulse amplification of 400 fs pulses, error-free amplification of a 640-Gbit/s optical time-division multiplexed signal with less than a 1-dB power penalty...

  4. High-efficiency, broad band, high-damage threshold high-index gratings for femtosecond pulse compression.

    Science.gov (United States)

    Canova, Frederico; Clady, Raphael; Chambaret, Jean-Paul; Flury, Manuel; Tonchev, Svtelen; Fechner, Renate; Parriaux, Olivier

    2007-11-12

    High efficiency, broad-band TE-polarization diffraction over a wavelength range centered at 800 nm is obtained by high index gratings placed on a non-corrugated mirror. More than 96% efficiency wide band top-hat diffraction efficiency spectra, as well as more than 1 J/cm(2) damage threshold under 50 fs pulses are demonstrated experimentally. This opens the way to high-efficiency Chirped Pulse Amplification for high average power laser machining by means of all-dielectric structures as well as for ultra-short high energy pulses by means of metal-dielectric structures.

  5. Water Clusters Observed by Chirped-Pulse Rotational Spectroscopy: Structures and Hydrogen Bonding

    Science.gov (United States)

    Kisiel, Zbigniew; Perez, Cristobal; Muckle, Matt T.; Zaleski, Daniel P.; Seifert, Nathan; Pate, Brooks H.; Temelso, Berhane; Shields, George C.

    2012-06-01

    The chirped-pulse rotational spectra of the hexamer, heptamer, and nonamer water clusters have been assigned and analysed as described in the preceding talk. The observation of all singly substituted 18O isotopologues for several clusters allowed direct determination of the r_s geometries of their oxygen atom frameworks. The r_s analysis was then complemented by least-squares determination of the r_0 geometries, which circumvented the problems with some imaginary substitution coordinates and allowed direct comparisons with computations. For the cage, prism and the book water hexamer clusters the agreement in O...O distances between experiment and vibrationally averaged computed geometries is typically at the 0.01Å level. This is a previously unanticipated level of agreement between experiment and theory, which facilitates more confident discussion of the internal properties of these clusters. The hexamer and larger water clusters begin to display the diversity of hydrogen bonding that is characteristic of condensed water and various aspects of this behaviour are discussed.

  6. An 18-26 GHz Segmented Chirped Pulse Fourier Transform Microwave Spectrometer for Astrochemical Applications

    Science.gov (United States)

    Steber, Amanda; Fatima, Mariyam; Perez, Cristobal; Schnell, Melanie

    2017-06-01

    In the past decade, astrochemistry has seen an increase in interest. As higher throughput and increased resolution radio astronomy facilities come online, faster laboratory instrumentation that directly covers the frequency ranges of these facilities is needed. The 18-26 GHz region is of interest astronomically as many cold organic molecules have their peak intensity in this region. We present here a new segmented chirped pulse Fourier transform microwave (CP-FTMW) spectrometer operating between 18-26 GHz. Using state-of-the-art digital electronics and the segmented approach[1], this design has the potential to be faster and cheaper than the previously presented broadband design. Characterization of the instrument using OCS will be presented, along with a comparison to the previously built and optimized 18-26 CP-FTMW built at the University of Virginia. It will be coupled with a discharge nozzle[2], and its applications to astrochemistry will be explored in this talk. [1] Neill, J.L., Harris, B.J., Steber, A.L., Douglass, K.O., Plusquellic, D.F., Pate, B.H. Opt. Express, 21, 19743-19749, 2013. [2] McCarthy, M.C., Chen, W., Travers, M.J., Thaddeus, P. Astrophys. J. Suppl. Ser., 129, 611-623 , 2000.

  7. Chirped Pulse-Fourier Transform Microwave Spectroscopy of Ethyl 3-METHYL-3-PHENYLGLYCIDATE (strawberry Aldehyde)

    Science.gov (United States)

    Shipman, Steven T.; Neill, Justin L.; Muckle, Matt T.; Suenram, Richard D.; Pate, Brooks H.

    2009-06-01

    Strawberry aldehyde (C_{12} O_3 H_{14}), a common artificial flavoring compound, has two non-interconvertible conformational families defined by the relative stereochemistry around its epoxide carbons. In one family, referred to as the trans because the two large substituents (a phenyl ring and an ethyl ester) are on opposite sides of the epoxide ring, these two substituents are unable to interact with each other. However, in the cis family, there is a long-range interaction that is difficult to accurately capture in electronic structure calculations. Three trans and two cis conformations have been assigned by broadband chirped pulse Fourier transform microwave spectroscopy, along with the C-13 isotopomers in natural abundance for one conformer from each of the families. The agreement of the rotational constants, relative dipole moments, and relative energies between theory and experiment is excellent, even at relatively crude levels of theory, for the trans family, but is quite poor for the cis conformers. In addition, due to the reactivity of strawberry aldehyde and the high temperature to which it must be heated to yield a suitable vapor pressure, several decomposition products have been assigned, and more, as of yet unassigned, are likely to be present. This project demonstrates some of the challenges in performing large-molecule rotational spectroscopy.

  8. Negative Kerr nonlinearity of graphene as seen via chirped-pulse-pumped self-phase modulation

    CERN Document Server

    Vermeulen, Nathalie; Cheng, JinLuo; Pasternak, Iwona; Krajewska, Aleksandra; Ciuk, Tymoteusz; Strupinski, Wlodek; Thienpont, Hugo; Van Erps, Jurgen

    2016-01-01

    We experimentally demonstrate a negative Kerr nonlinearity for quasi-undoped graphene. Hereto, we introduce the method of chirped-pulse-pumped self-phase modulation and apply it to graphene-covered silicon waveguides at telecom wavelengths. The extracted Kerr-nonlinear index for graphene equals n2,gr = -10^(-13) m^2/W. Whereas the sign of n2,gr turns out to be negative in contrast to what has been assumed so far, its magnitude is in correspondence with that observed in earlier experiments. Graphene's negative Kerr nonlinearity strongly impacts how graphene should be exploited for enhancing the nonlinear response of photonic (integrated) devices exhibiting a positive nonlinearity. It also opens up the possibility of using graphene to annihilate unwanted nonlinear effects in such devices, to develop unexplored approaches for establishing Kerr processes, and to extend the scope of the "periodic poling" method often used for second-order nonlinearities towards third-order Kerr processes. Because of the generic na...

  9. Highly depth-resolved chirped pulse photothermal radar for bone diagnostics

    Science.gov (United States)

    Kaiplavil, Sreekumar; Mandelis, Andreas

    2011-07-01

    A novel chirped pulse photothermal (PT) radiometric radar with improved sensitivity over the conventional harmonically modulated thermal-wave radar technique and alternative pulsed laser photothermal radiometry is introduced for the diagnosis of biological samples, especially bones with tissue and skin overlayers. The constraints imposed by the laser safety (maximum permissible exposure) ceiling on pump laser energy and the strong attenuation of thermal-wave signals in tissues significantly limit the photothermally active depth in most biological specimens to a level which is normally insufficient for practical applications (a few mm below the skin surface). A theoretical approach for improvement of signal-to-noise ratio (SNR), minimizing the static (dc) component of the photothermal signal and making use of the photothermal radiometric nonlinearity has been introduced and verified by comparing the SNR of four distinct excitation wave forms (sine-wave, square-wave, constant-width and constant duty-cycle pulses) for chirping the pump laser, under constant exposure energy. At low frequencies fixed-pulsewidth chirps of large peak power were found to be superior to all other equal-energy modalities, with an SNR improvement up to two orders of magnitude. Distinct thickness-dependent characteristic delay times in a goat bone were obtained, establishing an active depth resolution range of ˜2.8 mm in a layered skin-fat-bone structure, a favorable result compared to the maximum reported pulsed photothermal radiometric depth resolution <1 mm in turbid biological media.

  10. Isotopologue-Sensitive Detection Using Chirped-Pulse Ft-Mw Spectroscopy: Minor Species of Propofol

    Science.gov (United States)

    Lesarri, Alberto; Neill, Justin; Muckle, Matt; Shipman, Steven T.; Pate, Brooks H.; Suenram, Richard D.; Caminati, Walther

    2009-06-01

    The capabilities of chirped-pulse FT-microwave spectroscopy to achieve full-bandwidth (11 GHz) isotopologue-sensitive detection have been tested on the 13-heavy atoms molecule of propofol (2,6-diisopropylphenol). The analysis of the rotational spectrum using moderate signal averaging (10 k FIDs) had previously detected the presence of two conformers arising from the combined internal rotations of the hydroxyl and the two isopropyl groups. In the new experiment reported here 600 k FID's were coherently averaged, using three pulsed nozzle sources and reading multiple FIDs per sample injection cycle to reduce the total acquisition time and sample consumption. The new spectrum revealed a very large number of weak transitions, suggesting that full-band ^{13}C sensitivity had been surpassed. The new data have resulted in the assignment of a third conformer of propofol, followed by all twelve ^{13}C-monosubstituted species in natural abundance for the most stable conformer. The isotopic information confirmed the molecular structure for the preferred conformation of propofol, validating the ab initio predictions for this compound. The potential function for the OH internal rotation has been determined using a flexible model. A. Lesarri, S. T. Shipman, G. G. Brown, L. Alvarez-Valtierra, R. D. Suenram and B. H. Pate, 63^rd OSU Int. Symp. On Mol. Spectrosc., Columbus, OH, 2008, RH07 In the

  11. Femtosecond pulse generation and amplification in Yb-doped fibre ...

    Indian Academy of Sciences (India)

    mode-locking regimes are reviewed and the details of development and characterization of an all-fibre, high-power, ... components. Keywords. All-fibre amplifier; femtosecond pulse; chirped pulse amplification; mode- ... emerging as a promising candidate for high-power all-fibre integrated oscillator– amplifier system which ...

  12. Chirped Pulse Rotational Spectroscopy of a Single THUJONE+WATER Sample

    Science.gov (United States)

    Kisiel, Zbigniew; Perez, Cristobal; Schnell, Melanie

    2016-06-01

    Rotational spectroscopy of natural products dates over 35 years when six different species including thujone were investigated. Nevertheless, the technique of low-resolution microwave spectroscopy employed therein allowed determination of only a single conformational parameter. Advances in sensitivity and resolution possible with supersonic expansion techniques of rotational spectroscopy made possible much more detailed studies such that, for example, the structures of first camphor, and then of multiple clusters of camphor with water were determined. We revisited the rotational spectrum of the well known thujone molecule by using the chirped pulse spectrometer in Hamburg. The spectrum of a single thujone sample was recorded with an admixture of 18O enriched water and was successively analysed using an array of techniques, including the AUTOFIT program, the AABS package and the STRFIT program. We have, so far, been able to assign rotational transitions of α-thujone, β-thujone, another thujone isomer, fenchone, and several thujone-water clusters in the spectrum of this single sample. Natural abundance molecular populations were sufficient to determine precise heavy atom backbones of thujone and fenchone, and H_218O enrichment delivered water molecule orientations in the hydrated clusters. An overview of these results will be presented. Z.Kisiel, A.C.Legon, JACS 100, 8166 (1978) Z.Kisiel, O.Desyatnyk, E.Białkowska-Jaworska, L.Pszczółkowski, PCCP 5 820 (2003) C.Pérez, A.Krin, A.L.Steber, J.C.López, Z.Kisiel, M.Schnell, J.Phys.Chem.Lett. 7 154 (2016) N.A.Seifert, I.A.Finneran, C.Perez, et al. J.Mol.Spectrosc. 312, 12 (2015) Z.Kisiel, L.Pszczółkowski, B.J.Drouin, et al. J.Mol.Spectrosc. 280, 134 (2012). Z.Kisiel, J.Mol.Spectrosc. 218, 58 (2003)

  13. A chirped-pulse Fourier-transform microwave/pulsed uniform flow spectrometer. II. Performance and applications for reaction dynamics

    Science.gov (United States)

    Abeysekera, Chamara; Zack, Lindsay N.; Park, G. Barratt; Joalland, Baptiste; Oldham, James M.; Prozument, Kirill; Ariyasingha, Nuwandi M.; Sims, Ian R.; Field, Robert W.; Suits, Arthur G.

    2014-12-01

    This second paper in a series of two reports on the performance of a new instrument for studying chemical reaction dynamics and kinetics at low temperatures. Our approach employs chirped-pulse Fourier-transform microwave (CP-FTMW) spectroscopy to probe photolysis and bimolecular reaction products that are thermalized in pulsed uniform flows. Here we detail the development and testing of a new Ka-band CP-FTMW spectrometer in combination with the pulsed flow system described in Paper I [J. M. Oldham, C. Abeysekera, B. Joalland, L. N. Zack, K. Prozument, I. R. Sims, G. B. Park, R. W. Field, and A. G. Suits, J. Chem. Phys. 141, 154202 (2014)]. This combination delivers broadband spectra with MHz resolution and allows monitoring, on the μs timescale, of the appearance of transient reaction products. Two benchmark reactive systems are used to illustrate and characterize the performance of this new apparatus: the photodissociation of SO2 at 193 nm, for which the vibrational populations of the SO product are monitored, and the reaction between CN and C2H2, for which the HCCCN product is detected in its vibrational ground state. The results show that the combination of these two well-matched techniques, which we refer to as chirped-pulse in uniform flow, also provides insight into the vibrational and rotational relaxation kinetics of the nascent reaction products. Future directions are discussed, with an emphasis on exploring the low temperature chemistry of complex polyatomic systems.

  14. Efficient Wave Energy Amplification with Wave Reflectors

    OpenAIRE

    Kramer, Morten Mejlhede; Frigaard, Peter Bak

    2002-01-01

    Wave Energy Converters (WEC's) extract wave energy from a limited area, often a single point or line even though the wave energy is generally spread out along the wave crest. By the use of wave reflectors (reflecting walls) the wave energy is effectively focused and increased to approximately 130-140%. In the paper a procedure for calculating the efficiency and optimizing the geometry of wave reflectors are described, this by use of a 3D boundary element method. The calculations are verified ...

  15. Efficient Wave Energy Amplification with Wave Reflectors

    DEFF Research Database (Denmark)

    Kramer, Morten Mejlhede; Frigaard, Peter Bak

    2002-01-01

    Wave Energy Converters (WEC's) extract wave energy from a limited area, often a single point or line even though the wave energy is generally spread out along the wave crest. By the use of wave reflectors (reflecting walls) the wave energy is effectively focused and increased to approximately 130......-140%. In the paper a procedure for calculating the efficiency and optimizing the geometry of wave reflectors are described, this by use of a 3D boundary element method. The calculations are verified by laboratory experiments and a very good agreement is found. The paper gives estimates of possible power benifit...... for different geometries of the wave reflectors and optimal geometrical design parameters are specified. On this basis inventors of WEC's can evaluate whether a specific WEC possible could benefit from wave reflectors....

  16. A chirped-pulse Fourier-transform microwave/pulsed uniform flow spectrometer. I. The low-temperature flow system.

    Science.gov (United States)

    Oldham, James M; Abeysekera, Chamara; Joalland, Baptiste; Zack, Lindsay N; Prozument, Kirill; Sims, Ian R; Park, G Barratt; Field, Robert W; Suits, Arthur G

    2014-10-21

    We report the development of a new instrument that combines chirped-pulse microwave spectroscopy with a pulsed uniform supersonic flow. This combination promises a nearly universal detection method that can deliver isomer and conformer specific, quantitative detection and spectroscopic characterization of unstable reaction products and intermediates, product vibrational distributions, and molecular excited states. This first paper in a series of two presents a new pulsed-flow design, at the heart of which is a fast, high-throughput pulsed valve driven by a piezoelectric stack actuator. Uniform flows at temperatures as low as 20 K were readily achieved with only modest pumping requirements, as demonstrated by impact pressure measurements and pure rotational spectroscopy. The proposed technique will be suitable for application in diverse fields including fundamental studies in spectroscopy, kinetics, and reaction dynamics.

  17. 1 μJ, sub-500 fs chirped pulse amplification in a Tm-doped fiber system.

    Science.gov (United States)

    Sims, R Andrew; Kadwani, Pankaj; Shah, Alex Sincore Lawrence; Richardson, Martin

    2013-01-15

    We demonstrate a Tm-doped fiber laser system producing ~300 fs pulses with 1 μJ energy, corresponding to peak powers greater than 3 MW. Pulses of 150 fs with 30 nm spectral bandwidth and 3 nJ pulse energy are generated in a Raman-soliton self-frequency shift amplifier, then stretched to ~160 ps using a chirped Bragg grating. The 60 MHz oscillator repetition rate is reduced to 100 kHz using an electro-optic modulator. After a single-mode fiber preamplifier and a large-mode-area fiber power amplifier, pulses were compressed using a folded Treacy grating setup to below 500 fs with up to 1 μJ pulse energy. To the best of our knowledge, this is the highest energy yet demonstrated as well as the first demonstration of peak powers exceeding 1 MW from a Tm:fiber laser system.

  18. Unity-Efficiency Parametric Down-Conversion via Amplitude Amplification

    Science.gov (United States)

    Niu, Murphy Yuezhen; Sanders, Barry C.; Wong, Franco N. C.; Shapiro, Jeffrey H.

    2017-03-01

    We propose an optical scheme, employing optical parametric down-converters interlaced with nonlinear sign gates (NSGs), that completely converts an n -photon Fock-state pump to n signal-idler photon pairs when the down-converters' crystal lengths are chosen appropriately. The proof of this assertion relies on amplitude amplification, analogous to that employed in Grover search, applied to the full quantum dynamics of single-mode parametric down-conversion. When we require that all Grover iterations use the same crystal, and account for potential experimental limitations on crystal-length precision, our optimized conversion efficiencies reach unity for 1 ≤n ≤5 , after which they decrease monotonically for n values up to 50, which is the upper limit of our numerical dynamics evaluations. Nevertheless, our conversion efficiencies remain higher than those for a conventional (no NSGs) down-converter.

  19. Dynamic Time-Resolved Chirped-Pulse Rotational Spectroscopy of Vinyl Cyanide Photoproducts in a Room Temperature Flow Reactor

    Science.gov (United States)

    Zaleski, Daniel P.; Prozument, Kirill

    2017-06-01

    Chirped-pulsed (CP) Fourier transform rotational spectroscopy invented by Brooks Pate and coworkers a decade ago is an attractive tool for gas phase chemical dynamics and kinetics studies. A good reactor for such a purpose would have well-defined (and variable) temperature and pressure conditions to be amenable to accurate kinetic modeling. Furthermore, in low pressure samples with large enough number of molecular emitters, reaction dynamics can be observable directly, rather than mediated by supersonic expansion. In the present work, we are evaluating feasibility of in situ time-resolved CP spectroscopy in a room temperature flow tube reactor. Vinyl cyanide (CH_2CHCN), neat or mixed with inert gasses, flows through the reactor at pressures 1-50 μbar (0.76-38 mTorr) where it is photodissociated by a 193 nm laser. Millimeter-wave beam of the CP spectrometer co-propagates with the laser beam along the reactor tube and interacts with nascent photoproducts. Rotational transitions of HCN, HNC, and HCCCN are detected, with ≥10 μs time-steps for 500 ms following photolysis of CH_2CHCN. The post-photolysis evolution of the photoproducts' rotational line intensities is investigated for the effects of rotational and vibrational thermalization of energized photoproducts. Possible contributions from bimolecular and wall-mediated chemistry are evaluated as well.

  20. Laser plasma acceleration with a negatively chirped pulse: all-optical control over dark current in the blowout regime

    Science.gov (United States)

    Kalmykov, S. Y.; Beck, A.; Davoine, X.; Lefebvre, E.; Shadwick, B. A.

    2012-03-01

    Recent experiments with 100 terawatt-class, sub-50 femtosecond laser pulses show that electrons self-injected into a laser-driven electron density bubble can be accelerated above 0.5 gigaelectronvolt energy in a sub-centimetre-length rarefied plasma. To reach this energy range, electrons must ultimately outrun the bubble and exit the accelerating phase; this, however, does not ensure high beam quality. Wake excitation increases the laser pulse bandwidth by red-shifting its head, keeping the tail unshifted. Anomalous group velocity dispersion of radiation in plasma slows down the red-shifted head, compressing the pulse into a few-cycle-long piston of relativistic intensity. Pulse transformation into a piston causes continuous expansion of the bubble, trapping copious numbers of unwanted electrons (dark current) and producing a poorly collimated, polychromatic energy tail, completely dominating the electron spectrum at the dephasing limit. The process of piston formation can be mitigated by using a broad-bandwidth (corresponding to a few-cycle transform-limited duration), negatively chirped pulse. Initial blue-shift of the pulse leading edge compensates for the nonlinear frequency red-shift and delays the piston formation, thus significantly suppressing the dark current, making the leading quasi-monoenergetic bunch the dominant feature of the electron spectrum near dephasing. This method of dark current control may be feasible for future experiments with ultrahigh-bandwidth, multi-joule laser pulses.

  1. Chirped-Pulse and Cavity Based Fourier Transform Microwave Spectroscopy of the Methyl Lactate-Ammonia Adduct

    Science.gov (United States)

    Thomas, Javix; Sukhorukov, Oleksandr; Jaeger, Wolfgang; Xu, Yunjie

    2012-06-01

    The hydrogen bonded complex of ammonia with methyl lactate, a chiral alpha-hydroxyester, has been studied using rotational spectroscopy and high level ab initio calculations. Previous studies showed that methyl lactate can exist in a number of conformers. However, only the most stable one which has an intramolecular hydrogen bonded ring formed with its alcoholic hydroxyl and its carbonyl oxygen atom was detected experimentally An extensive ab initio search has been performed to locate all possible low energy conformers of the methyl lactate-ammonia contact pair. Five lowest energy conformers have been identified at the MP2/6-311++G(d,p) level. The lowest energy conformer favors an insertion arrangement, where ammonia is inserted into the existing intramolecular hydrogen bonded ring in the most stable methyl lactate conformer. Broadband scans for the rotational spectra of possible binary conformers have been carried out using a chirped-pulse Fourier transform microwave (FTMW) instrument. The most stable binary adduct was identified and assigned. The final frequency measurements have been done with a cavity based FTMW instrument. The spectrum observed shows complicated fine and hyperfine splitting patterns, likely due to the internal rotations of the methyl groups of methyl lactate and that of ammonia, as well as the 14N quadrupolar nucleus. The binary adduct with 15NH3 has also been studied to simplify the splitting pattern and to aid the assignments of the extensive splittings. The isotopic data and the fine and hyperfine structures will be discussed in terms of internal rotation dynamics and geometry of the hydrogen bonded adduct.

  2. High-average-power 2 μm few-cycle optical parametric chirped pulse amplifier at 100 kHz repetition rate.

    Science.gov (United States)

    Shamir, Yariv; Rothhardt, Jan; Hädrich, Steffen; Demmler, Stefan; Tschernajew, Maxim; Limpert, Jens; Tünnermann, Andreas

    2015-12-01

    Sources of long wavelengths few-cycle high repetition rate pulses are becoming increasingly important for a plethora of applications, e.g., in high-field physics. Here, we report on the realization of a tunable optical parametric chirped pulse amplifier at 100 kHz repetition rate. At a central wavelength of 2 μm, the system delivered 33 fs pulses and a 6 W average power corresponding to 60 μJ pulse energy with gigawatt-level peak powers. Idler absorption and its crystal heating is experimentally investigated for a BBO. Strategies for further power scaling to several tens of watts of average power are discussed.

  3. The Efficiency of Magnetic Field Amplification at Shocks by Turbulence

    Science.gov (United States)

    Ji, Suoqing; Oh, S. Peng; Ruszkowsi, M.; Markevitch, M.

    2016-01-01

    Turbulent dynamo field amplification has often been invoked to explain the strong field strengths in thin rims in supernova shocks (approx.100 micrograms) and in radio relics in galaxy clusters (approx. micrograms). We present high-resolution magnetohydrodynamic simulations of the interaction between pre-shock turbulence, clumping and shocks, to quantify the conditions under which turbulent dynamo amplification can be significant. We demonstrate numerically converged field amplification which scales with Alfven Mach number, B/B0 varies as MA, up to MA approx.150.This implies that the post-shock field strength is relatively independent of the seed field. Amplification is dominated by compression at low MA, and stretching (turbulent amplification) at high MA. For high MA, the B-field grows exponentially and saturates at equipartition with turbulence, while the vorticity jumps sharply at the shock and subsequently decays; the resulting field is orientated predominately along the shock normal (an effect only apparent in 3D and not 2D). This agrees with the radial field bias seen in supernova remnants. By contrast, for low MA, field amplification is mostly compressional, relatively modest, and results in a predominantly perpendicular field. The latter is consistent with the polarization seen in radio relics. Our results are relatively robust to the assumed level of gas clumping. Our results imply that the turbulent dynamo may be important for supernovae, but is only consistent with the field strength, and not geometry, for cluster radio relics. For the latter, this implies strong pre-existing B-fields in the ambient cluster outskirts.

  4. Highly efficient amplification of chronic wasting disease agent by protein misfolding cyclical amplification with beads (PMCAb)

    Science.gov (United States)

    Johnson, Chad J.; Aiken, Judd M.; McKenzie, Debbie; Samuel, Michael D.; Pedersen, Joel A.

    2012-01-01

    Protein misfolding cyclic amplification (PMCA) has emerged as an important technique for detecting low levels of pathogenic prion protein in biological samples. The method exploits the ability of the pathogenic prion protein to convert the normal prion protein to a proteinase K-resistant conformation. Inclusion of Teflon® beads in the PMCA reaction (PMCAb) has been previously shown to increase the sensitivity and robustness of detection for the 263 K and SSLOW strains of hamster-adapted prions. Here, we demonstrate that PMCAb with saponin dramatically increases the sensitivity of detection for chronic wasting disease (CWD) agent without compromising the specificity of the assay (i.e., no false positive results). Addition of Teflon® beads increased the robustness of the PMCA reaction, resulting in a decrease in the variability of PMCA results. Three rounds of serial PMCAb allowed detection of CWD agent from a 6.7×10−13 dilution of 10% brain homogenate (1.3 fg of source brain). Titration of the same brain homogenate in transgenic mice expressing cervid prion protein (Tg(CerPrP)1536+/−mice) allowed detection of CWD agent from the 10−6 dilution of 10% brain homogenate. PMCAb is, thus, more sensitive than bioassay in transgenic mice by a factor exceeding 105. Additionally, we are able to amplify CWD agent from brain tissue and lymph nodes of CWD-positive white-tailed deer having Prnp alleles associated with reduced disease susceptibility.

  5. Highly efficient amplification of chronic wasting disease agent by protein misfolding cyclic amplification with beads (PMCAb.

    Directory of Open Access Journals (Sweden)

    Chad J Johnson

    Full Text Available Protein misfolding cyclic amplification (PMCA has emerged as an important technique for detecting low levels of pathogenic prion protein in biological samples. The method exploits the ability of the pathogenic prion protein to convert the normal prion protein to a proteinase K-resistant conformation. Inclusion of Teflon® beads in the PMCA reaction (PMCAb has been previously shown to increase the sensitivity and robustness of detection for the 263 K and SSLOW strains of hamster-adapted prions. Here, we demonstrate that PMCAb with saponin dramatically increases the sensitivity of detection for chronic wasting disease (CWD agent without compromising the specificity of the assay (i.e., no false positive results. Addition of Teflon® beads increased the robustness of the PMCA reaction, resulting in a decrease in the variability of PMCA results. Three rounds of serial PMCAb allowed detection of CWD agent from a 6.7 × 10(-13 dilution of 10% brain homogenate (1.3 fg of source brain. Titration of the same brain homogenate in transgenic mice expressing cervid prion protein (Tg(CerPrP1536(+/- mice allowed detection of CWD agent from the 10(-6 dilution of 10% brain homogenate. PMCAb is, thus, more sensitive than bioassay in transgenic mice by a factor exceeding 10(5. Additionally, we are able to amplify CWD agent from brain tissue and lymph nodes of CWD-positive white-tailed deer having Prnp alleles associated with reduced disease susceptibility.

  6. Essential criteria for efficient pulse amplification via Raman and Brillouin scattering

    CERN Document Server

    Trines, R M G M; Webb, E; Vieira, J; Fiuza, F; Fonseca, R A; Silva, L O; Sadler, J; Ratan, N; Ceurvorst, L; Kasim, M F; Tabak, M; Froula, D; Haberberger, D; Norreys, P A; Cairns, R A; Bingham, R

    2016-01-01

    Raman and Brillouin amplification are two schemes for amplifying and compressing short laser pulses in plasma. Analytical models have already been derived for both schemes, but the full consequences of these models are little known or used. Here, we present new criteria that govern the evolution of the attractor solution for the seed pulse in Raman and Brillouin amplification, and show how the initial laser pulses need to be shaped to control the properties of the final amplified seed and improve the amplification efficiency.

  7. Random amplification of genomic ends (RAGE) as an efficient ...

    African Journals Online (AJOL)

    Isolation of complete coding sequences and regulatory regions is critical for the complete characterization of a gene. Efficient methods to obtain complete genomic or regulatory is important in the process of isolation. The utility of the available genome walking methods are influenced by factors like the size of the genome ...

  8. The Chirped-Pulse and Cavity Based Ftmw Spectroscopy of the Methyl Lactate-Water and Methyl Lactate-Deuterium Oxide Dimers

    Science.gov (United States)

    Thomas, Javix; Sukhorukov, Oleksandr; Jäger, Wolfgang; Xu, Yunjie

    2011-06-01

    The delicate competition between the inter- and intramolecular hydrogen-bonding in the complex consisting of a chiral alpha-hydroxy ester, methyl lactate, and water, has been studied using rotational spectroscopy and high level ab initio calculations. Extensive ab initio calculations have been performed to locate all possible low energy conformers of the methyl lactate-water contact pair and five lowest energy conformers have been identified. The most stable conformer forms a seven membered ring with two intermolecular hydrogen bonds: one between the alcoholic hydroxy group of methyl lactate and the oxygen of the water molecule and the other between the hydrogen of water and the oxygen of the carbonyl group. Broadband scans for the rotational spectra of these conformers have been carried out using a newly built chirped-pulse FTMW instrument and the final frequency measurements with a cavity based FTMW instrument. Spectral assignments have been made for the lowest energy conformer of methyl lactate-H2O and D2O. The hyperfine splitting and the source of the splitting will be discussed.

  9. Chirped-Pulse Fourier-Transform Microwave Spectroscopy of the Prototypical C-H\\cdotsπ Interaction: the BENZENE\\cdotsACETYLENE Weakly Bound Dimer

    Science.gov (United States)

    Ulrich, Nathan; Seifert, Nathan A.; Dorris, Rachel E.; Peebles, Rebecca A.; Peebles, Sean A.; Pate, Brooks

    2014-06-01

    The rotational spectrum of the CH\\cdotsπ bonded complex between benzene and acetylene has been measured in the 6-20 GHz range using chirped-pulse Fourier-transform microwave spectroscopy. The spectra for the normal isotopologue, three unique 13C substituted species, and the d_1-benzene\\cdotsHCCH species have allowed determination of the dimer structure. The spectrum is that of a symmetric top, with effective C6v symmetry, and a CH\\cdotsπ distance of 2.4921(1) Å. The dipole moment has been measured using the Stark effect, and is 0.438(11) D. In addition to the ground state spectrum, three additional sets of transitions corresponding to similar rotational constants have been observed, likely due to excitation of the three low energy intermolecular vibrational modes of the dimer. Analysis of these excited state transitions is in progress. Comparison of the binding energy and structure of the benzene\\cdotsHCCH dimer with other H\\cdotsπ complexes will be presented.

  10. Emulsion PCR: a high efficient way of PCR amplification of random DNA libraries in aptamer selection.

    Directory of Open Access Journals (Sweden)

    Keke Shao

    Full Text Available Aptamers are short RNA or DNA oligonucleotides which can bind with different targets. Typically, they are selected from a large number of random DNA sequence libraries. The main strategy to obtain aptamers is systematic evolution of ligands by exponential enrichment (SELEX. Low efficiency is one of the limitations for conventional PCR amplification of random DNA sequence library in aptamer selection because of relative low products and high by-products formation efficiency. Here, we developed emulsion PCR for aptamer selection. With this method, the by-products formation decreased tremendously to an undetectable level, while the products formation increased significantly. Our results indicated that by-products in conventional PCR amplification were from primer-product and product-product hybridization. In emulsion PCR, we can completely avoid the product-product hybridization and avoid the most of primer-product hybridization if the conditions were optimized. In addition, it also showed that the molecule ratio of template to compartment was crucial to by-product formation efficiency in emulsion PCR amplification. Furthermore, the concentration of the Taq DNA polymerase in the emulsion PCR mixture had a significant impact on product formation efficiency. So, the results of our study indicated that emulsion PCR could improve the efficiency of SELEX.

  11. Characterization of Intermolecular Interactions at Play in the 2,2,2-TRIFLUOROETHANOL Trimers Using Cavity and Chirped-Pulse Microwave Spectroscopy

    Science.gov (United States)

    Seifert, Nathan A.; Thomas, Javix; Jäger, Wolfgang; Xu, Yunjie

    2017-06-01

    2,2,2-trifluoroethanol (TFE) is a common aqueous co-solvent in biological chemistry which may induce or destabilize secondary structures of proteins and polypeptides, thanks to its diverse intermolecular linkages originating from the hydrogen bonding potential of both the hydroxyl and perfluoro groups. Theoretically, the TFE monomer is predicted to have two stable gauche (gauche^{+}/gauche^{-}) conformations whereas the trans form is unstable or is supported only by a very shallow potential. Only the gauche conformers have been identified in the gas phase, whereas liquid phase studies suggest a trans:gauche ratio of 2:3. The question at which sample (cluster) size the trans form of TFE would appear was one major motivation for our study. Here, we report the detection of three trimers of TFE using Balle-Flygare cavity and chirped-pulse Fourier transform microwave spectroscopy (CP-FTMW) techniques. The most stable observed trimer features one trans- and two gauche-TFE subunits. The other two trimers, observed using a newly constructed 2-6 GHz CP-FTMW spectrometer, consist of only the two gauche conformers of TFE. Quantum Theory of Atoms in Molecules (QTAIM) and non-covalent interactions (NCI) analyses give detailed insights into which intermolecular interactions are at play to stabilize the trans form of TFE in the most stable trimer. M. Buck, Q. Rev. Biophys. 1998, 31, 297-335. I. Bakó, T. Radnai, M. Claire, B. Funel, J. Chem. Phys. 2004, 121, 12472-12480. R. F. W. Bader, Chem. Rev. 1991, 91, 893-928. E. R. Johnson, S. Keinan, P. Mori-Sánchez, J. Contreras-Garcia, A. J. Cohen, W. Yang, J. Am. Chem. Soc., 2010, 132, 6498-6506.

  12. LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens

    Directory of Open Access Journals (Sweden)

    Lee Wah

    2008-09-01

    Full Text Available Abstract Background Pathogen detection using DNA microarrays has the potential to become a fast and comprehensive diagnostics tool. However, since pathogen detection chips currently utilize random primers rather than specific primers for the RT-PCR step, bias inherent in random PCR amplification becomes a serious problem that causes large inaccuracies in hybridization signals. Results In this paper, we study how the efficiency of random PCR amplification affects hybridization signals. We describe a model that predicts the amplification efficiency of a given random primer on a target viral genome. The prediction allows us to filter false-negative probes of the genome that lie in regions of poor random PCR amplification and improves the accuracy of pathogen detection. Subsequently, we propose LOMA, an algorithm to generate random primers that have good amplification efficiency. Wet-lab validation showed that the generated random primers improve the amplification efficiency significantly. Conclusion The blind use of a random primer with attached universal tag (random-tagged primer in a PCR reaction on a pathogen sample may not lead to a successful amplification. Thus, the design of random-tagged primers is an important consideration when performing PCR.

  13. Ultra-efficient PrP(Sc amplification highlights potentialities and pitfalls of PMCA technology.

    Directory of Open Access Journals (Sweden)

    Gian Mario Cosseddu

    2011-11-01

    Full Text Available In order to investigate the potential of voles to reproduce in vitro the efficiency of prion replication previously observed in vivo, we seeded protein misfolding cyclic amplification (PMCA reactions with either rodent-adapted Transmissible Spongiform Encephalopathy (TSE strains or natural TSE isolates. Vole brain homogenates were shown to be a powerful substrate for both homologous or heterologous PMCA, sustaining the efficient amplification of prions from all the prion sources tested. However, after a few serial automated PMCA (saPMCA rounds, we also observed the appearance of PK-resistant PrP(Sc in samples containing exclusively unseeded substrate (negative controls, suggesting the possible spontaneous generation of infectious prions during PMCA reactions. As we could not definitively rule out cross-contamination through a posteriori biochemical and biological analyses of de novo generated prions, we decided to replicate the experiments in a different laboratory. Under rigorous prion-free conditions, we did not observe de novo appearance of PrP(Sc in unseeded samples of M109M and I109I vole substrates, even after many consecutive rounds of saPMCA and working in different PMCA settings. Furthermore, when positive and negative samples were processed together, the appearance of spurious PrP(Sc in unseeded negative controls suggested that the most likely explanation for the appearance of de novo PrP(Sc was the occurrence of cross-contamination during saPMCA. Careful analysis of the PMCA process allowed us to identify critical points which are potentially responsible for contamination events. Appropriate technical improvements made it possible to overcome PMCA pitfalls, allowing PrP(Sc to be reliably amplified up to extremely low dilutions of infected brain homogenate without any false positive results even after many consecutive rounds. Our findings underline the potential drawback of ultrasensitive in vitro prion replication and warn on cautious

  14. Efficiency of the motion amplification device with viscous dampers and its application in high-rise buildings

    Science.gov (United States)

    Huang, Henry C.

    2009-12-01

    After nearly a decade of application and investigation, a motion amplification device with viscous dampers for energy dissipation has been recognized as an effective solution to mitigate wind or seismic excitation, especially for stiff structural systems. As a result of compensation of amplified motion, it has been proved that the efficiency of viscous damper largely depends on the motion amplification device configuration, particularly for device stiffness. In this paper, a “scissor-jack” type of motion amplification device, called a “toggle brace damper” system, is studied. It is demonstrated that the efficiency of such a device reflected by its amplification factor is not merely a function of its geometric configuration, but is highly dependent on the support elements’ stiffness as well, similar to the mechanism of a leverage arm. Accordingly, a mathematical model in terms of complex modulus of the viscous damper with consideration of the support brace’s stiffness is established. The results indicate that the efficiency of the motion amplification device with viscous dampers significantly depends on the stiffness of the support elements. Other parameters, such as toggle brace configuration and damping values of the viscous damper, are studied and compared. As an application example, numerical analyses are conducted to study the dynamic performance of a 39-story office tower installed with toggle brace dampers constructed on soft soil in a reclaimed area, under a combined effect of the vortex shedding of an adjacent existing 52-story building and earthquakes. The results show that viscous dampers with a motion amplification system using a properly designed toggle brace device proved to be an effective solution to alleviate the external excitations.

  15. Efficient Sub-Bandgap Light Absorption and Signal Amplification in Silicon Photodetectors

    Science.gov (United States)

    Liu, Yu-Hsin

    This thesis focuses on two areas in silicon photodetectors, the first being enhancing the sub-bandgap light absorption of IR wavelenghts in silicon, and the second being intrinsic signal amplification in silicon photodetectors. Both of these are achieved using heavily doped p-n junction devices which create localized states that relax the k-selection rule of indirect bandgap material. The probability of transitions between impurity band and the conduction/valence band would be much more efficient than the one between band-to-band transition. The waveguide-coupled epitaxial p-n photodetector was demonstrated for 1310 nm wavelength detection. Incorporated with the Franz-Keldysh effect and the quasi-confined epitaxial layer design, an absorption coefficient around 10 cm-1 has been measured and internal quantum efficiency nearly 100% at -2.5V. The absorption coefficient is calculated from the wave function of the electron and hole in p-n diode. The heavily doped impurity wave function can be formulated as a delta function, and the quasi-confined conduction band energy states, and the wave function on each level can be obtained from the Silvaco software. The calculated theoretical absorption coefficient increases with the increasing applied bias and the doping concentration, which matches the experimental results. To solve the issues of large excess noise and high operation bias for avalanche photodiodes based on impact ionization, I presented a detector using the Cycling Excitation Process (CEP) for signal amplification. This can be realized in a heavily doped and highly compensated Si p-n junction, showing ultra high gain about 3000 at very low bias (<4 V), and possessing an intrinsic, phonon-mediated regulation process to keep the device stable without any quenching device required in today's Geiger-mode avalanche detectors. The CEP can be formulated with the rate equations in conduction bands and impurity states. The gain expression, which is a function of the

  16. High-efficiency multilayer-dielectric diffraction gratings

    Energy Technology Data Exchange (ETDEWEB)

    Perry, M.D.; Boyd, R.D.; Britten, J.A.

    1996-06-01

    The ability to produce short laser pulses of extremely high power and high irradiance, as is needed for fast ignitor research in inertial confinement fusion, places increasing demands on optical components such as amplifiers, lenses, and mirrors that must remain undamaged by the radiation. The higher refractive index in the center of an intense laser beam acts as a focusing lens. The resulting wavefront distortion, left uncorrected, eventually leads to catastrophic filamentation. Major advances in energy extraction and resulting increases in focused irradiance have been made possible by the use of chirped-pulse amplification (CPA), long used in radar applications and newly applied to optical frequencies. Optical-frequency CPA systems begin with a mode-locked oscillator that produces low-energy seed pulses with durations of ten to a few hundred femtoseconds. As a result of the classical uncertainty relation between time and frequency, these short pulses have a very broad frequency distribution. A pair of diffraction gratings (or other dispersive elements) lengthens the laser pulse and induces a time-varying frequency (or chirp). Following amplification, diffraction gratings compress the pulse back to nearly the original duration. Typically a nanojoule, femtosecond pulse is stretched by a factor of several thousand and is amplified by as much as 12 orders of magnitude before recompression. By producing the short pulse only after amplification, this technique makes possible efficient extraction of energy from a variety of broadband solid state materials. Achieving high focused irradiance from a pulse ultimately requires both high peak power and excellent beam quality. There is therefore a demand for diffraction gratings that produce a high-quality diffracted wavefront, have high diffraction efficiency, and exhibit a high threshold for laser damage.

  17. Glycoform-independent prion conversion by highly efficient, cell-based, protein misfolding cyclic amplification

    Science.gov (United States)

    Moudjou, Mohammed; Chapuis, Jérôme; Mekrouti, Mériem; Reine, Fabienne; Herzog, Laetitia; Sibille, Pierre; Laude, Hubert; Vilette, Didier; Andréoletti, Olivier; Rezaei, Human; Dron, Michel; Béringue, Vincent

    2016-01-01

    Prions are formed of misfolded assemblies (PrPSc) of the variably N-glycosylated cellular prion protein (PrPC). In infected species, prions replicate by seeding the conversion and polymerization of host PrPC. Distinct prion strains can be recognized, exhibiting defined PrPSc biochemical properties such as the glycotype and specific biological traits. While strain information is encoded within the conformation of PrPSc assemblies, the storage of the structural information and the molecular requirements for self-perpetuation remain uncertain. Here, we investigated the specific role of PrPC glycosylation status. First, we developed an efficient protein misfolding cyclic amplification method using cells expressing the PrPC species of interest as substrate. Applying the technique to PrPC glycosylation mutants expressing cells revealed that neither PrPC nor PrPSc glycoform stoichiometry was instrumental to PrPSc formation and strainness perpetuation. Our study supports the view that strain properties, including PrPSc glycotype are enciphered within PrPSc structural backbone, not in the attached glycans. PMID:27384922

  18. Modeling high-peak-power few-cycle field waveform generation by optical parametric amplification in the long-wavelength infrared.

    Science.gov (United States)

    Voronin, A A; Lanin, A A; Zheltikov, A M

    2016-10-03

    Extended coupled-wave analysis of optical parametric chirped-pulse amplification (OPCPA) reveals regimes whereby high-peak-power few-cycle pulses can be generated in the long-wavelength infrared (LWIR) spectral range. Broadband OPCPA in suitable nonlinear crystals pumped at around 2 μm and seeded either through the signal or the idler input is shown to enable the generation of high-power field waveforms with pulse widths shorter than two field cycles within the entire LWIR range.

  19. Construction and optimization of an efficient breathing-based isothermal emulsion amplification method

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Yanting, E-mail: shenyanting798@126.com [Research Center for Learning Science, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); State Key Laboratory of Bioelectronics, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); Tian, Fei, E-mail: 642807827@qq.com [Research Center for Learning Science, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); Tu, Jing, E-mail: jtu@seu.edu.cn [State Key Laboratory of Bioelectronics, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); Li, Rui, E-mail: lirui901113@163.com [Research Center for Learning Science, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); Chen, Zhenzhu, E-mail: zzchen_seu@163.com [Research Center for Learning Science, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); Bai, Yunfei, E-mail: whitecf@seu.edu.cn [State Key Laboratory of Bioelectronics, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); Ge, Qinyu, E-mail: geqinyu@seu.edu.cn [State Key Laboratory of Bioelectronics, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); Lu, Zuhong, E-mail: zhlu@seu.edu.cn [State Key Laboratory of Bioelectronics, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China)

    2017-06-22

    The reaction temperature is one of the main factors that affect the stability of emulsion PCR (emPCR). Focusing on this point, we applied the “DNA breathing” mechanism in BEAMing (Bead, Emulsion, Amplification, and Magnetic) and proposed a more stable emulsion amplification method. Compared to the conventional emPCR, this method provided excellent results. Firstly, more stable emulsion system resulted in higher percentage of single-molecular amplifications (73.17%). Secondly, an ordinary temperature-controlling device was enough. Our outcome showed that the reaction temperature of this method was not strict so that the ordinary temperature-controlling device was enough for it (the heat block sets vs. the PCR instrument: 13.140 ± 0.110 vs. 13.008 ± 0.039, P = 0.120). Thirdly, the single-biotinylated emP{sub 1} coated streptavidin beads were stable enough to be used for this method (the control temperature vs. the reaction temperature: 2967.91 ± 409.045 vs. 3026.22 ± 442.129, P = 0.334), which could replace the double-biotinylated emP{sub 1} coated beads and was benefit for saving cost. In conclusion, the method presented here with stable emulsion system, simplified temperature-controlling device, and decreased investment would be a highly streamlined and inexpensive option for future single-molecular amplification based researches. - Highlights: • A breathing-based isothermal emulsion amplification (BIEA) method was developed. • BIEA showed excellent properties compared with conventional amplification method. • Terminal breathing of DNA duplex was firstly used in emulsion amplification.

  20. Experimental demonstration of spatially coherent beam combining using optical parametric amplification.

    Science.gov (United States)

    Kurita, Takashi; Sueda, Keiichi; Tsubakimoto, Koji; Miyanaga, Noriaki

    2010-07-05

    We experimentally demonstrated coherent beam combining using optical parametric amplification with a nonlinear crystal pumped by random-phased multiple-beam array of the second harmonic of a Nd:YAG laser at 10-Hz repetition rate. In the proof-of-principle experiment, the phase jump between two pump beams was precisely controlled by a motorized actuator. For the demonstration of multiple-beam combining a random phase plate was used to create random-phased beamlets as a pump pulse. Far-field patterns of the pump, the signal, and the idler indicated that the spatially coherent signal beams were obtained on both cases. This approach allows scaling of the intensity of optical parametric chirped pulse amplification up to the exa-watt level while maintaining diffraction-limited beam quality.

  1. Solid-phase PCR for rapid multiplex detection of Salmonella spp. at the subspecies level, with amplification efficiency comparable to conventional PCR

    DEFF Research Database (Denmark)

    Chin, Wai Hoe; Sun, Yi; Høgberg, Jonas

    2017-01-01

    Solid-phase PCR (SP-PCR) has attracted considerable interest in different research fields since it allows parallel DNA amplification on the surface of a solid substrate. However, the applications of SP-PCR have been hampered by the low efficiency of the solid-phase amplification. In order...

  2. Comparison of methods to preserve Rheum palmatum (Polygonaceae) for efficient DNA extraction and PCR amplification.

    Science.gov (United States)

    Huang, M; Sun, X J; Zhou, Y; Wang, X M

    2016-08-19

    In this study, we compared the quality of DNA extracted using the modified CTAB method, from Rheum palmatum leaves preserved using fourteen different methods, including ones used commonly in other species: under ultra-cold (-80°C) temperatures, after drying with an absorbent paper, desiccating using a silica gel, drying at 60°C, in 70% ethanol, absolute ethanol, 70% ethanol supplemented with 50 mM EDTA, SDS-DNA extracting solution, nuclear separation buffer, improved NaCl-CTAB solution, TE-buffer, I-solution, or II-solution. DNA extracted from fresh leaves was used as the control. The quality of extracted DNA was evaluated based on the success of PCR amplification of the ITS2 region and a microsatellite marker. DNA was not extracted from samples preserved in the nuclear separation buffer and II-solution. The purities of DNA extracted from leaves preserved in ultra-cold temperatures, 70% ethanol, and 70% ethanol with 50 mM EDTA, and after desiccating using a silica gel and drying were higher, and comparable to the purity of DNA extracted from fresh leaves, than those of leaves preserved using other methods. In the present study, combined with the PCR amplifications, the preservation using ultra-cold temperatures, silica gel desiccation, or drying, and PCR amplification of the extracted DNA can be used for further molecular studies in R. palmatum.

  3. Fabrication of Efficient, Large Aperture Transmission Diffraction Gratings by Ion-Beam Etching

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, H T; Bryan, S R; Britten, J A; Perry, M D

    2000-09-14

    The utilization of high-power short pulse laser employing chirped-pulse amplification (CPA) for material processing and inertial confinement research is widely increasing. The performance of these high-power CPA laser system continues to be limited by the ability of the pulse compression gratings to hold up to the high-average-power or high-peak-power of the laser. Pulse compression gratings used in transmission and fabricated out of bulk fused silica have intrinsically the highest laser damage threshold when compared with metal or multilayer dielectric gratings that work in reflection. LLNL has developed processing capability to produce high efficiency fused silica transmission gratings at sizes useful to future Petawatt-class systems, and has demonstrated high efficiency at smaller aperture. This report shows that fused silica diffraction exhibiting >95% efficiency into the -1 diffraction order in transmission (90{sup o} deflection of the incident light, at an incidence angle of 45{sup o} to the grating face). The microstructure of this grating consisted of grooves ion-beam etched to a depth of 1.6 microns with a pitch of 0.75 microns, using a holographically produced photoresist mask that was subsequently stripped away in significance to the fabrication of the small scale high efficiency grating was the development of the processing technology and infrastructure for production of such gratings at up to 65 cm diameter. LLNL is the currently the only location in the world with the ability to coat, interferometrically expose, and ion etch diffractive optics at this aperture. Below, we describe the design, fabrication, performance and, the scaleup process for a producing a high-efficiency transmission grating on a 65 cm fused silica substrate.

  4. Limited efficiency of universal mini-barcode primers for DNA amplification from desert reptiles, birds and mammals

    National Research Council Canada - National Science Library

    Arif, I A; Khan, H A; Al Sadoon, M; Shobrak, M

    2011-01-01

    .... We report an extended validation of a universal DNA mini-barcode for amplification of 130-bp COI segments from 23 specimens collected from a desert environment, including 11 reptiles, five mammals and seven birds...

  5. An efficient and reliable DNA extraction method for preimplantation genetic diagnosis: a comparison of allele drop out and amplification rates using different single cell lysis methods.

    Science.gov (United States)

    Kim, Sung Ah; Yoon, Jung Ah; Kang, Moon Joo; Choi, Young Min; Chae, Soo Jin; Moon, Shin Yong

    2009-08-01

    To evaluate methods of DNA extraction from single cells for their suitability to amplify and provide a correct diagnosis of target disease genes. Experimental study. University hospital laboratory. Two normal adult male and female blood donors. Exon 51 of the dystrophin gene and the ZFX/ZFY gene were amplified from single lymphocytes using nested PCR. Five different methods of DNA extraction were tested (lysis in distilled water with freezing and thawing using liquid nitrogen, lysis in distilled water, alkaline lysis buffer, Proteinase K/sodium dodecyl sulfate (SDS) buffer, and N-lauroylsarcosine salt solution). Allele drop out and amplification rate. The amplification efficiency from single unaffected lymphocytes was 89.0% using the liquid nitrogen method, 88.1% with the distilled water lysis method, 97.5% with the alkaline lysis buffer method, 91.5% with the Proteinase K/SDS lysis buffer method, and 84.8% using the N-lauroylsarcosine salt solution method. The mean allele drop out rate was 16.7%, 43.9%, 2.0%, 9.8%, and 18.9%, respectively, for each lysis method using single male lymphocytes as a template. Based on these results, DNA extraction using an alkaline lysis buffer results in more efficient rates of DNA amplification and less allele drop out than the other methods of DNA extraction tested. This method is suitable for the lysis of single cells in clinical preimplantation genetic diagnosis.

  6. High index contrast potassium double tungstate waveguides towards efficient rare-earth ion amplification on-chip

    NARCIS (Netherlands)

    Sefünç, Mustafa; Segerink, Franciscus B.; García Blanco, Sonia Maria

    2015-01-01

    Rare-earth ion doped KY(WO4)2 amplifiers are proposed to be a good candidate for many future applications by benefiting from the excellent gain characteristics of rare-earth ions, namely high bit rate amplification (

  7. An efficient and high fidelity method for amplification, cloning and sequencing of complete tospovirus genomic RNA segments

    Science.gov (United States)

    Amplification and sequencing of the complete M- and S-RNA segments of Tomato spotted wilt virus and Impatiens necrotic spot virus as a single fragment is useful for whole genome sequencing of tospoviruses co-infecting a single host plant. It avoids issues associated with overlapping amplicon-based ...

  8. Solid-phase PCR for rapid multiplex detection of Salmonella spp. at the subspecies level, with amplification efficiency comparable to conventional PCR.

    Science.gov (United States)

    Chin, Wai Hoe; Sun, Yi; Høgberg, Jonas; Hung, Tran Quang; Wolff, Anders; Bang, Dang Duong

    2017-04-01

    Solid-phase PCR (SP-PCR) has attracted considerable interest in different research fields since it allows parallel DNA amplification on the surface of a solid substrate. However, the applications of SP-PCR have been hampered by the low efficiency of the solid-phase amplification. In order to increase the yield of the solid-phase amplification, we studied various parameters including the length, the density, as well as the annealing position of the solid support primer. A dramatic increase in the signal-to-noise (S/N) ratio was observed when increasing the length of solid support primers from 45 to 80 bp. The density of the primer on the surface was found to be important for the S/N ratio of the SP-PCR, and the optimal S/N was obtained with a density of 1.49 × 1011 molecules/mm2. In addition, the use of solid support primers with a short overhang at the 5' end would help improve the S/N ratio of the SP-PCR. With optimized conditions, SP-PCR can achieve amplification efficiency comparable to conventional PCR, with a limit of detection of 1.5 copies/μl (37.5 copies/reaction). These improvements will pave the way for wider applications of SP-PCR in various fields such as clinical diagnosis, high-throughput DNA sequencing, and single-nucleotide polymorphism analysis. Graphical abstract Schematic representation of solid-phase PCR.

  9. Limited efficiency of universal mini-barcode primers for DNA amplification from desert reptiles, birds and mammals.

    Science.gov (United States)

    Arif, I A; Khan, H A; Al Sadoon, M; Shobrak, M

    2011-10-31

    In recent years, DNA barcoding has emerged as a powerful tool for species identification. We report an extended validation of a universal DNA mini-barcode for amplification of 130-bp COI segments from 23 specimens collected from a desert environment, including 11 reptiles, five mammals and seven birds. Besides the standard double-annealing protocol, we also tested a more stringent single-annealing protocol. The PCR success rate for the amplification of the mini-barcode region was: mammals (4/5), reptiles (5/11) and birds (4/7). These findings demonstrate the limited utility of universal primers for mini-barcoding, at least for these vertebrate taxa that we collected from the Saudi Arabian desert.

  10. High Fidelity, Efficiency and Functionalization of Ds-Px Unnatural Base Pairs in PCR Amplification for a Genetic Alphabet Expansion System.

    Science.gov (United States)

    Okamoto, Itaru; Miyatake, Yuya; Kimoto, Michiko; Hirao, Ichiro

    2016-11-18

    Genetic alphabet expansion of DNA using an artificial extra base pair (unnatural base pair) could augment nucleic acid and protein functionalities by increasing their components. We previously developed an unnatural base pair between 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px), which exhibits high fidelity as a third base pair in PCR amplification. Here, the fidelity and efficiency of Ds-Px pairing using modified Px bases with functional groups, such as diol, azide, ethynyl and biotin, were evaluated by an improved method with optimized PCR conditions. The results revealed that all of the base pairs between Ds and either one of the modified Px bases functioned with high amplification efficiency (0.76-0.81), high selectivity (≥99.96% per doubling), and less sequence dependency, in PCR using 3'-exonuclease-proficient Deep Vent DNA polymerase. We also demonstrated that the azide-Px in PCR-amplified DNA was efficiently modified with any functional groups by copper-free click reaction. This genetic alphabet expansion system could endow nucleic acids with a wide variety of increased functionalities by the site-specific incorporation of modified Px bases at desired positions in DNA.

  11. HaloTag mediated artificial cellulosome assembly on a rolling circle amplification DNA template for efficient cellulose hydrolysis.

    Science.gov (United States)

    Sun, Qing; Chen, Wilfred

    2016-05-10

    We report here the generation of four-component artificial cellulosomes onto a DNA scaffold using the self-labeling HaloTag for DNA conjugation. The resulting structures exhibited significantly improved cellulosome assembly as well as cellulose hydrolysis over compatible structures generated using protein scaffolds. Cellulose hydrolysis was further enhanced by 2-fold using the more complex cellulosome structures assembled onto DNA templates generated by rolling circle amplification (RCA). The flexibility to insert additional hybridization sites in a multiplexing manner using RCA should enable the assembly of a larger array of cellulases to better mimic the enzyme diversity of naturally occurring cellulosomes.

  12. Intercistronic as well as terminal sequences are required for efficient amplification of brome mosaic virus RNA3.

    OpenAIRE

    French, R; Ahlquist, P

    1987-01-01

    The genome of brome mosaic virus (BMV) is divided among messenger polarity RNA1, RNA2, and RNA3 (3.2, 2.9, and 2.1 kilobases, respectively). cis-Acting sequences required for BMV RNA amplification were investigated with RNA3. By using expressible cDNA clones, deletions were constructed throughout RNA3 and tested in barley protoplasts coinoculated with RNA1 and RNA2. In contrast to requirements for 5'- and 3'-terminal noncoding sequences, either of the two RNA3 coding regions can be deleted in...

  13. Hardness amplification in nondeterministic logspace

    OpenAIRE

    Gupta, Sushmita

    2007-01-01

    A hard problem is one which cannot be easily computed by efficient algorithms. Hardness amplification is a procedure which takes as input a problem of mild hardness and returns a problem of higher hardness. This is closely related to the task of decoding certain error-correcting codes. We show amplification from mild average case hardness to higher average case hardness for nondeterministic logspace and worst-to-average amplification for nondeterministic linspace. Finally we explore possible ...

  14. Intercistronic as well as terminal sequences are required for efficient amplification of brome mosaic virus RNA3.

    Science.gov (United States)

    French, R; Ahlquist, P

    1987-05-01

    The genome of brome mosaic virus (BMV) is divided among messenger polarity RNA1, RNA2, and RNA3 (3.2, 2.9, and 2.1 kilobases, respectively). cis-Acting sequences required for BMV RNA amplification were investigated with RNA3. By using expressible cDNA clones, deletions were constructed throughout RNA3 and tested in barley protoplasts coinoculated with RNA1 and RNA2. In contrast to requirements for 5'- and 3'-terminal noncoding sequences, either of the two RNA3 coding regions can be deleted individually and both can be simultaneously inactivated by N-terminal frameshift mutations without significantly interfering with amplification of RNA3 or production of its subgenomic mRNA. However, simultaneous major deletions in both coding regions greatly attenuate RNA3 accumulation. RNA3 levels can be largely restored by insertion of a heterologous, nonviral sequence in such mutants, suggesting that RNA3 requires physical separation of its terminal domains or a minimum overall size for normal replication or stability. Unexpectedly, deletions in a 150-base segment of the intercistronic noncoding region drastically reduce RNA3 accumulation. This segment contains a sequence element homologous to sequences found near the 5' ends of BMV RNA1 and RNA2 and in analogous positions in the three genomic RNAs of the related cucumber mosaic virus, suggesting a possible role in plus-strand synthesis.

  15. EFFICIENCY OF REAL-TIME PCR FOR 18S rRNA AMPLIFICATION OF SORBUS DOMESTICA, L.

    Directory of Open Access Journals (Sweden)

    Petronela Poláčeková

    2012-10-01

    Full Text Available Normal 0 21 false false false SK X-NONE X-NONE Nowadays, the awareness is given more and more to underutilized and  unusual fruits. One of them is Sorbus domestica, L. not only as an endangered species, but as well as a promising and economically usable crop. The work was aimed for finding a total genomic DNA isolating methods from fresh plant material and confirmation of the optimized method by the detection of 18S rRNA gene using real-time PCR. Two commercial isolation kits were tested -  Invisorb® Spin Plant Mini Kit and Wizard ® Genomic DNA. Higher purity and yield of DNA isolation kit showed Invisorb kit. The effective and pure PCR amplification was confirmed for Invisorb, too when 20 ng undiluted DNA at annealing temperature of 64.5 °C.doi:10.5219/203

  16. Development of an efficient signal amplification strategy for label-free enzyme immunoassay using two site-specific biotinylated recombinant proteins

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Jin-Bao [School of Pharmacy, Weifang Medical University, Weifang 261053 (China); Tang, Ying [Affiliated Hospital of Weifang Medical University, Weifang 261041 (China); Yang, Hong-Ming, E-mail: yanghongming2006@sohu.com [School of Pharmacy, Weifang Medical University, Weifang 261053 (China)

    2015-02-15

    Highlights: • An efficient signal amplification strategy for label-free EIA is proposed. • Divalent biotinylated AP and monovalent biotinylated ZZ were prepared via Avitag–BirA system. • The above site-specific biotinylated fusion proteins form complex via SA–biotin interaction. • The mechanism relies on the ZZ–Avi-B/SA/AP–(Avi-B){sub 2} complex. • The analytical signals are enhanced (32-fold) by the proposed strategy. - Abstract: Constructing a recombinant protein between a reporter enzyme and a detector protein to produce a homogeneous immunological reagent is advantageous over random chemical conjugation. However, the approach hardly recombines multiple enzymes in a difunctional fusion protein, which results in insufficient amplification of the enzymatic signal, thereby limiting its application in further enhancement of analytical signal. In this study, two site-specific biotinylated recombinant proteins, namely, divalent biotinylated alkaline phosphatase (AP) and monovalent biotinylated ZZ domain, were produced by employing the Avitag–BirA system. Through the high streptavidin (SA)–biotin interaction, the divalent biotinylated APs were clustered in the SA–biotin complex and then incorporated with the biotinylated ZZ. This incorporation results in the formation of a functional macromolecule that involves numerous APs, thereby enhancing the enzymatic signal, and in the production of several ZZ molecules for the interaction with immunoglobulin G (IgG) antibody. The advantage of this signal amplification strategy is demonstrated through ELISA, in which the analytical signal was substantially enhanced, with a 32-fold increase in the detection sensitivity compared with the ZZ–AP fusion protein approach. The proposed immunoassay without chemical modification can be an alternative strategy to enhance the analytical signals in various applications involving immunosensors and diagnostic chips, given that the label-free IgG antibody is suitable

  17. Design of phylum-specific hybrid primers for DNA barcoding: addressing the need for efficient COI amplification in the Echinodermata.

    Science.gov (United States)

    Hoareau, T B; Boissin, E

    2010-11-01

    Recent research has shown the usefulness of the Folmer region of the cytochrome oxidase I (COI) as a genetic barcode to assist in species delimitation of echinoderms. However, amplification of COI is often challenging in echinoderms (low success or pseudogenes). We present a method that allows the design of phylum-specific hybrid primers, and use this to develop COI primers for the Echinodermata. We aligned COI sequences from 310 echinoderm species and designed all possible primers along the consensus sequence with two methods (standard degenerate and hybrid). We found much lower degeneracy for hybrid primers (4-fold degeneracy) than for standard degenerate primers (≥48-fold degeneracy). We then designed the most conserved hybrid primers to amplify a >500-bp region within COI. These primers successfully amplified this gene region in all tested taxa (123 species across all echinoderm classes). Sequencing of 30 species among these confirmed both the quality of the sequences (>500 bp, no pseudogenes) and their utility as a DNA barcode. This method should be useful for developing primers for other mitochondrial genes and other phyla. The method will also be of interest for the development of future projects involving both community-based genetic assessments on macroorganisms and biodiversity assessment of environmental samples using high-throughput sequencing. © 2010 Blackwell Publishing Ltd.

  18. Efficient and Specific Detection of Salmonella in Food Samples Using a stn-Based Loop-Mediated Isothermal Amplification Method

    Science.gov (United States)

    2015-01-01

    The Salmonella enterotoxin (stn) gene exhibits high homology among S. enterica serovars and S. bongori. A set of 6 specific primers targeting the stn gene were designed for detection of Salmonella spp. using the loop-mediated isothermal amplification (LAMP) method. The primers amplified target sequences in all 102 strains of 87 serovars of Salmonella tested and no products were detected in 57 non-Salmonella strains. The detection limit in pure cultures was 5 fg DNA/reaction when amplified at 65°C for 25 min. The LAMP assay could detect Salmonella in artificially contaminated food samples as low as 220 cells/g of food without a preenrichment step. However, the sensitivity was increased 100-fold (~2 cells/g) following 5 hr preenrichment at 35°C. The LAMP technique, with a preenrichment step for 5 and 16 hr, was shown to give 100% specificity with food samples compared to the reference culture method in which 67 out of 90 food samples gave positive results. Different food matrixes did not interfere with LAMP detection which employed a simple boiling method for DNA template preparation. The results indicate that the LAMP method, targeting the stn gene, has great potential for detection of Salmonella in food samples with both high specificity and high sensitivity. PMID:26543859

  19. Strong enhancement of emission efficiency in GaN light-emitting diodes by plasmon-coupled light amplification of graphene

    Science.gov (United States)

    Kim, Jong Min; Kim, Sung; Hwang, Sung Won; Kim, Chang Oh; Shin, Dong Hee; Kim, Ju Hwan; Jang, Chan Wook; Kang, Soo Seok; Hwang, Euyheon; Choi, Suk-Ho; El-Gohary, Sherif H.; Byun, Kyung Min

    2018-02-01

    Recently, we have demonstrated that excitation of plasmon-polaritons in a mechanically-derived graphene sheet on the top of a ZnO semiconductor considerably enhances its light emission efficiency. If this scheme is also applied to device structures, it is then expected that the energy efficiency of light-emitting diodes (LEDs) increases substantially and the commercial potential will be enormous. Here, we report that the plasmon-induced light coupling amplifies emitted light by ∼1.6 times in doped large-area chemical-vapor-deposition-grown graphene, which is useful for practical applications. This coupling behavior also appears in GaN-based LEDs. With AuCl3-doped graphene on Ga-doped ZnO films that is used as transparent conducting electrodes for the LEDs, the average electroluminescence intensity is 1.2–1.7 times enhanced depending on the injection current. The chemical doping of graphene may produce the inhomogeneity in charge densities (i.e., electron/hole puddles) or roughness, which can play a role as grating couplers, resulting in such strong plasmon-enhanced light amplification. Based on theoretical calculations, the plasmon-coupled behavior is rigorously explained and a method of controlling its resonance condition is proposed.

  20. Efficient 1 kHz femtosecond optical parametric amplification in BiB(3)O(6) pumped at 800 nm.

    Science.gov (United States)

    Ghotbi, Masood; Ebrahim-Zadeh, Majid; Petrov, Valentin; Tzankov, Pancho; Noack, Frank

    2006-10-30

    We demonstrate efficient operation of a tunable femtosecond optical parametric amplifier based on BiB(3)O(6) pumped at 800 nm by a 1 kHz Ti:sapphire regenerative amplifier. The idler wavelength coverage extends to beyond 3 mum and the pulse duration at this wavelength is of the order of 110 fs. This new nonlinear borate crystal offers exceptionally high nonlinearity, making it a very promising candidate for power scaling of such frequency converters in the near-IR.

  1. Mixed-Signal Architectures for High-Efficiency and Low-Distortion Digital Audio Processing and Power Amplification

    Directory of Open Access Journals (Sweden)

    Pierangelo Terreni

    2010-01-01

    Full Text Available The paper addresses the algorithmic and architectural design of digital input power audio amplifiers. A modelling platform, based on a meet-in-the-middle approach between top-down and bottom-up design strategies, allows a fast but still accurate exploration of the mixed-signal design space. Different amplifier architectures are configured and compared to find optimal trade-offs among different cost-functions: low distortion, high efficiency, low circuit complexity and low sensitivity to parameter changes. A novel amplifier architecture is derived; its prototype implements digital processing IP macrocells (oversampler, interpolating filter, PWM cross-point deriver, noise shaper, multilevel PWM modulator, dead time compensator on a single low-complexity FPGA while off-chip components are used only for the power output stage (LC filter and power MOS bridge; no heatsink is required. The resulting digital input amplifier features a power efficiency higher than 90% and a total harmonic distortion down to 0.13% at power levels of tens of Watts. Discussions towards the full-silicon integration of the mixed-signal amplifier in embedded devices, using BCD technology and targeting power levels of few Watts, are also reported.

  2. Red-backed vole brain promotes highly efficient in vitro amplification of abnormal prion protein from macaque and human brains infected with variant Creutzfeldt-Jakob disease agent.

    Science.gov (United States)

    Nemecek, Julie; Nag, Nabanita; Carlson, Christina M.; Schneider, Jay R.; Heisey, Dennis M.; Johnson, Christopher J.; Asher, David M.; Gregori, Luisa

    2013-01-01

    Rapid antemortem tests to detect individuals with transmissible spongiform encephalopathies (TSE) would contribute to public health. We investigated a technique known as protein misfolding cyclic amplification (PMCA) to amplify abnormal prion protein (PrPTSE) from highly diluted variant Creutzfeldt-Jakob disease (vCJD)-infected human and macaque brain homogenates, seeking to improve the rapid detection of PrPTSE in tissues and blood. Macaque vCJD PrPTSE did not amplify using normal macaque brain homogenate as substrate (intraspecies PMCA). Next, we tested interspecies PMCA with normal brain homogenate of the southern red-backed vole (RBV), a close relative of the bank vole, seeded with macaque vCJD PrPTSE. The RBV has a natural polymorphism at residue 170 of the PrP-encoding gene (N/N, S/S, and S/N). We investigated the effect of this polymorphism on amplification of human and macaque vCJD PrPTSE. Meadow vole brain (170N/N PrP genotype) was also included in the panel of substrates tested. Both humans and macaques have the same 170S/S PrP genotype. Macaque PrPTSE was best amplified with RBV 170S/S brain, although 170N/N and 170S/N were also competent substrates, while meadow vole brain was a poor substrate. In contrast, human PrPTSE demonstrated a striking narrow selectivity for PMCA substrate and was successfully amplified only with RBV 170S/S brain. These observations suggest that macaque PrPTSE was more permissive than human PrPTSE in selecting the competent RBV substrate. RBV 170S/S brain was used to assess the sensitivity of PMCA with PrPTSE from brains of humans and macaques with vCJD. PrPTSE signals were reproducibly detected by Western blot in dilutions through 10-12 of vCJD-infected 10% brain homogenates. This is the first report showing PrPTSE from vCJD-infected human and macaque brains efficiently amplified with RBV brain as the substrate. Based on our estimates, PMCA showed a sensitivity that might be sufficient to detect PrPTSE in v

  3. Amplification of femtosecond pulses in large mode area Bragg fibers

    Science.gov (United States)

    Gaponov, Dmitry A.; Février, Sébastien; Roy, Philippe; Hanna, Marc; Papadopoulos, Dimitris N.; Druon, Frédéric; Daniault, Louis; Georges, Patrick; Likhachev, Mikhail E.; Salganskii, Mikhail Y.; Yashkov, Mikhail V.

    2010-04-01

    The increase of the output power in fiber lasers and amplifiers is directly related to the scaling of the core diameter. State of the art high power laser and amplifier setups are based on large mode area (LMA) photonic crystal fibers (PCF) exhibiting core diameters ranging from 40 μm up to 100 μm1 (rod-type PCF). For instance, a two-stage femtosecond chirped pulse amplification (CPA) system based on 80 μm core diameter rod-type PCF was demonstrated generating 270 fs 100 μJ pulses2. Although highly suited to reach very large mode areas, this fiber design suffers some drawbacks such as high bend sensitivity (for core diameter equal to or larger than 40 μm3) and practical handling (cleaving, splicing, etc.) due to presence of air holes. As an alternative we have recently proposed all-solid photonic bandgap (PBG) Bragg fiber (BF) design4. Due to their waveguiding mechanism completely different from total internal reflection this type of fiber offers a very flexible geometry for designing waveguide structures with demanding properties (singlemodedness in large core configuration5, chromatic dispersion6, polarization maintaining7, low bend sensitivity8). During the last few years our interest was mainly focused on the realization of an active BF and scaling up the core diameter. We showed that, in principle, core diameters in excess of 50 μm can be reached9. As an example, an Yb-doped LMA BF with 20 μm core diameter was realized and single transverse mode operation in continuous wave (cw)9 and mode-locking10 oscillation regimes was demonstrated. Moreover, operation of two dimensional all-solid PBG fibers in laser and amplifier regimes was recently demonstrated11-13. In this paper we report on the first demonstration of amplification of femtosecond pulses in LMA PBG BF. A single transverse mode was obtained and the BF allowed for generating 5 μJ 260 fs pulses in a system with a moderate stretching of 150 ps.

  4. Exawatt-Zettawatt Pulse Generation and Applications

    CERN Document Server

    Mourou, G A; Malkin, V M; Toroker, Z; Khazanov, E A; Sergeev, A M; Tajima, T

    2011-01-01

    A new amplification method, weaving the three basic compression techniques, Chirped Pulse Amplification (CPA), Optical Parametric Chirped Pulse Amplification (OPCPA) and Plasma Compression by Backward Raman Amplification (BRA) in plasma, is proposed. It is called C3 for Cascaded Conversion Compression. It has the capability to compress with good efficiency kilojoule to megajoule, nanosecond laser pulses into femtosecond pulses, to produce exawatt and beyond peak power. In the future, C3 could be used at large-scale facilities such as the National Ignition Facility (NIF) or the Laser Megajoule (LMJ) and open the way to zettawatt level pulses. The beam will be focused to a wavelength spot size with a f#1. The very small beam size, i.e. few centimeters, along with the low laser repetition rate laser system will make possible the use of inexpensive, precision, disposable optics. The resulting intensity will approach the Schwinger value, thus opening up new possibilities in fundamental physics.

  5. Amplification variable factor amplifier

    NARCIS (Netherlands)

    Akitsugu, Oshita; Nauta, Bram

    2007-01-01

    PROBLEM TO BE SOLVED: To provide an amplification factor variable amplifier capable of achieving temperature compensation of an amplification factor over a wide variable amplification factor range. ; SOLUTION: A Gilbert type amplification factor variable amplifier 11 amplifies an input signal and

  6. Amplification variable factor amplifier

    NARCIS (Netherlands)

    Akitsugu, O.; Nauta, Bram

    2006-01-01

    PROBLEM TO BE SOLVED: To provide an amplification factor variable amplifier capable of achieving temperature compensation of an amplification factor over a wide variable amplification factor range. ; SOLUTION: A Gilbert type amplification factor variable amplifier 11 amplifies an input signal and

  7. Study of the transverse lasing in big size crystals of Ti:Sa. Application to the design of the peta-watt high-energy amplifier of the pilot laser of the LASERIX facility; Etude de l'amplification parasite transverse de la fluorescence dans les cristaux de Ti:Sa de grandes dimensions. Application a la realisation de l'amplificateur petawatt haute energie du laser pilote de la station LASERIX

    Energy Technology Data Exchange (ETDEWEB)

    Ple, F

    2007-11-15

    This manuscript presents experimental and theoretical works accomplished for the development of the LASERIX laser driver. The main goal of this thesis work was to design a high energy and high repetition rate titanium doped sapphire amplifier (Ti:Sa) allowing to reach an energy of 40 J at a repetition rate of 0.1 Hz before compression. After a general description of amplification in chirped pulse amplification Ti:Sa laser systems (Chapter 1), I present the two particular developments we made during this work for high energy amplification (Chapter 2). First, the spatial shaping and the homogenization based on micro-lens array (MLA) systems of the eight Nd-Glass pump lasers dedicated to the pumping of the last booster amplifier.Secondly, the suppression of parasitic effects due to transverse amplification of the fluorescence in the last booster amplifier Ti:Sa crystal. The developments performed as part of this thesis allowed us to amplify an impulsion of 2 J of energy up to 39 J in a crystal of 10 cm diameter. I also present the simulation program I developed (Chapter 3) in order to simulate the three dimensional parasitic lasing effect and fluorescence transverse amplification phenomena in large Ti:Sa crystals. A parametric study of these parasitic effects is also presented. Finally, the last part of this manuscript (Chapter 4) gives prospects of this work as part of the large future ELI and ILE projects. (author)

  8. Deuterated Water Hexamer Observed by Chirped-Pulse Rotational Spectroscopy

    Science.gov (United States)

    Evangelisti, Luca; Perez, Cristobal; Lobsiger, Simon; Seifert, Nathan A.; Zaleski, Daniel P.; Pate, Brooks; Kisiel, Zbigniew; Temelso, Berhane; Shields, George C.

    2014-06-01

    The water hexamer is the first cluster size where three dimensional structures become the most stable. For cluster sizes up to the water decamer, the hexamer is unique because there are three low-lying isomers with distinct oxygen framework geometries that can be observed in pulsed molecular beams: the prism, cage, and book. Each structure has a different number of hydrogen bonds (prism: 9, cage: 8, book: 7). The prediction of the lowest energy form by different water potentials has become a benchmark in computational studies of water clusters. The experimental determination that the cage is the lowest energy form was presented by our group in 2012 using the population changes that occur when different carrier gases are used in the molecular beam expansion. Recently, it has been proposed by Babin and Paesani that the relative energy ordering of these isomers might be useful for testing the ability of theory to include zero-point energy effects. Their calculations suggested that the prism might become the lowest energy isomer in the fully deuterated water hexamer. At the simplest level, this can explained by the fact that the prism has the most hydrogen bonds and would, therefore, experience the most energy lowering upon isotopic substitution. Broadband rotational spectroscopy in a pulsed supersonic expansion has been used to study the cage, prism and book isomers of deuterated water hexamer. These data, in conjunction with new computational advances, quantify the changes in the oxygen framework structure respect to the normal water hexamers. Moreover, by using different gases in the expansion we have established that the prism isomer becomes the minimum energy structure as suggested by Babin and Paesani. V. Babin and F. Paesani, "The curious case of the water hexamer: Cage vs. Prism", Chem. Phys. Lett. 580, 1-8 (2013).

  9. Multiplex ligation-dependent probe amplification for genetic screening in autism spectrum disorders: Efficient identification of known microduplications and identification of a novel microduplication in ASMT

    Directory of Open Access Journals (Sweden)

    Reichert Jennifer G

    2008-10-01

    Full Text Available Abstract Background It has previously been shown that specific microdeletions and microduplications, many of which also associated with cognitive impairment (CI, can present with autism spectrum disorders (ASDs. Multiplex ligation-dependent probe amplification (MLPA represents an efficient method to screen for such recurrent microdeletions and microduplications. Methods In the current study, a total of 279 unrelated subjects ascertained for ASDs were screened for genomic disorders associated with CI using MLPA. Fluorescence in situ hybridization (FISH, quantitative polymerase chain reaction (Q-PCR and/or direct DNA sequencing were used to validate potential microdeletions and microduplications. Methylation-sensitive MLPA was used to characterize individuals with duplications in the Prader-Willi/Angelman (PWA region. Results MLPA showed two subjects with typical ASD-associated interstitial duplications of the 15q11-q13 PWA region of maternal origin. Two additional subjects showed smaller, de novo duplications of the PWA region that had not been previously characterized. Genes in these two novel duplications include GABRB3 and ATP10A in one case, and MKRN3, MAGEL2 and NDN in the other. In addition, two subjects showed duplications of the 22q11/DiGeorge syndrome region. One individual was found to carry a 12 kb deletion in one copy of the ASPA gene on 17p13, which when mutated in both alleles leads to Canavan disease. Two subjects showed partial duplication of the TM4SF2 gene on Xp11.4, previously implicated in X-linked non-specific mental retardation, but in our subsequent analyses such variants were also found in controls. A partial duplication in the ASMT gene, located in the pseudoautosomal region 1 (PAR1 of the sex chromosomes and previously suggested to be involved in ASD susceptibility, was observed in 6–7% of the cases but in only 2% of controls (P = 0.003. Conclusion MLPA proves to be an efficient method to screen for chromosomal

  10. Efficient amplification of chimeric adenovirus 5/40S vectors carrying the short fiber protein of Ad40 in suspension cell cultures.

    Directory of Open Access Journals (Sweden)

    Marta Miralles

    Full Text Available The human adenovirus 40 (Ad40 is a promising tool for gene therapy of intestinal diseases. Since the production of Ad40 in vitro is extremely inefficient, chimeric Adenovirus 5/40S vectors carrying the Ad40 short fiber on the Ad5 capsid have been developed. However, Ad5/40S productivity is low. We hypothesized that low productivity was a result of inefficient viral entry into producer cells during amplification. To this end, we have developed a production strategy based on using 211B cells (expressing Ad5 fiber during amplification steps, while Ad5/40S infectivity is further improved by adding polybrene during infections. In addition, the optimal harvesting time was determined by evaluating the Ad5/40S viral cycle. The developed production strategy significantly reduces the number of amplification cycles and duration of the process. Finally, to further facilitate Ad5/40S production, 211B cells were adapted to suspension thus allowing to easily upscale the production process in bioreactors.

  11. Improved amplification efficiency on stool samples by addition of spermidine and its use for non-invasive detection of colorectal cancer

    KAUST Repository

    Roperch, Jean-Pierre

    2015-05-29

    Background Using quantitative methylation-specific PCR (QM-MSP) is a promising method for colorectal cancer (CRC) diagnosis from stool samples. Difficulty in eliminating PCR inhibitors of this body fluid has been extensively reported. Here, spermidine is presented as PCR facilitator for the detection of stool DNA methylation biomarkers using QM-MSP. We examined its effectiveness with NPY, PENK and WIF1, three biomarkers which we have previously shown to be of relevance to CRC. Results We determined an optimal window for the amplification of the albumin (Alb) gene (100 ng of bisulfite-treated stool DNA added of 1 mM spermidine) at which we report that spermidine acts as a PCR facilitator (AE = 1680%) for SG RT-PCR. We show that the amplification of methylated PENK, NPY and WIF1 is considerably facilitated by QM-MSP as measured by an increase of CMI (Cumulative Methylation Index, i.e. the sum of the three methylation values) by a factor of 1.5 to 23 fold in individual samples, and of 10 fold in a pool of five samples. Conclusions We contend that spermidine greatly reduces the problems of PCR inhibition in stool samples. This observed feature, after validation on a larger sampling, could be used in the development of stool-based CRC diagnosis tests.

  12. Effects of humic acid on DNA quantification with Quantifiler® Human DNA Quantification kit and short tandem repeat amplification efficiency.

    Science.gov (United States)

    Seo, Seung Bum; Lee, Hye Young; Zhang, Ai Hua; Kim, Hye Yeon; Shin, Dong Hoon; Lee, Soong Deok

    2012-11-01

    Correct DNA quantification is an essential part to obtain reliable STR typing results. Forensic DNA analysts often use commercial kits for DNA quantification; among them, real-time-based DNA quantification kits are most frequently used. Incorrect DNA quantification due to the presence of PCR inhibitors may affect experiment results. In this study, we examined the alteration degree of DNA quantification results estimated in DNA samples containing a PCR inhibitor by using a Quantifiler® Human DNA Quantification kit. For experiments, we prepared approximately 0.25 ng/μl DNA samples containing various concentrations of humic acid (HA). The quantification results were 0.194-0.303 ng/μl at 0-1.6 ng/μl HA (final concentration in the Quantifiler reaction) and 0.003-0.168 ng/μl at 2.4-4.0 ng/μl HA. Most DNA quantity was undetermined when HA concentration was higher than 4.8 ng/μl HA. The C (T) values of an internal PCR control (IPC) were 28.0-31.0, 36.5-37.1, and undetermined at 0-1.6, 2.4, and 3.2 ng/μl HA. These results indicate that underestimated DNA quantification results may be obtained in the DNA sample with high C (T) values of IPC. Thus, researchers should carefully interpret the DNA quantification results. We additionally examined the effects of HA on the STR amplification by using an Identifiler® kit and a MiniFiler™ kit. Based on the results of this study, it is thought that a better understanding of various effects of HA would help researchers recognize and manipulate samples containing HA.

  13. Heralded amplification of photonic qubits.

    Science.gov (United States)

    Bruno, Natalia; Pini, Vittorio; Martin, Anthony; Verma, Varun B; Nam, Sae Woo; Mirin, Richard; Lita, Adriana; Marsili, Francesco; Korzh, Boris; Bussières, Félix; Sangouard, Nicolas; Zbinden, Hugo; Gisin, Nicolas; Thew, Rob

    2016-01-11

    We demonstrate postselection free heralded qubit amplification for Time-Bin qubits and single photon states in an all-fibre, telecom-wavelength, scheme that highlights the simplicity, stability and potential for fully integrated photonic solutions. Exploiting high-efficiency superconducting detectors, the gain, fidelity and the performance of the amplifier are studied as a function of loss. We also demonstrate the first heralded single photon amplifier with independent sources. This provides a significant advance towards demonstrating device-independent quantum key distribution as well as fundamental tests of quantum mechanics over extended distances.

  14. Temporal optimization of ultrabroadband high-energy OPCPA

    National Research Council Canada - National Science Library

    Jeffrey Moses; Cristian Manzoni; Shu-Wei Huang; Giulio Cerullo; Franz X. Kaertner

    2009-01-01

    We present general guidelines for the design of ultrabroadband, high-energy optical parametric chirped-pulse amplifiers, where maximization of both conversion efficiency and bandwidth and simultaneous...

  15. DHFR/MSH3 amplification in methotrexate-resistant cells alters the hMutSα/hMutSβ ratio and reduces the efficiency of base–base mismatch repair

    Science.gov (United States)

    Drummond, James T.; Genschel, Jochen; Wolf, Elisabeth; Modrich, Paul

    1997-01-01

    The level and fate of hMSH3 (human MutS homolog 3) were examined in the promyelocytic leukemia cell line HL-60 and its methotrexate-resistant derivative HL-60R, which is drug resistant by virtue of an amplification event that spans the dihydrofolate reductase (DHFR) and MSH3 genes. Nuclear extracts from HL-60 and HL-60R cells were subjected to an identical, rapid purification protocol that efficiently captures heterodimeric hMutSα (hMSH2⋅hMSH6) and hMutSβ (hMSH2⋅hMSH3). In HL-60 extracts the hMutSα to hMutSβ ratio is roughly 6:1, whereas in methotrexate-resistant HL-60R cells the ratio is less than 1:100, due to overproduction of hMSH3 and heterodimer formation of this protein with virtually all the nuclear hMSH2. This shift is associated with marked reduction in the efficiency of base–base mismatch and hypermutability at the hypoxanthine phosphoribosyltransferase (HPRT) locus. Purified hMutSα and hMutSβ display partial overlap in mismatch repair specificity: both participate in repair of a dinucleotide insertion–deletion heterology, but only hMutSα restores base–base mismatch repair to extracts of HL-60R cells or hMSH2-deficient LoVo colorectal tumor cells. PMID:9294177

  16. Quantum phase amplification for temporal pulse shaping and super-resolution in remote sensing

    Science.gov (United States)

    Yin, Yanchun

    The use of nonlinear optical interactions to perform nonclassical transformations of electromagnetic field is an area of considerable interest. Quantum phase amplification (QPA) has been previously proposed as a method to perform nonclassical manipulation of coherent light, which can be experimentally realized by use of nonlinear optical mixing processes, of which phase-sensitive three-wave mixing (PSTWM) is one convenient choice. QPA occurs when PSTWM is operated in the photon number deamplification mode, i.e., when the energy is coherently transferred among the low-frequency signal and idler waves and the high-frequency pump wave. The final state is nonclassical, with the field amplitude squeezed and the phase anti-squeezed. In the temporal domain, the use of QPA has been studied to facilitate nonlinear pulse shaping. This novel method directly shapes the temporal electric field amplitude and phase using the PSTWM in a degenerate and collinear configuration, which has been analyzed using a numerical model. Several representative pulse shaping capabilities of this technique have been identified, which can augment the performance of common passive pulse shaping methods operating in the Fourier domain. The analysis indicates that a simple quadratic variation of temporal phase facilitates pulse compression and self-steepening, with features significantly shorter than the original transform-limited pulse. Thus, PSTWM can act as a direct pulse compressor based on the combined effects of phase amplification and group velocity mismatch, even without the subsequent linear phase compensation. Furthermore, it is shown numerically that pulse doublets and pulse trains can be produced at the pump frequency by utilizing the residual linear phase of the signal. Such pulse shaping capabilities are found to be within reach of this technique in common nonlinear optical crystals pumped by pulses available from compact femtosecond chirped-pulse amplification laser systems. The use of

  17. Efficient PCR-Based Amplification of Diverse Alcohol Dehydrogenase Genes from Metagenomes for Improving Biocatalysis: Screening of Gene-Specific Amplicons from Metagenomes

    Science.gov (United States)

    Kariya, Satomi; Kurokawa, Junji

    2014-01-01

    Screening of gene-specific amplicons from metagenomes (S-GAM) has tremendous biotechnological potential. We used this approach to isolate alcohol dehydrogenase (adh) genes from metagenomes based on the Leifsonia species adh gene (lsadh), the enzyme product of which can produce various chiral alcohols. A primer combination was synthesized by reference to homologs of lsadh, and PCR was used to amplify nearly full-length adh genes from metagenomic DNAs. All adh preparations were fused with lsadh at the terminal region and used to construct Escherichia coli plasmid libraries. Of the approximately 2,000 colonies obtained, 1,200 clones were identified as adh positive (∼60%). Finally, 40 adh genes, Hladh-001 to Hladh-040 (for homologous Leifsonia adh), were identified from 223 clones with high efficiency, which were randomly sequenced from the 1,200 clones. The Hladh genes obtained via this approach encoded a wide variety of amino acid sequences (8 to 99%). After screening, the enzymes obtained (HLADH-012 and HLADH-021) were confirmed to be superior to LSADH in some respects for the production of anti-Prelog chiral alcohols. PMID:25085492

  18. Development of a cost-efficient novel method for rapid, concurrent genotyping of five common single nucleotide polymorphisms of the brain derived neurotrophic factor (BDNF) gene by tetra-primer amplification refractory mutation system.

    Science.gov (United States)

    Wang, Cathy K; Xu, Michael S; Ross, Colin J; Lo, Ryan; Procyshyn, Ric M; Vila-Rodriguez, Fidel; White, Randall F; Honer, William G; Barr, Alasdair M

    2015-09-01

    Brain derived neurotrophic factor (BDNF) is a molecular trophic factor that plays a key role in neuronal survival and plasticity. Single nucleotide polymorphisms (SNPs) of the BDNF gene have been associated with specific phenotypic traits in a large number of neuropsychiatric disorders and the response to psychotherapeutic medications in patient populations. Nevertheless, due to study differences and occasionally contrasting findings, substantial further research is required to understand in better detail the association between specific BDNF SNPs and these psychiatric disorders. While considerable progress has been made recently in developing advanced genotyping platforms of SNPs, many high-throughput probe- or array-based detection methods currently available are limited by high costs, slow processing times or access to advanced instrumentation. The polymerase chain reaction (PCR)-based, tetra-primer amplification refractory mutation system (T-ARMS) method is a potential alternative technique for detecting SNP genotypes efficiently, quickly, easily, and cheaply. As a tool in psychopathology research, T-ARMS was shown to be capable of detecting five common SNPs in the BDNF gene (rs6265, rs988748, rs11030104, 11757G/C and rs7103411), which are all SNPs with previously demonstrated clinical relevance to schizophrenia and depression. The present technique therefore represents a suitable protocol for many research laboratories to study the genetic correlates of BDNF in psychiatric disorders. Copyright Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  19. Biomaterials in light amplification

    Science.gov (United States)

    Mysliwiec, Jaroslaw; Cyprych, Konrad; Sznitko, Lech; Miniewicz, Andrzej

    2017-03-01

    Biologically produced or inspired materials can serve as optical gain media, i.e. they can exhibit the phenomenon of light amplification. Some of these materials, under suitable dye-doping and optical pumping conditions, show lasing phenomena. The emerging branch of research focused on obtaining lasing action in highly disordered and highly light scattering materials, i.e. research on random lasing, is perfectly suited for biological materials. The use of biomaterials in light amplification has been extensively reported in the literature. In this review we attempt to report on progress in the development of biologically derived systems able to show the phenomena of light amplification and random lasing together with the contribution of our group to this field. The rich world of biopolymers modified with molecular aggregates and nanocrystals, and self-organized at the nanoscale, offers a multitude of possibilities for tailoring luminescent and light scattering properties that are not easily replicated in conventional organic or inorganic materials. Of particular importance and interest are light amplification and lasing, or random lasing studies in biological cells and tissues. In this review we will describe nucleic acids and their complexes employed as gain media due to their favorable optical properties and ease of manipulation. We will report on research conducted on various biomaterials showing structural analogy to nucleic acids such as fluorescent proteins, gelatins in which the first distributed feedback laser was realized, and also amyloids or silks, which, due to their dye-doped fiber-like structure, allow for light amplification. Other materials that were investigated in that respect include polysaccharides, like starch exhibiting favorable photostability in comparison to other biomaterials, and chitosan, which forms photonic crystals or cellulose. Light amplification and random lasing was not only observed in processed biomaterials but also in living

  20. Improved PCR Amplification of Broad Spectrum GC DNA Templates.

    Science.gov (United States)

    Guido, Nicholas; Starostina, Elena; Leake, Devin; Saaem, Ishtiaq

    2016-01-01

    Many applications in molecular biology can benefit from improved PCR amplification of DNA segments containing a wide range of GC content. Conventional PCR amplification of DNA sequences with regions of GC less than 30%, or higher than 70%, is complex due to secondary structures that block the DNA polymerase as well as mispriming and mis-annealing of the DNA. This complexity will often generate incomplete or nonspecific products that hamper downstream applications. In this study, we address multiplexed PCR amplification of DNA segments containing a wide range of GC content. In order to mitigate amplification complications due to high or low GC regions, we tested a combination of different PCR cycling conditions and chemical additives. To assess the fate of specific oligonucleotide (oligo) species with varying GC content in a multiplexed PCR, we developed a novel method of sequence analysis. Here we show that subcycling during the amplification process significantly improved amplification of short template pools (~200 bp), particularly when the template contained a low percent of GC. Furthermore, the combination of subcycling and 7-deaza-dGTP achieved efficient amplification of short templates ranging from 10-90% GC composition. Moreover, we found that 7-deaza-dGTP improved the amplification of longer products (~1000 bp). These methods provide an updated approach for PCR amplification of DNA segments containing a broad range of GC content.

  1. Macromechanical Parametric Amplification

    DEFF Research Database (Denmark)

    Neumeyer, Stefan

    Parametric amplification is obtained by adding parametric excitation to direct (externally driven) excitation for boosting near-resonant oscillations. It is utilized for mass and force sensing, switching and signal processing, filtering, timing, signal amplification, and appears promising...... for energy harvesting. Using analytical, numerical, and experimental methods, the thesis focuses on superthreshold pumping (above the systems parametric instability threshold), nonlinear effects, frequency response backbones, and frequency detuning effects for parametric amplifiers. Part one of the thesis...... but parametrically excited frequency response backbone is proposed instead of the classic unforced and undamped backbone. With the modified and more general backbone, it is shown how the response of a superthreshold pumped amplifier is related to respectively the pure directly and pure parametrically excited...

  2. Superlinear Amplitude Amplification

    OpenAIRE

    Grover, Lov K.

    2008-01-01

    Quantum search/amplitude amplification algorithms are designed to be able to amplify the amplitude in the target state linearly with the number of operations. Since the probability is the square of the amplitude, this results in the success probability rising quadratically with the number of operations. This paper presents a new kind of quantum search algorithm in which the amplitude of the target state, itself increases quadratically with the number of operations. However, the domain of appl...

  3. Quantum Amplification by Superradiant Emission of Radiation

    Directory of Open Access Journals (Sweden)

    Anatoly A. Svidzinsky

    2013-10-01

    Full Text Available A laser generates light through stimulated emission of radiation and requires population inversion. Quantum interference can yield lasing without inversion. However, such phase-sensitive quantum amplification still requires some atomic population in the excited state. Here, we present a new kind of quantum amplifier based on collective superradiant emission which does not need any population in the excited state. We show that parametric resonance between the driving (e.g., infrared field and collective superradiant oscillations of the atomic polarization can yield light amplification at high (e.g., XUV frequencies. To achieve gain, one must suppress a time-dependent Stark shift caused by the driving field. The resulting superradiant amplifier is many orders of magnitude more efficient than the usual nonlinear multiphoton excitation and holds promise for a new kind of generator of high-frequency coherent radiation. In addition to a detailed analytical analysis, confirmed by numerical simulations, we provide a physically appealing explanation of the quantum amplification by superradiant emission of radiation (QASER operation in terms of coupled classical oscillators. We also present an experiment that demonstrates the QASER amplification mechanism in an electronic circuit, which, to the best of our knowledge, is the first experimental demonstration of the difference combination resonance.

  4. Quantitative reverse transcription strand displacement amplification: quantitation of nucleic acids using an isothermal amplification technique.

    Science.gov (United States)

    Nycz, C M; Dean, C H; Haaland, P D; Spargo, C A; Walker, G T

    1998-06-01

    Recent advances in nucleic acid amplification techniques have allowed for quantitation of viral nucleic acid levels in clinical specimens. The most prevalent testing is carried out for HIV viral load. Strand displacement amplification (SDA) is an isothermal DNA amplification system utilizing a restriction enzyme and a DNA polymerase with strand displacement properties. SDA was adapted for quantitative RNA amplification (QRT-SDA) of an HIV gag sequence by including AMV reverse transcriptase, a quantitative control sequence, and 32P-labeled detector oligonucleotides for the HIV and the control sequences. We have also improved the amplification efficiency by including the single-strand binding protein from gene 32 of T4 bacteriophage (T4gp32) to enhance strand displacement replication. In a preliminary analytical demonstration of the technique, RT-SDA was quantitative to within twofold over a range of 500-500,000 transcripts that were generated from a plasmid bearing an HIV gag sequence. QRT-SDA potentially represents a convenient alternative for viral load testing in a clinical setting. Copyright 1998 Academic Press.

  5. 152 W average power Tm-doped fiber CPA system.

    Science.gov (United States)

    Stutzki, Fabian; Gaida, Christian; Gebhardt, Martin; Jansen, Florian; Wienke, Andreas; Zeitner, Uwe; Fuchs, Frank; Jauregui, Cesar; Wandt, Dieter; Kracht, Dietmar; Limpert, Jens; Tünnermann, Andreas

    2014-08-15

    A high-power thulium (Tm)-doped fiber chirped-pulse amplification system emitting a record compressed average output power of 152 W and 4 MW peak power is demonstrated. This result is enabled by utilizing Tm-doped photonic crystal fibers with mode-field diameters of 35 μm, which mitigate detrimental nonlinearities, exhibit slope efficiencies of more than 50%, and allow for reaching a pump-power-limited average output power of 241 W. The high-compression efficiency has been achieved by using multilayer dielectric gratings with diffraction efficiencies higher than 98%.

  6. Frequency-domain nonlinear optics in two-dimensionally patterned quasi-phase-matching media.

    Science.gov (United States)

    Phillips, C R; Mayer, B W; Gallmann, L; Keller, U

    2016-07-11

    Advances in the amplification and manipulation of ultrashort laser pulses have led to revolutions in several areas. Examples include chirped pulse amplification for generating high peak-power lasers, power-scalable amplification techniques, pulse shaping via modulation of spatially-dispersed laser pulses, and efficient frequency-mixing in quasi-phase-matched nonlinear crystals to access new spectral regions. In this work, we introduce and demonstrate a new platform for nonlinear optics which has the potential to combine these separate functionalities (pulse amplification, frequency transfer, and pulse shaping) into a single monolithic device that is bandwidth- and power-scalable. The approach is based on two-dimensional (2D) patterning of quasi-phase-matching (QPM) gratings combined with optical parametric interactions involving spatially dispersed laser pulses. Our proof of principle experiment demonstrates this technique via mid-infrared optical parametric chirped pulse amplification of few-cycle pulses. Additionally, we present a detailed theoretical and numerical analysis of such 2D-QPM devices and how they can be designed.

  7. Optimizing direct amplification of forensic commercial kits for STR determination.

    Science.gov (United States)

    Caputo, M; Bobillo, M C; Sala, A; Corach, D

    2017-04-01

    Direct DNA amplification in forensic genotyping reduces analytical time when large sample sets are being analyzed. The amplification success depends mainly upon two factors: on one hand, the PCR chemistry and, on the other, the type of solid substrate where the samples are deposited. We developed a workflow strategy aiming to optimize times and cost when starting from blood samples spotted onto diverse absorbent substrates. A set of 770 blood samples spotted onto Blood cards, Whatman(®) 3 MM paper, FTA™ Classic cards, and Whatman(®) Grade 1 was analyzed by a unified working strategy including a low-cost pre-treatment, a PCR amplification volume scale-down, and the use of the 3500 Genetic Analyzer as the analytical platform. Samples were analyzed using three different commercial multiplex STR direct amplification kits. The efficiency of the strategy was evidenced by a higher percentage of high-quality profiles obtained (over 94%), a reduced number of re-injections (average 3.2%), and a reduced amplification failure rate (lower than 5%). Average peak height ratio among different commercial kits was 0.91, and the intra-locus balance showed values ranging from 0.92 to 0.94. A comparison with previously reported results was performed demonstrating the efficiency of the proposed modifications. The protocol described herein showed high performance, producing optimal quality profiles, and being both time and cost effective. Copyright © 2017 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  8. Superimposed chirped pulse parameter estimation based on the extended Kalman filter (EKF)

    CSIR Research Space (South Africa)

    Olivier, JC

    2009-05-01

    Full Text Available . Mean square error (MSE) performance is shown to compare well to the Cramer-Rao bounds even for difficult cases where the number of samples is close to the inverse of the difference in normalized frequencies....

  9. Genome position and gene amplification

    Czech Academy of Sciences Publication Activity Database

    Jirsová, Pavla; Snijders, A.M.; Kwek, S.; Roydasgupta, R.; Fridlyand, J.; Tokuyasu, T.; Pinkel, D.; Albertson, D. G.

    2007-01-01

    Roč. 8, č. 6 (2007), r120 ISSN 1474-760X Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : gene amplification * array comparative genomic hybridization * oncogene Subject RIV: BO - Biophysics Impact factor: 6.589, year: 2007

  10. Compression Amplification in Hearing Aids.

    Science.gov (United States)

    Hickson, L M

    1994-11-01

    In this tutorial, the characteristics of compression amplification in analog hearing aids and the experimental results obtained with single- and multichannel compression amplification systems are reviewed. Single-channel compression systems are classified into four broad groups on the basis of their static and dynamic characteristics: compression limiters, syllabic compressors, automatic volume control (AVC) systems, and "others," those with adaptive recovery time (aRT) and dual frontend automatic gain control (AGC) (Moore, 1990; Moore & Glasberg, 1988). Multichannel compression devices have, to date, used a variety of different types of compression, with syllabic compression in each frequency channel being the most popular. Experimental evidence suggests that compression limiting is generally superior to peak clipping as a means of controlling output, except for some individuals with severe to profound hearing loss. There is some evidence that syllabic compression and AVC systems enhance speech perception in quiet compared to conventional linear amplification; however, this improvement is not consistently maintained in the presence of background noise. The majority of recent research has focused on multichannel compression, and favorable results have been obtained with some systems. Research findings about the efficacy of using compression amplification for people with hearing loss have been extremely variable, and possible reasons for this are discussed.

  11. ExCyto PCR amplification.

    Directory of Open Access Journals (Sweden)

    Vinay Dhodda

    2010-09-01

    Full Text Available ExCyto PCR cells provide a novel and cost effective means to amplify DNA transformed into competent bacterial cells. ExCyto PCR uses host E. coli with a chromosomally integrated gene encoding a thermostable DNA polymerase to accomplish robust, hot-start PCR amplification of cloned sequences without addition of exogenous enzyme.Because the thermostable DNA polymerase is stably integrated into the bacterial chromosome, ExCyto cells can be transformed with a single plasmid or complex library, and then the expressed thermostable DNA polymerase can be used for PCR amplification. We demonstrate that ExCyto cells can be used to amplify DNA from different templates, plasmids with different copy numbers, and master mixes left on ice for up to two hours. Further, PCR amplification with ExCyto cells is comparable to amplification using commercial DNA polymerases. The ability to transform a bacterial strain and use the endogenously expressed protein for PCR has not previously been demonstrated.ExCyto PCR reduces pipetting and greatly increases throughput for screening EST, genomic, BAC, cDNA, or SNP libraries. This technique is also more economical than traditional PCR and thus broadly useful to scientists who utilize analysis of cloned DNAs in their research.

  12. An Intrinsically Digital Amplification Scheme for Hearing Aids

    Science.gov (United States)

    Blamey, Peter J.; Macfarlane, David S.; Steele, Brenton R.

    2005-12-01

    Results for linear and wide-dynamic range compression were compared with a new 64-channel digital amplification strategy in three separate studies. The new strategy addresses the requirements of the hearing aid user with efficient computations on an open-platform digital signal processor (DSP). The new amplification strategy is not modeled on prior analog strategies like compression and linear amplification, but uses statistical analysis of the signal to optimize the output dynamic range in each frequency band independently. Using the open-platform DSP processor also provided the opportunity for blind trial comparisons of the different processing schemes in BTE and ITE devices of a high commercial standard. The speech perception scores and questionnaire results show that it is possible to provide improved audibility for sound in many narrow frequency bands while simultaneously improving comfort, speech intelligibility in noise, and sound quality.

  13. Target amplification for broad spectrum microbial diagnostics and detection.

    Science.gov (United States)

    Leski, Tomasz A; Malanoski, Anthony P; Stenger, David A; Lin, Baochuan

    2010-02-01

    Microarrays are massively parallel detection platforms that were first used extensively for gene expression studies, but have also been successfully applied to microbial detection in a number of diverse fields requiring broad-range microbial identification. This technology has enabled researchers to gain an insight into the microbial diversity of environmental samples, facilitated discovery of a number of new pathogens and enabled studies of multipathogen infections. In contrast to gene expression studies, the concentrations of targets in analyzed samples for microbial detection are usually much lower, and require the use of nucleic acid amplification techniques. The rapid advancement of manufacturing technologies has increased the content of the microarrays; thus, the required amplification is a challenging problem. The constant parallel improvements in both microarray and sample amplification techniques in the near future may lead to a radical progression in medical diagnostics and systems for efficient detection of microorganisms in the environment.

  14. An Intrinsically Digital Amplification Scheme for Hearing Aids

    Directory of Open Access Journals (Sweden)

    Brenton R. Steele

    2005-11-01

    Full Text Available Results for linear and wide-dynamic range compression were compared with a new 64-channel digital amplification strategy in three separate studies. The new strategy addresses the requirements of the hearing aid user with efficient computations on an open-platform digital signal processor (DSP. The new amplification strategy is not modeled on prior analog strategies like compression and linear amplification, but uses statistical analysis of the signal to optimize the output dynamic range in each frequency band independently. Using the open-platform DSP processor also provided the opportunity for blind trial comparisons of the different processing schemes in BTE and ITE devices of a high commercial standard. The speech perception scores and questionnaire results show that it is possible to provide improved audibility for sound in many narrow frequency bands while simultaneously improving comfort, speech intelligibility in noise, and sound quality.

  15. Amplification of Information by Photons and the Quantum Chernoff Bound

    Science.gov (United States)

    Zwolak, Michael; Riedel, C. Jess; Zurek, Wojciech H.

    2014-03-01

    Amplification was regarded, since the early days of quantum theory, as a mysterious ingredient that endows quantum microstates with macroscopic consequences, key to the ``collapse of the wavepacket,'' and a way to avoid embarrassing problems exemplified by Schrödinger's cat. This bridge between the quantum microworld and the classical world of our experience was postulated ad hoc in the Copenhagen Interpretation. Quantum Darwinism views amplification as replication, in many copies, of information about quantum states. We show that such amplification is a natural consequence of a broad class of models of decoherence, including the photon environment we use to obtain most of our information. The resultant amplification is huge, proportional to # ξQCB . Here, #  is the environment size and ξQCB is the ``typical'' Quantum Chernoff Information, which quantifies the efficiency of the amplification. The information communicated though the environment is imprinted in the states of individual environment subsystems, e.g., in single photons, which document the transfer of information into the environment and result in the emergence of the classical world. See, http://mike.zwolak.org

  16. Quantum tomography enhanced through parametric amplification

    Science.gov (United States)

    Knyazev, E.; Spasibko, K. Yu; Chekhova, M. V.; Khalili, F. Ya

    2018-01-01

    Quantum tomography is the standard method of reconstructing the Wigner function of quantum states of light by means of balanced homodyne detection. The reconstruction quality strongly depends on the photodetectors quantum efficiency and other losses in the measurement setup. In this article we analyze in detail a protocol of enhanced quantum tomography, proposed by Leonhardt and Paul [1] which allows one to reduce the degrading effect of detection losses. It is based on phase-sensitive parametric amplification, with the phase of the amplified quadrature being scanned synchronously with the local oscillator phase. Although with sufficiently strong amplification the protocol enables overcoming any detection inefficiency, it was so far not implemented in the experiment, probably due to the losses in the amplifier. Here we discuss a possible proof-of-principle experiment with a traveling-wave parametric amplifier. We show that with the state-of-the-art optical elements, the protocol enables high fidelity tomographic reconstruction of bright non-classical states of light. We consider two examples: bright squeezed vacuum and squeezed single-photon state, with the latter being a non-Gaussian state and both strongly affected by the losses.

  17. 5  μm few-cycle pulses with multi-gigawatt peak power at a 1  kHz repetition rate.

    Science.gov (United States)

    von Grafenstein, Lorenz; Bock, Martin; Ueberschaer, Dennis; Zawilski, Kevin; Schunemann, Peter; Griebner, Uwe; Elsaesser, Thomas

    2017-10-01

    A mid-infrared (mid-IR) optical parametric chirped pulse amplification (OPCPA) system generating few-cycle pulses with multi-gigawatt peak power at a 1 kHz repetition rate is reported. The system is pumped by a highly stable 2 μm picosecond chirped pulse amplifier based on Ho:YLF gain media to exploit the high nonlinearity of ZnGeP2 (ZGP) crystals for parametric amplification. The ZGP optical parametric amplification (OPA) is characterized by a high conversion efficiency of >10 %, resulting in 1.3 mJ idler pulses at a center wavelength of 5.1 μm. Employing a dispersion management scheme based only on bulk materials, pulses as short as 160 fs are obtained. By adding a spatial light modulator in the OPCPA setup, the pulses are further recompressed to 75 fs duration which corresponds to less than five optical cycles. Taking into account the pulse energy of 0.65 mJ in this configuration, it translates into a peak power of 7.7 GW. The achieved pulse durations and peak powers, to the best of our knowledge, represent record values for high-energy mid-IR OPCPAs beyond 4 μm.

  18. An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community

    KAUST Repository

    Wang, Yong

    2016-02-23

    The low biomass in environmental samples is a major challenge for microbial metagenomic studies. The amplification of a genomic DNA was frequently applied to meeting the minimum requirement of the DNA for a high-throughput next-generation-sequencing technology. Using a synthetic bacterial community, the amplification efficiency of the Multiple Annealing and Looping Based Amplification Cycles (MALBAC) kit that is originally developed to amplify the single-cell genomic DNA of mammalian organisms is examined. The DNA template of 10 pg in each reaction of the MALBAC amplification may generate enough DNA for Illumina sequencing. Using 10 pg and 100 pg templates for each reaction set, the MALBAC kit shows a stable and homogeneous amplification as indicated by the highly consistent coverage of the reads from the two amplified samples on the contigs assembled by the original unamplified sample. Although GenomePlex whole genome amplification kit allows one to generate enough DNA using 100 pg of template in each reaction, the minority of the mixed bacterial species is not linearly amplified. For both of the kits, the GC-rich regions of the genomic DNA are not efficiently amplified as suggested by the low coverage of the contigs with the high GC content. The high efficiency of the MALBAC kit is supported for the amplification of environmental microbial DNA samples, and the concerns on its application are also raised to bacterial species with the high GC content.

  19. Centriole Amplification in Zebrafish Affects Proliferation and Survival but Not Differentiation of Neural Progenitor Cells

    Directory of Open Access Journals (Sweden)

    Edo Dzafic

    2015-10-01

    Full Text Available In animal cells, supernumerary centrosomes, resulting from centriole amplification, cause mitotic aberrations and have been associated with diseases, including microcephaly and cancer. To evaluate how centriole amplification impacts organismal development at the cellular and tissue levels, we used the in vivo imaging potential of the zebrafish. We demonstrate that centriole amplification can induce multipolar anaphase, resulting in binucleated cells. Such binucleation causes substantial apoptosis in the neuroepithelium. Interestingly, not all epithelia are similarly sensitive to binucleation, as skin cells tolerate it without entering apoptosis. In the neuroepithelium, however, binucleation leads to tissue degeneration and subsequent organismal death. Notably, this tissue degeneration can be efficiently counterbalanced by compensatory proliferation of wild-type cells. Because the risk for generating a binucleated daughter recurs at every cell division, centriole amplification in the neuroepithelium is especially deleterious during progenitor proliferation. Once cells reach the differentiation phase, however, centriole amplification does not impair neuronal differentiation.

  20. Resonant primordial gravitational waves amplification

    Directory of Open Access Journals (Sweden)

    Chunshan Lin

    2016-01-01

    Full Text Available We propose a mechanism to evade the Lyth bound in models of inflation. We minimally extend the conventional single-field inflation model in general relativity (GR to a theory with non-vanishing graviton mass in the very early universe. The modification primarily affects the tensor perturbation, while the scalar and vector perturbations are the same as the ones in GR with a single scalar field at least at the level of linear perturbation theory. During the reheating stage, the graviton mass oscillates coherently and leads to resonant amplification of the primordial tensor perturbation. After reheating the graviton mass vanishes and we recover GR.

  1. Dynamics and Control of DNA Sequence Amplification

    CERN Document Server

    Marimuthu, Karthikeyan

    2014-01-01

    DNA amplification is the process of replication of a specified DNA sequence \\emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction (PCR) as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reaction are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal tempe...

  2. Multiscale image contrast amplification (MUSICA)

    Science.gov (United States)

    Vuylsteke, Pieter; Schoeters, Emile P.

    1994-05-01

    This article presents a novel approach to the problem of detail contrast enhancement, based on multiresolution representation of the original image. The image is decomposed into a weighted sum of smooth, localized, 2D basis functions at multiple scales. Each transform coefficient represents the amount of local detail at some specific scale and at a specific position in the image. Detail contrast is enhanced by non-linear amplification of the transform coefficients. An inverse transform is then applied to the modified coefficients. This yields a uniformly contrast- enhanced image without artefacts. The MUSICA-algorithm is being applied routinely to computed radiography images of chest, skull, spine, shoulder, pelvis, extremities, and abdomen examinations, with excellent acceptance. It is useful for a wide range of applications in the medical, graphical, and industrial area.

  3. Risk Perception and Social Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Smith, R.E. [Environment Agency (United Kingdom)

    2001-07-01

    This paper seeks to consider social amplification as it applies to risk perception. Perceptions of the magnitude of a risk are conditioned by issues such as the degree of uncertainty in probability and consequences, the nature of the consequences and the relative weightings placed on probability and consequences. Risk perceptions are also influenced by factors such as confidence in the operator of an industrial process, trust in the regulator and the perceived fairness of regulatory decision-making. Different people may hold different views about these issues and there may also be difficulties in communication. The paper identifies and discusses self-reinforcing mechanisms, which will be labelled 'lock-in' here. They appear to apply in many situations where social amplification is observed. Historically, the term 'lock-in' has been applied mainly in the technological context but, in this paper, four types of lock-in are identified, namely scientific/technological, economic, social and institutional lock-in. One type of lock-in tends to lead to the next and all are buttressed by people's general acceptance of the familiar, fear of the unknown and resistance to change. The regulator seeks to make decisions which achieve the common good rather than supporting or perpetuating any set of vested interests. In this regard the locked-in positions of stakeholders, whether organisations, interest groups, or individual members of the public, are obstacles and challenges. Existing methods of consultation are unsatisfactory in terms of achieving a proper and productive level of dialogue with stakeholders.

  4. Rolling circle amplification of complete nematode mitochondrial genomes.

    Science.gov (United States)

    Tang, Sha; Hyman, Bradley C

    2005-06-01

    To enable investigation of nematode mitochondrial DNA evolution, methodology has been developed to amplify intact nematode mitochondrial genomes in preparative yields using a rolling circle replication strategy. Successful reactions were generated from whole cell template DNA prepared by alkaline lysis of the rhabditid nematode Caenorhabditis elegans and a mermithid nematode, Thaumamermis cosgrovei. These taxa, representing the two major nematode classes Chromodorea and Enoplea, maintain mitochondrial genomes of 13.8 kb and 20.0 kb, respectively. Efficient amplifications were conducted on template DNA isolated from individual or pooled nematodes that were alive or stored at -80 degrees C. Unexpectedly, these experiments revealed that multiple T. cosgrovei mitochondrial DNA haplotypes are maintained in our local population. Rolling circle amplification products can be used as templates for standard PCR reactions with specific primers that target mitochondrial genes or for direct DNA sequencing.

  5. High peak-power kilohertz laser system employing single-stage multi-pass amplification

    Science.gov (United States)

    Shan, Bing; Wang, Chun; Chang, Zenghu

    2006-05-23

    The present invention describes a technique for achieving high peak power output in a laser employing single-stage, multi-pass amplification. High gain is achieved by employing a very small "seed" beam diameter in gain medium, and maintaining the small beam diameter for multiple high-gain pre-amplification passes through a pumped gain medium, then leading the beam out of the amplifier cavity, changing the beam diameter and sending it back to the amplifier cavity for additional, high-power amplification passes through the gain medium. In these power amplification passes, the beam diameter in gain medium is increased and carefully matched to the pump laser's beam diameter for high efficiency extraction of energy from the pumped gain medium. A method of "grooming" the beam by means of a far-field spatial filter in the process of changing the beam size within the single-stage amplifier is also described.

  6. Increasingly branched rolling circle amplification for the cancer gene detection.

    Science.gov (United States)

    Li, Hongling; Xu, Jianguo; Wang, Zhenmeng; Wu, Zai-Sheng; Jia, Lee

    2016-12-15

    An increasingly branched rolling circle amplification (IB-RCA) which contains a padlock probe (PP) and a structurally tailored molecular beacon (MB) was innovatively developed for highly sensitive detection of cancer gene, Kras gene codon 12. In this system, the PP can be circularized after hybridization with the precisely-matched target DNA, while the stem of MB can be also opened by target DNA, resulting in hybridization with the circularized PP to generate a long tandem single-stranded DNA (ssDNA) product. Since the MB is also designed to hybridize with ssDNA product, the newly-opened MBs are able to trigger the next RCA reactions, therapy producing branched rolling circle amplification (RCA) products and in turn leading to the increasingly branched RCA (IB-RCA). This alternately and continuously operates hybridization-based MB opening and opened MBs-triggered RCA. As a result, a great number of MBs are opened that is associated with a dramatically amplified fluorescent signal, enabling to quantify target DNA down to 100 fM. This sensing method demonstrates a new concept of IB-RCA amplification even in a simple way to efficiently transduce the fluorescence signal, accomplishing the highly sensitive and selective detection of cancer gene. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Utility of amplification enhancers in low copy number DNA analysis.

    Science.gov (United States)

    Marshall, Pamela L; King, Jonathan L; Budowle, Bruce

    2015-01-01

    One parameter that impacts the robustness and reliability of forensic DNA analyses is the amount of template DNA used in the polymerase chain reaction (PCR). With short tandem repeat (STR) typing, low copy number (LCN) DNA samples can present exaggerated stochastic effects during the PCR that result in heterozygote peak height imbalance, allele drop out, and increased stutter. Despite these effects, there has been little progress toward decreasing the formation of stutter products and heterozygote peak imbalance effects during PCR. In an attempt to develop a more robust system that is less refractory to stochastic effects, the PCR additives, betaine, DMSO, PEG, and PCRboost®, were investigated on low-quantity DNA samples. The effects of the additives were assessed by evaluating STR typing results. Of the four additives, the only positive effects were observed with betaine treatment. Betaine, at a final concentration of 1.25 mol/L, was found to improve the robustness of the amplification, specifically by decreasing stutter in a dual locus system. In contrast, the addition of 1.25 mol/L betaine to commercial STR amplification kits did not affect stutter ratios. However, the addition of betaine did lead to increased yield of PCR products in all commercial kits tested. The results support that betaine can improve amplification efficiency of LCN DNA samples.

  8. Random amplification of genomic ends (RAGE) as an efficient ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-05

    Oct 5, 2009 ... 5Department of Biotechnology, Sri Ramachandra University, No.1, Ramachandra Nagar, Porur, Chennai - 600 116,. India. Accepted 23 ... technique can be used for cloning of full length gene and promoters in organisms where whole genome .... ting restriction enzymes Dra I, EcoR V, SnaB I, and Ssp I (all.

  9. Random amplification of genomic ends (RAGE) as an efficient ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-05

    Oct 5, 2009 ... The eukaryotic genes contain un- translated (UTR) regions at both the 5' and 3' region ... Even in prokaryotes with relatively simple genomes and gene sequences, the isolation of genes could be ... prokaryotic system for cloning the full length HetR gene from a partial genomic clone of a Cylindrospermum.

  10. Amplification of chirality in liquid crystals

    NARCIS (Netherlands)

    Eelkema, Rienk; Feringa, Ben L.

    2006-01-01

    The amplification of molecular chirality by liquid crystalline systems is widely applied in investigations towards enantioselective solvent - solute interactions, chiral supramolecular assemblies, smart materials, and the development of liquid crystal displays. Here we present an overview of recent

  11. Instrument for Real-Time Digital Nucleic Acid Amplification on Custom Microfluidic Devices.

    Directory of Open Access Journals (Sweden)

    David A Selck

    Full Text Available Nucleic acid amplification tests that are coupled with a digital readout enable the absolute quantification of single molecules, even at ultralow concentrations. Digital methods are robust, versatile and compatible with many amplification chemistries including isothermal amplification, making them particularly invaluable to assays that require sensitive detection, such as the quantification of viral load in occult infections or detection of sparse amounts of DNA from forensic samples. A number of microfluidic platforms are being developed for carrying out digital amplification. However, the mechanistic investigation and optimization of digital assays has been limited by the lack of real-time kinetic information about which factors affect the digital efficiency and analytical sensitivity of a reaction. Commercially available instruments that are capable of tracking digital reactions in real-time are restricted to only a small number of device types and sample-preparation strategies. Thus, most researchers who wish to develop, study, or optimize digital assays rely on the rate of the amplification reaction when performed in a bulk experiment, which is now recognized as an unreliable predictor of digital efficiency. To expand our ability to study how digital reactions proceed in real-time and enable us to optimize both the digital efficiency and analytical sensitivity of digital assays, we built a custom large-format digital real-time amplification instrument that can accommodate a wide variety of devices, amplification chemistries and sample-handling conditions. Herein, we validate this instrument, we provide detailed schematics that will enable others to build their own custom instruments, and we include a complete custom software suite to collect and analyze the data retrieved from the instrument. We believe assay optimizations enabled by this instrument will improve the current limits of nucleic acid detection and quantification, improving our

  12. Instrument for Real-Time Digital Nucleic Acid Amplification on Custom Microfluidic Devices.

    Science.gov (United States)

    Selck, David A; Ismagilov, Rustem F

    2016-01-01

    Nucleic acid amplification tests that are coupled with a digital readout enable the absolute quantification of single molecules, even at ultralow concentrations. Digital methods are robust, versatile and compatible with many amplification chemistries including isothermal amplification, making them particularly invaluable to assays that require sensitive detection, such as the quantification of viral load in occult infections or detection of sparse amounts of DNA from forensic samples. A number of microfluidic platforms are being developed for carrying out digital amplification. However, the mechanistic investigation and optimization of digital assays has been limited by the lack of real-time kinetic information about which factors affect the digital efficiency and analytical sensitivity of a reaction. Commercially available instruments that are capable of tracking digital reactions in real-time are restricted to only a small number of device types and sample-preparation strategies. Thus, most researchers who wish to develop, study, or optimize digital assays rely on the rate of the amplification reaction when performed in a bulk experiment, which is now recognized as an unreliable predictor of digital efficiency. To expand our ability to study how digital reactions proceed in real-time and enable us to optimize both the digital efficiency and analytical sensitivity of digital assays, we built a custom large-format digital real-time amplification instrument that can accommodate a wide variety of devices, amplification chemistries and sample-handling conditions. Herein, we validate this instrument, we provide detailed schematics that will enable others to build their own custom instruments, and we include a complete custom software suite to collect and analyze the data retrieved from the instrument. We believe assay optimizations enabled by this instrument will improve the current limits of nucleic acid detection and quantification, improving our fundamental

  13. Rolling circle amplification of metazoan mitochondrialgenomes

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Lindberg, D.R.; Boore, J.L.

    2005-07-31

    Here we report the successful use of rolling circle amplification (RCA) for the amplification of complete metazoan mt genomes to make a product that is amenable to high-throughput genome sequencing techniques. The benefits of RCA over PCR are many and with further development and refinement of RCA, the sequencing of organellar genomics will require far less time and effort than current long PCR approaches.

  14. Ultrafast, laser-based, x-ray science: the dawn of atomic-scale cinematography

    Energy Technology Data Exchange (ETDEWEB)

    Barty, C.P.J. [University of California, Department of Applied Mechanics and Engineering Science, Urey Hall, Mali Code 0339, San Diego, La Jolla, CA (United States)

    2000-03-01

    The characteristics of ultrafast chirped pulse amplification systems are reviewed. Application of ultrafast chirped pulse amplification to the generation of femtosecond, incoherent, 8-keV line radiation is outlined and the use of femtosecond laser-based, x-rays for novel time-resolved diffraction studies of crystalline dynamics with sub-picosecond temporal resolution and sub-picometer spatial resolution is reviewed in detail. Possible extensions of laser-based, x-ray technology and evaluation of alternative x-ray approaches for time-resolved studies of the atomic scale dynamics are given. (author)

  15. Onshore seismic amplifications due to bathymetric features

    Science.gov (United States)

    Rodríguez-Castellanos, A.; Carbajal-Romero, M.; Flores-Guzmán, N.; Olivera-Villaseñor, E.; Kryvko, A.

    2016-08-01

    We perform numerical calculations for onshore seismic amplifications, taking into consideration the effect of bathymetric features on the propagation of seismic movements. To this end, the boundary element method is applied. Boundary elements are employed to irradiate waves and, consequently, force densities can be obtained for each boundary element. From this assumption, Huygens’ principle is applied, and since the diffracted waves are built at the boundary from which they are radiated, this idea is equivalent to Somigliana’s representation theorem. The application of boundary conditions leads to a linear system being obtained (Fredholm integral equations). Several numerical models are analyzed, with the first one being used to verify the proposed formulation, and the others being used to estimate onshore seismic amplifications due to the presence of bathymetric features. The results obtained show that compressional waves (P-waves) generate onshore seismic amplifications that can vary from 1.2 to 5.2 times the amplitude of the incident wave. On the other hand, the shear waves (S-waves) can cause seismic amplifications of up to 4.0 times the incident wave. Furthermore, an important result is that in most cases the highest seismic amplifications from an offshore earthquake are located on the shoreline and not offshore, despite the seafloor configuration. Moreover, the influence of the incident angle of seismic waves on the seismic amplifications is highlighted.

  16. Signal amplification strategies for DNA and protein detection based on polymeric nanocomposites and polymerization: A review

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Shaohong; Yuan, Liang; Hua, Xin; Xu, Lingling; Liu, Songqin, E-mail: liusq@seu.edu.cn

    2015-06-02

    Highlights: • We review the innovative advances in polymer-based signal amplification. • Conceptual connectivity between different amplified methodologies is illustrated. • Examples explain the mechanisms of polymers/polymerizations-based amplification. • Several elegant applications are summarized that illustrate underlying concept. - Abstract: Demand is increasing for ultrasensitive bioassays for disease diagnosis, environmental monitoring and other research areas. This requires novel signal amplification strategies to maximize the signal output. In this review, we focus on a series of significant signal amplification strategies based on polymeric nanocomposites and polymerization. Some common polymers are used as carriers to increase the local concentration of signal probes and/or biomolecules on their surfaces or in their interiors. Some polymers with special fluorescence and optical properties can efficiently transfer the excitation energy from a single site to the whole polymer backbone. This results in superior fluorescence signal amplification due to the resulting collective effort (integration of signal). Recent polymerization-based signal amplification strategies that employ atom transfer radical polymerization (ATRP) and photo-initiated polymerization are also summarized. Several distinctive applications of polymers in ultrasensitive bioanalysis are highlighted.

  17. Simple System for Isothermal DNA Amplification Coupled to Lateral Flow Detection

    Science.gov (United States)

    Roskos, Kristina; Hickerson, Anna I.; Lu, Hsiang-Wei; Ferguson, Tanya M.; Shinde, Deepali N.; Klaue, Yvonne; Niemz, Angelika

    2013-01-01

    Infectious disease diagnosis in point-of-care settings can be greatly improved through integrated, automated nucleic acid testing devices. We have developed an early prototype for a low-cost system which executes isothermal DNA amplification coupled to nucleic acid lateral flow (NALF) detection in a mesofluidic cartridge attached to a portable instrument. Fluid handling inside the cartridge is facilitated through one-way passive valves, flexible pouches, and electrolysis-driven pumps, which promotes a compact and inexpensive instrument design. The closed-system disposable prevents workspace amplicon contamination. The cartridge design is based on standard scalable manufacturing techniques such as injection molding. Nucleic acid amplification occurs in a two-layer pouch that enables efficient heat transfer. We have demonstrated as proof of principle the amplification and detection of Mycobacterium tuberculosis (M.tb) genomic DNA in the cartridge, using either Loop Mediated Amplification (LAMP) or the Exponential Amplification Reaction (EXPAR), both coupled to NALF detection. We envision that a refined version of this cartridge, including upstream sample preparation coupled to amplification and detection, will enable fully-automated sample-in to answer-out infectious disease diagnosis in primary care settings of low-resource countries with high disease burden. PMID:23922706

  18. Simple system for isothermal DNA amplification coupled to lateral flow detection.

    Directory of Open Access Journals (Sweden)

    Kristina Roskos

    Full Text Available Infectious disease diagnosis in point-of-care settings can be greatly improved through integrated, automated nucleic acid testing devices. We have developed an early prototype for a low-cost system which executes isothermal DNA amplification coupled to nucleic acid lateral flow (NALF detection in a mesofluidic cartridge attached to a portable instrument. Fluid handling inside the cartridge is facilitated through one-way passive valves, flexible pouches, and electrolysis-driven pumps, which promotes a compact and inexpensive instrument design. The closed-system disposable prevents workspace amplicon contamination. The cartridge design is based on standard scalable manufacturing techniques such as injection molding. Nucleic acid amplification occurs in a two-layer pouch that enables efficient heat transfer. We have demonstrated as proof of principle the amplification and detection of Mycobacterium tuberculosis (M.tb genomic DNA in the cartridge, using either Loop Mediated Amplification (LAMP or the Exponential Amplification Reaction (EXPAR, both coupled to NALF detection. We envision that a refined version of this cartridge, including upstream sample preparation coupled to amplification and detection, will enable fully-automated sample-in to answer-out infectious disease diagnosis in primary care settings of low-resource countries with high disease burden.

  19. Carboxylesterase gene amplifications associated with insecticide resistance in Aedes albopictus: Geographical distribution and evolutionary origin.

    Directory of Open Access Journals (Sweden)

    Linda Grigoraki

    2017-04-01

    Full Text Available Aedes albopictus is one of the most invasive human disease vectors. Its control has been largely based on insecticides, such as the larvicide temephos. Temephos resistance has been associated with the up-regulation, through gene amplification, of two carboxylesterase (CCE genes closely linked on the genome, capable of sequestering and metabolizing temephos oxon, the activated form of temephos.Here, we investigated the occurrence, geographical distribution and origin of the CCE amplicon in Ae. albopictus populations from several geographical regions worldwide. The haplotypic diversity at the CCEae3a locus revealed high polymorphism, while phylogenetic analysis showed an absence of correlation between haplotype similarity and geographic origin. Two types of esterase amplifications were found, in two locations only (Athens and Florida: one, previously described, results in the amplification of both CCEae3a and CCEae6a; the second is being described for the first time and results in the amplification of CCEae3a only. The two amplification events are independent, as confirmed by sequence analysis. All individuals from Athens and Florida carrying the CCEae3a-CCEae6a co-amplicon share a common haplotype, indicating a single amplification event, which spread between the two countries.The importance of passive transportation of disease vectors, including individuals carrying resistance mechanisms, is discussed in the light of efficient and sustainable vector control strategies.

  20. Magnetic Field Amplification and Blazar Flares

    Directory of Open Access Journals (Sweden)

    Chen Xuhui

    2013-12-01

    Full Text Available Recent multiwavelength observations of PKS 0208-512 by SMARTS, Fermi, and Swift revealed that γ-ray and optical light curves of this flat spectrum radio quasars are highly correlated, but with an exception of one large optical flare having no corresponding gamma-ray activity or even detection. On the other hand, recent advances in SNRs observations and plasma simulations both reveal that magnetic field downstream of astrophysical shocks can be largely amplified beyond simple shock compression. These amplifications, along with their associated particle acceleration, might contribute to blazar flares, including the peculiar flare of PKS 0208-512. Using our time dependent multizone blazar emission code, we evaluate several scenarios that may represent such phenomena. This code combines Monte Carlo method that tracks the radiative processes including inverse Compton scattering, and Fokker-Planck equation that follows the cooling and acceleration of particles. It is a comprehensive time dependent code that fully takes into account the light travel time effects. In this study, both the changes of the magnetic field and acceleration efficiency are explored as the cause of blazar flares. Under these assumption, synchrotron self-Compton and external Compton scenarios produce distinct features that favor the external Compton scenario. The optical flares with/without gamma-ray counterparts can be explained by different allocations of energy between the magnetization and particle acceleration, which in turn can be affected by the relative orientation between the magnetic field and the shock flow. We compare the details of the observations and simulation, and highlight what implications this study has on our understanding of relativistic jets.

  1. Heat induces gene amplification in cancer cells

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Bin, E-mail: yanbin@mercyhealth.com [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS 39213 (United States); Mercy Cancer Center, Mercy Medical Center-North Iowa, Mason City, IA 50401 (United States); Ouyang, Ruoyun [Department of Respiratory Medicine, The Second Xiangya Hospital, Xinagya School of Medicine, Central South University, Changsha 410011 (China); Huang, Chenghui [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS 39213 (United States); Department of Oncology, The Third Xiangya Hospital, Xinagya School of Medicine, Central South University, Changsha 410013 (China); Liu, Franklin [Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710 (United States); Neill, Daniel [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS 39213 (United States); Li, Chuanyuan [Dermatology, Duke University Medical Center, Durham, NC 27710 (United States); Dewhirst, Mark [Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710 (United States)

    2012-10-26

    Highlights: Black-Right-Pointing-Pointer This study discovered that heat exposure (hyperthermia) results in gene amplification in cancer cells. Black-Right-Pointing-Pointer Hyperthermia induces DNA double strand breaks. Black-Right-Pointing-Pointer DNA double strand breaks are considered to be required for the initiation of gene amplification. Black-Right-Pointing-Pointer The underlying mechanism of heat-induced gene amplification is generation of DNA double strand breaks. -- Abstract: Background: Hyperthermia plays an important role in cancer therapy. However, as with radiation, it can cause DNA damage and therefore genetic instability. We studied whether hyperthermia can induce gene amplification in cancer cells and explored potential underlying molecular mechanisms. Materials and methods: (1) Hyperthermia: HCT116 colon cancer cells received water-submerged heating treatment at 42 or 44 Degree-Sign C for 30 min; (2) gene amplification assay using N-(phosphoacetyl)-L-aspartate (PALA) selection of cabamyl-P-synthetase, aspartate transcarbarmylase, dihydro-orotase (cad) gene amplified cells; (3) southern blotting for confirmation of increased cad gene copies in PALA-resistant cells; (4) {gamma}H2AX immunostaining to detect {gamma}H2AX foci as an indication for DNA double strand breaks. Results: (1) Heat exposure at 42 or 44 Degree-Sign C for 30 min induces gene amplification. The frequency of cad gene amplification increased by 2.8 and 6.5 folds respectively; (2) heat exposure at both 42 and 44 Degree-Sign C for 30 min induces DNA double strand breaks in HCT116 cells as shown by {gamma}H2AX immunostaining. Conclusion: This study shows that heat exposure can induce gene amplification in cancer cells, likely through the generation of DNA double strand breaks, which are believed to be required for the initiation of gene amplification. This process may be promoted by heat when cellular proteins that are responsible for checkpoints, DNA replication, DNA repair and

  2. Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Triggered Isothermal Amplification for Site-Specific Nucleic Acid Detection.

    Science.gov (United States)

    Huang, Mengqi; Zhou, Xiaoming; Wang, Huiying; Xing, Da

    2018-02-06

    A novel CRISPR/Cas9 triggered isothermal exponential amplification reaction (CAS-EXPAR) strategy based on CRISPR/Cas9 cleavage and nicking endonuclease (NEase) mediated nucleic acids amplification was developed for rapid and site-specific nucleic acid detection. CAS-EXPAR was primed by the target DNA fragment produced by cleavage of CRISPR/Cas9, and the amplification reaction performed cyclically to generate a large number of DNA replicates which were detected using a real-time fluorescence monitoring method. This strategy that combines the advantages of CRISPR/Cas9 and exponential amplification showed high specificity as well as rapid amplification kinetics. Unlike conventional nucleic acids amplification reactions, CAS-EXPAR does not require exogenous primers, which often cause target-independent amplification. Instead, primers are first generated by Cas9/sgRNA directed site-specific cleavage of target and accumulated during the reaction. It was demonstrated this strategy gave a detection limit of 0.82 amol and showed excellent specificity in discriminating single-base mismatch. Moreover, the applicability of this method to detect DNA methylation and L. monocytogenes total RNA was also verified. Therefore, CAS-EXPAR may provide a new paradigm for efficient nucleic acid amplification and hold the potential for molecular diagnostic applications.

  3. Monodisperse Picoliter Droplets for Low-Bias and Contamination-Free Reactions in Single-Cell Whole Genome Amplification.

    Directory of Open Access Journals (Sweden)

    Yohei Nishikawa

    Full Text Available Whole genome amplification (WGA is essential for obtaining genome sequences from single bacterial cells because the quantity of template DNA contained in a single cell is very low. Multiple displacement amplification (MDA, using Phi29 DNA polymerase and random primers, is the most widely used method for single-cell WGA. However, single-cell MDA usually results in uneven genome coverage because of amplification bias, background amplification of contaminating DNA, and formation of chimeras by linking of non-contiguous chromosomal regions. Here, we present a novel MDA method, termed droplet MDA, that minimizes amplification bias and amplification of contaminants by using picoliter-sized droplets for compartmentalized WGA reactions. Extracted DNA fragments from a lysed cell in MDA mixture are divided into 105 droplets (67 pL within minutes via flow through simple microfluidic channels. Compartmentalized genome fragments can be individually amplified in these droplets without the risk of encounter with reagent-borne or environmental contaminants. Following quality assessment of WGA products from single Escherichia coli cells, we showed that droplet MDA minimized unexpected amplification and improved the percentage of genome recovery from 59% to 89%. Our results demonstrate that microfluidic-generated droplets show potential as an efficient tool for effective amplification of low-input DNA for single-cell genomics and greatly reduce the cost and labor investment required for determination of nearly complete genome sequences of uncultured bacteria from environmental samples.

  4. The Discovery of Rolling Circle Amplification and Rolling Circle Transcription.

    Science.gov (United States)

    Mohsen, Michael G; Kool, Eric T

    2016-11-15

    Nucleic acid amplification is a hugely important technology for biology and medicine. While the polymerase chain reaction (PCR) has been highly useful and effective, its reliance on heating and cooling cycles places some constraints on its utility. For example, the heating step of PCR can destroy biological molecules under investigation and heat/cool cycles are not applicable in living systems. Thus, isothermal approaches to DNA and RNA amplification are under widespread study. Perhaps the simplest of these are the rolling circle approaches, including rolling circle amplification (RCA) and rolling circle transcription (RCT). In this strategy, a very small circular oligonucleotide (e.g., 25-100 nucleotides in length) acts as a template for a DNA or an RNA polymerase, producing long repeating product strands that serve as amplified copies of the circle sequence. Here we describe the early developments and studies involving circular oligonucleotides that ultimately led to the burgeoning rolling circle technologies currently under development. This Account starts with our studies on the design of circular oligonucleotides as novel DNA- and RNA-binding motifs. We describe how we developed chemical and biochemical strategies for synthesis of well-defined circular oligonucleotides having defined sequence and open (unpaired) structure, and we outline the unusual ways in which circular DNAs can interact with other nucleic acids. We proceed next to the discovery of DNA and RNA polymerase activity on these very small cyclic DNAs. DNA polymerase "rolling circle" activities were discovered concurrently in our laboratory and that of Andrew Fire. We describe the surprising efficiency of this process even on shockingly small circular DNAs, producing repeating DNAs thousands of nucleotides in length. RNA polymerase activity on circular oligonucleotides was first documented in our group in 1995; especially surprising in this case was the finding that the process occurs efficiently

  5. Visual Detection of Potato leafroll virus by One-step Reverse Transcription Loop-Mediated Isothermal Amplification of DNA with Hydroxynaphthol Blue Dye

    NARCIS (Netherlands)

    Ahmadi, S.; Almasi, A.M.; Fatehi, F.; Struik, P.C.; Moradi, A.

    2013-01-01

    Loop-mediated isothermal amplification (LAMP) assay is a novel technique for amplifying DNA under constant temperature, with high specificity, sensitivity, rapidity and efficiency. We applied reverse transcription loop-mediated isothermal amplification (RT-LAMP) to visually detect Potato leafroll

  6. Rapid Newcastle Disease Virus Detection Based on Loop-Mediated Isothermal Amplification and Optomagnetic Readout

    DEFF Research Database (Denmark)

    Tian, Bo; Ma, Jing; Zardán Gómez de la Torre, Teresa

    2016-01-01

    efficiency of loop-mediated isothermal amplification (LAMP) with an optomagnetic nanoparticle-based readout system, we demonstrate ultrasensitive and rapid detection of Newcastle disease virus RNA. Biotinylated amplicons of LAMP and reverse transcription LAMP (RT-LAMP) bind to streptavidin-coated magnetic...

  7. ESTIMATION OF AMPLIFICATION FACTOR IN EARTHQUAKE ENGINEERING

    Directory of Open Access Journals (Sweden)

    Nazarov Yuriy Pavlovich

    2015-03-01

    Full Text Available The authors are the developers of Odyssey Software (Eurosoft Co. for the analysis of seismological data and computing of seismic loads and their parameters. While communicating with the users of the software, the authors have revealed some uncertainty about both understanding of the term "amplification factor (AF" and calculation of the amplification factor using various methods. In this article, a simple example shows that the determination of the amplification factor as the ratio of the acceleration’s spectrum to the maximal acceleration is derived from the classical definition of AF in the form of the ratio of maximal dynamic displacement to the displacement by the action of static load. Deterministic and probabilistic ap-proaches for the calculating of the AF were discussed. There was an example of AFs calculation and their envelopes for translational and rotational components of seismic impact by using Odyssey Software.

  8. Time varying arctic climate change amplification

    Energy Technology Data Exchange (ETDEWEB)

    Chylek, Petr [Los Alamos National Laboratory; Dubey, Manvendra K [Los Alamos National Laboratory; Lesins, Glen [DALLHOUSIE U; Wang, Muyin [NOAA/JISAO

    2009-01-01

    During the past 130 years the global mean surface air temperature has risen by about 0.75 K. Due to feedbacks -- including the snow/ice albedo feedback -- the warming in the Arctic is expected to proceed at a faster rate than the global average. Climate model simulations suggest that this Arctic amplification produces warming that is two to three times larger than the global mean. Understanding the Arctic amplification is essential for projections of future Arctic climate including sea ice extent and melting of the Greenland ice sheet. We use the temperature records from the Arctic stations to show that (a) the Arctic amplification is larger at latitudes above 700 N compared to those within 64-70oN belt, and that, surprisingly; (b) the ratio of the Arctic to global rate of temperature change is not constant but varies on the decadal timescale. This time dependence will affect future projections of climate changes in the Arctic.

  9. Amplification, Redundancy, and Quantum Chernoff Information

    Science.gov (United States)

    Zwolak, Michael; Riedel, C. Jess; Zurek, Wojciech H.

    2014-04-01

    Amplification was regarded, since the early days of quantum theory, as a mysterious ingredient that endows quantum microstates with macroscopic consequences, key to the "collapse of the wave packet," and a way to avoid embarrassing problems exemplified by Schrödinger's cat. Such a bridge between the quantum microworld and the classical world of our experience was postulated ad hoc in the Copenhagen interpretation. Quantum Darwinism views amplification as replication, in many copies, of the information about quantum states. We show that such amplification is a natural consequence of a broad class of models of decoherence, including the photon environment we use to obtain most of our information. This leads to objective reality via the presence of robust and widely accessible records of selected quantum states. The resulting redundancy (the number of copies deposited in the environment) follows from the quantum Chernoff information that quantifies the information transmitted by a typical elementary subsystem of the environment.

  10. Amplification, redundancy, and quantum Chernoff information.

    Science.gov (United States)

    Zwolak, Michael; Riedel, C Jess; Zurek, Wojciech H

    2014-04-11

    Amplification was regarded, since the early days of quantum theory, as a mysterious ingredient that endows quantum microstates with macroscopic consequences, key to the "collapse of the wave packet," and a way to avoid embarrassing problems exemplified by Schrödinger's cat. Such a bridge between the quantum microworld and the classical world of our experience was postulated ad hoc in the Copenhagen interpretation. Quantum Darwinism views amplification as replication, in many copies, of the information about quantum states. We show that such amplification is a natural consequence of a broad class of models of decoherence, including the photon environment we use to obtain most of our information. This leads to objective reality via the presence of robust and widely accessible records of selected quantum states. The resulting redundancy (the number of copies deposited in the environment) follows from the quantum Chernoff information that quantifies the information transmitted by a typical elementary subsystem of the environment.

  11. Amplification of hofmeister effect by alcohols.

    Science.gov (United States)

    Xu, Yun; Liu, Guangming

    2014-07-03

    We have demonstrated that Hofmeister effect can be amplified by adding alcohols to aqueous solutions. The lower critical solution temperature behavior of poly(N-isopropylacrylamide) has been employed as the model system to study the amplification of Hofmeister effect. The alcohols can more effectively amplify the Hofmeister effect following the series methanol alcohols and following the series d-sorbitol ≈ xylitol ≈ meso-erythritol alcohols. Our study reveals that the relative extent of amplification of Hofmeister effect is determined by the stability of the water/alcohol complex, which is strongly dependent on the chemical structure of alcohols. The more stable solvent complex formed via stronger hydrogen bonds can more effectively differentiate the anions through the anion-solvent complex interactions, resulting in a stronger amplification of Hofmeister effect. This study provides an alternative method to tune the relative strength of Hofmeister effect besides salt concentration.

  12. Phase sensitive degenerate parametric amplification using directly-bonded PPLN ridge waveguides.

    Science.gov (United States)

    Umeki, Takeshi; Tadanaga, Osamu; Takada, Atsushi; Asobe, Masaki

    2011-03-28

    We constructed the first CW pumped degenerate parametric amplifier based on periodically poled and ZnO-doped LiNbO3 ridge waveguides. An in-phase gain of + 11 dB was achieved owing to the high conversion efficiency and high damage resistance of the waveguide obtained by employing direct bonding and dry etching techniques. Nearly identical amplification and deamplification were obtained owing to a sufficient spatial and temporal overlap between the pump and signal beams. No secondary wavelength conversion process was observed, and a maximum output of 22 dBm was obtained. We also successfully demonstrated the phase sensitive amplification of a modulated signal light.

  13. An Exact Formula to Describe the Amplification Process in a Photomultiplier Tube

    CERN Document Server

    Rademacker, J

    2002-01-01

    An analytical function is derived that exactly describes the amplification process due to a series of discrete, Poisson-like amplifications like those in a photo multiplier tube (PMT). A numerical recipe is provided that implements this function as a computer program. It is shown how the program can be used as the core-element of a faster, simplified routine to fit PMT spectra with high efficiency. The functionality of the method is demonstrated by fitting both, Monte Carlo generated and measured PMT spectra.

  14. Influence of interfacial Dzyaloshinskii-Moriya interaction on the parametric amplification of spin waves

    Energy Technology Data Exchange (ETDEWEB)

    Verba, Roman, E-mail: verrv@ukr.net [Institute of Magnetism, National Academy of Sciences of Ukraine, Kyiv 03142 (Ukraine); Tiberkevich, Vasil; Slavin, Andrei [Department of Physics, Oakland University, Rochester, Michigan 48309 (United States)

    2015-09-14

    The influence of the interfacial Dzyaloshinskii-Moriya interaction (IDMI) on the parametric amplification of spin waves propagating in ultrathin ferromagnetic film is considered theoretically. It is shown that the IDMI changes the relation between the group velocities of the signal and idler spin waves in a parametric amplifier, which may result in the complete vanishing of the reversed idler wave. In the optimized case, the idler spin wave does not propagate from the pumping region at all, which increases the efficiency of the amplification of the signal wave and suppresses the spurious impact of the idler waves on neighboring spin-wave processing devices.

  15. The polar amplification asymmetry: role of Antarctic surface height

    Science.gov (United States)

    Salzmann, Marc

    2017-05-01

    Previous studies have attributed an overall weaker (or slower) polar amplification in Antarctica compared to the Arctic to a weaker Antarctic surface albedo feedback and also to more efficient ocean heat uptake in the Southern Ocean in combination with Antarctic ozone depletion. Here, the role of the Antarctic surface height for meridional heat transport and local radiative feedbacks, including the surface albedo feedback, was investigated based on CO2-doubling experiments in a low-resolution coupled climate model. When Antarctica was assumed to be flat, the north-south asymmetry of the zonal mean top of the atmosphere radiation budget was notably reduced. Doubling CO2 in a flat Antarctica (flat AA) model setup led to a stronger increase in southern hemispheric poleward atmospheric and oceanic heat transport compared to the base model setup. Based on partial radiative perturbation (PRP) computations, it was shown that local radiative feedbacks and an increase in the CO2 forcing in the deeper atmospheric column also contributed to stronger Antarctic warming in the flat AA model setup, and the roles of the individual radiative feedbacks are discussed in some detail. A considerable fraction (between 24 and 80 % for three consecutive 25-year time slices starting in year 51 and ending in year 126 after CO2 doubling) of the polar amplification asymmetry was explained by the difference in surface height, but the fraction was subject to transient changes and might to some extent also depend on model uncertainties. In order to arrive at a more reliable estimate of the role of land height for the observed polar amplification asymmetry, additional studies based on ensemble runs from higher-resolution models and an improved model setup with a more realistic gradual increase in the CO2 concentration are required.

  16. a New 2.0-6.0 GHz Chirped Pulse Fourier Transform Microwave Spectrometer: Instrumental Analysis and Initial Molecular Results

    Science.gov (United States)

    Seifert, Nathan A.; Thomas, Javix; Jäger, Wolfgang; Xu, Yunjie

    2017-06-01

    Low frequency microwave spectroscopy (lactate as a benchmark. Finally, initial results for several novel molecular systems studied using this new spectrometer, including the tetramer of 2-fluoroethanol, will be presented. C. Perez, S. Lobsiger, N. A. Seifert, D. P. Zaleski, B. Temelso, G. C. Shields, Z. Kisiel, B. H. Pate, Chem. Phys. Lett., 2013, 571, 1-15.

  17. Multi-channel, fiber-based seed pulse distribution system for femtosecond-level synchronized chirped pulse amplifiers.

    Science.gov (United States)

    Horáček, Martin; Indra, Lukáš; Green, Jonathan T; Naylon, Jack A; Tykalewicz, Boguslaw; Novák, Jakub; Batysta, František; Mazanec, Tomáš; Horáček, Jakub; Antipenkov, Roman; Hubka, Zbyněk; Boge, Robert; Bakule, Pavel; Rus, Bedřich

    2017-01-01

    We report on the design and performance of a fiber-based, multi-channel laser amplifier seed pulse distribution system. The device is designed to condition and distribute low energy laser pulses from a mode-locked oscillator to multiple, highly synchronized, high energy amplifiers integrated into a laser beamline. Critical functions such as temporal pulse stretching well beyond 100 ps/nm, pulse picking, and fine control over the pulse delay up to 300 ps are all performed in fiber eliminating the need for bulky and expensive grating stretchers, Pockels cells, and delay lines. These functions are characterized and the system as a whole is demonstrated by seeding two high energy amplifiers in the laser beamline. The design of this system allows for complete computer control of all functions, including tuning of dispersion, and is entirely hands-free. The performance of this device and its subsystems will be relevant to those developing lasers where reliability, size, and cost are key concerns in addition to performance; this includes those developing large-scale laser systems similar to ours and also those developing table-top experiments and commercial systems.

  18. Grism compressor for carrier-envelope phase-stable millijoule-energy chirped pulse amplifier lasers featuring bulk material stretcher.

    Science.gov (United States)

    Ricci, A; Jullien, A; Forget, N; Crozatier, V; Tournois, P; Lopez-Martens, R

    2012-04-01

    We demonstrate compression of amplified carrier-envelope phase (CEP)-stable laser pulses using paired transmission gratings and high-index prisms, or grisms, with chromatic dispersion matching that of a bulk material pulse stretcher. Grisms enable the use of larger bulk stretching factors and thereby higher energy pulses with lower B-integral in a compact amplifier design suitable for long-term CEP control.

  19. Intelligence amplification framework for enhancing scheduling processes

    NARCIS (Netherlands)

    Dobrkovic, Andrej; Liu, Luyao; Iacob, Maria Eugenia; van Hillegersberg, Jos

    2016-01-01

    The scheduling process in a typical business environment consists of predominantly repetitive tasks that have to be completed in limited time and often containing some form of uncertainty. The intelligence amplification is a symbiotic relationship between a human and an intelligent agent. This

  20. Optical Pattern Recognition With Self-Amplification

    Science.gov (United States)

    Liu, Hua-Kuang

    1994-01-01

    In optical pattern recognition system with self-amplification, no reference beam used in addressing mode. Polarization of laser beam and orientation of photorefractive crystal chosen to maximize photorefractive effect. Intensity of recognition signal is orders of magnitude greater than other optical correlators. Apparatus regarded as real-time or quasi-real-time optical pattern recognizer with memory and reprogrammability.

  1. Desert Amplification in a Warming Climate

    Science.gov (United States)

    Zhou, Liming

    2016-01-01

    Here I analyze the observed and projected surface temperature anomalies over land between 50°S-50°N for the period 1950–2099 by large-scale ecoregion and find strongest warming consistently and persistently seen over driest ecoregions such as the Sahara desert and the Arabian Peninsula during various 30-year periods, pointing to desert amplification in a warming climate. This amplification enhances linearly with the global mean greenhouse gases(GHGs) radiative forcing and is attributable primarily to a stronger GHGs-enhanced downward longwave radiation forcing reaching the surface over drier ecoregions as a consequence of a warmer and thus moister atmosphere in response to increasing GHGs. These results indicate that desert amplification may represent a fundamental pattern of global warming associated with water vapor feedbacks over land in low- and mid- latitudes where surface warming rates depend inversely on ecosystem dryness. It is likely that desert amplification might involve two types of water vapor feedbacks that maximize respectively in the tropical upper troposphere and near the surface over deserts, with both being very dry and thus extremely sensitive to changes of water vapor. PMID:27538725

  2. PHAGE AMPLIFICATION TECHNOLOGY IN THE DIAGNOSIS OF ...

    African Journals Online (AJOL)

    The World Health Organization recognizes the need for new, affordable, rapid and highly sensitive diagnostics for use in developing countries. Phage amplification technology employs a specific mycobacteriophage which infects a live TB bacillus if represent in a sample. These replicate and lyse the cells to release progeny ...

  3. Characterization of Metarhizium anisopliae using amplifed ...

    African Journals Online (AJOL)

    Characterization of Metarhizium anisopliae using amplifed ribossomal DNA restriction analysis (ARDRA) and internal transcribed spacer (ITS) sequence analysis. Maria do Carmo Catanho Pereira de Lyra, Maria Luiza Ribeiro Bastos da Silva, Vanildo Alberto Leal Bezerra Cavalcanti, Adália Cavalcanti Espírito Santo ...

  4. Enhance XL-III Facility to Petawatt with Improved Front-Stage Amplifier and Optimized Output Energy

    Science.gov (United States)

    Wang, Zhaohua; Wei, Zhiyi; Liu, Cheng; Liu, Feng; Wang, Nan; Ma, Jinglong; Zhang, Jie

    2010-04-01

    This paper reports the recent progresses on the XL-III facility by using a new front-end stage and increasing the gain efficiency in the final amplifier. An improved scheme of double chirped pulse amplification (DCPA) with a long cavity ring regenerative amplifier and technique of cross-polarized wave generation (XPW) was used. Pumped the finial stage with 110J laser energy at 527 nm, the 800 nm chirped laser was boosted to the energy of 45 J by efficiently eliminating the paralasing. After optimized alignment the compressors combined with a far-filed monitor, we obtained the pulse duration of 31fs and contrast ratio of about 10-8 in the preliminary measurement, beam was focused to a spot of about 25 μm with a f/10 OAP. Considered the throughout of the compressor, it promises a peak power of around 1 PW.

  5. Thermostable Mismatch-Recognizing Protein MutS Suppresses Nonspecific Amplification during Polymerase Chain Reaction (PCR

    Directory of Open Access Journals (Sweden)

    Seiki Kuramitsu

    2013-03-01

    Full Text Available Polymerase chain reaction (PCR-related technologies are hampered mainly by two types of error: nonspecific amplification and DNA polymerase-generated mutations. Here, we report that both errors can be suppressed by the addition of a DNA mismatch-recognizing protein, MutS, from a thermophilic bacterium. Although it had been expected that MutS has a potential to suppress polymerase-generated mutations, we unexpectedly found that it also reduced nonspecific amplification. On the basis of this finding, we propose that MutS binds a mismatched primer-template complex, thereby preventing the approach of DNA polymerase to the 3' end of the primer. Our simple methodology improves the efficiency and accuracy of DNA amplification and should therefore benefit various PCR-based applications, ranging from basic biological research to applied medical science.

  6. Ultrafast Capillary Electrophoresis Isolation of DNA Aptamer for the PCR Amplification-Based Small Analyte Sensing

    Directory of Open Access Journals (Sweden)

    Emmanuelle eFiore

    2015-08-01

    Full Text Available Here, we report a new homogeneous DNA amplification-based aptamer assay for small analyte sensing. The aptamer of adenosine chosen as the model analyte was split into two fragments able to assemble in the presence of target. Primers were introduced at extremities of one fragment in order to generate the amplifiable DNA component. The amount of amplifiable fragment was quantifiable by Real-Time Polymerase Chain Reaction (RT-PCR amplification and directly reliable on adenosine concentration. This approach combines the very high separation efficiency and the homogeneous format (without immobilization of capillary electrophoresis and the sensitivity of real time PCR amplification. An ultrafast isolation of target-bound split aptamer (60 s was developed by designing a capillary electrophoresis input/ouput scheme. Such method was successfully applied to the determination of adenosine with a LOD of 1 µM.

  7. High amplification and low noise achieved by a double-stage non-collinear Brillouin amplifier.

    Science.gov (United States)

    Lu, Zhiwei; Gao, Wei; He, Weiming; Zhang, Zan; Hasi, Wuliji

    2009-06-22

    We report a double-stage non-collinear Brillouin amplifier structure with high amplification and low noise, achieving an energy amplification of 6 x 10(11) and a signal-to-noise ratio of 10(3) for an input signal of 5.5 x 10(-14)J in the regime above the pump's stimulated Brillouin scattering threshold. The signal of the first-stage amplifier is efficiently amplified and separated from the noise output. The saturation amplification with noise suppressing is implemented in the second stage. The design principles of system parameters such as the intersection angle between the pump and signal beams, the pump energy, and the beam diameter are given.

  8. External and semi-internal controls for PCR amplification of homologous sequences in mixed templates

    DEFF Research Database (Denmark)

    Kalle, Elena; Gulevich, Alexander; Rensing, Christopher Günther T

    2013-01-01

    . This study demonstrated the efficiency of a model mixed template as an adequate external amplification control for a particular PCR application. The conditions of multi-template PCR do not allow implementation of a classic internal control; therefore we developed a convenient semi-internal control...... as an acceptable alternative. In order to evaluate the effects of inhibitors, a model multi-template mix was amplified in a mixture with DNAse-treated sample. Semi-internal control allowed establishment of intervals for robust PCR performance for different samples, thus enabling correct comparison of the samples....... The complexity of the external and semi-internal amplification controls must be comparable with the assumed complexity of the samples. We also emphasize that amplification controls should be applied in multi-template PCR regardless of the post-assay method used to analyze products....

  9. Site amplifications for generic rock sites

    Science.gov (United States)

    Boore, D.M.; Joyner, W.B.

    1997-01-01

    Seismic shear-wave velocity as a function of depth for generic rock sites has been estimated from borehole data and studies of crustal velocities, and these velocities have been used to compute frequency-dependent amplifications for zero attenuation for use in simulations of strong ground motion. We define a generic rock site as one whose velocity at shallow depths equals the average of those from the rock sites sampled by the borehole data. Most of the boreholes are in populated areas; for that reason, the rock sites sampled are of particular engineering significance. We consider two generic rock sites: rock, corresponding to the bulk of the borehole data, and very hard rock, such as is found in glaciated regions in large areas of eastern North America or in portions of western North America. The amplifications on rock sites can be in excess of 3.5 at high frequencies, in contrast to the amplifications of less than 1.2 on very hard rock sites. The consideration of unattenuated amplification alone is computationally convenient, but what matters for ground-motion estimation is the combined effect of amplification and attenuation. For reasonable values of the attenuation parameter K0, the combined effect of attenuation and amplification for rock sites peaks between about 2 and 5 Hz with a maximum level of less than 1.8. The combined effect is about a factor of 1.5 at 1 Hz and is less than unity for frequencies in the range of 10 to 20 Hz (depending on K0). Using these amplifications, we find provisional values of about ???? = 70 bars and K0 = 0.035 sec for rock sites in western North America by fitting our empirically determined response spectra for an M 6.5 event to simulated values. The borehole data yield shear velocities (V??30) of 618 and 306 m/sec for "rock" and "soil" sites, respectively, when averaged over the upper 30 m. From this, we recommend that V??30 equals 620 and 310 m/sec for applications requiring the average velocity for rock and soil sites in

  10. First demonstration of high-order QAM signal amplification in PPLN-based phase sensitive amplifier.

    Science.gov (United States)

    Umeki, T; Tadanaga, O; Asobe, M; Miyamoto, Y; Takenouchi, H

    2014-02-10

    We demonstrate the phase sensitive amplification of a high-order quadrature amplitude modulation (QAM) signal using non-degenerate parametric amplification in a periodically poled lithium niobate (PPLN) waveguide. The interaction between the pump, signal, and phase-conjugated idler enables us to amplify arbitrary phase components of the signal. The 16QAM signals are amplified without distortion because of the high gain linearity of the PPLN-based phase sensitive amplifier (PSA). Both the phase and amplitude noise reduction capabilities of the PSA are ensured. Phase noise cancellation is achieved by using the interaction with the phase-conjugated idler. A degraded signal-to-noise ratio (SNR) is restored by using the gain difference between a phase-correlated signal-idler pair and uncorrelated excess noise. The applicability of the simultaneous amplification of multi-carrier signals and the amplification of two independent polarization signals are also confirmed with a view to realizing ultra-high spectrally efficient signal amplification.

  11. Nucleic acid tool enzymes-aided signal amplification strategy for biochemical analysis: status and challenges.

    Science.gov (United States)

    Qing, Taiping; He, Dinggeng; He, Xiaoxiao; Wang, Kemin; Xu, Fengzhou; Wen, Li; Shangguan, Jingfang; Mao, Zhengui; Lei, Yanli

    2016-04-01

    Owing to their highly efficient catalytic effects and substrate specificity, the nucleic acid tool enzymes are applied as 'nano-tools' for manipulating different nucleic acid substrates both in the test-tube and in living organisms. In addition to the function as molecular scissors and molecular glue in genetic engineering, the application of nucleic acid tool enzymes in biochemical analysis has also been extensively developed in the past few decades. Used as amplifying labels for biorecognition events, the nucleic acid tool enzymes are mainly applied in nucleic acids amplification sensing, as well as the amplification sensing of biorelated variations of nucleic acids. With the introduction of aptamers, which can bind different target molecules, the nucleic acid tool enzymes-aided signal amplification strategies can also be used to sense non-nucleic targets (e.g., ions, small molecules, proteins, and cells). This review describes and discusses the amplification strategies of nucleic acid tool enzymes-aided biosensors for biochemical analysis applications. Various analytes, including nucleic acids, ions, small molecules, proteins, and cells, are reviewed briefly. This work also addresses the future trends and outlooks for signal amplification in nucleic acid tool enzymes-aided biosensors.

  12. Kinetic Simulations of Laser Parametric Amplification in Magnetized Plasmas

    Science.gov (United States)

    Jia, Qing; Shi, Yuan; Qin, Hong; Fisch, Nathaniel

    2017-10-01

    Laser pulse compression using magnetized resonance near the upper-hybrid frequency is promising for achieving higher output intensity in regimes previously thought impossible using unmagnetized plasmas. Using one-dimensional particle-in-cell simulations, we verify that, by partially replacing plasma with an external transverse magnetic field of megagauss scale, the output pulse can be intensified by a factor of a few, due to the increased allowable amplification time despite a decreased growth rate. Further improvement is impeded by the generation of an electromagnetic wakefield, to which the amplified pulse loses more energy than it does in the unmagnetized case. This limitation can however be circumvented by the use of a stronger pump. In contrast to unmagnetized compression, the magnetized amplification remains efficient when the pump intensity is well above the wavebreaking threshold, until a higher phase-mixing threshold is exceeded. This surprising resilience to wavebreaking in magnetized plasma is of great benefit for magnetized compression. Work supported by the NNSA Grant No. DE274-FG52-08NA28553 and AFOSR Grant No. FA9550-15-1-0391.

  13. Whole genome amplification: Use of advanced isothermal method

    African Journals Online (AJOL)

    Yomi

    2010-12-29

    TLAD), balanced-PCR amplification and restriction and circularization-aided rolling circle amplification. (RCA-RCA) have been suggested to ... (specific to the restriction enzyme used) are ligated to the ends of the genomic DNA ...

  14. Coherent amplification of ultrashort pulses in activated crystals

    Energy Technology Data Exchange (ETDEWEB)

    Varnavskii, O.P.; Kirkin, A.N.; Leontovich, A.M.; Malikov, R.F.; Mozharovskii, A.M.; Trifonov, E.D.

    1984-04-01

    Coherent amplification of picosecond pulses in Nd:YAG and ruby at a temperature of 100 K is investigated. The main features of coherent amplification which distinguish it from incoherent amplification are observed. Alternating sign oscillations of the field envelope at the trailing edge of the amplified pulse, unrestricted pulse duration in relation to the amplification line width, and a doublet structure in the emission spectrum were found. Good agreement was obtained between the experimental and theoretical results. 39 references.

  15. Plasmonic Terahertz Amplification in Graphene-Based Asymmetric Hyperbolic Metamaterial

    Directory of Open Access Journals (Sweden)

    Igor Nefedov

    2015-05-01

    Full Text Available We propose and theoretically explore terahertz amplification, based on stimulated generation of plasmons in graphene asymmetric hyperbolic metamaterials (AHMM, strongly coupled to terahertz radiation. In contrast to the terahertz amplification in resonant nanocavities, AHMM provides a wide-band THz amplification without any reflection in optically thin graphene multilayers.

  16. nucleic acid amplification as used in the diagnosis and management ...

    African Journals Online (AJOL)

    DR. AMINU

    2014-06-01

    Jun 1, 2014 ... thus, amplification based methods offer superior performance ... self-sustaining sequence replication), Amplification of nucleic acid probe (e.g., ligase chain reaction and Q-beta replicase) and Signal amplification (e.g., branched-probe DNA assay). PCR ... advantages, limitations and clinical utility (Fredricks.

  17. Comparison of the Soil Dynamic Amplification Factor and Soil Amplification by Using Microtremor and MASW Methods Respectively

    Science.gov (United States)

    Tuncel, Aykut; Cevdet Özdag, Özkan; Pamuk, Eren; Akgün, Mustafa

    2017-12-01

    Single Station Microtremor method, which is widely used nowadays, is an effective and easy applicable method. In this study, dynamic amplification factor distributions of the study area were obtained using scenario earthquake parameters with single station microtremor data gathered at 112 points. In addition, a surface wave active method, which is known as MASW (Multichannel Analysis of Surface Waves), was applied at 43 profiles to calculate the soil amplification values. Dynamic amplification factor (DAF), soil amplification, the predominant soil period (PSP), geology and topography data of the study area were analysed together. Dynamic amplification factor and soil amplification values were obtained 2 or higher at about sea level parts of the study area which are generally composed of alluvial units. Additionally, in high altitude regions that are composed of volcanic rocks, relatively lower dynamic amplification factor and soil amplification values were obtained. The minimum amplification value in the study area was 1.15, while the maximum amplification value was 3.05 according to the dynamic amplification results and the soil amplification values were between 1.16 and 3.85 in harmony. It is seen that the obtained DAF values and the soil amplification values calculated from the seismic velocities are very similar to each other numerically and regionally. Because of this, it is concluded that the values of the soil amplification obtained by the MASW method and the calculated DAF values in this study are in harmony with each other. Although the depths of research in these two calculation methods are different from each other, the similarity of the results allows us to arrive at the result of how effective the ground layer is on the amplification. It has a great importance to calculate the amplification values and other dynamic parameters by in situ measurements for a planned plot because geological units can vary even at very short distances in heterogeneously

  18. Differential pre-amplification of STR loci for fragmented forensic DNA profiling.

    Science.gov (United States)

    Ham, Seon-Kyu; Kim, Se-Yong; Seo, Bo Young; Woo, Kwang-Man; Lee, Seung-Hwan; Choi, Cheol Yong

    2016-11-01

    DNA profiling of short tandem repeats (STR) has been successfully used for the identification of individuals in forensic samples, accidents and natural disasters. However, STR profiling of DNA isolated from old crime scenes and damaged biological samples is difficult due to DNA degradation and fragmentation. Here, we show that pre-amplification of STR loci using biotinylated primers for the STR loci is an efficient strategy to obtain STR profiling results from fragmented forensic samples. Analysis of STR loci with longer amplicon sizes is generally hampered, since these relatively long loci are vulnerable to DNA fragmentation. This problem was overcome by using reduced or increased primer concentrations for loci with shorter or longer amplicon sizes, respectively, in our pre-amplification strategy. In addition, pre-amplification of STR loci into two groups of short or long amplicon size increases the efficiency of STR profiling from highly fragmented forensic DNA samples. Therefore, differential pre-amplification of STR loci is an effective way to obtain DNA profiling results from fragmented forensic samples. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Resonant amplification of quantum fluctuations in a spinor gas

    DEFF Research Database (Denmark)

    Topic, O.; Scherer, M.; Gebreyesus, G.

    2010-01-01

    and classical fluctuations. This is strikingly manifested in a sample initially prepared in the m F = 0 state, where spin-changing collisions triggered by quantum fluctuations may lead to the creation of correlated pairs in m F = ±1. We show that the pair creation efficiency is strongly influenced...... of seed atoms is triggered purely by quantum fluctuations and thus the system acts as a matter-wave amplifier for the vacuum state.......Bose-Einstein condensates of atoms with non-zero spin are known to constitute an ideal system to investigate fundamental properties of magnetic superfluids. More recently it was realized that they also provide the fascinating opportunity to investigate the macroscopic amplification of quantum...

  20. Measurement-induced amplification of optical cat-like states

    DEFF Research Database (Denmark)

    Laghaout, Amine; Neergaard-Nielsen, Jonas Schou; Rigas, J.

    2013-01-01

    with pairs of small cats and then to interfere them on a balanced beam splitter. The projective measurement of one of the outputs is used to herald a larger cat resulting from the constructive interference of the initial states. The scheme proposed here uses the projection |x = 0〉〈x = 0| as the heralding...... attain amplitudes too small for practical use. This is for example the case for photon-subtracted squeezed vacuum (PSSV), which can be used to approximate cat states of amplitude no larger than y = 1.5 if the fidelity is to be maintained above 95%. One way to reach larger amplitudes is to start...... condition. Homodyning is proposed, as opposed to photon counting, because homodyne detection has high a quantum efficiency, and - as demonstrated in the paper - can be tuned to increase the success probability of the amplification without heavily compromising the output's fidelity....

  1. Numerical simulations for performance optimization of a few-cycle terawatt NOPCPA system

    NARCIS (Netherlands)

    Witte, S.; Zinkstok, R.T.; Hogervorst, W.; Eikema, K.S.E.

    2007-01-01

    We present a systematic numerical design and performance study of an ultra-broadband noncollinear optical parametric chirped pulse amplification (NOPCPA) system. Using a split-step Fourier approach, we model a three-stage amplifier system which is designed for the generation of 7 fs pulses with

  2. Surface roughness-aided hard X-ray emission from carbon nanotubes

    Indian Academy of Sciences (India)

    The simple analytical model explains the basic experimental observations and also serves as a ... Os; 79.20.Ds; 52.50.Jm. 1. Introduction. The advent of intense, ultrashort solid-state chirped pulse amplification lasers. (USUIL) have come up with possibilities of realizing ultrashort high peak brightness sources of photons ...

  3. Iodometric microdetermination of hydrazines by amplification reactions.

    Science.gov (United States)

    Gawargious, Y A; Besada, A

    1975-09-01

    Two new, simple, rapid, and accurate iodometric amplification methods are described for the micro and submicro determination of hydrazine. The first depends on oxidation with a chloroform solution of iodine and removal of its excess, oxidation of the resulting iodide with bromine, and iodometric titration of the liberated iodate. The second method is based on oxidation with periodate at pH 8, masking of the excess of periodate with molybdate at pH 3, and iodometric titration of the iodate. The order of amplification involved in the two methods is 6- and 3-fold, respectively. Micro amounts of hydrazine sulphate and dihydrochloride were determined satisfactorily by both methods, the average recoveries being 98.6 and 99.4%.

  4. Digital Microfluidics for Nucleic Acid Amplification.

    Science.gov (United States)

    Coelho, Beatriz; Veigas, Bruno; Fortunato, Elvira; Martins, Rodrigo; Águas, Hugo; Igreja, Rui; Baptista, Pedro V

    2017-06-25

    Digital Microfluidics (DMF) has emerged as a disruptive methodology for the control and manipulation of low volume droplets. In DMF, each droplet acts as a single reactor, which allows for extensive multiparallelization of biological and chemical reactions at a much smaller scale. DMF devices open entirely new and promising pathways for multiplex analysis and reaction occurring in a miniaturized format, thus allowing for healthcare decentralization from major laboratories to point-of-care with accurate, robust and inexpensive molecular diagnostics. Here, we shall focus on DMF platforms specifically designed for nucleic acid amplification, which is key for molecular diagnostics of several diseases and conditions, from pathogen identification to cancer mutations detection. Particular attention will be given to the device architecture, materials and nucleic acid amplification applications in validated settings.

  5. Parametric nanomechanical amplification at very high frequency.

    Science.gov (United States)

    Karabalin, R B; Feng, X L; Roukes, M L

    2009-09-01

    Parametric resonance and amplification are important in both fundamental physics and technological applications. Here we report very high frequency (VHF) parametric resonators and mechanical-domain amplifiers based on nanoelectromechanical systems (NEMS). Compound mechanical nanostructures patterned by multilayer, top-down nanofabrication are read out by a novel scheme that parametrically modulates longitudinal stress in doubly clamped beam NEMS resonators. Parametric pumping and signal amplification are demonstrated for VHF resonators up to approximately 130 MHz and provide useful enhancement of both resonance signal amplitude and quality factor. We find that Joule heating and reduced thermal conductance in these nanostructures ultimately impose an upper limit to device performance. We develop a theoretical model to account for both the parametric response and nonequilibrium thermal transport in these composite nanostructures. The results closely conform to our experimental observations, elucidate the frequency and threshold-voltage scaling in parametric VHF NEMS resonators and sensors, and establish the ultimate sensitivity limits of this approach.

  6. Digital Microfluidics for Nucleic Acid Amplification

    Directory of Open Access Journals (Sweden)

    Beatriz Coelho

    2017-06-01

    Full Text Available Digital Microfluidics (DMF has emerged as a disruptive methodology for the control and manipulation of low volume droplets. In DMF, each droplet acts as a single reactor, which allows for extensive multiparallelization of biological and chemical reactions at a much smaller scale. DMF devices open entirely new and promising pathways for multiplex analysis and reaction occurring in a miniaturized format, thus allowing for healthcare decentralization from major laboratories to point-of-care with accurate, robust and inexpensive molecular diagnostics. Here, we shall focus on DMF platforms specifically designed for nucleic acid amplification, which is key for molecular diagnostics of several diseases and conditions, from pathogen identification to cancer mutations detection. Particular attention will be given to the device architecture, materials and nucleic acid amplification applications in validated settings.

  7. Amplification of postwildfire peak flow by debris

    Science.gov (United States)

    Kean, Jason W.; McGuire, Luke; Rengers, Francis; Smith, Joel B.; Staley, Dennis M.

    2016-01-01

    In burned steeplands, the peak depth and discharge of postwildfire runoff can substantially increase from the addition of debris. Yet methods to estimate the increase over water flow are lacking. We quantified the potential amplification of peak stage and discharge using video observations of postwildfire runoff, compiled data on postwildfire peak flow (Qp), and a physically based model. Comparison of flood and debris flow data with similar distributions in drainage area (A) and rainfall intensity (I) showed that the median runoff coefficient (C = Qp/AI) of debris flows is 50 times greater than that of floods. The striking increase in Qp can be explained using a fully predictive model that describes the additional flow resistance caused by the emergence of coarse-grained surge fronts. The model provides estimates of the amplification of peak depth, discharge, and shear stress needed for assessing postwildfire hazards and constraining models of bedrock incision.

  8. Parametric amplification by coupled flux qubits

    OpenAIRE

    Rehak, M.; Neilinger, P.; Grajcar, M.; Oelsner, G.; Huebner, U.; Il'ichev, E.; Meyer, H. -G.

    2014-01-01

    We report the parametric amplification of a microwave signal in a Kerr medium formed from superconducting qubits. Two mutually coupled flux qubits, embedded in the current antinode of a superconducting coplanar waveguide resonator, are used as a nonlinear element. Shared Josephson junctions provide the qubit-resonator coupling, resulting in a device with a measured gain of about 20 dB. We argue, that this arrangement represents a unit cell which can be straightforwardly extended to a quasi on...

  9. A mechanism for ramified rolling circle amplification

    Directory of Open Access Journals (Sweden)

    Smith James H

    2010-12-01

    Full Text Available Abstract Background Amplification of single-stranded DNA circles has wide utility for a variety of applications. The two-primer ramified rolling circle amplification (RAM reaction provides exponential DNA amplification under isothermal conditions, creating a regular laddered series of double-stranded DNA products. However, the molecular mechanism of the RAM reaction remains unexplained. Results A RAM reaction model predicts exponential accumulation of a double-stranded DNA product size series, and product-size ratios, that are consistent with observed RAM reaction products. The mechanism involves generation of a series of increasing size intermediate templates; those templates produce RAM products and recursively generate smaller intermediate templates. The model allows prediction of the number of rounds of circular template replication. Real-time RAM reaction data are consistent with the model. Analysis of RAM reaction products shows exponential growth limitation consistent with the model's predictions. Conclusions The model provides a rationale for the observed products of the RAM reaction, and the molecular yield among those products. Experimental results are consistent with the model.

  10. Morphology of ablation craters generated by ultra-short laser pulses in dentin surfaces: AFM and ESEM evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Daskalova, A., E-mail: a_daskalova@code.bg [Institute of Electronics, Bulgarian Academy of Sciences, 72, Tsarigradsko Chaussee Blvd., 1784 Sofia (Bulgaria); Bashir, S.; Husinsky, W. [IAP, Vienna University of Technology, Wiedner Hauptstrasse 8-10, 1040 Vienna (Austria)

    2010-11-15

    In this study, the surface morphology and structure of dentin after ablation by ultra-short pulses were evaluated using environmental scanning electron microscopy (ESEM) and atomic force microscopy (AFM). The dentin specimens examined were irradiated by a chirped-pulse-amplification (CPA) Ti:sapphire laser (800 nm) and the optimal conditions for producing various nanostructures were determined. Based on the ESEM results, it was possible to identify an energy density range as the ablation threshold for dentin. The laser-induced damage was characterized over the fluence range 1.3-2.1 J/cm{sup 2}. The results demonstrate that by selecting suitable parameters one can obtain efficient dentin surface preparation without evidence of thermal damage, i.e., with minimized heat affected zones and reduced collateral damage, the latter being normally characterized by formation of microcracks, grain growth and recrystallization in the heat affected zones.

  11. Octave-spanning coherent mid-IR generation via adiabatic difference frequency conversion.

    Science.gov (United States)

    Suchowski, Haim; Krogen, Peter R; Huang, Shu-Wei; Kärtner, Franz X; Moses, Jeffrey

    2013-11-18

    We demonstrate efficient downconversion of a near-IR broadband optical parametric chirped pulse amplifier (OPCPA) pulse to a 1.1-octave-spanning mid-IR pulse (measured at -10 dB of peak) via a single nonlinearly and adiabatically chirped quasi-phase-matching grating in magnesium oxide doped lithium niobate. We report a spectrum spanning from 2 to 5 μm and obtained by near full photon number conversion of μJ-energy OPCPA pulses spanning 680-870 nm mixed with a narrowband 1047-nm pulse. The conversion process is shown to be robust for various input broadband OPA pulses and suitable for post-amplification conversion for many near-IR systems.

  12. Prognostic impact of HER-2 Subclonal Amplification in breast cancer.

    Science.gov (United States)

    Di Oto, Enrico; Brandes, Alba A; Cucchi, Maria C; Foschini, Maria P

    2017-06-02

    The presence of a limited number of cells with HER-2 amplification (Subclonal Amplification) in breast carcinomas is occasionally encountered, but its prognostic impact is poorly known. The purpose of this study is to evaluate the prognostic impact of HER-2 Subclonal Amplification in a retrospective series of breast cancers. Accordingly, 81 consecutive breast carcinomas showing HER-2 Subclonal Amplification were obtained from the histology files (case series). These cases were subdivided into two groups: (a) those cases in which the HER-2 Subclonal Amplification was consonant to the accepted criteria for amplification, showing clusters of amplified cells, and (b) those cases with rare HER-2 Subclonal Amplification that did not reflect the accepted criteria for amplification, showing scattered amplified cells only. The incidence of metastases and late recurrences of the case series was compared with a series composed of 109 consecutive cases, being HER-2 homogeneous (comprising 14 Amplified and 95 Non-Amplified cases), matched for grade and stage (control series). It appeared that cases showing Subclonal Amplification had an incidence of metastases intermediate between the cases Amplified and Non-Amplified. Specifically, Subclonal Amplification with clustered cells had a lower incidence of metastases than Amplified cases (12.9 versus 21.4%). On the contrary, Subclonal Amplification with scattered cells showed an incidence of metastases higher than Non-Amplified cases (14 versus 9.47%). In addition, patients Subclonal Amplification with clustered cells, who were treated with the specific monoclonal antibody, had a lower incidence of metastases than patients showing Subclonal Amplification with scattered cells, who did not receive target therapy. These data, together with those recently published, indicate that Subclonal Amplification has an impact on prognosis and should be taken into consideration to correctly plan the treatment of breast cancer patients.

  13. A Tympanal Insect Ear Exploits a Critical Oscillator for Active Amplification and Tuning

    OpenAIRE

    Mhatre, Natasha; Robert, Daniel

    2013-01-01

    Summary A dominant theme of acoustic communication is the partitioning of acoustic space into exclusive, species-specific niches to enable efficient information transfer. In insects, acoustic niche partitioning is achieved through auditory frequency filtering, brought about by the mechanical properties of their ears [1]. The tuning of the antennal ears of mosquitoes [2] and flies [3], however, arises from active amplification, a process similar to that at work in the mammalian cochlea [4]. Ye...

  14. Parametric amplification by coupled flux qubits

    Science.gov (United States)

    Rehák, M.; Neilinger, P.; Grajcar, M.; Oelsner, G.; Hübner, U.; Il'ichev, E.; Meyer, H.-G.

    2014-04-01

    We report parametric amplification of a microwave signal in a Kerr medium formed from superconducting qubits. Two mutually coupled flux qubits, embedded in the current antinode of a superconducting coplanar waveguide resonator, are used as a nonlinear element. Shared Josephson junctions provide the qubit-resonator coupling, resulting in a device with a tunable Kerr constant (up to 3 × 10-3) and a measured gain of about 20 dB. This arrangement represents a unit cell which can be straightforwardly extended to a quasi one-dimensional quantum metamaterial with large tunable Kerr nonlinearity, providing a basis for implementation of wide-band travelling wave parametric amplifiers.

  15. Does the Arctic Amplification peak this decade?

    Science.gov (United States)

    Martin, Torge; Haine, Thomas W. N.

    2017-04-01

    Temperatures rise faster in the Arctic than on global average, a phenomenon known as Arctic Amplification. While this is well established from observations and model simulations, projections of future climate (here: RCP8.5) with models of the Coupled Model Intercomparison Project phase 5 (CMIP5) also indicate that the Arctic Amplification has a maximum. We show this by means of an Arctic Amplification factor (AAF), which we define as the ratio of Arctic mean to global mean surface air temperature (SAT) anomalies. The SAT anomalies are referenced to the period 1960-1980 and smoothed by a 30-year running mean. For October, the multi-model ensemble-mean AAF reaches a maximum in 2017. The maximum moves however to later years as Arctic winter progresses: for the autumn mean SAT (September to November) the maximum AAF is found in 2028 and for winter (December to February) in 2060. Arctic Amplification is driven, amongst others, by the ice-albedo feedback (IAF) as part of the more general surface albedo feedback (involving clouds, snow cover, vegetation changes) and temperature effects (Planck and lapse-rate feedbacks). We note that sea ice retreat and the associated warming of the summer Arctic Ocean are not only an integral part of the IAF but are also involved in the other drivers. In the CMIP5 simulations, the timing of the AAF maximum coincides with the period of fastest ice retreat for the respective month. Presence of at least some sea ice is crucial for the IAF to be effective because of the contrast in surface albedo between ice and open water and the need to turn ocean warming into ice melt. Once large areas of the Arctic Ocean are ice-free, the IAF should be less effective. We thus hypothesize that the ice retreat significantly affects AAF variability and forces a decline of its magnitude after at least half of the Arctic Ocean is ice-free and the ice cover becomes basically seasonal.

  16. Amplification Effects and Unconventional Monetary Policies

    Directory of Open Access Journals (Sweden)

    Cécile BASTIDON GILLES

    2012-02-01

    Full Text Available Global financial crises trigger off amplification effects, which allow relatively small shocks to propagate through the whole financial system. For this reason, the range of Central banks policies is now widening beyond conventional monetary policies and lending of last resort. The aim of this paper is to establish a rule for this practice. The model is based on the formalization of funding conditions in various types of markets. We conduct a comprehensive analysis of the “unconventional monetary policies”, and especially quantify government bonds purchases by the Central bank.

  17. Plasmonic nanostructures for multiscale light amplification

    Science.gov (United States)

    Chen, Aiqing; Welp, Ulrich; Vlasko-Vlasov, Vitalii; Miller, Ryan; Shevchenko, Elena; Ocola, Leonidas; Gray, Stephen; Deprinceiii, Eugene

    2012-02-01

    We demonstrate experimentally a multiscale plasmonic design for giant light amplification using gold nanoparticles self-assembled in gratings on a metal mirror with thin dielectric spacer. The successive increase of the light enhancement factors upon addition of individual plasmonic elements in the design is tested by measurement of the Raman signal from R6G and benzenethiol molecules on clusters of nanoparticles, their ordered arrays on dielectric, semiconducting, and metal substrates, and on metal substrate with gratings. High fidelity of our structures as SERS substrates are confirmed by areal maps of the Raman response. FDTD numerical calculations are in a good agreement with our experimental measurements.

  18. Hybridization and amplification rate correction for affymetrix SNP arrays

    Directory of Open Access Journals (Sweden)

    Wang Quan

    2012-06-01

    Full Text Available Abstract Background Copy number variation (CNV is essential to understand the pathology of many complex diseases at the DNA level. Affymetrix SNP arrays, which are widely used for CNV studies, significantly depend on accurate copy number (CN estimation. Nevertheless, CN estimation may be biased by several factors, including cross-hybridization and training sample batch, as well as genomic waves of intensities induced by sequence-dependent hybridization rate and amplification efficiency. Since many available algorithms only address one or two of the three factors, a high false discovery rate (FDR often results when identifying CNV. Therefore, we have developed a new CNV detection pipeline which is based on hybridization and amplification rate correction (CNVhac. Methods CNVhac first estimates the allelic concentrations (ACs of target sequences by using the sample independent parameters trained through physicochemical hybridization law. Then the raw CN is estimated by taking the ratio of AC to the corresponding average AC from a reference sample set for one specific site. Finally, a hidden Markov model (HMM segmentation process is implemented to detect CNV regions. Results Based on public HapMap data, the results show that CNVhac effectively smoothes the genomic waves and facilitates more accurate raw CN estimates compared to other methods. Moreover, CNVhac alleviates, to a certain extent, the sample dependence of inference and makes CNV calling with appreciable low FDRs. Conclusion CNVhac is an effective approach to address the common difficulties in SNP array analysis, and the working principles of CNVhac can be easily extended to other platforms.

  19. Parallel pumping for magnon spintronics: Amplification and manipulation of magnon spin currents on the micron-scale

    Science.gov (United States)

    Brächer, T.; Pirro, P.; Hillebrands, B.

    2017-06-01

    Magnonics and magnon spintronics aim at the utilization of spin waves and magnons, their quanta, for the construction of wave-based logic networks via the generation of pure all-magnon spin currents and their interfacing with electric charge transport. The promise of efficient parallel data processing and low power consumption renders this field one of the most promising research areas in spintronics. In this context, the process of parallel parametric amplification, i.e., the conversion of microwave photons into magnons at one half of the microwave frequency, has proven to be a versatile tool to excite and to manipulate spin waves. Its beneficial and unique properties such as frequency and mode-selectivity, the possibility to excite spin waves in a wide wavevector range and the creation of phase-correlated wave pairs, have enabled the achievement of important milestones like the magnon Bose-Einstein condensation and the cloning and trapping of spin-wave packets. Parallel parametric amplification, which allows for the selective amplification of magnons while conserving their phase is, thus, one of the key methods of spin-wave generation and amplification. The application of parallel parametric amplification to CMOS-compatible micro- and nano-structures is an important step towards the realization of magnonic networks. This is motivated not only by the fact that amplifiers are an important tool for the construction of any extended logic network but also by the unique properties of parallel parametric amplification. In particular, the creation of phase-correlated wave pairs allows for rewarding alternative logic operations such as a phase-dependent amplification of the incident waves. Recently, the successful application of parallel parametric amplification to metallic microstructures has been reported which constitutes an important milestone for the application of magnonics in practical devices. It has been demonstrated that parametric amplification provides an

  20. Parametric amplification in MoS2drum resonator.

    Science.gov (United States)

    Prasad, Parmeshwar; Arora, Nishta; Naik, A K

    2017-11-30

    Parametric amplification is widely used in diverse areas from optics to electronic circuits to enhance low level signals by varying relevant system parameters. Parametric amplification has also been performed in several micro-nano resonators including nano-electromechanical system (NEMS) resonators based on a two-dimensional (2D) material. Here, we report the enhancement of mechanical response in a MoS 2 drum resonator using degenerate parametric amplification. We use parametric pumping to modulate the spring constant of the MoS 2 resonator and achieve a 10 dB amplitude gain. We also demonstrate quality factor enhancement in the resonator with parametric amplification. We investigate the effect of cubic nonlinearity on parametric amplification and show that it limits the gain of the mechanical resonator. Amplifying ultra-small displacements at room temperature and understanding the limitations of the amplification in these devices is key for using these devices for practical applications.

  1. Fidelity of DNA polymerases in DNA amplification

    Energy Technology Data Exchange (ETDEWEB)

    Keohavong, P.; Thilly, W.G. (Massachusetts Institute of Technology, Cambridge (USA))

    1989-12-01

    Denaturing gradient gel electrophoresis (DGGE) was used to separate and isolate the products of DNA amplification by polymerase chain reaction (PCR). The strategy permitted direct enumeration and identification of point mutations created by T4, modified T7, Klenow fragment of polymerase I, and Thermus aquaticus (Tag) DNA polymerases. Incorrectly synthesized sequences were separated from the wild type by DGGE as mutant/wild-type heteroduplexes and the heteroduplex fraction was used to calculate the average error rate (mutations per base duplication). The error rate induced in the 104-base-pair low-temperature melting domain of exon 3 of the human hypoxanthine/guanine phosphoribosyltransferase (HPRT) gene was {approx} 3.4 {times} 10{sup {minus}5} for modified T7, 1.3 {times} 10{sup {minus}4} for Klenow fragment, and 2.1 {times} 10{sup {minus}4} for Taq polymerases after a 10{sup 6}-fold amplification. The error rate for T4 DNA polymerase was not more than 3 {times} 10{sup {minus}6} error per base duplication. The predominant mutations were sequenced and found to be transitions of G{center dot}C to A{center dot}T for T4 and modified T7 DNA polymerases, and A{center dot}T to G{center dot}C for Taq polymerase. Klenow fragment induced both possible transitions and deletions of 2 and 4 base pairs.

  2. Space Optical Communications Using Laser Beam Amplification

    Science.gov (United States)

    Agrawal, Govind

    2015-01-01

    The Space Optical Communications Using Laser Beam Amplification (SOCLBA) project will provide a capability to amplify a laser beam that is received in a modulating retro-reflector (MRR) located in a satellite in low Earth orbit. It will also improve the pointing procedure between Earth and spacecraft terminals. The technology uses laser arrays to strengthen the reflected laser beam from the spacecraft. The results of first year's work (2014) show amplification factors of 60 times the power of the signal beam. MMRs are mirrors that reflect light beams back to the source. In space optical communications, a high-powered laser interrogator beam is directed from the ground to a satellite. Within the satellite, the beam is redirected back to ground using the MMR. In the MMR, the beam passes through modulators, which encode a data signal onto the returning beam. MMRs can be used in small spacecraft for optical communications. The SOCLBA project is significant to NASA and small spacecraft due to its application to CubeSats for optical data transmission to ground stations, as well as possible application to spacecraft for optical data transmission.

  3. Direct loop mediated isothermal amplification on filters for quantification of Dehalobacter in groundwater.

    Science.gov (United States)

    Stedtfeld, Robert D; Stedtfeld, Tiffany M; Samhan, Farag; Kanitkar, Yogendra H; Hatzinger, Paul B; Cupples, Alison M; Hashsham, Syed A

    2016-12-01

    Nucleic acid amplification of biomarkers is increasingly used to monitor microbial activity and assess remedial performance in contaminated aquifers. Previous studies described the use of filtration, elution, and direct isothermal amplification (i.e. no DNA extraction and purification) as a field-able means to quantify Dehalococcoides spp. in groundwater. This study expands previous work with direct loop mediated isothermal amplification (LAMP) for the detection and quantification of Dehalobacter spp. in groundwater. Experiments tested amplification of DNA with and without crude lysis and varying concentrations of humic acid. Three separate field-able methods of biomass concentration with eight aquifer samples were also tested, comparing direct LAMP with traditional DNA extraction and quantitative PCR (qPCR). A new technique was developed where filters were amplified directly within disposable Gene-Z chips. The direct filter amplification (DFA) method eliminated an elution step and provided a detection limit of 10(2)Dehalobacter cells per 100mL. LAMP with crudely lysed Dehalobacter had a negligible effect on threshold time and sensitivity compared to lysed samples. The LAMP assay was more resilient than traditional qPCR to humic acid in sample, amplifying with up to 100mg per L of humic acid per reaction compared to 1mg per L for qPCR. Of the tested field-able concentrations methods, DFA had the lowest coefficient of variation among Dehalobacter spiked groundwater samples and lowest threshold time indicating high capture efficiency and low inhibition. While demonstrated with Dehalobacter, the DFA method can potentially be used for a number of applications requiring field-able, rapid (<60min) and highly sensitive quantification of microorganisms in environmental water samples. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Directional random oligonucleotide primed (DROP) global amplification of cDNA: its application to subtractive cDNA cloning.

    OpenAIRE

    Hampson, I N; Hampson, L; Dexter, T M

    1996-01-01

    We describe a method of global PCR amplification of cDNA such that the strand sense is maintained. The products of this process are random primed fragments ranging in size from 100 to 500 bp which facilitates uniform PCR amplification of total cDNA. Directional incorporation of a T7 RNA polymerase initiator/promoter sequence allows efficient synthesis of total sense RNA from this material and the use of a biotinylated primer permits the separation of single-stranded cDNA. Isolation of these p...

  5. Effects of Amplification Facilitators on Diagnostic PCR in the Presence of Blood, Feces, and Meat

    Science.gov (United States)

    Abu Al-Soud, Waleed; Rådström, Peter

    2000-01-01

    The full potential of diagnostic PCR is limited, in part, by the presence of inhibitors in complex biological samples that reduce the amplification efficiency. Therefore, different pre-PCR treatments are being used to reduce the effects of PCR inhibitors. The aim of the present study was to investigate the effects of 16 amplification facilitators to enhance DNA amplification in the presence of blood, feces, or meat. Different concentrations of amplification facilitators and inhibitory samples were added to PCR mixtures containing rTth or Taq DNA polymerase. The addition of 0.6% (wt/vol) bovine serum albumin to reaction mixtures containing Taq DNA polymerase reduced the inhibitory effect of blood and allowed DNA amplification in the presence of 2% instead of 0.2% (vol/vol) blood. Furthermore, the addition of bovine serum albumin (BSA) to reaction mixtures containing feces or meat enhanced the amplification capacities of both polymerases. Taq DNA polymerase was able to amplify DNA in the presence of 4% instead of 0.4% (vol/vol) feces and 4% instead of 0.2% (vol/vol) meat, and rTth was able to amplify DNA in the presence of 4% instead of 0.4% (vol/vol) feces and 20% instead of 2% (vol/vol) meat. The single-stranded DNA binding T4 gene 32 protein (gp32) had a relieving effect similar to that of BSA, except when it was added to PCR mixtures of rTth containing meat and of Taq DNA polymerase containing feces. The relieving effects of betaine and a cocktail of proteinase inhibitors were more sample specific. The addition of 11.7% (wt/vol) betaine allowed Taq DNA polymerase to amplify DNA in the presence of 2% (vol/vol) blood, while the addition of proteinase inhibitors allowed DNA amplification by both polymerases in the presence of 4% (vol/vol) feces. When various combinations of betaine, BSA, gp32, and proteinase inhibitors were tested, no synergistic or additive effects were observed. The effects of facilitators on real-time DNA synthesis instead of conventional PCR

  6. Parametric amplification by coupled flux qubits

    Energy Technology Data Exchange (ETDEWEB)

    Rehák, M.; Neilinger, P.; Grajcar, M. [Department of Experimental Physics, Comenius University, SK-84248 Bratislava (Slovakia); Institute of Physics, Slovak Academy of Science, 845 11 Bratislava (Slovakia); Oelsner, G.; Hübner, U.; Meyer, H.-G. [Leibniz Institute of Photonic Technology, P.O. Box 100239, D-07702 Jena (Germany); Il' ichev, E. [Leibniz Institute of Photonic Technology, P.O. Box 100239, D-07702 Jena (Germany); Novosibirsk State Technical University, 20 K. Marx Ave., 630092 Novosibirsk (Russian Federation)

    2014-04-21

    We report parametric amplification of a microwave signal in a Kerr medium formed from superconducting qubits. Two mutually coupled flux qubits, embedded in the current antinode of a superconducting coplanar waveguide resonator, are used as a nonlinear element. Shared Josephson junctions provide the qubit-resonator coupling, resulting in a device with a tunable Kerr constant (up to 3 × 10{sup −3}) and a measured gain of about 20 dB. This arrangement represents a unit cell which can be straightforwardly extended to a quasi one-dimensional quantum metamaterial with large tunable Kerr nonlinearity, providing a basis for implementation of wide-band travelling wave parametric amplifiers.

  7. Control and amplification of cortical neurodynamics

    Science.gov (United States)

    Liljenstroem, Hans; Aronsson, P.

    1999-03-01

    We investigate different mechanisms for the control and amplification of cortical neurodynamics, using a neural network model of a three layered cortical structure. We show that different dynamical states can be obtained by changing a control parameter of the input-output relation, or by changing the noise level. Point attractor, limit cycle, and strange attractor dynamics occur at different values of the control parameter. For certain, optimal noise levels, system performance is maximized, analogous to stochastic resonance phenomena. Noise can also be used to induce different dynamical states. A few noisy network units distributed in a network layer can result in global synchronous oscillations, or waves of activity moving across the network. We further demonstrate that fast synchronization of network activity can be obtained by implementing electromagnetic interactions between network units.

  8. Heralded amplification of path entangled quantum states

    Science.gov (United States)

    Monteiro, F.; Verbanis, E.; Caprara Vivoli, V.; Martin, A.; Gisin, N.; Zbinden, H.; Thew, R. T.

    2017-06-01

    Device-independent quantum key distribution (DI-QKD) represents one of the most fascinating challenges in quantum communication, exploiting concepts of fundamental physics, namely Bell tests of nonlocality, to ensure the security of a communication link. This requires the loophole-free violation of a Bell inequality, which is intrinsically difficult due to losses in fibre optic transmission channels. Heralded photon amplification (HPA) is a teleportation-based protocol that has been proposed as a means to overcome transmission loss for DI-QKD. Here we demonstrate HPA for path entangled states and characterise the entanglement before and after loss by exploiting a recently developed displacement-based detection scheme. We demonstrate that by exploiting HPA we are able to reliably maintain high fidelity entangled states over loss-equivalent distances of more than 50 km.

  9. Protein Misfolding Cyclic Amplification of Infectious Prions.

    Science.gov (United States)

    Moda, Fabio

    2017-01-01

    Transmissible spongiform encephalopathies, or prion diseases, are a group of incurable disorders caused by the accumulation of an abnormally folded prion protein (PrP Sc ) in the brain. According to the "protein-only" hypothesis, PrP Sc is the infectious agent able to propagate the disease by acting as a template for the conversion of the correctly folded prion protein (PrP C ) into the pathological isoform. Recently, the mechanism of PrP C conversion has been mimicked in vitro using an innovative technique named protein misfolding cyclic amplification (PMCA). This technology represents a great tool for studying diverse aspects of prion biology in the field of basic research and diagnosis. Moreover, PMCA can be expanded for the study of the misfolding process associated to other neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and frontotemporal lobar degeneration. © 2017 Elsevier Inc. All rights reserved.

  10. Principles of Whole-Genome Amplification.

    Science.gov (United States)

    Czyz, Zbigniew Tadeusz; Kirsch, Stefan; Polzer, Bernhard

    2015-01-01

    Modern molecular biology relies on large amounts of high-quality genomic DNA. However, in a number of clinical or biological applications this requirement cannot be met, as starting material is either limited (e.g., preimplantation genetic diagnosis (PGD) or analysis of minimal residual cancer) or of insufficient quality (e.g., formalin-fixed paraffin-embedded tissue samples or forensics). As a consequence, in order to obtain sufficient amounts of material to analyze these demanding samples by state-of-the-art modern molecular assays, genomic DNA has to be amplified. This chapter summarizes available technologies for whole-genome amplification (WGA), bridging the last 25 years from the first developments to currently applied methods. We will especially elaborate on research application, as well as inherent advantages and limitations of various WGA technologies.

  11. Markovian Dynamics of Josephson Parametric Amplification

    Directory of Open Access Journals (Sweden)

    W. Kaiser

    2017-09-01

    Full Text Available In this work, we derive the dynamics of the lossy DC pumped non-degenerate Josephson parametric amplifier (DCPJPA. The main element in a DCPJPA is the superconducting Josephson junction. The DC bias generates the AC Josephson current varying the nonlinear inductance of the junction. By this way the Josephson junction acts as the pump oscillator as well as the time varying reactance of the parametric amplifier. In quantum-limited amplification, losses and noise have an increased impact on the characteristics of an amplifier. We outline the classical model of the lossy DCPJPA and derive the available noise power spectral densities. A classical treatment is not capable of including properties like spontaneous emission which is mandatory in case of amplification at the quantum limit. Thus, we derive a quantum mechanical model of the lossy DCPJPA. Thermal losses are modeled by the quantum Langevin approach, by coupling the quantized system to a photon heat bath in thermodynamic equilibrium. The mode occupation in the bath follows the Bose-Einstein statistics. Based on the second quantization formalism, we derive the Heisenberg equations of motion of both resonator modes. We assume the dynamics of the system to follow the Markovian approximation, i.e. the system only depends on its actual state and is memory-free. We explicitly compute the time evolution of the contributions to the signal mode energy and give numeric examples based on different damping and coupling constants. Our analytic results show, that this model is capable of including thermal noise into the description of the DC pumped non-degenerate Josephson parametric amplifier.

  12. Markovian Dynamics of Josephson Parametric Amplification

    Science.gov (United States)

    Kaiser, Waldemar; Haider, Michael; Russer, Johannes A.; Russer, Peter; Jirauschek, Christian

    2017-09-01

    In this work, we derive the dynamics of the lossy DC pumped non-degenerate Josephson parametric amplifier (DCPJPA). The main element in a DCPJPA is the superconducting Josephson junction. The DC bias generates the AC Josephson current varying the nonlinear inductance of the junction. By this way the Josephson junction acts as the pump oscillator as well as the time varying reactance of the parametric amplifier. In quantum-limited amplification, losses and noise have an increased impact on the characteristics of an amplifier. We outline the classical model of the lossy DCPJPA and derive the available noise power spectral densities. A classical treatment is not capable of including properties like spontaneous emission which is mandatory in case of amplification at the quantum limit. Thus, we derive a quantum mechanical model of the lossy DCPJPA. Thermal losses are modeled by the quantum Langevin approach, by coupling the quantized system to a photon heat bath in thermodynamic equilibrium. The mode occupation in the bath follows the Bose-Einstein statistics. Based on the second quantization formalism, we derive the Heisenberg equations of motion of both resonator modes. We assume the dynamics of the system to follow the Markovian approximation, i.e. the system only depends on its actual state and is memory-free. We explicitly compute the time evolution of the contributions to the signal mode energy and give numeric examples based on different damping and coupling constants. Our analytic results show, that this model is capable of including thermal noise into the description of the DC pumped non-degenerate Josephson parametric amplifier.

  13. Nucleic Acid Amplification Testing in Suspected Child Sexual Abuse

    Science.gov (United States)

    Esernio-Jenssen, Debra; Barnes, Marilyn

    2011-01-01

    The American Academy of Pediatrics recommends that site-specific cultures be obtained, when indicated, for sexually victimized children. Nucleic acid amplification testing is a highly sensitive and specific methodology for identifying sexually transmitted infections. Nucleic acid amplification tests are also less invasive than culture, and this…

  14. Evaluation of loop mediated isothermal amplification for diagnosis of ...

    African Journals Online (AJOL)

    Tuberculosis (TB) remains an important global public health problem. The lack of rapid and accurate diagnostic testing is an important impediment to global tuberculosis control. Loop mediated isothermal amplification (LAMP) is a rapid method for nucleic acid amplification. In this study, we assessed the performance of an ...

  15. Centrosome Amplification Is Sufficient to Promote Spontaneous Tumorigenesis in Mammals

    NARCIS (Netherlands)

    Levine, Michelle S.; Bakker, Bjorn; Boeckx, Bram; Moyett, Julia; Lu, James; Vitre, Benjamin; Spierings, Diana C.; Lansdorp, Peter M.; Cleveland, Don W.; Lambrechts, Diether; Foijer, Floris; Holland, Andrew J.

    2017-01-01

    Centrosome amplification is a common feature of human tumors, but whether this is a cause or a consequence of cancer remains unclear. Here, we test the consequence of centrosome amplification by creating mice in which centrosome number can be chronically increased in the absence of additional

  16. Quantum Darwinism: Amplification and the Acquisition of Information by Spin Environments

    Energy Technology Data Exchange (ETDEWEB)

    Zwolak, Michael P. [Oregon State Univ., Corvallis, OR (United States) Dept. of Physics; Riedel, Jess [IBM, Yorktown Heights, NY (United States). Thomas J. Watson Research Center; Zurek, Wojciech H. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2014-07-09

    Quantum Darwinism recognizes the role of the environment as a communication channel: Decoherence can amplify select information – information about the pointer states of a system of interest (preventing access to complementary information about superpositions of those states). We examine the amplification process for a spin environment under a variety of conditions. For initially pure environment states, the contribution to decoherence and the partial record deposited in an environment spin are both determined by the overlap of conditional states generated on the spin. For mixed environments, however, decoherence and a partial record are no longer directly related. The partial record, though, is given by a generalized measure of overlap – the quantum Chernoff information. The latter quantity is a measure of distinguishability and gives the efficiency of the amplification process. We calculate the Chernoff information and show explicitly that, except for a set of measure zero, there is always redundant information acquired by the environment.

  17. Plasmon Field Effect Transistor for Plasmon to Electric Conversion and Amplification.

    Science.gov (United States)

    Shokri Kojori, Hossein; Yun, Ju-Hyung; Paik, Younghun; Kim, Joondong; Anderson, Wayne A; Kim, Sung Jin

    2016-01-13

    Direct coupling of electronic excitations of optical energy via plasmon resonances opens the door to improving gain and selectivity in various optoelectronic applications. We report a new device structure and working mechanisms for plasmon resonance energy detection and electric conversion based on a thin film transistor device with a metal nanostructure incorporated in it. This plasmon field effect transistor collects the plasmonically induced hot electrons from the physically isolated metal nanostructures. These hot electrons contribute to the amplification of the drain current. The internal electric field and quantum tunneling effect at the metal-semiconductor junction enable highly efficient hot electron collection and amplification. Combined with the versatility of plasmonic nanostructures in wavelength tunability, this device architecture offers an ultrawide spectral range that can be used in various applications.

  18. Rapid Identification of Black Grain Eumycetoma Causative Agents Using Rolling Circle Amplification

    Science.gov (United States)

    Ahmed, Sarah A.; van den Ende, Bert H. G. Gerrits; Fahal, Ahmed H.; van de Sande, Wendy W. J.; de Hoog, G. S.

    2014-01-01

    Accurate identification of mycetoma causative agent is a priority for treatment. However, current identification tools are far from being satisfactory for both reliable diagnosis and epidemiological investigations. A rapid, simple, and highly efficient molecular based method for identification of agents of black grain eumycetoma is introduced, aiming to improve diagnostic in endemic areas. Rolling Circle Amplification (RCA) uses species-specific padlock probes and isothermal DNA amplification. The tests were based on ITS sequences and developed for Falciformispora senegalensis, F. tompkinsii, Madurella fahalii, M. mycetomatis, M. pseudomycetomatis, M. tropicana, Medicopsis romeroi, and Trematosphaeria grisea. With the isothermal RCA assay, 62 isolates were successfully identified with 100% specificity and no cross reactivity or false results. The main advantage of this technique is the low-cost, high specificity, and simplicity. In addition, it is highly reproducible and can be performed within a single day. PMID:25474355

  19. Rapid identification of black grain eumycetoma causative agents using rolling circle amplification.

    Directory of Open Access Journals (Sweden)

    Sarah A Ahmed

    2014-12-01

    Full Text Available Accurate identification of mycetoma causative agent is a priority for treatment. However, current identification tools are far from being satisfactory for both reliable diagnosis and epidemiological investigations. A rapid, simple, and highly efficient molecular based method for identification of agents of black grain eumycetoma is introduced, aiming to improve diagnostic in endemic areas. Rolling Circle Amplification (RCA uses species-specific padlock probes and isothermal DNA amplification. The tests were based on ITS sequences and developed for Falciformispora senegalensis, F. tompkinsii, Madurella fahalii, M. mycetomatis, M. pseudomycetomatis, M. tropicana, Medicopsis romeroi, and Trematosphaeria grisea. With the isothermal RCA assay, 62 isolates were successfully identified with 100% specificity and no cross reactivity or false results. The main advantage of this technique is the low-cost, high specificity, and simplicity. In addition, it is highly reproducible and can be performed within a single day.

  20. The effects of different maceration techniques on nuclear DNA amplification using human bone.

    Science.gov (United States)

    Lee, Esther J; Luedtke, Jennifer G; Allison, Jamie L; Arber, Carolyn E; Merriwether, D Andrew; Steadman, Dawnie Wolfe

    2010-07-01

    Forensic anthropologists routinely macerate human bone for the purposes of identity and trauma analysis, but the heat and chemical treatments used can destroy genetic evidence. As a follow-up to a previous study on nuclear DNA recovery that used pig ribs, this study utilizes human skeletal remains treated with various bone maceration techniques for nuclear DNA amplification using the standard Combined DNA Index System (CODIS) markers. DNA was extracted from 18 samples of human lower leg bones subjected to nine chemical and heat maceration techniques. Genotyping was carried out using the AmpFlSTR COfiler and AmpFlSTR Profiler Plus ID kits. Results showed that heat treatments via microwave or Biz/Na(2)CO(3) in sub-boiling water efficiently macerate bone and produce amplifiable nuclear DNA for genetic analysis. Long-term use of chemicals such as hydrogen peroxide is discouraged as it results in poor bone quality and has deleterious effects on DNA amplification.

  1. Recyclable amplification for single-photon entanglement from photon loss and decoherence

    Science.gov (United States)

    Zhou, Lan; Chen, Ling-Quan; Zhong, Wei; Sheng, Yu-Bo

    2018-01-01

    We put forward a highly efficient recyclable single-photon assisted amplification protocol, which can protect single-photon entanglement (SPE) from photon loss and decoherence. Making use of quantum nondemolition detection gates constructed with the help of cross-Kerr nonlinearity, our protocol has some attractive advantages. First, the parties can recover less-entangled SPE to be maximally entangled SPE, and reduce photon loss simultaneously. Second, if the protocol fails, the parties can repeat the protocol to reuse some discarded items, which can increase the success probability. Third, when the protocol is successful, they can similarly repeat the protocol to further increase the fidelity of the SPE. Thereby, our protocol provides a possible way to obtain high entanglement, high fidelity and high success probability simultaneously. In particular, our protocol shows higher success probability in the practical high photon loss channel. Based on the above features, our amplification protocol has potential for future application in long-distance quantum communication.

  2. Clinical application of somatosensory amplification in psychosomatic medicine

    Directory of Open Access Journals (Sweden)

    Nakao Mutsuhiro

    2007-10-01

    Full Text Available Abstract Many patients with somatoform disorders are frequently encountered in psychosomatic clinics as well as in primary care clinics. To assess such patients objectively, the concept of somatosensory amplification may be useful. Somatosensory amplification refers to the tendency to experience a somatic sensation as intense, noxious, and disturbing. It may have a role in a variety of medical conditions characterized by somatic symptoms that are disproportionate to demonstrable organ pathology. It may also explain some of the variability in somatic symptomatology found among different patients with the same serious medical disorder. It has been assessed with a self-report questionnaire, the Somatosensory Amplification Scale. This instrument was developed in a clinical setting in the U.S., and the reliability and validity of the Japanese and Turkish versions have been confirmed as well. Many studies have attempted to clarify the specific role of somatosensory amplification as a pathogenic mechanism in somatization. It has been reported that somatosensory amplification does not correlate with heightened sensitivity to bodily sensations and that emotional reactivity exerts its influence on somatization via a negatively biased reporting style. According to our recent electroencephalographic study, somatosensory amplification appears to reflect some aspects of long-latency cognitive processing rather than short-latency interoceptive sensitivity. The concept of somatosensory amplification can be useful as an indicator of somatization in the therapy of a broad range of disorders, from impaired self-awareness to various psychiatric disorders. It also provides useful information for choosing appropriate pharmacological or psychological therapy. While somatosensory amplification has a role in the presentation of somatic symptoms, it is closely associated with other factors, namely, anxiety, depression, and alexithymia that may also influence the same

  3. How a replication origin and matrix attachment region accelerate gene amplification under replication stress in mammalian cells.

    Directory of Open Access Journals (Sweden)

    Shun-suke Tanaka

    Full Text Available The gene amplification plays a critical role in the malignant transformation of mammalian cells. The most widespread method for amplifying a target gene in cell culture is the use of methotrexate (Mtx treatment to amplify dihydrofolate reductase (Dhfr. Whereas, we found that a plasmid bearing both a mammalian origin of replication (initiation region; IR and a matrix attachment region (MAR was spontaneously amplified in mammalian cells. In this study, we attempted to uncover the underlying mechanism by which the IR/MAR sequence might accelerate Mtx induced Dhfr amplification. The plasmid containing the IR/MAR was extrachromosomally amplified, and then integrated at multiple chromosomal locations within individual cells, increasing the likelihood that the plasmid might be inserted into a chromosomal environment that permits high expression and further amplification. Efficient amplification of this plasmid alleviated the genotoxicity of Mtx. Clone-based cytogenetic and sequence analysis revealed that the plasmid was amplified in a chromosomal context by breakage-fusion-bridge cycles operating either at the plasmid repeat or at the flanking fragile site activated by Mtx. This mechanism explains how a circular molecule bearing IR/MAR sequences of chromosomal origin might be amplified under replication stress, and also provides insight into gene amplification in human cancer.

  4. In vitro amplification of PrPSc derived from the brain and blood of sheep infected with scrapie.

    Science.gov (United States)

    Thorne, Leigh; Terry, Linda A

    2008-12-01

    Scrapie is a fatal, naturally transmissible, neurodegenerative prion disease that affects sheep and goats and is characterized by the accumulation of a misfolded protein, PrPSc, converted from host-encoded PrPc, in the central nervous system of affected animals. Highly efficient in vitro conversion of host PrPc to PrPSc has been achieved in models of scrapie and in natural prion diseases by protein misfolding cyclic amplification (PMCA). Here, we demonstrate amplification, by serial PMCA, of PrPSc from individual sources of scrapie-infected sheep. Efficiency of amplification was affected by the pairing of the source of PrPSc with the control brain substrate of different genotypes of PrP. In line with previous studies, efficiency of amplification was greatly enhanced with the addition of a synthetic polyanion, polyadenylic acid (PolyA), facilitating rapid detection of low levels of PrPSc from body fluids such as blood. To this end PrPSc was amplified, in a 3 day PMCA assay, from blood leukocyte preparations from VRQ/VRQ scrapie-affected sheep at clinical end point. While PolyA-assisted PMCA resulted in spontaneous conversion of PrPc, we were able to distinguish blood samples from unaffected and affected sheep under controlled conditions. This study demonstrates that highly efficient amplification of PrPSc can be achieved for ovine scrapie from both brain and blood from naturally infected sheep and shows potential applications for improvements in current diagnostics and pre-mortem testing.

  5. Towards rapid prototyped convective microfluidic DNA amplification platform

    Science.gov (United States)

    Ajit, Smrithi; Praveen, Hemanth Mithun; Puneeth, S. B.; Dave, Abhishek; Sesham, Bharat; Mohan, K. N.; Goel, Sanket

    2017-02-01

    Today, Polymerase Chain Reaction (PCR) based DNA amplification plays an indispensable role in the field of biomedical research. Its inherent ability to exponentially amplify sample DNA has proven useful for the identification of virulent pathogens like those causing Multiple Drug-Resistant Tuberculosis (MDR-TB). The intervention of Microfluidics technology has revolutionized the concept of PCR from being a laborious and time consuming process into one that is faster, easily portable and capable of being multifunctional. The Microfluidics based PCR outweighs its traditional counterpart in terms of flexibility of varying reaction rate, operation simplicity, need of a fraction of volume and capability of being integrated with other functional elements. The scope of the present work involves the development of a real-time continuous flow microfluidic device, fabricated by 3D printing-governed rapid prototyping method, eventually leading to an automated and robust platform to process multiple DNA samples for detection of MDRTB-associated mutations. The thermal gradient characteristic to the PCR process is produced using peltier units appropriate to the microfluidic environment fully monitored and controlled by a low cost controller driven by a Data Acquisition System. The process efficiency achieved in the microfluidic environment in terms of output per cycle is expected to be on par with the traditional PCR and capable of earning the additional advantages of being faster and minimizing the handling.

  6. Current Developments in Prokaryotic Single Cell Whole Genome Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Goudeau, Danielle; Nath, Nandita; Ciobanu, Doina; Cheng, Jan-Fang; Malmstrom, Rex

    2014-03-14

    Our approach to prokaryotic single-cell Whole Genome Amplification at the JGI continues to evolve. To increase both the quality and number of single-cell genomes produced, we explore all aspects of the process from cell sorting to sequencing. For example, we now utilize specialized reagents, acoustic liquid handling, and reduced reaction volumes eliminate non-target DNA contamination in WGA reactions. More specifically, we use a cleaner commercial WGA kit from Qiagen that employs a UV decontamination procedure initially developed at the JGI, and we use the Labcyte Echo for tip-less liquid transfer to set up 2uL reactions. Acoustic liquid handling also dramatically reduces reagent costs. In addition, we are exploring new cell lysis methods including treatment with Proteinase K, lysozyme, and other detergents, in order to complement standard alkaline lysis and allow for more efficient disruption of a wider range of cells. Incomplete lysis represents a major hurdle for WGA on some environmental samples, especially rhizosphere, peatland, and other soils. Finding effective lysis strategies that are also compatible with WGA is challenging, and we are currently assessing the impact of various strategies on genome recovery.

  7. The amplification of risk in experimental diffusion chains.

    Science.gov (United States)

    Moussaïd, Mehdi; Brighton, Henry; Gaissmaier, Wolfgang

    2015-05-05

    Understanding how people form and revise their perception of risk is central to designing efficient risk communication methods, eliciting risk awareness, and avoiding unnecessary anxiety among the public. However, public responses to hazardous events such as climate change, contagious outbreaks, and terrorist threats are complex and difficult-to-anticipate phenomena. Although many psychological factors influencing risk perception have been identified in the past, it remains unclear how perceptions of risk change when propagated from one person to another and what impact the repeated social transmission of perceived risk has at the population scale. Here, we study the social dynamics of risk perception by analyzing how messages detailing the benefits and harms of a controversial antibacterial agent undergo change when passed from one person to the next in 10-subject experimental diffusion chains. Our analyses show that when messages are propagated through the diffusion chains, they tend to become shorter, gradually inaccurate, and increasingly dissimilar between chains. In contrast, the perception of risk is propagated with higher fidelity due to participants manipulating messages to fit their preconceptions, thereby influencing the judgments of subsequent participants. Computer simulations implementing this simple influence mechanism show that small judgment biases tend to become more extreme, even when the injected message contradicts preconceived risk judgments. Our results provide quantitative insights into the social amplification of risk perception, and can help policy makers better anticipate and manage the public response to emerging threats.

  8. Phase-Sensitive Control Of Molecular Dissociation Through Attosecond Pump/Strong-Field Mid-IR Probe Spectroscopy

    Science.gov (United States)

    2016-04-15

    developed a cryocooled laser and optical parametric chirped pulse amplification based light pulse architecture , producing, by high harmonic generation, a 16...micron optical parametric amplifier (OPA). 9. Demonstrated compressibility of the mid-IR seed pulses down to 1.1-cycle duration. 10. Designed a...18 eV isolated single-femtosecond EUV pulse source, and by adiabatic difference frequency generation and optical parametric amplification

  9. Strong correlation between cross-amplification success and genetic distance across all members of 'True Salamanders' (Amphibia: Salamandridae) revealed by Salamandra salamandra-specific microsatellite loci.

    Science.gov (United States)

    Hendrix, Ralf; Susanne Hauswaldt, J; Veith, Michael; Steinfartz, Sebastian

    2010-11-01

    The unpredictable and low cross-amplification success of microsatellite loci tested for congeneric amphibian species has mainly been explained by the size and complexity of amphibian genomes, but also by taxonomy that is inconsistent with phylogenetic relationships among taxa. Here, we tested whether the cross-amplification success of nine new and 11 published microsatellite loci cloned for an amphibian source species, the fire salamander (Salamandra salamandra), correlated with the genetic distance across all members of True Salamanders (genera Chioglossa, Lyciasalamandra, Mertensiella and Salamandra that form a monophyletic clade within the family of Salamandridae) serving as target species. Cross-amplification success varied strongly among the species and showed a highly significant negative relationship with genetic distance and amplification success. Even though lineages of S. salamandra and Lyciasalamndra have separated more than 30 Ma, a within genus amplification success rate of 65% was achieved for species of Lyciasalamandra thus demonstrating that an efficient cross-species amplification of microsatellite loci in amphibians is feasible even across large evolutionary distances. A decrease in genome size, on the other hand, paralleled also a decrease in amplified loci and therefore contradicted previous results and expectations that amplification success should increase with a decrease in genome size. However, in line with other studies, our comprehensive dataset clearly shows that cross-amplification success of microsatellite loci is well explained by phylogenetic divergence between species. As taxonomic classifications on the species and genus level do not necessarily mirror phylogenetic divergence between species, the pure belonging of species to the same taxonomic units (i.e. species or genus) might be less useful to predict cross-amplification success of microsatellite loci between such species. © 2010 Blackwell Publishing Ltd.

  10. A mechanism of gene amplification driven by small DNA fragments.

    Directory of Open Access Journals (Sweden)

    Kuntal Mukherjee

    Full Text Available DNA amplification is a molecular process that increases the copy number of a chromosomal tract and often causes elevated expression of the amplified gene(s. Although gene amplification is frequently observed in cancer and other degenerative disorders, the molecular mechanisms involved in the process of DNA copy number increase remain largely unknown. We hypothesized that small DNA fragments could be the trigger of DNA amplification events. Following our findings that small fragments of DNA in the form of DNA oligonucleotides can be highly recombinogenic, we have developed a system in the yeast Saccharomyces cerevisiae to capture events of chromosomal DNA amplification initiated by small DNA fragments. Here we demonstrate that small DNAs can amplify a chromosomal region, generating either tandem duplications or acentric extrachromosomal DNA circles. Small fragment-driven DNA amplification (SFDA occurs with a frequency that increases with the length of homology between the small DNAs and the target chromosomal regions. SFDA events are triggered even by small single-stranded molecules with as little as 20-nt homology with the genomic target. A double-strand break (DSB external to the chromosomal amplicon region stimulates the amplification event up to a factor of 20 and favors formation of extrachromosomal circles. SFDA is dependent on Rad52 and Rad59, partially dependent on Rad1, Rad10, and Pol32, and independent of Rad51, suggesting a single-strand annealing mechanism. Our results reveal a novel molecular model for gene amplification, in which small DNA fragments drive DNA amplification and define the boundaries of the amplicon region. As DNA fragments are frequently found both inside cells and in the extracellular environment, such as the serum of patients with cancer or other degenerative disorders, we propose that SFDA may be a common mechanism for DNA amplification in cancer cells, as well as a more general cause of DNA copy number variation

  11. Small Sample Whole-Genome Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Hara, C A; Nguyen, C P; Wheeler, E K; Sorensen, K J; Arroyo, E S; Vrankovich, G P; Christian, A T

    2005-09-20

    Many challenges arise when trying to amplify and analyze human samples collected in the field due to limitations in sample quantity, and contamination of the starting material. Tests such as DNA fingerprinting and mitochondrial typing require a certain sample size and are carried out in large volume reactions; in cases where insufficient sample is present whole genome amplification (WGA) can be used. WGA allows very small quantities of DNA to be amplified in a way that enables subsequent DNA-based tests to be performed. A limiting step to WGA is sample preparation. To minimize the necessary sample size, we have developed two modifications of WGA: the first allows for an increase in amplified product from small, nanoscale, purified samples with the use of carrier DNA while the second is a single-step method for cleaning and amplifying samples all in one column. Conventional DNA cleanup involves binding the DNA to silica, washing away impurities, and then releasing the DNA for subsequent testing. We have eliminated losses associated with incomplete sample release, thereby decreasing the required amount of starting template for DNA testing. Both techniques address the limitations of sample size by providing ample copies of genomic samples. Carrier DNA, included in our WGA reactions, can be used when amplifying samples with the standard purification method, or can be used in conjunction with our single-step DNA purification technique to potentially further decrease the amount of starting sample necessary for future forensic DNA-based assays.

  12. Magnetic Field Amplification in Supernova Remnants

    Science.gov (United States)

    Xu, Siyao; Lazarian, Alex

    2017-12-01

    Based on the new findings on the turbulent dynamo in Xu & Lazarian, we examine the magnetic field amplification in the context of supernova remnants. Due to the strong ion-neutral collisional damping in the weakly ionized interstellar medium, the dynamo in the preshock turbulence remains in the damping kinematic regime, which leads to a linear-in-time growth of the magnetic field strength. The resultant magnetic field structure enables effective diffusion upstream and shock acceleration of cosmic rays to energies above the “knee.” Differently, the nonlinear dynamo in the postshock turbulence leads to a linear-in-time growth of the magnetic energy due to the turbulent magnetic diffusion. Given a weak initial field strength in the postshock region, the magnetic field saturates at a significant distance from the shock front as a result of the inefficiency of the nonlinear dynamo. This result is in a good agreement with existing numerical simulations and well explains the X-ray spots detected far behind the shock front.

  13. Amplification and chromosomal dispersion of human endogenous retroviral sequences

    Energy Technology Data Exchange (ETDEWEB)

    Steele, P.E.; Martin, M.A.; Rabson, A.B.; Bryan, T.; O' Brien, S.J.

    1986-09-01

    Endogenous retroviral sequences have undergone amplification events involving both viral and flanking cellular sequences. The authors cloned members of an amplified family of full-length endogenous retroviral sequences. Genomic blotting, employing a flanking cellular DNA probe derived from a member of this family, revealed a similar array of reactive bands in both humans and chimpanzees, indicating that an amplification event involving retroviral and associated cellular DNA sequences occurred before the evolutionary separation of these two primates. Southern analyses of restricted somatic cell hybrid DNA preparations suggested that endogenous retroviral segments are widely dispersed in the human genome and that amplification and dispersion events may be linked.

  14. A tympanal insect ear exploits a critical oscillator for active amplification and tuning.

    Science.gov (United States)

    Mhatre, Natasha; Robert, Daniel

    2013-10-07

    A dominant theme of acoustic communication is the partitioning of acoustic space into exclusive, species-specific niches to enable efficient information transfer. In insects, acoustic niche partitioning is achieved through auditory frequency filtering, brought about by the mechanical properties of their ears. The tuning of the antennal ears of mosquitoes and flies, however, arises from active amplification, a process similar to that at work in the mammalian cochlea. Yet, the presence of active amplification in the other type of insect ears--tympanal ears--has remained uncertain. Here we demonstrate the presence of active amplification and adaptive tuning in the tympanal ear of a phylogenetically basal insect, a tree cricket. We also show that the tree cricket exploits critical oscillator-like mechanics, enabling high auditory sensitivity and tuning to conspecific songs. These findings imply that sophisticated auditory mechanisms may have appeared even earlier in the evolution of hearing and acoustic communication than currently appreciated. Our findings also raise the possibility that frequency discrimination and directional hearing in tympanal systems may rely on physiological nonlinearities, in addition to mechanical properties, effectively lifting some of the physical constraints placed on insects by their small size [6] and prompting an extensive reexamination of invertebrate audition. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  15. GMO detection in food and feed through screening by visual loop-mediated isothermal amplification assays.

    Science.gov (United States)

    Wang, Cong; Li, Rong; Quan, Sheng; Shen, Ping; Zhang, Dabing; Shi, Jianxin; Yang, Litao

    2015-06-01

    Isothermal DNA/RNA amplification techniques are the primary methodology for developing on-spot rapid nucleic acid amplification assays, and the loop-mediated isothermal amplification (LAMP) technique has been developed and applied in the detection of foodborne pathogens, plant/animal viruses, and genetically modified (GM) food/feed contents. In this study, one set of LAMP assays targeting on eight frequently used universal elements, marker genes, and exogenous target genes, such as CaMV35S promoter, FMV35S promoter, NOS, bar, cry1Ac, CP4 epsps, pat, and NptII, were developed for visual screening of GM contents in plant-derived food samples with high efficiency and accuracy. For these eight LAMP assays, their specificity was evaluated by testing commercial GM plant events and their limits of detection were also determined, which are 10 haploid genome equivalents (HGE) for FMV35S promoter, cry1Ac, and pat assays, as well as five HGE for CaMV35S promoter, bar, NOS terminator, CP4 epsps, and NptII assays. The screening applicability of these LAMP assays was further validated successfully using practical canola, soybean, and maize samples. The results suggested that the established visual LAMP assays are applicable and cost-effective for GM screening in plant-derived food samples.

  16. A Digital Microfluidics Platform for Loop-Mediated Isothermal Amplification Detection

    Directory of Open Access Journals (Sweden)

    Beatriz Jorge Coelho

    2017-11-01

    Full Text Available Digital microfluidics (DMF arises as the next step in the fast-evolving field of operation platforms for molecular diagnostics. Moreover, isothermal schemes, such as loop-mediated isothermal amplification (LAMP, allow for further simplification of amplification protocols. Integrating DMF with LAMP will be at the core of a new generation of detection devices for effective molecular diagnostics at point-of-care (POC, providing simple, fast, and automated nucleic acid amplification with exceptional integration capabilities. Here, we demonstrate for the first time the role of coupling DMF and LAMP, in a dedicated device that allows straightforward mixing of LAMP reagents and target DNA, as well as optimum temperature control (reaction droplets undergo a temperature variation of just 0.3 °C, for 65 °C at the bottom plate. This device is produced using low-temperature and low-cost production processes, adaptable to disposable and flexible substrates. DMF-LAMP is performed with enhanced sensitivity without compromising reaction efficacy or losing reliability and efficiency, by LAMP-amplifying 0.5 ng/µL of target DNA in just 45 min. Moreover, on-chip LAMP was performed in 1.5 µL, a considerably lower volume than standard bench-top reactions.

  17. A Digital Microfluidics Platform for Loop-Mediated Isothermal Amplification Detection.

    Science.gov (United States)

    Coelho, Beatriz Jorge; Veigas, Bruno; Águas, Hugo; Fortunato, Elvira; Martins, Rodrigo; Baptista, Pedro Viana; Igreja, Rui

    2017-11-16

    Digital microfluidics (DMF) arises as the next step in the fast-evolving field of operation platforms for molecular diagnostics. Moreover, isothermal schemes, such as loop-mediated isothermal amplification (LAMP), allow for further simplification of amplification protocols. Integrating DMF with LAMP will be at the core of a new generation of detection devices for effective molecular diagnostics at point-of-care (POC), providing simple, fast, and automated nucleic acid amplification with exceptional integration capabilities. Here, we demonstrate for the first time the role of coupling DMF and LAMP, in a dedicated device that allows straightforward mixing of LAMP reagents and target DNA, as well as optimum temperature control (reaction droplets undergo a temperature variation of just 0.3 °C, for 65 °C at the bottom plate). This device is produced using low-temperature and low-cost production processes, adaptable to disposable and flexible substrates. DMF-LAMP is performed with enhanced sensitivity without compromising reaction efficacy or losing reliability and efficiency, by LAMP-amplifying 0.5 ng/µL of target DNA in just 45 min. Moreover, on-chip LAMP was performed in 1.5 µL, a considerably lower volume than standard bench-top reactions.

  18. Direct PCR amplification of the HVSI region in mitochondrial DNA from buccal cell swabs

    Directory of Open Access Journals (Sweden)

    Kovačević-Grujičić Nataša

    2012-01-01

    Full Text Available Amplification of human mitochondrial DNA (mtDNA has been widely used in population genetics, human evolutionary and molecular anthropology studies. mtDNA hypervariable segments I and II (HVSI and HVSII were shown to be a suitable tool in genetic analyses due to the unique properties of mtDNA, such as the lack of recombination, maternal mode of inheritance, rapid evolutionary rate and high population-specific polymorphisms. Here we present a rapid and low-cost method for direct PCR amplification of a 330 bp fragment of HVSI from buccal cell samples. Avoiding the DNA isolation step makes this method appropriate for the analysis of a large number of samples in a short period of time. Since the transportation of samples and fieldwork conditions can affect the quality of samples and subsequent DNA analysis, we tested the effects of long-term storage of buccal cell swabs on the suitability of such samples for direct PCR amplification. We efficiently amplified a 330 bp fragment of HVSI even after the long-term storage of buccal cells at room temperature, +4°C or at -20°C, for up to eight months. All examined PCR products were successfully sequenced, regardless of sample storage time and conditions. Our results suggest that the direct PCR amplification of the HVSI region from buccal cells is a method well suited for large-scale mtDNA population studies.[Acknowledgments. This work was supported by the Ministry of Education and Science of the Republic of Serbia (Grant no. III 47025.

  19. Amplification of surface temperature trends and variability in thetropical atmosphere

    Energy Technology Data Exchange (ETDEWEB)

    Santer, B.D.; Wigley, T.M.L.; Mears, C.; Wentz, F.J.; Klein,S.A.; Seidel, D.J.; Taylor, K.E.; Thorne, P.W.; Wehner, M.F.; Gleckler,P.J.; Boyle, J.S.; Collins, W.D.; Dixon, K.W.; Doutriaux, C.; Free, M.; Fu, Q.; Hansen, J.E.; Jones, G.S.; Ruedy, R.; Karl, T.R.; Lanzante, J.R.; Meehl, G.A.; Ramaswamy, V.; Russell, G.; Schmidt, G.A.

    2005-08-11

    The month-to-month variability of tropical temperatures is larger in the troposphere than at the Earth's surface. This amplification behavior is similar in a range of observations and climate model simulations, and is consistent with basic theory. On multi-decadal timescales, tropospheric amplification of surface warming is a robust feature of model simulations, but occurs in only one observational dataset. Other observations show weak or even negative amplification. These results suggest that either different physical mechanisms control amplification processes on monthly and decadal timescales, and models fail to capture such behavior, or (more plausibly) that residual errors in several observational datasets used here affect their representation of long-term trends.

  20. Nonlinear Zel'dovich Effect: Parametric Amplification from Medium Rotation

    Science.gov (United States)

    Faccio, Daniele; Wright, Ewan M.

    2017-03-01

    The interaction of light with rotating media has attracted recent interest for both fundamental and applied studies including rotational Doppler shift measurements. It is also possible to obtain amplification through the scattering of light with orbital angular momentum from a rotating and absorbing cylinder, as proposed by Zel'dovich more than forty years ago. This amplification mechanism has never been observed experimentally yet has connections to other fields such as Penrose superradiance in rotating black holes. Here we propose a nonlinear optics system whereby incident light carrying orbital angular momentum drives parametric interaction in a rotating medium. The crystal rotation is shown to take the phase-mismatched parametric interaction with negligible energy exchange at zero rotation to amplification for sufficiently large rotation rates. The amplification is shown to result from breaking of anti-P T symmetry induced by the medium rotation.

  1. EGFR intragenic loss and gene amplification in astrocytic gliomas.

    Science.gov (United States)

    Arjona, Dolores; Bello, M Josefa; Rey, Juan A

    2006-01-01

    We have studied EGFR gene amplification and allelic status of chromosome 7 in 68 tumors consisting of 34 WHO grade IV glioblastomas (26 primary and 8 secondary), 14 WHO grade III anaplastic astrocytomas, and 20 WHO grade II astrocytomas, by polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP), quantitative PCR, and microsatellite analysis. EGFR gene amplification was present in 27 of these tumors (40%), and we identified allelic losses at 7p11 approximately p14 in 38 of the 68 cases (56%), including 17 tumors displaying loss for EGFR intragenic markers. The positive correlation (P < 0.05, chi(2)) between tumors with EGFR intragenic loss and EGFR gene amplification, frequently displaying the EGFR vIII form, suggests that EGFR gene rearrangement leading to intragenic loss is a molecular event that participates in the amplification process of this gene.

  2. Integration of random amplification of polymorphic DNA-polymerase ...

    African Journals Online (AJOL)

    adjusted reaction conditions strain-distinctive PCR-restriction fragment lenght polymorphism (RFLP) can be designed. Key words: Echinococcus granulosus, strain-specificity, random amplification of polymorphic DNA-polymerase chain reaction ...

  3. FAST MAGNETIC FIELD AMPLIFICATION IN THE EARLY UNIVERSE: GROWTH OF COLLISIONLESS PLASMA INSTABILITIES IN TURBULENT MEDIA

    Energy Technology Data Exchange (ETDEWEB)

    Falceta-Gonçalves, D. [SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SS (United Kingdom); Kowal, G. [Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, Rua Arlindo Bettio, 1000, São Paulo, SP 03828-000 (Brazil)

    2015-07-20

    In this work we report on a numerical study of the cosmic magnetic field amplification due to collisionless plasma instabilities. The collisionless magnetohydrodynamic equations derived account for the pressure anisotropy that leads, in specific conditions, to the firehose and mirror instabilities. We study the time evolution of seed fields in turbulence under the influence of such instabilities. An approximate analytical time evolution of the magnetic field is provided. The numerical simulations and the analytical predictions are compared. We found that (i) amplification of the magnetic field was efficient in firehose-unstable turbulent regimes, but not in the mirror-unstable models; (ii) the growth rate of the magnetic energy density is much faster than the turbulent dynamo; and (iii) the efficient amplification occurs at small scales. The analytical prediction for the correlation between the growth timescales and pressure anisotropy is confirmed by the numerical simulations. These results reinforce the idea that pressure anisotropies—driven naturally in a turbulent collisionless medium, e.g., the intergalactic medium, could efficiently amplify the magnetic field in the early universe (post-recombination era), previous to the collapse of the first large-scale gravitational structures. This mechanism, though fast for the small-scale fields (∼kpc scales), is unable to provide relatively strong magnetic fields at large scales. Other mechanisms that were not accounted for here (e.g., collisional turbulence once instabilities are quenched, velocity shear, or gravitationally induced inflows of gas into galaxies and clusters) could operate afterward to build up large-scale coherent field structures in the long time evolution.

  4. In vitro amplification of ovine prions from scrapie-infected sheep from Great Britain reveals distinct patterns of propagation

    Directory of Open Access Journals (Sweden)

    Thorne Leigh

    2012-11-01

    Full Text Available Abstract Background Protein misfolding cyclic amplification (PMCA is a method that facilitates the detection of prions from many sources of transmissible spongiform encephalopathy (TSE. Sheep scrapie represents a unique diversity of prion disease agents in a range of susceptible PRNP genotypes. In this study PMCA was assessed on a range of Great Britain (GB sheep scrapie isolates to determine the applicability to veterinary diagnosis of ovine TSE. Results PrPSc amplification by protein misfolding cyclic amplification (PMCA was assessed as a diagnostic tool for field cases of scrapie. The technique was initially applied to thirty-seven isolates of scrapie from diverse geographical locations around GB, and involved sheep of various breeds and PRNP genotypes. All samples were amplified in either VRQ and/or ARQ PrPC substrate. For PrPSc from sheep with at least one VRQ allele, all samples amplified efficiently in VRQ PrPC but only PrPSc from ARH/VRQ sheep amplified in both substrates. PrPSc from ARQ/ARQ sheep displayed two amplification patterns, one that amplified in both substrates and one that only amplified in ARQ PrPC. These amplification patterns were consistent for a further 14/15 flock/farm mates of these sheep. Furthermore experimental scrapie strains SSBP1, Dawson, CH1641 and MRI were analysed. SSBP1 and Dawson (from VRQ/VRQ sheep amplified in VRQ but not ARQ substrate. MRI scrapie (from ARQ/ARQ sheep nor CH1641 did not amplify in ARQ or VRQ substrate; these strains required an enhanced PMCA method incorporating polyadenylic acid (poly(A to achieve amplification. Conclusions PrPsc from 52 classical scrapie GB field isolates amplified in VRQ or ARQ or both substrates and supports the use of PMCA as a rapid assay for the detection of a wide range of ovine classical scrapie infections involving multiple PRNP genotypes and scrapie strains.

  5. Quantum amplitude amplification algorithm: an explanation of availability bias

    OpenAIRE

    Franco, Riccardo

    2008-01-01

    In this article, I show that a recent family of quantum algorithms, based on the quantum amplitude amplification algorithm, can be used to describe a cognitive heuristic called availability bias. The amplitude amplification algorithm is used to define quantitatively the ease of a memory task, while the quantum amplitude estimation and the quantum counting algorithms to describe cognitive tasks such as estimating probability or approximate counting.

  6. Raman parametric generation of anti-Stokes radiation under amplification of an external Stokes signal

    Energy Technology Data Exchange (ETDEWEB)

    Grasiuk, A.Z.; Losev, L.L.; Lutsenko, A.P.; Sazonov, S.N. (Fizicheskii Institut, Moscow (USSR))

    1990-05-01

    Parametric generation of anti-Stokes radiation in a Raman amplifier was calculated and implemented experimentally. In the experiments, the external Stokes signal propagated at an angle to the pumping direction which corresponded to phase matching. It is shown that, in the amplification regime, the second harmonic radiation of an Nd laser (0.53 micron) in compressed (to about 20 atm) hydrogen can be converted into the first anti-Stokes component (0.43 micron) with efficiency of about 11 percent. 5 refs.

  7. Evaluation of techniques for human bone decalcification and amplification using sixteen STR markers

    Directory of Open Access Journals (Sweden)

    Ajay Balayan

    2015-03-01

    Full Text Available Efficient DNA extraction procedures, as well as accurate DNA amplification, are critical steps involved in the process of successful DNA analysis of skeletal samples. Unfortunately, at present there is no infallible method to recover DNA from highly degraded samples due to variations in DNA yield from larger bone fragments, which may be attributed to heterogeneity within bones. We evaluated two different protocols for bone decalcification in the DNA extraction procedure for bones. This study is important for analysis of challenging forensic samples.

  8. Terahertz amplification in RTD-gated HEMTs with a grating-gate wave coupling topology

    Energy Technology Data Exchange (ETDEWEB)

    Condori Quispe, Hugo O.; Sensale-Rodriguez, Berardi [The University of Utah, Salt Lake City, Utah 84112 (United States); Encomendero-Risco, Jimy J.; Xing, Huili Grace [University of Notre Dame, Notre Dame, Indiana 46556 (United States); Cornell University, Ithaca, New York 14853 (United States)

    2016-08-08

    We theoretically analyze the operation of a terahertz amplifier consisting of a resonant-tunneling-diode gated high-electron-mobility transistor (RTD-gated HEMT) in a grating-gate topology. In these devices, the key element enabling substantial power gain is the efficient coupling of terahertz waves into and out of plasmons in the RTD-gated HEMT channel, i.e., the gain medium, via the grating-gate itself, part of the active device, rather than by an external antenna structure as discussed in previous works, therefore potentially enabling terahertz amplification with associated power gains >40 dB.

  9. Theory of phase-mixing amplification in an optomechanical system

    Science.gov (United States)

    Ockeloen-Korppi, C. F.; Heikkilä, T. T.; Sillanpää, M. A.; Massel, F.

    2017-09-01

    The investigation of the ultimate limits imposed by quantum mechanics on amplification represents an important topic both on a fundamental level and from the perspective of potential applications. We discuss here a novel regime for bosonic linear amplifiers—beside phase-insensitive and phase-sensitive amplification—which we term here phase-mixing amplification. Furthermore, we show that phase-mixing amplification can be realised in a cavity optomechanical setup, constituted by a mechanical resonator which is dispersively coupled to an optomechanical cavity asymmetrically driven around both mechanical sidebands. While, in general, this amplifier is phase-mixing, for a suitable choice of parameters, the amplifier proposed here operates as a phase-sensitive amplifier. We show that both configurations allow amplification with an added noise below the quantum limit of (phase-insensitive) amplification in a parameter range compatible with current experiments in microwave circuit optomechanics. In particular, we show that introducing phase-mixing amplification typically allows for a significant reduction of the added noise.

  10. Targeting MET Amplification as a New Oncogenic Driver

    Energy Technology Data Exchange (ETDEWEB)

    Kawakami, Hisato [Department of Medical Oncology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511 (Japan); Okamoto, Isamu, E-mail: okamotoi@kokyu.med.kyushu-u.ac.jp [Department of Medical Oncology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511 (Japan); Center for Clinical and Translational Research, Kyushu University Hospital, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582 (Japan); Okamoto, Wataru [Department of Medical Oncology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511 (Japan); Division of Transrlational Research, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577 (Japan); Tanizaki, Junko [Department of Medical Oncology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511 (Japan); Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, HIM223, 450 Brookline Avenue, Boston, MA 02215 (United States); Nakagawa, Kazuhiko [Department of Medical Oncology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511 (Japan); Nishio, Kazuto [Department of Genome Biology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511 (Japan)

    2014-07-22

    Certain genetically defined cancers are dependent on a single overactive oncogene for their proliferation and survival, a phenomenon known as “oncogene addiction”. A new generation of drugs that selectively target such “driver oncogenes” manifests a clinical efficacy greater than that of conventional chemotherapy in appropriate genetically defined patients. MET is a proto-oncogene that encodes a receptor tyrosine kinase, and aberrant activation of MET signaling occurs in a subset of advanced cancers as result of various genetic alterations including gene amplification, polysomy, and gene mutation. Our preclinical studies have shown that inhibition of MET signaling either with the small-molecule MET inhibitor crizotinib or by RNA interference targeted to MET mRNA resulted in marked antitumor effects in cancer cell lines with MET amplification both in vitro and in vivo. Furthermore, patients with non-small cell lung cancer or gastric cancer positive for MET amplification have shown a pronounced clinical response to crizotinib. Accumulating preclinical and clinical evidence thus suggests that MET amplification is an “oncogenic driver” and therefore a valid target for treatment. However, the prevalence of MET amplification has not been fully determined, possibly in part because of the difficulty in evaluating gene amplification. In this review, we provide a rationale for targeting this genetic alteration in cancer therapy.

  11. Tumor hypoxia: Impact on gene amplification in glioblastoma.

    Science.gov (United States)

    Fischer, Ulrike; Radermacher, Jens; Mayer, Jens; Mehraein, Yasmin; Meese, Eckart

    2008-09-01

    Gene amplification is frequently found in human glioblastoma but the mechanisms driving amplifications remain to be elucidated. Hypoxia as hallmark of glioblastoma is known to be involved in the induction of fragile sites that are central to gene amplification. We analyzed the potential of hypoxia (pO2 0%) and mini hypoxia (pO2 5%) to induce fragile sites within a homogeneously staining region (HSR) at 12q14-15 in a glioblastoma cell line (TX3868). Treatment of cells by hypoxia or by mini hypoxia induced double minutes (DMs) and caused breakage of the HSR structure at 12q14-15, suggesting a novel hypoxia inducible fragile site on 12q. Treatment with aphidicolin, a known fragile site inducer, indicates that the hypoxia inducible fragile site is a common fragile site. Reintegration of amplified sequences and occurrence of anaphase-bridge-like structures shows that mini hypoxia and hypoxia are able to initiate amplification processes in human glioblastoma cells. Hypoxia as known tumor microenvironment factor is crucial for the development of amplifications in glioblastoma. The identification and characterization of novel common fragile sites induced by hypoxia will improve the understanding of mechanisms underlying amplifications in glioblastoma.

  12. A novel power amplification scheme for nuclear magnetic resonance/nuclear quadrupole resonance systems.

    Science.gov (United States)

    Zhang, Xinwang; Schemm, Nathan; Balkır, Sina

    2011-03-01

    Nuclear magnetic resonance (NMR) and nuclear quadrupole resonance (NQR)-based chemical analysis systems have been widely utilized in various areas such as medicine, security, and academic research. In these applications, the power amplifier stage plays a key role in generating the required oscillating magnetic fields within a radio frequency coil that serves as the probe. However, the bulky size and relatively low efficiency of the traditional power amplification schemes employed present a bottleneck for the realization of compact sized and portable NMR and NQR systems. To address this problem, this work presents a class D voltage-switching power amplification scheme with novel fast-start and fast-stop functions that are suitable for generating ideal NMR and NQR excitation signals. Compared to the traditional analog power amplifiers (PAs), the proposed switched-mode PA can achieve significant improvement on the power efficiency as well as the physical volume. A PA circuit for portable NQR-based explosive detection systems has been designed and built using the proposed scheme with 1 kW possible maximum output power and 10 MHz maximum operating frequency. Test results show that the presented PA achieves more than 60% measured efficiency within a highly compact volume while sustaining fast start and stop of excitation signals in the order of microseconds.

  13. ASAP: Amplification, sequencing & annotation of plastomes

    Directory of Open Access Journals (Sweden)

    Folta Kevin M

    2005-12-01

    Full Text Available Abstract Background Availability of DNA sequence information is vital for pursuing structural, functional and comparative genomics studies in plastids. Traditionally, the first step in mining the valuable information within a chloroplast genome requires sequencing a chloroplast plasmid library or BAC clones. These activities involve complicated preparatory procedures like chloroplast DNA isolation or identification of the appropriate BAC clones to be sequenced. Rolling circle amplification (RCA is being used currently to amplify the chloroplast genome from purified chloroplast DNA and the resulting products are sheared and cloned prior to sequencing. Herein we present a universal high-throughput, rapid PCR-based technique to amplify, sequence and assemble plastid genome sequence from diverse species in a short time and at reasonable cost from total plant DNA, using the large inverted repeat region from strawberry and peach as proof of concept. The method exploits the highly conserved coding regions or intergenic regions of plastid genes. Using an informatics approach, chloroplast DNA sequence information from 5 available eudicot plastomes was aligned to identify the most conserved regions. Cognate primer pairs were then designed to generate ~1 – 1.2 kb overlapping amplicons from the inverted repeat region in 14 diverse genera. Results 100% coverage of the inverted repeat region was obtained from Arabidopsis, tobacco, orange, strawberry, peach, lettuce, tomato and Amaranthus. Over 80% coverage was obtained from distant species, including Ginkgo, loblolly pine and Equisetum. Sequence from the inverted repeat region of strawberry and peach plastome was obtained, annotated and analyzed. Additionally, a polymorphic region identified from gel electrophoresis was sequenced from tomato and Amaranthus. Sequence analysis revealed large deletions in these species relative to tobacco plastome thus exhibiting the utility of this method for structural and

  14. Ultrasensitive detection of scrapie prion protein derived from ARQ and AHQ homozygote sheep by interspecies in vitro amplification.

    Science.gov (United States)

    Murayama, Yuichi; Imamura, Morikazu; Masujin, Kentaro; Shimozaki, Noriko; Yoshioka, Miyako; Mohri, Shirou; Yokoyama, Takashi

    2012-08-01

    Prions, infectious agents causing TSEs, are composed primarily of the pathogenic form (PrP(Sc)) of the PrP(C). The susceptibility of sheep to scrapie is determined by polymorphisms in the coding region of the PRNP, mainly at codons 136, 154, and 171. The efficiency of in vitro amplification of sheep PrP(Sc) seems to be linked also to the PrP genotype. PrP(Sc) derived from sheep with V(136)R(154)Q(171)-associated genotypes can be amplified efficiently by PMCA in the presence of additional polyanion such as poly A, but there are no reports that cite ultrasensitive detection of PrP(Sc) derived from sheep of other PrP genotypes. We report here that sheep PrP(Sc) derived from ARQ and AHQ homozygotes was amplified efficiently by serial PMCA using mouse brain homogenate as PrP(C) substrate. ARQ/ARQ PrP(Sc) was detected in infected brain homogenates diluted up to 10(-10) after five rounds of amplification, and AHQ/AHQ PrP(Sc) was detected in samples diluted up to 10(-8) after four rounds of amplification. On the other hand, amplification of PrP(Sc) from VRQ/ARQ sheep seemed to be less efficient under the experimental conditions used. The interspecies PMCA developed in this study may be useful in the detailed analysis of PrP(Sc) distribution in classical scrapie-infected ARQ and AHQ homozygote sheep. © 2012 The Societies and Blackwell Publishing Asia Pty Ltd.

  15. Lack of correlation between reaction speed and analytical sensitivity in isothermal amplification reveals the value of digital methods for optimization: validation using digital real-time RT-LAMP.

    Science.gov (United States)

    Khorosheva, Eugenia M; Karymov, Mikhail A; Selck, David A; Ismagilov, Rustem F

    2016-01-29

    In this paper, we asked if it is possible to identify the best primers and reaction conditions based on improvements in reaction speed when optimizing isothermal reactions. We used digital single-molecule, real-time analyses of both speed and efficiency of isothermal amplification reactions, which revealed that improvements in the speed of isothermal amplification reactions did not always correlate with improvements in digital efficiency (the fraction of molecules that amplify) or with analytical sensitivity. However, we observed that the speeds of amplification for single-molecule (in a digital device) and multi-molecule (e.g. in a PCR well plate) formats always correlated for the same conditions. Also, digital efficiency correlated with the analytical sensitivity of the same reaction performed in a multi-molecule format. Our finding was supported experimentally with examples of primer design, the use or exclusion of loop primers in different combinations, and the use of different enzyme mixtures in one-step reverse-transcription loop-mediated amplification (RT-LAMP). Our results show that measuring the digital efficiency of amplification of single-template molecules allows quick, reliable comparisons of the analytical sensitivity of reactions under any two tested conditions, independent of the speeds of the isothermal amplification reactions. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Transmission comparison of ultra-long Raman fibre laser based amplification with first and dual order Raman amplification using 10×118 Gbit/s DP-QPSK

    OpenAIRE

    Tan, Mingming; Rosa, Pawel; Phillips, Ian D.; Stephens, M.F.C.; Sygletos, Stylianos; Ellis, Andrew; Harper, Paul

    2014-01-01

    Experimental investigations of 10×118 Gbit/s DP-QPSK WDM transmission using three types of distributed Raman amplification techniques are presented. Novel ultra-long Raman fibre laser based amplification with second order counter-propagated pumping is compared with conventional first order and dual order counter-pumped Raman amplification. We demonstrate that URFL based amplification can extend the transmission reach up to a distance of 7520 km in comparison with 5010 km and 6180 km using fir...

  17. Frequency of Drug Resistance Gene Amplification in Clinical Leishmania Strains

    Directory of Open Access Journals (Sweden)

    C. Mary

    2010-01-01

    Full Text Available Experimental studies about Leishmania resistance to metal and antifolates have pointed out that gene amplification is one of the main mechanisms of drug detoxification. Amplified genes code for adenosine triphosphate-dependent transporters (multidrug resistance and P-glycoproteins P, enzymes involved in trypanothione pathway, particularly gamma glutamyl cysteine synthase, and others involved in folates metabolism, such as dihydrofolate reductase and pterine reductase. The aim of this study was to detect and quantify the amplification of these genes in clinical strains of visceral leishmaniasis agents: Leishmania infantum, L. donovani, and L. archibaldi. Relative quantification experiments by means of real-time polymerase chain reaction showed that multidrug resistance gene amplification is the more frequent event. For P-glycoproteins P and dihydrofolate reductase genes, level of amplification was comparable to the level observed after in vitro selection of resistant clones. Gene amplification is therefore a common phenomenon in wild strains concurring to Leishmania genomic plasticity. This finding, which corroborates results of experimental studies, supports a better understanding of metal resistance selection and spreading in endemic areas.

  18. Modeling the amplification dynamics of human alu retrotransposons.

    Directory of Open Access Journals (Sweden)

    2005-09-01

    Full Text Available Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed a computer simulation that incorporates several known aspects of primate Alu retrotransposon biology and accommodates sampling effects resulting from the methods by which mobile elements are typically discovered and characterized. By modeling a number of amplification scenarios and comparing simulation-generated expectations to empirical data gathered from existing Alu subfamilies, we were able to statistically reject a number of amplification scenarios for individual subfamilies, including that of a rapid expansion or explosion of Alu amplification at the time of human-chimpanzee divergence.

  19. Modeling the amplification dynamics of human Alu retrotransposons.

    Directory of Open Access Journals (Sweden)

    Dale J Hedges

    2005-09-01

    Full Text Available Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed a computer simulation that incorporates several known aspects of primate Alu retrotransposon biology and accommodates sampling effects resulting from the methods by which mobile elements are typically discovered and characterized. By modeling a number of amplification scenarios and comparing simulation-generated expectations to empirical data gathered from existing Alu subfamilies, we were able to statistically reject a number of amplification scenarios for individual subfamilies, including that of a rapid expansion or explosion of Alu amplification at the time of human-chimpanzee divergence.

  20. Loopback rolling circle amplification for ultrasensitive detection of Kras gene.

    Science.gov (United States)

    Xu, Huo; Wu, Dong; Jiang, Yifan; Zhang, Rongbo; Wu, Qingzheng; Liu, Yiyun; Li, Feng; Wu, Zai-Sheng

    2017-03-01

    Mutations in Kras gene may be used as a diagnostic marker and a target for treatment of the broad spectrum of human cancers. In this study, we developed a new class of amplification assay, double-hairpin molecular beacon (DHMB)-based cascade rolling circle amplification (RCA), for ultrasensitive and selective detection of Kras gene in a homogenous solution. Specifically, target DNA can hybridize with DHMB and activate cyclical target strand-displacement polymerization (CTDP) and nicking-mediated strand-displacement polymerization (NMDP). The resulting nicked/displaced fragments substantially outnumber target DNA and cause the cascade rolling circle amplification (C-RCA) and nicked fragment-induced strand-displacement polymerization (NFDP). Even if four amplification processes are designed, only DHMB, padlock probe and polymerization primer are involved. Under optimized conditions, this screening system exhibits a linear range of 5 orders of magnitude (from 100fM to 20nM), and the detection limit is down to 16fM. Moreover, the developed biosensing system offers a high assay specificity for perfectly matched target DNA, and the measured data from practical samples demonstrated the potential application in the cancer diagnoses. As a proof-of-concept genetic assay, the novel signaling strategy, as well as desirable analytical capability, would significantly benefit the development of versatile amplification gene profiling platforms, revealing great promise in biological studies and medical diagnostics. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Isolation of eicosapentaenoic acid-producing fungi from soil based on polymerase chain reaction amplification.

    Science.gov (United States)

    Hu, Jing-Rong; Zhou, Peng-Peng; Zhu, Yuan-Min; Ren, Liang; Yu, Long-Jiang

    2011-01-01

    A method was developed for rapid screening and isolation of eicosapentaenoic acid (EPA)-producing soil fungi through polymerase chain reaction (PCR) amplification. Genes coding for delta6 fatty acid desaturase and delta5 fatty acid desaturase were used as molecular markers for screening these EPA-producing fungi from soil. Three out of 65 soil fungi gave positive results through PCR amplification. Two out of these three strains were found to produce EPA when they had grown in 80 ml potato/dextrose liquid medium at (25 +/- 1) degrees C for 144 h. The EPA yields were 215.81 mg 1(-1) and 263.80 mg 1(-1), respectively. The other positive strain was detected to produce arachidonic acid (AA). This study indicates that molecular detection of genes encoding delta6 and delta5 desaturases is an efficient method for primary screening of EPA- or its related polyunsaturated fatty acids (PuFAs)-producing fungi, which can improve the screening efficiency prominently.

  2. Determining Parameters for Images Amplification by Pulses Interpolation

    Directory of Open Access Journals (Sweden)

    Morera-Delfín Leandro

    2015-01-01

    Full Text Available This paper presents the implementation of a method for image samples interpolation based on a physical scanning model. It uses the theory to take digital image samples and to perform an implementation of such mechanism through software. This allows us to get the appropriate parameters for the images amplification using a truncated sampler arrangement. The shown process copies the physical model of image acquisition in order to incorporate the required samples for the amplification. This process is useful in the reconstruction of details in low resolution images and for images compression. The proposed method studies the conservation of high frequency in the high resolution plane for the generation of the amplification kernel. A new way of direct application of the physical model for scanning images in analytic mode is presented.

  3. Current Amplification Characteristics of BJT on Fast Neutron Irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, Sung Ho; Sun, Gwang Min; Baek, Hani [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2016-10-15

    BJT (Bipolar Junction Transistor) is a three-terminal device with an important feature in that the current through two terminals can be controlled by small changes we make in the current or voltage at the third terminal. This control feature allows us to amplify small AC signals or to switch the device from an on state and off state and back. Fast neutron irradiation incurs lattice damage in bulk Si. The recombination rate of minority carriers and register are increased by the lattice damage. This study will investigate the current amplification characteristics of a pnp Si BJT through fast neutron irradiation experiments. In this paper, the current amplification characteristics of a pnp Si BJT were investigated for fast neutron irradiation. The experimental results show that base-tocollector current amplification ratio is decreased with an increase in the fast neutron irradiation. These indicate that the lattice damage caused by fast neutron irradiation increases the recombination rate of minority carriers and resistor.

  4. Multi-chamber nucleic acid amplification and detection device

    Energy Technology Data Exchange (ETDEWEB)

    Dugan, Lawrence

    2017-10-25

    A nucleic acid amplification and detection device includes an amplification cartridge with a plurality of reaction chambers for containing an amplification reagent and a visual detection reagent, and a plurality of optically transparent view ports for viewing inside the reaction chambers. The cartridge also includes a sample receiving port which is adapted to receive a fluid sample and fluidically connected to distribute the fluid sample to the reaction chamber, and in one embodiment, a plunger is carried by the cartridge for occluding fluidic communication to the reaction chambers. The device also includes a heating apparatus having a heating element which is activated by controller to generate heat when a trigger event is detected. The heating apparatus includes a cartridge-mounting section which positioned a cartridge in thermal communication with the heating element so that visual changes to the contents of the reaction chambers are viewable through the view ports.

  5. A geostatistical approach to mapping site response spectral amplifications

    Science.gov (United States)

    Thompson, E.M.; Baise, L.G.; Kayen, R.E.; Tanaka, Y.; Tanaka, H.

    2010-01-01

    If quantitative estimates of the seismic properties do not exist at a location of interest then the site response spectral amplifications must be estimated from data collected at other locations. Currently, the most common approach employs correlations of site class with maps of surficial geology. Analogously, correlations of site class with topographic slope can be employed where the surficial geology is unknown. Our goal is to identify and validate a method to estimate site response with greater spatial resolution and accuracy for regions where additional effort is warranted. This method consists of three components: region-specific data collection, a spatial model for interpolating seismic properties, and a theoretical method for computing spectral amplifications from the interpolated seismic properties. We consider three spatial interpolation schemes: correlations with surficial geology, termed the geologic trend (GT), ordinary kriging (OK), and kriging with a trend (KT). We estimate the spectral amplifications from seismic properties using the square root of impedance method, thereby linking the frequency-dependent spectral amplifications to the depth-dependent seismic properties. Thus, the range of periods for which this method is applicable is limited by the depth of exploration. A dense survey of near-surface S-wave slowness (Ss) throughout Kobe, Japan shows that the geostatistical methods give more accurate estimates of Ss than the topographic slope and GT methods, and the OK and KT methods perform equally well. We prefer the KT model because it can be seamlessly integrated with geologic maps that cover larger regions. Empirical spectral amplifications show that the region-specific data achieve more accurate estimates of observed median short-period amplifications than the topographic slope method. ?? 2010 Elsevier B.V.

  6. Identification of Genetic Elements Associated with EPSPS Gene Amplification

    Science.gov (United States)

    Gaines, Todd A.; Wright, Alice A.; Molin, William T.; Lorentz, Lothar; Riggins, Chance W.; Tranel, Patrick J.; Beffa, Roland; Westra, Philip; Powles, Stephen B.

    2013-01-01

    Weed populations can have high genetic plasticity and rapid responses to environmental selection pressures. For example, 100-fold amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene evolved in the weed species Amaranthus palmeri to confer resistance to glyphosate, the world’s most important herbicide. However, the gene amplification mechanism is unknown. We sequenced the EPSPS gene and genomic regions flanking EPSPS loci in A. palmeri, and searched for mobile genetic elements or repetitive sequences. The EPSPS gene was 10,229 bp, containing 8 exons and 7 introns. The gene amplification likely proceeded through a DNA-mediated mechanism, as introns exist in the amplified gene copies and the entire amplified sequence is at least 30 kb in length. Our data support the presence of two EPSPS loci in susceptible (S) A. palmeri, and that only one of these was amplified in glyphosate-resistant (R) A. palmeri. The EPSPS gene amplification event likely occurred recently, as no sequence polymorphisms were found within introns of amplified EPSPS copies from R individuals. Sequences with homology to miniature inverted-repeat transposable elements (MITEs) were identified next to EPSPS gene copies only in R individuals. Additionally, a putative Activator (Ac) transposase and a repetitive sequence region were associated with amplified EPSPS genes. The mechanism controlling this DNA-mediated amplification remains unknown. Further investigation is necessary to determine if the gene amplification may have proceeded via DNA transposon-mediated replication, and/or unequal recombination between different genomic regions resulting in replication of the EPSPS gene. PMID:23762434

  7. Photoacoustic remote sensing microscopy with lock-in amplification

    Science.gov (United States)

    Shi, Wei; Hajireza, Parsin; Bell, Kevan; Zemp, Roger

    2017-03-01

    High sensitive detection with lock-in amplification can provide high signal noise ratio even when noise is in orders of magnitude higher than the signal. Here we report to combine lock-in amplification with a novel photoacoustic remote sensing (PARS) technology to achieve high resolution, high contrast, all optical non-contact photoacoustic imaging at depth beyond optical scattering limitation. We demonstrate phantom measurements from PARS with lock-in technology were several orders of magnitude more sensitive than those from PARS with the broadband detection techniques.

  8. Methods for microbial DNA extraction from soil for PCR amplification

    Directory of Open Access Journals (Sweden)

    Yeates C

    1998-01-01

    Full Text Available Amplification of DNA from soil is often inhibited by co-purified contaminants. A rapid, inexpensive, large-scale DNA extraction method involving minimal purification has been developed that is applicable to various soil types (1. DNA is also suitable for PCR amplification using various DNA targets. DNA was extracted from 100g of soil using direct lysis with glass beads and SDS followed by potassium acetate precipitation, polyethylene glycol precipitation, phenol extraction and isopropanol precipitation. This method was compared to other DNA extraction methods with regard to DNA purity and size.

  9. Digital laser mode amplification using ND: YAG amplifier

    CSIR Research Space (South Africa)

    Bell, Teboho

    2016-07-01

    Full Text Available amplification using Nd: YAG amplifier T. Bell1,2,* , & S. Ngcobo1 1CSIR-NLC, PO Box 395, Pretoria 0001, RSA. 2UKZN, Westville Private Bag X 54001, Durban 4000, RSA. *Email: tbell@csir.co.za ABSTRACT In this work we demonstrate the output power amplification... ranging from white to black, in 256 levels (8-bit encoding). . was used to measure the amplified LG beam power. RESULTS The seed intensity profiles of the input LGp,l modes are shown in Fig. 3(a). The amplified seed intensity profiles are also illustrated...

  10. Strongly coupled stimulated Brillouin amplification in pump-ionizing plasma

    Science.gov (United States)

    Peng, H.; Wu, Z. H.; Zuo, Y. L.; Zhou, K. N.; Wang, X. D.; Li, Q.; Zhu, H. Y.; Su, J. Q.

    2018-02-01

    Laser amplification based on strongly coupled stimulated Brillouin scattering in plasma is investigated. The pump and seed are at the same wavelength of 800 nm and the same duration of 3.5 ps, but with a different intensity. The plasma is produced by the front part of the pump via tunnel ionization from hydrogen. The hydrogen is fully ionized to eliminate small-scale density fluctuations in the plasma, so the transmission level of the seed is enhanced to 22%, and a relative amplification factor of 6 is obtained.

  11. Phase-Fitted and Amplification-Fitted Higher Order Two-Derivative Runge-Kutta Method for the Numerical Solution of Orbital and Related Periodical IVPs

    Directory of Open Access Journals (Sweden)

    N. A. Ahmad

    2017-01-01

    Full Text Available A phase-fitted and amplification-fitted two-derivative Runge-Kutta (PFAFTDRK method of high algebraic order for the numerical solution of first-order Initial Value Problems (IVPs which possesses oscillatory solutions is derived. We present a sixth-order four-stage two-derivative Runge-Kutta (TDRK method designed using the phase-fitted and amplification-fitted property. The stability of the new method is analyzed. The numerical experiments are carried out to show the efficiency of the derived methods in comparison with other existing Runge-Kutta (RK methods.

  12. Amplification of nonspecific products in quantitative polymerase chain reactions (qPCR

    Directory of Open Access Journals (Sweden)

    Adrián Ruiz-Villalba

    2017-12-01

    Full Text Available Quantitative PCR allows the precise measurement of DNA concentrations and is generally considered to be straightforward and trouble free. However, a survey with 93 validated assays for genes in the Wnt-pathway showed that the amplification of nonspecific products occurs frequently and is unrelated to Cq or PCR efficiency values. Titration experiments showed that the occurrence of low and high melting temperature artifacts was shown to be determined by annealing temperature, primer concentration and cDNA input. To explore the range of input variations that occur in the normal use of the Cre assay these conditions were mimicked in a complete two-way design of template −plasmid DNA- and non-template −mouse cDNA- concentrations. These experiments showed that the frequency of the amplification of the correct product and the artifact, as well as the valid quantification of the correct product, depended on the concentration of the non-template cDNA. This finding questions the interpretation of dilution series in which template as well as non-template concentrations are simultaneously decreasing. Repetition of this cDNA concentration experiment with other templates revealed that exact reproduction qPCR experiments was affected by the time it takes to complete the pipetting of a qPCR plate. Long bench times were observed to lead to significantly more artifacts. However, the measurement of artifact-associated fluorescence can be avoided by inclusion of a small heating step after the elongation phase in the amplification protocol. Taken together, this trouble-shooting journey showed that reliability and reproducibility of qPCR experiments not only depends on standardization and reporting of the biochemistry and technical aspects but also on hitherto neglected factors as sample dilution and waiting times in the laboratory work flow. Keywords: RT-qPCR, Melting curve analysis, Reaction parameters, Artifacts

  13. High-power X- and Ka-band Gallium Nitride Amplifiers with Exceptional Efficiency Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Achieving very high-power amplification with maximum efficiency at X- and Ka-band is challenging using solid-state technology. Gallium Arsenide (GaAs) has been the...

  14. Optimization and validation of a fast amplification protocol for AmpFlSTR® Profiler Plus® for rapid forensic human identification.

    Science.gov (United States)

    Laurin, Nancy; Frégeau, Chantal

    2012-01-01

    The goal of this work was to optimize and validate a fast amplification protocol for the multiplex amplification of the STR loci included in AmpFlSTR(®) Profiler Plus(®) to expedite human DNA identification. By modifying the cycling conditions and by combining the use of a DNA polymerase optimized for high speed PCR (SpeedSTAR™ HS) and a more efficient thermal cycler instrument (Bio-RAD C1000™), we were able to reduce the amplification process from 4h to 26 min. No modification to the commercial AmpFlSTR(®) Profiler Plus(®) primer mix was required. When compared to the current Royal Canadian Mounted Police (RCMP) amplification protocol, no differences with regards to specificity, sensitivity, heterozygote peak height ratios and overall profile balance were noted. Moreover, complete concordance was obtained with profiles previously generated with the standard amplification protocol and minor alleles in mixture samples were reliably typed. An increase in n-4 stutter ratios (2.2% on average for all loci) was observed for profiles amplified with the fast protocol compared to the current procedure. Our results document the robustness of this rapid amplification protocol for STR profiling using the AmpFlSTR(®) Profiler Plus(®) primer set and demonstrate that comparable data can be obtained in substantially less time. This new approach could provide an alternative option to current multiplex STR typing amplification protocols in order to increase throughput or expedite time-sensitive cases. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  15. A novel approach for evaluating the performance of real time quantitative loop-mediated isothermal amplification-based methods.

    Science.gov (United States)

    Nixon, Gavin J; Svenstrup, Helle F; Donald, Carol E; Carder, Caroline; Stephenson, Judith M; Morris-Jones, Stephen; Huggett, Jim F; Foy, Carole A

    2014-12-01

    Molecular diagnostic measurements are currently underpinned by the polymerase chain reaction (PCR). There are also a number of alternative nucleic acid amplification technologies, which unlike PCR, work at a single temperature. These 'isothermal' methods, reportedly offer potential advantages over PCR such as simplicity, speed and resistance to inhibitors and could also be used for quantitative molecular analysis. However there are currently limited mechanisms to evaluate their quantitative performance, which would assist assay development and study comparisons. This study uses a sexually transmitted infection diagnostic model in combination with an adapted metric termed isothermal doubling time (IDT), akin to PCR efficiency, to compare quantitative PCR and quantitative loop-mediated isothermal amplification (qLAMP) assays, and to quantify the impact of matrix interference. The performance metric described here facilitates the comparison of qLAMP assays that could assist assay development and validation activities.

  16. A novel approach for evaluating the performance of real time quantitative loop-mediated isothermal amplification-based methods

    Directory of Open Access Journals (Sweden)

    Gavin J. Nixon

    2014-12-01

    Full Text Available Molecular diagnostic measurements are currently underpinned by the polymerase chain reaction (PCR. There are also a number of alternative nucleic acid amplification technologies, which unlike PCR, work at a single temperature. These ‘isothermal’ methods, reportedly offer potential advantages over PCR such as simplicity, speed and resistance to inhibitors and could also be used for quantitative molecular analysis. However there are currently limited mechanisms to evaluate their quantitative performance, which would assist assay development and study comparisons. This study uses a sexually transmitted infection diagnostic model in combination with an adapted metric termed isothermal doubling time (IDT, akin to PCR efficiency, to compare quantitative PCR and quantitative loop-mediated isothermal amplification (qLAMP assays, and to quantify the impact of matrix interference. The performance metric described here facilitates the comparison of qLAMP assays that could assist assay development and validation activities.

  17. Active amplification in insect ears: mechanics, models and molecules.

    Science.gov (United States)

    Mhatre, Natasha

    2015-01-01

    Active amplification in auditory systems is a unique and sophisticated mechanism that expends energy in amplifying the mechanical input to the auditory system, to increase its sensitivity and acuity. Although known for decades from vertebrates, active auditory amplification was only discovered in insects relatively recently. It was first discovered from two dipterans, mosquitoes and flies, who hear with their light and compliant antennae; only recently has it been observed in the stiffer and heavier tympanal ears of an orthopteran. The discovery of active amplification in two distinct insect lineages with independently evolved ears, suggests that the trait may be ancestral, and other insects may possess it as well. This opens up extensive research possibilities in the field of acoustic communication, not just in auditory biophysics, but also in behaviour and neurobiology. The scope of this review is to establish benchmarks for identifying the presence of active amplification in an auditory system and to review the evidence we currently have from different insect ears. I also review some of the models that have been posited to explain the mechanism, both from vertebrates and insects and then review the current mechanical, neurobiological and genetic evidence for each of these models.

  18. mediated isothermal amplification of the pat selectable marker gene

    African Journals Online (AJOL)

    ajl yemi

    2011-11-28

    Nov 28, 2011 ... *Corresponding author. E-mail: wuzhongyi@yahoo.com. Tel: 86-10-51503668; Fax: 86-10-51503980. Abbreviations: LAMP, Loop-mediated isothermal amplification;. PCR, polymerase chain reaction; FIP, forward inner primer;. BIP, backward inner primer; GMOs, genetically modified organisms; CTAB, cetyl ...

  19. Phase-shift amplification for precision measurements without nonclassical states

    OpenAIRE

    Luis Aina, Alfredo

    2002-01-01

    We propose a practical arrangement that allows one to reach the Heisenberg limit in precision phase-shift measurements. This is achieved via phase-shift amplification. The arrangement we propose is based on experimental processes already carried out and does not require the use of any special quantum state.

  20. Factors Affecting the Benefits of High-Frequency Amplification

    Science.gov (United States)

    Horwitz, Amy R.; Ahlstrom, Jayne B.; Dubno, Judy R.

    2008-01-01

    Purpose: This study was designed to determine the extent to which high-frequency amplification helped or hindered speech recognition as a function of hearing loss, gain-frequency response, and background noise. Method: Speech recognition was measured monaurally under headphones for nonsense syllables low-pass filtered in one-third-octave steps…

  1. Recent Arctic amplification and extreme mid-latitude weather

    NARCIS (Netherlands)

    Cohen, Judah; Screen, James A.; Furtado, Jason C.; Barlow, Mathew; Whittleston, David; Coumou, Dim; Francis, Jennifer; Dethloff, Klaus; Entekhabi, Dara; Overland, James; Jones, Justin

    2014-01-01

    The Arctic region has warmed more than twice as fast as the global average-a phenomenon known as Arctic amplification. The rapid Arctic warming has contributed to dramatic melting of Arctic sea ice and spring snow cover, at a pace greater than that simulated by climate models. These profound changes

  2. Whole genome amplification: Use of advanced isothermal method

    African Journals Online (AJOL)

    Yomi

    2010-12-29

    Dec 29, 2010 ... Whole genome amplification: Use of advanced isothermal method. Sima Moghaddaszadeh Ahrabi1, Safar Farajnia2,3*, Ghodratollah Rahimi-Mianji4, Soheila. Montazer Saheb3 ... Moreover, application of high fidelity and high possessive DNA ..... between I-PEP with MDA by using serial dilutions of.

  3. New Technologies in Amplification: Applications to the Pediatric Population.

    Science.gov (United States)

    Kopun, Judy

    1995-01-01

    Discussion of technological advances in amplification for children with hearing impairments focuses on the advantages and limitations of fitting children with devices that have features such as dynamic-range compression, multiband signal processing, multimemory capability, digital feedback reduction, and frequency transposition. (Author/DB)

  4. Cross-genus amplification and characterisation of microsatellite loci ...

    African Journals Online (AJOL)

    There was no evidence of linkage disequilibrium among pairs of loci, or of deviation from Hardy-Weinberg equilibrium. These six loci were informative in studies of population genetic structure of C. pumilus sensu lato. Keywords: Bats, Chaerephon pumilus, Chiroptera, microsatellites, Molossidae, cross-genus amplification

  5. Whole genome amplification: Use of advanced isothermal method ...

    African Journals Online (AJOL)

    Laboratory method for amplifying genomic deoxyribonucleic acid (DNA) samples aiming to generate more amounts and sufficient quantity DNA for subsequent specific analysis is named whole genome amplification (WGA). This method is only way to increase input material from few cells and limited DNA contents.

  6. The rolling circle amplification and next generation sequencing ...

    African Journals Online (AJOL)

    This is an innovative approach that utilizes the robustness of the bacteriophage phi29 DNA polymerase used in circle amplification, together with deep sequencing using Illumina Miseq and bioinformatics to assess population diversity of begomoviruses in naturally infected cassava. The approach is suitable for detecting ...

  7. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification.

    Science.gov (United States)

    Berry, David; Ben Mahfoudh, Karim; Wagner, Michael; Loy, Alexander

    2011-11-01

    "Barcode-tagged" PCR primers used for multiplex amplicon sequencing generate a thus-far-overlooked amplification bias that produces variable terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing data from the same environmental DNA template. We propose a simple two-step PCR approach that increases reproducibility and consistently recovers higher genetic diversity in pyrosequencing libraries.

  8. Algebraic Geometry of Error Amplification: the Prony leaves

    OpenAIRE

    Batenkov, Dmitry; Goldman, Gil; Salman, Yehonatan; Yomdin, Yosef

    2017-01-01

    We provide an overview of some results on the "geometry of error amplification" in solving Prony system, in situations where the nodes near-collide. It turns out to be governed by the "Prony foliations" $S_q$, whose leaves are "equi-moment surfaces" in the parameter space. Next, we prove some new results concerning explicit parametrization of the Prony leaves.

  9. Parametric amplification in a micro Coriolis mass flow sensor

    NARCIS (Netherlands)

    Groenesteijn, Jarno; Droogendijk, H.; Wiegerink, Remco J.; Lammerink, Theodorus S.J.; Lötters, Joost Conrad; Sanders, Remco G.P.; Krijnen, Gijsbertus J.M.

    2014-01-01

    We report on the application of parametric amplification to a micro Coriolis mass flow sensor. We demonstrate that this mechanism allows for reduction of the system's power dissipation while retaining sensitivity to flow. By reducing this power dissipation, less heat will be transferred to the fluid

  10. Graphene Ambipolar Nanoelectronics for High Noise Rejection Amplification.

    Science.gov (United States)

    Liu, Che-Hung; Chen, Qi; Liu, Chang-Hua; Zhong, Zhaohui

    2016-02-10

    In a modern wireless communication system, signal amplification is critical for overcoming losses during multiple data transformations/processes and long-distance transmission. Common mode and differential mode are two fundamental amplification mechanisms, and they utilize totally different circuit configurations. In this paper, we report a new type of dual-gate graphene ambipolar device with capability of operating under both common and differential modes to realize signal amplification. The signal goes through two stages of modulation where the phase of signal can be individually modulated to be either in-phase or out-of-phase at two stages by exploiting the ambipolarity of graphene. As a result, both common and differential mode amplifications can be achieved within one single device, which is not possible in the conventional circuit configuration. In addition, a common-mode rejection ratio as high as 80 dB can be achieved, making it possible for low noise circuit application. These results open up new directions of graphene-based ambipolar electronics that greatly simplify the RF circuit complexity and the design of multifunction device operation.

  11. Whole genome amplification and its impact on CGH array profiles

    Directory of Open Access Journals (Sweden)

    Meldrum Cliff

    2008-07-01

    Full Text Available Abstract Background Some array comparative genomic hybridisation (array CGH platforms require a minimum of micrograms of DNA for the generation of reliable and reproducible data. For studies where there are limited amounts of genetic material, whole genome amplification (WGA is an attractive method for generating sufficient quantities of genomic material from miniscule amounts of starting material. A range of WGA methods are available and the multiple displacement amplification (MDA approach has been shown to be highly accurate, although amplification bias has been reported. In the current study, WGA was used to amplify DNA extracted from whole blood. In total, six array CGH experiments were performed to investigate whether the use of whole genome amplified DNA (wgaDNA produces reliable and reproducible results. Four experiments were conducted on amplified DNA compared to unamplified DNA and two experiments on unamplified DNA compared to unamplified DNA. Findings All the experiments involving wgaDNA resulted in a high proportion of losses and gains of genomic material. Previously, amplification bias has been overcome by using amplified DNA in both the test and reference DNA. Our data suggests that this approach may not be effective, as the gains and losses introduced by WGA appears to be random and are not reproducible between different experiments using the same DNA. Conclusion In light of these findings, the use of both amplified test and reference DNA on CGH arrays may not provide an accurate representation of copy number variation in the DNA.

  12. Detection of M. tuberculosis DNA using thermophilic strand displacement amplification.

    Science.gov (United States)

    Spargo, C A; Fraiser, M S; Van Cleve, M; Wright, D J; Nycz, C M; Spears, P A; Walker, G T

    1996-08-01

    Strand Displacement Amplification (SDA) is an isothermal, in vitro method of amplifying DNA that is based upon the combined action of a DNA polymerase and restriction enzyme. Previously, a form of SDA was developed which utilizes the exonuclease deficient Klenow fragment of E. coli polymerase I (exo Klenow) and the restriction enzyme HincII to achieve 10(8)-fold amplification in 2 h at 37 degrees C (Walker, G.T., 1993, PCR Methods and Applications 3; 1-6). A new thermophilic form of SDA is reported here which uses a restriction endonuclease from Bacillus stearothermophilus (BsoBI) and a 5'-->3' exonuclease deficient polymerase from Bacillus caldotenax (exo Bca). SDA was used to amplify DNA from Mycobacterium tuberculosis. An amplification factor of 10(10)-fold was achieved after 15 min of SDA at 60 degrees C. The new thermophilic system is much more specific than the previous mesophilic system as evidenced by a dramatic decrease in background amplification products. Thermophilic SDA was also optimized with dUTP substituted for TTP to enable amplicon decontamination using uracil-DNA glycosylase.

  13. Observation of non-degenerate photorefractive parametric amplification

    DEFF Research Database (Denmark)

    Pedersen, H.C.; Johansen, P.M.

    1996-01-01

    We report on the first experimental observation of so-called nondegenerate photorefractive parametric amplification. We show that due to this effect it is possible for a weakly modulated photoinduced grating to be parametrically amplified via nonlinear interaction with a strongly modulated...

  14. Amplification and Attenuation across USArray using Ambient Noise Wavefront Tracking

    KAUST Repository

    Bowden, Daniel C.

    2017-11-15

    As seismic travel-time tomography continues to be refined using data from the vast USArray dataset, it is advantageous to also exploit the amplitude information carried by seismic waves. We use ambient noise cross correlation to make observations of surface-wave amplification and attenuation at shorter periods (8 – 32 seconds) than can be observed with only traditional teleseismic earthquake sources. We show that the wavefront tracking approach of [Lin et al., 2012a] can be successfully applied to ambient noise correlations, yielding results quite similar to those from earthquake observations at periods of overlap. This consistency indicates that the wavefront tracking approach is viable for use with ambient noise correlations, despite concerns of the inhomogeneous and unknown distribution of noise sources. The resulting amplification and attenuation maps correlate well with known tectonic and crustal structure; at the shortest periods, our amplification and attenuation maps correlate well with surface geology and known sedimentary basins, while our longest period amplitudes are controlled by crustal thickness and begin to probe upper mantle materials. These amplification and attenuation observations are sensitive to crustal materials in different ways than travel-time observations and may be used to better constrain temperature or density variations. We also value them as an independent means of describing the lateral variability of observed Rayleigh-wave amplitudes without the need for 3D tomographic inversions.

  15. Four-quadrant flyback converter for direct audio power amplification

    DEFF Research Database (Denmark)

    Ljusev, Petar; Andersen, Michael Andreas E.

    2005-01-01

    This paper presents a bidirectional, four-quadrant flyback converter for use in direct audio power amplification. When compared to the standard Class-D switching audio power amplifier with a separate power supply, the proposed four-quadrant flyback converter provides simple solution with better...

  16. Chirped-pulse Fourier transform millimeter-wave spectroscopy of ten vibrationally excited states of i-propyl cyanide: exploring the far-infrared region.

    Science.gov (United States)

    Arenas, Benjamin E; Gruet, Sébastien; Steber, Amanda L; Giuliano, Barbara M; Schnell, Melanie

    2017-01-18

    We report here further spectroscopic investigation of the astrochemically relevant molecule i-propyl cyanide. We observed and analysed the rotational spectra of the ground state of the molecule and ten vibrationally excited states with energies between 180-500 cm(-1). For this, we used a segmented W-band spectrometer (75-110 GHz) and performed the experiments under room temperature conditions. This approach thus provides access to high-resolution, pure rotational data of vibrational modes that occur in the far-infrared fingerprint region, and that can be difficult to access with other techniques. The obtained, extensive data set will support further astronomical searches and identifications, such as in warmer regions of the interstellar space where contributions from vibrationally excited states become increasingly relevant.

  17. Population inversion in hyperfine states of Rb with a single nanosecond chirped pulse in the framework of a four-level system

    Science.gov (United States)

    Liu, G.; Zakharov, V.; Collins, T.; Gould, P.; Malinovskaya, S. A.

    2014-04-01

    We implement a four-level semiclassical model of a single pulse interacting with the hyperfine structure in ultracold rubidium aimed at control of population dynamics and quantum state preparation. We discuss a method based on pulse chirping to achieve population inversion between hyperfine states of the 5S shell. The results may prove useful for quantum operations with ultracold atoms.

  18. The Chirped-Pulse Fourier Transform Microwave Cp-Ftmw Spectrum and Potential Energy Calculations for AN Aromatic Claisen Rearrangement Molecule, Allyl Phenyl Ether

    Science.gov (United States)

    Grubbs, G. S. Grubbs, Ii; Cooke, S. A.; Novick, Stewart E.

    2012-06-01

    Claisen rearrangement ethers are a fundamental organic, pericyclic rearrangement reaction reagent. In the mechanism of a Claisen rearrangement, a vinyl allyl ether is needed to provide the necessary Lewis acid/base sites on the molecule for the rearrangement and are simply heated. This rearrangement was first discovered by heating up the title molecule, allyl phenyl ether. However, much like the Diels-Alder, Cope, and other pericyclic reactions, conformation and coordination of chemical groups is key to the Claisen mechanism. In this study, the authors present some structural characteristics of allyl phenyl ether from an analysis of the microwave spectra in the 8-14 GHz region using a CP-FTMW spectrometer. This is, to the authors knowledge, the first known microwave region study of the title molecule. Three conformers have been observed and assigned to date and will be discussed. Along with the rotational spectra, geometry calculations and potential energy surfaces performed at the MP2/6-311G++(3d,2p) level will be discussed and compared to the experimental results. Modeling the Claisen aromatic rearrangement mechanism using CP-FTMW spectroscopy will also be discussed. L. Claisen Chemische Berichte 45, 3157, October 1912.

  19. Carrier-Envelope Phase stabilization of a 20 W, grating based, chirped-pulse amplified laser, using electro-optic effect in a LiNbO₃ crystal.

    Science.gov (United States)

    Hergott, J-F; Tcherbakoff, O; Paul, P-M; Demengeot, Ph; Perdrix, M; Lepetit, F; Garzella, D; Guillaumet, D; Comte, M; Oliveira, P D'; Gobert, O

    2011-10-10

    Using an original CEP stabilization technique based on the linear electro-optical effect in a specific crystal, we achieved long term CEP stabilization of a 20 W, 1 kHz laser with residual noise as low as 440 mrad (rms). At 3 W, the CEP shot to shot noise is kept as low as 320 mrad (rms) over half an hour.

  20. Voltage-dependent amplification of synaptic inputs in respiratory motoneurones

    Science.gov (United States)

    Enríquez Denton, M; Wienecke, J; Zhang, M; Hultborn, H; Kirkwood, P A

    2012-01-01

    The role of persistent inward currents (PICs) in cat respiratory motoneurones (phrenic inspiratory and thoracic expiratory) was investigated by studying the voltage-dependent amplification of central respiratory drive potentials (CRDPs), recorded intracellularly, with action potentials blocked with the local anaesthetic derivative, QX-314. Decerebrate unanaesthetized or barbiturate-anaesthetized preparations were used. In expiratory motoneurones, plateau potentials were observed in the decerebrates, but not under anaesthesia. For phrenic motoneurones, no plateau potentials were observed in either state (except in one motoneurone after the abolition of the respiratory drive by means of a medullary lesion), but all motoneurones showed voltage-dependent amplification of the CRDPs, over a wide range of membrane potentials, too wide to result mainly from PIC activation. The measurements of the amplification were restricted to the phase of excitation, thus excluding the inhibitory phase. Amplification was found to be greatest for the smallest CRDPs in the lowest resistance motoneurones and was reduced or abolished following intracellular injection of the NMDA channel blocker, MK-801. Plateau potentials were readily evoked in non-phrenic cervical motoneurones in the same (decerebrate) preparations. We conclude that the voltage-dependent amplification of synaptic excitation in phrenic motoneurones is mainly the result of NMDA channel modulation rather than the activation of Ca2+ channel mediated PICs, despite phrenic motoneurones being strongly immunohistochemically labelled for CaV1.3 channels. The differential PIC activation in different motoneurones, all of which are CaV1.3 positive, leads us to postulate that the descending modulation of PICs is more selective than has hitherto been believed. PMID:22495582

  1. Development of high energy, sub-15 fs OPCPA system operating at 1 kHz repetition rate for ELI-Beamlines facility

    Science.gov (United States)

    Bakule, Pavel; Antipenkov, Roman; Green, Jonathan T.; Novák, Jakub; Batysta, František; Rus, Bedřich; Boge, Robert; Hubka, Zbyněk.; Naylon, Jack A.; Horáček, Martin; Horáček, Jakub; Strkula, Petr; Snopek, David; Indra, Lukaš; Tykalewicz, Boguslaw

    2017-05-01

    We report on the status of the high repetition rate, high energy, L1 laser beamline at the ELI-Beamlines facility. The beamline is based on picosecond optical parametric chirped pulse amplification (OPCPA) of pulses from a mode-locked Ti:Sapphire oscillator and has a target energy/repetition rate of 100 mJ/1 kHz with architecture design considerations to achieve our goals of long term stability are discussed.

  2. Enzymatic Synthesis, Amplification, and Application of DNA with a Functionalized Backbone.

    Science.gov (United States)

    Chen, Tingjian; Romesberg, Floyd E

    2017-11-06

    The ability to amplify DNA along with its unprecedented sequence control has led to its use for different applications, but all are limited by the properties available to natural nucleotides. We previously reported the evolution of polymerase SFM4-3, which better tolerates 2'-modified substrates. To explore the utility of SFM4-3, we now report the characterization of its recognition of substrates with 2'-azido, 2'-chloro, 2'-amino, or arabinose sugars. We find that SFM4-3 can efficiently synthesize polymers composed of these nucleotides, and most interestingly, that SFM4-3 can also PCR amplify these modified oligonucleotides. When combined with post-amplification modification, the latter allows for the exponential amplification of polymers that may be functionalized with desired moieties arrayed in a controlled fashion, the utility of which we demonstrate with extensive small molecule functionalization and the production and initial characterization of a novel DNA hydrogel. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Enhanced primers for amplification of DNA barcodes from a broad range of marine metazoans.

    Science.gov (United States)

    Lobo, Jorge; Costa, Pedro M; Teixeira, Marcos A L; Ferreira, Maria S G; Costa, Maria H; Costa, Filipe O

    2013-09-10

    Building reference libraries of DNA barcodes is relatively straightforward when specifically designed primers are available to amplify the COI-5P region from a relatively narrow taxonomic group (e.g. single class or single order). DNA barcoding marine communities have been comparatively harder to accomplish due to the broad taxonomic diversity and lack of consistently efficient primers. Although some of the so-called "universal" primers have been relatively successful, they still fail to amplify COI-5P of many marine animal groups, while displaying random success even among species within each group. Here we propose a new pair of primers designed to enhance amplification of the COI-5P region in a wide range of marine organisms. Amplification tests conducted on a wide range of marine animal taxa, rendered possible the first-time sequencing of DNA barcodes from eight separated phyla (Annelida, Arthropoda, Chordata, Cnidaria, Echinodermata, Mollusca, Nemertea and Platyhelminthes), comprising a total of 14 classes, 28 orders, 57 families, 68 genus and 76 species. These primers demonstrated to be highly cost-effective, which is of key importance for DNA barcoding procedures, such as for building comprehensive DNA barcode libraries of marine communities, where the processing of a large numbers of specimens from a wide variety of marine taxa is compulsory.

  4. Loop-mediated isothermal amplification (LAMP) based detection of Colletotrichum falcatum causing red rot in sugarcane.

    Science.gov (United States)

    Chandra, Amaresh; Keizerweerd, Amber T; Que, Youxiong; Grisham, Michael P

    2015-08-01

    Red rot, caused by Colletotrichum falcatum, is a destructive disease prevalent in most sugarcane-producing countries. Disease-free sugarcane planting materials (setts) are essential as the pathogen spreads primarily through infected setts. The present study was undertaken to develop a loop-mediated isothermal amplification (LAMP) assay for the detection of C. falcatum. C. falcatum genomic DNA was isolated from pure mycelium culture and infected tissues. Four sets of primers corresponding to a unique DNA sequence specific to C. falcatum were designed. Specificity of the LAMP test was checked with DNA of another fungal pathogen of sugarcane, Puccinia melanocephala, as well as two closely-related species, Colletotrichum fructivorum and Colletotrichum acutatum. No reaction was found with the three pathogens. When C. falcatum DNA from pure culture was used in a detection limit analysis, sensitivity of the LAMP method was observed to be ten times higher than that of conventional PCR; however, sensitivity was only 5 times higher when DNA from C. falcatum-infected tissues was used. Using the LAMP assay, C. falcatum DNA is amplified with high specificity, efficiency, and rapidity under isothermal conditions. Moreover, visual judgment of color change in <1 h without further post-amplification processing makes the LAMP method convenient, economical, and useful in diagnostic laboratories and the field.

  5. Chiral amplification in a cyanobiphenyl nematic liquid crystal doped with helicene-like derivatives

    Directory of Open Access Journals (Sweden)

    Alberta Ferrarini

    2009-10-01

    Full Text Available The addition of a chiral non-racemic dopant to a nematic liquid crystal (LC has the effect of transferring the molecular chirality to the phase organization and a chiral nematic phase is formed. This molecular chirality amplification in the LC provides a unique possibility for investigating the relationship between molecular structure, intermolecular interactions, and mesoscale organization. It is known that axially chiral or helical-shaped molecules with reduced conformational disorder are good candidates for high helical twisting power derivatives. In particular, biaryl derivatives are known to be efficient chiral inducers in biaryl nematic mesophases. In this paper, we focus on a new series of helicene-like molecules of known absolute configuration. We have integrated cholesteric pitch measurements with geometry optimization by DFT calculations and analysis of the twisting ability by the Surface Chirality model to shed light on the structural features responsible for the analogies and differences exhibited by these derivatives. The investigation of these dopants with well-defined geometry, by virtue of the low conformational freedom, and the substituents variously distributed around the core, allows us to extend our knowledge of the molecular origin of the chirality amplification in liquid crystals and to confirm the simple relationship “molecular P-helicity” → “cholesteric P-handedness” for helical-shaped helicene-like derivatives.

  6. Rapid DNA amplification using a battery-powered thin-film resistive thermocycler.

    Science.gov (United States)

    Herold, Keith E; Sergeev, Nikolay; Matviyenko, Andriy; Rasooly, Avraham

    2009-01-01

    A prototype handheld, compact, rapid thermocycler was developed for multiplex analysis of nucleic acids in an inexpensive, portable configuration. Instead of the commonly used Peltier heating/cooling element, electric thin-film resistive heater and a miniature fan enable rapid heating and cooling of glass capillaries leading to a simple, low-cost Thin-Film Resistive Thermocycler (TFRT). Computer-based pulse width modulation control yields heating rates of 6-7 K/s and cooling rates of 5 K/s. The four capillaries are closely coupled to the heater, resulting in low power consumption. The energy required by a nominal PCR cycle (20 s at each temperature) was found to be 57+/-2 J yielding an average power of approximately 1.0 W (not including the computer and the control system). Thus the device can be powered by a standard 9 V alkaline battery (or other 9 V power supply). The prototype TFRT was demonstrated (in a benchtop configuration) for detection of three important food pathogens (E. coli ETEC, Shigella dysenteriae, and Salmonella enterica). PCR amplicons were analyzed by gel electrophoresis. The 35 cycle PCR protocol using a single channel was completed in less then 18 min. Simple and efficient heating/cooling, low cost, rapid amplification, and low power consumption make the device suitable for portable DNA amplification applications including clinical point of care diagnostics and field use.

  7. Loop Mediated Isothermal Amplification (LAMP): A Versatile Technique for Detection of Microorganisms.

    Science.gov (United States)

    Wong, Yien-Ping; Othman, Shuhaidah; Lau, Yee-Ling; Son, Radu; Chee, Hui-Yee

    2017-11-22

    Loop mediated isothermal amplification (LAMP) amplifies DNA with high specificity, efficiency, and rapidity under isothermal conditions by using a DNA polymerase with high displacement strand activity and a set of specifically designed primers to amplify targeted DNA strands. Following its first discovery by Notomi et al. in the year 2000, LAMP was further developed over the years which involved the combination of this technique with other molecular approaches, such as reverse transcription and multiplex amplification for the detection of infectious diseases caused by microorganisms in humans, livestock and plants. In this review, available types of LAMP techniques will be discussed together with their applications in detection of various microorganisms'. Up to date, there are varieties of LAMP detection methods available including colorimetric and fluorescent detection, real-time monitoring using turbidity meter and detection using lateral flow device which will also be highlighted in this review. Apart from that, commercialization of LAMP technique had also been reported such as lyophilized form of LAMP reagents kit and LAMP primer sets for detection of pathogenic microorganisms. On top of that, advantages and limitations of this molecular detection method are also described together with its future potential as a diagnostic method for infectious disease. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  8. Generation of high-power few-cycle lasers via Brillouin-based plasma amplification

    Science.gov (United States)

    Zhang, Z. M.; Zhang, B.; Hong, W.; Deng, Z. G.; Teng, J.; He, S. K.; Zhou, W. M.; Gu, Y. Q.

    2017-11-01

    Strong coupling stimulated Brillouin backscattering (sc-SBS) in plasma is potentially an efficient method of amplifying laser pulses to reach exawatt powers. Here, we report on a new regime of brillouin-based plasma amplification, producing an amplified pulse with a duration of 5 fs and unfocused intensity of 6 × 1017 W/cm2. The results are obtained from 2D particle-in-cell simulations, using two circularly polarized pump and seed pulse with Gaussian transverse profile, both at an intensity of 2.74 × 1016 W/cm2, counter-propagating in a 0.3nc plasma. The significant compression of amplified seed is achieved as a result of sc-SBS amplification as well as additional compression by the interplay between self-phase modulation and negative group delay dispersion. We show that the amplified seed retains high beam qualities since the filamentation can be prevented due to the fast compression. This scheme may pave the way for few-cycle laser pulses to reach exawatt or even zetawatt regime.

  9. Radon hazard in shallow groundwaters: Amplification and long term variability induced by rainfall

    Energy Technology Data Exchange (ETDEWEB)

    De Francesco, S., E-mail: stefano.defrancesco@unina2.it [Department of Environmental Sciences, Second University of Naples, Via Vivaldi, 43, 81100 Caserta (Italy); Tommasone, F. Pascale [Office of Civil Protection, Meteorology, Climatology and Natural Hazards, Piazza Municipio, 81051 Pietramelara, Caserta (Italy); Cuoco, E.; Verrengia, G. [Department of Environmental Sciences, Second University of Naples, Via Vivaldi, 43, 81100 Caserta (Italy); Tedesco, D. [Department of Environmental Sciences, Second University of Naples, Via Vivaldi, 43, 81100 Caserta (Italy); C.N.R. (Italian Council for Research), Institute of Environmental Geology and Geological Engineering, Piazzale Aldo Moro, 00100 Roma (Italy)

    2010-01-15

    {sup 222}Rn concentrations have been determined with a RAD7 radon detector in shallow groundwaters of the Pietramelara Plain, north-western Campania, southern Italy, where pyroclastic deposits, along with recent stream alluvial sediments, come in contact with Mesozoic carbonate reservoirs. The aim of this study has been to study the annual variation of {sup 222}Rn concentration in the shallow groundwaters, scarcely considered in the literature and of obvious relevance for radon hazard evaluation. Our results definitely show that {sup 222}Rn levels are characterized by a clear annual periodicity, strictly related to rainfall and water table levels, with a pronounced difference between the dry and the wet season. In this last case with concentrations increasing up to two orders of magnitude (up to two times the lower threshold given in the Recommendation 2001/928/EURATOM for public waters). In relation to this, experimental field data will be presented to demonstrate that this variability is due to purely hydrological mechanisms, mainly rinse out and discharge that control leaching efficiency. The detected cycle (Radon Hydrological Amplification Cycle, RHAC) has been generalized for the Mediterranean Tyrrhenian climate. The marked and seasonally persistent amplification in {sup 222}Rn levels poses the problem of evaluating the epidemiological risk brought up by this previously not yet reported mechanism. This mechanism, occurring in shallow groundwaters, very likely should strongly influence indoor radon levels via groundwater-soil-building exchange.

  10. Simulation of Redox-Cycling Phenomena at Interdigitated Array (IDA) Electrodes: Amplification and Selectivity

    NARCIS (Netherlands)

    Odijk, Mathieu; Olthuis, Wouter; Dam, T.V.A.; van den Berg, Albert

    2008-01-01

    We present Finite Element Method (FEM) simulations of interdigitated array (IDA) electrode geometries to study and verify redox selectivity and redox cycling amplification factor. The simulations provide an adequate explanation of an earlier found, but poorly understood, high amplification factor

  11. Adaptive gene amplification as an intermediate step in the expansion of virus host range.

    Directory of Open Access Journals (Sweden)

    Greg Brennan

    2014-03-01

    Full Text Available The majority of recently emerging infectious diseases in humans is due to cross-species pathogen transmissions from animals. To establish a productive infection in new host species, viruses must overcome barriers to replication mediated by diverse and rapidly evolving host restriction factors such as protein kinase R (PKR. Many viral antagonists of these restriction factors are species specific. For example, the rhesus cytomegalovirus PKR antagonist, RhTRS1, inhibits PKR in some African green monkey (AGM cells, but does not inhibit human or rhesus macaque PKR. To model the evolutionary changes necessary for cross-species transmission, we generated a recombinant vaccinia virus that expresses RhTRS1 in a strain that lacks PKR inhibitors E3L and K3L (VVΔEΔK+RhTRS1. Serially passaging VVΔEΔK+RhTRS1 in minimally-permissive AGM cells increased viral replication 10- to 100-fold. Notably, adaptation in these AGM cells also improved virus replication 1000- to 10,000-fold in human and rhesus cells. Genetic analyses including deep sequencing revealed amplification of the rhtrs1 locus in the adapted viruses. Supplying additional rhtrs1 in trans confirmed that amplification alone was sufficient to improve VVΔEΔK+RhTRS1 replication. Viruses with amplified rhtrs1 completely blocked AGM PKR, but only partially blocked human PKR, consistent with the replication properties of these viruses in AGM and human cells. Finally, in contrast to AGM-adapted viruses, which could be serially propagated in human cells, VVΔEΔK+RhTRS1 yielded no progeny virus after only three passages in human cells. Thus, rhtrs1 amplification in a minimally permissive intermediate host was a necessary step, enabling expansion of the virus range to previously nonpermissive hosts. These data support the hypothesis that amplification of a weak viral antagonist may be a general evolutionary mechanism to permit replication in otherwise resistant host species, providing a molecular foothold

  12. Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

    DEFF Research Database (Denmark)

    Hou, Yong; Wu, Kui; Shi, Xulian

    2015-01-01

    BACKGROUND: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleoti......BACKGROUND: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate...

  13. Added value of HER-2 amplification testing by multiplex ligation-dependent probe amplification in invasive breast cancer.

    Directory of Open Access Journals (Sweden)

    Chantal C H J Kuijpers

    Full Text Available BACKGROUND: HER-2 is a prognostic and predictive marker, but as yet no technique is perfectly able to identify patients likely to benefit from HER-2 targeted therapies. We aimed to prospectively assess the added value of first-line co-testing by IHC, and multiplex ligation-dependent probe amplification (MLPA and chromogenic in situ hybridization (CISH. METHODS: As local validation, HER-2 MLPA and CISH were compared in 99 breast cancers. Next, we reviewed 937 invasive breast cancers, from 4 Dutch pathology laboratories, that were prospectively assessed for HER-2 by IHC and MLPA (and CISH in selected cases. RESULTS: The validation study demonstrated 100% concordance between CISH and MLPA, if both methods were assessable and conclusive (81.8% of cases. Significant variation regarding percentages IHC 0/1+ and 2+ cases was observed between the laboratories (p<0.0001. Overall concordance between IHC and MLPA/CISH was 98.1% (575/586 (Kappa = 0.94. Of the IHC 3+ cases, 6.7% failed to reveal gene amplification, whereas 0.8% of the IHC 0/1+ cases demonstrated gene amplification. Results remained discordant after retrospective review in 3/11 discordant cases. In the remaining 8 cases the original IHC score was incorrect or adapted after repeated IHC staining. CONCLUSIONS: MLPA is a low-cost and quantitative high-throughput technique with near perfect concordance with CISH. The use of MLPA in routinely co-testing all breast cancers may reduce HER-2 testing variation between laboratories, may serve as quality control for IHC, will reveal IHC 0/1+ patients with gene amplification, likely responsive to trastuzumab, and identify IHC 3+ cases without gene amplification that may respond less well.

  14. High-energy infrared femtosecond pulses generated by dual-chirped optical parametric amplification.

    Science.gov (United States)

    Fu, Yuxi; Takahashi, Eiji J; Midorikawa, Katsumi

    2015-11-01

    We demonstrate high-energy infrared femtosecond pulse generation by a dual-chirped optical parametric amplification (DC-OPA) scheme [Opt. Express19, 7190 (2011)]. By employing a 100 mJ pump laser, a signal pulse energy exceeding 20 mJ at a wavelength of 1.4 μm was achieved before dispersion compensation. A total output energy of 33 mJ was recorded. Under a further energy scaling condition, the signal pulse was compressed to an almost transform-limited duration of 27 fs using a fused silica prism compressor. Since the DC-OPA scheme is efficient and energy scalable, design parameters for obtaining 100 mJ level infrared pulses are presented, which are suitable as driver lasers for the energy scaling of high-order harmonic generation with sub-keV photon energy.

  15. Backward Raman amplification in plasmas with chirped wideband pump and seed pulses

    Science.gov (United States)

    Wu, Zhao-Hui; Wei, Xiao-Feng; Zuo, Yan-Lei; Liu, Lan-Qin; Zhang, Zhi-Meng; Li, Min; Zhou, Yu-Liang; Su, Jing-Qin

    2015-01-01

    Chirped wideband pump and seed pulses are usually considered for backward Raman amplification (BRA) in plasmas to achieve an extremely high-power laser pulse. However, current theoretical models only contain either a chirped pump or a chirped seed. In this paper, modified three-wave coupling equations are proposed for the BRA in the plasmas with both chirped wideband pump and seed. The simulation results can more precisely describe the experiments, such as the Princeton University experiment. The optimized chirp and bandwidth are determined based on the simulation to enhance the output intensity and efficiency. Project supported by the National Natural Science Foundation of China (Grant No. 11305157) and the Development Foundation of China Academy of Engineering Physics Laboratory (CAEPL) (Grant No. 2013A0401019).

  16. Biosensors for breast cancer diagnosis: A review of bioreceptors, biotransducers and signal amplification strategies.

    Science.gov (United States)

    Mittal, Sunil; Kaur, Hardeep; Gautam, Nandini; Mantha, Anil K

    2017-02-15

    Breast cancer is highly prevalent in females and accounts for second highest number of deaths, worldwide. Cumbersome, expensive and time consuming detection techniques presently available for detection of breast cancer potentiates the need for development of novel, specific and ultrasensitive devices. Biosensors are the promising and selective detection devices which hold immense potential as point of care (POC) tools. Present review comprehensively scrutinizes various breast cancer biosensors developed so far and their technical evaluation with respect to efficiency and potency of selected bioreceptors and biotransducers. Use of glycoproteins, DNA biomarkers, micro-RNA, circulatory tumor cells (CTC) and some potential biomarkers are introduced briefly. The review also discusses various strategies used in signal amplification such as nanomaterials, redox mediators, p19 protein, duplex specific nucleases (DSN) and redox cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Whole genome amplification - Review of applications and advances

    Energy Technology Data Exchange (ETDEWEB)

    Hawkins, Trevor L.; Detter, J.C.; Richardson, Paul

    2001-11-15

    The concept of Whole Genome Amplification is something that has arisen in the past few years as modifications to the polymerase chain reaction (PCR) have been adapted to replicate regions of genomes which are of biological interest. The applications here are many--forensics, embryonic disease diagnosis, bio terrorism genome detection, ''imoralization'' of clinical samples, microbial diversity, and genotyping. The key question is if DNA can be replicated a genome at a time without bias or non random distribution of the target. Several papers published in the last year and currently in preparation may lead to the conclusion that whole genome amplification may indeed be possible and therefore open up a new avenue to molecular biology.

  18. Detection of Botrytis cinerea by loop-mediated isothermal amplification.

    Science.gov (United States)

    Tomlinson, J A; Dickinson, M J; Boonham, N

    2010-12-01

    To develop a sensitive, rapid and simple method for detection of Botrytis cinerea based on loop-mediated isothermal amplification (LAMP) that would be suitable for use outside a conventional laboratory setting. A LAMP assay was designed based on the intergenic spacer of the B. cinerea nuclear ribosomal DNA (rDNA). The resulting assay was characterized in terms of sensitivity and specificity using DNA extracted from cultures. The assay consistently amplified 65 pg B. cinerea DNA. No cross-reactivity was observed with a range of other fungal pathogens, with the exception of the closely related species Botrytis pelargonii. Use of a novel real-time LAMP platform (the OptiGene Genie I) allowed detection of B. cinerea in infected rose petals, with amplification occurring in cut flowers, fruit and vegetables. © 2010 British Crown Copyright. Letters in Applied Microbiology 51, 650-657 © 2010 The Society for Applied Microbiology.

  19. Amplification, Decoherence, and the Acquisition of Information by Spin Environments.

    Science.gov (United States)

    Zwolak, Michael; Riedel, C Jess; Zurek, Wojciech H

    2016-05-19

    Quantum Darwinism recognizes the role of the environment as a communication channel: Decoherence can selectively amplify information about the pointer states of a system of interest (preventing access to complementary information about their superpositions) and can make records of this information accessible to many observers. This redundancy explains the emergence of objective, classical reality in our quantum Universe. Here, we demonstrate that the amplification of information in realistic spin environments can be quantified by the quantum Chernoff information, which characterizes the distinguishability of partial records in individual environment subsystems. We show that, except for a set of initial states of measure zero, the environment always acquires redundant information. Moreover, the Chernoff information captures the rich behavior of amplification in both finite and infinite spin environments, from quadratic growth of the redundancy to oscillatory behavior. These results will considerably simplify experimental testing of quantum Darwinism, e.g., using nitrogen vacancies in diamond.

  20. Parametric Amplification of Vacuum Fluctuations in a Spinor Condensate

    DEFF Research Database (Denmark)

    Klempt, C.; Topic, O.; Gebreyesus, G.

    2010-01-01

    Parametric amplification of vacuum fluctuations is crucial in modern quantum optics, enabling the creation of squeezing and entanglement. We demonstrate the parametric amplification of vacuum fluctuations for matter waves using a spinor F=2 87Rb condensate. Interatomic interactions lead...... to correlated pair creation in the mF=±1 states from an initial mF=0 condensate, which acts as a vacuum for mF≠0. Although this pair creation from a pure mF=0 condensate is ideally triggered by vacuum fluctuations, unavoidable spurious initial mF=±1 atoms induce a classical seed which may become the dominant...... triggering mechanism. We show that pair creation is insensitive to a classical seed for sufficiently large magnetic fields, demonstrating the dominant role of vacuum fluctuations. The presented system thus provides a direct path towards the generation of nonclassical states of matter....

  1. Extrachromosomal oncogene amplification drives tumor evolution and genetic heterogeneity

    Science.gov (United States)

    Turner, Kristen M.; Deshpande, Viraj; Beyter, Doruk; Koga, Tomoyuki; Rusert, Jessica; Lee, Catherine; Li, Bin; Arden, Karen; Ren, Bing; Nathanson, David A.; Kornblum, Harley I.; Taylor, Michael D.; Kaushal, Sharmeela; Cavenee, Webster K.; Wechsler-Reya, Robert; Furnari, Frank B.; Vandenberg, Scott R.; Rao, P. Nagesh; Wahl, Geoffrey M.; Bafna, Vineet; Mischel, Paul S.

    2017-01-01

    Human cells have twenty-three pairs of chromosomes but in cancer, genes can be amplified in chromosomes or in circular extrachromosomal DNA (ECDNA), whose frequency and functional significance are not understood1–4. We performed whole genome sequencing, structural modeling and cytogenetic analyses of 17 different cancer types, including 2572 metaphases, and developed ECdetect to conduct unbiased integrated ECDNA detection and analysis. ECDNA was found in nearly half of human cancers varying by tumor type, but almost never in normal cells. Driver oncogenes were amplified most commonly on ECDNA, elevating transcript level. Mathematical modeling predicted that ECDNA amplification elevates oncogene copy number and increases intratumoral heterogeneity more effectively than chromosomal amplification, which we validated by quantitative analyses of cancer samples. These results suggest that ECDNA contributes to accelerated evolution in cancer. PMID:28178237

  2. Surface plasmon polariton amplification in semiconductor-graphene-dielectric structure

    Energy Technology Data Exchange (ETDEWEB)

    Dadoenkova, Yuliya S. [Ulyanovsk State University, Ulyanovsk (Russian Federation); Novgorod State University, Veliky Novgorod (Russian Federation); Donetsk Institute for Physics and Technology, Donetsk (Ukraine); Moiseev, Sergey G. [Ulyanovsk State University, Ulyanovsk (Russian Federation); Kotelnikov Institute of Radio Engineering and Electronics, Russian Academy of Sciences, Ulyanovsk (Russian Federation); Abramov, Aleksei S. [Ulyanovsk State University, Ulyanovsk (Russian Federation); Kadochkin, Aleksei S.; Zolotovskii, Igor O. [Ulyanovsk State University, Ulyanovsk (Russian Federation); Institute of Nanotechnologies of Microelectronics of the Russian Academy of Sciences, 32A Leninskiy Prosp., 119991, Moscow (Russian Federation); Fotiadi, Andrei A. [Ulyanovsk State University, Ulyanovsk (Russian Federation); Universite de Mons (Belgium)

    2017-05-15

    A mechanism of amplification of surface plasmon polaritons due to the transfer of electromagnetic energy from a drift current wave into a far-infrared surface wave propagating along a semiconductor-dielectric boundary in waveguide geometry is proposed. A necessary condition of the interaction of these waves is phase matching condition, i. e., when the phase velocity of the surface wave approaches the drift velocity of charge carriers. It is shown that in the spectral region of the surface plasmon polariton slowing-down its amplification coefficient can reach values substantially exceeding the ohmic loss coefficient of the surface wave in the structure. (copyright 2017 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  3. Phase Sensitive Amplification using Parametric Processes in Optical Fibers

    DEFF Research Database (Denmark)

    Kang, Ning

    , in specific, the design and optimization of such phase sensitive amplifiers (PSAs). For phase sensitive amplification in highly nonlinear fibers, optima points of operation have been identified for both the standard and the novel high stimulated Brillouin scattering (SBS) threshold highly nonlinear fiber......Phase sensitive amplification using the parametric processes in fiber has the potential of delivering high gain and broadband operation with ultralow noise. It is able to regenerate both amplitude and phase modulated signals, simultaneously, with the appropriate design. This thesis concerns...... types. The regeneration capability of PSAs on phase encoded signal in an optical link has been optimized. Flat-top phase sensitive profile has been synthesized. It is able to provide simultaneous amplitude and phase noise squeezing, with enhanced phase noise margin compared to conventional designs...

  4. Spin noise amplification and giant noise in optical microcavity

    Energy Technology Data Exchange (ETDEWEB)

    Ryzhov, I. I.; Poltavtsev, S. V.; Kozlov, G. G.; Zapasskii, V. S. [Spin-Optics Laboratory, St. Petersburg State University, 198504 St. Petersburg (Russian Federation); Kavokin, A. V. [Department of Physics and Astronomy, University of Southampton, Southampton SO17 1BJ (United Kingdom); Spin-Optics Laboratory, St. Petersburg State University, 198504 St. Petersburg (Russian Federation); Lagoudakis, P. V. [Department of Physics and Astronomy, University of Southampton, Southampton SO17 1BJ (United Kingdom)

    2015-06-14

    When studying the spin-noise-induced fluctuations of Kerr rotation in a quantum-well microcavity, we have found a dramatic increase of the noise signal (by more than two orders of magnitude) in the vicinity of anti-crossing of the polariton branches. The effect is explained by nonlinear optical instability of the microcavity giving rise to the light-power-controlled amplification of the polarization noise signal. In the framework of the developed model of built-in amplifier, we also interpret the nontrivial spectral and intensity-related properties of the observed noise signal below the region of anti-crossing of polariton branches. The discovered effect of optically controllable amplification of broadband polarization signals in microcavities in the regime of optical instability may be of interest for detecting weak oscillations of optical anisotropy in fundamental research and for other applications in optical information processing.

  5. The Energy Amplification Characteristic Research of a Multimodal Actuator

    Directory of Open Access Journals (Sweden)

    Han Yali

    2016-05-01

    Full Text Available A multimodal actuator is proposed to fulfil the different walking patterns of a power-assisted knee exoskeleton. With this actuator, the exoskeleton leg can realize several modes of operation, including series elastic actuation, stiff position control and energy storage and release. The energy amplification characteristics of the multimodal actuator in the series elastic mode are analysed. A dynamics model was established to study how series elasticity and the equivalent mass of transmission influence a power source, such as an electric motor. The results, in both simulation and experiment, show that series elasticity can amplify actuator power output, and the power output of a multimodal actuator is greater when the equivalent mass of the transmission mechanism is smaller. This research into multimodal actuator energy amplification supplies important insights into the design of artificial systems that can more closely approximate the performance of biological systems.

  6. A novel whole genome amplification method using type IIS restriction enzymes to create overhangs with random sequences.

    Science.gov (United States)

    Pan, Xiaoming; Wan, Baihui; Li, Chunchuan; Liu, Yu; Wang, Jing; Mou, Haijin; Liang, Xingguo

    2014-08-20

    Ligation-mediated polymerase chain reaction (LM-PCR) is a whole genome amplification (WGA) method, for which genomic DNA is cleaved into numerous fragments and then all of the fragments are amplified by PCR after attaching a universal end sequence. However, the self-ligation of these fragments could happen and may cause biased amplification and restriction of its application. To decrease the self-ligation probability, here we use type IIS restriction enzymes to digest genomic DNA into fragments with 4-5nt long overhangs with random sequences. After ligation to an adapter with random end sequences to above fragments, PCR is carried out and almost all present DNA sequences are amplified. In this study, whole genome of Vibrio parahaemolyticus was amplified and the amplification efficiency was evaluated by quantitative PCR. The results suggested that our approach could provide sufficient genomic DNA with good quality to meet requirements of various genetic analyses. Copyright © 2014. Published by Elsevier B.V.

  7. Loop-mediated isothermal amplification for the rapid detection of Chrysanthemum chlorotic mottle viroid (CChMVd).

    Science.gov (United States)

    Park, Jungan; Jung, Yuchul; Kil, Eui-Joon; Kim, Jaedeok; Thi Tran, Dung; Choi, Seung-Kook; Yoon, Ju-Yeon; Cho, Won Kyong; Lee, Sukchan

    2013-10-01

    Loop-mediated isothermal amplification (LAMP) is an established nucleic acid amplification method offering rapid, sensitive, and convenient diagnosis of infectious diseases. Chrysanthemum chlorotic mottle viroid (CChMVd) causes one of the most serious viral diseases in chrysanthemum in Korea. A sensitive LAMP assay was developed for rapidly detecting CChMVd infection. The assay was based on a set of four primers matching the specific region of the CChMVd genome. The CChMVd LAMP primer sets were designed using the sequences from nonsymptomatic and symptomatic CChMVd isolates in Korea. The efficiency and specificity of this method were optimized using Bst DNA polymerase, which allowed for increased viroid detection sensitivity. The reaction was carried out at 65 °C for 90 min, and was improved by adding SYBR Green I dye to the inside of the reaction tube lid prior to amplification. The results indicate that this LAMP method will be useful for chrysanthemum viroid disease monitoring and detecting CChMVd infectious disease. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

  8. Direct visualization of the reaction transformation and signal amplification in a DNA molecular machine with total internal reflection fluorescence microscopy.

    Science.gov (United States)

    Ren, Rui; Wang, Haiyan; Liu, Rui; Zhang, Shusheng

    2013-01-01

    In this study, as a proof of concept, the signal amplification in an artificial DNA molecular machine was directly visualized via total internal reflection fluorescence microscopy (TIRFM). The molecular machine brought about obvious morphology change in DNA nanostructures as well as signal amplifications. On one hand, through a triggered and autonomically repeated RCA, a DNA nano-complex featuring a "locked" circular DNA template (serving as raw feed) was converted into a long periodically repeated strand, i.e., the RCA products. On the other hand, this RCA was repeated in three controllable reaction phases, bring about progressive signal amplification. It was testified that the RCA products (presented as long thread-like fluorescent objects) can be easily distinguished from the inputted DNA probes (presented as fluorescent dots), thus the transformation in reaction can be visualized. Also, by quantitive counting of the aforementioned fluorescence objects, the progress of the reaction through the phases, along with time, and over the lysozyme concentration can be demonstrated through TIRFM visualization. Overall, it was demonstrated that TIRFM is an efficient approach to quantitatively visualize the biochemical processes at single-molecule level.

  9. A novel CMOS image sensor system for quantitative loop-mediated isothermal amplification assays to detect food-borne pathogens.

    Science.gov (United States)

    Wang, Tiantian; Kim, Sanghyo; An, Jeong Ho

    2017-02-01

    Loop-mediated isothermal amplification (LAMP) is considered as one of the alternatives to the conventional PCR and it is an inexpensive portable diagnostic system with minimal power consumption. The present work describes the application of LAMP in real-time photon detection and quantitative analysis of nucleic acids integrated with a disposable complementary-metal-oxide semiconductor (CMOS) image sensor. This novel system works as an amplification-coupled detection platform, relying on a CMOS image sensor, with the aid of a computerized circuitry controller for the temperature and light sources. The CMOS image sensor captures the light which is passing through the sensor surface and converts into digital units using an analog-to-digital converter (ADC). This new system monitors the real-time photon variation, caused by the color changes during amplification. Escherichia coli O157 was used as a proof-of-concept target for quantitative analysis, and compared with the results for Staphylococcus aureus and Salmonella enterica to confirm the efficiency of the system. The system detected various DNA concentrations of E. coli O157 in a short time (45min), with a detection limit of 10fg/μL. The low-cost, simple, and compact design, with low power consumption, represents a significant advance in the development of a portable, sensitive, user-friendly, real-time, and quantitative analytic tools for point-of-care diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Rolling circle amplification detection of RNA and DNA

    Science.gov (United States)

    Christian, Allen T.; Pattee, Melissa S.; Attix, Cristina M.; Tucker, James D.

    2004-08-31

    Rolling circle amplification (RCA) has been useful for detecting point mutations in isolated nucleic acids, but its application in cytological preparations has been problematic. By pretreating cells with a combination of restriction enzymes and exonucleases, we demonstrate RCA in solution and in situ to detect gene copy number and single base mutations. It can also detect and quantify transcribed RNA in individual cells, making it a versatile tool for cell-based assays.

  11. Uncertainty of site amplification derived from ground response analysis

    OpenAIRE

    Afshari, K; Stewart, JP

    2015-01-01

    Site-specific geotechnical ground response analyses (GRAs) are typically performed to evaluate stress and strain demands within soil profiles and/or to improve the estimation of site response relative to generic site terms from empirical prediction equations. Implementation of GRA results in probabilistic seismic hazard analysis (PSHA) requires knowledge of the mean and standard deviation of site amplification from GRA. We provide expressions for evaluating within-event standard deviations of...

  12. Spectral amplification models for response spectrum addressing the directivity effect

    Science.gov (United States)

    Moghimi, Saed; Akkar, Sinan

    2017-04-01

    Ground motions with forward directivity effects are known with their significantly large spectral ordinates in medium-to-long periods. The large spectral ordinates stem from the impulsive characteristics of the forward directivity ground motions. The quantification of these spectral amplifications requires the identification of major seismological parameters that play a role in their generation. After running a suite of probabilistic seismic hazard analysis, Moghimi and Akkar (2016) have shown that fault slip rate, fault characteristic magnitude, fault-site geometry as well as mean annual exceedance rate are important parameters that determine the level of spectral amplification due to directivity. These parameters are considered to develop two separate spectral amplification equations in this study. The proposed equations rely on Shahi and Baker (SHB11; 2011) and Chiou and Spudich (CHS13; Spudic et al., 2013) narrow-band forward directivity models. The presented equations only focus on the estimation of maximum spectral amplifications that occur at the ends of the fault segments. This way we eliminate the fault-site parameter in our equations for simplification. The proposed equations show different trends due to differences in the narrow-band directivity models of SHB11 and CHS13. The equations given in this study can form bases for describing forward directivity effects in seismic design codes. REFERENCES Shahi. S., Baker, J.W. (2011), "An Empirically Calibrated Framework for Including the Effects of Near-Fault Directivity in Probabilistic Seismic Hazard Analysis", Bulletin of the Seismological Society of America, 101(2): 742-755. Spudich, P., Watson-Lamprey, J., Somerville, P., Bayless, J., Shahi, S. K., Baker, J. W., Rowshandel, B., and Chiou, B. (2013), "Final Report of the NGA-West2 Directivity Working Group", PEER Report 2013/09. Moghimi. S., Akkar, S. (2016), "Implications of Forward Directivity Effects on Design Ground Motions", Seismological Society of

  13. A Window into Domain Amplification Through Piccolo in Teleost Fish

    Science.gov (United States)

    Nonet, Michael L.

    2012-01-01

    I describe and characterize the extensive amplification of the zinc finger domain of Piccolo selectively in teleost fish. Piccolo and Bassoon are partially functionally redundant and play roles in regulating the pool of neurotransmitter-filled synaptic vesicles present at synapses. In mice, each protein contains two N-terminal zinc finger domains that have been implicated in interacting with synaptic vesicles. In all teleosts examined, both the Bassoon and Piccolo genes are duplicated. Both teleost bassoon genes and one piccolo gene show very similar domain structure and intron-exon organization to their mouse homologs. In contrast, in piccolo b a single exon that encodes a zinc finger domain is amplified 8 to 16 times in different teleost species. Analysis of the amplified exons suggests they were added and/or deleted from the gene as individual exons in rare events that are likely the result of unequal crossovers between homologous sequences. Surprisingly, the structure of the repeats from cod and zebrafish suggest that amplification of this exon has occurred independently multiple times in the teleost lineage. Based on the structure of the exons, I propose a model in which selection for high sequence similarity at the 5′ and 3′ ends of the exon drives amplification of the repeats and diversity in repeat length likely promotes the stability of the repeated exons by minimizing the likelihood of mispairing of adjacent repeat sequences. Further analysis of piccolo b in teleosts should provide a window through which to examine the process of domain amplification. PMID:23173084

  14. Rapid and Sensitive Detection of Norovirus Genomes in Oysters by a Two-Step Isothermal Amplification Assay System Combining Nucleic Acid Sequence-Based Amplification and Reverse Transcription-Loop-Mediated Isothermal Amplification Assays▿

    Science.gov (United States)

    Fukuda, Shinji; Sasaki, Yukie; Seno, Masato

    2008-01-01

    We developed a two-step isothermal amplification assay system, which achieved the detection of norovirus (NoV) genomes in oysters with a sensitivity similar to that of reverse transcription-seminested PCR. The time taken for the amplification of NoV genomes from RNA extracts was shortened to about 3 h. PMID:18456857

  15. Rapid and Sensitive Detection of Norovirus Genomes in Oysters by a Two-Step Isothermal Amplification Assay System Combining Nucleic Acid Sequence-Based Amplification and Reverse Transcription-Loop-Mediated Isothermal Amplification Assays▿

    OpenAIRE

    Fukuda, Shinji; Sasaki, Yukie; Seno, Masato

    2008-01-01

    We developed a two-step isothermal amplification assay system, which achieved the detection of norovirus (NoV) genomes in oysters with a sensitivity similar to that of reverse transcription-seminested PCR. The time taken for the amplification of NoV genomes from RNA extracts was shortened to about 3 h.

  16. Rapid and sensitive detection of norovirus genomes in oysters by a two-step isothermal amplification assay system combining nucleic acid sequence-based amplification and reverse transcription-loop-mediated isothermal amplification assays.

    Science.gov (United States)

    Fukuda, Shinji; Sasaki, Yukie; Seno, Masato

    2008-06-01

    We developed a two-step isothermal amplification assay system, which achieved the detection of norovirus (NoV) genomes in oysters with a sensitivity similar to that of reverse transcription-seminested PCR. The time taken for the amplification of NoV genomes from RNA extracts was shortened to about 3 h.

  17. Drivers of trophic amplification of ocean productivity trends in a changing climate

    Science.gov (United States)

    Stock, C. A.; Dunne, J. P.; John, J. G.

    2014-07-01

    Pronounced projected 21st century trends in regional oceanic net primary production (NPP) raise the prospect of significant redistributions of marine resources. Recent results further suggest that NPP changes may be amplified at higher trophic levels. Here, we elucidate the role of planktonic food web dynamics in driving projected changes in mesozooplankton production (MESOZP) found to be, on average, twice as large as projected changes in NPP by the latter half of the 21st century under a high emissions scenario. Globally, MESOZP was projected to decline by 7.9% but regional MESOZP changes sometimes exceeded 50%. Changes in three planktonic food web properties - zooplankton growth efficiency (ZGE), the trophic level of mesozooplankton (MESOTL), and the fraction of NPP consumed by zooplankton (zooplankton-phytoplankton coupling, ZPC), were demonstrated to be responsible for the projected amplification. Zooplankton growth efficiencies (ZGE) changed with NPP, amplifying both NPP increases and decreases. Negative amplification (i.e., exacerbation) of projected subtropical NPP declines via this mechanism was particularly strong since consumers in the subtropics already have limited surplus energy above basal metabolic costs. Increased mesozooplankton trophic level (MESOTL) resulted from projected declines in large phytoplankton production, the primary target of herbivorous mesozooplankton. This further amplified negative subtropical NPP declines but was secondary to ZGE and, at higher latitudes, was often offset by increased ZPC. Marked ZPC increases were projected for high latitude regions experiencing shoaling of deep winter mixing or decreased winter sea ice - both tending to increase winter zooplankton biomass and enhance grazer control of spring blooms. Increased ZPC amplified projected NPP increases associated with declining sea ice in the Artic and damped projected NPP declines associated with decreased mixing in the Northwest Atlantic and Southern Ocean

  18. Arctic amplification: does it impact the polar jet stream?

    Directory of Open Access Journals (Sweden)

    Valentin P. Meleshko

    2016-10-01

    Full Text Available It has been hypothesised that the Arctic amplification of temperature changes causes a decrease in the northward temperature gradient in the troposphere, thereby enhancing the oscillation of planetary waves leading to extreme weather in mid-latitudes. To test this hypothesis, we study the response of the atmosphere to Arctic amplification for a projected summer sea-ice-free period using an atmospheric model with prescribed surface boundary conditions from a state-of-the-art Earth system model. Besides a standard global warming simulation, we also conducted a sensitivity experiment with sea ice and sea surface temperature anomalies in the Arctic. We show that when global climate warms, enhancement of the northward heat transport provides the major contribution to decrease the northward temperature gradient in the polar troposphere in cold seasons, causing more oscillation of the planetary waves. However, while Arctic amplification significantly enhances near-surface air temperature in the polar region, it is not large enough to invoke an increased oscillation of the planetary waves.

  19. Nucleic acid amplification of individual molecules in a microfluidic device.

    Science.gov (United States)

    Dettloff, Roger; Yang, Esther; Rulison, Aaron; Chow, Andrea; Farinas, Javier

    2008-06-01

    A microfluidic device was developed that enabled rapid polymerase chain reaction (PCR) analysis of individual DNA molecules. The device combined a means for accessing samples serially from a microtiter plate, channels for assembling eight parallel PCR reactions, and integrated resistive heaters for rapid thermocycling (>5 degrees C/s heating, >7 degrees C/s cooling) of samples as they flowed continuously through PCR channels. Amplification was monitored by fluorescence detection of Taqman probes. The long, narrow channels (10 microm x 180 microm x 40 mm) allowed sufficient separation between neighboring DNA templates to enable amplification of discreet DNA molecules. The functionality of the device was demonstrated by reproducibly amplifying a 2D6.6 CYP450 template and distinguishing between wild-type and mutant sequences using Taqman probes. A comparison of the rate of individual amplification events to the expected Poisson distribution confirmed that the device could reliably analyze individual DNA molecules. This work establishes the feasibility of rapid, single-molecule interrogation of nucleic acids.

  20. Mechanism of seasonal Arctic sea ice evolution and Arctic amplification

    Directory of Open Access Journals (Sweden)

    K.-Y. Kim

    2016-09-01

    Full Text Available Sea ice loss is proposed as a primary reason for the Arctic amplification, although the physical mechanism of the Arctic amplification and its connection with sea ice melting is still in debate. In the present study, monthly ERA-Interim reanalysis data are analyzed via cyclostationary empirical orthogonal function analysis to understand the seasonal mechanism of sea ice loss in the Arctic Ocean and the Arctic amplification. While sea ice loss is widespread over much of the perimeter of the Arctic Ocean in summer, sea ice remains thin in winter only in the Barents–Kara seas. Excessive turbulent heat flux through the sea surface exposed to air due to sea ice reduction warms the atmospheric column. Warmer air increases the downward longwave radiation and subsequently surface air temperature, which facilitates sea surface remains to be free of ice. This positive feedback mechanism is not clearly observed in the Laptev, East Siberian, Chukchi, and Beaufort seas, since sea ice refreezes in late fall (November before excessive turbulent heat flux is available for warming the atmospheric column in winter. A detailed seasonal heat budget is presented in order to understand specific differences between the Barents–Kara seas and Laptev, East Siberian, Chukchi, and Beaufort seas.

  1. Spatial distribution of laminar flow-assisted dendritic amplification.

    Science.gov (United States)

    Hosokawa, Kazuo; Maeda, Mizuo

    2009-02-07

    In this paper, we report spatial distribution of laminar flow-assisted dendritic amplification (LFDA) product. LFDA is a recently invented signal amplification method dedicated to biomolecular binding events on microchannel walls. Onto the bound biomolecule, a dendritic structure is constructed by supplying two building blocks from laminar streams produced by a Y-shaped microchannel. In view of the extension of LFDA to simultaneous amplification of multiple binding spots, we have investigated the distribution of the LFDA product across and along the microchannel with the course of time. We fabricated a Y-shaped microchannel with a cross section of 110 microm x 22 microm using poly(dimethylsiloxane). As the LFDA building blocks, FITC-labeled streptavidin and biotinylated anti-streptavidin were injected from the two inlets of the microchannel at a mean flow velocity of 6.2 mm s(-1) (after the confluence). Nonspecific adsorption of the building blocks formed the seed layer of LFDA. The progress of LFDA was monitored with a fluorescence microscope up to 10.1 mm of microchannel length. After 5 min or later, the fluorescence intensity profile across the microchannel showed a peak at the center of the channel. With the course of time, the peak height grew exponentially except for slight saturation, but the peak width was almost constant. Along the microchannel, the peak height decreased almost linearly with the increasing logarithm of the distance, and the peak width was broadened in accordance with the 1/3 power law.

  2. Current amplification models of sensorineurall and conductive hearing loss

    Directory of Open Access Journals (Sweden)

    Ostojić Sanja

    2012-01-01

    Full Text Available The main function of a hearing aid is to improve auditory and language abilities of hearing impaired users. The amplification model has to be adapted according to age, degree and type of hearing loss. The goal of this paper is to analyze the current amplification models of sensorineural and conductive hearing loss which can provide a high quality of speech perception and sounds at any degree of hearing loss. The BAHA is a surgically implantable system for treatment of conductive hearing loss that works through direct bone conduction. BAHA is used to help people with chronic ear infections, congenital external auditory canal atresia and single sided deafness who cannot benefit from conventional hearing aids. The last generation of hearing aid for sensorineural hearing loss is cochlear implant. Bimodal amplification improves binaural hearing. Hearing aids alone do not make listening easier in all situations. The things that can interfere with listening are background noises, distance from a sound and reverberation or echo. The device used most often today is the Frequency Modulated (FM system.

  3. Ancient DNA: genomic amplification of Roman and medieval bovine bones

    Directory of Open Access Journals (Sweden)

    A. Valentini

    2010-04-01

    Full Text Available Cattle remains (bones and teeth of both roman and medieval age were collected in the archaeological site of Ferento (Viterbo, Italy with the aim of extracting and characterising nucleic acids. Procedures to minimize contamination with modern DNA and to help ancient DNA (aDNA preservation of the archaeological remains were adopted. Different techniques to extract aDNA (like Phenol/chloroform extraction from bovine bones were tested to identify the method that applies to the peculiar characteristics of the study site. Currently, aDNA investigation is mainly based on mtDNA, due to the ease of amplification of the small and high-copied genome and to its usefulness in evolutionary studies. Preliminary amplification of both mitochondrial and nuclear aDNA fragments from samples of Roman and medieval animals were performed and partial specific sequences of mitochondrial D-loop as well as of nuclear genes were obtained. The innovative amplification of nuclear aDNA could enable the analysis of genes involved in specific animal traits, giving insights of ancient economic and cultural uses, as well as providing information on the origin of modern livestock population.

  4. Diagnosis of brugian filariasis by loop-mediated isothermal amplification.

    Directory of Open Access Journals (Sweden)

    Catherine B Poole

    Full Text Available In this study we developed and evaluated a Brugia Hha I repeat loop-mediated isothermal amplification (LAMP assay for the rapid detection of Brugia genomic DNA. Amplification was detected using turbidity or fluorescence as readouts. Reactions generated a turbidity threshold value or a clear visual positive within 30 minutes using purified genomic DNA equivalent to one microfilaria. Similar results were obtained using DNA isolated from blood samples containing B. malayi microfilariae. Amplification was specific to B. malayi and B. timori, as no turbidity was observed using DNA from the related filarial parasites Wuchereria bancrofti, Onchocerca volvulus or Dirofilaria immitis, or from human or mosquito. Furthermore, the assay was most robust using a new strand-displacing DNA polymerase termed Bst 2.0 compared to wild-type Bst DNA polymerase, large fragment. The results indicate that the Brugia Hha I repeat LAMP assay is rapid, sensitive and Brugia-specific with the potential to be developed further as a field tool for diagnosis and mapping of brugian filariasis.

  5. Determining generic velocity and density models for crustal amplification calculations, with an update of the Boore and Joyner (1997) Generic Site Amplification for Graphic Site Amplification

    Science.gov (United States)

    Boore, David

    2016-01-01

    This short note contains two contributions related to deriving depth‐dependent velocity and density models for use in computing generic crustal amplifications. The first contribution is a method for interpolating two velocity profiles to obtain a third profile with a time‐averaged velocity  to depth Z that is equal to a specified value (e.g., for shear‐wave velocity VS,  for Z=30  m, in which the subscript S has been added to indicate that the average is for shear‐wave velocities). The second contribution is a procedure for obtaining densities from VS. The first contribution is used to extend and revise the Boore and Joyner (1997) generic rock VS model, for which , to a model with the more common . This new model is then used with the densities from the second contribution to compute crustal amplifications for a generic site with .

  6. Glycoform-independent prion conversion by highly efficient, cell-based, protein misfolding cyclic amplification

    OpenAIRE

    Moudjou, Mohammed; Chapuis, J?r?me; Mekrouti, M?riem; Reine, Fabienne; Herzog, Laetitia; Sibille, Pierre; Laude, Hubert; Vilette, Didier; Andr?oletti, Olivier; Rezaei, Human; Dron, Michel; B?ringue, Vincent

    2016-01-01

    Prions are formed of misfolded assemblies (PrPSc) of the variably N-glycosylated cellular prion protein (PrPC). In infected species, prions replicate by seeding the conversion and polymerization of host PrPC. Distinct prion strains can be recognized, exhibiting defined PrPSc biochemical properties such as the glycotype and specific biological traits. While strain information is encoded within the conformation of PrPSc assemblies, the storage of the structural information and the molecular req...

  7. Comparison between NuGEN's WT-Ovation Pico and one-direct amplification systems.

    Science.gov (United States)

    Morse, Alison M; Carballo, Valentina; Baldwin, Donald A; Taylor, Christopher G; McIntyre, Lauren M

    2010-09-01

    Differential gene expression between groups of homogenous cell types is a biological question whose time has come. RNA can be extracted from small numbers of cells, such as those isolated by laser-capture microdissection, but the small amounts obtained often require amplification to enable whole genome transcriptome profiling by technologies such as microarray analysis and RNA-seq. Recently, advances in amplification procedures make amplification directly from whole cell lysates possible. The aim of this study was to compare two amplification systems for variations in observed RNA abundance attributable to the amplification procedure for use with small quantities of cells isolated by laser-capture microdissection. Arabidopsis root cells undergoing giant cell formation as a result of nematode infestation and uninfested control root cells were laser-captured and used to evaluate two amplification systems. One, NuGEN's WT-Ovation Pico (Pico) amplification system, uses total RNA as starting material, and the other, NuGEN's WT-One-Direct (One-Direct) amplification system, uses lysate containing the captured cells. The reproducibility of whole genome transcript profiling and correlations of both systems were investigated after microarray analysis. The One-Direct system was less reproducible and more variable than the Pico system. The Pico amplification kit resulted in the detection of thousands of differentially expressed genes between giant cells and control cells. This is in marked contrast to the relatively few genes detected after amplification with the One-Direct amplification kit.

  8. Magnetic nanobeads present during enzymatic amplification and labeling for a simplified DNA detection protocol based on AC susceptometry

    Science.gov (United States)

    Bejhed, Rebecca S.; Strømme, Maria; Svedlindh, Peter; Ahlford, Annika; Strömberg, Mattias

    2015-12-01

    Magnetic biosensors are promising candidates for low-cost point-of-care biodiagnostic devices. For optimal efficiency it is crucial to minimize the time and complexity of the assay protocol including target recognition, amplification, labeling and read-out. In this work, possibilities for protocol simplifications for a DNA biodetection principle relying on hybridization of magnetic nanobeads to rolling circle amplification (RCA) products are investigated. The target DNA is recognized through a padlock ligation assay resulting in DNA circles serving as templates for the RCA process. It is found that beads can be present during amplification without noticeably interfering with the enzyme used for RCA (phi29 polymerase). As a result, the bead-coil hybridization can be performed immediately after amplification in a one-step manner at elevated temperature within a few minutes prior to read-out in an AC susceptometer setup, i.e. a combined protocol approach. Moreover, by recording the phase angle ξ = arctan(χ″/χ'), where χ and χ″ are the in-phase and out-of-phase components of the AC susceptibility, respectively, at one single frequency the total assay time for the optimized combined protocol would be no more than 1.5 hours, often a relevant time frame for diagnosis of cancer and infectious disease. Also, applying the phase angle method normalization of AC susceptibility data is not needed. These findings are useful for the development of point-of-care biodiagnostic devices relying on bead-coil binding and magnetic AC susceptometry.

  9. Magnetic nanobeads present during enzymatic amplification and labeling for a simplified DNA detection protocol based on AC susceptometry

    Directory of Open Access Journals (Sweden)

    Rebecca S. Bejhed

    2015-12-01

    Full Text Available Magnetic biosensors are promising candidates for low-cost point-of-care biodiagnostic devices. For optimal efficiency it is crucial to minimize the time and complexity of the assay protocol including target recognition, amplification, labeling and read-out. In this work, possibilities for protocol simplifications for a DNA biodetection principle relying on hybridization of magnetic nanobeads to rolling circle amplification (RCA products are investigated. The target DNA is recognized through a padlock ligation assay resulting in DNA circles serving as templates for the RCA process. It is found that beads can be present during amplification without noticeably interfering with the enzyme used for RCA (phi29 polymerase. As a result, the bead-coil hybridization can be performed immediately after amplification in a one-step manner at elevated temperature within a few minutes prior to read-out in an AC susceptometer setup, i.e. a combined protocol approach. Moreover, by recording the phase angle ξ = arctan(χ″/χ′, where χ and χ″ are the in-phase and out-of-phase components of the AC susceptibility, respectively, at one single frequency the total assay time for the optimized combined protocol would be no more than 1.5 hours, often a relevant time frame for diagnosis of cancer and infectious disease. Also, applying the phase angle method normalization of AC susceptibility data is not needed. These findings are useful for the development of point-of-care biodiagnostic devices relying on bead-coil binding and magnetic AC susceptometry.

  10. Self-Assembled DNA Tetrahedral Scaffolds for the Construction of Electrochemiluminescence Biosensor with Programmable DNA Cyclic Amplification.

    Science.gov (United States)

    Feng, Qiu-Mei; Guo, Yue-Hua; Xu, Jing-Juan; Chen, Hong-Yuan

    2017-05-24

    A novel DNA tetrahedron-structured electrochemiluminescence (ECL) platform for bioanalysis with programmable DNA cyclic amplification was developed. In this work, glucose oxidase (GOD) was labeled to a DNA sequence (S) as functional conjugation (GOD-S), which could hybridize with other DNA sequences (L and P) to form GOD-S:L:P probe. In the presence of target DNA and a help DNA (A), the programmable DNA cyclic amplification was activated and released GOD-S via toehold-mediated strand displacement. Then, the obtained GOD-S was further immobilized on the DNA tetrahedral scaffolds with a pendant capture DNA and Ru(bpy)32+-conjugated silica nanoparticles (RuSi NPs) decorated on the electrode surface. Thus, the amount of GOD-S assembled on the electrode surface depended on the concentration of target DNA and GOD could catalyze glucose to generate H2O2 in situ. The ECL signal of Ru(bpy)32+-TPrA system was quenched by the presence of H2O2. By integrating the programmable DNA cyclic amplification and in situ generating H2O2 as Ru(bpy)32+ ECL quencher, a sensitive DNA tetrahedron-structured ECL sensing platform was proposed for DNA detection. Under optimized conditions, this biosensor showed a wide linear range from 100 aM to 10 pM with a detection limit of 40 aM, indicating a promising application in DNA analysis. Furthermore, by labeling GOD to different recognition elements, the proposed strategy could be used for the detection of various targets. Thus, this programmable cascade amplification strategy not only retains the high selectivity and good capturing efficiency of tetrahedral-decorated electrode surface but also provides potential applications in the construction of ECL biosensor.

  11. Impact of whole-genome amplification on the reliability of pre-transfer cattle embryo breeding value estimates.

    Science.gov (United States)

    Shojaei Saadi, Habib A; Vigneault, Christian; Sargolzaei, Mehdi; Gagné, Dominic; Fournier, Éric; de Montera, Béatrice; Chesnais, Jacques; Blondin, Patrick; Robert, Claude

    2014-10-12

    Genome-wide profiling of single-nucleotide polymorphisms is receiving increasing attention as a method of pre-implantation genetic diagnosis in humans and of commercial genotyping of pre-transfer embryos in cattle. However, the very small quantity of genomic DNA in biopsy material from early embryos poses daunting technical challenges. A reliable whole-genome amplification (WGA) procedure would greatly facilitate the procedure. Several PCR-based and non-PCR based WGA technologies, namely multiple displacement amplification, quasi-random primed library synthesis followed by PCR, ligation-mediated PCR, and single-primer isothermal amplification were tested in combination with different DNA extractions protocols for various quantities of genomic DNA inputs. The efficiency of each method was evaluated by comparing the genotypes obtained from 15 cultured cells (representative of an embryonic biopsy) to unamplified reference gDNA. The gDNA input, gDNA extraction method and amplification technology were all found to be critical for successful genome-wide genotyping. The selected WGA platform was then tested on embryo biopsies (n = 226), comparing their results to that of biopsies collected after birth. Although WGA inevitably leads to a random loss of information and to the introduction of erroneous genotypes, following genomic imputation the resulting genetic index of both sources of DNA were highly correlated (r = 0.99, P<0.001). It is possible to generate high-quality DNA in sufficient quantities for successful genome-wide genotyping starting from an early embryo biopsy. However, imputation from parental and population genotypes is a requirement for completing and correcting genotypic data. Judicious selection of the WGA platform, careful handling of the samples and genomic imputation together, make it possible to perform extremely reliable genomic evaluations for pre-transfer embryos.

  12. Cytogenetic manifestation of chromosome 11 duplication/amplification in acute myeloid leukemia.

    Science.gov (United States)

    Sárová, Iveta; Brezinová, Jana; Zemanová, Zuzana; Izáková, Silvia; Lizcová, Libuse; Malinová, Eva; Berková, Adéla; Cermák, Jaroslav; Maaloufová, Jacqueline; Nováková, Ludmila; Michalová, Kyra

    2010-06-01

    Gene amplification is a frequent genetic abnormality in solid tumors, and many oncogenes are activated in this way. In acute myeloid leukemia (AML), a frequent target of gene amplification is chromosome 11, particularly chromosome region 11q23, including the MLL (myeloid/lymphoid leukemia) gene. However, the number of other amplicons from the long arm of chromosome 11 has also been described. Duplication/amplification of chromosome 11 was found by cytogenetic methods in 10 of 119 newly diagnosed patients with AML. The amplification was presented as: amplification including only the 5' segment of the MLL gene (1 patient), trisomy 11 (3 patients), partial trisomy 11q (2 patients), isochromosome 11q (1 patient), and multiple amplification of specific regions (3 patients). In two cases, amplification involved parts of not only long arm but also of short arm of the chromosome 11: 11p15 and 11p11.1 to 11p13. Copyright 2010 Elsevier Inc. All rights reserved.

  13. KRAS and MAPK1 Gene Amplification in Type II Ovarian Carcinomas

    Directory of Open Access Journals (Sweden)

    Noriyuki Ishikawa

    2013-07-01

    Full Text Available In this study, we examined the clinical significance of KRAS and MAPK1 amplification and assessed whether these amplified genes were potential therapeutic targets in type II ovarian carcinoma. Using fluorescence in situ hybridization, immunohistochemistry, and retrospectively collected clinical data, KRAS and MAPK1 amplifications were identified in 9 (13.2% and 5 (7.4% of 68 type II ovarian carcinoma tissue samples, respectively. Interestingly, co-amplification of KRAS and MAPK1 seemed to be absent in the type II ovarian carcinomas tested, except one case. Active phospho-ERK1/2 was identified in 26 (38.2% out of 68 type II ovarian carcinomas and did not correlate with KRAS or MAPK1 amplification. There was no significant relationship between KRAS amplification and overall or progression-free survival in patients with type II ovarian carcinoma. However, patients with MAPK1 amplification had significantly poorer progression-free survival than patients without MAPK1 amplification. Moreover, type II ovarian carcinoma cells with concomitant KRAS amplification and mutation exhibited dramatic growth reduction following treatment with the MEK inhibitor PD0325901. These findings indicate that KRAS/MAPK1 amplification is critical for the growth of a subset of type II ovarian carcinomas. Additionally, RAS/RAF/MEK/ERK pathway-targeted therapy may benefit selected patients with type II ovarian carcinoma harboring KRAS/MAPK1 amplifications.

  14. Randomness Amplification under Minimal Fundamental Assumptions on the Devices

    Science.gov (United States)

    Ramanathan, Ravishankar; Brandão, Fernando G. S. L.; Horodecki, Karol; Horodecki, Michał; Horodecki, Paweł; Wojewódka, Hanna

    2016-12-01

    Recently, the physically realistic protocol amplifying the randomness of Santha-Vazirani sources producing cryptographically secure random bits was proposed; however, for reasons of practical relevance, the crucial question remained open regarding whether this can be accomplished under the minimal conditions necessary for the task. Namely, is it possible to achieve randomness amplification using only two no-signaling components and in a situation where the violation of a Bell inequality only guarantees that some outcomes of the device for specific inputs exhibit randomness? Here, we solve this question and present a device-independent protocol for randomness amplification of Santha-Vazirani sources using a device consisting of two nonsignaling components. We show that the protocol can amplify any such source that is not fully deterministic into a fully random source while tolerating a constant noise rate and prove the composable security of the protocol against general no-signaling adversaries. Our main innovation is the proof that even the partial randomness certified by the two-party Bell test [a single input-output pair (u* , x* ) for which the conditional probability P (x*|u*) is bounded away from 1 for all no-signaling strategies that optimally violate the Bell inequality] can be used for amplification. We introduce the methodology of a partial tomographic procedure on the empirical statistics obtained in the Bell test that ensures that the outputs constitute a linear min-entropy source of randomness. As a technical novelty that may be of independent interest, we prove that the Santha-Vazirani source satisfies an exponential concentration property given by a recently discovered generalized Chernoff bound.

  15. Limits of femtosecond fiber amplification by parabolic pre-shaping

    Science.gov (United States)

    Fu, Walter; Tang, Yuxing; McComb, Timothy S.; Lowder, Tyson L.; Wise, Frank W.

    2017-03-01

    We explore parabolic pre-shaping as a means of generating and amplifying ultrashort pulses. We develop a theoretical framework for modeling the technique and use its conclusions to design a femtosecond fiber amplifier. Starting from 9 ps pulses, we obtain 4.3 $\\mu$J, nearly transform-limited pulses 275 fs in duration, simultaneously achieving over 40 dB gain and 33-fold compression. Finally, we show that this amplification scheme is limited by Raman scattering, and outline a method by which the pulse duration and energy may be further improved and tailored for a given application.

  16. Rapid detection of Mycobacterium tuberculosis by recombinase polymerase amplification.

    Directory of Open Access Journals (Sweden)

    David S Boyle

    Full Text Available Improved access to effective tests for diagnosing tuberculosis (TB has been designated a public health priority by the World Health Organisation. In high burden TB countries nucleic acid based TB tests have been restricted to centralised laboratories and specialised research settings. Requirements such as a constant electrical supply, air conditioning and skilled, computer literate operators prevent implementation of such tests in many settings. Isothermal DNA amplification technologies permit the use of simpler, less energy intensive detection platforms more suited to low resource settings that allow the accurate diagnosis of a disease within a short timeframe. Recombinase Polymerase Amplification (RPA is a rapid, low temperature isothermal DNA amplification reaction. We report here RPA-based detection of Mycobacterium tuberculosis complex (MTC DNA in <20 minutes at 39 °C. Assays for two MTC specific targets were investigated, IS6110 and IS1081. When testing purified MTC genomic DNA, limits of detection of 6.25 fg (IS6110 and 20 fg (IS1081were consistently achieved. When testing a convenience sample of pulmonary specimens from suspected TB patients, RPA demonstrated superior accuracy to indirect fluorescence microscopy. Compared to culture, sensitivities for the IS1081 RPA and microscopy were 91.4% (95%CI: 85, 97.9 and 86.1% (95%CI: 78.1, 94.1 respectively (n = 71. Specificities were 100% and 88.6% (95% CI: 80.8, 96.1 respectively. For the IS6110 RPA and microscopy sensitivities of 87.5% (95%CI: 81.7, 93.2 and 70.8% (95%CI: 62.9, 78.7 were obtained (n = 90. Specificities were 95.4 (95% CI: 92.3,98.1 and 88% (95% CI: 83.6, 92.4 respectively. The superior specificity of RPA for detecting tuberculosis was due to the reduced ability of fluorescence microscopy to distinguish Mtb complex from other acid fast bacteria. The rapid nature of the RPA assay and its low energy requirement compared to other amplification technologies suggest RPA-based TB

  17. Utilization of non-linear converters for audio amplification

    DEFF Research Database (Denmark)

    Iversen, Niels Elkjær; Birch, Thomas; Knott, Arnold

    2012-01-01

    Class D amplifiers fits the automotive demands quite well. The traditional buck-based amplifier has reduced both the cost and size of amplifiers. However the buck topology is not without its limitations. The maximum peak AC output voltage produced by the power stage is only equal the supply voltage....... The introduction of non-linear converters for audio amplification defeats this limitation. A Cuk converter, designed to deliver an AC peak output voltage twice the supply voltage, is presented in this paper. A 3V prototype has been developed to prove the concept. The prototype shows that it is possible to achieve...

  18. Direct field measurement of the dynamic amplification in a bridge

    Science.gov (United States)

    Carey, Ciarán; OBrien, Eugene J.; Malekjafarian, Abdollah; Lydon, Myra; Taylor, Su

    2017-02-01

    In this paper, the level of dynamics, as described by the Assessment Dynamic Ratio (ADR), is measured directly through a field test on a bridge in the United Kingdom. The bridge was instrumented using fiber optic strain sensors and piezo-polymer weigh-in-motion sensors were installed in the pavement on the approach road. Field measurements of static and static-plus-dynamic strains were taken over 45 days. The results show that, while dynamic amplification is large for many loading events, these tend not to be the critical events. ADR, the allowance that should be made for dynamics in an assessment of safety, is small.

  19. Multiple Endonuclease Restriction Real-Time Loop-Mediated Isothermal Amplification: A Novel Analytically Rapid, Sensitive, Multiplex Loop-Mediated Isothermal Amplification Detection Technique.

    Science.gov (United States)

    Wang, Yi; Wang, Yan; Lan, Ruiting; Xu, Huaqing; Ma, Aijing; Li, Dongxun; Dai, Hang; Yuan, Xuejiao; Xu, Jianguo; Ye, Changyun

    2015-07-01

    Loop-mediated isothermal amplification (LAMP) is restricted to detecting a single target, limiting the usefulness of this method. To achieve multiplex LAMP-based detection, we developed a novel approach we called the multiple endonuclease restriction real-time-LAMP assay. In this system, the LAMP forward or backward inner primers contain 5' end short sequences that are recognized by the restriction endonuclease Nb.BsrDI, and the new forward or backward inner primers were modified at the 5' end with a fluorophore and in the middle with a dark quencher. Nb.BsrDI digests the newly synthesized double-stranded terminal sequences (5' end short sequences and their complementary sequences), which releases the quenching, resulting in a gain of signal. The assay permitted real-time detection of single or multiple target sequences in a single tube, and the positive results can be obtained in as short as 12 minutes. The novel methodology is highly efficient and specific, detecting down to 250 fg of DNA per reaction of Listeria DNA tested, and was successful in evaluating raw meat samples. The multiple endonuclease restriction real-time-LAMP technology, which is an extension of LAMP to accommodate robust, target-specific, and multiplex detection, provides a molecular diagnostic tool with less detection time and high sensitivity and specificity compared with those of LAMP and quantitative real-time PCR. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  20. Comparison of three DNA extraction methods for feed products and four amplification methods for the 5'-junction fragment of Roundup Ready soybean.

    Science.gov (United States)

    Wang, Xiumin; Teng, Da; Tian, Fang; Guan, Qingfeng; Wang, Jianhua

    2012-05-09

    Three methods of DNA extraction from feed products and four detection methods for the 5'-junction fragment of genetically modified (GM) Roundup Ready soybean (RRS) were compared and evaluated. The DNA extraction methods, including cetyltrimethylammonium bromide (CTAB), sodium dodecyl sulfate (SDS), and guanidine hydrochloride (Kit), were assessed for their yields and purity of DNA, extraction time, and reagent cost. The DNA yields of CTAB, SDS, and Kit were 52-694, 164-1750 and 23-105 ng/mg sample, and their extraction time was 2.5-3, 2-2.5, and 1.5-2 h with reagent cost about US dollar 0.24, 0.13, and 1.9 per extraction, respectively. The SDS method was generally well suited to all kinds of feed matrices tested. The limits of detection for the four amplification protocols, including loop-mediated isothermal amplification (LAMP), hyperbranched rolling circle amplification (HRCA), conventional polymerase chain reaction (PCR), and real-time PCR, were 48.5, 4.85, 485, and 9 copies of the pTLH10 plasmid, respectively. The ranked results of the four detection methods were based on multiattribute utility theory as follows (from best to worse): HRCA, LAMP, PCR, and real-time PCR. This comparative evaluation was specifically useful for selection of a highly efficient DNA extraction or amplification method for detecting different GM ingredients.

  1. [Automated RNA amplification for the rapid identification of Mycobacterium tuberculosis complex in respiratory specimens].

    Science.gov (United States)

    Drouillon, V; Houriez, F; Buze, M; Lagrange, P; Herrmann, J-L

    2006-01-01

    Rapid and sensitive detection of Mycobacterium tuberculosis complex (MTB) directly on clinical respiratory specimens is essential for a correct management of patients suspected of tuberculosis. For this purpose PCR-based kits are available to detect MTB in respiratory specimen but most of them need at least 4 hours to be completed. New methods, based on TRC method (TRC: Transcription Reverse transcription Concerted--TRCRapid M. Tuberculosis--Tosoh Bioscience, Tokyo, Japon) and dedicated monitor have been developed. A new kit (TRC Rapid M. tuberculosis and Real-time monitor TRCRapid-160, Tosoh Corporation, Japan) enabling one step amplification and real-time detection of MTB 16S rRNA by a combination of intercalative dye oxazole yellow-linked DNA probe and isothermal RNA amplification directly on respiratory specimens has been tested in our laboratory. 319 respiratory specimens were tested in this preliminary study and results were compared to smear and culture. Fourteen had a positive culture for MTB. Among theses samples, smear was positive in 11 cases (78.6%) and TRC process was positive in 8 cases (57.1%). Overall sensitivity of TRC compared to smear positive samples is 73%. Theses first results demonstrated that a rapid identification of MTB was possible (less than 2 processing hours for 14 specimens and about 1 hour for 1 specimen) in most cases of smear positive samples using ready to use reagents for real time detection of MTB rRNA in clinical samples. New pretreatment and extraction reagents kits to increase the stability of the sputum RNA and the extraction efficiency are now tested in our laboratory.

  2. Platinum Nanocatalyst Amplification: Redefining the Gold Standard for Lateral Flow Immunoassays with Ultrabroad Dynamic Range.

    Science.gov (United States)

    Loynachan, Colleen N; Thomas, Michael R; Gray, Eleanor R; Richards, Daniel A; Kim, Jeongyun; Miller, Benjamin S; Brookes, Jennifer C; Agarwal, Shweta; Chudasama, Vijay; McKendry, Rachel A; Stevens, Molly M

    2018-01-23

    Paper-based lateral flow immunoassays (LFIAs) are one of the most widely used point-of-care (PoC) devices; however, their application in early disease diagnostics is often limited due to insufficient sensitivity for the requisite sample sizes and the short time frames of PoC testing. To address this, we developed a serum-stable, nanoparticle catalyst-labeled LFIA with a sensitivity surpassing that of both current commercial and published sensitivities for paper-based detection of p24, one of the earliest and most conserved biomarkers of HIV. We report the synthesis and characterization of porous platinum core-shell nanocatalysts (PtNCs), which show high catalytic activity when exposed to complex human blood serum samples. We explored the application of antibody-functionalized PtNCs with strategically and orthogonally modified nanobodies with high affinity and specificity toward p24 and established the key larger nanoparticle size regimes needed for efficient amplification and performance in LFIA. Harnessing the catalytic amplification of PtNCs enabled naked-eye detection of p24 spiked into sera in the low femtomolar range (ca. 0.8 pg·mL -1 ) and the detection of acute-phase HIV in clinical human plasma samples in under 20 min. This provides a versatile absorbance-based and rapid LFIA with sensitivity capable of significantly reducing the HIV acute phase detection window. This diagnostic may be readily adapted for detection of other biomolecules as an ultrasensitive screening tool for infectious and noncommunicable diseases and can be capitalized upon in PoC settings for early disease detection.

  3. Autocatalytic loop, amplification and diffusion: a mathematical and computational model of cell polarization in neural chemotaxis.

    Directory of Open Access Journals (Sweden)

    Paola Causin

    2009-08-01

    Full Text Available The chemotactic response of cells to graded fields of chemical cues is a complex process that requires the coordination of several intracellular activities. Fundamental steps to obtain a front vs. back differentiation in the cell are the localized distribution of internal molecules and the amplification of the external signal. The goal of this work is to develop a mathematical and computational model for the quantitative study of such phenomena in the context of axon chemotactic pathfinding in neural development. In order to perform turning decisions, axons develop front-back polarization in their distal structure, the growth cone. Starting from the recent experimental findings of the biased redistribution of receptors on the growth cone membrane, driven by the interaction with the cytoskeleton, we propose a model to investigate the significance of this process. Our main contribution is to quantitatively demonstrate that the autocatalytic loop involving receptors, cytoplasmic species and cytoskeleton is adequate to give rise to the chemotactic behavior of neural cells. We assess the fact that spatial bias in receptors is a precursory key event for chemotactic response, establishing the necessity of a tight link between upstream gradient sensing and downstream cytoskeleton dynamics. We analyze further crosslinked effects and, among others, the contribution to polarization of internal enzymatic reactions, which entail the production of molecules with a one-to-more factor. The model shows that the enzymatic efficiency of such reactions must overcome a threshold in order to give rise to a sufficient amplification, another fundamental precursory step for obtaining polarization. Eventually, we address the characteristic behavior of the attraction/repulsion of axons subjected to the same cue, providing a quantitative indicator of the parameters which more critically determine this nontrivial chemotactic response.

  4. A High-Energy, Ultrashort-Pulse X-Ray System for the Dynamic Study of Heavy, Dense Materials

    Energy Technology Data Exchange (ETDEWEB)

    Gibson, David Jeremy [Univ. of California, Davis, CA (United States)

    2004-01-01

    -power ultrafast laser systems. This system combines an optical-parametric chirped-pulse amplification (OPCPA) system with a titanium:sapphire-based four-pass amplifier to provide the high pre-pulse contrast and ease of assembly of an OPCPA using a commercial pump laser while avoiding the loss of efficiency such a system would normally entail.

  5. Transmission performance improvement using random DFB laser based Raman amplification and bidirectional second-order pumping

    OpenAIRE

    Tan, M.; Rosa, P; Le, S.T.; Iqbal, Md A.; Phillips, I.D.; Harper, P.

    2016-01-01

    We demonstrate that a distributed Raman amplification scheme based on random distributed feedback (DFB) fiber laser enables bidirectional second-order Raman pumping without increasing relative intensity noise (RIN) of the signal. This extends the reach of 10 × 116 Gb/s DP-QPSK WDM transmission up to 7915 km, compared with conventional Raman amplification schemes. Moreover, this scheme gives the longest maximum transmission distance among all the Raman amplification schemes presented in this p...

  6. Tuning backbones and side-chains of cationic conjugated polymers for optical signal amplification of fluorescent DNA detection.

    Science.gov (United States)

    Huang, Yan-Qin; Liu, Xing-Fen; Fan, Qu-Li; Wang, Lihua; Song, Shiping; Wang, Lian-Hui; Fan, Chunhai; Huang, Wei

    2009-06-15

    Three cationic conjugated polymers (CCPs) exhibiting different backbone geometries and charge densities were used to investigate how their conjugated backbone and side chain properties, together with the transitions of DNA amphiphilic properties, interplay in the CCP/DNA-C* (DNA-C*: fluorophore-labeled DNA) complexes to influence the optical signal amplification of fluorescent DNA detection based on Förster resonance energy transfer (FRET). By examining the FRET efficiencies to dsDNA-C* (dsDNA: double-stranded DNA) and ssDNA-C* (ssDNA: single-stranded DNA) for each CCP, twisted conjugated backbones and higher charge densities were proved to facilitate electrostatic attraction in CCP/dsDNA-C* complexes, and induced improved sensitivity to DNA hybridization. Especially, by using the CCP with twisted conjugated backbone and the highest charge density, a more than 7-fold higher efficiency of FRET to dsDNA-C* was found than to ssDNA-C*, indicating a high signal amplification for discriminating between dsDNA and ssDNA. By contrast, linear conjugated backbones and lower charge density were demonstrated to favor hydrophobic interactions in CCP/ssDNA-C* complexes. These findings provided guidelines for the design of novel sensitive CCP, which can be useful to recognize many other important DNA activities involving transitions of DNA amphiphilic properties like DNA hybridization, such as specific DNA binding with ions, some secondary or tertiary structural changes of DNA, and so forth.

  7. Constraining Magnetic Field Amplification in SN Shocks Using Radio Observations of SNe 2011fe and 2014J

    Science.gov (United States)

    Kundu, E.; Lundqvist, P.; Pérez-Torres, M. A.; Herrero-Illana, R.; Alberdi, A.

    2017-06-01

    We modeled the radio non-detection of two Type Ia supernovae (SNe), SN 2011fe and SN 2014J, considering synchrotron emission from the interaction between SN ejecta and the circumstellar medium. For ejecta whose outer parts have a power-law density structure, we compare synchrotron emission with radio observations. Assuming that 20% of the bulk shock energy is being shared equally between electrons and magnetic fields, we found a very low-density medium around both the SNe. A less tenuous medium with particle density ˜1 cm-3, which could be expected around both SNe, can be estimated when the magnetic field amplification is less than that presumed for energy equipartition. This conclusion also holds if the progenitor of SN 2014J was a rigidly rotating white dwarf (WD) with a main-sequence (MS) or red giant companion. For a He star companion, or a MS for SN 2014J, with 10% and 1% of bulk kinetic energy in magnetic fields, we obtain mass-loss rates of wind velocity of 100 {km} {{{s}}}-1. The former requires a mass accretion efficiency of >99% onto the WD, but is less restricted for the latter case. However, if the tenuous medium is due to a recurrent nova, it is difficult from our model to predict synchrotron luminosities. Although the formation channels of SNe 2011fe and 2014J are not clear, the null detection in radio wavelengths could point toward a low amplification efficiency for magnetic fields in SN shocks.

  8. Long-term in vitro system for maintenance and amplification of root-knot nematodes in Cucumis sativus roots

    Directory of Open Access Journals (Sweden)

    Fernando E. eDíaz-Manzano

    2016-02-01

    Full Text Available Root-knot nematodes (RKN are polyphagous plant-parasitic roundworms that produce large crop losses, representing a relevant agricultural pest worldwide. After infection, they induce swollen root structures called galls containing giant cells (GCs indispensable for nematode development. Among efficient control methods are biotechnology-based strategies that require a deep knowledge of underlying molecular processes during the plant-nematode interaction. Methods of achieving this knowledge include the application of molecular biology techniques such as transcriptomics (massive sequencing or microarray hybridization, proteomics or metabolomics. These require aseptic experimental conditions, as undetected contamination with other microorganisms could compromise the interpretation of the results. Herein, we present a simple, efficient and long-term method for nematode amplification on cucumber roots grown in vitro. Amplification of juveniles (J2 from the starting inoculum is around 40-fold. The method was validated for three Meloidogyne species (M. javanica, M. incognita and M. arenaria, producing viable and robust freshly hatched J2s. These can be used for further in vitro infection of different plant species such as Arabidopsis, tobacco and tomato, as well as enough J2s to maintain the population. The method allowed maintenance of around 90 Meloidogyne spp. generations (one every two months from a single initial female over 15 years.

  9. Development and Application of Surface Plasmon Polaritons on Optical Amplification

    Directory of Open Access Journals (Sweden)

    Tong Zhang

    2014-01-01

    Full Text Available Propagation of surface plasmon polaritons (SPPs along the interface between a metal and a dielectric has attracted significant attention due to its unique optical properties, which has inspired a plethora of fascinating applications in photonics and optoelectronics. However, SPPs suffer from large attenuation because of the ohmic losses in the metal layer. It has become the main bottom-neck problem for the development of high performance plasmonic devices. This limitation can be overcome by providing the material adjacent to the metal with optical gain. In this paper, a review of gain compensation to SPPs is presented. We focus on the spontaneous radiation amplification and simulated radiation amplification. The ohmic loss of metal was greatly improved by introducing optical gain. Then we introduce several gain mediums of dye doped, quantum dots, erbium ion, and semiconductor to compensate optical loss of SPPs. Using gain medium mentioned above can compensate losses and achieve many potential applications, for example, laser, amplifier, and LRSPP discussed.

  10. Health Risk Information Engagement and Amplification on Social Media.

    Science.gov (United States)

    Strekalova, Yulia A

    2017-04-01

    Emerging pandemics call for unique health communication and education strategies in which public health agencies need to satisfy the public's information needs about possible risks while preventing risk exaggeration and dramatization. As a route to providing a framework for understanding public information behaviors in response to an emerging pandemic, this study examined the characteristics of communicative behaviors of social media audiences in response to Ebola outbreak news. Grounded in the social amplification of risks framework, this study adds to an understanding of information behaviors of online audiences by showing empirical differences in audience engagement with online health information. The data were collected from the Centers for Disease Control and Prevention (CDC) Facebook channel. The final data set included 809 CDC posts and 35,916 audience comments. The analysis identified the differences in audience information behaviors in response to an emerging pandemic, Ebola, and health promotion posts. While the CDC had fewer posts on Ebola than health promotion topics, the former received more attention from active page users. Furthermore, audience members who actively engaged with Ebola news had a small overlap with those who engaged with non-Ebola information during the same period. Overall, this study demonstrated that information behavior and audience engagement is topic dependent. Furthermore, audiences who commented on news about an emerging pandemic were homogenous and varied in their degree of information amplification.

  11. Beyond Words: Amplification of Cancer Risk Communication on Social Media.

    Science.gov (United States)

    Strekalova, Yulia A; Krieger, Janice L

    2017-10-01

    Social media provide a unique channel for disseminating evidence-based information to diverse audiences and organizational and private stakeholders, thus facilitating a dialog about health and health risks. Guided by the social amplification of risk framework, the goal of this study was to assess the level of audience engagement with messages posted on the National Cancer Institute (NCI) Facebook page and evaluate the differences in the audience information behavior toward risk-related and non-risk posts. Data included 1,975 posts published on the NCI Facebook page as well as the corresponding 4,537 comments, 77,298 shares, and 145,462 likes. Links and images were the top two most frequent types of content for both risk-related and non-risk posts, but risk-related messages were more amplified through comments, shares, and likes. Comparing the modality of risk-related messages, videos, contrary to the prediction, were not more effective in attracting audience engagement than images. Finally, comments to risk-related posts did not repeat risk-related language suggesting that future studies should examine risk signal recognition and dissemination as separate behaviors. This study's findings emphasize the importance of focused investigation of message design strategies and message effects on the dissemination and amplification of communication related to health risks.

  12. When Amplification with Weak Values Fails to Suppress Technical Noise

    Directory of Open Access Journals (Sweden)

    George C. Knee

    2014-03-01

    Full Text Available The application of postselection to a weak quantum measurement leads to the phenomenon of weak values. Expressed in units of the measurement strength, the displacement of a quantum coherent measuring device is ordinarily bounded by the eigenspectrum of the measured observable. Postselection can enable an interference effect that moves the average displacement far outside this range, bringing practical benefits in certain situations. Employing the Fisher-information metric, we argue that the amplified displacement offers no fundamental metrological advantage, due to the necessarily reduced probability of success. Our understanding of metrological advantage is the possibility of a lower uncertainty in the estimate of an unknown parameter with a large number of trials. We analyze a situation in which the detector is pixelated with a finite resolution and in which the detector is afflicted by random displacements: imperfections that degrade the fundamental limits of parameter estimation. Surprisingly, weak-value amplification is no more robust to them than a technique making no use of the amplification effect brought about by a final, postselected measurement.

  13. Static and Dynamic Amplification Using Strong Mechanical Coupling

    KAUST Repository

    Ilyas, Saad

    2016-07-28

    Amplifying the signal-to-noise ratio of resonant sensors is vital toward the effort to miniaturize devices into the sub-micro and nano regimes. In this paper, we demonstrate theoretically and experimentally, amplification through mechanically coupled microbeams. The device is composed of two identical clamped-clamped beams, made of polyimide, connected at their middle through a third beam, which acts as a mechanical coupler. Each of the clamped-clamped microbeams and the coupler are designed to be actuated separately, hence providing various possibilities of actuation and sensing. The coupled resonator is driven into resonance near its first resonance mode and its dynamic behavior is explored via frequency sweeps. The results show significant amplification in the resonator amplitude when the signal is measured at the midpoint of the coupler compared with the response of the individual uncoupled beams. The static pull-in characteristics of the resonator are also studied. It is shown that the compliant mechanical coupler can serve as a low-power radio frequency switch actuated at low voltage loads. [2016-0100

  14. Amplification of traveling magnetostatic waves by parametric pumping

    Science.gov (United States)

    Bashkovskiy, A. V.; Zubkov, V. I.; Krutsenko, I. V.; Melkov, G. A.

    1984-07-01

    An experiment was performed with traveling surface magnetostatic waves in a structure consisting of two parallel microstrip lines isolated from one another on a common Polycor base, both covered with a YIG (yttrium-iron garnet) film on a GGG (gallium-gadolinum garnet) substrate. An open dielectric pumping cavity resonator at the center of the 9.6 micron thick YIG film on its substrate side was operating in the parallel mode, with its magnetic field parallel to the constant external magnetic field, this mode of operation requiring less power than the transverse mode. The frequency of surface magneto-static waves on the YIG film (saturation magnetization 4 pi m sub o = 1750 Gs, width of resonance line 2 delta H= 0.5 Oe) was approx 4.7 GHz and the pumping frequency was approx. 9.4 GHz, with the intensity of the external magnetic field approx. 940 Oe. Heating of the film was avoided by pumping with pulses of 20 micro sec duration at a repetition rate of 50 Hz rather than with a continuous wave. This experiment for the first time revealed amplification of surface magnetostatic waves, the gain reaching 16 dB at a pumping powr of 2.2 W with 8 MHz bandwidth and 3 micro sec. delay time. Amplification occurred in a magnetic field of intensity H0 corresponding to maximum signal transmission from input to output microstrip line.

  15. RESONANT AMPLIFICATION OF TURBULENCE BY THE BLAST WAVES

    Energy Technology Data Exchange (ETDEWEB)

    Zankovich, A. M.; Kovalenko, I. G., E-mail: ilya.g.kovalenko@gmail.com [Physicotechnical Institute, Volgograd State University, Volgograd 400062 (Russian Federation)

    2015-02-10

    We discuss the idea of whether spherical blast waves can amplify by a nonlocal resonant hydrodynamic mechanism inhomogeneities formed by turbulence or phase segregation in the interstellar medium. We consider the problem of a blast-wave-turbulence interaction in the Linear Interaction Approximation. Mathematically, this is an eigenvalue problem for finding the structure and amplitude of eigenfunctions describing the response of the shock-wave flow to forced oscillations by external perturbations in the ambient interstellar medium. Linear analysis shows that the blast wave can amplify density and vorticity perturbations for a wide range of length scales with amplification coefficients of up to 20, with increasing amplification the larger the length. There also exist resonant harmonics for which the gain becomes formally infinite in the linear approximation. Their orbital wavenumbers are within the range of macro- (l ∼ 1), meso- (l ∼ 20), and microscopic (l > 200) scales. Since the resonance width is narrow (typically, Δl < 1), resonance should select and amplify discrete isolated harmonics. We speculate on a possible explanation of an observed regular filamentary structure of regularly shaped round supernova remnants such as SNR 1572, 1006, or 0509-67.5. Resonant mesoscales found (l ≈ 18) are surprisingly close to the observed scales (l ≈ 15) of ripples in the shell's surface of SNR 0509-67.5.

  16. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity.

    Science.gov (United States)

    Turner, Kristen M; Deshpande, Viraj; Beyter, Doruk; Koga, Tomoyuki; Rusert, Jessica; Lee, Catherine; Li, Bin; Arden, Karen; Ren, Bing; Nathanson, David A; Kornblum, Harley I; Taylor, Michael D; Kaushal, Sharmeela; Cavenee, Webster K; Wechsler-Reya, Robert; Furnari, Frank B; Vandenberg, Scott R; Rao, P Nagesh; Wahl, Geoffrey M; Bafna, Vineet; Mischel, Paul S

    2017-03-02

    Human cells have twenty-three pairs of chromosomes. In cancer, however, genes can be amplified in chromosomes or in circular extrachromosomal DNA (ecDNA), although the frequency and functional importance of ecDNA are not understood. We performed whole-genome sequencing, structural modelling and cytogenetic analyses of 17 different cancer types, including analysis of the structure and function of chromosomes during metaphase of 2,572 dividing cells, and developed a software package called ECdetect to conduct unbiased, integrated ecDNA detection and analysis. Here we show that ecDNA was found in nearly half of human cancers; its frequency varied by tumour type, but it was almost never found in normal cells. Driver oncogenes were amplified most commonly in ecDNA, thereby increasing transcript level. Mathematical modelling predicted that ecDNA amplification would increase oncogene copy number and intratumoural heterogeneity more effectively than chromosomal amplification. We validated these predictions by quantitative analyses of cancer samples. The results presented here suggest that ecDNA contributes to accelerated evolution in cancer.

  17. Immigration, political trust, and Brexit - Testing an aversion amplification hypothesis.

    Science.gov (United States)

    Abrams, Dominic; Travaglino, Giovanni A

    2018-01-10

    A few weeks prior to the EU referendum (23rd June 2016) two broadly representative samples of the electorate were drawn in Kent (the south-east of England, N = 1,001) and Scotland (N = 1,088) for online surveys that measured their trust in politicians, concerns about acceptable levels of immigration, threat from immigration, European identification, and voting intention. We tested an aversion amplification hypothesis that the impact of immigration concerns on threat and identification would be amplified when political trust was low. We hypothesized that the effect of aversion amplification on voting intentions would be mediated first by perceived threat from immigration, and then by (dis) identification with Europe. Results in both samples were consistent with this hypothesis and suggest that voters were most likely to reject the political status quo (choose Brexit) when concerns that immigration levels were too high were combined with a low level of trust in politicians. © 2018 The Authors. British Journal of Social Psychology published by John Wiley & Sons Ltd on behalf of British Psychological Society.

  18. DNA Extraction and Amplification from Contemporary Polynesian Bark-Cloth

    Science.gov (United States)

    Moncada, Ximena; Payacán, Claudia; Arriaza, Francisco; Lobos, Sergio; Seelenfreund, Daniela; Seelenfreund, Andrea

    2013-01-01

    Background Paper mulberry has been used for thousands of years in Asia and Oceania for making paper and bark-cloth, respectively. Museums around the world hold valuable collections of Polynesian bark-cloth. Genetic analysis of the plant fibers from which the textiles were made may answer a number of questions of interest related to provenance, authenticity or species used in the manufacture of these textiles. Recovery of nucleic acids from paper mulberry bark-cloth has not been reported before. Methodology We describe a simple method for the extraction of PCR-amplifiable DNA from small samples of contemporary Polynesian bark-cloth (tapa) using two types of nuclear markers. We report the amplification of about 300 bp sequences of the ITS1 region and of a microsatellite marker. Conclusions Sufficient DNA was retrieved from all bark-cloth samples to permit successful PCR amplification. This method shows a means of obtaining useful genetic information from modern bark-cloth samples and opens perspectives for the analyses of small fragments derived from ethnographic materials. PMID:23437166

  19. Post-Fragmentation Whole Genome Amplification-Based Method

    Science.gov (United States)

    Benardini, James; LaDuc, Myron T.; Langmore, John

    2011-01-01

    This innovation is derived from a proprietary amplification scheme that is based upon random fragmentation of the genome into a series of short, overlapping templates. The resulting shorter DNA strands (fragmentation whole genome amplification-based technology provides a robust and accurate method of amplifying femtogram levels of starting material into microgram yields with no detectable allele bias. The amplified DNA also facilitates the preservation of samples (spacecraft samples) by amplifying scarce amounts of template DNA into microgram concentrations in just a few hours. Based on further optimization of this technology, this could be a feasible technology to use in sample preservation for potential future sample return missions. The research and technology development described here can be pivotal in dealing with backward/forward biological contamination from planetary missions. Such efforts rely heavily on an increasing understanding of the burden and diversity of microorganisms present on spacecraft surfaces throughout assembly and testing. The development and implementation of these technologies could significantly improve the comprehensiveness and resolving power of spacecraft-associated microbial population censuses, and are important to the continued evolution and advancement of planetary protection capabilities. Current molecular procedures for assaying spacecraft-associated microbial burden and diversity have inherent sample loss issues at practically every step, particularly nucleic acid extraction. In engineering a molecular means of amplifying nucleic acids directly from single cells in their native state within the sample matrix, this innovation has circumvented entirely the need for DNA extraction regimes in the sample processing scheme.

  20. CDK4 amplification predicts recurrence of well-differentiated liposarcoma of the abdomen.

    Directory of Open Access Journals (Sweden)

    Sanghoon Lee

    Full Text Available The absence of CDK4 amplification in liposarcomas is associated with favorable prognosis. We aimed to identify the factors associated with tumor recurrence in patients with well-differentiated (WD and dedifferentiated (DD liposarcomas.From 2000 to 2010, surgical resections for 101 WD and DD liposarcomas were performed. Cases in which complete surgical resections with curative intent were carried out were selected. MDM2 and CDK4 gene amplification were analyzed by quantitative real-time polymerase chain reaction (Q-PCR.There were 31 WD and 17 DD liposarcomas. Locoregional recurrence was observed in 11 WD and 3 DD liposarcomas. WD liposarcomas showed better patient survival compared to DD liposarcomas (P<0.05. Q-PCR analysis of the liposarcomas revealed the presence of CDK4 amplification in 44 cases (91.7% and MDM2 amplification in 46 cases (95.8%. WD liposarcomas with recurrence after surgical resection had significantly higher levels of CDK4 amplification compared to those without recurrence (P = 0.041. High level of CDK4 amplification (cases with CDK4 amplification higher than the median 7.54 was associated with poor recurrence-free survival compared to low CDK4 amplification in both univariate (P = 0.012 and multivariate analyses (P = 0.020.Level of CDK4 amplification determined by Q-PCR was associated with the recurrence of WD liposarcomas after surgical resection.

  1. Sensitive fluorescent detection of DNA methyltransferase using nicking endonuclease-mediated multiple primers-like rolling circle amplification.

    Science.gov (United States)

    Huang, Juan; Li, Xiao-Yu; Du, Yi-Chen; Zhang, Li-Na; Liu, Ke-Ke; Zhu, Li-Na; Kong, De-Ming

    2017-05-15

    Sensitive and reliable detection of DNA methyltransferase (MTase) is of great significance for both early tumor diagnosis and therapy. In this study, a simple, label-free and sensitive DNA MTase-sensing method was developed on the basis of a nicking endonuclease-mediated multiple primers-like rolling circle amplification (RCA) strategy. In this method, a dumbbell RCA template was prepared by blunt-end ligation of two molecules of hairpin DNA. In addition to the primer-binding sequence, the dumbbell template contained another three important parts: 5'-CCGG-3' sequences in double-stranded stems, nicking endonuclease recognition sites and C-rich sequences in single-stranded loops. The introduction of 5'-CCGG-3' sequences allows the dumbbell template to be destroyed by the restriction endonuclease, HpaII, but is not destroyed in the presence of the target MTase-M.SssI MTase. The introduction of nicking endonuclease recognition sites makes the M.SssI MTase-protected dumbbell template-mediated RCA proceed in a multiple primers-like exponential mode, thus providing the RCA with high amplification efficiency. The introduction of C-rich sequences may promote the folding of amplification products into a G-quadruplex structure, which is specifically recognized by the commercially available fluorescent probe thioflavin T. Improved RCA amplification efficiency and specific fluorescent recognition of RCA products provide the M.SssI MTase-sensing platform with high sensitivity. When a dumbbell template containing four nicking endonuclease sites is used, highly specific M.SssI MTase activity detection can be achieved in the range of 0.008-50U/mL with a detection limit as low as 0.0011U/mL. Simple experimental operation and mix-and-detection fluorescent sensing mode ensures that M.SssI MTase quantitation works well in a real-time RCA mode, thus further simplifying the sensing performance and making high throughput detection possible. The proposed MTase-sensing strategy was also

  2. Highly sensitive MicroRNA 146a detection using a gold nanoparticle-based CTG repeat probing system and isothermal amplification.

    Science.gov (United States)

    Le, Binh Huy; Seo, Young Jun

    2018-01-25

    We have developed a gold nanoparticle (AuNP)-based CTG repeat probing system displaying high quenching capability and combined it with isothermal amplification for the detection of miRNA 146a. This method of using a AuNP-based CTG repeat probing system with isothermal amplification allowed the highly sensitive (14 aM) and selective detection of miRNA 146a. A AuNP-based CTG repeat probing system having a hairpin structure and a dT F fluorophore exhibited highly efficient quenching because the CTG repeat-based stable hairpin structure imposed a close distance between the AuNP and the dT F residue. A small amount of miRNA 146a induced multiple copies of the CAG repeat sequence during rolling circle amplification; the AuNP-based CTG repeat probing system then bound to the complementary multiple-copy CAG repeat sequence, thereby inducing a structural change from a hairpin to a linear structure with amplified fluorescence. This AuNP-based CTG probing system combined with isothermal amplification could also discriminate target miRNA 146a from one- and two-base-mismatched miRNAs (ORN 1 and ORN 2, respectively). This simple AuNP-based CTG probing system, combined with isothermal amplification to induce a highly sensitive change in fluorescence, allows the detection of miRNA 146a with high sensitivity (14 aM) and selectivity. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Comparative evaluation of DNA extraction methods for amplification by qPCR of superficial vs intracellular DNA from Bacillus spores.

    Science.gov (United States)

    Brauge, Thomas; Faille, Christine; Inglebert, Gaëlle; Dubois, Thomas; Morieux, Paul; Slomianny, Christian; Midelet-Bourdin, Graziella

    2018-02-02

    This study was designed to assess the efficiency of eight extraction methods regarding their ability to release superficial (exogenous) and intracellular (endogenous) DNA from B. cereus spores for subsequent analysis by quantitative PCR (qPCR). B. cereus spore suspensions were subjected to both commercial DNA extraction kits and mechanical DNA extraction methods. The spores were observed by transmission electron microscopy to evaluate any damage caused during extraction. The efficiency of both extraction and purification were assessed using a qPCR assay targeting the bclA gene. Most of the extraction methods assessed, except the passage through the French press or the use of the QIAamp DNA Blood Mini kit without 95°C treatment, allowed the amplification of significant amounts of DNA. By using propidium monoazide, which is a photoreactive DNA-binding dye, the presence of non-negligible amounts of amplifiable DNA at the spore surface was highlighted. A further set of extraction assays was then performed on spores previously treated with PMA. The results of this study show that both superficial and intracellular spore DNA can be released by extraction methods to a greater or lesser extent and then further amplified by qPCR. The Precellys extraction allowed the detection of both intracellular and superficial DNA, the DNeasy Blood & Tissue kit the specific detection of intracellular DNA, while the Instagene kit detected only superficial DNA. Of the methods tested in this study, the Precellys extraction was the most efficient in terms of further DNA detection. In order to verify the presence or absence of B. cereus spores in food or on surfaces in the food environment, the use of an efficient extraction method is required, followed by a qPCR analysis on the DNA released. Conversely, in order to quantify the population of Bacillus spores, any superficial DNA must be blocked, e.g. with PMA, prior to intracellular DNA extraction and further amplification. Copyright © 2018

  4. Statistical study of ground motion amplification in the Mississippi embayment

    Science.gov (United States)

    Malekmohammadi, Mojtaba

    Three important topics have been studied in this dissertation. First, the effects of deep soil deposits of the Mississippi embayment in ground motion amplification have been studied. Using the results of one-dimensional analyses, a parametric model is developed for the region to estimate the ground motion amplification. The averaged shear-wave velocity in the upper 30 meter, Vs30, ranging from 220 to 800 m/s and deposit thickness varying from 70 to 750m, are considered in the estimation of the ground motion amplification with respect to a generic bedrock profile of the Mississippi embayment. Results indicate that site factors suggested by seismic codes cannot capture the site properties of the Mississippi embayment and are not appropriate for the region. In the second part, a new step-by-step method is developed to select a set of ground motions which takes into account a site-specific Probabilistic Seismic Hazard Analysis (PSHA) and the associated uncertainties through the defined logic tree. In the proposed method, after capturing the variability of the Uniform Hazard Response Spectrum (UHRS), I used a Monte Carlo procedure to produce a set of response spectra that has mean equals to the target and variability close to the variability of the target at all the spectral periods. Each member of the generated set is called individual target response spectra, and ground motions from the database of real data and also synthetic ground motions are selected based on their similarity with the individual target response spectra. The method's procedure is defined through studying a sample site in North of the Mississippi embayment. In the last part of the study I developed a model for the ratio of Vertical to Horizontal component of earthquakes (V/H ratio) for the Mississippi embayment. This model can be used in developing the site-specific vertical design spectrum for the region by scaling the horizontal design spectrum resulting from a PSHA. The input parameters of the

  5. Social Amplification of Risk and Crisis Communication Planing - Case Study

    Science.gov (United States)

    Stanciugelu, I.; Frunzaru, V.; Armas, I.; Duntzer, A.; Stan, S.

    2012-04-01

    Risk management has become a dominant concern of public policy and the ability of government to anticipate the strength and focus of public concerns remains weak. The Social Amplification of Risk Framework (SARF) was designed to assist in this endeavor. It aims to facilitate a greater understanding of the social processes that can mediate between a hazard event and its consequences. SARF identifies categories of mediator/moderator that intervene between risk event and its consequences and suggests a causal and temporal sequence in which they act. Information flows first through various sources and then channels, triggering social stations of amplification, initiating individual station of amplification and precipitating behavioral reactions. The International Risk Governance Council Framework is an interdisciplinary and multilevel approach, linking risk management and risk assessment sphere through communication. This study aims to identify categories of mediator/moderator that intervene between the risk event and its consequences, using a survey on earthquake risk perception addressing population of Bucharest city. Romania has a unique seismic profile in Europe, being the country with the biggest surface affected in case of a serious earthquake. Considering the development of the urban area that took place in the last two decades and the growing number of inhabitants, Bucharest is the largest city in Romania and is exposed to extensive damages in case of an earthquake. The sociological survey has been conducted in December 2009 on a representative sample of the Bucharest population aged 18 and over (N=1376) using one stage sampling design. We used a stratified sample method shearing the investigated populations in six layers according to the six sectors of Bucharest. The respondents were selected using random digit dialling method (RDD) and the questionnaires were administered by research staff with computer assisted telephone interviewing method (CATI). The

  6. Quantitative analysis of night skyglow amplification under cloudy conditions

    Science.gov (United States)

    Kocifaj, Miroslav; Solano Lamphar, Héctor Antonio

    2014-10-01

    The radiance produced by artificial light is a major source of nighttime over-illumination. It can, however, be treated experimentally using ground-based and satellite data. These two types of data complement each other and together have a high information content. For instance, the satellite data enable upward light emissions to be normalized, and this in turn allows skyglow levels at the ground to be modelled under cloudy or overcast conditions. Excessive night lighting imposes an unacceptable burden on nature, humans and professional astronomy. For this reason, there is a pressing need to determine the total amount of downwelling diffuse radiation. Undoubtedly, cloudy periods can cause a significant increase in skyglow as a result of amplification owing to diffuse reflection from clouds. While it is recognized that the amplification factor (AF) varies with cloud cover, the effects of different types of clouds, of atmospheric turbidity and of the geometrical relationships between the positions of an individual observer, the cloud layer, and the light source are in general poorly known. In this paper the AF is quantitatively analysed considering different aerosol optical depths (AODs), urban layout sizes and cloud types with specific albedos and altitudes. The computational results show that the AF peaks near the edges of a city rather than at its centre. In addition, the AF appears to be a decreasing function of AOD, which is particularly important when modelling the skyglow in regions with apparent temporal or seasonal variability of atmospheric turbidity. The findings in this paper will be useful to those designing engineering applications or modelling light pollution, as well as to astronomers and environmental scientists who aim to predict the amplification of skyglow caused by clouds. In addition, the semi-analytical formulae can be used to estimate the AF levels, especially in densely populated metropolitan regions for which detailed computations may be CPU

  7. Combined Amplification and Sound Generation for Tinnitus: A Scoping Review.

    Science.gov (United States)

    Tutaj, Lindsey; Hoare, Derek J; Sereda, Magdalena

    2017-11-17

    In most cases, tinnitus is accompanied by some degree of hearing loss. Current tinnitus management guidelines recognize the importance of addressing hearing difficulties, with hearing aids being a common option. Sound therapy is the preferred mode of audiological tinnitus management in many countries, including in the United Kingdom. Combination instruments provide a further option for those with an aidable hearing loss, as they combine amplification with a sound generation option. The aims of this scoping review were to catalog the existing body of evidence on combined amplification and sound generation for tinnitus and consider opportunities for further research or evidence synthesis. A scoping review is a rigorous way to identify and review an established body of knowledge in the field for suggestive but not definitive findings and gaps in current knowledge. A wide variety of databases were used to ensure that all relevant records within the scope of this review were captured, including gray literature, conference proceedings, dissertations and theses, and peer-reviewed articles. Data were gathered using scoping review methodology and consisted of the following steps: (1) identifying potentially relevant records; (2) selecting relevant records; (3) extracting data; and (4) collating, summarizing, and reporting results. Searches using 20 different databases covered peer-reviewed and gray literature and returned 5959 records. After exclusion of duplicates and works that were out of scope, 89 records remained for further analysis. A large number of records identified varied considerably in methodology, applied management programs, and type of devices. There were significant differences in practice between different countries and clinics regarding candidature and fitting of combination aids, partly driven by the application of different management programs. Further studies on the use and effects of combined amplification and sound generation for tinnitus are

  8. Experimental evidence for short-pulse laser heating of solid-density target to high bulk temperatures.

    Science.gov (United States)

    Soloviev, A; Burdonov, K; Chen, S N; Eremeev, A; Korzhimanov, A; Pokrovskiy, G V; Pikuz, T A; Revet, G; Sladkov, A; Ginzburg, V; Khazanov, E; Kuzmin, A; Osmanov, R; Shaikin, I; Shaykin, A; Yakovlev, I; Pikuz, S; Starodubtsev, M; Fuchs, J

    2017-09-22

    Heating efficiently solid-density, or even compressed, matter has been a long-sought goal in order to allow investigation of the properties of such state of matter of interest for various domains, e.g. astrophysics. High-power lasers, pinches, and more recently Free-Electron-Lasers (FELs) have been used in this respect. Here we show that by using the high-power, high-contrast "PEARL" laser (Institute of Applied Physics-Russian Academy of Science, Nizhny Novgorod, Russia) delivering 7.5 J in a 60 fs laser pulse, such coupling can be efficiently obtained, resulting in heating of a slab of solid-density Al of 0.8 µm thickness at a temperature of 300 eV, and with minimal density gradients. The characterization of the target heating is achieved combining X-ray spectrometry and measurement of the protons accelerated from the Al slab. The measured heating conditions are consistent with a three-temperatures model that simulates resistive and collisional heating of the bulk induced by the hot electrons. Such effective laser energy deposition is achieved owing to the intrinsic high contrast of the laser which results from the Optical Parametric Chirped Pulse Amplification technology it is based on, allowing to attain high target temperatures in a very compact manner, e.g. in comparison with large-scale FEL facilities.

  9. Nonlinear whistler-mode Chorus Amplification: a lasing mechanism

    Science.gov (United States)

    Soto-chavez, A.; Bhattacharjee, A.

    2013-12-01

    A mechanism for chorus wave amplification is presented. We show [1] that the whistler-mode chorus dynamical equations can be put in a form similar to the ones describing the physics of Free-electron lasers (underscoring the well known observational fact that the intensity of whistler-mode chorus demand a quasi-coherent mechanism [2]). We solve these dynamical equations numerically in the nonlinear regime [3]. In this regime our numerical results exhibit strong amplitude modulation and particle trapping, consistent with observations and numerical results previously obtained in the literature. Finally, our model gives simplified analytical expressions of wave growth rate in terms of a few measurable plasma parameters that can be used by observers without further simplification. 1. A. R. Soto-Chavez et al. Phys. Plasmas, 19, 010701, (2012). 2. P. A. Isenberg et al. J. Geophys. Res., 87, 1495, (1982). 3. A. R. Soto-Chavez and A. Bhattacharjee, JGR, (2013) submitted.

  10. Cognitive and affective matching effects in persuasion: an amplification perspective.

    Science.gov (United States)

    Clarkson, Joshua J; Tormala, Zakary L; Rucker, Derek D

    2011-11-01

    Past research suggests that cognitive and affective attitudes are more open to change toward cognitive and affective (i.e., matched) persuasive attacks, respectively. The present research investigates how attitude certainty influences this openness. Although an extensive literature suggests that certainty generally reduces an attitude's openness to change, the authors explore the possibility that certainty might increase an attitude's openness to change in the context of affective or cognitive appeals. Based on the recently proposed amplification hypothesis, the authors posit that high (vs. low) attitude certainty will boost the resistance of attitudes to mismatched attacks (e.g., affective attitudes attacked by cognitive messages) but boost the openness of attitudes to matched attacks (e.g., affective attitudes attacked by affective messages). Two experiments provide support for this hypothesis. Implications for increasing the openness of attitudes to both matched and mismatched attacks are discussed.

  11. Detection of fish nocardiosis by loop-mediated isothermal amplification.

    Science.gov (United States)

    Itano, T; Kawakami, H; Kono, T; Sakai, M

    2006-06-01

    Loop-mediated isothermal amplification (LAMP) is a novel method that amplifies DNA with high specificity and rapidity under isothermal conditions. In this study, using the LAMP method, a protocol for detecting Nocardia seriolae which is a causative agent of fish nocardiosis, was designed. A set of four primers, two inner and two outer, were designed based on the sequence of the 16S-23S ribosomal RNA internal transcribed spacer region of N. seriolae. Time and temperature conditions for detection of N. seriolae were optimized for 60 min at 65 degrees C. Other fish pathogen was not amplified by this LAMP system. The detection of N. seriola using LAMP was found to be more sensitive than that by polymerase chain reaction. LAMP is a highly sensitive and rapid diagnostic procedure for detection of N. seriolae. LAMP is a useful diagnostic method for fish nocardiosis.

  12. 'Social Laser': action amplification by stimulated emission of social energy.

    Science.gov (United States)

    Khrennikov, Andrei

    2016-01-13

    The problem of the 'explanation' of recent social explosions, especially in the Middle East, but also in Southern Europe and the USA, has been debated actively in the social and political literature. We can mention the contributions of P. Mason, F. Fukuyama, E. Schmidt, J. Cohen and I. Krastev to this debate. We point out that the diversity of opinions and conclusions is really amazing. At the moment, there is no consistent and commonly acceptable theory of these phenomena. We present a model of social explosions based on a novel approach for the description of social processes, namely the quantum-like approach. Here quantum theory is treated simply as an operational formalism-without any direct relation to physics. We explore the quantum-like laser model to describe the possibility of action amplification by stimulated emission of social energy. © 2015 The Author(s).

  13. Amplification of large-scale magnetic field in nonhelical magnetohydrodynamics

    KAUST Repository

    Kumar, Rohit

    2017-08-11

    It is typically assumed that the kinetic and magnetic helicities play a crucial role in the growth of large-scale dynamo. In this paper, we demonstrate that helicity is not essential for the amplification of large-scale magnetic field. For this purpose, we perform nonhelical magnetohydrodynamic (MHD) simulation, and show that the large-scale magnetic field can grow in nonhelical MHD when random external forcing is employed at scale 1/10 the box size. The energy fluxes and shell-to-shell transfer rates computed using the numerical data show that the large-scale magnetic energy grows due to the energy transfers from the velocity field at the forcing scales.

  14. Amplification and Re-Generation of LNA-Modified Libraries

    DEFF Research Database (Denmark)

    Doessing, Holger; Hansen, Lykke H.; Veedu, Rakesh N.

    2012-01-01

    Locked nucleic acids (LNA) confer high thermal stability and nuclease resistance to oligonucleotides. The discovery of polymerases that accept LNA triphosphates has led us to propose a scheme for the amplification and re-generation of LNA-containing oligonucleotide libraries. Such libraries could...... be used for in vitro selection of e.g., native LNA aptamers. We maintained an oligonucleotide library encoding 40 randomized positions with LNA ATP, GTP, CTP, and TTP for 7 rounds of ‘mock’ in vitro selection in the absence of a target and analyzed the sequence composition after rounds 1, 4 and 7. We...... observed a decrease in LNA-A content from 20.5% in round 1 to 6.6% in round 7. This decrease was accompanied by a substantial bias against successive LNA-As (poly-LNA adenosine tracts) and a relative over-representation of single LNA-As. Maintaining a library with LNA TTP yielded similar results. Together...

  15. Signal amplification for impedimetric genosensing using gold-streptavidin nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Bonanni, A.; Esplandiu, M.J. [Sensors and Biosensors Group, Department of Chemistry, Universitat Autonoma de Barcelona, Edifici Cn, 08193 Bellaterra, Barcelona (Spain); Valle, M. del [Sensors and Biosensors Group, Department of Chemistry, Universitat Autonoma de Barcelona, Edifici Cn, 08193 Bellaterra, Barcelona (Spain)], E-mail: manel.delvalle@uab.es

    2008-04-20

    Streptavidin-coated gold nanoparticles (strept-AuNPs) were used in this work to amplify the impedimetric signal generated in a biosensor detecting the DNA hybridization event. Probe oligomer was adsorbed onto a graphite epoxy composite (GEC) electrode surface and the impedance measurement was performed in a solution containing the redox marker ferrocyanide/ferricyanide. The biotinylated complementary oligomer was used as target. The change of interfacial charge transfer resistance (R{sub ct}), experimented by the redox marker, was recorded to confirm the hybrid formation. The addition of strept-AuNPs, binding to the target due to the strong streptavidin-biotin interaction, led to a further increment of R{sub ct} thus obtaining significant signal amplification. Strept-AuNPs on the electrode surface were observed by scanning electron microscopy (SEM) after silver enhancement treatment. A competitive binding assay was also performed using unlabelled DNA target to demonstrate its applicability to real sample analysis.

  16. Near quantum limited amplification from inelastic Cooper-pair tunneling

    Science.gov (United States)

    Hofheinz, Max; Jebari, Salha; Blanchet, Florian; Grimm, Alexander; Hazra, Dibyendu; Albert, Romain; Portier, Fabien

    Josephson parametric amplifiers approach quantum-limited noise performance but require strong external microwave pump tones which make them more difficult to use than DC powered amplifiers: The pump tone can affect the device under test and requires expensive room-temperature equipment. Inelastic Cooper pair tunneling processes through a small DC voltage-biased Josephson junction, where a tunneling Cooper pair dissipates its energy 2 eV in the form of two photons are reminiscent of parametric down conversion. We show that these processes can be used to provide amplification near the quantum limit without external microwave pump tone. We explain the measured gain and noise based on the P (E) theory of inelastic Cooper pair tunneling and general fluctuation-dissipation relations.

  17. Detection of Entamoeba histolytica by Recombinase Polymerase Amplification

    Science.gov (United States)

    Nair, Gayatri; Rebolledo, Mauricio; White, A. Clinton; Crannell, Zachary; Richards-Kortum, R. Rebecca; Pinilla, A. Elizabeth; Ramírez, Juan David; López, M. Consuelo; Castellanos-Gonzalez, Alejandro

    2015-01-01

    Amebiasis is an important cause of diarrheal disease worldwide and has been associated with childhood malnutrition. Traditional microscopy approaches are neither sensitive nor specific for Entamoeba histolytica. Antigen assays are more specific, but many cases are missed unless tested by molecular methods. Although polymerase chain reaction (PCR) is effective, the need for sophisticated, expensive equipment, infrastructure, and trained personnel limits its usefulness, especially in the resource-limited, endemic areas. Here, we report development of a recombinase polymerase amplification (RPA) method to detect E. histolytica specifically. Using visual detection by lateral flow (LF), the test was highly sensitive and specific and could be performed without additional equipment. The availability of this inexpensive, sensitive, and field-applicable diagnostic test could facilitate rapid diagnosis and treatment of amebiasis in endemic regions. PMID:26123960

  18. Organo-erbium systems for optical amplification at telecommunications wavelengths.

    Science.gov (United States)

    Ye, H Q; Li, Z; Peng, Y; Wang, C C; Li, T Y; Zheng, Y X; Sapelkin, A; Adamopoulos, G; Hernández, I; Wyatt, P B; Gillin, W P

    2014-04-01

    Modern telecommunications rely on the transmission and manipulation of optical signals. Optical amplification plays a vital part in this technology, as all components in a real telecommunications system produce some loss. The two main issues with present amplifiers, which rely on erbium ions in a glass matrix, are the difficulty in integration onto a single substrate and the need of high pump power densities to produce gain. Here we show a potential organic optical amplifier material that demonstrates population inversion when pumped from above using low-power visible light. This system is integrated into an organic light-emitting diode demonstrating that electrical pumping can be achieved. This opens the possibility of direct electrically driven optical amplifiers and optical circuits. Our results provide an alternative approach to producing low-cost integrated optics that is compatible with existing silicon photonics and a different route to an effective integrated optics technology.

  19. Rhetorical Tools for Discovery and Amplification of Design Arguments

    DEFF Research Database (Denmark)

    Halstrøm, Per Liljenberg

    2017-01-01

    the argumentative perspective is to demonstrate how rhetorical theory on discovery and amplification of arguments may lend support to designers in two ways. One is for the purpose of exploring abundant ways of designing design methods and processes. Two is to support designers in discovering persuasive arguments......In this article design processes and designed artifacts are perceived as instances of argumentation. A design process is defined as a process of deliberation about what to do when seeking to design artifacts that aim to be persuasive about how we are to lead our lives. The intention of employing...... about their choices. The article provides examples of how such a rhetorical design process may be carried out in practice....

  20. Surface plasmon amplification by stimulated emission of radiation (SPASER)

    Science.gov (United States)

    Stockman, Mark I [Atlanta, GA; Bergman, David J [Ramat Hasharon, IL

    2009-08-04

    A nanostructure is used to generate a highly localized nanoscale optical field. The field is excited using surface plasmon amplification by stimulated emission of radiation (SPASER). The SPASER radiation consists of surface plasmons that undergo stimulated emission, but in contrast to photons can be localized within a nanoscale region. A SPASER can incorporate an active medium formed by two-level emitters, excited by an energy source, such as an optical, electrical, or chemical energy source. The active medium may be quantum dots, which transfer excitation energy by radiationless transitions to a resonant nanosystem that can play the same role as a laser cavity in a conventional laser. The transitions are stimulated by the surface plasmons in the nanostructure, causing the buildup of a macroscopic number of surface plasmons in a single mode.

  1. Recombinase Polymerase Amplification Assay for Rapid Diagnostics of Dengue Infection.

    Directory of Open Access Journals (Sweden)

    Ahmed Abd El Wahed

    Full Text Available Over 2.5 billion people are exposed to the risk of contracting dengue fever (DF. Early diagnosis of DF helps to diminish its burden on public health. Real-time reverse transcription polymerase amplification assays (RT-PCR are the standard method for molecular detection of the dengue virus (DENV. Real-time RT-PCR analysis is not suitable for on-site screening since mobile devices are large, expensive, and complex. In this study, two RT-recombinase polymerase amplification (RT-RPA assays were developed to detect DENV1-4.Using two quantitative RNA molecular standards, the analytical sensitivity of a RT-RPA targeting the 3´non-translated region of DENV1-4 was found to range from 14 (DENV4 to 241 (DENV1-3 RNA molecules detected. The assay was specific and did not cross detect other Flaviviruses. The RT-RPA assay was tested in a mobile laboratory combining magnetic-bead based total nucleic acid extraction and a portable detection device in Kedougou (Senegal and in Bangkok (Thailand. In Kedougou, the RT-RPA was operated at an ambient temperature of 38 °C with auxiliary electricity tapped from a motor vehicle and yielded a clinical sensitivity and specificity of 98% (n=31 and 100% (n=23, respectively. While in the field trial in Bangkok, the clinical sensitivity and specificity were 72% (n=90 and 100%(n=41, respectively.During the first 5 days of infection, the developed DENV1-4 RT-RPA assays constitute a suitable accurate and rapid assay for DENV diagnosis. Moreover, the use of a portable fluorescence-reading device broadens its application potential to the point-of-care for outbreak investigations.

  2. Whole genome amplification and sequencing of a Daphnia resting egg.

    Science.gov (United States)

    Lack, Justin B; Weider, Lawrence J; Jeyasingh, Punidan D

    2017-09-19

    Resting eggs banks are unique windows that allow us to directly observe shifts in population genetics, and phenotypes over time as natural populations evolve. Though a variety of planktonic organisms also produce resting stages, the keystone freshwater consumer, Daphnia, is a well-known model for paleogenetics and resurrection ecology. Nevertheless, paleogenomic investigations are limited largely because resting eggs do not contain enough DNA for genomic sequencing. In fact, genomic studies even on extant populations include a laborious preparatory phase of batch culturing dozens of individuals to generate sufficient genomic DNA. Here, we furnish a protocol to generate whole genomes of single ephippial (resting) eggs and single daphniids. Whole genomes of single ephippial eggs and single adults were amplified using Qiagen REPLI-g Single Cell kit reaction, followed by NEBNext Ultra DNA Library Prep Kit for library construction and Illumina sequencing. We compared the quality of the single-egg and single-individual amplified genomes to the standard batch genomic DNA extraction in the absence of genome amplification. At mean 20× depth, coverage was essentially identical for the amplified single individual relative to the unamplified batch extracted genome (>90% of the genome was covered and callable). Finally, while amplification resulted in the slight loss of heterozygosity for the amplified genomes, estimates were largely comparable and illustrate the utility and limitations of this approach in estimating population genetic parameters over long periods of time in natural populations of Daphnia and also other small species known to produce resting stages. © 2017 John Wiley & Sons Ltd.

  3. Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification

    Directory of Open Access Journals (Sweden)

    Michael G. Mauk

    2015-10-01

    Full Text Available Microfluidic components and systems for rapid (<60 min, low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs are described. A microfluidic point-of-care (POC diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1 nucleic acids (NAs are extracted from relatively large (~mL volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane” to capture sample NAs in a flow-through, filtration mode; (2 NAs captured on the membrane are isothermally (~65 °C amplified; (3 amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4 paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD better than 103 virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed.

  4. Mechanism of chimera formation during the Multiple Displacement Amplification reaction

    Directory of Open Access Journals (Sweden)

    Stockwell Timothy B

    2007-04-01

    Full Text Available Abstract Background Multiple Displacement Amplification (MDA is a method used for amplifying limiting DNA sources. The high molecular weight amplified DNA is ideal for DNA library construction. While this has enabled genomic sequencing from one or a few cells of unculturable microorganisms, the process is complicated by the tendency of MDA to generate chimeric DNA rearrangements in the amplified DNA. Determining the source of the DNA rearrangements would be an important step towards reducing or eliminating them. Results Here, we characterize the major types of chimeras formed by carrying out an MDA whole genome amplification from a single E. coli cell and sequencing by the 454 Life Sciences method. Analysis of 475 chimeras revealed the predominant reaction mechanisms that create the DNA rearrangements. The highly branched DNA synthesized in MDA can assume many alternative secondary structures. DNA strands extended on an initial template can be displaced becoming available to prime on a second template creating the chimeras. Evidence supports a model in which branch migration can displace 3'-ends freeing them to prime on the new templates. More than 85% of the resulting DNA rearrangements were inverted sequences with intervening deletions that the model predicts. Intramolecular rearrangements were favored, with displaced 3'-ends reannealing to single stranded 5'-strands contained within the same branched DNA molecule. In over 70% of the chimeric junctions, the 3' termini had initiated priming at complimentary sequences of 2–21 nucleotides (nts in the new templates. Conclusion Formation of chimeras is an important limitation to the MDA method, particularly for whole genome sequencing. Identification of the mechanism for chimera formation provides new insight into the MDA reaction and suggests methods to reduce chimeras. The 454 sequencing approach used here will provide a rapid method to assess the utility of reaction modifications.

  5. Offset-Free Gigahertz Midinfrared Frequency Comb Based on Optical Parametric Amplification in a Periodically Poled Lithium Niobate Waveguide

    Science.gov (United States)

    Mayer, A. S.; Phillips, C. R.; Langrock, C.; Klenner, A.; Johnson, A. R.; Luke, K.; Okawachi, Y.; Lipson, M.; Gaeta, A. L.; Fejer, M. M.; Keller, U.

    2016-11-01

    We report the generation of an optical-frequency comb in the midinfrared region with 1-GHz comb-line spacing and no offset with respect to absolute-zero frequency. This comb is tunable from 2.5 to 4.2 μ m and covers a critical spectral region for important environmental and industrial applications, such as molecular spectroscopy of trace gases. We obtain such a comb using a highly efficient frequency conversion of a near-infrared frequency comb. The latter is based on a compact diode-pumped semiconductor saturable absorber mirror-mode-locked ytterbium-doped calcium-aluminum gadolynate (Yb:CALGO) laser operating at 1 μ m . The frequency-conversion process is based on optical parametric amplification (OPA) in a periodically poled lithium niobate (PPLN) chip containing buried waveguides fabricated by reverse proton exchange. The laser with a repetition rate of 1 GHz is the only active element of the system. It provides the pump pulses for the OPA process as well as seed photons in the range of 1.4 - 1.8 μ m via supercontinuum generation in a silicon-nitride (Si3 N4 ) waveguide. Both the PPLN and Si3 N4 waveguides represent particularly suitable platforms for low-energy nonlinear interactions; they allow for mid-IR comb powers per comb line at the microwatt level and signal amplification levels up to 35 dB, with 2 orders of magnitude less pulse energy than reported in OPA systems using bulk devices. Based on numerical simulations, we explain how high amplification can be achieved at low energy using the interplay between mode confinement and a favorable group-velocity mismatch configuration where the mid-IR pulse moves at the same velocity as the pump.

  6. Parametric amplification of matter waves in dipolar spinor Bose-Einstein condensates

    DEFF Research Database (Denmark)

    Deuretzbacher, F.; Gebreyesus, G.; Topic, O.

    2010-01-01

    Spin-changing collisions may lead under proper conditions to the parametric amplification of matter waves in spinor Bose-Einstein condensates. Magnetic dipole-dipole interactions, although typically very weak in alkali-metal atoms, are shown to play a very relevant role in the amplification process...

  7. Pulse train amplification and regeneration based on semiconductor quantum dots waveguide

    DEFF Research Database (Denmark)

    Chen, Yaohui; Öhman, Filip; Mørk, Jesper

    2008-01-01

    We numerical analyze pulse train amplification up to 200 Gbit/s in quantum dot amplifiers and present regeneration properties with saturable absorber based on semiconductor quantum dot waveguides.......We numerical analyze pulse train amplification up to 200 Gbit/s in quantum dot amplifiers and present regeneration properties with saturable absorber based on semiconductor quantum dot waveguides....

  8. The effect of whole genome amplification on samples originating from more than one donor

    DEFF Research Database (Denmark)

    Thacker, C.R.; Balogh, M.K.; Børsting, Claus

    2006-01-01

    In this study, the GenomiPhi(TM) DNA Amplification Kit (Amersham Biosciences) was used to investigate the potential of whole genome amplification (WGA) when considering samples originating from more than one donor. DNA was extracted from blood samples, quantified and normalised before being mixed...

  9. Quantitative PCR Detection of c-erbB-2 Gene Amplification.

    Science.gov (United States)

    Dobianer, K; Medl, M; Spona, J

    2001-01-01

    The association of c-erbB-2 oncogene amplification and prognostic factors was intensively studied in human gynecological carcinomas, especially in mammary carcinoma (1). Positive lymph nodes, estrogen and progesterone receptor negative tumors, and short survival time correlate with c-erbB-2 amplification.

  10. The Media and Genetically Modified Foods : Evidence in Support of Social Amplification of Risk

    NARCIS (Netherlands)

    Frewer, L.J.; Miles, S.; Marsh, R.

    2002-01-01

    Empirical examinations of the "social amplification of risk" framework are rare, partly because of the difficulties in predicting when conditions likely to result in amplification effects will occur. This means that it is difficult to examine changes in risk perception that are contemporaneous with

  11. Catalytic signal amplification using [Fe(III)(biuret-amide)]-mesoporous silica nanoparticles: visual cyanide detection.

    Science.gov (United States)

    Panda, Chakadola; Dhar, Basab B; Malvi, Bharmana; Bhattacharjee, Yudhajit; Gupta, Sayam Sen

    2013-03-18

    Catalytic signal amplification was used for the colorimetric detection of CN(-) in aqueous media by using the enzyme catalase in tandem with mesoporous silica nanoparticle based synthetic HRP enzyme mimic Fe-MSNs. Signal amplification up to a maximum of eight fold was observed for the reporter "oxidized TMB" with respect to the added CN(-) ion.

  12. Quantum noise in optical parametric amplification: a means to achieve noiseless optical functions

    Science.gov (United States)

    Levenson, J. A.; Bencheikh, K.; Lovering, D. J.; Vidakovic, P.; Simonneau, C.

    1997-04-01

    We describe some limitations of the noise performance of classical optical devices which are directly related to the Poissonian statistics associated with ordinary laser beams. We show that quantum optics, via optical parametric amplification, allows us to circumvent these limitations in order to realize certain noiseless optical functions such as amplification, duplication, detection and distribution of optical signals.

  13. Plasma HER2 amplification in cell-free DNA during neoadjuvant chemotherapy in breast cancer

    DEFF Research Database (Denmark)

    Bechmann, Troels; Andersen, Rikke Fredslund; Pallisgaard, Niels

    2013-01-01

    Measurement of human epidermal growth factor receptor 2 (HER2) gene amplification in cell-free DNA (cfDNA) is an evolving technique in breast cancer, enabling liquid biopsies and treatment monitoring. The present study investigated the dynamics of plasma HER2 gene copy number and amplification...

  14. Generation of recombinant pestiviruses using a full-genome amplification strategy

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Reimann, I.; Uttenthal, Åse

    2010-01-01

    Complete genome amplification of viral RNA provides a new tool for the generation of modified viruses. We have recently reported a full-genome amplification strategy for recovery of pestiviruses (Rasmussen et al., 2008). A full-length cDNA amplicon corresponding to the Border disease virus-Gifhor...

  15. High efficiency poplar transformation.

    Science.gov (United States)

    Cseke, Leland J; Cseke, Sarah Beth; Podila, Gopi K

    2007-09-01

    With the completion of the poplar tree genome database, Populus species have become one of the most useful model systems for the study of woody plant biology. Populus tremuloides (quaking aspen) is the most wide-spread tree species in North America, and its rapid growth generates the most abundant wood-based biomass out of any other plant species. To study such beneficial traits, there is a need for easier and more efficient transformation procedures that will allow the study of large numbers of tree genes. We have developed transformation procedures that are suitable for high-throughput format transformations using either Agrobacterium tumefaciens to produce transformed trees or Agrobacterium rhizogenes to generate hairy roots. Our method uses Agrobacterium inoculated aspen seedling hypocotyls followed by direct thidiazuron (TDZ)-mediated shoot regeneration on selective media. Transformation was verified through beta-glucuronidase (GUS) reporter gene expression in all tree tissues, PCR amplification of appropriate vector products from isolated genomic DNA, and northern hybridization of incorporated and expressed transgenes. The hairy root protocol follows the same inoculation procedures and was tested using GUS reporter gene integration and antibiotic selection. The benefit of these procedures is that they are simple and efficient, requiring no maintenance of starting materials and allowing fully formed transgenic trees (or hairy roots) to be generated in only 3-4 months, rather than the 6-12 months required by more traditional methods. Likewise, the fact that the protocols are amenable to high-throughput formats makes them better suited for large-scale functional genomics studies in poplars.

  16. Development of reverse transcription loop-mediated isothermal amplification assay as a simple detection method of Chrysanthemum stem necrosis virus in chrysanthemum and tomato.

    Science.gov (United States)

    Suzuki, Ryoji; Fukuta, Shiro; Matsumoto, Yuho; Hasegawa, Toru; Kojima, Hiroko; Hotta, Makiko; Miyake, Noriyuki

    2016-10-01

    For a simple and rapid detection of Chrysanthemum stem necrosis virus (CSNV) from chrysanthemum and tomato, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed. A primer set designed to the genome sequences of CSNV worked most efficiently at 63°C and could detect CSNV RNA within 12min by fluorescence monitoring using an isothermal DNA amplification and fluorescence detection device. The result of a specificity test using seven other viruses and one viroid-infectable chrysanthemum or tomato showed that the assay could amplify CSNV specifically, and a sensitivity comparison showed that the RT-LAMP assay was as sensitive as the reverse transcriptase polymerase chain reaction. The RT-LAMP assay using crude RNA, extracted simply, could detect CSNV. Overall, the RT-LAMP assay was found to be a simple, specific, convenient, and time-saving method for CSNV detection. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. HER2 and TOP2A Gene Amplification and Protein Expression in Upper Tract Urothelial Carcinomas.

    Science.gov (United States)

    Aumayr, Klaus; Klatte, Tobias; Neudert, Barbara; Birner, Peter; Shariat, Shahrokh; Schmidinger, Manuela; Susani, Martin; Haitel, Andrea

    2017-07-28

    HER2, a potential target for therapy, has been described to be amplified in urothelial carcinomas. As the topoisomerase II alpha (TOP2A) gene is located close to the HER2 gene on chromosome 17q12-q21, it is frequently either co-amplified or deleted with HER2 amplification. The purpose of this study was to assess the impact HER2 and TOP2A gene amplification as well as protein expression on outcomes of upper tract urothelial carcinoma (UTUC). HER2 and TOP2A gene amplification and protein expression were assessed in 81 patients with radical nephroureterectomy for UTUC. Immunohistochemistry and chromogenic in-situ hybridization was performed on formalin-fixed, paraffin-embedded samples. HER2 protein expression was observed in 27/81 (33%) cases, of which 8 cases exhibited amplification of HER2. One of them had an additional polysomy 17, whereas 6/67 HER2 non-amplified cases revealed a polysomy 17. Coamplification of HER2 and TOP2A was found in 4 cases, whereas 3 cases showed only HER2 amplification and 20 cases only TOP2A amplification. HER2 IHC overexpression was associated with higher-grade tumors (p = 0.001), non-organ confined carcinomas (p = 0.017), HER2 amplification (p HER2 amplification was association with higher tumor grade (p = 0.001) and lymphnode metastasis (p = 0.003). TOP2A IHC positivity was significantly associated with higher tumor grade (p = 0.0004), TOP2A amplification (p = 0.0003), polysomy 17 (p = 0.035) and HER2 IHC overexpression (p = 0.28), whereas all categories of tumor stage and HER2 amplification remained not related. TOP2A amplification was significantly more frequent in tumors with higher grade, higher tumor stage, polysomy 17 and distant metastasis (p = 0.015; p = 0.042; p = 0.032; p = 0.011), respectively. In univariate analyses HER2 IHC positivity, TOP2A amplification, and polysomy 17 were associated with poor clinical outcome after surgery. HER2 IHC overexpression and TOP2A amplification are associated with

  18. Strategies for Amplification of Trinucleotide Repeats: Optimization of Fragile X and Androgen Receptor PCR.

    Science.gov (United States)

    Papp; Snyder; Sedra; Guida; Prior

    1996-06-01

    Background: Trinucleotide repeat regions are heritable unstable elements that change in copy number from generation to generation. Amplification of these triplet repeats is an important diagnostic tool for molecular medicine. However, these repeats are often difficult to amplify and may require the use of different cosolvents or amplification strategies. Methods and Results: We used the fragile X and androgen receptor triplet repeat regions to demonstrate a series of conditions that may be used to optimize the amplification of repeat sequences. Conclusions: For androgen receptor, we show that predigestion of the template DNA was sufficient to generate consistent amplification. In the case of fragile X we found that predigestion, when combined with use of betaine as a destabilizing additive, was superior to other methods and yielded consistent amplification of normal and premutation alleles in both isotopic and nonisotopic reactions.

  19. Effect of Cognitive and Central Auditory Impairments on Satisfaction of Amplification in Hearing Impaired Older Adults

    Directory of Open Access Journals (Sweden)

    Younes Lotfi

    2012-07-01

    Full Text Available Objectives: Older adults show many difficulties of speech perception in noisy situations due to peripheral and central auditory impairments, and cognitive dysfunctions. One of the most common rehabilitative procedures for older adults with hearing loss is amplification. However, there is some evidence of dissatisfaction of amplification in older adults. Methods & Materials: We assessed cognitive station, central auditory function, and satisfaction of 19 participants with hearing aids using mini-mental state examination (MMSE, dichotic digits test (DDT, and the satisfaction with amplification in daily life scale respectively. Our cases had moderate sensory hearing loss in both ears. Results: Kruskal-Wallis statistics showed significant correlation between cognitive impairments (MMSE scores and satisfaction of amplification (P0.05. Conclusion: We showed central auditory processing impairments in hearing impaired older adults with cognitive dysfunctions. It is indicated that older adults with hearing loss might have cognitive impairments inducing dissatisfaction of amplification.

  20. Amplification of realistic Schrödinger-cat-state-like states by homodyne heralding

    DEFF Research Database (Denmark)

    Laghaout, Amine; Neergaard-Nielsen, Jonas S.; Rigas, Ioannes

    2013-01-01

    We present a scheme for the amplification of Schrödinger cat states that collapses two smaller states onto their constructive interference via a homodyne projection. We analyze the performance of the amplification in terms of fidelity and success rate when the input consists of either exact coher...... coherent state superpositions or of photon-subtracted squeezed vacua. The impact of imprecise homodyne detection and of impure squeezing is quantified. We also assess the scalability of iterated amplifications.......We present a scheme for the amplification of Schrödinger cat states that collapses two smaller states onto their constructive interference via a homodyne projection. We analyze the performance of the amplification in terms of fidelity and success rate when the input consists of either exact...

  1. Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications.

    Directory of Open Access Journals (Sweden)

    Jennifer L Guler

    Full Text Available Malaria drug resistance contributes to up to a million annual deaths. Judicious deployment of new antimalarials and vaccines could benefit from an understanding of early molecular events that promote the evolution of parasites. Continuous in vitro challenge of Plasmodium falciparum parasites with a novel dihydroorotate dehydrogenase (DHODH inhibitor reproducibly selected for resistant parasites. Genome-wide analysis of independently-derived resistant clones revealed a two-step strategy to evolutionary success. Some haploid blood-stage parasites first survive antimalarial pressure through fortuitous DNA duplications that always included the DHODH gene. Independently-selected parasites had different sized amplification units but they were always flanked by distant A/T tracks. Higher level amplification and resistance was attained using a second, more efficient and more accurate, mechanism for head-to-tail expansion of the founder unit. This second homology-based process could faithfully tune DNA copy numbers in either direction, always retaining the unique DNA amplification sequence from the original A/T-mediated duplication for that parasite line. Pseudo-polyploidy at relevant genomic loci sets the stage for gaining additional mutations at the locus of interest. Overall, we reveal a population-based genomic strategy for mutagenesis that operates in human stages of P. falciparum to efficiently yield resistance-causing genetic changes at the correct locus in a successful parasite. Importantly, these founding events arise with precision; no other new amplifications are seen in the resistant haploid blood stage parasite. This minimizes the need for meiotic genetic cleansing that can only occur in sexual stage development of the parasite in mosquitoes.

  2. Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications.

    Science.gov (United States)

    Guler, Jennifer L; Freeman, Daniel L; Ahyong, Vida; Patrapuvich, Rapatbhorn; White, John; Gujjar, Ramesh; Phillips, Margaret A; DeRisi, Joseph; Rathod, Pradipsinh K

    2013-01-01

    Malaria drug resistance contributes to up to a million annual deaths. Judicious deployment of new antimalarials and vaccines could benefit from an understanding of early molecular events that promote the evolution of parasites. Continuous in vitro challenge of Plasmodium falciparum parasites with a novel dihydroorotate dehydrogenase (DHODH) inhibitor reproducibly selected for resistant parasites. Genome-wide analysis of independently-derived resistant clones revealed a two-step strategy to evolutionary success. Some haploid blood-stage parasites first survive antimalarial pressure through fortuitous DNA duplications that always included the DHODH gene. Independently-selected parasites had different sized amplification units but they were always flanked by distant A/T tracks. Higher level amplification and resistance was attained using a second, more efficient and more accurate, mechanism for head-to-tail expansion of the founder unit. This second homology-based process could faithfully tune DNA copy numbers in either direction, always retaining the unique DNA amplification sequence from the original A/T-mediated duplication for that parasite line. Pseudo-polyploidy at relevant genomic loci sets the stage for gaining additional mutations at the locus of interest. Overall, we reveal a population-based genomic strategy for mutagenesis that operates in human stages of P. falciparum to efficiently yield resistance-causing genetic changes at the correct locus in a successful parasite. Importantly, these founding events arise with precision; no other new amplifications are seen in the resistant haploid blood stage parasite. This minimizes the need for meiotic genetic cleansing that can only occur in sexual stage development of the parasite in mosquitoes.

  3. Short-pulse propagation in fiber optical parametric amplifiers

    DEFF Research Database (Denmark)

    Cristofori, Valentina

    Fiber optical parametric amplifiers (FOPAs) are attractive because they can provide large gain over a broad range of central wavelengths, depending only on the availability of a suitable pump laser. In addition, FOPAs are suitable for the realization of all-optical signal processing functionalities...... is implemented to obtain an all-fiber system. The advantages of all fiber-systems are related to their reliability, long-term stability and compactness. Fiber optical parametric chirped pulse amplification is promising for the amplification of such signals thanks to the inherent compatibility of FOPAs with fiber...

  4. Juggling Efficiency

    DEFF Research Database (Denmark)

    Andersen, Rikke Sand; Vedsted, Peter

    2015-01-01

    on institutional logics, we illustrate how a logic of efficiency organise and give shape to healthcare seeking practices as they manifest in local clinical settings. Overall, patient concerns are reconfigured to fit the local clinical setting and healthcare professionals and patients are required to juggle...... efficiency in order to deal with uncertainties and meet more complex or unpredictable needs. Lastly, building on the empirical case of cancer diagnostics, we discuss the implications of the pervasiveness of the logic of efficiency in the clinical setting and argue that provision of medical care in today......'s primary care settings requires careful balancing of increasing demands of efficiency, greater complexity of biomedical knowledge and consideration for individual patient needs....

  5. Principes et réalisation d'une chaîne laser femtoseconde haute intensité basée sur le saphir dopé au titane

    Science.gov (United States)

    Le Blanc, Catherine

    We present the initial study, the realisation and the characterisation of a high intensity femtosecond laser chain. This chain is able to produce intensities higher than 10^18 W/cm2 on target, at a 10 Hertz repetition rate. We present first fondamentals principles of chirped pulse propagation mechanisms: group velocity dispersion, self-phase modulation, self-focusing, and gain saturation. Then after describing the spectroscopic properties of titanium doped sapphire (Ti:S), we discuss near infrared femtosecond oscillators able to be amplified in Ti:S medium, and describe our home made Kerr Lens mode locked femtosecond Ti:S oscillator. The high intensity laser chain is based on the Chirped Pulse Amplification concept, which consists in stretching the pulse before its amplification in order to avoid non-linear effects such self-focusing or breakdown, and then recompressing it to its initial pulse duration. We have developed two compact and efficient multipass amplifiers for femtosecond chirped pulse amplification. With only two of these devices, we obtain an amplification factor of 10^8, which corresponds to a peak power of ˜ 0.5 terawatt after compression. We analyse in details the performances of this system and its advantages in terms of its high quantum yield (0.3), flexibility, and optical quality. Some observed spectral distortion on chirped pulses is simply explained by a gain saturation model. High dynamic pulse temporal control is crucial for interaction experiments. For this reason, we have developed a third order sampling autocorrelator. This device is able to measure 100 fs pulses with more than 8 orders of magnitude. I compare our obtained performances to other femtosecond systems and I analyse the best way to increase the energy, reduce the pulse duration and optimise focusing in order to reach the 10^19 W/cm2 regime. Ce mémoire présente les études préliminaires, la réalisation et la caractérisation d'une chaîne dite "de haute intensité" en r

  6. One-step nucleic acid amplification: the possible value in assessing sentinel lymph node metastasis during mastectomy

    Directory of Open Access Journals (Sweden)

    Hunter-Smith AE

    2018-01-01

    Full Text Available Alison E Hunter-Smith, Zenon Rayter Breast Surgery Unit, Bristol Breast Care Centre, North Bristol NHS Trust, Southmead Hospital, Westbury-on-Trym, Bristol, UK Abstract: Breast cancer is the most common cancer in women, worldwide, and 1,400 deaths per day are attributed to it. The success of national screening programs has seen breast cancers being diagnosed at an earlier stage. With conservative surgery to the breast demonstrating equivalent long-term outcomes, the last 10 years have seen a growing interest in the safety of less invasive management for the axilla in breast cancer patients. One-step nucleic acid amplification (OSNA is a validated, reliable, and efficient tool in identifying micro- and macro-metastases intraoperatively. It is the most widely used intraoperative analysis tool within the United Kingdom, and is employed by over 320 units across Europe and Asia. Recent evidence from the AMAROS, IBCSG 23-01, and ACOSOG Z0011 trials has changed surgical practice in managing the axilla of patients with breast cancer. We propose a clinical algorithm demonstrating the role of OSNA as an intraoperative analysis tool in today’s management of breast cancer as well as prospects for the future use of OSNA. Keywords: breast cancer, sentinel lymph node, intraoperative assessment, one-stop nucleic acid amplification, mastectomy

  7. Development of a loop-mediated isothermal amplification method for rapid mass-screening of sand flies for Leishmania infection.

    Science.gov (United States)

    Nzelu, Chukwunonso O; Gomez, Eduardo A; Cáceres, Abraham G; Sakurai, Tatsuya; Martini-Robles, Luiggi; Uezato, Hiroshi; Mimori, Tatsuyuki; Katakura, Ken; Hashiguchi, Yoshihisa; Kato, Hirotomo

    2014-04-01

    Entomological monitoring of Leishmania infection in leishmaniasis endemic areas offers epidemiologic advantages for predicting the risk and expansion of the disease, as well as evaluation of the effectiveness of control programs. In this study, we developed a highly sensitive loop-mediated isothermal amplification (LAMP) method for the mass screening of sand flies for Leishmania infection based on the 18S rRNA gene. The LAMP technique could detect 0.01 parasites, which was more sensitive than classical PCR. The method was robust and could amplify the target DNA within 1h from a crude sand fly template without DNA purification. Amplicon detection could be accomplished by the newly developed colorimetric malachite green (MG)--mediated naked eye visualization. Pre-addition of MG to the LAMP reaction solution did not inhibit amplification efficiency. The field applicability of the colorimetric MG-based LAMP assay was demonstrated with 397 field-caught samples from the endemic areas of Ecuador and eight positive sand flies were detected. The robustness, superior sensitivity, and ability to produce better visual discriminatory reaction products than existing LAMP fluorescence and turbidity assays indicated the field potential usefulness of this new method for surveillance and epidemiological studies of leishmaniasis in developing countries. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Application of Europium Multiwalled Carbon Nanotubes as Novel Luminophores in an Electrochemiluminescent Aptasensor for Thrombin Using Multiple Amplification Strategies.

    Science.gov (United States)

    Wu, Dan; Xin, Xia; Pang, Xuehui; Pietraszkiewicz, Marek; Hozyst, Robert; Sun, Xian'ge; Wei, Qin

    2015-06-17

    A novel electrochemiluminescent (ECL) aptasensor was proposed for the determination of thrombin (TB) using exonuclease-catalyzed target recycling and hybridization chain reaction (HCR) to amplify the signal. The capture probe was immobilized on an Au-GS-modified electrode through a Au-S bond. Subsequently, the hybrid between the capture probe and the complementary thrombin binding aptamer (TBA) was aimed at obtaining double-stranded DNA (dsDNA). The interaction between TB and its aptamer led to the dissociation of dsDNA because TB has a higher affinity to TBA than the complementary strands. In the presence of exonuclease, aptamer was selectively digested and TB could be released for target recycling. Extended dsDNA was formed through HCR of the capture probe and two hairpin DNA strands (NH2-DNA1 and NH2-DNA1). Then, numerous europium multiwalled carbon nanotubes (Eu-MWCNTs) could be introduced through amidation reaction between NH2-terminated DNA strands and carboxyl groups on the Eu-MWCNTs, resulting in an increased ECL signal. The multiple amplification strategies, including the amplification of analyte recycling and HCR, and high ECL efficiency of Eu-MWCNTs lead to a wide linear range (1.0×10(-12)-5.0×10(-9) mol/L) and a low detection limit (0.23 pmol/L). The method was applied to serum sample analysis with satisfactory results.

  9. DNA Barcoding: Amplification and sequence analysis of rbcl and matK genome regions in three divergent plant species

    Directory of Open Access Journals (Sweden)

    Javed Iqbal Wattoo

    2016-11-01

    Full Text Available Background: DNA barcoding is a novel method of species identification based on nucleotide diversity of conserved sequences. The establishment and refining of plant DNA barcoding systems is more challenging due to high genetic diversity among different species. Therefore, targeting the conserved nuclear transcribed regions would be more reliable for plant scientists to reveal genetic diversity, species discrimination and phylogeny. Methods: In this study, we amplified and sequenced the chloroplast DNA regions (matk+rbcl of Solanum nigrum, Euphorbia helioscopia and Dalbergia sissoo to study the functional annotation, homology modeling and sequence analysis to allow a more efficient utilization of these sequences among different plant species. These three species represent three families; Solanaceae, Euphorbiaceae and Fabaceae respectively. Biological sequence homology and divergence of amplified sequences was studied using Basic Local Alignment Tool (BLAST. Results: Both primers (matk+rbcl showed good amplification in three species. The sequenced regions reveled conserved genome information for future identification of different medicinal plants belonging to these species. The amplified conserved barcodes revealed different levels of biological homology after sequence analysis. The results clearly showed that the use of these conserved DNA sequences as barcode primers would be an accurate way for species identification and discrimination. Conclusion: The amplification and sequencing of conserved genome regions identified a novel sequence of matK in native species of Solanum nigrum. The findings of the study would be applicable in medicinal industry to establish DNA based identification of different medicinal plant species to monitor adulteration.

  10. A Loop-Mediated Isothermal Amplification Assay and Sample Preparation Procedure for Sensitive Detection of Xanthomonas fragariae in Strawberry

    Science.gov (United States)

    Wang, Hehe; Turechek, William W.

    2016-01-01

    Xanthomonas fragariae is a bacterium that causes angular leaf spot of strawberry. Asymptomatic infection is common and contributes to the difficulties in disease management. The aim of this study was to develop a loop-mediated isothermal amplification (LAMP) assay as an efficient method for detection of asymptomatic infections of X. fragariae. In addition, a new method of sample preparation was developed that allows sampling of a larger amount of plant tissue, hence increasing the detection rate in real-life samples. The sample preparation procedure includes an overnight incubation of strawberry tissues in phosphate-buffered saline (PBS), followed by a quick sample concentration and a boiling step to extract DNA for amplification. The detection limit of the LAMP assay was approximately 2×103 CFU/mL for pure bacteria culture and 300 CFU/mL for bacteria spiked strawberry leaf and petiole samples. LAMP provided a 2–3 fold lower detection limit than the standard qPCR assay but was faster, and more user-friendly. The LAMP assay should serve as a rapid, sensitive and cost-effective tool for detecting asymptomatic infections of X. fragariae in strawberry nursery stock and contribute to improved disease management. PMID:26766068

  11. Evolution of thermophilic DNA polymerases for the recognition and amplification of C2'-modified DNA.

    Science.gov (United States)

    Chen, Tingjian; Hongdilokkul, Narupat; Liu, Zhixia; Adhikary, Ramkrishna; Tsuen, Shujian S; Romesberg, Floyd E

    2016-06-01

    The PCR amplification of oligonucleotides enables the evolution of sequences called aptamers that bind specific targets with antibody-like affinity. However, in many applications the use of these aptamers is limited by nuclease-mediated degradation. In contrast, oligonucleotides that are modified at their sugar C2' positions with methoxy or fluorine substituents are stable to nucleases, but they cannot be synthesized by natural polymerases. Here we report the development of a polymerase-evolution system and its use to evolve thermostable polymerases that efficiently interconvert C2'-OMe-modified oligonucleotides and their DNA counterparts via 'transcription' and 'reverse transcription' or, more importantly, that PCR-amplify partially C2'-OMe- or C2'-F-modified oligonucleotides. A mechanistic analysis demonstrates that the ability to amplify the modified oligonucleotides evolved by optimizing interdomain interactions that stabilize the catalytically competent closed conformation of the polymerase. The evolved polymerases should find practical applications and the developed evolution system should be a powerful tool for tailoring polymerases to have other types of novel function.

  12. Detection of coat protein gene of nervous necrosis virus using loop-mediated isothermal amplification.

    Science.gov (United States)

    Hwang, Jinik; Suh, Sung-Suk; Park, Mirye; Oh, Myung-Joo; Kim, Jong-Oh; Lee, Sukchan; Lee, Taek-Kyun

    2016-03-01

    To establish a novel and highly specific loop-mediated isothermal amplification (LAMP) assay for the identification of nervous necrosis virus (NNV) infection. A set of synthesized primers was used to match the sequences of a specific region of the nnv gene from the National Center for Biotechnology Information database, not originating from NNV-infected fish, the efficiency and specificity of LAMP were measured dependent on the concentration of DNA polymerase and the reaction temperature and time. In addition, to determine species-specific LAMP primers, cross reactivity testing was applied to the reaction between NVV and other virus families including viral hemorrhagic septicemia virus and marine birnavirus. The optimized LAMP reaction carried out at 64 °C for 60 min, and above 4 U Bst DNA polymerase. The sensitivity of LAMP for the detection of nnv was thus about 10 times greater than the sensitivity of polymerase chain reaction. The LAMP assay primers were specific for the detection NNV infection in Epinephelus septemfasciatus. The development of LAMP primers based on genetic information from a public database, not virus-infected samples, may provide a very simple and convenient method to identify viral infection in aquatic organisms. Copyright © 2016 Hainan Medical College. Production and hosting by Elsevier B.V. All rights reserved.

  13. Loop-Mediated Isothermal Amplification Targeting Actin DNA of Trichomonas vaginalis.

    Science.gov (United States)

    Goo, Youn-Kyoung; Shin, Won-Sik; Yang, Hye-Won; Joo, So-Young; Song, Su-Min; Ryu, Jae-Sook; Kong, Hyun-Hee; Lee, Won-Ki; Chung, Dong-Il; Hong, Yeonchul

    2016-06-01

    Trichomoniasis caused by Trichomonas vaginalis is a common sexually transmitted disease. Its association with several health problems, including preterm birth, pelvic inflammatory disease, cervical cancer, and transmission of human immunodeficiency virus, emphasizes the importance of improved access to early and accurate detection of T. vaginalis. In this study, a rapid and efficient loop-mediated isothermal amplification-based method for the detection of T. vaginalis was developed and validated, using vaginal swab specimens from subjects suspected to have trichomoniasis. The LAMP assay targeting the actin gene was highly sensitive with detection limits of 1 trichomonad and 1 pg of T. vaginalis DNA per reaction, and specifically amplified the target gene only from T. vaginalis. Validation of this assay showed that it had the highest sensitivity and better agreement with PCR (used as the gold standard) compared to microscopy and multiplex PCR. This study showed that the LAMP assay, targeting the actin gene, could be used to diagnose early infections of T. vaginalis. Thus, we have provided an alternative molecular diagnostic tool and a point-of-care test that may help to prevent trichomoniasis transmission and associated complications.

  14. Heaving displacement amplification characteristics of a power buoy in shoaling water with insufficient draft

    Directory of Open Access Journals (Sweden)

    Hyuck-Min Kweon

    2013-12-01

    Full Text Available The resonance power buoy is a convincing tool that can increase the extraction efficiency of wave energy. The buoy needs a corresponding draft, to move in resonance with waves within the peak frequency band where wave energy is concentrated. However, it must still be clarified if the buoy acts as an effective displacement amplifier, when there is insufficient water depth. In this study, the vertical displacement of a circular cylinder-type buoy was calculated, with the spectrum data observed in a real shallow sea as the external wave force, and with the corresponding draft, according to the mode frequency of normal waves. Such numerical investigation result, without considering Power Take-Off (PTO damping, confirmed that the area of the heave responses spectrum can be amplified by up to about tenfold, compared with the wave energy spectrum, if the draft corresponds to the peak frequency, even with insufficient water depth. Moreover, the amplification factor of the buoy varied, according to the seasonal changes in the wave spectra.

  15. Combining isothermal rolling circle amplification and electrochemiluminescence for highly sensitive point mutation detection

    Science.gov (United States)

    Su, Qiang; Zhou, Xiaoming

    2008-12-01

    Many pathogenic and genetic diseases are associated with changes in the sequence of particular genes. We describe here a rapid and highly efficient assay for the detection of point mutation. This method is a combination of isothermal rolling circle amplification (RCA) and high sensitive electrochemluminescence (ECL) detection. In the design, a circular template generated by ligation upon the recognition of a point mutation on DNA targets was amplified isothermally by the Phi29 polymerase using a biotinylated primer. The elongation products were hybridized with tris (bipyridine) ruthenium (TBR)-tagged probes and detected in a magnetic bead based ECL platform, indicating the mutation occurrence. P53 was chosen as a model for the identification of this method. The method allowed sensitive determination of the P53 mutation from wild-type and mutant samples. The main advantage of RCA-ECL is that it can be performed under isothermal conditions and avoids the generation of false-positive results. Furthermore, ECL provides a faster, more sensitive, and economical option to currently available electrophoresis-based methods.

  16. Discovery and cross-amplification of microsatellite polymorphisms in asterinid sea stars.

    Science.gov (United States)

    Keever, Carson C; Sunday, Jennifer; Wood, Charlene; Byrne, Maria; Hart, Michael W

    2008-10-01

    Variation in tandem repeats of two- to six-base nucleotide motifs (microsatellites) can be used to obtain inexpensive and highly informative multi-locus data on population genetics.We developed and tested a large set of cross-amplifiable sea star (Asterinidae) microsatellite markers from a mixed pool of genomic DNA from eight species. We describe cloned sequences, primers, and PCR conditions, and characterize population-level variation for some species and markers. A few clones containing microsatellites showed considerable similarity to sequences (including genes of known function) in other sea stars and in sea urchins (from the Strongylocentrotus purpuratus complete genome). The pooled genomic DNA method was an efficient way to sample microsatellites from many species: we cloned 2-10 microsatellites from each of eight species, and most could be cross-amplified in 1-7 other species. At 12 loci in two species, we found 1-10 alleles per microsatellite, with a broad range of inbreeding coefficients. Measures of polymorphism were negatively correlated with the extent of cross-amplification.

  17. Use of reverse transcription loop-mediated isothermal amplification for the detection of Plum pox virus.

    Science.gov (United States)

    Varga, Aniko; James, Delano

    2006-12-01

    A one step, accelerated reverse transcription loop-mediated isothermal amplification (RT-LAMP) procedure was developed for the detection of Plum pox virus (PPV). The six primers required for accelerated RT-LAMP were designed using a conserved region in the C-terminus of the coat protein coding region of PPV. RT-LAMP was used to detect isolates of five strains of PPV including the strains D, M, EA, C, and W. The virus was detected reliably in both infected herbaceous and woody hosts. RT-LAMP was compared to real-time RT-PCR with SYBR Green I and melting curve analysis, using serial dilutions of total RNA extracts. Similar sensitivities were observed, except that real-time RT-PCR was more consistent at lower template concentrations. The purity of the FIP and BIP primers affected the efficiency of the reaction, and incubation time and template concentration affected the ladder-like pattern observed after agarose gel electrophoresis. Although PPV could be detected after 30min of incubation at 63 degrees C, a longer incubation time was required for lower concentrations of the target. RT-LAMP is a very sensitive, low cost diagnostic tool that should be of value in more accurate determination of the distribution of PPV. This should assist in preventing further spread of this devastating virus.

  18. 3'-RACE Amplification of Aminopeptidase N Gene from Anopheles stephensi Applicable in Transmission Blocking Vaccines.

    Science.gov (United States)

    Bokharaei, Hanieh; Raz, Abbasali; Zakeri, Sedigheh; Djadid, Navid Dinparast

    2012-07-01

    Because of the lack of an effective and economical control strategy against malaria (the most devastating infectious disease in developing countries) Transmission-Blocking Vaccines (TBVs) concept has been raised in recent years, promising a more efficient way to malaria control. TBVs aim at interfering and/or blocking pathogen development within the vector, halting transmission to non-infected vertebrate host. Aminopeptidase N (APN) is one of the most potent proteins in parasite development in Anopheles malaria vectors, which is strongly co-localized with human malaria parasites in the mosquito midgut epithelium. Therefore, Aminopeptidase N is one of the best choices for a new TBV. In this study for the first time we used 3'-RACE to amplify APN gene in Anopheles stephensi (An.stephensi), a major malaria vector in Iran, Indian subcontinent up to China by using different sets of primers including exon junction, conserved and specific region primers. Full length of APN was sequenced stepwise, which could be applied in designing a new regional TBV and act as an essential component of malaria elimination program in An.stephensi distribution areas. Primers design and method modification should be set up exactly in approach based amplifications. From results we came to this conclusion that that 3'-RACE could be applied to amplified key regions which are beyond reach.

  19. Broad-Range Bacterial Capture from Fluid-Samples: Implications for Amplification-Free Contamination Detection

    Directory of Open Access Journals (Sweden)

    Monika WEBER

    2016-08-01

    Full Text Available Fluid-Screen, Inc. presents a bacterial concentration and filtration method based on dielectrophoresis and alternating current kinetics. Dielectrophoresis has been previously shown to induce particle motion; however, bacterial capture efficiency and reproducibility have consistently been low, reducing its potential for practical applications. In this study, we introduce a novel, patent-pending electrode system optimized to simultaneously capture a wide range of bacterial species from a variety of aqueous solutions. Specifically, we show that the method of dielectrophoresis used induces responses in both characteristic Gram- negative Escherichia coli and Gram-positive Enterococcus faecalis bacteria, as well as with Bacillus subtilis and Aestuariimicrobium kwangyangense. We have adapted the electrode design to create a bacterial sample preparatio unit, termed the sample sorter, that is able to capture multiple bacterial species and release them simultaneously for bacterial concentration and exchange from complex matrices to defined buffer media. This technology can be used on its own or in conjunction with standard bacterial detection methods such as mass spectroscopy. The Fluid-Screen product will dramatically improve testing and identification of bacterial contaminants in various industrial settings by eliminating the need for amplification of samples and by reducing the time to identification.

  20. Rapid and sensitive detection of Bordetella bronchiseptica by loop-mediated isothermal amplification (LAMP

    Directory of Open Access Journals (Sweden)

    Hui Zhang

    2013-10-01

    Full Text Available Bordetella bronchiseptica causes acute and chronic respiratory infections in diverse animal species and occasionally in humans. In this study, we described the establishment of a simple, sensitive and cost-efficient loop-mediated isothermal amplification (LAMP assay for the detection of B. bronchiseptica. A set of primers towards a 235 bp region within the flagellum gene of B. bronchiseptica was designed with online software.. The specificity of the LAMP assay was examined by using 6 porcine pathogens and 100 nasal swabs collected from healthy pigs and suspect infected pigs. The results indicated that positive reactions were confirmed for all B. bronchiseptica and no cross-reactivity was observed from other non-B. bronchiseptica. In sensitivity evaluations, the technique successfully detected a serial dilutions of extracted B. bronchiseptica DNA with a detection limit of 9 copies, which was 10 times more sensitive than that of PCR. Compared with conventional PCR, the higher sensitivity of LAMP method and no need for the complex instrumentation make this LAMP assay a promising alternative for the diagnosis of B. bronchiseptica in rural areas and developing countries where there lacks of complex laboratory services.

  1. Faithful PCR Amplification of an Unnatural Base-Pair Analogue with Four Hydrogen Bonds.

    Science.gov (United States)

    Tarashima, Noriko; Komatsu, Yasuo; Furukawa, Kazuhiro; Minakawa, Noriaki

    2015-07-20

    In vitro replication of an unnatural imidazopyridopyridine:naphthyridine base pair, (i.e., ImN(N):NaO(O)), having four hydrogen bonds was investigated. Kinetic studies of single-nucleotide insertion revealed that ImN(N) and NaO(O) were recognized as complementary bases by an exonuclease-deficient Klenow fragment with higher specificity and efficiency than two previously described pairs (ImN(O):NaO(N) and ImO(N):NaN(O)) because of higher thermal and thermodynamic stabilities and the DAAD:ADDA (D=donor, A=acceptor) hydrogen-bonding pattern of the ImN(N):NaO(O) pair. Faithful polymerase chain reaction (PCR) amplification of a DNA fragment containing the ImN(N):NaO(O) pair was achieved by using DNA polymerases possessing 3'→5' exonuclease activity (≈99.5 % per doubling). © 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Status of the High Average Power Diode-Pumped Solid State Laser Development at HiLASE

    Directory of Open Access Journals (Sweden)

    Ondřej Novák

    2015-09-01

    Full Text Available An overview of the latest developments of kilowatt-level diode pumped solid state lasers for advanced applications at the HiLASE Centre is presented. An overview of subcontracted and in-house-developed laser beamlines is presented. The aim of development is to build kW-class beamlines delivering picosecond pulses between 1- and 100-kHz repetition rates and high-energy nanosecond pulses at 10 Hz. The picosecond beamlines are based on Yb:YAG thin-disk amplifiers and chirped pulse amplification. The current status of the beamlines’ performance is reported. The advantages of zero-phonon line and pulsed pumping are demonstrated with respect to efficiency, thin disk temperature and beam quality. New diagnostics methods supporting the high average power lasers’ development, such as the high-resolution spectroscopy of Yb-doped materials, in situ thin disk deformation measurements, single-shot M2 measurement, realization of wavefront correction by a deformable mirror and the laser performance of a new mixed garnet ceramics, are described. The energetic, thermal and fluid-mechanical numerical modeling for the optimization of the multi-slab amplifiers is also described.

  3. Visual and Real-Time Event-Specific Loop-Mediated Isothermal Amplification Based Detection Assays for Bt Cotton Events MON531 and MON15985.

    Science.gov (United States)

    Randhawa, Gurinder Jit; Chhabra, Rashmi; Bhoge, Rajesh K; Singh, Monika

    2015-01-01

    Bt cotton events MON531 and MON15985 are authorized for commercial cultivation in more than 18 countries. In India, four Bt cotton events have been commercialized; more than 95% of total area under genetically modified (GM) cotton cultivation comprises events MON531 and MON15985. The present study reports on the development of efficient event-specific visual and real-time loop-mediated isothermal amplification (LAMP) assays for detection and identification of cotton events MON531 and MON15985. Efficiency of LAMP assays was compared with conventional and real-time PCR assays. Real-time LAMP assay was found time-efficient and most sensitive, detecting up to two target copies within 35 min. The developed real-time LAMP assays, when combined with efficient DNA extraction kit/protocol, may facilitate onsite GM detection to check authenticity of Bt cotton seeds.

  4. Remote Optical Imagery of Obscured Objects in Low-Visibility Environments Using Parametric Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Asher, R.B.; Bliss, D.E.; Cameron, S.M.; Hamil, R.A.

    1998-10-14

    The development of unconventional active optical sensors to remotely detect and spatially resolve suspected threats obscured by low-visibility observation conditions (adverse weather, clouds, dust, smoke, precipitation, etc.) is fundamental to maintaining tactical supremacy in the battlespace. In this report, the authors describe an innovative frequency-agile image intensifier technology based on time-gated optical parametic amplification (OPA) for enhanced light-based remote sensing through pervasive scattering and/or turbulent environments. Improved dynamic range characteristics derived from the amplified passband of the OPA receiver combined with temporal discrimination in the image capture process will offset radiant power extinction losses, while defeating the deugradative effects & multipath dispersion and ,diffuse backscatter noise along the line-of-sight on resultant image contrast and range resolution. Our approach extends the operational utility of the detection channel in existing laser radar systems by increasing sensitivity to low-level target reffectivities, adding ballistic rejection of scatter and clutter in the range coordinate, and introducing multispectral and polarization discrimination capability in a wavelen~h-tunable, high gain nonlinear optical component with strong potential for source miniaturization. A key advantage of integrating amplification and tlequency up-conversion functions within a phasematched three-wave mixing parametric device is the ability to petiorm background-free imaging with eye-safe or longer inilared illumination wavelengths (idler) less susceptible to scatter without sacrificing quantum efficiency in the detection process at the corresponding signal wavelength. We report benchmark laboratory experiments in which the OPA gating process has been successfidly demonstrated in both transillumination and reflection test geometries with extended pathlengths representative of realistic coastal sea water and cumulus cloud

  5. Word Recognition and Learning: Effects of Hearing Loss and Amplification Feature

    Science.gov (United States)

    Stewart, Elizabeth C.; Willman, Amanda P.; Odgear, Ian S.

    2017-01-01

    Two amplification features were examined using auditory tasks that varied in stimulus familiarity. It was expected that the benefits of certain amplification features would increase as the familiarity with the stimuli decreased. A total of 20 children and 15 adults with normal hearing as well as 21 children and 17 adults with mild to severe hearing loss participated. Three models of ear-level devices were selected based on the quality of the high-frequency amplification or the digital noise reduction (DNR) they provided. The devices were fitted to each participant and used during testing only. Participants completed three tasks: (a) word recognition, (b) repetition and lexical decision of real and nonsense words, and (c) novel word learning. Performance improved significantly with amplification for both the children and the adults with hearing loss. Performance improved further with wideband amplification for the children more than for the adults. In steady-state noise and multitalker babble, performance decreased for both groups with little to no benefit from amplification or from the use of DNR. When compared with the listeners with normal hearing, significantly poorer performance was observed for both the children and adults with hearing loss on all tasks with few exceptions. Finally, analysis of across-task performance confirmed the hypothesis that benefit increased as the familiarity of the stimuli decreased for wideband amplification but not for DNR. However, users who prefer DNR for listening comfort are not likely to jeopardize their ability to detect and learn new information when using this feature.

  6. Functionally distinct, sequence-specific replicator and origin elements are required for Drosophila chorion gene amplification.

    Science.gov (United States)

    Lu, L; Zhang, H; Tower, J

    2001-01-15

    To meet the demand for the rapid synthesis of chorion (eggshell) proteins, Drosophila ovarian follicle cells amplify the chromosomal loci containing the chorion gene clusters up to 60-fold. Amplification occurs by repeated firing of one or more origins located within each gene cluster. Deletion analyses of transgenic constructs derived from the third chromosome cluster have identified a 320-bp amplification control element (ACE3) required for amplification, as well as several stimulatory amplification enhancing regions (AERs). Two-dimensional (2D) gel analyses have identified multiple DNA replication initiation sites (origins) that partially overlap in location with ACE3 and the AERs. To further study sequence requirements for amplification, a vector was used in which transgenic constructs are protected from chromosomal position effects by flanking insulator elements, the suppressor Hairy-wing protein binding site (SHWBS). Using the buffered vector, the 320-bp ACE3 and an 884-bp element designated ori-beta were found to be necessary and sufficient for amplification. Two-dimensional gels revealed that ori-beta was acting as the origin. In contrast, origin activity could not be detected for ACE3. An insulator placed between ACE3 and ori-beta inhibited amplification, indicating that ACE3 activates ori-beta in cis. The results suggest that ACE3 acts as a replicator and support and extend the replicator model for the organization of metazoan chromosomal replicons.

  7. Analysis of p53 mutational events and MDM2 amplification in canine soft-tissue sarcomas.

    Science.gov (United States)

    Nasir, L; Rutteman, G R; Reid, S W; Schulze, C; Argyle, D J

    2001-12-10

    Canine cancer is of major significance in terms of animal health and welfare and soft tissue sarcomas are an important group of tumours accounting for approximately 15% of all canine tumours presented. Abnormal p53 protein expression and gene mutations have been identified in a number of different canine tumour types. However, mdm2 gene amplification has only been investigated in a limited number of canine osteosarcomas. In this present study a series of canine soft-tissue sarcomas (STS) were examined for p53 mutations and/or mdm2 amplification. For p53 mutational studies polymerase chain reaction and direct DNA sequencing was used. Gene mutations were identified in 6 of 30 (20%) primary tumour cases including MPNST (n=3) leiomysarcoma (n=1), heamangiosarcoma (n=1) and sarcoma (n=1). mdm2 gene amplification was assessed by Southern Blot. Although there was no evidence for major gene rearrangements, gene amplification was detected in 4 of 35 (11.4 %) primary tumours including MPNST (n=2), rhabdomyosarcoma (n=2). A total of 33 cases were examined for both p53 mutations and mdm2 amplification. Seven of the tumours were positive for p53 mutations, while five were positive for mdm2 amplification. With the exception of one case, a reciprocal relationship between the presence of a p53 mutation and mdm2 gene amplification was demonstrated.

  8. N- myc oncogene amplification is correlated to trace metal concentrations in neuroblastoma cultured cells

    Science.gov (United States)

    Gouget, B.; Sergeant, C.; Benard, J.; Llabador, Y.; Simonoff, M.

    2000-10-01

    N- myc oncogene amplification is a powerful predictor of aggressive behavior of neuroblastoma (NB), the most common solid tumor of the early childhood. Since N- myc overexpression - subsequent to amplification - determines a phenotype of invasiveness and metastatic spreading, it is assumed that N- myc amplified neuroblasts synthesize zinc metalloenzymes leading to tumor invasion and formation of metastases. In order to test a possible relation between N- myc oncogene amplification and trace metal contents in human NB cells, Fe, Cu and Zn concentrations have been measured by nuclear microprobe analysis in three human neuroblastoma cell lines with various degrees of N- myc amplification. Elemental determinations show uniform distribution of trace metals within the cells, but variations of intracellular trace metal concentrations with respect to the degree of N- myc amplification are highly dependent on the nature of the element. Zinc concentration is higher in both N- myc amplified cell lines (IMR-32 and IGR-N-91) than in the non-amplified cells (SK-N-SH). In contrast, intracellular iron content is particularly low in N- myc amplified cell lines. Moreover, copper concentrations showed an increase with the degree of N- myc amplification. These results indicate that a relationship exists between intracellular trace metals and N- myc oncogene amplification. They further suggest that trace metals very probably play a determinant role in mechanisms of the neuroblastoma invasiveness.

  9. Genome-wide gene amplification during differentiation of neural progenitor cells in vitro.

    Directory of Open Access Journals (Sweden)

    Ulrike Fischer

    Full Text Available DNA sequence amplification is a phenomenon that occurs predictably at defined stages during normal development in some organisms. Developmental gene amplification was first described in amphibians during gametogenesis and has not yet been described in humans. To date gene amplification in humans is a hallmark of many tumors. We used array-CGH (comparative genomic hybridization and FISH (fluorescence in situ hybridization to discover gene amplifications during in vitro differentiation of human neural progenitor cells. Here we report a complex gene amplification pattern two and five days after induction of differentiation of human neural progenitor cells. We identified several amplified genes in neural progenitor cells that are known to be amplified in malignant tumors. There is also a striking overlap of amplified chromosomal regions between differentiating neural progenitor cells and malignant tumor cells derived from astrocytes. Gene amplifications in normal human cells as physiological process has not been reported yet and may bear resemblance to developmental gene amplifications in amphibians and insects.

  10. Digital Droplet Multiple Displacement Amplification (ddMDA for Whole Genome Sequencing of Limited DNA Samples.

    Directory of Open Access Journals (Sweden)

    Minsoung Rhee

    Full Text Available Multiple displacement amplification (MDA is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA technique where partitioning of the template DNA into thousands of sub-nanoliter droplets, each containing a small number of DNA fragments, greatly reduces the competition among DNA fragments for primers and polymerase thereby greatly reducing amplification bias. Consequently, the ddMDA approach enabled a more uniform coverage of amplification over the entire length of the genome, with significantly lower bias and non-specific amplification than conventional MDA. For a sample containing 0.1 pg/μL of E. coli DNA (equivalent of ~3/1000 of an E. coli genome per droplet, ddMDA achieves a 65-fold increase in coverage in de novo assembly, and more than 20-fold increase in specificity (percentage of reads mapping to E. coli compared to the conventional tube MDA. ddMDA offers a powerful method useful for many applications including medical diagnostics, forensics, and environmental microbiology.

  11. Basin amplification of seismic waves in the city of Pahrump, Nevada.

    Energy Technology Data Exchange (ETDEWEB)

    Abbott, Robert E.

    2005-07-01

    Sedimentary basins can increase the magnitude and extend the duration of seismic shaking. This potential for seismic amplification is investigated for Pahrump Valley, Nevada-California. The Pahrump Valley is located approximately 50 km northwest of Las Vegas and 75 km south of the Nevada Test Site. Gravity data suggest that the city of Pahrump sits atop a narrow, approximately 5 km deep sub-basin within the valley. The seismic amplification, or ''site effect'', was investigated using a combination of in situ velocity modeling and comparison of the waveforms and spectra of weak ground motion recorded in the city of Pahrump, Nevada, and those recorded in the nearby mountains. Resulting spectral ratios indicate seismic amplification factors of 3-6 over the deepest portion of Pahrump Valley. This amplification predominantly occurs at 2-2.5 Hz. Amplification over the deep sub-basin is lower than amplification at the sub-basin edge, location of the John Blume and Associates PAHA seismic station, which recorded many underground nuclear tests at the Nevada Test Site. A comprehensive analysis of basin amplification for the city of Pahrump should include 3-D basin modeling, due to the extreme basement topography of the Pahrump Valley.

  12. N-myc oncogene amplification is correlated to trace metal concentrations in neuroblastoma cultured cells

    Energy Technology Data Exchange (ETDEWEB)

    Gouget, B. E-mail: gouget@drecam.cea.fr; Sergeant, C.; Benard, J.; Llabador, Y.; Simonoff, M

    2000-10-01

    N-myc oncogene amplification is a powerful predictor of aggressive behavior of neuroblastoma (NB), the most common solid tumor of the early childhood. Since N-myc overexpression - subsequent to amplification - determines a phenotype of invasiveness and metastatic spreading, it is assumed that N-myc amplified neuroblasts synthesize zinc metalloenzymes leading to tumor invasion and formation of metastases. In order to test a possible relation between N-myc oncogene amplification and trace metal contents in human NB cells, Fe, Cu and Zn concentrations have been measured by nuclear microprobe analysis in three human neuroblastoma cell lines with various degrees of N-myc amplification. Elemental determinations show uniform distribution of trace metals within the cells, but variations of intracellular trace metal concentrations with respect to the degree of N-myc amplification are highly dependent on the nature of the element. Zinc concentration is higher in both N-myc amplified cell lines (IMR-32 and IGR-N-91) than in the non-amplified cells (SK-N-SH). In contrast, intracellular iron content is particularly low in N-myc amplified cell lines. Moreover, copper concentrations showed an increase with the degree of N-myc amplification. These results indicate that a relationship exists between intracellular trace metals and N-myc oncogene amplification. They further suggest that trace metals very probably play a determinant role in mechanisms of the neuroblastoma invasiveness.

  13. Batch efficiency

    CERN Document Server

    Schwickerath, U; Uria, C; CERN. Geneva. IT Department

    2010-01-01

    A frequent source of concern for resource providers is the efficient use of computing resources in their centers. This has a direct impact on requests for new resources. There are two different but strongly correlated aspects to be considered: while users are mostly interested in a good turn-around time for their jobs, resource providers are mostly interested in a high and efficient usage of their available resources. Both things, the box usage and the efficiency of individual user jobs, need to be closely monitored so that the sources of the inefficiencies can be identified. At CERN, the Lemon monitoring system is used for both purposes. Examples of such sources are poorly written user code, inefficient access to mass storage systems, and dedication of resources to specific user groups. As a first step for improvements CERN has launched a project to develop a scheduler add-on that allows careful overloading of worker nodes that run idle jobs.

  14. Fibroblast growth factor receptor (FGFR) gene amplifications are rare events in bladder cancer.

    Science.gov (United States)

    Fischbach, Anna; Rogler, Anja; Erber, Ramona; Stoehr, Robert; Poulsom, Richard; Heidenreich, Axel; Schneevoigt, Birte-Swantje; Hauke, Sven; Hartmann, Arndt; Knuechel, Ruth; Veeck, Jürgen; Gaisa, Nadine T

    2015-04-01

    Activating point mutations and protein overexpression of fibroblast growth factor receptors (FGFRs), especially FGFR3, are frequent events in bladder cancer. Little is known about gene amplifications, therefore we characterized amplification of FGFR1-3 by fluorescence in-situ hybridization (FISH). Tumours of 153 patients (n = 65 pTa low-grade, n = 15 pTa high-grade, n = 37 pT1, n = 20 pT2, n = 10 pT3, n = 6 pT4) were analysed by FISH for FGFR1-3 copy numbers and screened for FGFR3 mutations and immunohistochemical protein expression. Amplifications of FGFR1 were found in 1.6% (two of 122), FGFR2 in 0.8% (one of 121) and FGFR3 in 3.4% (five of 145). All amplifications were high-level amplifications, not overlapping with polysomy. Amplifications were found in papillary/papillary-invasive tumour parts, and predominantly in tumours with enhanced Ki67 index (>10%), aberrant CK20 expression, and low p53 expression. All FGFR3-amplified samples showed concomitant FGFR3 mutations and FGFR3 protein overexpression. FGFR amplifications were not associated significantly with gender, age, grade or stage in statistical analyses. FGFR amplifications are rare events in bladder cancer, with FGFR3 amplification being the most prevalent (3.4% of cases). Concomitant FGFR3 mutations and protein overexpression indicate that FGFR3-mediated signalling in these tumours would probably be highly active. This patient subgroup may be particularly suited to FGFR-targeted pharmacotherapy. © 2014 John Wiley & Sons Ltd.

  15. MYC amplification in breast cancer: a chromogenic in situ hybridisation study

    Science.gov (United States)

    Rodriguez‐Pinilla, S Maria; Jones, Robin L; Lambros, Maryou B K; Arriola, Edurne; Savage, Kay; James, Michelle; Pinder, Sarah E; Reis‐Filho, Jorge S

    2007-01-01

    Aims To analyse the correlation between MYC amplification and various clinicopathological features and outcome in a cohort of 245 patients with invasive breast carcinoma treated with surgery followed by anthracycline‐based chemotherapy. Given the high prevalence of MYC amplification in tumours of BRCA1 mutation carriers and the similarities between these and sporadic “basal‐like” carcinomas, the prevalence of MYC amplification in “basal‐like” breast carcinomas was investigated. Methods MYC gene copy number was assessed on tissue microarrays containing duplicate cores of 245 invasive breast carcinomas by means of chromogenic in situ hybridisation using SpotLight C‐MYC amplification probe and chromosome 8 centromeric probe (CEP8). Signals were evaluated at 400× magnification; 30 morphologically unequivocal neoplastic cells in each core were counted for the presence of the gene and CEP8 probes. Results Amplification was defined as a MYC:CEP8 ratio >2. Signals for both MYC and CEP8 were assessable in 196/245 (80%) tumours. MYC amplification was found in 19/196 cases (9.7%) and was not associated with tumour size, histological grade, positivity for oestrogen receptor, progesterone receptor, HER2, epidermal growth factor, cytokeratins 14, 5/6 and 17, MIB1 or p53. Only 4% of basal‐like carcinomas showed MYC amplification, compared to 8.75% and 10.7% of luminal and HER2 tumours respectively. On univariate analysis, MYC amplification displayed a significant association with shorter metastasis‐free and overall survival and proved to be an independent prognostic factor on multivariate survival analysis. Conclusion MYC amplification is not associated with “basal‐like” phenotype and proved to be an independent prognostic factor for breast cancer patients treated with anthracycline‐based chemotherapy. PMID:17158641

  16. Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations

    Directory of Open Access Journals (Sweden)

    Ivell Richard

    2003-11-01

    Full Text Available Abstract Background The amplification of RNA with the T7-System is a widely used technique for obtaining increased amounts of RNA starting from limited material. The amplified RNA (aRNA can subsequently be used for microarray hybridizations, warranting sufficient signal for image analysis. We describe here an amplification-time dependent degradation of aRNA in prolonged standard T7 amplification protocols, that results in lower average size aRNA and decreased yields. Results A time-dependent degradation of amplified RNA (aRNA could be observed when using the classical "Eberwine" T7-Amplification method. When the amplification was conducted for more than 4 hours, the resulting aRNA showed a significantly smaller size distribution on gel electrophoresis and a concomitant reduction of aRNA yield. The degradation of aRNA could be correlated to the presence of the T7 RNA Polymerase in the amplification cocktail. The aRNA degradation resulted in a strong bias in microarray hybridizations with a high coefficient of variation and a significant reduction of signals of certain transcripts, that seem to be susceptible to this RNA degrading activity. The time-dependent degradation of these transcripts was verified by a real-time PCR approach. Conclusions It is important to perform amplifications not longer than 4 hours as there is a characteristic 'quality vs. yield' situation for longer amplification times. When conducting microarray hybridizations it is important not to compare results obtained with aRNA from different amplification times.

  17. Two-Tone Interference Caused by Active Amplification

    Science.gov (United States)

    Duke, T. A. J.; Andor, D.; Jülicher, F.

    2003-02-01

    To capture faint sounds, the ear uses an active system of amplification. We and our colleagues have put forward the idea that the amplifier comprises a set of "self-tuned critical oscillators": each hair cell contains a force-generating dynamical system which is maintained at the threshold of an oscillatory instability, or Hopf bifurcation. Our analysis shows that the active response to a pure tone is perfectly suited to the ear's needs, since it provides frequency selectivity, exquisite sensitivity and wide dynamic range. However, the intrinsic nonlinearity of the mechanism causes tones of different frequency to interfere with one another in the cochlea. In order to provide a framework for understanding how the ear processes the more complex sounds of speech and music, we have examined the response of a critical Hopf oscillator to two tones. Our calculations indicate how the response to one tone is suppressed by the presence of a second tone of similar frequency. They also show how a characteristic spectrum of distortion products is generated. Based on this analysis, we discuss to what extent psychophysical phenomena such as the sensation of dissonance and auditory illusions can be attributed to the physical nature of the peripheral detection apparatus.

  18. Stochastic amplification of fluctuations in cortical up-states.

    Directory of Open Access Journals (Sweden)

    Jorge Hidalgo

    Full Text Available Cortical neurons are bistable; as a consequence their local field potentials can fluctuate between quiescent and active states, generating slow 0.5 2 Hz oscillations which are widely known as transitions between Up and Down States. Despite a large number of studies on Up-Down transitions, deciphering its nature, mechanisms and function are still today challenging tasks. In this paper we focus on recent experimental evidence, showing that a class of spontaneous oscillations can emerge within the Up states. In particular, a non-trivial peak around 20 Hz appears in their associated power-spectra, what produces an enhancement of the activity power for higher frequencies (in the 30-90 Hz band. Moreover, this rhythm within Ups seems to be an emergent or collective phenomenon given that individual neurons do not lock to it as they remain mostly unsynchronized. Remarkably, similar oscillations (and the concomitant peak in the spectrum do not appear in the Down states. Here we shed light on these findings by using different computational models for the dynamics of cortical networks in presence of different levels of physiological complexity. Our conclusion, supported by both theory and simulations, is that the collective phenomenon of "stochastic amplification of fluctuations"--previously described in other contexts such as Ecology and Epidemiology--explains in an elegant and parsimonious manner, beyond model-dependent details, this extra-rhythm emerging only in the Up states but not in the Downs.

  19. Using DNS amplification DDoS attack for hiding data

    Science.gov (United States)

    Mehić, M.; Voznak, M.; Safarik, J.; Partila, P.; Mikulec, M.

    2014-05-01

    This paper concerns available steganographic techniques that can be used for sending hidden data through public network. Typically, in steganographic communication it is advised to use popular/often used method for sending hidden data and amount of that data need to be high as much as possible. We confirmed this by choosing a Domain Name System (DNS) as a vital protocol of each network and choosing Distributed denial of service (DDoS) attacks that are most popular network attacks currently represented in the world. Apart from characterizing existing steganographic methods we provide new insights by presenting two new techniques. The first one is network steganography solution which exploits free/unused protocols fields and is known for IP, UDP or TCP protocols, but has never been applied to DNS (Domain Name Server) which are the fundamental part of network communications. The second explains the usage of DNS Amplification DDoS Attack to send seamlessly data through public network. The calculation that was performed to estimate the total amount of data that can be covertly transferred by using these technique, regardless of steganalysis, is included in this paper.

  20. Stochastic Amplification of Fluctuations in Cortical Up-States

    Science.gov (United States)

    Hidalgo, Jorge; Seoane, Luís F.; Cortés, Jesús M.; Muñoz, Miguel A.

    2012-01-01

    Cortical neurons are bistable; as a consequence their local field potentials can fluctuate between quiescent and active states, generating slow Hz oscillations which are widely known as transitions between Up and Down States. Despite a large number of studies on Up-Down transitions, deciphering its nature, mechanisms and function are still today challenging tasks. In this paper we focus on recent experimental evidence, showing that a class of spontaneous oscillations can emerge within the Up states. In particular, a non-trivial peak around Hz appears in their associated power-spectra, what produces an enhancement of the activity power for higher frequencies (in the Hz band). Moreover, this rhythm within Ups seems to be an emergent or collective phenomenon given that individual neurons do not lock to it as they remain mostly unsynchronized. Remarkably, similar oscillations (and the concomitant peak in the spectrum) do not appear in the Down states. Here we shed light on these findings by using different computational models for the dynamics of cortical networks in presence of different levels of physiological complexity. Our conclusion, supported by both theory and simulations, is that the collective phenomenon of “stochastic amplification of fluctuations” – previously described in other contexts such as Ecology and Epidemiology – explains in an elegant and parsimonious manner, beyond model-dependent details, this extra-rhythm emerging only in the Up states but not in the Downs. PMID:22879879

  1. NEW ERBIUM DOPED ANTIMONY GLASSES FOR LASER AND GLASS AMPLIFICATION

    Directory of Open Access Journals (Sweden)

    B. Tioua

    2015-07-01

    Full Text Available Because of the special spectroscopic properties of the rare earth ions, rare earth doped glasses are widely used in bulk and fiber lasers or amplifiers. The modelling of lasers and searching for new laser transitions require a precise knowledge of the spectroscopic properties of rare earth ions in different host glasses. In this poster will offer new doped erbium glasses synthesized in silicate crucibles were obtained in the combination Sb2O3-WO3-Na2O. Several properties are measured and correlated with glass compositions. The absorption spectral studies have been performed for erbium doped glasses. The intensities of various absorption bands of the doped glasses are measured and the Judd-Ofelt parameters have been computed. From the theory of Judd-Ofelt, various radiative properties, such as transition probability, branching ratio and radiative life time for various emission levels of these doped glasses have been determined and reported. These results confirm the ability of antimony glasses for glass amplification.

  2. Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification

    Science.gov (United States)

    Mauk, Michael G.; Liu, Changchun; Song, Jinzhao; Bau, Haim H.

    2015-01-01

    Microfluidic components and systems for rapid (nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane”) to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD) better than 103 virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed. PMID:27600235

  3. Competing disturbance amplification mechanisms in two-fluid boundary layers

    Science.gov (United States)

    Saha, Sandeep; Page, Jacob; Zaki, Tamer

    2015-11-01

    The linear stability of boundary layers above a thin wall film of lower viscosity is analyzed. Appropriate choice of the film thickness and viscosity excludes the possibility of interfacial instabilities. Transient amplification of disturbances is therefore the relevant destabilizing influence, and can take place via three different mechanisms in the two-fluid configuration. Each is examined in detail by solving an initial value problem whose initial condition comprises a pair of appropriately chosen eigenmodes from the discrete, continuous and interface modes. Two regimes are driven by the lift-up mechanism: (i) The response to a streamwise vortex and (ii) the normal vorticity generated by a stable Tollmien-Schlichting wave. Both are damped due to the film. The third regime is associated with the wall-normal vorticity that is generated by the interface displacement. It can lead to appreciable streamwise velocity disturbances in the near-wall region at relatively low viscosity ratios. The results demonstrate that a wall film can stabilize the early linear stages of boundary-layer transition, and explain the observations from the recent nonlinear direct numerical simulations of this configuration by Jung & Zaki (J. Fluid Mech., vol 772, 2015, 330-360).

  4. Period doubling induced by thermal noise amplification in genetic circuits

    Science.gov (United States)

    Ruocco, G.; Fratalocchi, A.

    2014-11-01

    Rhythms of life are dictated by oscillations, which take place in a wide rage of biological scales. In bacteria, for example, oscillations have been proven to control many fundamental processes, ranging from gene expression to cell divisions. In genetic circuits, oscillations originate from elemental block such as autorepressors and toggle switches, which produce robust and noise-free cycles with well defined frequency. In some circumstances, the oscillation period of biological functions may double, thus generating bistable behaviors whose ultimate origin is at the basis of intense investigations. Motivated by brain studies, we here study an ``elemental'' genetic circuit, where a simple nonlinear process interacts with a noisy environment. In the proposed system, nonlinearity naturally arises from the mechanism of cooperative stability, which regulates the concentration of a protein produced during a transcription process. In this elemental model, bistability results from the coherent amplification of environmental fluctuations due to a stochastic resonance of nonlinear origin. This suggests that the period doubling observed in many biological functions might result from the intrinsic interplay between nonlinearity and thermal noise.

  5. Parametric Amplification of Coupled Atomic and Optical Fields

    Science.gov (United States)

    Moore, M. G.; Meystre, P.

    One of the earliest and still most important spin-offs of the invention of the laser is without a doubt nonlinear optics. Following the pioneering experiments carried out by P. A. Franken and his students [1], N. Bloembergen, Y. R. Shen and their collaborators made a series of crucial advances that led to the rapid development of the field [2]. In the early days, it was generally understood that what made nonlinear optics possible was the high optical powers provided by lasers. For such fields, a classical description of the light fields was clearly sufficient. Yet, a few visionaries insisted on a fully quantum mechanical description of radiation in the analysis of nonlinear optical phenomena such as parametric amplification. A central character in these developments was R. J. Glauber, who, together with his students, developed many of the tools, and much of the early quantum theory of nonlinear optics [3,4]. One of his students was Dan Walls, who upon his return to New Zealand after spe nding a short time in Germany developed one of the leading schools of quantum optics in the world.

  6. Period doubling induced by thermal noise amplification in genetic circuits

    KAUST Repository

    Ruocco, G.

    2014-11-18

    Rhythms of life are dictated by oscillations, which take place in a wide rage of biological scales. In bacteria, for example, oscillations have been proven to control many fundamental processes, ranging from gene expression to cell divisions. In genetic circuits, oscillations originate from elemental block such as autorepressors and toggle switches, which produce robust and noise-free cycles with well defined frequency. In some circumstances, the oscillation period of biological functions may double, thus generating bistable behaviors whose ultimate origin is at the basis of intense investigations. Motivated by brain studies, we here study an “elemental” genetic circuit, where a simple nonlinear process interacts with a noisy environment. In the proposed system, nonlinearity naturally arises from the mechanism of cooperative stability, which regulates the concentration of a protein produced during a transcription process. In this elemental model, bistability results from the coherent amplification of environmental fluctuations due to a stochastic resonance of nonlinear origin. This suggests that the period doubling observed in many biological functions might result from the intrinsic interplay between nonlinearity and thermal noise.

  7. Current Technologies of Electrochemical Immunosensors: Perspective on Signal Amplification

    Directory of Open Access Journals (Sweden)

    Il-Hoon Cho

    2018-01-01

    Full Text Available An electrochemical immunosensor employs antibodies as capture and detection means to produce electrical charges for the quantitative analysis of target molecules. This sensor type can be utilized as a miniaturized device for the detection of point-of-care testing (POCT. Achieving high-performance analysis regarding sensitivity has been one of the key issues with developing this type of biosensor system. Many modern nanotechnology efforts allowed for the development of innovative electrochemical biosensors with high sensitivity by employing various nanomaterials that facilitate the electron transfer and carrying capacity of signal tracers in combination with surface modification and bioconjugation techniques. In this review, we introduce novel nanomaterials (e.g., carbon nanotube, graphene, indium tin oxide, nanowire and metallic nanoparticles in order to construct a high-performance electrode. Also, we describe how to increase the number of signal tracers by employing nanomaterials as carriers and making the polymeric enzyme complex associated with redox cycling for signal amplification. The pros and cons of each method are considered throughout this review. We expect that these reviewed strategies for signal enhancement will be applied to the next versions of lateral-flow paper chromatography and microfluidic immunosensor, which are considered the most practical POCT biosensor platforms.

  8. Gold Nanowire Based Electrical DNA Detection Using Rolling Circle Amplification

    Science.gov (United States)

    2014-01-01

    We present an electrical sensor that uses rolling circle amplification (RCA) of DNA to stretch across the gap between two electrodes, interact with metal nanoparticle seeds to generate an electrically conductive nanowire, and produce electrical signals upon detection of specific target DNA sequences. RCA is a highly specific molecular detection mechanism based on DNA probe circularization. With this technique, long single-stranded DNA with simple repetitive sequences are produced. Here we show that stretched RCA products can be metalized using silver or gold solutions to form metal wires. Upon metallization, the resistance drops from TΩ to kΩ for silver and to Ω for gold. Metallization is seeded by gold nanoparticles aligned along the single-stranded DNA product through hybridization of functionalized oligonucleotides. We show that combining RCA with electrical DNA detection produces results in readout with very high signal-to-noise ratio, an essential feature for sensitive and specific detection assays. Finally, we demonstrate detection of 10 ng of Escherichia coli genomic DNA using the sensor concept. PMID:24433087

  9. Microfluidic continuous flow digital loop-mediated isothermal amplification (LAMP).

    Science.gov (United States)

    Rane, Tushar D; Chen, Liben; Zec, Helena C; Wang, Tza-Huei

    2015-02-07

    Digital nucleic acid detection is rapidly becoming a popular technique for ultra-sensitive and quantitative detection of nucleic acid molecules in a wide range of biomedical studies. Digital polymerase chain reaction (PCR) remains the most popular way of conducting digital nucleic acid detection. However, due to the need for thermocycling, digital PCR is difficult to implement in a streamlined manner on a single microfluidic device, leading to complex fragmented workflows and multiple separate devices and instruments. Loop-mediated isothermal amplification (LAMP) is an excellent isothermal alternative to PCR with potentially better specificity than PCR because of the use of multiple primer sets for a nucleic acid target. Here we report a microfluidic droplet device implementing all the steps required for digital nucleic acid detection including droplet generation, incubation and in-line detection for digital LAMP. As compared to microchamber or droplet array-based digital assays, the continuous flow operation of this device eliminates the constraints on the number of total reactions imposed by the footprint of the device and the analysis throughput caused by the time for lengthy incubation and transfer of materials between instruments.

  10. Hyperpolarized xenon NMR and MRI signal amplification by gas extraction

    Science.gov (United States)

    Zhou, Xin; Graziani, Dominic; Pines, Alexander

    2009-01-01

    A method is reported for enhancing the sensitivity of NMR of dissolved xenon by detecting the signal after extraction to the gas phase. We demonstrate hyperpolarized xenon signal amplification by gas extraction (Hyper-SAGE) in both NMR spectra and magnetic resonance images with time-of-flight information. Hyper-SAGE takes advantage of a change in physical phase to increase the density of polarized gas in the detection coil. At equilibrium, the concentration of gas-phase xenon is ≈10 times higher than that of the dissolved-phase gas. After extraction the xenon density can be further increased by several orders of magnitude by compression and/or liquefaction. Additionally, being a remote detection technique, the Hyper-SAGE effect is further enhanced in situations where the sample of interest would occupy only a small proportion of the traditional NMR receiver. Coupled with targeted xenon biosensors, Hyper-SAGE offers another path to highly sensitive molecular imaging of specific cell markers by detection of exhaled xenon gas. PMID:19805177

  11. A new ultrasonic signal amplification method for detection of bacteria

    Science.gov (United States)

    Kant Shukla, Shiva; Resa López, Pablo; Sierra Sánchez, Carlos; Urréjola, José; Segura, Luis Elvira

    2012-10-01

    A new method is presented that increases the sensitivity of ultrasound-based techniques for detection of bacteria. The technique was developed for the detection of catalase-positive microorganisms. It uses a bubble trapping medium containing hydrogen peroxide that is mixed with the sample for microbiological evaluation. The enzyme catalase is present in catalase-positive bacteria, which induces a rapid hydrolysis of hydrogen peroxide, forming bubbles which remain in the medium. This reaction results in the amplification of the mechanical changes that the microorganisms produce in the medium. The effect can be detected by means of ultrasonic wave amplitude continuous measurement since the bubbles increase the ultrasonic attenuation significantly. It is shown that microorganism concentrations of the order of 105 cells ml-1 can be detected using this method. This allows an improvement of three orders of magnitude in the ultrasonic detection threshold of microorganisms in conventional culture media, and is competitive with modern rapid microbiological methods. It can also be used for the characterization of the enzymatic activity.

  12. Whole genome amplification and real-time PCR in forensic casework

    Directory of Open Access Journals (Sweden)

    Asili Paola

    2009-04-01

    Full Text Available Abstract Background WGA (Whole Genome Amplification in forensic genetics can eliminate the technical limitations arising from low amounts of genomic DNA (gDNA. However, it has not been used to date because any amplification bias generated may complicate the interpretation of results. Our aim in this paper was to assess the applicability of MDA to forensic SNP genotyping by performing a comparative analysis of genomic and amplified DNA samples. A 26-SNPs TaqMan panel specifically designed for low copy number (LCN and/or severely degraded genomic DNA was typed on 100 genomic as well as amplified DNA samples. Results Aliquots containing 1, 0.1 and 0.01 ng each of 100 DNA samples were typed for a 26-SNPs panel. Similar aliquots of the same DNA samples underwent multiple displacement amplification (MDA before being typed for the same panel. Genomic DNA samples showed 0% PCR failure rate for all three dilutions, whilst the PCR failure rate of the amplified DNA samples was 0% for the 1 ng and 0.1 ng dilutions and 0.077% for the 0.01 ng dilution. The genotyping results of both the amplified and genomic DNA samples were also compared with reference genotypes of the same samples obtained by direct sequencing. The genomic DNA samples showed genotype concordance rates of 100% for all three dilutions while the concordance rates of the amplified DNA samples were 100% for the 1 ng and 0.1 ng dilutions and 99.923% for the 0.01 ng dilution. Moreover, ten artificially-degraded DNA samples, which gave no results when analyzed by current forensic methods, were also amplified by MDA and genotyped with 100% concordance. Conclusion We investigated the suitability of MDA material for forensic SNP typing. Comparative analysis of amplified and genomic DNA samples showed that a large number of SNPs could be accurately typed starting from just 0.01 ng of template. We found that the MDA genotyping call and accuracy rates were only slightly lower than those for genomic DNA

  13. Whole genome amplification and real-time PCR in forensic casework

    Science.gov (United States)

    Giardina, Emiliano; Pietrangeli, Ilenia; Martone, Claudia; Zampatti, Stefania; Marsala, Patrizio; Gabriele, Luciano; Ricci, Omero; Solla, Gianluca; Asili, Paola; Arcudi, Giovanni; Spinella, Aldo; Novelli, Giuseppe

    2009-01-01

    Background WGA (Whole Genome Amplification) in forensic genetics can eliminate the technical limitations arising from low amounts of genomic DNA (gDNA). However, it has not been used to date because any amplification bias generated may complicate the interpretation of results. Our aim in this paper was to assess the applicability of MDA to forensic SNP genotyping by performing a comparative analysis of genomic and amplified DNA samples. A 26-SNPs TaqMan panel specifically designed for low copy number (LCN) and/or severely degraded genomic DNA was typed on 100 genomic as well as amplified DNA samples. Results Aliquots containing 1, 0.1 and 0.01 ng each of 100 DNA samples were typed for a 26-SNPs panel. Similar aliquots of the same DNA samples underwent multiple displacement amplification (MDA) before being typed for the same panel. Genomic DNA samples showed 0% PCR failure rate for all three dilutions, whilst the PCR failure rate of the amplified DNA samples was 0% for the 1 ng and 0.1 ng dilutions and 0.077% for the 0.01 ng dilution. The genotyping results of both the amplified and genomic DNA samples were also compared with reference genotypes of the same samples obtained by direct sequencing. The genomic DNA samples showed genotype concordance rates of 100% for all three dilutions while the concordance rates of the amplified DNA samples were 100% for the 1 ng and 0.1 ng dilutions and 99.923% for the 0.01 ng dilution. Moreover, ten artificially-degraded DNA samples, which gave no results when analyzed by current forensic methods, were also amplified by MDA and genotyped with 100% concordance. Conclusion We investigated the suitability of MDA material for forensic SNP typing. Comparative analysis of amplified and genomic DNA samples showed that a large number of SNPs could be accurately typed starting from just 0.01 ng of template. We found that the MDA genotyping call and accuracy rates were only slightly lower than those for genomic DNA. Indeed, when 10 pg of

  14. Amplification of surface acoustic waves by transverse electric current in piezoelectric semiconductors

    DEFF Research Database (Denmark)

    Gulyaev, Yuri V.

    1974-01-01

    It is shown that the principal characteristic feature of the surface acoustic waves in piezoelectrics—the presence of an alternating electric field transverse to the surface, which can be of the same order of magnitude as the longitudinal field—may not only give rise to the known transverse...... acoustoelectric effect but also lead to amplification of surface acoustic waves by electron drift perpendicular to the surface. For Love waves in a piezoelectric semiconductor film on a highly conducting substrate, the amplification coefficient is found and the conditions necessary for amplification...

  15. Dynamic Characteristics of a Hydraulic Amplification Mechanism for Large Displacement Actuators Systems

    Directory of Open Access Journals (Sweden)

    Xavier Arouette

    2010-03-01

    Full Text Available We have developed a hydraulic displacement amplification mechanism (HDAM and studied its dynamic response when combined with a piezoelectric actuator. The HDAM consists of an incompressible fluid sealed in a microcavity by two largely deformable polydimethylsiloxane (PDMS membranes. The geometry with input and output surfaces having different cross-sectional areas creates amplification. By combining the HDAM with micro-actuators, we can amplify the input displacement generated by the actuators, which is useful for applications requiring large deformation, such as tactile displays. We achieved a mechanism offering up to 18-fold displacement amplification for static actuation and 12-fold for 55 Hz dynamic actuation.

  16. Quantification of HER2 autoantibodies in the amplification phenomenon of HER2 in breast cancer

    DEFF Research Database (Denmark)

    Lauterlein, Jens-Jacob L; Petersen, Eva R B; Olsen, Dorte Aa

    2011-01-01

    Gene amplification of HER2 (human epidermal growth factor receptor 2) is a well-known phenomenon in various cancers. However, little is known about the mechanism of the gene amplification phenomenon itself. Autoantibodies to cellular receptors have been described in several cancer types. We...... hypothesised that autoantibodies against HER2 might have a stimulatory capacity and could be the cause of the HER2 gene amplification phenomenon. To investigate this, we developed a test for the detection of autoantibodies against HER2 in serum (S-HER2Ab)....

  17. Anisotropic amplification of proton transport in proton exchange membrane fuel cells

    Science.gov (United States)

    Thimmappa, Ravikumar; Fawaz, Mohammed; Devendrachari, Mruthyunjayachari Chattanahalli; Gautam, Manu; Kottaichamy, Alagar Raja; Shafi, Shahid Pottachola; Thotiyl, Musthafa Ottakam

    2017-07-01

    Though graphene oxide (GO) membrane shuttles protons under humid conditions, it suffer severe disintegration and anhydrous conditions lead to abysmal ionic conductivity. The trade-off between mechanical integrity and ionic conductivity challenge the amplification of GO's ionic transport under anhydrous conditions. We show anisotropic amplification of GO's ionic transport with a selective amplification of in plane contribution under anhydrous conditions by doping it with a plant extract, phytic acid (PA). The hygroscopic nature of PA stabilized interlayer water molecules and peculiar geometry of sbnd OH functionalities around saturated hydrocarbon ring anisotropically enhanced ionic transport amplifying the fuel cell performance metrics.

  18. Loop-Mediated Isothermal Amplification (LAMP) for Detection of Campylobacter jejuni and C. coli in Thai Children with Diarrhea.

    Science.gov (United States)

    Pham, Ngan Thi Kim; Trinh, Quang Duy; Khamrin, Pattara; Ukarapol, Nuthapong; Kongsricharoern, Tipachan; Yamazaki, Wataru; Komine-Aizawa, Shihoko; Okitsu, Shoko; Maneekarn, Niwat; Hayakawa, Satoshi; Ushijima, Hiroshi

    2015-01-01

    Campylobacter species are common causes of bacterial diarrhea, and Campylobacter jejuni and C. coli are known as the predominant causative agents in humans. Recent studies suggested that loop-mediated isothermal amplification (LAMP) is an efficient and practical tool for rapid detection of C. jejuni and C. coli in clinical samples. We used LAMP to screen 151 stool samples for Campylobacter; these samples were collected in 2012 from Thai children with diarrhea. The PCR method discriminated C. jejuni and C. coli among the detected Campylobacter strains; these species were subjected to sequencing of the hipO gene (in C. jejuni) or the ask gene (in C. coli). The results suggest that the prevalence of Campylobacter infection among Thai children with diarrhea is 8.6%, and C. jejuni is the most prevalent species.

  19. Inability of 'Whole Genome Amplification' to Improve Success Rates for the Biomolecular Detection of Tuberculosis in Archaeological Samples.

    Directory of Open Access Journals (Sweden)

    Jannine Forst

    Full Text Available We assessed the ability of whole genome amplification (WGA to improve the efficiency of downstream polymerase chain reactions (PCRs directed at ancient DNA (aDNA of members of the Mycobacterium tuberculosis complex (MTBC. Using extracts from a variety of bones and a tooth from human skeletons with or without lesions indicative of tuberculosis, from multiple time periods, we obtained inconsistent results. We conclude that WGA does not provide any advantage in studies of MTBC aDNA. The sporadic nature of our results are probably due to the fact that WGA is itself a PCR-based procedure which, although designed to deal with fragmented DNA, might be inefficient with the low concentration of templates in an aDNA extract. As such, WGA is subject to similar, if not the same, restrictions as PCR when applied to aDNA.

  20. [Application of combined chromosome karyotype analysis and multiplex ligation probe amplification technique for the prenatal diagnosis of fetal abnormalities].

    Science.gov (United States)

    Jiang, Nan; Yu, Dongyi

    2016-12-10

    To assess the value of combined chromosome karyotype analysis and multiplex ligation probe amplification (MLPA) assay for the prenatal diagnosis of fetuses with abnormalities detected by ultrasonography. With informed consent obtained, 72 pregnant women with ultrasound detected fetal structural abnormalities underwent percutaneous umbilical cord blood sampling. Routine karyotype analysis and MLPA assay were used to detect potential chromosomal deletions and duplications. Five cases were found with an abnormal karyotype. In addition, the MLPA has detected 2 chromosomal microdeletions and 1 microduplication. Together the two methods have yielded a detection rate of 11.11%. For fetal abnormalities revealed by ultrasonography, combined karyotype analysis and MLPA assay can provide a better option for its efficiency and simplicity.