Solving the jitter problem in microwave compressed ultrafast electron diffraction instruments: Robust sub-50 fs cavity-laser phase stabilization

PubMed Central

Otto, M. R.; René de Cotret, L. P.; Stern, M. J.; Siwick, B. J.

2017-01-01

We demonstrate the compression of electron pulses in a high-brightness ultrafast electron diffraction instrument using phase-locked microwave signals directly generated from a mode-locked femtosecond oscillator. Additionally, a continuous-wave phase stabilization system that accurately corrects for phase fluctuations arising in the compression cavity from both power amplification and thermal drift induced detuning was designed and implemented. An improvement in the microwave timing stability from 100 fs to 5 fs RMS is measured electronically, and the long-term arrival time stability (>10 h) of the electron pulses improves to below our measurement resolution of 50 fs. These results demonstrate sub-relativistic ultrafast electron diffraction with compressed pulses that is no longer limited by laser-microwave synchronization. PMID:28852686

Phase sensitive amplification in integrated waveguides (Conference Presentation)

NASA Astrophysics Data System (ADS)

Schroeder, Jochen B.; Zhang, Youngbin; Husko, Chad A.; LeFrancois, Simon; Eggleton, Benjamin J.

2017-02-01

Phase sensitive amplification (PSA) is an attractive technology for integrated all-optical signal processing, due to it's potential for noiseless amplification, phase regeneration and generation of squeezed light. In this talk I will review our results on implementing four-wave-mixing based PSA inside integrated photonic devices. In particular I will discuss PSA in chalcogenide ridge waveguides and silicon slow-light photonic crystals. We achieve PSA in both pump- and signal-degenerate schemes with maximum extinction ratios of 11 (silicon) and 18 (chalcogenide) dB. I will further discuss the influence of two-photon absorption and free carrier effects on the performance of silicon-based PSAs.

Precision phase estimation based on weak-value amplification

NASA Astrophysics Data System (ADS)

Qiu, Xiaodong; Xie, Linguo; Liu, Xiong; Luo, Lan; Li, Zhaoxue; Zhang, Zhiyou; Du, Jinglei

2017-02-01

In this letter, we propose a precision method for phase estimation based on the weak-value amplification (WVA) technique using a monochromatic light source. The anomalous WVA significantly suppresses the technical noise with respect to the intensity difference signal induced by the phase delay when the post-selection procedure comes into play. The phase measured precision of this method is proportional to the weak-value of a polarization operator in the experimental range. Our results compete well with the wide spectrum light phase weak measurements and outperform the standard homodyne phase detection technique.

Graphene Ambipolar Nanoelectronics for High Noise Rejection Amplification.

PubMed

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.

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

PubMed

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.

Gain-phase modulation in chirped-pulse amplification

NASA Astrophysics Data System (ADS)

Shen, Yijie; Gao, Gan; Meng, Yuan; Fu, Xing; Gong, Mali

2017-10-01

The cross-modulation between the gain and chirped phase in chirped-pulse amplification (CPA) is theoretically and experimentally demonstrated. We propose a gain-phase coupled nonlinear Schrödinger equation (GPC-NLSE) for solving chirped-pulse propagation in a nonlinear gain medium involved in the gain-phase modulation (GPM) process. With the GPC-NLSE, the space-time-frequency-dependent gain, chirped phase, pulse, and spectrum evolutions can be precisely calculated. Moreover, a short-length high-gain Yb-doped fiber CPA experiment is presented in which a self-steepening distortion of the seed pulse is automatically compensated after amplification. This phenomenon can be explained by the GPM theory whereas conventional models cannot. The experimental results for the temporal and spectral intensities show excellent agreement with our theory. Our GPM theory paves the way for further investigations of the finer structures of the pulse and spectrum in CPA systems.

The G1 phase Cdks regulate the centrosome cycle and mediate oncogene-dependent centrosome amplification

PubMed Central

2011-01-01

Because centrosome amplification generates aneuploidy and since centrosome amplification is ubiquitous in human tumors, a strong case is made for centrosome amplification being a major force in tumor biogenesis. Various evidence showing that oncogenes and altered tumor suppressors lead to centrosome amplification and aneuploidy suggests that oncogenes and altered tumor suppressors are a major source of genomic instability in tumors, and that they generate those abnormal processes to initiate and sustain tumorigenesis. We discuss how altered tumor suppressors and oncogenes utilize the cell cycle regulatory machinery to signal centrosome amplification and aneuploidy. PMID:21272329

Anomalous amplification of a homodyne signal via almost-balanced weak values.

PubMed

Liu, Wei-Tao; Martínez-Rincón, Julián; Viza, Gerardo I; Howell, John C

2017-03-01

We propose precision measurements of ultra-small angular velocities of a mirror within a modified Sagnac interferometer, where the counter-propagating beams are spatially separated, using the recently proposed technique of almost-balanced weak values amplification (ABWV) [Phys. Rev. Lett.116, 100803 (2016)PRLTAO0031-900710.1103/PhysRevLett.116.100803]. The separation between the two beams provides additional amplification with respect to using collinear beams in a Sagnac interferometer. Within the same setup, the weak-value amplification technique is also performed for comparison. Much higher amplification factors can be obtained using the almost-balanced weak values technique, with the best one achieved in our experiments being as high as 1.2×10⁷. In addition, the amplification factor monotonically increases with decreasing of the post-selection phase for the ABWV case in our experiments, which is not the case for weak-value amplification (WVA) at small post-selection phases. Both techniques consist of measuring the angular velocity. The sensitivity of the ABWV technique is ∼38  nrad/s per averaged pulse for a repetition rate of 1 Hz and ∼33  nrad/s per averaged pulse for the WVA technique.

Optical Parametric Amplification of Single Photon: Statistical Properties and Quantum Interference

NASA Astrophysics Data System (ADS)

Xu, Xue-Xiang; Yuan, Hong-Chun

2014-05-01

By using phase space method, we theoretically investigate the quantum statistical properties and quantum interference of optical parametric amplification of single photon. The statistical properties, such as the Wigner function (WF), average photon number, photon number distribution and parity, are derived analytically for the fields of the two output ports. The results indicate that the fields in the output ports are multiphoton states rather than single photon state due to the amplification of the optical parametric amplifiers (OPA). In addition, the phase sensitivity is also examined by using the detection scheme of parity measurement.

Raman-noise-induced quantum limits for χ(3) nondegenerate phase-sensitive amplification and quadrature squeezing

NASA Astrophysics Data System (ADS)

Voss, Paul L.; Köprülü, Kahraman G.; Kumar, Prem

2006-04-01

We present a quantum theory of nondegenerate phase-sensitive parametric amplification in a χ(3) nonlinear medium. The nonzero response time of the Kerr (χ(3)) nonlinearity determines the quantum-limited noise figure of χ(3) parametric amplification, as well as the limit on quadrature squeezing. This nonzero response time of the nonlinearity requires coupling of the parametric process to a molecular vibration phonon bath, causing the addition of excess noise through spontaneous Raman scattering. We present analytical expressions for the quantum-limited noise figure of frequency nondegenerate and frequency degenerate χ(3) parametric amplifiers operated as phase-sensitive amplifiers. We also present results for frequency nondegenerate quadrature squeezing. We show that our nondegenerate squeezing theory agrees with the degenerate squeezing theory of Boivin and Shapiro as degeneracy is approached. We have also included the effect of linear loss on the phase-sensitive process.

Adsorption-induced auto-amplification of enantiomeric excess on an achiral surface

NASA Astrophysics Data System (ADS)

Yun, Yongju; Gellman, Andrew J.

2015-06-01

The homochirality of biomolecules is a signature of life on Earth and has significant implications in, for example, the production of pharmaceutical compounds. It has been suggested that biomolecular homochirality may have arisen from the amplification of a spontaneously formed small enantiomeric excess (e.e.). Many minerals exhibit naturally chiral surfaces and so adsorption has been proposed as one possible mechanism for such an amplification of e.e. Here we show that when gas-phase mixtures of D- and L-aspartic acid are exposed to an achiral Cu(111) surface, a small e.e. in the gas phase, e.e.g, leads to an amplification of the e.e. on the surface, e.e.s, under equilibrium conditions. Adsorption-induced amplification of e.e. does not require a chiral surface. The dependence of e.e.s on e.e.g has been modelled successfully using a Langmuir-like adsorption isotherm that incorporates the formation of homochiral adsorbate clusters on the surface.

Magnetic nanobeads present during enzymatic amplification and labeling for a simplified DNA detection protocol based on AC susceptometry

NASA Astrophysics Data System (ADS)

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.

Enhanced solid-phase recombinase polymerase amplification and electrochemical detection.

PubMed

Del Río, Jonathan Sabaté; Lobato, Ivan Magriñà; Mayboroda, Olena; Katakis, Ioanis; O'Sullivan, Ciara K

2017-05-01

Recombinase polymerase amplification (RPA) is an elegant method for the rapid, isothermal amplification of nucleic acids. Here, we elucidate the optimal surface chemistry for rapid and efficient solid-phase RPA, which was fine-tuned in order to obtain a maximum signal-to-noise ratio, defining the optimal DNA probe density, probe-to-lateral spacer ratio (1:0, 1:1, 1:10 and 1:100) and length of a vertical spacer of the probe as well as investigating the effect of different types of lateral spacers. The use of different labelling strategies was also examined in order to reduce the number of steps required for the analysis, using biotin or horseradish peroxidase-labelled reverse primers. Optimisation of the amplification temperature used and the use of surface blocking agents were also pursued. The combination of these changes facilitated a significantly more rapid amplification and detection protocol, with a lowered limit of detection (LOD) of 1 · 10 -15 M. The optimised protocol was applied to the detection of Francisella tularensis in real samples from hares and a clear correlation with PCR and qPCR results observed and the solid-phase RPA demonstrated to be capable of detecting 500 fM target DNA in real samples. Graphical abstract Relative size of thiolated lateral spacers tested versus the primer and the uvsx recombinase protein.

Construction Strategy for an Internal Amplification Control for Real-Time Diagnostic Assays Using Nucleic Acid Sequence-Based Amplification: Development and Clinical Application

PubMed Central

Rodríguez-Lázaro, David; D'Agostino, Martin; Pla, Maria; Cook, Nigel

2004-01-01

An important analytical control in molecular amplification-based methods is an internal amplification control (IAC), which should be included in each reaction mixture. An IAC is a nontarget nucleic acid sequence which is coamplified simultaneously with the target sequence. With negative results for the target nucleic acid, the absence of an IAC signal indicates that amplification has failed. A general strategy for the construction of an IAC for inclusion in molecular beacon-based real-time nucleic acid sequence-based amplification (NASBA) assays is presented. Construction proceeds in two phases. In the first phase, a double-stranded DNA molecule that contains nontarget sequences flanked by target sequences complementary to the NASBA primers is produced. At the 5′ end of this DNA molecule is a T7 RNA polymerase binding sequence. In the second phase of construction, RNA transcripts are produced from the DNA by T7 RNA polymerase. This RNA is the IAC; it is amplified by the target NASBA primers and is detected by a molecular beacon probe complementary to the internal nontarget sequences. As a practical example, an IAC for use in an assay for the detection of Mycobacterium avium subsp. paratuberculosis is described, its incorporation and optimization within the assay are detailed, and its application to spiked and natural clinical samples is shown to illustrate the correct interpretation of the diagnostic results. PMID:15583319

Carrier-envelope phase stabilization and control using a transmission grating compressor and an AOPDF.

PubMed

Canova, Lorenzo; Chen, Xiaowei; Trisorio, Alexandre; Jullien, Aurélie; Assion, Andreas; Tempea, Gabriel; Forget, Nicolas; Oksenhendler, Thomas; Lopez-Martens, Rodrigo

2009-05-01

Carrier-envelope phase (CEP) stabilization of a femtosecond chirped-pulse amplification system featuring a compact transmission grating compressor is demonstrated. The system includes two amplification stages and routinely generates phase-stable (approximately 250 mrad rms) 2 mJ, 25 fs pulses at 1 kHz. Minimizing the optical pathway in the compressor enables phase stabilization without feedback control of the grating separation or beam pointing. We also demonstrate for the first time to the best of our knowledge, out-of-loop control of the CEP using an acousto-optic programmable dispersive filter inside the laser chain.

Pressure waves in a supersaturated bubbly magma

USGS Publications Warehouse

Kurzon, I.; Lyakhovsky, V.; Navon, O.; Chouet, B.

2011-01-01

We study the interaction of acoustic pressure waves with an expanding bubbly magma. The expansion of magma is the result of bubble growth during or following magma decompression and leads to two competing processes that affect pressure waves. On the one hand, growth in vesicularity leads to increased damping and decreased wave amplitudes, and on the other hand, a decrease in the effective bulk modulus of the bubbly mixture reduces wave velocity, which in turn, reduces damping and may lead to wave amplification. The additional acoustic energy originates from the chemical energy released during bubble growth. We examine this phenomenon analytically to identify conditions under which amplification of pressure waves is possible. These conditions are further examined numerically to shed light on the frequency and phase dependencies in relation to the interaction of waves and growing bubbles. Amplification is possible at low frequencies and when the growth rate of bubbles reaches an optimum value for which the wave velocity decreases sufficiently to overcome the increased damping of the vesicular material. We examine two amplification phase-dependent effects: (1) a tensile-phase effect in which the inserted wave adds to the process of bubble growth, utilizing the energy associated with the gas overpressure in the bubble and therefore converting a large proportion of this energy into additional acoustic energy, and (2) a compressive-phase effect in which the pressure wave works against the growing bubbles and a large amount of its acoustic energy is dissipated during the first cycle, but later enough energy is gained to amplify the second cycle. These two effects provide additional new possible mechanisms for the amplification phase seen in Long-Period (LP) and Very-Long-Period (VLP) seismic signals originating in magma-filled cracks.

Novel Bioluminescent Quantitative Detection of Nucleic Acid Amplification in Real-Time

PubMed Central

Gandelman, Olga A.; Church, Vicki L.; Moore, Cathy A.; Kiddle, Guy; Carne, Christopher A.; Parmar, Surendra; Jalal, Hamid; Tisi, Laurence C.; Murray, James A. H.

2010-01-01

Background The real-time monitoring of polynucleotide amplification is at the core of most molecular assays. This conventionally relies on fluorescent detection of the amplicon produced, requiring complex and costly hardware, often restricting it to specialised laboratories. Principal Findings Here we report the first real-time, closed-tube luminescent reporter system for nucleic acid amplification technologies (NAATs) enabling the progress of amplification to be continuously monitored using simple light measuring equipment. The Bioluminescent Assay in Real-Time (BART) continuously reports through bioluminescent output the exponential increase of inorganic pyrophosphate (PPi) produced during the isothermal amplification of a specific nucleic acid target. BART relies on the coupled conversion of inorganic pyrophosphate (PPi) produced stoichiometrically during nucleic acid synthesis to ATP by the enzyme ATP sulfurylase, and can therefore be coupled to a wide range of isothermal NAATs. During nucleic acid amplification, enzymatic conversion of PPi released during DNA synthesis into ATP is continuously monitored through the bioluminescence generated by thermostable firefly luciferase. The assay shows a unique kinetic signature for nucleic acid amplifications with a readily identifiable light output peak, whose timing is proportional to the concentration of original target nucleic acid. This allows qualitative and quantitative analysis of specific targets, and readily differentiates between negative and positive samples. Since quantitation in BART is based on determination of time-to-peak rather than absolute intensity of light emission, complex or highly sensitive light detectors are not required. Conclusions The combined chemistries of the BART reporter and amplification require only a constant temperature maintained by a heating block and are shown to be robust in the analysis of clinical samples. Since monitoring the BART reaction requires only a simple light detector, the iNAAT-BART combination is ideal for molecular diagnostic assays in both laboratory and low resource settings. PMID:21152399

Explanatory Model for Sound Amplification in a Stethoscope

ERIC Educational Resources Information Center

Eshach, H.; Volfson, A.

2015-01-01

In the present paper we suggest an original physical explanatory model that explains the mechanism of the sound amplification process in a stethoscope. We discuss the amplification of a single pulse, a continuous wave of certain frequency, and finally we address the resonant frequencies. It is our belief that this model may provide students with…

High-power parametric amplification of 11.8-fs laser pulses with carrier-envelope phase control.

PubMed

Zinkstok, R Th; Witte, S; Hogervorst, W; Eikema, K S E

2005-01-01

Phase-stable parametric chirped-pulse amplification of ultrashort pulses from a carrier-envelope phase-stabilized mode-locked Ti:sapphire oscillator (11.0 fs) to 0.25 mJ/pulse at 1 kHz is demonstrated. Compression with a grating compressor and a LCD shaper yields near-Fourier-limited 11.8-fs pulses with an energy of 0.12 mJ. The amplifier is pumped by 532-nm pulses from a synchronized mode-locked laser, Nd:YAG amplifier system. This approach is shown to be promising for the next generation of ultrafast amplifiers aimed at producing terawatt-level phase-controlled few-cycle laser pulses.

Instrument-free exothermic heating with phase change temperature control for paper microfluidic devices

NASA Astrophysics Data System (ADS)

Singleton, Jered; Zentner, Chris; Buser, Josh; Yager, Paul; LaBarre, Paul; Weigl, Bernhard H.

2013-03-01

Many infectious diseases, as well as some cancers, that affect global health are most accurately diagnosed through nucleic acid amplification and detection. There is a great need to simplify nucleic acid-based assay systems for use in global health in low-resource settings as well as in settings that do not have convenient access to laboratory staff and equipment such as doctors' offices and home care settings. In developing countries, unreliable electric power, inadequate supply chains, and lack of maintenance for complex diagnostic instruments are all common infrastructure shortfalls. Many elements of instrument-free, disposable, nucleic acid amplification assays have been demonstrated in recent years. However, the problem of instrument-free,1 low-cost, temperature-controlled chemical heating remains unsolved. In this paper we present the current status and results of work towards developing disposable, low-cost, temperature-controlled heaters designed to support isothermal nucleic acid amplification assays that are integrated with a two-dimensional paper network. Our approach utilizes the heat generated through exothermic chemical reactions and controls the heat through use of engineered phase change materials to enable sustained temperatures required for nucleic acid amplification. By selecting appropriate exothermic and phase change materials, temperatures can be controlled over a wide range, suitable for various isothermal amplification methods, and maintained for over an hour at an accuracy of +/- 1°C.

Instrument-free exothermic heating with phase change temperature control for paper microfluidic devices.

PubMed

Singleton, Jered; Zentner, Chris; Buser, Josh; Yager, Paul; LaBarre, Paul; Weigl, Bernhard H

2013-03-09

Many infectious diseases, as well as some cancers, that affect global health are most accurately diagnosed through nucleic acid amplification and detection. There is a great need to simplify nucleic acid-based assay systems for use in global health in low-resource settings as well as in settings that do not have convenient access to laboratory staff and equipment such as doctors' offices and home care settings. In developing countries, unreliable electric power, inadequate supply chains, and lack of maintenance for complex diagnostic instruments are all common infrastructure shortfalls. Many elements of instrument-free, disposable, nucleic acid amplification assays have been demonstrated in recent years. However, the problem of instrument-free, low-cost, temperature-controlled chemical heating remains unsolved. In this paper we present the current status and results of work towards developing disposable, low-cost, temperature-controlled heaters designed to support isothermal nucleic acid amplification assays that are integrated with a two-dimensional paper network. Our approach utilizes the heat generated through exothermic chemical reactions and controls the heat through use of engineered phase change materials to enable sustained temperatures required for nucleic acid amplification. By selecting appropriate exothermic and phase change materials, temperatures can be controlled over a wide range, suitable for various isothermal amplification methods, and maintained for over an hour at an accuracy of +/- 1°C.

Instrument-free exothermic heating with phase change temperature control for paper microfluidic devices

PubMed Central

Singleton, Jered; Zentner, Chris; Buser, Josh; Yager, Paul; LaBarre, Paul; Weigl, Bernhard H.

2014-01-01

Many infectious diseases, as well as some cancers, that affect global health are most accurately diagnosed through nucleic acid amplification and detection. There is a great need to simplify nucleic acid-based assay systems for use in global health in low-resource settings as well as in settings that do not have convenient access to laboratory staff and equipment such as doctors' offices and home care settings. In developing countries, unreliable electric power, inadequate supply chains, and lack of maintenance for complex diagnostic instruments are all common infrastructure shortfalls. Many elements of instrument-free, disposable, nucleic acid amplification assays have been demonstrated in recent years. However, the problem of instrument-free,1 low-cost, temperature-controlled chemical heating remains unsolved. In this paper we present the current status and results of work towards developing disposable, low-cost, temperature-controlled heaters designed to support isothermal nucleic acid amplification assays that are integrated with a two-dimensional paper network. Our approach utilizes the heat generated through exothermic chemical reactions and controls the heat through use of engineered phase change materials to enable sustained temperatures required for nucleic acid amplification. By selecting appropriate exothermic and phase change materials, temperatures can be controlled over a wide range, suitable for various isothermal amplification methods, and maintained for over an hour at an accuracy of +/- 1°C. PMID:25426269

Bulk Viscosity of Bubbly Magmas and the Amplification of Pressure Waves

NASA Astrophysics Data System (ADS)

Navon, O.; Lensky, N. G.; Neuberg, J. W.; Lyakhovsky, V.

2001-12-01

The bulk viscosity of magma is needed in order to describe the dynamics of a compressible bubbly magma flowing in conduits and to follow the attenuation of pressure waves travelling through a compressible magma. We developed a model for the bulk viscosity of a suspension of gas bubbles in an incompressible Newtonian liquid that exsolves volatiles (e.g. magma). The suspension is modeled as a close pack of spherical cells, consisting of gas bubbles centered in spherical shells of a volatile-bearing liquid. Following a drop in the ambient pressure the resulting dilatational motion and driving pressure are obtained in terms of the two-phase cell parameters, i.e. bubble radius and gas pressure. By definition, the bulk viscosity of a fluid is the relation between changes of the driving pressure with respect to changes in the resulted expansion strain-rate. Thus, we can use the two-phase solution to define the bulk viscosity of a hypothetical cell, composed of a homogeneously compressible, one-phase, continuous fluid. The resulted bulk viscosity is highly non-linear. At the beginning of the expansion process, when gas exsolution is efficient, the expansion rate grows exponentially while the driving pressure decreases slightly. That means that bulk viscosity is formally negative. The negative value reflects the release of the energy stored in the supersaturated liquid (melt) and its conversion to mechanical work during exsolution. Later, when bubbles are large enough and the gas influx decreases significantly, the strain rate decelerates and the bulk viscosity becomes positive as expected in a dissipative system. We demonstrate that amplification of seismic wave travelling through a volcanic conduit filled with a volatile saturated magma may be attributed to the negative bulk viscosity of the compressible magma. Amplification of an expansion wave may, at some level in the conduit, damage the conduit walls and initiate opening of new pathways for magma to erupt.

Explanatory model for sound amplification in a stethoscope

NASA Astrophysics Data System (ADS)

Eshach, H.; Volfson, A.

2015-01-01

In the present paper we suggest an original physical explanatory model that explains the mechanism of the sound amplification process in a stethoscope. We discuss the amplification of a single pulse, a continuous wave of certain frequency, and finally we address the resonant frequencies. It is our belief that this model may provide students with opportunities to not only better understand the amplification mechanism of a stethoscope, but also to strengthen their understanding of sound, pressure, waves, resonance modes, etc.

Frequency-degenerate phase-sensitive optical parametric amplification based on four-wave mixing in graphene–silicon slot waveguide

NASA Astrophysics Data System (ADS)

Li, Zhen; Liu, Hongjun; Huang, Nan; Wang, Zhaolu; Han, Jing

2018-06-01

The phase-sensitive amplification process of a hybrid graphene–silicon (HyGS) slot waveguide with trilayers of graphene is investigated in this paper. Numerical simulation shows that a relatively high extinction ratio (42 dB) is achieved, because of the ultrahigh nonlinear coefficients, with a waveguide length of only 680 µm. In addition, the graphene layer provides the possibility of modulating the phase status and gain of the output signal. This study is expected to be highly beneficial to applications such as integrated optics and graphene-related active optical devices.

Control of Brillouin short-pulse seed amplification by chirping the pump pulse

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lehmann, G.; Spatschek, K. H.

Seed amplification via Brillouin backscattering of a long pump pulse is considered. Similar to Raman amplification, several obstructive effects may occur during short-pulse Brillouin amplification. One is the spontaneous Raman backscattering of the pump before interacting with the seed. Preforming the plasma and/or chirping the pump will reduce unwanted pump backscattering. Optimized regions for low-loss pump propagation were proposed already in conjunction with Raman seed amplification. Hence, the influence of the chirp of the pump during Brillouin interaction with the seed becomes important and will be considered here. Both, the linear as well as the nonlinear evolution phases of themore » seed caused by Brillouin amplification under the action of a chirped pump are investigated. The amplification rate as well as the seed profiles are presented as function of the chirping rate. Also the dependence of superradiant scaling rates on the chirp parameter is discussed.« less

Direct solar-pumped iodine laser amplifier

NASA Technical Reports Server (NTRS)

Han, Kwang S.; Hwang, In Heon

1990-01-01

The optimum conditions of a solar pumped iodine laser are found in this research for the case of a continuous wave operation and a pulsed operation. The optimum product of the pressure(p) inside the laser tube and the tube diameter(d) was pd=40 approx. 50 torr-cm on the contrary to the case of a high intensity flashlamp pumped iodine laser where the optimum value of the product is known to be pd=150 torr-cm. The pressure-diameter product is less than 1/3 of that of the high power iodine laser. During the research period, various laser materials were also studied for solar pumping. Among the laser materials, Nd:YAG is found to have the lowest laser threshold pumping intensity of about 200 solar constant. The Rhodamine 6G was also tested as the solar pumped laser material. The threshold pumping power was measured to be about 20,000 solar constant. The amplification experiment for a continuously pumped iodine laser amplifier was performed using Vortek solar simulator and the amplification factors were measured for single pass amplification and triple pass amplification of the 15 cm long amplifier tube. The amplification of 5 was obtained for the triple pass amplification.

Free electron laser designs for laser amplification

DOEpatents

Prosnitz, Donald; Szoke, Abraham

1985-01-01

Method for laser beam amplification by means of free electron laser techniques. With wiggler magnetic field strength B.sub.w and wavelength .lambda..sub.w =2.pi./k.sub.w regarded as variable parameters, the method(s) impose conditions such as substantial constancy of B.sub.w /k.sub.w or k.sub.w or B.sub.w and k.sub.w (alternating), coupled with a choice of either constant resonant phase angle or programmed phase space "bucket" area.

The role of the global phase in the spatio-temporal evolution of strong-coupling Brillouin scattering

NASA Astrophysics Data System (ADS)

Amiranoff, F.; Riconda, C.; Chiaramello, M.; Lancia, L.; Marquès, J. R.; Weber, S.

2018-01-01

The role of the global phase in the spatio-temporal evolution of the 3-wave coupled equations for backscattering is analyzed in the strong-coupling regime of Brillouin scattering. This is of particular interest for controlled backscattering in the case of plasma-based amplification to produce short and intense laser pulses. It is shown that the analysis of the envelope equations of the three waves involved, pump, seed, and ion wave, in terms of phase and amplitude fully describes the coupling dynamics. In particular, it helps understanding the role of the chirp of the laser beams and of the plasma density profile. The results can be used to optimize or quench the coupling mechanism. It is found that the directionality of the energy transfer is imposed by the phase relation at the leading edge of the pulse. This actually ensures continued energy transfer even if the intensity of the seed pulse is already higher than the pump pulse intensity.

Theory of remote entanglement via quantum-limited phase-preserving amplification

NASA Astrophysics Data System (ADS)

Silveri, Matti; Zalys-Geller, Evan; Hatridge, Michael; Leghtas, Zaki; Devoret, Michel H.; Girvin, S. M.

2016-06-01

We show that a quantum-limited phase-preserving amplifier can act as a which-path information eraser when followed by heterodyne detection. This "beam splitter with gain" implements a continuous joint measurement on the signal sources. As an application, we propose heralded concurrent remote entanglement generation between two qubits coupled dispersively to separate cavities. Dissimilar qubit-cavity pairs can be made indistinguishable by simple engineering of the cavity driving fields providing further experimental flexibility and the prospect for scalability. Additionally, we find an analytic solution for the stochastic master equation, a quantum filter, yielding a thorough physical understanding of the nonlinear measurement process leading to an entangled state of the qubits. We determine the concurrence of the entangled states and analyze its dependence on losses and measurement inefficiencies.

Phase-sensitive, through-amplification with a double-pumped JPC

NASA Astrophysics Data System (ADS)

Sliwa, K. M.; Hatridge, M.; Frattini, N. E.; Narla, A.; Shankar, S.; Devoret, M. H.

The Josephson Parametric Converter (JPC) is now routinely used as a quantum-limited signal processing device for superconducting qubit experiments. The JPC consists of two modes, the signal and the idler, that are coupled by a ring of Josephson junctions that implements a non-degenerate, three-wave mixing process. This device is conventionally operated as either a phase-preserving parametric amplifier, or a coherent frequency converter, by pumping it at the sum or difference of the signal and idler frequencies, respectively. Here we present a novel double-pumping scheme based on theory by Metelmann and Clerk where a coherent conversion process and a gain process are simultaneously imposed between the signal and idler modes. The interference of these two processes results in a phase-sensitive amplifier with only forward gain, and which breaks the traditional gain-bandwidth limit of parametric amplification. We present results on phase-sensitive amplification with increased bandwidth, and on noise performance and dynamic range that are comparable to the traditional mode of operation. Work supported by ARO, AFOSR, NSF and YINQE.

The effectiveness of robotic training depends on motor task characteristics.

PubMed

Marchal-Crespo, Laura; Rappo, Nicole; Riener, Robert

2017-12-01

Previous research suggests that the effectiveness of robotic training depends on the motor task to be learned. However, it is still an open question which specific task's characteristics influence the efficacy of error-modulating training strategies. Motor tasks can be classified based on the time characteristics of the task, in particular the task's duration (discrete vs. continuous). Continuous tasks require movements without distinct beginning or end. Discrete tasks require fast movements that include well-defined postures at the beginning and the end. We developed two games, one that requires a continuous movement-a tracking task-and one that requires discrete movements-a fast reaching task. We conducted an experiment with thirty healthy subjects to evaluate the effectiveness of three error-modulating training strategies-no guidance, error amplification (i.e., repulsive forces proportional to errors) and haptic guidance-on self-reported motivation and learning of the continuous and discrete games. Training with error amplification resulted in better motor learning than haptic guidance, besides the fact that error amplification reduced subjects' interest/enjoyment and perceived competence during training. Only subjects trained with error amplification improved their performance after training the discrete game. In fact, subjects trained without guidance improved the performance in the continuous game significantly more than in the discrete game, probably because the continuous task required greater attentional levels. Error-amplifying training strategies have a great potential to provoke better motor learning in continuous and discrete tasks. However, their long-lasting negative effects on motivation might limit their applicability in intense neurorehabilitation programs.

Brillouin Amplification--A Powerful New Scheme for Microwave Photonic Communications

NASA Technical Reports Server (NTRS)

Yao, S.; Maleki, L.

1997-01-01

We introduce the Brillouin selective sideband amplification technique and demonstrate many important applications of this technique in photonic microwave systems, including efficient phase modulation to amplitude modulation conversion, photonic frequency multiplication, photonic signal mixing with gain, and frequency multiplied signal up conversion.

Increasing the sensitivity of reverse phase protein arrays by antibody-mediated signal amplification

PubMed Central

2010-01-01

Background Reverse phase protein arrays (RPPA) emerged as a useful experimental platform to analyze biological samples in a high-throughput format. Different signal detection methods have been described to generate a quantitative readout on RPPA including the use of fluorescently labeled antibodies. Increasing the sensitivity of RPPA approaches is important since many signaling proteins or posttranslational modifications are present at a low level. Results A new antibody-mediated signal amplification (AMSA) strategy relying on sequential incubation steps with fluorescently-labeled secondary antibodies reactive against each other is introduced here. The signal quantification is performed in the near-infrared range. The RPPA-based analysis of 14 endogenous proteins in seven different cell lines demonstrated a strong correlation (r = 0.89) between AMSA and standard NIR detection. Probing serial dilutions of human cancer cell lines with different primary antibodies demonstrated that the new amplification approach improved the limit of detection especially for low abundant target proteins. Conclusions Antibody-mediated signal amplification is a convenient and cost-effective approach for the robust and specific quantification of low abundant proteins on RPPAs. Contrasting other amplification approaches it allows target protein detection over a large linear range. PMID:20569466

Design of multi-phase dynamic chemical networks

NASA Astrophysics Data System (ADS)

Chen, Chenrui; Tan, Junjun; Hsieh, Ming-Chien; Pan, Ting; Goodwin, Jay T.; Mehta, Anil K.; Grover, Martha A.; Lynn, David G.

2017-08-01

Template-directed polymerization reactions enable the accurate storage and processing of nature's biopolymer information. This mutualistic relationship of nucleic acids and proteins, a network known as life's central dogma, is now marvellously complex, and the progressive steps necessary for creating the initial sequence and chain-length-specific polymer templates are lost to time. Here we design and construct dynamic polymerization networks that exploit metastable prion cross-β phases. Mixed-phase environments have been used for constructing synthetic polymers, but these dynamic phases emerge naturally from the growing peptide oligomers and create environments suitable both to nucleate assembly and select for ordered templates. The resulting templates direct the amplification of a phase containing only chain-length-specific peptide-like oligomers. Such multi-phase biopolymer dynamics reveal pathways for the emergence, self-selection and amplification of chain-length- and possibly sequence-specific biopolymers.

Raman amplification in the coherent wave-breaking regime.

PubMed

Farmer, J P; Pukhov, A

2015-12-01

In regimes far beyond the wave-breaking threshold of Raman amplification, we show that significant amplification can occur after the onset of wave breaking, before phase mixing destroys the coherent coupling between pump, probe, and plasma wave. Amplification in this regime is therefore a transient effect, with the higher-efficiency "coherent wave-breaking" (CWB) regime accessed by using a short, intense probe. Parameter scans illustrate the marked difference in behavior between below wave breaking, in which the energy-transfer efficiency is high but total energy transfer is low, wave breaking, in which efficiency is low, and CWB, in which moderate efficiencies allow the highest total energy transfer.

Joint Inversion of Phase and Amplitude Data of Surface Waves for North American Upper Mantle

NASA Astrophysics Data System (ADS)

Hamada, K.; Yoshizawa, K.

2015-12-01

For the reconstruction of the laterally heterogeneous upper-mantle structure using surface waves, we generally use phase delay information of seismograms, which represents the average phase velocity perturbation along a ray path, while the amplitude information has been rarely used in the velocity mapping. Amplitude anomalies of surface waves contain a variety of information such as anelastic attenuation, elastic focusing/defocusing, geometrical spreading, and receiver effects. The effects of elastic focusing/defocusing are dependent on the second derivative of phase velocity across the ray path, and thus, are sensitive to shorter-wavelength structure than the conventional phase data. Therefore, suitably-corrected amplitude data of surface waves can be useful for improving the lateral resolution of phase velocity models. In this study, we collect a large-number of inter-station phase velocity and amplitude ratio data for fundamental-mode surface waves with a non-linear waveform fitting between two stations of USArray. The measured inter-station phase velocity and amplitude ratios are then inverted simultaneously for phase velocity maps and local amplification factor at receiver locations in North America. The synthetic experiments suggest that, while the phase velocity maps derived from phase data only reflect large-scale tectonic features, those from phase and amplitude data tend to exhibit better recovery of the strength of velocity perturbations, which emphasizes local-scale tectonic features with larger lateral velocity gradients; e.g., slow anomalies in Snake River Plain and Rio Grande Rift, where significant local amplification due to elastic focusing are observed. Also, the spatial distribution of receiver amplification factor shows a clear correlation with the velocity structure. Our results indicate that inter-station amplitude-ratio data can be of help in reconstructing shorter-wavelength structures of the upper mantle.

Noise-figure limit of fiber-optical parametric amplifiers and wavelength converters: experimental investigation

NASA Astrophysics Data System (ADS)

Tang, Renyong; Voss, Paul L.; Lasri, Jacob; Devgan, Preetpaul; Kumar, Prem

2004-10-01

Recent theoretical work predicts that the quantum-limited noise figure of a chi(3)-based fiber-optical parametric amplifier operating as a phase-insensitive in-line amplifier or as a wavelength converter exceeds the standard 3-dB limit at high gain. The degradation of the noise figure is caused by the excess noise added by the unavoidable Raman gain and loss occurring at the signal and the converted wavelengths. We present detailed experimental evidence in support of this theory through measurements of the gain and noise-figure spectra for phase-insensitive parametric amplification and wavelength conversion in a continuous-wave amplifier made from 4.4 km of dispersion-shifted fiber. The theory is also extended to include the effect of distributed linear loss on the noise figure of such a long-length parametric amplifier and wavelength converter.

Electrochemical detection of Piscirickettsia salmonis genomic DNA from salmon samples using solid-phase recombinase polymerase amplification.

PubMed

Del Río, Jonathan Sabaté; Svobodova, Marketa; Bustos, Paulina; Conejeros, Pablo; O'Sullivan, Ciara K

2016-12-01

Electrochemical detection of solid-phase isothermal recombinase polymerase amplification (RPA) of Piscirickettsia salmonis in salmon genomic DNA is reported. The electrochemical biosensor was constructed by surface functionalization of gold electrodes with a thiolated forward primer specific to the genomic region of interest. Solid-phase RPA and primer elongation were achieved in the presence of the specific target sequence and biotinylated reverse primers. The formation of the subsequent surface-tethered duplex amplicons was electrochemically monitored via addition of streptavidin-linked HRP upon completion of solid-phase RPA. Successful quantitative amplification and detection were achieved in less than 1 h at 37 °C, calibrating with PCR-amplified genomic DNA standards and achieving a limit of detection of 5 · 10 -8  μg ml -1 (3 · 10 3 copies in 10 μl). The presented system was applied to the analysis of eight real salmon samples, and the method was also compared to qPCR analysis, observing an excellent degree of correlation. Graphical abstract Schematic of use of electrochemical RPA for detection of Psiricketessia salmonis in salmon liver.

Quantum-Enhanced Sensing Based on Time Reversal of Nonlinear Dynamics.

PubMed

Linnemann, D; Strobel, H; Muessel, W; Schulz, J; Lewis-Swan, R J; Kheruntsyan, K V; Oberthaler, M K

2016-07-01

We experimentally demonstrate a nonlinear detection scheme exploiting time-reversal dynamics that disentangles continuous variable entangled states for feasible readout. Spin-exchange dynamics of Bose-Einstein condensates is used as the nonlinear mechanism which not only generates entangled states but can also be time reversed by controlled phase imprinting. For demonstration of a quantum-enhanced measurement we construct an active atom SU(1,1) interferometer, where entangled state preparation and nonlinear readout both consist of parametric amplification. This scheme is capable of exhausting the quantum resource by detecting solely mean atom numbers. Controlled nonlinear transformations widen the spectrum of useful entangled states for applied quantum technologies.

Kibble-Zurek Scaling and String-Net Coarsening in Topologically Ordered Systems

NASA Astrophysics Data System (ADS)

Khemani, Vedika; Chandran, Anushya; Burnell, F. J.; Sondhi, S. L.

2013-03-01

We consider the non-equilibrium dynamics of topologically ordered systems, such as spin liquids, driven across a continuous phase transition into proximate phases with no, or reduced, topological order. This dynamics exhibits scaling in the spirit of Kibble and Zurek but now without the presence of symmetry breaking and a local order parameter. The non-equilibrium dynamics near the critical point is universal in a particular scaling limit. The late stages of the process are seen to exhibit slow, quantum coarsening dynamics for the extended string-nets characterizing the topological phase, a potentially interesting signature of topological order. Certain gapped degrees of freedom that could potentially destroy coarsening are, at worst, dangerously irrelevant in the scaling limit. We also note a time dependent amplification of the energy splitting between topologically degenerate states on closed manifolds. We illustrate these phenomena in the context of particular phase transitions out of the abelian Z2 topologically ordered phase of the toric code, and the non-abelian SU(2)k ordered phases of the relevant Levin-Wen models. This research was supported in part by the National Science Foundation under Grant No. NSF PHY11-25915 and DMR 10-06608.

Direct solar-pumped iodine laser amplifier

NASA Technical Reports Server (NTRS)

Han, Kwang S.; Hwang, In Heon; Stock, Larry V.

1989-01-01

This semiannual progress report covers the period from September 1, 1988 to February 28, 1989 under NASA grant NAG-1-441 entitled, Direct Solar-Pumped Iodine Laser Amplifier. During this period, the research effort was concentrated on the solar pumped master oscillator power amplifier (MOPA) system using n-C3F7I. In the experimental work, the amplification measurement was conducted to identify the optimum conditions for amplification of the center's Vortek solar simulator pumped iodine laser amplifier. A modeling effort was also pursued to explain the experimental results in the theoretical work. The amplification measurement of the solar simulator pumped iodine laser amplifier is the first amplification experiment on the continuously pumped amplifier. The small signal amplification of 5 was achieved for the triple pass geometry of the 15 cm long solar simulator pumped amplifier at the n-C3F7I pressure of 20 torr, at the flow velocity of 6 m/sec and at the pumping intensity of 1500 solar constants. The XeCl laser pumped iodine laser oscillator, which was developed in the previous research, was employed as the master oscillator for the amplification measurement. In the theoretical work, the rate equations of the amplifier was established and the small signal amplification was calculated for the solar simulator pumped iodine laser amplifier. The amplification calculated from the kinetic equations with the previously measured rate coefficients reveals very large disagreement with experimental measurement. Moreover, the optimum condition predicted by the kinetic equation is quite discrepant with that measured by experiment. This fact indicates the necessity of study in the measurement of rate coefficients of the continuously pumped iodine laser system.

Role of Frequency Chirp and Energy Flow Directionality in the Strong Coupling Regime of Brillouin-Based Plasma Amplification.

PubMed

Chiaramello, M; Amiranoff, F; Riconda, C; Weber, S

2016-12-02

A detailed analysis is presented of the various stages of strong coupling Brillouin plasma amplification, emphasizing the importance of the chirp which can be of threefold origin: the intrinsic one driven by the amplification process, the one originating from the chirped-pulse-generated laser pulses, and the one associated with the plasma profile. Control of the overall chirp can optimize or quench the energy transfer. The time-dependent phase relation explains the energy flow direction during amplification and is characteristic for this strong coupling process. The study is also of potential importance to understand and maybe control cross-beam-energy transfer in inertial confinement fusion.

Single-molecule dilution and multiple displacement amplification for molecular haplotyping.

PubMed

Paul, Philip; Apgar, Josh

2005-04-01

Separate haploid analysis is frequently required for heterozygous genotyping to resolve phase ambiguity or confirm allelic sequence. We demonstrate a technique of single-molecule dilution followed by multiple strand displacement amplification to haplotype polymorphic alleles. Dilution of DNA to haploid equivalency, or a single molecule, is a simple method for separating di-allelic DNA. Strand displacement amplification is a robust method for non-specific DNA expansion that employs random hexamers and phage polymerase Phi29 for double-stranded DNA displacement and primer extension, resulting in high processivity and exceptional product length. Single-molecule dilution was followed by strand displacement amplification to expand separated alleles to microgram quantities of DNA for more efficient haplotype analysis of heterozygous genes.

Numerical investigation of differential phase noise and its power penalty for optical amplification using semiconductor optical amplifiers in DPSK applications

NASA Astrophysics Data System (ADS)

Hong, Wei; Huang, Dexiu; Zhang, Xinliang; Zhu, Guangxi

2007-11-01

A thorough simulation and evaluation of phase noise for optical amplification using semiconductor optical amplifier (SOA) is very important for predicting its performance in differential phase shift keyed (DPSK) applications. In this paper, standard deviation and probability distribution of differential phase noise are obtained from the statistics of simulated differential phase noise. By using a full-wave model of SOA, the noise performance in the entire operation range can be investigated. It is shown that nonlinear phase noise substantially contributes to the total phase noise in case of a noisy signal amplified by a saturated SOA and the nonlinear contribution is larger with shorter SOA carrier lifetime. Power penalty due to differential phase noise is evaluated using a semi-analytical probability density function (PDF) of receiver noise. Obvious increase of power penalty at high signal input powers can be found for low input OSNR, which is due to both the large nonlinear differential phase noise and the dependence of BER vs. receiving power curvature on differential phase noise standard deviation.

All-optical simultaneous multichannel quadrature phase shift keying signal regeneration based on phase-sensitive amplification

NASA Astrophysics Data System (ADS)

Wang, Hongxiang; Wang, Qi; Bai, Lin; Ji, Yuefeng

2018-01-01

A scheme is proposed to realize the all-optical phase regeneration of four-channel quadrature phase shift keying (QPSK) signal based on phase-sensitive amplification. By utilizing conjugate pump and common pump in a highly nonlinear optical fiber, degenerate four-wave mixing process is observed, and QPSK signals are regenerated. The number of waves is reduced to decrease the cross talk caused by undesired nonlinear interaction during the coherent superposition process. In addition, to avoid the effect of overlapping frequency, frequency spans between pumps and signals are set to be nonintegral multiples. Optical signal-to-noise ratio improvement is validated by bit error rate measurements. Compared with single-channel regeneration, multichannel regeneration brings 0.4-dB OSNR penalty when the value of BER is 10-3, which shows the cross talk in regeneration process is negligible.

Genome amplification of single sperm using multiple displacement amplification.

PubMed

Jiang, Zhengwen; Zhang, Xingqi; Deka, Ranjan; Jin, Li

2005-06-07

Sperm typing is an effective way to study recombination rate on a fine scale in regions of interest. There are two strategies for the amplification of single meiotic recombinants: repulsion-phase allele-specific PCR and whole genome amplification (WGA). The former can selectively amplify single recombinant molecules from a batch of sperm but is not scalable for high-throughput operation. Currently, primer extension pre-amplification is the only method used in WGA of single sperm, whereas it has limited capacity to produce high-coverage products enough for the analysis of local recombination rate in multiple large regions. Here, we applied for the first time a recently developed WGA method, multiple displacement amplification (MDA), to amplify single sperm DNA, and demonstrated its great potential for producing high-yield and high-coverage products. In a 50 mul reaction, 76 or 93% of loci can be amplified at least 2500- or 250-fold, respectively, from single sperm DNA, and second-round MDA can further offer >200-fold amplification. The MDA products are usable for a variety of genetic applications, including sequencing and microsatellite marker and single nucleotide polymorphism (SNP) analysis. The use of MDA in single sperm amplification may open a new era for studies on local recombination rates.

Quantum tomography enhanced through parametric amplification

NASA Astrophysics Data System (ADS)

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.

Concentrating the phase of a coherent state by means of probabilistic amplification

NASA Astrophysics Data System (ADS)

Usuga, Mario A.; Müller, Christian R.; Wittmann, Christoffer; Marek, Petr; Filip, Radim; Marquardt, Christoph; Leuchs, Gerd; Andersen, Ulrik L.

2011-10-01

We discuss the recent implementation of phase concentration of an optical coherent state by use of a probabilistic noiseless amplifier. The operation of the amplifier is described pictorially with phase space diagrams, and the experimental results are outlined.

Inverse four-wave-mixing and self-parametric amplification effect in optical fibre

PubMed Central

Turitsyn, Sergei K.; Bednyakova, Anastasia E.; Fedoruk, Mikhail P.; Papernyi, Serguei B.; Clements, Wallace R.L.

2015-01-01

An important group of nonlinear processes in optical fibre involves the mixing of four waves due to the intensity dependence of the refractive index. It is customary to distinguish between nonlinear effects that require external/pumping waves (cross-phase modulation and parametric processes such as four-wave mixing) and self-action of the propagating optical field (self-phase modulation and modulation instability). Here, we present a new nonlinear self-action effect, self-parametric amplification (SPA), which manifests itself as optical spectrum narrowing in normal dispersion fibre, leading to very stable propagation with a distinctive spectral distribution. The narrowing results from an inverse four-wave mixing, resembling an effective parametric amplification of the central part of the spectrum by energy transfer from the spectral tails. SPA and the observed stable nonlinear spectral propagation with random temporal waveform can find applications in optical communications and high power fibre lasers with nonlinear intra-cavity dynamics. PMID:26345290

Frequency domain optical parametric amplification

PubMed Central

Schmidt, Bruno E.; Thiré, Nicolas; Boivin, Maxime; Laramée, Antoine; Poitras, François; Lebrun, Guy; Ozaki, Tsuneyuki; Ibrahim, Heide; Légaré, François

2014-01-01

Today’s ultrafast lasers operate at the physical limits of optical materials to reach extreme performances. Amplification of single-cycle laser pulses with their corresponding octave-spanning spectra still remains a formidable challenge since the universal dilemma of gain narrowing sets limits for both real level pumped amplifiers as well as parametric amplifiers. We demonstrate that employing parametric amplification in the frequency domain rather than in time domain opens up new design opportunities for ultrafast laser science, with the potential to generate single-cycle multi-terawatt pulses. Fundamental restrictions arising from phase mismatch and damage threshold of nonlinear laser crystals are not only circumvented but also exploited to produce a synergy between increased seed spectrum and increased pump energy. This concept was successfully demonstrated by generating carrier envelope phase stable, 1.43 mJ two-cycle pulses at 1.8 μm wavelength. PMID:24805968

Biochip for Real-Time Monitoring of Hepatitis B Virus (HBV) by Combined Loop-Mediated Isothermal Amplification and Solution-Phase Electrochemical Detection

NASA Astrophysics Data System (ADS)

Tien, Bui Quang; Ngoc, Nguyen Thy; Loc, Nguyen Thai; Thu, Vu Thi; Lam, Tran Dai

2017-06-01

Accurate in situ diagnostic tests play a key role in patient management and control of most infectious diseases. To achieve this, use of handheld biochips that implement sample handling, sample analysis, and result readout together is an ideal approach. We present herein a fluid-handling biochip for real-time electrochemical monitoring of nucleic acid amplification based on loop-mediated isothermal amplification and real-time electrochemical detection on a microfluidic platform. Intercalation between amplifying DNA and free redox probe in solution phase was used to monitor the number of DNA copies. The whole diagnostic process is completed within 70 min. Our platform offers a fast and easy tool for quantification of viral pathogens in shorter time and with limited risk of all potential forms of cross-contamination. Such diagnostic tools have potential to make a huge difference to the lives of millions of people worldwide.

Phase reversal of vibratory signals in honeycomb may assist dancing honeybees to attract their audience.

PubMed

Tautz, J; Casas, J; Sandeman, D

2001-11-01

Forager honeybees dancing on the comb are able to attract dance-followers from distances across the comb that are too remote for tactile or visual signals to play a role. An alternative signal could be the vibrations of the comb at 200-300 Hz generated by dancing bees but which, without amplification, may not be large enough to alert remote dance-followers. We describe here, however, an unexpected property of honeycomb when it is subjected to vibration at around 200 Hz that would represent an effective amplification of the vibratory signals for remote dance-followers. We find that, at a specific distance from the origin of an imposed vibration, the walls across a single comb cell abruptly reverse the phase of their displacement and move in opposite directions to one another. Behavioural measurements show that the distance from which the majority of remote dance-followers are recruited coincides with the location of this phase-reversal phenomenon relative to the signal source. We propose that effective signal amplification by the phase-reversal phenomenon occurs when bees straddle a cell across which the phase reversal is expressed. Such a bee would be subjected to a situation in which the legs were moving towards and away from one another instead of in the same direction. In this manner, remote dance-followers could be alerted to a dancer performing in their vicinity.

Continuous in vitro evolution of catalytic function.

PubMed

Wright, M C; Joyce, G F

1997-04-25

A population of RNA molecules that catalyze the template-directed ligation of RNA substrates was made to evolve in a continuous manner in the test tube. A simple serial transfer procedure was used to achieve approximately 300 successive rounds of catalysis and selective amplification in 52 hours. During this time, the population size was maintained against an overall dilution of 3 x 10(298). Both the catalytic rate and amplification rate of the RNAs improved substantially as a consequence of mutations that accumulated during the evolution process. Continuous in vitro evolution makes it possible to maintain laboratory "cultures" of catalytic molecules that can be perpetuated indefinitely.

Continuous in vitro evolution of catalytic function

NASA Technical Reports Server (NTRS)

Wright, M. C.; Joyce, G. F.

1997-01-01

A population of RNA molecules that catalyze the template-directed ligation of RNA substrates was made to evolve in a continuous manner in the test tube. A simple serial transfer procedure was used to achieve approximately 300 successive rounds of catalysis and selective amplification in 52 hours. During this time, the population size was maintained against an overall dilution of 3 x 10(298). Both the catalytic rate and amplification rate of the RNAs improved substantially as a consequence of mutations that accumulated during the evolution process. Continuous in vitro evolution makes it possible to maintain laboratory "cultures" of catalytic molecules that can be perpetuated indefinitely.

Entangled-Pair Transmission Improvement Using Distributed Phase-Sensitive Amplification

NASA Astrophysics Data System (ADS)

Agarwal, Anjali; Dailey, James M.; Toliver, Paul; Peters, Nicholas A.

2014-10-01

We demonstrate the transmission of time-bin entangled photon pairs through a distributed optical phase-sensitive amplifier (OPSA). We utilize four-wave mixing at telecom wavelengths in a 5-km dispersion-shifted fiber OPSA operating in the low-gain limit. Measurements of two-photon interference curves show no statistically significant degradation in the fringe visibility at the output of the OPSA. In addition, coincidence counting rates are higher than direct passive transmission because of constructive interference between amplitudes of input photon pairs and those generated in the OPSA. Our results suggest that application of distributed phase-sensitive amplification to transmission of entangled photon pairs could be highly beneficial towards advancing the rate and scalability of future quantum communications systems.

Pediatric Audiology in North America: Current Clinical Practice and How It Relates to the American Academy of Audiology Pediatric Amplification Guideline.

PubMed

Moodie, Sheila; Rall, Eileen; Eiten, Leisha; Lindley, George; Gordey, Dave; Davidson, Lisa; Bagatto, Marlene; Scollie, Susan

2016-03-01

There is broad consensus that screening and diagnosis of permanent hearing loss in children must be embedded within a comprehensive, evidence-based, family-centered intervention program. Clinical practice guidelines (CPGs) for pediatric hearing assessment and hearing aid verification aim to reduce variability in practice and increase the use of effective evidence-based diagnostic and treatment options so that optimal outcomes may be achieved. To be of value, guidelines must be translated and implemented into practice and ongoing monitoring of their use in practice should occur. This paper provides the results of two studies that aim to examine current pediatric audiology and amplification practice in North America. A concurrent embedded mixed methods design was used. An electronic survey was distributed to North American audiologists who delivered pediatric audiology services with 350 audiologists participating in study 1 and 63 audiologists participating in study 2. A quantitative approach was the predominant method of data collection. Respondents were prompted to provide additional qualitative text and detail regarding their quantitative response choice. This qualitative text was used during the analysis phase and combined with quantitative results to assist understanding of respondents' knowledge, skills, and barriers/facilitators to implement best practice in pediatric amplification. Approximately 70% of audiologists reported using best-practice protocols for pediatric hearing aid fitting. Despite widespread knowledge and increased use of CPGs over the last 18 yrs, results of these studies show that variation in practice patterns continue to exist. Several examples of implementation challenges are discussed with recommendations provided. In order for audiologists working with children who are deaf or hard of hearing and their families to achieve the principles of family-centered early intervention, practice guidelines must continue to be developed, disseminated, and translated as they have a positive impact on the services provided. Researchers and clinical audiologists who deliver services must continue to collaborate to understand the "how" and "why" of implementing guidelines into practice and to identify the barriers/facilitators encountered in trying to do so. American Academy of Audiology.

On the role of dealing with quantum coherence in amplitude amplification

NASA Astrophysics Data System (ADS)

Rastegin, Alexey E.

2018-07-01

Amplitude amplification is one of primary tools in building algorithms for quantum computers. This technique generalizes key ideas of the Grover search algorithm. Potentially useful modifications are connected with changing phases in the rotation operations and replacing the intermediate Hadamard transform with arbitrary unitary one. In addition, arbitrary initial distribution of the amplitudes may be prepared. We examine trade-off relations between measures of quantum coherence and the success probability in amplitude amplification processes. As measures of coherence, the geometric coherence and the relative entropy of coherence are considered. In terms of the relative entropy of coherence, complementarity relations with the success probability seem to be the most expository. The general relations presented are illustrated within several model scenarios of amplitude amplification processes.

Dual phase multiplex polymerase chain reaction

DOEpatents

Pemov, Alexander [Charlottesville, VA; Bavykin, Sergei [Darien, IL

2008-10-07

Highly specific and sensitive methods were developed for multiplex amplification of nucleic acids on supports such as microarrays. Based on a specific primer design, methods include five types of amplification that proceed in a reaction chamber simultaneously. These relate to four types of multiplex amplification of a target DNA on a solid support, directed by forward and reverse complex primers immobilized to the support and a fifth type--pseudo-monoplex polymerase chain reaction (PCR) of multiple targets in solution, directed by a single pair of unbound universal primers. The addition of the universal primers in the reaction mixture increases the yield over the traditional "bridge" amplification on a solid support by approximately ten times. Methods that provide multitarget amplification and detection of as little as 0.45-4.5.times.10.sup.-12 g (equivalent to 10.sup.2-10.sup.3 genomes) of a bacterial genomic DNA are disclosed.

Amplification of thermostable lipase genes fragment from thermogenic phase of domestic waste composting process

NASA Astrophysics Data System (ADS)

Nurhasanah, Nurbaiti, Santi; Madayanti, Fida; Akhmaloka

2015-09-01

Lipases are lipolytic enzymes, catalyze the hydrolysis of fatty acid ester bonds of triglycerides to produce free fatty acids and glycerol. The enzyme is widely used in various fields of biotechnological industry. Hence, lipases with unique properties (e.g.thermostable lipase) are still being explored by variation methods. One of the strategy is by using metagenomic approach to amplify the gene directly from environmental sample. This research was focused on amplification of lipase gene fragment directly from the thermogenic phase of domestic waste composting in aerated trenches. We used domestic waste compost from waste treatment at SABUGA, ITB for the sample. Total chromosomal DNA were directly extracted from several stages at thermogenic phase of compost. The DNA was then directly used as a template for amplification of thermostable lipase gene fragments using a set of internal primers namely Flip-1a and Rlip-1a that has been affixed with a GC clamp in reverse primer. The results showed that the primers amplified the gene from four stages of thermogenic phase with the size of lipase gene fragment of approximately 570 base pairs (bp). These results were further used for Denaturing Gradient Gel Electrophoresis (DGGE) analysis to determine diversity of thermostable lipase gene fragments.

The theory of optical black hole lasers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gaona-Reyes, José L., E-mail: jgaona@fis.cinvestav.mx; Bermudez, David, E-mail: dbermudez@fis.cinvestav.mx

The event horizon of black holes and white holes can be achieved in the context of analogue gravity. It was proven for a sonic case that if these two horizons are close to each other their dynamics resemble a laser, a black hole laser, where the analogue of Hawking radiation is trapped and amplified. Optical analogues are also very successful and a similar system can be achieved there. In this work we develop the theory of optical black hole lasers and prove that the amplification is also possible. Then, we study the optical system by determining the forward propagation ofmore » modes, obtaining an approximation for the phase difference which governs the amplification, and performing numerical simulations of the pulse propagation of our system. - Highlights: • We develop the conditions to obtain the kinematics of the optical black hole laser. • We prove the amplification of Hawking radiation for the optical case. • We derive the forward propagation of modes and check the result of the backward case. • A model is proposed to calculate the phase difference and the amplification rate. • We perform numerical simulations of a pulse between two solitons forming a cavity.« less

Secret information reconciliation based on punctured low-density parity-check codes for continuous-variable quantum key distribution

NASA Astrophysics Data System (ADS)

Jiang, Xue-Qin; Huang, Peng; Huang, Duan; Lin, Dakai; Zeng, Guihua

2017-02-01

Achieving information theoretic security with practical complexity is of great interest to continuous-variable quantum key distribution in the postprocessing procedure. In this paper, we propose a reconciliation scheme based on the punctured low-density parity-check (LDPC) codes. Compared to the well-known multidimensional reconciliation scheme, the present scheme has lower time complexity. Especially when the chosen punctured LDPC code achieves the Shannon capacity, the proposed reconciliation scheme can remove the information that has been leaked to an eavesdropper in the quantum transmission phase. Therefore, there is no information leaked to the eavesdropper after the reconciliation stage. This indicates that the privacy amplification algorithm of the postprocessing procedure is no more needed after the reconciliation process. These features lead to a higher secret key rate, optimal performance, and availability for the involved quantum key distribution scheme.

Exploration of S-wave velocity profiles at strong motion stations in Eskisehir, Turkey, using microtremor phase velocity and S-wave amplification

NASA Astrophysics Data System (ADS)

Yamanaka, Hiroaki; Özmen, Ögur Tuna; Chimoto, Kosuke; Alkan, Mehmet Akif; Tün, Muammer; Pekkan, Emrah; Özel, Oguz; Polat, Derya; Nurlu, Murat

2018-05-01

We have explored 1D S-wave velocity profiles of shallow and deep soil layers over a basement at strong motion stations in Eskisehir Province, Turkey. Microtremor array explorations were conducted at eight strong motion stations in the area to know shallow 1D S-wave velocity models. Rayleigh wave phase velocity at a frequency range from 3 to 30 Hz was estimated with the spatial autocorrelation analysis of array records of vertical microtremors at each station. Individual phase velocity was inverted to a shallow S-wave velocity profile. Low-velocity layers were identified at the stations in the basin. Site amplification factors from S-wave parts of earthquake records that had been estimated at the strong motion stations by Yamanaka et al. (2017) were inverted to the S-wave velocities and Q-values of the sedimentary layers. The depths to the basement with an S-wave velocity of 2.2 km/s are about 1 km in the central part of the basin, while the basement becomes shallow as 0.3 km in the marginal part of the basin. We finally discussed the effects of the shallow and deep sedimentary layers on the 1D S-wave amplification characteristics using the revealed profiles. It is found that the shallow soil layers have no significant effects in the amplification at a frequency range lower than 3 Hz in the area.

Control over high peak-power laser light and laser-driven X-rays

NASA Astrophysics Data System (ADS)

Zhao, Baozhen; Banerjee, Sudeep; Yan, Wenchao; Zhang, Ping; Zhang, Jun; Golovin, Grigory; Liu, Cheng; Fruhling, Colton; Haden, Daniel; Chen, Shouyuan; Umstadter, Donald

2018-04-01

An optical system was demonstrated that enables continuous control over the peak power level of ultrashort duration laser light. The optical characteristics of amplified and compressed femtosecond-duration light from a chirped-pulse amplification laser are shown to remain invariant and maintain high-fidelity using this system. When the peak power was varied by an order-of-magnitude, up to its maximum attainable value, the phase, spectral bandwidth, polarization state, and focusability of the light remained constant. This capability led to precise control of the focused laser intensity and enabled a correspondingly high level of control over the power of an all-laser-driven Thomson X-ray light source.

A Strategy for Minimizing Background Signal in Autoinductive Signal Amplification Reactions for Point-of-Need Assays.

PubMed

Brooks, Adam D; Yeung, Kimy; Lewis, Gregory G; Phillips, Scott T

2015-09-07

Rapid point-of-need assays are used to detect abundant biomarkers. The development of in situ signal amplification reactions could extend these assays to screening and triaging of patients for trace levels of biomarkers, even in resource-limited settings. We, and others, have developed small molecule-based in situ signal amplification reactions that eventually may be useful in this context. Herein we describe a design strategy for minimizing background signal that may occur in the absence of the target analyte, thus moving this in situ signal amplification approach one step closer to practical applications. Specifically, we describe allylic ethers as privileged connectors for linking detection and propagating functionality in a small molecule signal amplification reagent. Allylic ethers minimize background reactions while still enabling controlled release of a propagating signal in order to continue the signal amplification reaction. This paper characterizes the ability of allylic ethers to provide an amplified response, and offers insight into additional design considerations that are needed before in situ small molecule-based signal amplification becomes a viable strategy for point-of-need diagnostics.

A Strategy for Minimizing Background Signal in Autoinductive Signal Amplification Reactions for Point-of-Need Assays

PubMed Central

Brooks, Adam D.; Yeung, Kimy; Lewis, Gregory G.

2015-01-01

Rapid point-of-need assays are used to detect abundant biomarkers. The development of in situ signal amplification reactions could extend these assays to screening and triaging of patients for trace levels of biomarkers, even in resource-limited settings. We, and others, have developed small molecule-based in situ signal amplification reactions that eventually may be useful in this context. Herein we describe a design strategy for minimizing background signal that may occur in the absence of the target analyte, thus moving this in situ signal amplification approach one step closer to practical applications. Specifically, we describe allylic ethers as privileged connectors for linking detection and propagating functionality in a small molecule signal amplification reagent. Allylic ethers minimize background reactions while still enabling controlled release of a propagating signal in order to continue the signal amplification reaction. This paper characterizes the ability of allylic ethers to provide an amplified response, and offers insight into additional design considerations that are needed before in situ small molecule-based signal amplification becomes a viable strategy for point-of-need diagnostics. PMID:26604988

3-dB signal-ASE beat noise reduction of coherent multi-carrier signal utilizing phase sensitive amplification.

PubMed

Umeki, Takeshi; Takara, Hidehiko; Miyamoto, Yutaka; Asobe, Masaki

2012-10-22

We demonstrated the simultaneous amplification of a coherent multi-carrier signal using a χ(2)-based non-degenerate phase sensitive amplifier (PSA). The signal-to-noise ratio (SNR), which is degraded by the additional amplified spontaneous emission (ASE) noise, can be recovered due to the gain difference between a phase-correlated signal-idler pair and uncorrelated excess noise. Utilizing the second harmonic pumping of a χ(2)-based PSA enables us to observe the SNR recovery directly by comparing the SNR for the input with that for the PSA output. A 3-dB optical-SNR (OSNR) improvement was obtained as a result of the gain difference. We also achieved a 3-dB SNR improvement in the electric domain by reducing the signal-ASE beat noise. The receiver sensitivity for a 10 Gbit/s phase shift keying signal was clearly improved with the PSA.

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

NASA Astrophysics Data System (ADS)

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 QPA in the spatial domain has also been studied as a method to enhance the spatial resolution of imaging systems. A detailed model has been developed for achieving both super-resolution and detection of phase-amplified light. The imaging resolution problem considered here is treated as a binary hypotheses testing problem. Resolution enhancement is achieved by magnification of the angular separation of two targets in the sub-Rayleigh regime. The detection model includes optimization of detector segmentation, detector noise, and detection in both the spatial and the spatial frequency domain, which provide strategies for the optimization of the signal-to-noise ratio that take advantage of both the change of the field distribution and the change of energy of the signal in the QPA process. Proof-of-principle experiments have been conducted in the spatial domain. For the first time, beam angular amplification has been demonstrated, and the experimental result is in good agreement with simulations. The experimental demonstration has been achieved by observing the correlation of amplitude and angular phase in the phase-sensitive three-wave mixing process using ultrashort laser pulses and utilizing a type I three-wave mixing process. Several diagnostics have been developed and employed in the experimental measurements, including the near-field diagnostic, the far-field diagnostic, and the interferometry diagnostic. They have all been used to confirm the existence and study the properties of the QPA process on a shot-to-shot basis. Specifically, amplitude was measured in the near-field diagnostic, while the angular phase was indirectly measured in the far-field diagnostic by determining the position of the beam centroid. Interferometric measurements have been found to be of insufficient accuracy for this measurement in the way they were implemented. The demonstration of beam angular amplification by use of QPA lays the foundation for future integrated demonstration of imaging resolution enhancement, while the results of the modeling in the time domain open opportunities for development of flexible pulse shaping benefitting a variety of ultrafast applications.

Nondegenerate parametric generation of 2.2-mJ, few-cycle 2.05-μm pulses using a mixed phase matching scheme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Guibao; Wandel, Scott F.; Jovanovic, Igor, E-mail: ijovanovic@psu.edu

2014-02-15

We describe the production of 2.2-mJ, ∼6 optical-cycle-long mid-infrared laser pulses with a carrier wavelength of 2.05 μm in a two-stage β-BaB{sub 2}O{sub 4} nondegenerate optical parametric amplifier design with a mixed phase matching scheme, which is pumped by a standard Ti:sapphire chirped-pulse amplification system. It is demonstrated that relatively high pulse energies, short pulse durations, high stability, and excellent beam profiles can be obtained using this simple approach, even without the use of optical parametric chirped-pulse amplification.

Enhancement of quantum-enhanced LADAR receiver in nonideal phase-sensitive amplification

NASA Astrophysics Data System (ADS)

Zhang, Shuan; Liu, Hongjun; Huang, Nan; Wang, Zhaolu; Han, Jing

2017-07-01

The phase-sensitive amplification (PSA) with an injected squeezed vacuum field is theoretically investigated in quantum-enhanced laser detection and ranging (LADAR) receiver. The theoretical model of the amplified process is derived to investigate the quantum fluctuations in detail. A new method of mitigating the unflat gain of nonideal PSA is proposed by adjusting the squeezed angle of the squeezed vacuum field. The simulation results indicate that signal-noise ratio (SNR) of system can be efficiently improved and close to the ideal case by this method. This research will provide an important potential in the applications of quantum-enhanced LADAR receiver.

Role of monkeys in the sylvatic cycle of chikungunya virus in Senegal.

PubMed

Althouse, Benjamin M; Guerbois, Mathilde; Cummings, Derek A T; Diop, Ousmane M; Faye, Ousmane; Faye, Abdourahmane; Diallo, Diawo; Sadio, Bakary Djilocalisse; Sow, Abdourahmane; Faye, Oumar; Sall, Amadou A; Diallo, Mawlouth; Benefit, Brenda; Simons, Evan; Watts, Douglas M; Weaver, Scott C; Hanley, Kathryn A

2018-03-13

Arboviruses spillover into humans either as a one-step jump from a reservoir host species into humans or as a two-step jump from the reservoir to an amplification host species and thence to humans. Little is known about arbovirus transmission dynamics in reservoir and amplification hosts. Here we elucidate the role of monkeys in the sylvatic, enzootic cycle of chikungunya virus (CHIKV) in the region around Kédougou, Senegal. Over 3 years, 737 monkeys were captured, aged using anthropometry and dentition, and tested for exposure to CHIKV by detection of neutralizing antibodies. Infant monkeys were positive for CHIKV even when the virus was not detected in a concurrent survey of mosquitoes and when population immunity was too high for monkeys alone to support continuous transmission. We conclude that monkeys in this region serve as amplification hosts of CHIKV. Additional efforts are needed to identify other hosts capable of supporting continuous circulation.

Reduction of B-integral accumulation in lasers

DOEpatents

Meyerhofer, David D.; Konoplev, Oleg A.

2000-01-01

A pulsed laser is provided wherein the B-integral accumulated in the laser pulse is reduced using a semiconductor wafer. A laser pulse is generated by a laser pulse source. The laser pulse passes through a semiconductor wafer that has a negative nonlinear index of refraction. Thus, the laser pulse accumulates a negative B-integral. The laser pulse is then fed into a laser amplification medium, which has a positive nonlinear index of refraction. The laser pulse may make a plurality of passes through the laser amplification medium and accumulate a positive B-integral during a positive non-linear phase change. The semiconductor and laser pulse wavelength are chosen such that the negative B-integral accumulated in the semiconductor wafer substantially cancels the positive B-integral accumulated in the laser amplification medium. There may be additional accumulation of positive B-integral if the laser pulse passes through additional optical mediums such as a lens or glass plates. Thus, the effects of self-phase modulation in the laser pulse are substantially reduced.

Optomechanical transistor with mechanical gain

NASA Astrophysics Data System (ADS)

Zhang, X. Z.; Tian, Lin; Li, Yong

2018-04-01

We study an optomechanical transistor, where an input field can be transferred and amplified unidirectionally in a cyclic three-mode optomechanical system. In this system, the mechanical resonator is coupled simultaneously to two cavity modes. We show that it only requires a finite mechanical gain to achieve the nonreciprocal amplification. Here the nonreciprocity is caused by the phase difference between the linearized optomechanical couplings that breaks the time-reversal symmetry of this system. The amplification arises from the mechanical gain, which provides an effective phonon bath that pumps the mechanical mode coherently. This effect is analogous to the stimulated emission of atoms, where the probe field can be amplified when its frequency is in resonance with that of the anti-Stokes transition. We show that by choosing optimal parameters, this optomechanical transistor can reach perfect unidirectionality accompanied with strong amplification. In addition, the presence of the mechanical gain can result in ultralong delay in the phase of the probe field, which provides an alternative to controlling light transport in optomechanical systems.

Simulation and evaluation of phase noise for optical amplification using semiconductor optical amplifiers in DPSK applications

NASA Astrophysics Data System (ADS)

Hong, Wei; Huang, Dexiu; Zhang, Xinliang; Zhu, Guangxi

2008-01-01

A thorough simulation and evaluation of phase noise for optical amplification using semiconductor optical amplifier (SOA) is very important for predicting its performance in differential phase-shift keyed (DPSK) applications. In this paper, standard deviation and probability distribution of differential phase noise at the SOA output are obtained from the statistics of simulated differential phase noise. By using a full-wave model of SOA, the noise performance in the entire operation range can be investigated. It is shown that nonlinear phase noise substantially contributes to the total phase noise in case of a noisy signal amplified by a saturated SOA and the nonlinear contribution is larger with shorter SOA carrier lifetime. It is also shown that Gaussian distribution can be useful as a good approximation of the total differential phase noise statistics in the whole operation range. Power penalty due to differential phase noise is evaluated using a semi-analytical probability density function (PDF) of receiver noise. Obvious increase of power penalty at high signal input powers can be found for low input OSNR, which is due to both the large nonlinear differential phase noise and the dependence of BER vs. receiving power curvature on differential phase noise standard deviation.

Quality control for quantitative PCR based on amplification compatibility test.

PubMed

Tichopad, Ales; Bar, Tzachi; Pecen, Ladislav; Kitchen, Robert R; Kubista, Mikael; Pfaffl, Michael W

2010-04-01

Quantitative qPCR is a routinely used method for the accurate quantification of nucleic acids. Yet it may generate erroneous results if the amplification process is obscured by inhibition or generation of aberrant side-products such as primer dimers. Several methods have been established to control for pre-processing performance that rely on the introduction of a co-amplified reference sequence, however there is currently no method to allow for reliable control of the amplification process without directly modifying the sample mix. Herein we present a statistical approach based on multivariate analysis of the amplification response data generated in real-time. The amplification trajectory in its most resolved and dynamic phase is fitted with a suitable model. Two parameters of this model, related to amplification efficiency, are then used for calculation of the Z-score statistics. Each studied sample is compared to a predefined reference set of reactions, typically calibration reactions. A probabilistic decision for each individual Z-score is then used to identify the majority of inhibited reactions in our experiments. We compare this approach to univariate methods using only the sample specific amplification efficiency as reporter of the compatibility. We demonstrate improved identification performance using the multivariate approach compared to the univariate approach. Finally we stress that the performance of the amplification compatibility test as a quality control procedure depends on the quality of the reference set. Copyright 2010 Elsevier Inc. All rights reserved.

Parametric amplification in a resonant sensing array

NASA Astrophysics Data System (ADS)

Yie, Zi; Miller, Nicholas J.; Shaw, Steven W.; Turner, Kimberly L.

2012-03-01

We demonstrate parametric amplification of a multidegree of freedom resonant mass sensing array via an applied base motion containing the appropriate frequency content and phases. Applying parametric forcing in this manner is simple and aligns naturally with the vibrational properties of the sensing structure. Using this technique, we observe an increase in the quality factors of the coupled array resonances, which provides an effective means of improving device sensitivity.

Self-induced parametric amplification arising from nonlinear elastic coupling in a micromechanical resonating disk gyroscope

PubMed Central

Nitzan, Sarah H.; Zega, Valentina; Li, Mo; Ahn, Chae H.; Corigliano, Alberto; Kenny, Thomas W.; Horsley, David A.

2015-01-01

Parametric amplification, resulting from intentionally varying a parameter in a resonator at twice its resonant frequency, has been successfully employed to increase the sensitivity of many micro- and nano-scale sensors. Here, we introduce the concept of self-induced parametric amplification, which arises naturally from nonlinear elastic coupling between the degenerate vibration modes in a micromechanical disk-resonator, and is not externally applied. The device functions as a gyroscope wherein angular rotation is detected from Coriolis coupling of elastic vibration energy from a driven vibration mode into a second degenerate sensing mode. While nonlinear elasticity in silicon resonators is extremely weak, in this high quality-factor device, ppm-level nonlinear elastic effects result in an order-of-magnitude increase in the observed sensitivity to Coriolis force relative to linear theory. Perfect degeneracy of the primary and secondary vibration modes is achieved through electrostatic frequency tuning, which also enables the phase and frequency of the parametric coupling to be varied, and we show that the resulting phase and frequency dependence of the amplification follow the theory of parametric resonance. We expect that this phenomenon will be useful for both fundamental studies of dynamic systems with low dissipation and for increasing signal-to-noise ratio in practical applications such as gyroscopes. PMID:25762243

Self-induced parametric amplification arising from nonlinear elastic coupling in a micromechanical resonating disk gyroscope.

PubMed

Nitzan, Sarah H; Zega, Valentina; Li, Mo; Ahn, Chae H; Corigliano, Alberto; Kenny, Thomas W; Horsley, David A

2015-03-12

Parametric amplification, resulting from intentionally varying a parameter in a resonator at twice its resonant frequency, has been successfully employed to increase the sensitivity of many micro- and nano-scale sensors. Here, we introduce the concept of self-induced parametric amplification, which arises naturally from nonlinear elastic coupling between the degenerate vibration modes in a micromechanical disk-resonator, and is not externally applied. The device functions as a gyroscope wherein angular rotation is detected from Coriolis coupling of elastic vibration energy from a driven vibration mode into a second degenerate sensing mode. While nonlinear elasticity in silicon resonators is extremely weak, in this high quality-factor device, ppm-level nonlinear elastic effects result in an order-of-magnitude increase in the observed sensitivity to Coriolis force relative to linear theory. Perfect degeneracy of the primary and secondary vibration modes is achieved through electrostatic frequency tuning, which also enables the phase and frequency of the parametric coupling to be varied, and we show that the resulting phase and frequency dependence of the amplification follow the theory of parametric resonance. We expect that this phenomenon will be useful for both fundamental studies of dynamic systems with low dissipation and for increasing signal-to-noise ratio in practical applications such as gyroscopes.

Electrochemical detection of Francisella tularensis genomic DNA using solid-phase recombinase polymerase amplification.

PubMed

del Río, Jonathan Sabaté; Yehia Adly, Nouran; Acero-Sánchez, Josep Lluis; Henry, Olivier Y F; O'Sullivan, Ciara K

2014-04-15

Solid-phase isothermal DNA amplification was performed exploiting the homology protein recombinase A (recA). The system was primarily tested on maleimide activated microtitre plates as a proof-of-concept and later translated to an electrochemical platform. In both cases, forward primer for Francisella tularensis holarctica genomic DNA was surface immobilised via a thiol or an amino moiety and then elongated during the recA mediated amplification, carried out in the presence of specific target sequence and reverse primers. The formation of the subsequent surface tethered amplicons was either colorimetrically or electrochemically monitored using a horseradish peroxidase (HRP)-labelled DNA secondary probe complementary to the elongated strand. The amplification time was optimised to amplify even low amounts of DNA copies in less than an hour at a constant temperature of 37°C, achieving a limit of detection of 1.3×10(-13) M (4×10(6) copies in 50 μL) for the colorimetric assay and 3.3×10(-14) M (2×10(5) copies in 10 μL) for the chronoamperometric assay. The system was demonstrated to be highly specific with negligible cross-reactivity with non-complementary targets or primers. © 2013 Elsevier B.V. All rights reserved.

Mid-infrared Raman amplification and wavelength conversion in dispersion engineered silicon-on-sapphire waveguides

NASA Astrophysics Data System (ADS)

Wang, Zhaolu; Liu, Hongjun; Huang, Nan; Sun, Qibing; Li, Xuefeng

2014-01-01

Raman amplification based on stimulated Stokes Raman scattering (SSRS) and wavelength conversion based on coherent anti-Stokes Raman scattering (CARS) are theoretically investigated in silicon-on-sapphire (SOS) waveguides in the mid-infrared (IR) region. When the linear phase mismatch Δk is close to zero, the Stokes gain and conversion efficiency drop down quickly due to the effect of parametric gain suppression when the Stokes-pump input ratio is sufficiently large. The Stokes gain increases with the increase of Δk, whereas efficient wavelength conversion needs appropriate Δk under different pump intensities. The conversion efficiency at exact linear phase matching (Δk = 0) is smaller than that at optimal linear phase mismatch by a factor of about 28 dB when the pump intensity is 2 GW cm-2.

Amplification of a seed pumped by a chirped laser in the strong coupling Brillouin regime

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schluck, F.; Lehmann, G.; Spatschek, K. H.

Seed amplification via Brillouin backscattering of a long pump laser-pulse is considered. The interaction takes place in the so called strong coupling regime. Pump chirping is applied to mitigate spontaneous Raman backscattering of the pump before interacting with the seed. The strong coupling regime facilitates stronger exponential growth and narrower seeds compared to the so called weak coupling regime, although in the latter the scaling with pump amplitude is stronger. Strong coupling is achieved when the pump laser amplitude exceeds a certain threshold. It is shown how the chirp influences both the linear as well as the nonlinear amplification process.more » First, linear amplification as well as the seed profiles are determined in dependence of the chirping rate. In contrast to the weak coupling situation, the evolution is not symmetric with respect to the sign of the chirping rate. In the nonlinear stage of the amplification, we find an intrinsic chirp of the seed pulse even for an un-chirped pump. We show that chirping the pump may have a strong influence on the shape of the seed in the nonlinear amplification phase. Also, the influence of pump chirp on the efficiency of Brillouin seed amplification is discussed.« less

Noiseless optical amplification in quasi-phase-matched bulk lithium niobate

NASA Astrophysics Data System (ADS)

Lovering, D. J.; Levenson, J. A.; Vidakovic, P.; Webjörn, J.; Russell, P. St. J.

1996-09-01

An optical parametric amplifier (OPA) has been demonstrated in bulk, periodically poled lithium niobate and is shown to operate with a noise figure well below the classical limit. In contrast to conventional OPA's, this device uses quasi-phase matching to provide the coupling between the pump and the signal. Comparison of the measured performance with that of a theoretical model reveals that the main intrinsic contribution to the output noise is due to spatial and temporal mode mixing, which arises as a consequence of tight focusing of the incident beams. Factors that affect the performance of this amplifier are identified theoretically and their relative importance investigated for both amplification and squeezing.

Quantum dot SOA input power dynamic range improvement for differential-phase encoded signals.

PubMed

Vallaitis, T; Bonk, R; Guetlein, J; Hillerkuss, D; Li, J; Brenot, R; Lelarge, F; Duan, G H; Freude, W; Leuthold, J

2010-03-15

Experimentally we find a 10 dB input power dynamic range advantage for amplification of phase encoded signals with quantum dot SOA as compared to low-confinement bulk SOA. An analysis of amplitude and phase effects shows that this improvement can be attributed to the lower alpha-factor found in QD SOA.

2D and 3D graphical representation of the propagation of electromagnetic waves at the interface with a material with general effective complex permittivity and permeability

NASA Astrophysics Data System (ADS)

Diaz, A.; Ramos, J. G.; Friedman, J. S.

2017-09-01

We developed a web-based instructional and research tool that demonstrates the behavior of electromagnetic waves as they propagate through a homogenous medium and through an interface where the second medium can be characterized by an effective complex permittivity and permeability. Either p- or s-polarization wave components can be chosen and the graphical interface includes 2D wave and 3D component representations. The program enables the study of continuity of electromagnetic components, critical angle, Brewster angle, absorption and amplification, behavior of light in sub-unity and negative-index materials, Poynting vector and phase velocity behavior, and positive and negative Goos- Hänchen shifts.

Hyperpolarized xenon NMR and MRI signal amplification by gas extraction

PubMed Central

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

Simple Approaches to Minimally-Instrumented, Microfluidic-Based Point-of-Care Nucleic Acid Amplification Tests

PubMed Central

Mauk, Michael G.; Song, Jinzhao; Liu, Changchun; Bau, Haim H.

2018-01-01

Designs and applications of microfluidics-based devices for molecular diagnostics (Nucleic Acid Amplification Tests, NAATs) in infectious disease testing are reviewed, with emphasis on minimally instrumented, point-of-care (POC) tests for resource-limited settings. Microfluidic cartridges (‘chips’) that combine solid-phase nucleic acid extraction; isothermal enzymatic nucleic acid amplification; pre-stored, paraffin-encapsulated lyophilized reagents; and real-time or endpoint optical detection are described. These chips can be used with a companion module for separating plasma from blood through a combined sedimentation-filtration effect. Three reporter types: Fluorescence, colorimetric dyes, and bioluminescence; and a new paradigm for end-point detection based on a diffusion-reaction column are compared. Multiplexing (parallel amplification and detection of multiple targets) is demonstrated. Low-cost detection and added functionality (data analysis, control, communication) can be realized using a cellphone platform with the chip. Some related and similar-purposed approaches by others are surveyed. PMID:29495424

Amplification of the BCR/ABL fusion gene clustered on a masked Philadelphia chromosome in a patient with myeloblastic crisis of chronic myelocytic leukemia.

PubMed

Gargallo, Patricia M; Cuello, Maria Teresa; Aranguren, Pedro Negri; Larripa, Irene B

2003-06-01

Although the chronic phase of chronic myelocytic leukemia (CML) is characterized by the Philadelphia (Ph) chromosome creating a hybrid BCR/ABL gene, additional genetic changes involved in blast crisis are poorly understood. We report a 4-8-fold amplification by tandem duplication of the BCR/ABL fusion gene clustered on a masked Ph chromosome in a 61-year-old male patient with CML in myeloblastic crisis. Our finding suggests that the BCR/ABL amplification may play a role as a novel mechanism in the progression to an aggressive blast transformation in some cases of Ph-positive CML.

Unraveling the sub-processes of selective attention: insights from dynamic modeling and continuous behavior.

PubMed

Frisch, Simon; Dshemuchadse, Maja; Görner, Max; Goschke, Thomas; Scherbaum, Stefan

2015-11-01

Selective attention biases information processing toward stimuli that are relevant for achieving our goals. However, the nature of this bias is under debate: Does it solely rely on the amplification of goal-relevant information or is there a need for additional inhibitory processes that selectively suppress currently distracting information? Here, we explored the processes underlying selective attention with a dynamic, modeling-based approach that focuses on the continuous evolution of behavior over time. We present two dynamic neural field models incorporating the diverging theoretical assumptions. Simulations with both models showed that they make similar predictions with regard to response times but differ markedly with regard to their continuous behavior. Human data observed via mouse tracking as a continuous measure of performance revealed evidence for the model solely based on amplification but no indication of persisting selective distracter inhibition.

Real-time and label-free ring-resonator monitoring of solid-phase recombinase polymerase amplification.

PubMed

Sabaté Del Río, Jonathan; Steylaerts, Tim; Henry, Olivier Y F; Bienstman, Peter; Stakenborg, Tim; Van Roy, Wim; O'Sullivan, Ciara K

2015-11-15

In this work we present the use of a silicon-on-insulator (SOI) chip featuring an array of 64 optical ring resonators used as refractive index sensors for real-time and label-free DNA detection. Single ring functionalisation was achieved using a click reaction after precise nanolitre spotting of specific hexynyl-terminated DNA capture probes to link to an azido-silanised chip surface. To demonstrate detectability using the ring resonators and to optimise conditions for solid-phase amplification, hybridisation between short 25-mer single stranded DNA (ssDNA) fragments and a complementary capture probe immobilised on the surface of the ring resonators was carried out and detected through the shift in the resonant wavelength. Using the optimised conditions demonstrated via the solid-phase hybridisation, a 144-bp double stranded DNA (dsDNA) was then detected directly using recombinase and polymerase proteins through on-chip target amplification and solid-phase elongation of immobilised forward primers on specific rings, at a constant temperature of 37°C and in less than 60min, achieving a limit of detection of 7.8·10(-13)M (6·10(5) copies in 50µL). The use of an automatic liquid handler injection instrument connected to an integrated resealable chip interface (RCI) allowed programmable multiple injection protocols. Air plugs between different solutions were introduced to prevent intermixing and a proportional-integral-derivative (PID) temperature controller minimised temperature based drifts. Published by Elsevier B.V.

Phase estimation of coherent states with a noiseless linear amplifier

NASA Astrophysics Data System (ADS)

Assad, Syed M.; Bradshaw, Mark; Lam, Ping Koy

Amplification of quantum states is inevitably accompanied with the introduction of noise at the output. For protocols that are probabilistic with heralded success, noiseless linear amplification in theory may still be possible. When the protocol is successful, it can lead to an output that is a noiselessly amplified copy of the input. When the protocol is unsuccessful, the output state is degraded and is usually discarded. Probabilistic protocols may improve the performance of some quantum information protocols, but not for metrology if the whole statistics is taken into consideration. We calculate the precision limits on estimating the phase of coherent states using a noiseless linear amplifier by computing its quantum Fisher information and we show that on average, the noiseless linear amplifier does not improve the phase estimate. We also discuss the case where abstention from measurement can reduce the cost for estimation.

Electrically controlled microvalves to integrate microchip polymerase chain reaction and capillary electrophoresis.

PubMed

Kaigala, Govind V; Hoang, Viet N; Backhouse, Christopher J

2008-07-01

Microvalves are key in realizing portable miniaturized diagnostic platforms. We present a scalable microvalve that integrates well with standard lab on a chip (LOC) implementations, yet which requires essentially no external infrastructure for its operation. This electrically controlled, phase-change microvalve is used to integrate genetic amplification and analysis via capillary electrophoresis--the basis of many diagnostics. The microvalve is actuated using a polymer (polyethylene glycol, PEG) that exhibits a large volumetric change between its solid and liquid phases. Both the phase change of the PEG and the genetic amplification via polymerase chain reaction (PCR) are thermally controlled using thin film resistive elements that are patterned using standard microfabrication methods. By contrast with many other valve technologies, these microvalves and their control interface scale down in size readily. The novelty here lies in the use of fully integrated microvalves that require only electrical connections to realize a portable and inexpensive genetic analysis platform.

Optical back propagation for fiber optic networks with hybrid EDFA Raman amplification.

PubMed

Liang, Xiaojun; Kumar, Shiva

2017-03-06

We have investigated an optical back propagation (OBP) method to compensate for propagation impairments in fiber optic networks with lumped Erbium doped fiber amplifier (EDFA) and/or distributed Raman amplification. An OBP module consists of an optical phase conjugator (OPC), optical amplifiers and dispersion varying fibers (DVFs). We derived a semi-analytical expression that calculates the dispersion profile of DVF. The OBP module acts as a nonlinear filter that fully compensates for the nonlinear distortions due to signal propagation in a transmission fiber, and is applicable for fiber optic networks with reconfigurable optical add-drop multiplexers (ROADMs). We studied a wavelength division multiplexing (WDM) network with 3000 km transmission distance and 64-quadrature amplitude modulation (QAM) modulation. OBP brings 5.8 dB, 5.9 dB and 6.1 dB Q-factor gains over linear compensation for systems with full EDFA amplification, hybrid EDFA/Raman amplification, and full Raman amplification, respectively. In contrast, digital back propagation (DBP) or OPC-only systems provide only 0.8 ~ 1.5 dB Q-factor gains.

Linear analysis of active-medium two-beam accelerator

NASA Astrophysics Data System (ADS)

Voin, Miron; Schächter, Levi

2015-07-01

We present detailed development of the linear theory of wakefield amplification by active medium and its possible application to a two-beam accelerator (TBA) is discussed. A relativistic train of triggering microbunches traveling along a vacuum channel in an active medium confined by a cylindrical waveguide excites Cherenkov wake in the medium. The wake is a superposition of azimuthally symmetric transverse magnetic modes propagating along a confining waveguide, with a phase velocity equal to the velocity of the triggering bunches. The structure may be designed in such a way that the frequency of one of the modes is close to active-medium resonant frequency, resulting in amplification of the former and domination of a single mode far behind the trigger bunches. Another electron bunch placed in proper phase with the amplified wakefield may be accelerated by the latter. Importantly, the energy for acceleration is provided by the active medium and not the drive bunch as in a traditional TBA. Based on a simplified model, we analyze extensively the impact of various parameters on the wakefield amplification process.

High-power Yb-fiber comb based on pre-chirped-management self-similar amplification

NASA Astrophysics Data System (ADS)

Luo, Daping; Liu, Yang; Gu, Chenglin; Wang, Chao; Zhu, Zhiwei; Zhang, Wenchao; Deng, Zejiang; Zhou, Lian; Li, Wenxue; Zeng, Heping

2018-02-01

We report a fiber self-similar-amplification (SSA) comb system that delivers a 250-MHz, 109-W, 42-fs pulse train with a 10-dB spectral width of 85 nm at 1056 nm. A pair of grisms is employed to compensate the group velocity dispersion and third-order dispersion of pre-amplified pulses for facilitating a self-similar evolution and a self-phase modulation (SPM). Moreover, we analyze the stabilities and noise characteristics of both the locked carrier envelope phase and the repetition rate, verifying the stability of the generated high-power comb. The demonstration of the SSA comb at such high power proves the feasibility of the SPM-based low-noise ultrashort comb.

Microfluidic magnetic fluidized bed for DNA analysis in continuous flow mode.

PubMed

Hernández-Neuta, Iván; Pereiro, Iago; Ahlford, Annika; Ferraro, Davide; Zhang, Qiongdi; Viovy, Jean-Louis; Descroix, Stéphanie; Nilsson, Mats

2018-04-15

Magnetic solid phase substrates for biomolecule manipulation have become a valuable tool for simplification and automation of molecular biology protocols. However, the handling of magnetic particles inside microfluidic chips for miniaturized assays is often challenging due to inefficient mixing, aggregation, and the advanced instrumentation required for effective actuation. Here, we describe the use of a microfluidic magnetic fluidized bed approach that enables dynamic, highly efficient and simplified magnetic bead actuation for DNA analysis in a continuous flow platform with minimal technical requirements. We evaluate the performance of this approach by testing the efficiency of individual steps of a DNA assay based on padlock probes and rolling circle amplification. This assay comprises common nucleic acid analysis principles, such as hybridization, ligation, amplification and restriction digestion. We obtained efficiencies of up to 90% for these reactions with high throughput processing up to 120μL of DNA dilution at flow rates ranging from 1 to 5μL/min without compromising performance. The fluidized bed was 20-50% more efficient than a commercially available solution for microfluidic manipulation of magnetic beads. Moreover, to demonstrate the potential of this approach for integration into micro-total analysis systems, we optimized the production of a low-cost polymer based microarray and tested its analytical performance for integrated single-molecule digital read-out. Finally, we provide the proof-of-concept for a single-chamber microfluidic chip that combines the fluidized bed with the polymer microarray for a highly simplified and integrated magnetic bead-based DNA analyzer, with potential applications in diagnostics. Copyright © 2017 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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 to pulse compression is investigated using numerical simulation.

Amplification of light in one-dimensional vibrating metal photonic crystal

NASA Astrophysics Data System (ADS)

Ueta, Tsuyoshi

2012-04-01

Photon-phonon interaction on the analogy of electron-phonon interaction is considered in one-dimensional metal photonic crystal. When lattice vibration is artificially introduced to the photonic crystal, a governing equation of electromagnetic field is derived. A simple model is numerically analyzed, and the following novel phenomena are found out. The lattice vibration generates the light of frequency which added the integral multiple of the vibration frequency to that of the incident wave and also amplifies the incident wave resonantly. On a resonance, the amplification factor increases very rapidly with the number of layers. Resonance frequencies change with the phases of lattice vibration. The amplification phenomenon is analytically discussed for low frequency of the lattice vibration and is confirmed by numerical works.

Nonenzymatic microorganism identification based on ribosomal RNA

NASA Astrophysics Data System (ADS)

Ives, Jeffrey T.; Pierini, Alicia M.; Stokes, Jeffrey A.; Wahlund, Thomas M.; Read, Betsy; Bechtel, James H.; Bronk, Burt V.

1999-11-01

Effective defense against biological warfare (BW) agents requires rapid, fieldable and accurate systems. For micro- organisms like bacteria and viruses, ribosomal RNA (rRNA) provides a valuable target with multiple advantages of species specificity and intrinsic target amplification. Vegetative and spore forms of bacteria contain approximately 104 copies of rRNA. Direct detection of rRNA copies can eliminate some of the interference and preparation difficulties involved in enzymatic amplification methods. In order to apply the advantages of rRNA to BW defense, we are developing a fieldable system based on 16S rRNA, physical disruption of the micro-organism, solid phase hybridization, and fluorescence detection. Our goals include species-specific identification, complete operation from raw sample to identification in 15 minutes or less, and compact, fieldable instrumentation. Initial work on this project has investigated the lysis and hybridization steps, the species-specificity of oligonucleotides probes, and the development of a novel electromagnetic method to physically disrupt the micro- organisms. Target bacteria have been Escherichia coli (E. coli) and Bacillus subtilis (B. subtilis). Continuing work includes further development of methods to rapidly disrupt the micro-organisms and release the rRNA, improved integration and processing, and extension to bacterial and mammalian viruses like MS2 and vesicular stomatitis virus.

Parametric amplification in quasi-PT symmetric coupled waveguide structures

NASA Astrophysics Data System (ADS)

Zhong, Q.; Ahmed, A.; Dadap, J. I.; Osgood, R. M., Jr.; El-Ganainy, R.

2016-12-01

The concept of non-Hermitian parametric amplification was recently proposed as a means to achieve an efficient energy conversion throughout the process of nonlinear three wave mixing in the absence of phase matching. Here we investigate this effect in a waveguide coupler arrangement whose characteristics are tailored to introduce passive PT symmetry only for the idler component. By means of analytical solutions and numerical analysis, we demonstrate the utility of these novel schemes and obtain the optimal design conditions for these devices.

Programmable Iterative Optical Image And Data Processing

NASA Technical Reports Server (NTRS)

Jackson, Deborah J.

1995-01-01

Proposed method of iterative optical image and data processing overcomes limitations imposed by loss of optical power after repeated passes through many optical elements - especially, beam splitters. Involves selective, timed combination of optical wavefront phase conjugation and amplification to regenerate images in real time to compensate for losses in optical iteration loops; timing such that amplification turned on to regenerate desired image, then turned off so as not to regenerate other, undesired images or spurious light propagating through loops from unwanted reflections.

Flux amplification and sustainment of ST plasmas by multi-pulsed coaxial helicity injection on HIST

NASA Astrophysics Data System (ADS)

Higashi, T.; Ishihara, M.; Kikuchi, Y.; Fukumoto, N.; Nagata, M.

2010-11-01

The Helicity Injected Spherical Torus (HIST) device has been developed towards high-current start up and sustainment by Multi-pulsed Coaxial Helicity Injection (M-CHI) method. Multiple pulses operation of the coaxial plasma gun can build the magnetic field of STs and spheromak plasmas in a stepwise manner. So far, successive gun pulses on SSPX at LLNL were demonstrated to maintain the magnetic field of spheromak in a quasi-steady state against resistive decay [1]. The resistive 3D-MHD numerical simulation [2] for STs reproduced the current amplification by the M-CHI method and confirmed that stochastic magnetic field was reduced during the decay phase. By double pulsed operation on HIST, the plasma current was effectively amplified against the resistive decay. The life time increases up to 10 ms which is longer than that in the single CHI case (4 ms). The edge poloidal fields last between 0.5 ms and 6 ms like a repetitive manner. During the second driven phase, the toroidal ion flow is driven in the same direction as the plasma current as well as in the initial driven phase. At the meeting, we will discuss a current amplification mechanism based on the merging process with the plasmoid injected secondly from the gun. [1] B. Hudson et al., Phys. Plasmas Vol.15, 056112 (2008). [2] Y. Kagei et al., J. Plasma Fusion Res. Vol.79, 217 (2003).

Rapid identification of Yersinia pestis and Brucella melitensis by chip-based continuous flow PCR

NASA Astrophysics Data System (ADS)

Dietzsch, Michael; Hlawatsch, Nadine; Melzer, Falk; Tomaso, Herbert; Gärtner, Claudia; Neubauer, Heinrich

2012-06-01

To combat the threat of biological agents like Yersinia pestis and Brucella melitensis in bioterroristic scenarios requires fast, easy-to-use and safe identification systems. In this study we describe a system for rapid amplification of specific genetic markers for the identification of Yersinia pestis and Brucella melitensis. Using chip based PCR and continuous flow technology we were able to amplify the targets simultaneously with a 2-step reaction profile within 20 minutes. The subsequent analysis of amplified fragments by standard gel electrophoresis requires another 45 minutes. We were able to detect both pathogens within 75 minutes being much faster than most other nucleic acid amplification technologies.

Changes in southern hemispheric polar amplification over the past 5 million years revealed by climate modelling

NASA Astrophysics Data System (ADS)

Hoencamp, Jori; Stap, Lennert; Tuenter, Erik; Lourens, Luc; van de Wal, Roderik

2016-04-01

Knowledge on polar amplification is important to relate high latitude climate records to global mean temperature changes. Several studies have pointed out that the strength of polar amplification in the Northern Hemisphere varies considerably due to the presence of large ice sheets and more sea ice during colder climate conditions. As a result, the polar amplification in the Northern Hemisphere decreases for warmer climates. In this study, we address the fact that these changes in the Northern Hemisphere also affect the polar amplification in the Southern Hemisphere. We study the Southern and Northern Hemisphere amplification together over the past 5 million years with the CLIMBER-2 intermediate complexity model. Radiation, land ice extent and height, and greenhouse gases are prescribed as forcing. We find that in contrast to the reduction in polar amplification in the Northern Hemisphere, polar amplification in the Southern Hemisphere increases for warmer climates. The amplification decreases in the Northern Hemisphere from 2.7 during glacial conditions to 1.6 for a pre-industrial climate, which is line with other climate simulations. Over the same CO2 range the southern hemispheric polar amplification increases from 1 to 1.6. This is caused by the fact that the atmospheric transport needed to balance the radiation surplus in the equatorial region needs to be compensated by relatively stronger transport of energy in Southern direction while the transport in Northern direction reduces. This reduction in Northern direction is driven by less (land and sea) ice resulting in a smaller meridional gradient in Northern direction and hence a smaller atmospheric transport. As a consequence, the traditional scaled (with LGM temperature) Dome C record needs to be corrected with a maximum of 0.6 degrees half-way glacial and interglacial conditions, if it is to be interpreted as global mean temperature change indicator. While this changes the amplitude, the phasing of temperature records from the Southern Hemisphere remains unaffected.

Parametric amplification of a superconducting plasma wave

DOE PAGES

Rajasekaran, S.; Casandruc, E.; Laplace, Y.; ...

2016-07-11

Many applications in photonics require all-optical manipulation of plasma waves, which can concentrate electromagnetic energy on sub-wavelength length scales. This is difficult in metallic plasmas because of their small optical nonlinearities. Some layered superconductors support Josephson plasma waves, involving oscillatory tunnelling of the superfluid between capacitively coupled planes. Josephson plasma waves are also highly nonlinear, and exhibit striking phenomena such as cooperative emission of coherent terahertz radiation, superconductor–metal oscillations and soliton formation. In this paper, we show that terahertz Josephson plasma waves can be parametrically amplified through the cubic tunnelling nonlinearity in a cuprate superconductor. Finally, parametric amplification is sensitivemore » to the relative phase between pump and seed waves, and may be optimized to achieve squeezing of the order-parameter phase fluctuations or terahertz single-photon devices.« less

Chronic centrosome amplification without tumorigenesis

PubMed Central

Vitre, Benjamin; Holland, Andrew J.; Kulukian, Anita; Shoshani, Ofer; Hirai, Maretoshi; Wang, Yin; Maldonado, Marcus; Cho, Thomas; Boubaker, Jihane; Swing, Deborah A.; Tessarollo, Lino; Evans, Sylvia M.; Fuchs, Elaine; Cleveland, Don W.

2015-01-01

Centrosomes are microtubule-organizing centers that facilitate bipolar mitotic spindle assembly and chromosome segregation. Recognizing that centrosome amplification is a common feature of aneuploid cancer cells, we tested whether supernumerary centrosomes are sufficient to drive tumor development. To do this, we constructed and analyzed mice in which centrosome amplification can be induced by a Cre-recombinase–mediated increase in expression of Polo-like kinase 4 (Plk4). Elevated Plk4 in mouse fibroblasts produced supernumerary centrosomes and enhanced the expected mitotic errors, but proliferation continued only after inactivation of the p53 tumor suppressor. Increasing Plk4 levels in mice with functional p53 produced centrosome amplification in liver and skin, but this did not promote spontaneous tumor development in these tissues or enhance the growth of chemically induced skin tumors. In the absence of p53, Plk4 overexpression generated widespread centrosome amplification, but did not drive additional tumors or affect development of the fatal thymic lymphomas that arise in animals lacking p53. We conclude that, independent of p53 status, supernumerary centrosomes are not sufficient to drive tumor formation. PMID:26578792

Multi-mJ energy extraction using Yb-fiber based coherent pulse stacking amplification of fs pulses (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ruppe, John M.; Pei, Hanzhang; Chen, Siyun; Sheikhsofla, Morteza; Wilcox, Russell B.; Nees, John A.; Galvanauskas, Almantas

2017-03-01

We report multi-mJ energy (>5mJ) extraction from femtosecond-pulse Yb-doped fiber CPA using coherent pulse stacking amplification (CPSA) technique. This high energy extraction has been enabled by amplifying 10's of nanosecond long pulse sequence, and by using 85-µm core Yb-doped CCC fiber based power amplification stage. The CPSA system consists of 1-GHz repetition rate mode-locked fiber oscillator, followed by a pair of fast phase and amplitude electro-optic modulators, a diffraction-grating based pulse stretcher, a fiber amplifier chain, a GTI-cavity based pulse stacker, and a diffraction grating pulse compressor. Electro-optic modulators are used to carve out from the 1-GHz mode-locked pulse train an amplitude and phase modulated pulse burst, which after stretching and amplification, becomes equal-amplitude pulse burst consisting of 27 stretched pulses, each approximately 1-ns long. Initial pulse-burst shaping accounts for the strong amplifier saturation effects, so that it is compensated at the power amplifier output. This 27-pulse burst is then coherently stacked into a single pulse using a multiplexed sequence of 5 GTI cavities. The compact-footprint 4+1 multiplexed pulse stacker consists of 4 cavities having rountrip of 1 ns, and one Herriott-cell folded cavity - with 9ns roundtrip. After stacking, stretched pulses are compressed down to the bandwidth-limited 300 fs duration using a standard diffraction-grating pulse compressor.

Achieving High Levels of NMR-Hyperpolarization in Aqueous Media With Minimal Catalyst Contamination Using SABRE.

PubMed

Iali, Wissam; Olaru, Alexandra M; Green, Gary G R; Duckett, Simon B

2017-08-04

Signal amplification by reversible exchange (SABRE) is shown to allow access to strongly enhanced 1 H NMR signals in a range of substrates in aqueous media. To achieve this outcome, phase-transfer catalysis is exploited, which leads to less than 1.5×10 -6  mol dm -3 of the iridium catalyst in the aqueous phase. These observations reflect a compelling route to produce a saline-based hyperpolarized bolus in just a few seconds for subsequent in vivo MRI monitoring. The new process has been called catalyst separated hyperpolarization through signal amplification by reversible exchange or CASH-SABRE. We illustrate this method for the substrates pyrazine, 5-methylpyrimidine, 4,6-d 2 -methyl nicotinate, 4,6-d 2 -nicotinamide and pyridazine achieving 1 H signal gains of approximately 790-, 340-, 3000-, 260- and 380-fold per proton at 9.4 T at the time point at which phase separation is complete. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Parametric amplification of orbital angular momentum beams based on light-acoustic interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Wei, E-mail: wei-g@163.com, E-mail: zhuzhihandd@sina.com; Mu, Chunyuan; Yang, Yuqiang

A high fidelity amplification of beams carrying orbital angular momentum (OAM) is very crucial for OAM multiplexing and other OAM-based applications. Here, we report a demonstration of stimulated Brillouin amplification for OAM beams, and the energy conversion efficiency of photon-phonon coupling and the phase structure of amplified signals are investigated in collinear and noncollinear frame systems, respectively. Our results demonstrate that the OAM signals can be efficiently amplified without obvious noise introduced, and the modes of output signal are independent of the pump modes or the geometrical frames. Meanwhile, an OAM state depending on the optical modes and the geometricalmore » frames is loaded into phonons by coherent light-acoustic interaction, which reveals more fundamental significance and a great application potential in OAM-multiplexing.« less

Experimental Implementation of a Quantum Optical State Comparison Amplifier

NASA Astrophysics Data System (ADS)

Donaldson, Ross J.; Collins, Robert J.; Eleftheriadou, Electra; Barnett, Stephen M.; Jeffers, John; Buller, Gerald S.

2015-03-01

We present an experimental demonstration of a practical nondeterministic quantum optical amplification scheme that employs two mature technologies, state comparison and photon subtraction, to achieve amplification of known sets of coherent states with high fidelity. The amplifier uses coherent states as a resource rather than single photons, which allows for a relatively simple light source, such as a diode laser, providing an increased rate of amplification. The amplifier is not restricted to low amplitude states. With respect to the two key parameters, fidelity and the amplified state production rate, we demonstrate significant improvements over previous experimental implementations, without the requirement of complex photonic components. Such a system may form the basis of trusted quantum repeaters in nonentanglement-based quantum communications systems with known phase alphabets, such as quantum key distribution or quantum digital signatures.

Product differentiation during continuous-flow thermal gradient PCR.

PubMed

Crews, Niel; Wittwer, Carl; Palais, Robert; Gale, Bruce

2008-06-01

A continuous-flow PCR microfluidic device was developed in which the target DNA product can be detected and identified during its amplification. This in situ characterization potentially eliminates the requirement for further post-PCR analysis. Multiple small targets have been amplified from human genomic DNA, having sizes of 108, 122, and 134 bp. With a DNA dye in the PCR mixture, the amplification and unique melting behavior of each sample is observed from a single fluorescent image. The melting behavior of the amplifying DNA, which depends on its molecular composition, occurs spatially in the thermal gradient PCR device, and can be observed with an optical resolution of 0.1 degrees C pixel(-1). Since many PCR cycles are within the field of view of the CCD camera, melting analysis can be performed at any cycle that contains a significant quantity of amplicon, thereby eliminating the cycle-selection challenges typically associated with continuous-flow PCR microfluidics.

Nonreciprocal Microwave Signal Processing with a Field-Programmable Josephson Amplifier

NASA Astrophysics Data System (ADS)

Lecocq, F.; Ranzani, L.; Peterson, G. A.; Cicak, K.; Simmonds, R. W.; Teufel, J. D.; Aumentado, J.

2017-02-01

We report on the design and implementation of a field-programmable Josephson amplifier (FPJA)—a compact and lossless superconducting circuit that can be programmed in situ by a set of microwave drives to perform reciprocal and nonreciprocal frequency conversion and amplification. In this work, we demonstrate four modes of operation: frequency conversion (transmission of -0.5 dB, reflection of -30 dB), circulation (transmission of -0.5 dB, reflection of -30 dB, isolation of 30 dB), phase-preserving amplification (gain >20 dB , one photon of added noise) and directional phase-preserving amplification (reflection of -10 dB, forward gain of 18 dB, reverse isolation of 8 dB, one photon of added noise). The system exhibits quantitative agreement with the theoretical prediction. Based on a gradiometric superconducting quantum-interference device with Nb /Al -Al Ox/Nb Josephson junctions, the FPJA is first-order insensitive to flux noise and can be operated without magnetic shielding at low temperature. Owing to its flexible design and compatibility with existing superconducting fabrication techniques, the FPJA offers a straightforward route toward on-chip integration with superconducting quantum circuits such as qubits and microwave optomechanical systems.

Parametric amplification and bidirectional invisibility in PT -symmetric time-Floquet systems

NASA Astrophysics Data System (ADS)

Koutserimpas, Theodoros T.; Alù, Andrea; Fleury, Romain

2018-01-01

Parity-time (PT )-symmetric wave devices, which exploit balanced interactions between material gain and loss, exhibit extraordinary properties, including lasing and flux-conserving scattering processes. In a seemingly different research field, periodically driven systems, also known as time-Floquet systems, have been widely studied as a relevant platform for reconfigurable active wave control and manipulation. In this article, we explore the connection between PT -symmetry and parametric time-Floquet systems. Instead of relying on material gain, we use parametric amplification by considering a time-periodic modulation of the refractive index at a frequency equal to twice the incident signal frequency. We show that the scattering from a simple parametric slab, whose dynamics follows the Mathieu equation, can be described by a PT -symmetric scattering matrix, whose PT -breaking threshold corresponds to the Mathieu instability threshold. By combining different parametric slabs modulated out of phase, we create PT -symmetric time-Floquet systems that feature exceptional scattering properties, such as coherent perfect absorption (CPA)-laser operation and bidirectional invisibility. These bidirectional properties, rare for regular PT -symmetric systems, are related to a compensation of parametric amplification due to multiple scattering between two parametric systems modulated with a phase difference.

Regenerative Amplification of Femtosecond Pulses: Design andConstruction of a sub-100fs, muon J Laser System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schumacher, Andreas B.

1996-10-01

Femtosecond lasers are a powerful tool for a wealth of applications in physics, chemistry and biology. In most cases, however, their use is fundamentally restricted to a rather narrow spectral range. This thesis deals with the construction and characterization of a femtosecond light source for spectroscopic applications which overcomes that restriction. It is demonstrated how the output of a continuously pumped Ti:sapphire femtosecond oscillator is amplified to the μJ level,while the pulse duration remains below 100 fs. A combination of continuous pumping, acousto-optic switching and Ti:Al 2O 3 as a gain medium allows amplification at high repetition rates. By focusingmore » the high energy pulses into a sapphire crystal, a broad-band continuum can be generated, extended in wavelengths over several hundred nanometers. To accomplish amplification of three orders of magnitude while maintaining the pulse length, a regenerative multipass amplifier system was built. The thesis describes theoretical design, realization and characterization of the system. Theoretical calculations and preliminary measurements were carried out and allow a critical evaluation of the final performance.« less

A Label-Free and Sensitive Fluorescent Qualitative Assay for Bisphenol A Based on Rolling Circle Amplification/Exonuclease III-Combined Cascade Amplification.

PubMed

Li, Xia; Song, Juan; Xue, Qing-Wang; You, Fu-Heng; Lu, Xia; Kong, Yan-Cong; Ma, Shu-Yi; Jiang, Wei; Li, Chen-Zhong

2016-10-21

Bisphenol A (BPA) detection in drinking water and food packaging materials has attracted much attention since the discovery that BPA can interfere with normal physiological processes and cause adverse health effects. Here, we constructed a label-free aptamer fluorescent assay for selective and sensitive detection of BPA based on the rolling circle amplification (RCA)/Exonuclease III (Exo III)-combined cascade amplification strategy. First, the duplex DNA probe (RP) with anti-BPA aptamer and trigger sequence was designed for BPA recognition and signal amplification. Next, under the action of BPA, the trigger probe was liberated from RP to initiate RCA reaction as primary amplification. Subsequently, the RCA products were used to trigger Exo III assisted secondary amplification with the help of hairpin probes, producing plenty of "G-quadruplex" in lantern-like structures. Finally, the continuously enriched "G-quadruplex lanterns" were lightened by zinc(II)-protoporphyrin IX (ZnPPIX) generating enhanced fluorescence signals. By integrating the primary RCA and secondary Exo III mediated cascade amplification strategy, this method displayed an excellent sensitivity with the detection limits of 5.4 × 10 -17 M. In addition, the anti-BPA aptamer exhibits high recognition ability with BPA, guaranteeing the specificity of detection. The reporter signal probe (G-quadruplex with ZnPPIX) provides a label-free fluorescence signals readout without complicated labeling procedures, making the method simple in design and cost-effective in operation. Moreover, environmental samples analysis was also performed, suggesting that our strategy was reliable and had a great potential application in environmental monitoring.

chipPCR: an R package to pre-process raw data of amplification curves.

PubMed

Rödiger, Stefan; Burdukiewicz, Michał; Schierack, Peter

2015-09-01

Both the quantitative real-time polymerase chain reaction (qPCR) and quantitative isothermal amplification (qIA) are standard methods for nucleic acid quantification. Numerous real-time read-out technologies have been developed. Despite the continuous interest in amplification-based techniques, there are only few tools for pre-processing of amplification data. However, a transparent tool for precise control of raw data is indispensable in several scenarios, for example, during the development of new instruments. chipPCR is an R: package for the pre-processing and quality analysis of raw data of amplification curves. The package takes advantage of R: 's S4 object model and offers an extensible environment. chipPCR contains tools for raw data exploration: normalization, baselining, imputation of missing values, a powerful wrapper for amplification curve smoothing and a function to detect the start and end of an amplification curve. The capabilities of the software are enhanced by the implementation of algorithms unavailable in R: , such as a 5-point stencil for derivative interpolation. Simulation tools, statistical tests, plots for data quality management, amplification efficiency/quantification cycle calculation, and datasets from qPCR and qIA experiments are part of the package. Core functionalities are integrated in GUIs (web-based and standalone shiny applications), thus streamlining analysis and report generation. http://cran.r-project.org/web/packages/chipPCR. Source code: https://github.com/michbur/chipPCR. stefan.roediger@b-tu.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A Label-Free and Sensitive Fluorescent Qualitative Assay for Bisphenol A Based on Rolling Circle Amplification/Exonuclease III-Combined Cascade Amplification

PubMed Central

Li, Xia; Song, Juan; Xue, Qing-Wang; You, Fu-Heng; Lu, Xia; Kong, Yan-Cong; Ma, Shu-Yi; Jiang, Wei; Li, Chen-Zhong

2016-01-01

Bisphenol A (BPA) detection in drinking water and food packaging materials has attracted much attention since the discovery that BPA can interfere with normal physiological processes and cause adverse health effects. Here, we constructed a label-free aptamer fluorescent assay for selective and sensitive detection of BPA based on the rolling circle amplification (RCA)/Exonuclease III (Exo III)-combined cascade amplification strategy. First, the duplex DNA probe (RP) with anti-BPA aptamer and trigger sequence was designed for BPA recognition and signal amplification. Next, under the action of BPA, the trigger probe was liberated from RP to initiate RCA reaction as primary amplification. Subsequently, the RCA products were used to trigger Exo III assisted secondary amplification with the help of hairpin probes, producing plenty of “G-quadruplex” in lantern-like structures. Finally, the continuously enriched “G-quadruplex lanterns” were lightened by zinc(II)-protoporphyrin IX (ZnPPIX) generating enhanced fluorescence signals. By integrating the primary RCA and secondary Exo III mediated cascade amplification strategy, this method displayed an excellent sensitivity with the detection limits of 5.4 × 10−17 M. In addition, the anti-BPA aptamer exhibits high recognition ability with BPA, guaranteeing the specificity of detection. The reporter signal probe (G-quadruplex with ZnPPIX) provides a label-free fluorescence signals readout without complicated labeling procedures, making the method simple in design and cost-effective in operation. Moreover, environmental samples analysis was also performed, suggesting that our strategy was reliable and had a great potential application in environmental monitoring. PMID:28335318

A multi-module microfluidic platform for continuous pre-concentration of water-soluble ions and separation of oil droplets from oil-in-water (O/W) emulsions using a DC-biased AC electrokinetic technique.

PubMed

Das, Dhiman; Phan, Dinh-Tuan; Zhao, Yugang; Kang, Yuejun; Chan, Vincent; Yang, Chun

2017-03-01

A novel continuous flow microfluidic platform specifically designed for environmental monitoring of O/W emulsions during an aftermath of oil spills is reported herein. Ionized polycyclic aromatic hydrocarbons which are toxic are readily released from crude oil to the surrounding water phase through the smaller oil droplets with enhanced surface area. Hence, a multi-module microfluidic device is fabricated to form ion enrichment zones in the water phase of O/W emulsions for the ease of detection and to separate micron-sized oil droplets from the O/W emulsions. Fluorescein ions in the water phase are used to simulate the presence of these toxic ions in the O/W emulsion. A DC-biased AC electric field is employed in both modules. In the first module, a nanoporous Nafion membrane is used for activating the concentration polarization effect on the fluorescein ions, resulting in the formation of stable ion enrichment zones in the water phase of the emulsion. A 35.6% amplification of the fluorescent signal is achieved in the ion enrichment zone; corresponding to 100% enrichment of the fluorescent dye concentration. In this module, the main inlet is split into two channels by using a Y-junction so that there are two outlets for the oil droplets. The second module located downstream of the first module consists of two oil droplet entrapment zones at two outlets. By switching on the appropriate electrodes, either one of the two oil droplet entrapment zones can be activated and the droplets can be blocked in the corresponding outlet. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

SITE AMPLIFICATION OF EARTHQUAKE GROUND MOTION.

USGS Publications Warehouse

Hays, Walter W.

1986-01-01

When analyzing the patterns of damage in an earthquake, physical parameters of the total earthquake-site-structure system are correlated with the damage. Soil-structure interaction, the cause of damage in many earthquakes, involves the frequency-dependent response of both the soil-rock column and the structure. The response of the soil-rock column (called site amplification) is controversial because soil has strain-dependent properties that affect the way the soil column filters the input body and surface seismic waves, modifying the amplitude and phase spectra and the duration of the surface ground motion.

Optical parametric amplification of arbitrarily polarized light in periodically poled LiNbO3.

PubMed

Shao, Guang-hao; Song, Xiao-shi; Xu, Fei; Lu, Yan-qing

2012-08-13

Optical parametric amplification (OPA) of arbitrarily polarized light is proposed in a multi-section periodically poled Lithium Niobate (PPLN). External electric field is applied on selected sections to induce the polarization rotation of involved lights, thus the quasi-phase matched optical parametric processes exhibit polarization insensitivity under suitable voltage. In addition to the amplified signal wave, an idler wave with the same polarization is generated simultaneously. As an example, a ~10 times OPA showing polarization independency is simulated. Applications of this technology are also discussed.

Statistical mechanics of self-driven Carnot cycles.

PubMed

Smith, E

1999-10-01

The spontaneous generation and finite-amplitude saturation of sound, in a traveling-wave thermoacoustic engine, are derived as properties of a second-order phase transition. It has previously been argued that this dynamical phase transition, called "onset," has an equivalent equilibrium representation, but the saturation mechanism and scaling were not computed. In this work, the sound modes implementing the engine cycle are coarse-grained and statistically averaged, in a partition function derived from microscopic dynamics on criteria of scale invariance. Self-amplification performed by the engine cycle is introduced through higher-order modal interactions. Stationary points and fluctuations of the resulting phenomenological Lagrangian are analyzed and related to background dynamical currents. The scaling of the stable sound amplitude near the critical point is derived and shown to arise universally from the interaction of finite-temperature disorder, with the order induced by self-amplification.

Trirotron: triode rotating beam radio frequency amplifier

DOEpatents

Lebacqz, Jean V.

1980-01-01

High efficiency amplification of radio frequencies to very high power levels including: establishing a cylindrical cloud of electrons; establishing an electrical field surrounding and coaxial with the electron cloud to bias the electrons to remain in the cloud; establishing a rotating electrical field that surrounds and is coaxial with the steady field, the circular path of the rotating field being one wavelength long, whereby the peak of one phase of the rotating field is used to accelerate electrons in a beam through the bias field in synchronism with the peak of the rotating field so that there is a beam of electrons continuously extracted from the cloud and rotating with the peak; establishing a steady electrical field that surrounds and is coaxial with the rotating field for high-energy radial acceleration of the rotating beam of electrons; and resonating the rotating beam of electrons within a space surrounding the second field, the space being selected to have a phase velocity equal to that of the rotating field to thereby produce a high-power output at the frequency of the rotating field.

Site Amplification in the Central U.S.: Towards and understanding of factors influencing the site effect

NASA Astrophysics Data System (ADS)

Yassminh, R.; Sandvol, E. A.

2017-12-01

We have mapped site amplification using a Reverse Two Station (RTS) approach across much of the Central United States. We have found several unexpected results including a lack of amplification in Paleozoic basins such as the Illinois and Michigan basins. In general, we found that the amplification of high frequency regional waves is related to the topography. We also suggest that the HVSR spectra are primarily a function of the shallow velocity structure. The Central United States Seismic Observatory (CUSSO) is a vertical seismic array located adjacent to the central segment of the NMSZ. CUSSO data gives us the opportunity to understand the amplification of the ground motion at different depths within the uppermost crust. Simulating ground motions throughout the CUSSO borehole and examining the factors affecting the ground amplification, such as the velocity and thicknesses of the model layers and the source sizes, is an effective way to understand the role different factors playing in modifying the ground motion for both the local and regional seismic phases. We have used the spectral-element method (SEMs) with a 1D crustal velocity structure derived from logging data taken from CUSSO borehole. This model is comprised of near surface sediment layers and a Paleozoic basement. Utilizing the software package SPECFEM2D with virtual seismometers located on the surface and in the bottom of the different sediment layers, we have computed the true synthetic site amplification for frequencies between 0.01-3 Hz. For the local model, we have tested the sensitivity of the ground motion amplification to the source magnitude. For frequencies>0.6, the ground motions have been amplified with decreasing the magnitudes while for HZ<0.6 the the horizontal amplification increases with increasing the magnitudes. The effect of the velocity of the upper 30m was tested and the result shows that decreasing the Vs30m resulted in amplifying of the ground motion and decreasing of the resonant frequency. The velocity of the lower part of the sediment basin modifies the ground motion amplification and the result shows that increasing the velocity resulted in shifting the horizontal amplification peak frequency toward a lower frequency and increasing the amplification for frequencies >2Hz.

Phase-stable, multi-µJ femtosecond pulses from a repetition-rate tunable Ti:Sa-oscillator-seeded Yb-fiber amplifier

NASA Astrophysics Data System (ADS)

Saule, T.; Holzberger, S.; De Vries, O.; Plötner, M.; Limpert, J.; Tünnermann, A.; Pupeza, I.

2017-01-01

We present a high-power, MHz-repetition-rate, phase-stable femtosecond laser system based on a phase-stabilized Ti:Sa oscillator and a multi-stage Yb-fiber chirped-pulse power amplifier. A 10-nm band around 1030 nm is split from the 7-fs oscillator output and serves as the seed for subsequent amplification by 54 dB to 80 W of average power. The µJ-level output is spectrally broadened in a solid-core fiber and compressed to 30 fs with chirped mirrors. A pulse picker prior to power amplification allows for decreasing the repetition rate from 74 MHz by a factor of up to 4 without affecting the pulse parameters. To compensate for phase jitter added by the amplifier to the feed-forward phase-stabilized seeding pulses, a self-referencing feed-back loop is implemented at the system output. An integrated out-of-loop phase noise of less than 100 mrad was measured in the band from 0.4 Hz to 400 kHz, which to the best of our knowledge corresponds to the highest phase stability ever demonstrated for high-power, multi-MHz-repetition-rate ultrafast lasers. This system will enable experiments in attosecond physics at unprecedented repetition rates, it offers ideal prerequisites for the generation and field-resolved electro-optical sampling of high-power, broadband infrared pulses, and it is suitable for phase-stable white light generation.

Protein detection using biobarcodes.

PubMed

Müller, Uwe R

2006-10-01

Over the past 50 years the development of assays for the detection of protein analytes has been driven by continuing demands for higher levels of sensitivity and multiplexing. The result has been a progression of sandwich-type immunoassays, starting with simple radioisotopic, colorimetric, or fluorescent labeling systems to include various enzymatic or nanostructure-based signal amplification schemes, with a concomitant sensitivity increase of over 1 million fold. Multiplexing of samples and tests has been enabled by microplate and microarray platforms, respectively, or lately by various molecular barcoding systems. Two different platforms have emerged as the current front-runners by combining a nucleic acid amplification step with the standard two-sided immunoassay. In both, the captured protein analyte is replaced by a multiplicity of oligonucleotides that serve as surrogate targets. One of these platforms employs DNA or RNA polymerases for the amplification step, while detection is by fluorescence. The other is based on gold nanoparticles for both amplification as well as detection. The latter technology, now termed Biobarcode, is completely enzyme-free and offers potentially much higher multiplexing power.

Sensitivity analysis of reactive ecological dynamics.

PubMed

Verdy, Ariane; Caswell, Hal

2008-08-01

Ecological systems with asymptotically stable equilibria may exhibit significant transient dynamics following perturbations. In some cases, these transient dynamics include the possibility of excursions away from the equilibrium before the eventual return; systems that exhibit such amplification of perturbations are called reactive. Reactivity is a common property of ecological systems, and the amplification can be large and long-lasting. The transient response of a reactive ecosystem depends on the parameters of the underlying model. To investigate this dependence, we develop sensitivity analyses for indices of transient dynamics (reactivity, the amplification envelope, and the optimal perturbation) in both continuous- and discrete-time models written in matrix form. The sensitivity calculations require expressions, some of them new, for the derivatives of equilibria, eigenvalues, singular values, and singular vectors, obtained using matrix calculus. Sensitivity analysis provides a quantitative framework for investigating the mechanisms leading to transient growth. We apply the methodology to a predator-prey model and a size-structured food web model. The results suggest predator-driven and prey-driven mechanisms for transient amplification resulting from multispecies interactions.

21 CFR 880.2460 - Electrically powered spinal fluid pressure monitor.

Code of Federal Regulations, 2013 CFR

2013-04-01

... SERVICES (CONTINUED) MEDICAL DEVICES GENERAL HOSPITAL AND PERSONAL USE DEVICES General Hospital and... electrical signal. The device includes signal amplification, conditioning, and display equipment. (b...

21 CFR 880.2460 - Electrically powered spinal fluid pressure monitor.

Code of Federal Regulations, 2012 CFR

2012-04-01

... SERVICES (CONTINUED) MEDICAL DEVICES GENERAL HOSPITAL AND PERSONAL USE DEVICES General Hospital and... electrical signal. The device includes signal amplification, conditioning, and display equipment. (b...

21 CFR 880.2460 - Electrically powered spinal fluid pressure monitor.

Code of Federal Regulations, 2014 CFR

2014-04-01

... SERVICES (CONTINUED) MEDICAL DEVICES GENERAL HOSPITAL AND PERSONAL USE DEVICES General Hospital and... electrical signal. The device includes signal amplification, conditioning, and display equipment. (b...

PHYSICAL EFFECTS OCCURRING DURING GENERATION AND AMPLIFICATION OF LASER RADIATION: Spatial phase fluctuations of the fundamental laser mode caused by spontaneous emission

NASA Astrophysics Data System (ADS)

Belinskiĭ, A. V.; Chirkin, Anatolii S.

1989-02-01

A calculation is reported of the degree of spatial coherence of the fundamental radiation mode subject to phase fluctuations in space. It is shown that the degree of spatial coherence (within the beam width) is perturbed only slightly by these fluctuations, compared with subthreshold excitation of higher transverse modes.

Interference effects in a cavity for optical amplification

NASA Astrophysics Data System (ADS)

Cardimona, D. A.; Alsing, P. M.

2009-08-01

In space situational awareness scenarios, the objects needed to be characterized and identified are usually quite far away and quite dim. Thus, optical detectors need to be able to sense these very dim optical signals. Quantum interference in a three-level system can lead to amplification of optical signals. If we put a three-level system into a cavity tuned to the frequency of an incoming optical signal, we anticipate the amplification possibilities should be increased proportional to the quality factor of the cavity. Our vision is to utilize quantum dots in photonic crystal cavities, but as a stepping stone we first investigate a simple three-level system in a free-space optical cavity. We investigate quantum interference and classical interference effects when a three-level system interacts with both a cavity field mode and an external driving field mode. We find that under certain circumstances the cavity field evolves to be equal in magnitude to, but 180° out-of-phase with the external pump field when the pump field frequency equals the cavity frequency. At this point the resonance fluorescence from the atom in the cavity goes to zero due to a purely classical interference effect between the two out-of-phase fields. This is quite different from the quantum interference that occurs under the right circumstances, when the state populations are coherently driven into a linear combination that is decoupled from any applied field - and population is trapped in the excited states, thus allowing for a population inversion and an amplification of incoming optical signals.

Quinone Methide Signal Amplification: Covalent Reporter Labeling of Cancer Epitopes using Alkaline Phosphatase Substrates.

PubMed

Polaske, Nathan W; Kelly, Brian D; Ashworth-Sharpe, Julia; Bieniarz, Christopher

2016-03-16

Diagnostic assays with the sensitivity required to improve cancer therapeutics depend on the development of new signal amplification technologies. Herein, we report the development and application of a novel amplification system which utilizes latent quinone methides (QMs) activated by alkaline phosphatase (AP) for signal amplification in solid-phase immunohistochemical (IHC) assays. Phosphate-protected QM precursor substrates were prepared and conjugated to either biotin or a fluorophore through an amine-functionalized linker group. Upon reaction with AP, the phosphate group is cleaved, followed by elimination of the leaving group and formation of the highly reactive and short-lived QM. The QMs either react with tissue nucleophiles in close proximity to their site of generation, or are quenched by nucleophiles in the reaction media. The reporter molecules that covalently bind to the tissue were then detected visually by fluorescence microscopy in the case of fluorophore reporters, or brightfield microscopy using diaminobenzidine (DAB) in the case of biotin reporters. With multiple reporters deposited per enzyme, significant signal amplification was observed utilizing QM precursor substrates containing either benzyl difluoro or benzyl monofluoro leaving group functionalities. However, the benzyl monofluoro leaving group gave superior results with respect to both signal intensity and discretion, the latter of which was found to be imperative for use in diagnostic IHC assays.

Targeting HER2 aberrations as actionable drivers in lung cancers: phase II trial of the pan-HER tyrosine kinase inhibitor dacomitinib in patients with HER2-mutant or amplified tumors

PubMed Central

Kris, M. G.; Camidge, D. R.; Giaccone, G.; Hida, T.; Li, B. T.; O'Connell, J.; Taylor, I.; Zhang, H.; Arcila, M. E.; Goldberg, Z.; Jänne, P. A.

2015-01-01

Background HER2 mutations and amplifications have been identified as oncogenic drivers in lung cancers. Dacomitinib, an irreversible inhibitor of HER2, EGFR (HER1), and HER4 tyrosine kinases, has demonstrated activity in cell-line models with HER2 exon 20 insertions or amplifications. Here, we studied dacomitinib in patients with HER2-mutant or amplified lung cancers. Patients and methods As a prespecified cohort of a phase II study, we included patients with stage IIIB/IV lung cancers with HER2 mutations or amplification. We gave oral dacomitinib at 30–45 mg daily in 28-day cycles. End points included partial response rate, overall survival, and toxicity. Results We enrolled 30 patients with HER2-mutant (n = 26, all in exon 20 including 25 insertions and 1 missense mutation) or HER2-amplified lung cancers (n = 4). Three of 26 patients with tumors harboring HER2 exon 20 mutations [12%; 95% confidence interval (CI) 2% to 30%] had partial responses lasting 3+, 11, and 14 months. No partial responses occurred in four patients with tumors with HER2 amplifications. The median overall survival was 9 months from the start of dacomitinib (95% CI 7–21 months) for patients with HER2 mutations and ranged from 5 to 22 months with amplifications. Treatment-related toxicities included diarrhea (90%; grade 3/4: 20%/3%), dermatitis (73%; grade 3/4: 3%/0%), and fatigue (57%; grade 3/4: 3%/0%). One patient died on study likely due to an interaction of dacomitinib with mirtazapine. Conclusions Dacomitinib produced objective responses in patients with lung cancers with specific HER2 exon 20 insertions. This observation validates HER2 exon 20 insertions as actionable targets and justifies further study of HER2-targeted agents in specific HER2-driven lung cancers. ClinicalTrials.gov NCT00818441. PMID:25899785

Icotinib in Patients with Pretreated Advanced Esophageal Squamous Cell Carcinoma with EGFR Overexpression or EGFR Gene Amplification: A Single-Arm, Multicenter Phase 2 Study.

PubMed

Huang, Jing; Fan, Qingxia; Lu, Ping; Ying, Jianming; Ma, Changwu; Liu, Wei; Liu, Ying; Tan, Fenlai; Sun, Yan

2016-06-01

Epidermal growth factor receptor (EGFR) has been reported to be overexpressed and amplified in a high percentage of patients with esophageal squamous cell carcinoma (ESCC). The activity of icotinib, an EGFR tyrosine kinase inhibitor, was assessed in previously treated ESCC with EGFR overexpression or amplification. For this phase 2, single-arm, multicenter trial undertaken at six hospitals in China, we included Chinese patients with previously treated, histologically confirmed advanced ESCC and EGFR overexpression (immunohistochemical staining sore of 3+) or amplification (positive fluorescence in situ hybridization result). These patients received oral icotinib (250 mg, three times daily).The primary end point was the proportion of patients with objective responses as assessed by an independent radiology review committee. Between December 5, 2013, and May 28, 2015, a total of 281 patients were screened. Fifty-four eligible patients were enrolled. Nine responses were observed, including one complete response and eight partial responses, and 16 patients had stable disease, resulting in a 16.7% objective response rate (95% confidence interval [CI]: 6.7-26.6) and 46.3% disease control rate (95% CI: 33.0-59.6). The median progression-free survival and overall survival times were 52 (95% CI: 40-95) days and 153 (95% CI: 139-218) days, respectively. A total of 43 patients experienced at least one adverse event, but most were only grade 1 to 2 in severity. The most frequent was rash (48.1%), followed by diarrhea (22.2%). Icotinib showed favorable activity in patients with advanced, previously treated ESCC with EGFR overexpression or amplification. These findings suggest further research into EGFR overexpression or amplification for selecting responsive patients. Copyright © 2016 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Control of the amplifications of large-band amplitude-modulated pulses in an Nd-glass amplifier chain

NASA Astrophysics Data System (ADS)

Videau, Laurent; Bar, Emmanuel; Rouyer, Claude; Gouedard, Claude; Garnier, Josselin C.; Migus, Arnold

1999-07-01

We study nonlinear effects in amplification of partially coherent pulses in a high power laser chain. We compare statistical models with experimental results for temporal and spatial effects. First we show the interplay between self-phase modulation which broadens spectrum bandwidth and gain narrowing which reduces output spectrum. Theoretical results are presented for spectral broadening and energy limitation in case of time-incoherent pulses. In a second part, we introduce spatial incoherence with a multimode optical fiber which provides a smoothed beam. We show with experimental result that spatial filter pinholes are responsible for additive energy losses in the amplification. We develop a statistical model which takes into account the deformation of the focused beam as a function of B integral. We estimate the energy transmission of the spatial filter pinholes and compare this model with experimental data. We find a good agreement between theory and experiments. As a conclusion, we present an analogy between temporal and spatial effects with spectral broadening and spectral filter. Finally, we propose some solutions to control energy limitations in smoothed pulses amplification.

Peroxy Radical Measurements during the IRRONIC Field Project by C2H6 - NO Chemical Amplification

NASA Astrophysics Data System (ADS)

Wood, E. C. D.; Kundu, S.; Deming, B.; Lew, M.; Stevens, P. S.; Sklaveniti, S.; Dusanter, S.

2015-12-01

We present measurements of total peroxy radicals (HO2 + RO2) during the Indiana Radical, Reactivity and Ozone Production Intercomparison (IRRONIC) field project in Bloomington, Indiana during July 2015. Peroxy radicals were measured by chemical amplification using ethane and nitric oxide in dual PFA reaction chambers, and the amplification product NO2 was quantified by cavity attenuated phase shift spectroscopy. On sunny days mid-day peroxy radical mixing ratios were typically between 20 and 70 ppt and were well correlated with "HO2*" measured by the Indiana University Laser-Induced Fluorescence with Fluorescence Assay by Gas Expansion (IU-FAGE) instrument. The ratio of total peroxy radicals (UMass) to the IU-FAGE HO2* measurements was greater than two. We also describe results from an informal intercomparison of the two instruments' calibration sources, which are based on acetone photolysis (UMass) and water photolysis (IU). In addition to sampling the IU calibration source in "amplification" mode, the UMass instrument also separately quantified the HO2 mixing ratio in the IU calibration gas by reaction with excess NO and subsequent quantification of the NO2 produced.

0.4 mJ quasi-continuously pumped picosecond Nd:GdVO4 laser with selectable pulse duration

NASA Astrophysics Data System (ADS)

Kubeček, V.; Jelínek, M.; Čech, M.; Hiršl, P.; Diels, J.-C.

2010-02-01

A quasi-continuously pumped picosecond oscillator-amplifier Nd:GdVO4 laser system based on two identical slabs in a single bounce geometry is reported. Pulse duration is from 160 to 55 ps resulting from the pulse shortening along the extended mode locked train from passively mode locked oscillator, which was measured directly from a single laser shot. The shortest 55 ps long cavity dumped single pulses from the oscillator with the energy of 15±1 μJ and the contrast better than 10-3 were amplified to the energy of 150 μJ with the contrast better than 10-3 after the single-pass amplification and to the energy of 400 μJ after the double-pass amplification.

Carrier-envelope phase stabilization and control of 1 kHz, 6 mJ, 30 fs laser pulses from a Ti:sapphire regenerative amplifier.

PubMed

Chen, Shouyuan; Chini, Michael; Wang, He; Yun, Chenxia; Mashiko, Hiroki; Wu, Yi; Chang, Zenghu

2009-10-20

Carrier-envelope (CE) phase stabilization of a two-stage chirped pulse amplifier laser system with regenerative amplification as the preamplifier is demonstrated. The CE phase stability of this laser system is found to have a 90 mrad rms error averaged over 50 laser shots for a locking period of 4.5 h. The CE phase locking was confirmed unambiguously by experimental observation of the 2pi periodicity of the high-order harmonic spectrum generated by double optical gating.

Strand Displacement Amplification Reaction on Quantum Dot-Encoded Silica Bead for Visual Detection of Multiplex MicroRNAs.

PubMed

Qu, Xiaojun; Jin, Haojun; Liu, Yuqian; Sun, Qingjiang

2018-03-06

The combination of microbead array, isothermal amplification, and molecular signaling enables the continuous development of next-generation molecular diagnostic techniques. Herein we reported the implementation of nicking endonuclease-assisted strand displacement amplification reaction on quantum dots-encoded microbead (Qbead), and demonstrated its feasibility for multiplexed miRNA assay in real sample. The Qbead featured with well-defined core-shell superstructure with dual-colored quantum dots loaded in silica core and shell, respectively, exhibiting remarkably high optical encoding stability. Specially designed stem-loop-structured probes were immobilized onto the Qbead for specific target recognition and amplification. In the presence of low abundance of miRNA target, the target triggered exponential amplification, producing a large quantity of stem-G-quadruplexes, which could be selectively signaled by a fluorescent G-quadruplex intercalator. In one-step operation, the Qbead-based isothermal amplification and signaling generated emissive "core-shell-satellite" superstructure, changing the Qbead emission-color. The target abundance-dependent emission-color changes of the Qbead allowed direct, visual detection of specific miRNA target. This visualization method achieved limit of detection at the subfemtomolar level with a linear dynamic range of 4.5 logs, and point-mutation discrimination capability for precise miRNA analyses. The array of three encoded Qbeads could simultaneously quantify three miRNA biomarkers in ∼500 human hepatoma carcinoma cells. With the advancements in ease of operation, multiplexing, and visualization capabilities, the isothermal amplification-on-Qbead assay could potentially enable the development of point-of-care diagnostics.

High peak-power laser system tuneable from 8 to 10 μm

NASA Astrophysics Data System (ADS)

Gutty, François; Grisard, Arnaud; Larat, Christian; Papillon, Dominique; Schwarz, Muriel; Gérard, Bruno; Ostendorf, Ralf; Wagner, Joachim; Lallier, Eric

2017-04-01

A high peak-power rapidly tuneable laser system in the long-wave infrared is obtained using an external cavity quantum-cascade laser (EC-QCL) broadly tuneable from 8 to 10 μm and an optical parametric amplifier (OPA) based on quasi phase-matching in orientation-patterned gallium arsenide (OP-GaAs). To provide an efficient amplification, the nonlinear crystal is pumped by a pulsed fiber laser source. With a pump laser source tuneable around 2 μm, quasi phase-matching remains satisfied with a fixed grating period in the OP-GaAs crystal when the EC-QCL wavelength is swept from 8 to 10 μm. The OPA demonstrates parametric amplification from 8 to 10 μm and achieves output peak powers up to 140 W, with spectral linewidths below 3.5 cm-1 and a beam profile quality (M2) below 3.4 in both horizontal and vertical directions.

Molecular alignment and orientation with a hybrid Raman scattering technique

NASA Astrophysics Data System (ADS)

Bustard, Philip J.; Lausten, R.; Sussman, Benjamin J.

2012-11-01

We demonstrate a scheme for the preparation of molecular alignment and angular momentum orientation using a hybrid combination of two limits of Raman scattering. First a weak, impulsive pump pulse initializes the system via the nonresonant dynamic Stark effect. Then, having overcome the influence of the vacuum fluctuations, an amplification pulse selectively enhances the initial coherences by transient stimulated Raman scattering, generating alignment and angular momentum orientation of molecular hydrogen. The amplitude and phase of the resulting coherent dynamics are experimentally probed, indicating an amplification factor of 4.5. An analytic theory is developed to model the dynamics.

High energy, high average power solid state green or UV laser

DOEpatents

Hackel, Lloyd A.; Norton, Mary; Dane, C. Brent

2004-03-02

A system for producing a green or UV output beam for illuminating a large area with relatively high beam fluence. A Nd:glass laser produces a near-infrared output by means of an oscillator that generates a high quality but low power output and then multi-pass through and amplification in a zig-zag slab amplifier and wavefront correction in a phase conjugator at the midway point of the multi-pass amplification. The green or UV output is generated by means of conversion crystals that follow final propagation through the zig-zag slab amplifier.

FIBER OPTICS: Schrödinger soliton in a fiber waveguide exhibiting both gain and losses: squeezed states and growth of noise in the linear approximation

NASA Astrophysics Data System (ADS)

Belinskiĭ, A. V.

1992-09-01

An investigation is made of the evolution of quantum fluctuations of a fundamental soliton in the course of its propagation in a nonlinear fiber waveguide characterized by losses and compensated by amplification. Simple relationships are obtained for the amplitude and phase noise, quantum uncertainty of the position and momentum, and also fluctuations of the quadrature components of the radiation field. Numerical estimates are obtained. It is shown that loss-compensating amplification is unnecessary for efficient formation of squeezed states of a soliton.

Phase stabilization of multidimensional amplification architectures for ultrashort pulses

NASA Astrophysics Data System (ADS)

Müller, M.; Kienel, M.; Klenke, A.; Eidam, T.; Limpert, J.; Tünnermann, A.

2015-03-01

The active phase stabilization of spatially and temporally combined ultrashort pulses is investigated theoretically and experimentally. Particularly, considering a combining scheme applying 2 amplifier channels and 4 divided-pulse replicas a bistable behavior is observed. The reason is mutual influence of the optical error signals that is intrinsic to temporal polarization beam combining. A successful mitigation strategy is proposed and is analyzed theoretically and experimentally.

Marking the Emergence of Rhetoric and Composition Since 1950: Snapshots from the Founding of Eight Academic Journals.

ERIC Educational Resources Information Center

Goggin, Maureen Daly

The emergence of rhetoric and composition as a scholarly field can be described as having occurred in three phases: (1) the establishment of the field; (2) the amplification of the field; and (3) the consolidation of disciplinary practices. These three stages are reflected in the activity of scholarly journals since 1950. The first phase (1950 to…

Biomaterials in light amplification

NASA Astrophysics Data System (ADS)

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 cells and tissues or separated phase systems like phosphatydylcholine liposomes. All of the above-mentioned light amplification possibilities of biomaterials also have potential for several interesting applications in biology, medicine, sensing and imaging, which will be described and discussed in this review.

MET Amplification Identifies a Small and Aggressive Subgroup of Esophagogastric Adenocarcinoma With Evidence of Responsiveness to Crizotinib

PubMed Central

Lennerz, Jochen K.; Kwak, Eunice L.; Ackerman, Allison; Michael, Michael; Fox, Stephen B.; Bergethon, Kristin; Lauwers, Gregory Y.; Christensen, James G.; Wilner, Keith D.; Haber, Daniel A.; Salgia, Ravi; Bang, Yung-Jue; Clark, Jeffrey W.; Solomon, Benjamin J.; Iafrate, A. John

2011-01-01

Purpose Amplification of the MET proto-oncogene in gastroesophageal cancer (GEC) may constitute a molecular marker for targeted therapy. We examined a GEC cohort with follow-up and reported the clinical response of four additional patients with MET-amplified tumors to the small molecule inhibitor crizotinib as part of an expanded phase I cohort study. Patients and Methods From 2007 to 2009, patients with GEC were genetically screened as a consecutive series of 489 tumors (stages 0, I, and II, 39%; III, 25%; IV, 36%; n = 222 esophageal, including n = 21 squamous carcinomas). MET, EGFR, and HER2 amplification status was assessed by using fluorescence in situ hybridization. Results Ten (2%) of 489 patients screened harbored MET amplification; 23 (4.7%) harbored EGFR amplification; 45 (8.9%) harbored HER2 amplification; and 411 (84%) were wild type for all three genes (ie, negative). MET-amplified tumors were typically high-grade adenocarcinomas that presented at advanced stages (5%; n = 4 of 80). EGFR-amplified tumors showed the highest fraction of squamous cell carcinoma (17%; n = 4 of 23). HER2, MET, and EGFR amplification were, with one exception (MET and EGFR positive), mutually exclusive events. Survival analysis in patients with stages III and IV disease showed substantially shorter median survival in MET/EGFR-amplified groups, with a rank order for all groups by median survival (from most to least aggressive): MET (7.1 months; P < .001) less than EGFR (11.2 months; P = .16) less than HER2 (16.9 months; P = .89) when compared with the negative group (16.2 months). Two of four patients with MET-amplified tumors treated with crizotinib experienced tumor shrinkage (−30% and −16%) and experienced progression after 3.7 and 3.5 months. Conclusion MET amplification defines a small and aggressive subset of GEC with indications of transient sensitivity to the targeted MET inhibitor crizotinib (PF-02341066). PMID:22042947

MET amplification identifies a small and aggressive subgroup of esophagogastric adenocarcinoma with evidence of responsiveness to crizotinib.

PubMed

Lennerz, Jochen K; Kwak, Eunice L; Ackerman, Allison; Michael, Michael; Fox, Stephen B; Bergethon, Kristin; Lauwers, Gregory Y; Christensen, James G; Wilner, Keith D; Haber, Daniel A; Salgia, Ravi; Bang, Yung-Jue; Clark, Jeffrey W; Solomon, Benjamin J; Iafrate, A John

2011-12-20

Amplification of the MET proto-oncogene in gastroesophageal cancer (GEC) may constitute a molecular marker for targeted therapy. We examined a GEC cohort with follow-up and reported the clinical response of four additional patients with MET-amplified tumors to the small molecule inhibitor crizotinib as part of an expanded phase I cohort study. From 2007 to 2009, patients with GEC were genetically screened as a consecutive series of 489 tumors (stages 0, I, and II, 39%; III, 25%; IV, 36%; n = 222 esophageal, including n = 21 squamous carcinomas). MET, EGFR, and HER2 amplification status was assessed by using fluorescence in situ hybridization. Ten (2%) of 489 patients screened harbored MET amplification; 23 (4.7%) harbored EGFR amplification; 45 (8.9%) harbored HER2 amplification; and 411 (84%) were wild type for all three genes (ie, negative). MET-amplified tumors were typically high-grade adenocarcinomas that presented at advanced stages (5%; n = 4 of 80). EGFR-amplified tumors showed the highest fraction of squamous cell carcinoma (17%; n = 4 of 23). HER2, MET, and EGFR amplification were, with one exception (MET and EGFR positive), mutually exclusive events. Survival analysis in patients with stages III and IV disease showed substantially shorter median survival in MET/EGFR-amplified groups, with a rank order for all groups by median survival (from most to least aggressive): MET (7.1 months; P < .001) less than EGFR (11.2 months; P = .16) less than HER2 (16.9 months; P = .89) when compared with the negative group (16.2 months). Two of four patients with MET-amplified tumors treated with crizotinib experienced tumor shrinkage (-30% and -16%) and experienced progression after 3.7 and 3.5 months. MET amplification defines a small and aggressive subset of GEC with indications of transient sensitivity to the targeted MET inhibitor crizotinib (PF-02341066).

Amplification of curvature perturbations in cyclic cosmology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang Jun; Liu Zhiguo; Piao Yunsong

2010-12-15

We analytically and numerically show that through the cycles with nonsingular bounce, the amplitude of curvature perturbation on a large scale will be amplified and the power spectrum will redden. In some sense, this amplification will eventually destroy the homogeneity of the background, which will lead to the ultimate end of cycles of the global universe. We argue that for the model with increasing cycles, it might be possible that a fissiparous multiverse will emerge after one or several cycles, in which the cycles will continue only at corresponding local regions.

Fidelity criterion for quantum-domain transmission and storage of coherent states beyond the unit-gain constraint.

PubMed

Namiki, Ryo; Koashi, Masato; Imoto, Nobuyuki

2008-09-05

We generalize the experimental success criterion for quantum teleportation (memory) in continuous-variable quantum systems to be suitable for a non-unit-gain condition by considering attenuation (amplification) of the coherent-state amplitude. The new criterion can be used for a nonideal quantum memory and long distance quantum communication as well as quantum devices with amplification process. It is also shown that the framework to measure the average fidelity is capable of detecting all Gaussian channels in the quantum domain.

Vibration of the organ of Corti within the cochlear apex in mice

PubMed Central

Gao, Simon S.; Wang, Rosalie; Raphael, Patrick D.; Moayedi, Yalda; Groves, Andrew K.; Zuo, Jian; Applegate, Brian E.

2014-01-01

The tonotopic map of the mammalian cochlea is commonly thought to be determined by the passive mechanical properties of the basilar membrane. The other tissues and cells that make up the organ of Corti also have passive mechanical properties; however, their roles are less well understood. In addition, active forces produced by outer hair cells (OHCs) enhance the vibration of the basilar membrane, termed cochlear amplification. Here, we studied how these biomechanical components interact using optical coherence tomography, which permits vibratory measurements within tissue. We measured not only classical basilar membrane tuning curves, but also vibratory responses from the rest of the organ of Corti within the mouse cochlear apex in vivo. As expected, basilar membrane tuning was sharp in live mice and broad in dead mice. Interestingly, the vibratory response of the region lateral to the OHCs, the “lateral compartment,” demonstrated frequency-dependent phase differences relative to the basilar membrane. This was sharply tuned in both live and dead mice. We then measured basilar membrane and lateral compartment vibration in transgenic mice with targeted alterations in cochlear mechanics. Prestin499/499, Prestin−/−, and TectaC1509G/C1509G mice demonstrated no cochlear amplification but maintained the lateral compartment phase difference. In contrast, SfswapTg/Tg mice maintained cochlear amplification but did not demonstrate the lateral compartment phase difference. These data indicate that the organ of Corti has complex micromechanical vibratory characteristics, with passive, yet sharply tuned, vibratory characteristics associated with the supporting cells. These characteristics may tune OHC force generation to produce the sharp frequency selectivity of mammalian hearing. PMID:24920025

Architecture and Bloch-Maxwell modelling of multi-mJ 100 fs fully-coherent soft X-ray laser based on X-ray CPA

NASA Astrophysics Data System (ADS)

Zeitoun, Ph.; Oliva, E.; Fajardo, M.; Cheriaux, G.; Le, T. T. T.; Li, L.; Pitman, M.; Ros, D.; Sebban, S.; Velarde, P.

2012-07-01

By seeding amplifying plasmas pumped with the so-called Transient collisionnal excitation scheme, the amplified pulse seems to be limited to an energy of several 10's of μJ. Aiming to attain several mJ, we study the seeding of plasma pumped by long laser pulse. Thanks to our time-dependent Maxwell-Bloch code, we demonstrate that direct seeding with femtosecond pulse is inefficient. We also study the amplification of pulse train with the drawback of re-synchronizing the pulses. We proposed and studied the amplification of high harmonic seed stretched by a grating pair, amplified finally compressed. We consider off-axis diffraction on the gratings for maximizing their efficiency. Considering the phase deformation induced by the amplification and the spectral narrowing the final pulse is 230 fs in duration and 5 mJ.

Light amplification by seeded Kerr instability

NASA Astrophysics Data System (ADS)

Vampa, G.; Hammond, T. J.; Nesrallah, M.; Naumov, A. Yu.; Corkum, P. B.; Brabec, T.

2018-02-01

Amplification of femtosecond laser pulses typically requires a lasing medium or a nonlinear crystal. In either case, the chemical properties of the lasing medium or the momentum conservation in the nonlinear crystal constrain the frequency and the bandwidth of the amplified pulses. We demonstrate high gain amplification (greater than 1000) of widely tunable (0.5 to 2.2 micrometers) and short (less than 60 femtosecond) laser pulses, up to intensities of 1 terawatt per square centimeter, by seeding the modulation instability in an Y3Al5O12 crystal pumped by femtosecond near-infrared pulses. Our method avoids constraints related to doping and phase matching and therefore can occur in a wider pool of glasses and crystals even at far-infrared frequencies and for single-cycle pulses. Such amplified pulses are ideal to study strong-field processes in solids and highly excited states in gases.

Architecture and Bloch-Maxwell modelling of multi-mJ 100 fs fully-coherent soft X-ray laser based on X-ray CPA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeitoun, Ph.; Oliva, E.; Fajardo, M.

2012-07-09

By seeding amplifying plasmas pumped with the so-called Transient collisionnal excitation scheme, the amplified pulse seems to be limited to an energy of several 10's of {mu}J. Aiming to attain several mJ, we study the seeding of plasma pumped by long laser pulse. Thanks to our time-dependent Maxwell-Bloch code, we demonstrate that direct seeding with femtosecond pulse is inefficient. We also study the amplification of pulse train with the drawback of re-synchronizing the pulses. We proposed and studied the amplification of high harmonic seed stretched by a grating pair, amplified finally compressed. We consider off-axis diffraction on the gratings formore » maximizing their efficiency. Considering the phase deformation induced by the amplification and the spectral narrowing the final pulse is 230 fs in duration and 5 mJ.« less

Directional amplifier in an optomechanical system with optical gain

NASA Astrophysics Data System (ADS)

Jiang, Cheng; Song, L. N.; Li, Yong

2018-05-01

Directional amplifiers are crucial nonreciprocal devices in both classical and quantum information processing. Here we propose a scheme for realizing a directional amplifier between optical and microwave fields based on an optomechanical system with optical gain, where an active optical cavity and two passive microwave cavities are coupled to a common mechanical resonator via radiation pressure. The two passive cavities are coupled via hopping interaction to facilitate the directional amplification between the active and passive cavities. We obtain the condition of achieving optical directional amplification and find that the direction of amplification can be controlled by the phase differences between the effective optomechanical couplings. The effects of the gain rate of the active cavity and the effective coupling strengths on the maximum gain of the amplifier are discussed. We show that the noise added to this amplifier can be greatly suppressed in the large cooperativity limit.

Amplification and Attenuation Across USArray Using Ambient Noise Wavefront Tracking

NASA Astrophysics Data System (ADS)

Bowden, Daniel C.; Tsai, Victor C.; Lin, Fan-Chi

2017-12-01

As seismic traveltime tomography continues to be refined using data from the vast USArray data set, 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 s) than can be observed with only traditional teleseismic earthquake sources. We show that the wavefront tracking approach 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 traveltime 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 3-D tomographic inversions.

Amplification of Dynamic Nuclear Polarization at 200 GHz by Arbitrary Pulse Shaping of the Electron Spin Saturation Profile.

PubMed

Kaminker, Ilia; Han, Songi

2018-06-07

Dynamic nuclear polarization (DNP) takes center stage in nuclear magnetic resonance (NMR) as a tool to amplify its signal by orders of magnitude through the transfer of polarization from electron to nuclear spins. In contrast to modern NMR and electron paramagnetic resonance (EPR) that extensively rely on pulses for spin manipulation in the time domain, the current mainstream DNP technology exclusively relies on monochromatic continuous wave (CW) irradiation. This study introduces arbitrary phase shaped pulses that constitute a train of coherent chirp pulses in the time domain at 200 GHz (7 T) to dramatically enhance the saturation bandwidth and DNP performance compared to CW DNP, yielding up to 500-fold in NMR signal enhancements. The observed improvement is attributed to the recruitment of additional electron spins contributing to DNP via the cross-effect mechanism, as experimentally confirmed by two-frequency pump-probe electron-electron double resonance (ELDOR).

Grain boundary diffusion of Dy films prepared by magnetron sputtering for sintered Nd–Fe–B magnets

NASA Astrophysics Data System (ADS)

Chen, W.; Luo, J. M.; Guan, Y. W.; Huang, Y. L.; Chen, M.; Hou, Y. H.

2018-05-01

Dy films, deposited on the surface of sintered Nd–Fe–B magnets by magnetron sputtering, were employed for grain boundary diffusion source. High coercivity sintered Nd–Fe–B magnets were successfully prepared. Effects of sputtering power and grain boundary diffusion processes (GBDP) on the microstructure and magnetic properties were investigated in detail. The dense and uniform Dy films were beneficial to prepare high coercivity magnets by GBDP. The maximum coercivity value of 1189 kA m‑1 could be shown, which was an amplification of 22.3%, compared with that of as-prepared Nd–Fe–B magnet. Furthermore, the improved remanence and maximum energy product were also achieved through tuning grain boundary diffusion processes. Our results demonstrated that the formation of (Nd, Dy)2Fe14B shell surrounding Nd2Fe14B grains and fine, uniform and continuous intergranular RE-rich phases jointly contribute to the improved coercivity.

Novel approach to quantitative polymerase chain reaction using real-time detection: application to the detection of gene amplification in breast cancer.

PubMed

Bièche, I; Olivi, M; Champème, M H; Vidaud, D; Lidereau, R; Vidaud, M

1998-11-23

Gene amplification is a common event in the progression of human cancers, and amplified oncogenes have been shown to have diagnostic, prognostic and therapeutic relevance. A kinetic quantitative polymerase-chain-reaction (PCR) method, based on fluorescent TaqMan methodology and a new instrument (ABI Prism 7700 Sequence Detection System) capable of measuring fluorescence in real-time, was used to quantify gene amplification in tumor DNA. Reactions are characterized by the point during cycling when PCR amplification is still in the exponential phase, rather than the amount of PCR product accumulated after a fixed number of cycles. None of the reaction components is limited during the exponential phase, meaning that values are highly reproducible in reactions starting with the same copy number. This greatly improves the precision of DNA quantification. Moreover, real-time PCR does not require post-PCR sample handling, thereby preventing potential PCR-product carry-over contamination; it possesses a wide dynamic range of quantification and results in much faster and higher sample throughput. The real-time PCR method, was used to develop and validate a simple and rapid assay for the detection and quantification of the 3 most frequently amplified genes (myc, ccndl and erbB2) in breast tumors. Extra copies of myc, ccndl and erbB2 were observed in 10, 23 and 15%, respectively, of 108 breast-tumor DNA; the largest observed numbers of gene copies were 4.6, 18.6 and 15.1, respectively. These results correlated well with those of Southern blotting. The use of this new semi-automated technique will make molecular analysis of human cancers simpler and more reliable, and should find broad applications in clinical and research settings.

A Simple, Inexpensive Device for Nucleic Acid Amplification without Electricity—Toward Instrument-Free Molecular Diagnostics in Low-Resource Settings

PubMed Central

LaBarre, Paul; Hawkins, Kenneth R.; Gerlach, Jay; Wilmoth, Jared; Beddoe, Andrew; Singleton, Jered; Boyle, David; Weigl, Bernhard

2011-01-01

Background Molecular assays targeted to nucleic acid (NA) markers are becoming increasingly important to medical diagnostics. However, these are typically confined to wealthy, developed countries; or, to the national reference laboratories of developing-world countries. There are many infectious diseases that are endemic in low-resource settings (LRS) where the lack of simple, instrument-free, NA diagnostic tests is a critical barrier to timely treatment. One of the primary barriers to the practicality and availability of NA assays in LRS has been the complexity and power requirements of polymerase chain reaction (PCR) instrumentation (another is sample preparation). Methodology/Principal Findings In this article, we investigate the hypothesis that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays. We assess the heater's equivalence to commercially available PCR instruments through the characterization of the temperature profiles produced, and a minimal method comparison. Versions of the prototype for several different isothermal techniques are presented. Conclusions/Significance We demonstrate that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays, and that the results of those assays are not significantly different from ones incubated in parallel in commercially available PCR instruments. These results clearly suggest the potential of the non-instrumented nucleic acid amplification (NINA) heater for molecular diagnostics in LRS. When combined with other innovations in development that eliminate power requirements for sample preparation, cold reagent storage, and readout, the NINA heater will comprise part of a kit that should enable electricity-free NA testing for many important analytes. PMID:21573065

Evidence that selected amplification of a bacterial lac frameshift allele stimulates Lac(+) reversion (adaptive mutation) with or without general hypermutability.

PubMed Central

Slechta, E Susan; Liu, Jing; Andersson, Dan I; Roth, John R

2002-01-01

In the genetic system of Cairns and Foster, a nongrowing population of an E. coli lac frameshift mutant appears to specifically accumulate Lac(+) revertants when starved on medium including lactose (adaptive mutation). This behavior has been attributed to stress-induced general mutagenesis in a subpopulation of starved cells (the hypermutable state model). We have suggested that, on the contrary, stress has no direct effect on mutability but favors only growth of cells that amplify their leaky mutant lac region (the amplification mutagenesis model). Selection enhances reversion primarily by increasing the mutant lac copy number within each developing clone on the selection plate. The observed general mutagenesis is attributed to a side effect of growth with an amplification-induction of SOS by DNA fragments released from a tandem array of lac copies. Here we show that the S. enterica version of the Cairns system shows SOS-dependent general mutagenesis and behaves in every way like the original E. coli system. In both systems, lac revertants are mutagenized during selection. Eliminating the 35-fold increase in mutation rate reduces revertant number only 2- to 4-fold. This discrepancy is due to continued growth of amplification cells until some clones manage to revert without mutagenesis solely by increasing their lac copy number. Reversion in the absence of mutagenesis is still dependent on RecA function, as expected if it depends on lac amplification (a recombination-dependent process). These observations support the amplification mutagenesis model. PMID:12136002

Smart Cup: A Minimally-Instrumented, Smartphone-Based Point-of-Care Molecular Diagnostic Device.

PubMed

Liao, Shih-Chuan; Peng, Jing; Mauk, Michael G; Awasthi, Sita; Song, Jinzhao; Friedman, Harvey; Bau, Haim H; Liu, Changchun

2016-06-28

Nucleic acid amplification-based diagnostics offer rapid, sensitive, and specific means for detecting and monitoring the progression of infectious diseases. However, this method typically requires extensive sample preparation, expensive instruments, and trained personnel. All of which hinder its use in resource-limited settings, where many infectious diseases are endemic. Here, we report on a simple, inexpensive, minimally-instrumented, smart cup platform for rapid, quantitative molecular diagnostics of pathogens at the point of care. Our smart cup takes advantage of water-triggered, exothermic chemical reaction to supply heat for the nucleic acid-based, isothermal amplification. The amplification temperature is regulated with a phase-change material (PCM). The PCM maintains the amplification reactor at a constant temperature, typically, 60-65°C, when ambient temperatures range from 12 to 35°C. To eliminate the need for an optical detector and minimize cost, we use the smartphone's flashlight to excite the fluorescent dye and the phone camera to record real-time fluorescence emission during the amplification process. The smartphone can concurrently monitor multiple amplification reactors and analyze the recorded data. Our smart cup's utility was demonstrated by amplifying and quantifying herpes simplex virus type 2 (HSV-2) with LAMP assay in our custom-made microfluidic diagnostic chip. We have consistently detected as few as 100 copies of HSV-2 viral DNA per sample. Our system does not require any lab facilities and is suitable for use at home, in the field, and in the clinic, as well as in resource-poor settings, where access to sophisticated laboratories is impractical, unaffordable, or nonexistent.

A self-heating cartridge for molecular diagnostics.

PubMed

Liu, Changchun; Mauk, Michael G; Hart, Robert; Qiu, Xianbo; Bau, Haim H

2011-08-21

A disposable, water-activated, self-heating, easy-to-use, polymeric cartridge for isothermal nucleic acid amplification and visual fluorescent detection of the amplification products is described. The device is self-contained and does not require any special instruments to operate. The cartridge integrates chemical, water-triggered, exothermic heating with temperature regulation facilitated with a phase-change material (PCM) and isothermal nucleic acid amplification. The water flows into the exothermic reactor by wicking through a porous paper. The porous paper's characteristics control the rate of water supply, which in turn controls the rate of exothermic reaction. The PCM material enables the cartridge to maintain a desired temperature independent of ambient temperatures in the range between 20 °C and 40 °C. The utility of the cartridge is demonstrated by amplifying and detecting Escherichia coli DNA with loop mediated isothermal amplification (LAMP). The device can detect consistently as few as 10 target molecules in the sample. With proper modifications, the cartridge also can work with other isothermal nucleic acid amplification technologies for detecting nucleic acids associated with various pathogens borne in blood, saliva, urine, and other body fluids as well as in water and food. The device is suitable for use at home, in the field, and in poor-resource settings, where access to sophisticated laboratories is impractical, unaffordable, or nonexistent. This journal is © The Royal Society of Chemistry 2011

High power, high contrast hybrid femtosecond laser systems

NASA Astrophysics Data System (ADS)

Dabu, Razvan

2017-06-01

For many research applications a very high laser intensity of more than 1022 W/cm2 in the focused beam is required. If a laser intensity of about 1011W/cm2 is reached on the target before the main laser pulse, the generated pre-plasma disturbs the experiment. High power femtosecond lasers must be tightly focused to get high intensity and in the same time must have a high enough intensity contrast of the temporally compressed amplified pulses. Reaching an intensity contrast in the range of 1012 represents a challenging task for a Ti:sapphire CPA laser. Hybrid femtosecond lasers combine optical parametric chirped pulsed amplification (OPCPA) in nonlinear crystals with the chirped pulse amplification (CPA) in laser active media. OPCPA provides large amplification spectral bandwidth and improves the intensity contrast of the amplified pulses. A key feature of these systems consists in the adaptation of the parametric amplification phase-matching bandwidth of nonlinear crystals to the spectral gain bandwidth of laser amplifying Ti:sapphire crystals. OPCPA in BBO crystals up to mJ energy level in the laser Front-End, followed by CPA up to ten/hundred Joules in large aperture Ti:sapphire crystals, represents a suitable solution for PW-class femtosecond lasers. The configuration and expected output beam characteristics of the hybrid amplification 2 × 10 PW ELI-NP laser are described.

A novel signal amplification technology for ELISA based on catalyzed reporter deposition. Demonstration of its applicability for measuring aflatoxin B(1).

PubMed

Bhattacharya, D; Bhattacharya, R; Dhar, T K

1999-11-19

In an earlier communication we have described a novel signal amplification technology termed Super-CARD, which is able to significantly improve antigen detection sensitivity in conventional Dot-ELISA by approximately 10(5)-fold. The method utilizes hitherto unreported synthesized electron rich proteins containing multiple phenolic groups which, when immobilized over a solid phase as blocking agent, markedly increases the signal amplification capability of the existing CARD method (Bhattacharya, R., Bhattacharya, D., Dhar, T.K., 1999. A novel signal amplification technology based on catalyzed reporter deposition and its application in a Dot-ELISA with ultra high sensitivity. J. Immunol. Methods 227, 31.). In this paper we describe the utilization of this Super-CARD amplification technique in ELISA and its applicability for the rapid determination of aflatoxin B(1) (AFB(1)) in infected seeds. Using this method under identical conditions, the increase in absorbance over the CARD method was approximately 400%. The limit of detection of AFB(1) by this method was 0.1 pg/well, the sensitivity enhancement being 5-fold over the optimized CARD ELISA. Furthermore, the total incubation time was reduced to 16 min compared to 50 min for the CARD method. Assay specificity was not adversely affected and the amount of AFB(1) measured in seed extracts correlated well with the values obtained by conventional ELISA.

Formation of template-switching artifacts by linear amplification.

PubMed

Chakravarti, Dhrubajyoti; Mailander, Paula C

2008-07-01

Linear amplification is a method of synthesizing single-stranded DNA from either a single-stranded DNA or one strand of a double-stranded DNA. In this protocol, molecules of a single primer DNA are extended by multiple rounds of DNA synthesis at high temperature using thermostable DNA polymerases. Although linear amplification generates the intended full-length single-stranded product, it is more efficient over single-stranded templates than double-stranded templates. We analyzed linear amplification over single- or double-stranded mouse H-ras DNA (exon 1-2 region). The single-stranded H-ras template yielded only the intended product. However, when the double-stranded template was used, additional artifact products were observed. Increasing the concentration of the double-stranded template produced relatively higher amounts of these artifact products. One of the artifact DNA bands could be mapped and analyzed by sequencing. It contained three template-switching products. These DNAs were formed by incomplete DNA strand extension over the template strand, followed by switching to the complementary strand at a specific Ade nucleotide within a putative hairpin sequence, from which DNA synthesis continued over the complementary strand.

Partially deuterated potassium dihydrogen phosphate optimized for ultra-broadband optical parametric amplification

NASA Astrophysics Data System (ADS)

Fujioka, K.; Fujimoto, Y.; Tsubakimoto, K.; Kawanaka, J.; Shoji, I.; Miyanaga, N.

2015-03-01

The refractive index of a potassium dihydrogen phosphate (KDP) crystal strongly depends on the deuteration fraction of the crystal. The wavelength dependence of the phase-matching angle in the near-infrared optical parametric process shows convex and concave characteristics for pure KDP and pure deuterated KDP (DKDP), respectively, when pumped by the second harmonic of Nd- or Yb-doped solid state lasers. Using these characteristics, ultra-broadband phase matching can be realized by optimization of the deuteration fraction. The refractive index of DKDP that was grown with a different deuteration fraction (known as partially deuterated KDP or pDKDP) was measured over a wide wavelength range of 0.4-1.5 μm by the minimum deviation method. The wavelength dispersions of the measured refractive indices were fitted using a modified Sellmeier equation, and the deuteration fraction dependence was analyzed using the Lorentz-Lorenz equation. The wavelength-dependent phase-matching angle for an arbitrary deuteration fraction was then calculated for optical parametric amplification with pumping at a wavelength of 526.5 nm. The results revealed that a refractive index database with precision of more than 2 × 10-5 was necessary for exact evaluation of the phase-matching condition. An ultra-broad gain bandwidth of up to 490 nm will be feasible when using the 68% pDKDP crystal.

CSDP: The seismology of continental thermal regimes

NASA Astrophysics Data System (ADS)

Aki, K.

1991-05-01

The past year continued to be extremely productive following up two major breakthroughs made in the preceding year. One of the breakthroughs was the derivation of an integral equation for time-dependent power spectra, which unified all the existing theories on seismic scattering including the radiative transfer theory for total energy and single-multiple scattering theories based on the ray approach. We successfully applied the method to the data from the United States Geological Survey (USGS) regional seismic arrays in central California, Long Valley and Island of Hawaii, and obtained convincing results on the scattering Q(sup -1) and intrinsic Q(sup -1) in these areas for the frequency range from 1 Hz to 20 Hz. The frequency dependence of scattering Q(sup -1) is, then, interpreted in terms of random medium with continuous or discrete scatterers. The other breakthrough was the application of T-matrix formulation to the seismic scattering problem. We are currently working on two dimensional inclusions with high and low velocity contrast with the surrounding medium. In addition to the above two main lines of research, we were able to use so-called 'T-phase' observed on the Island of Hawaii to map the Q value with a good spatial resolution. The T-phase is seismic waves converted from acoustic waves propagated through the sofar channel of the ocean. We found that we can eliminate remarkably well the frequency dependent recording site effect from the T-phase amplitude using the amplification factor for coda waves, further confirming the fundamental separability of source, path and site effects for coda waves, and proving the effectiveness of stochastic modeling of high-frequency seismic waves.

A multiplex primer design algorithm for target amplification of continuous genomic regions.

PubMed

Ozturk, Ahmet Rasit; Can, Tolga

2017-06-19

Targeted Next Generation Sequencing (NGS) assays are cost-efficient and reliable alternatives to Sanger sequencing. For sequencing of very large set of genes, the target enrichment approach is suitable. However, for smaller genomic regions, the target amplification method is more efficient than both the target enrichment method and Sanger sequencing. The major difficulty of the target amplification method is the preparation of amplicons, regarding required time, equipment, and labor. Multiplex PCR (MPCR) is a good solution for the mentioned problems. We propose a novel method to design MPCR primers for a continuous genomic region, following the best practices of clinically reliable PCR design processes. On an experimental setup with 48 different combinations of factors, we have shown that multiple parameters might effect finding the first feasible solution. Increasing the length of the initial primer candidate selection sequence gives better results whereas waiting for a longer time to find the first feasible solution does not have a significant impact. We generated MPCR primer designs for the HBB whole gene, MEFV coding regions, and human exons between 2000 bp to 2100 bp-long. Our benchmarking experiments show that the proposed MPCR approach is able produce reliable NGS assay primers for a given sequence in a reasonable amount of time.

Glucose acutely decreases pH of secretory granules in mouse pancreatic islets. Mechanisms and influence on insulin secretion.

PubMed

Stiernet, Patrick; Guiot, Yves; Gilon, Patrick; Henquin, Jean-Claude

2006-08-04

Glucose-induced insulin secretion requires a rise in beta-cell cytosolic Ca2+ ([Ca2+]c) that triggers exocytosis and a mechanistically unexplained amplification of the action of [Ca2+]c. Insulin granules are kept acidic by luminal pumping of protons with simultaneous Cl- uptake to maintain electroneutrality. Experiments using patched, dialyzed beta-cells prompted the suggestion that acute granule acidification by glucose underlies amplification of insulin secretion. However, others found glucose to increase granular pH in intact islets. In this study, we measured islet granular pH with Lysosensor DND-160, a fluorescent dye that permits ratiometric determination of pH < 6 in acidic compartments. Stimulation of mouse islets with glucose reversibly decreased granular pH by mechanisms that are dependent on metabolism and Cl- ions but independent of changes in [Ca2+]c and protein kinase A or C activity. Granular pH was increased by concanamycin (blocker of the vesicular type H+-ATPase) > methylamine (weak base) > Cl- omission. Concanamycin and methylamine did not alter glucose-induced [Ca2+]c increase in islets but strongly inhibited the two phases of insulin secretion. Omission of Cl- did not affect the first phase but decreased the second phase of both [Ca2+]c and insulin responses. Neither experimental condition affected the [Ca2+]c rise induced by 30 mM KCl, but the insulin responses were inhibited by concanamycin > methylamine and not affected by Cl- omission. The amplification of insulin secretion by glucose was not suppressed. We conclude that an acidic granular pH is important for insulin secretion but that the acute further acidification produced by glucose is not essential for the augmentation of secretion via the amplifying pathway.

Optofluidic analysis system for amplification-free, direct detection of Ebola infection

NASA Astrophysics Data System (ADS)

Cai, H.; Parks, J. W.; Wall, T. A.; Stott, M. A.; Stambaugh, A.; Alfson, K.; Griffiths, A.; Mathies, R. A.; Carrion, R.; Patterson, J. L.; Hawkins, A. R.; Schmidt, H.

2015-09-01

The massive outbreak of highly lethal Ebola hemorrhagic fever in West Africa illustrates the urgent need for diagnostic instruments that can identify and quantify infections rapidly, accurately, and with low complexity. Here, we report on-chip sample preparation, amplification-free detection and quantification of Ebola virus on clinical samples using hybrid optofluidic integration. Sample preparation and target preconcentration are implemented on a PDMS-based microfluidic chip (automaton), followed by single nucleic acid fluorescence detection in liquid-core optical waveguides on a silicon chip in under ten minutes. We demonstrate excellent specificity, a limit of detection of 0.2 pfu/mL and a dynamic range of thirteen orders of magnitude, far outperforming other amplification-free methods. This chip-scale approach and reduced complexity compared to gold standard RT-PCR methods is ideal for portable instruments that can provide immediate diagnosis and continued monitoring of infectious diseases at the point-of-care.

Selective Precipitation and Concentrating of Perovskite Crystals from Titanium-Bearing Slag Melt in Supergravity Field

NASA Astrophysics Data System (ADS)

Gao, Jintao; Zhong, Yiwei; Guo, Zhancheng

2016-08-01

Selective precipitation and concentrating of perovskite crystals from titanium-bearing slag melt in the supergravity field was investigated in this study. Since perovskite was the first precipitated phase from the slag melt during the cooling process, and a greater precipitation quantity and larger crystal sizes of perovskite were obtained at 1593 K to 1563 K (1320 °C to 1290 °C), concentrating of perovskite crystals from the slag melt was carried out at this temperature range in the supergravity field, at which the perovskite transforms into solid particles while the other minerals remain in the liquid melt. The layered structures appeared significantly in the sample obtained by supergravity treatment, and all the perovskite crystals moved along the supergravity direction and concentrated as the perovskite-rich phase in the bottom area, whereas the molten slag concentrated in the upper area along the opposite direction, in which it was impossible to find any perovskite crystals. With the gravity coefficient of G = 750, the mass fraction of TiO2 in the perovskite-rich phase was up to 34.65 wt pct, whereas that of the slag phase was decreased to 12.23 wt pct, and the recovery ratio of Ti in the perovskite-rich phase was up to 75.28 pct. On this basis, an amplification experimental centrifugal apparatus was exploited and the continuous experiment with larger scale was further carried out, the results confirming that selective precipitation and concentrating of perovskite crystals from the titanium-bearing slag melt by supergravity was a feasible method.

Experimental phase-space-based optical amplification of scar modes.

PubMed

Michel, C; Tascu, S; Doya, V; Aschiéri, P; Blanc, W; Legrand, O; Mortessagne, F

2012-04-01

Wave billiards which are chaotic in the geometrical limit are known to support nongeneric spatially localized modes called scar modes. The interaction of the scar modes with gain has been recently investigated in optics in microcavity lasers and vertical-cavity surface-emitting lasers. Exploiting the localization properties of scar modes in their wave-analogous phase-space representation, we report experimental results of scar mode selection by gain in a doped D-shaped optical fiber.

Phase noise mitigation of QPSK signal utilizing phase-locked multiplexing of signal harmonics and amplitude saturation.

PubMed

Mohajerin-Ariaei, Amirhossein; Ziyadi, Morteza; Chitgarha, Mohammad Reza; Almaiman, Ahmed; Cao, Yinwen; Shamee, Bishara; Yang, Jeng-Yuan; Akasaka, Youichi; Sekiya, Motoyoshi; Takasaka, Shigehiro; Sugizaki, Ryuichi; Touch, Joseph D; Tur, Moshe; Langrock, Carsten; Fejer, Martin M; Willner, Alan E

2015-07-15

We demonstrate an all-optical phase noise mitigation scheme based on the generation, delay, and coherent summation of higher order signal harmonics. The signal, its third-order harmonic, and their corresponding delayed variant conjugates create a staircase phase-transfer function that quantizes the phase of quadrature-phase-shift-keying (QPSK) signal to mitigate phase noise. The signal and the harmonics are automatically phase-locked multiplexed, avoiding the need for phase-based feedback loop and injection locking to maintain coherency. The residual phase noise converts to amplitude noise in the quantizer stage, which is suppressed by parametric amplification in the saturation regime. Phase noise reduction of ∼40% and OSNR-gain of ∼3  dB at BER 10(-3) are experimentally demonstrated for 20- and 30-Gbaud QPSK input signals.

A parity-time symmetric coherent plasmonic absorber-amplifier

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baum, Brian, E-mail: bbaum@stanford.edu; Dionne, Jennifer, E-mail: jdionne@stanford.edu; Alaeian, Hadiseh

Non-Hermitian parity-time (PT)-symmetric optical potentials have led to a new class of unidirectional photonic components based on the spatially symmetric and balanced inclusion of loss and gain. While most proposed and implemented PT-symmetric optical devices have wavelength-scale dimensions, no physical constraints preclude development of subwavelength PT-symmetric components. We theoretically demonstrate a nanoscale PT-symmetric, all-optical plasmonic modulator capable of phase-controlled amplification and directional absorption. The modulator consists of two deeply subwavelength channels composed of either gain or loss dielectric material, embedded in a metallic cladding. When illuminating on-resonance by two counter-propagating plane waves, the aperture's total output can be modulated bymore » changing the phase offset between the two waves. Modulation depths are greater than 10 dB, with output power varying from less than one half of the incident power to more than six times amplification. Off-resonance, the aperture possesses strong phase-controlled directionality with the output from one side varying from perfect absorption to strong scattering and transmission. The device design provides a platform for nanoscale all-optical modulators with gain while potentially enabling coherent perfect absorption and lasing in a single, compact structure.« less

Electricity-free amplification and detection for molecular point-of-care diagnosis of HIV-1.

PubMed

Singleton, Jered; Osborn, Jennifer L; Lillis, Lorraine; Hawkins, Kenneth; Guelig, Dylan; Price, Will; Johns, Rachel; Ebels, Kelly; Boyle, David; Weigl, Bernhard; LaBarre, Paul

2014-01-01

In resource-limited settings, the lack of decentralized molecular diagnostic testing and sparse access to centralized medical facilities can present a critical barrier to timely diagnosis, treatment, and subsequent control and elimination of infectious diseases. Isothermal nucleic acid amplification methods, including reverse transcription loop-mediated isothermal amplification (RT-LAMP), are well-suited for decentralized point-of-care molecular testing in minimal infrastructure laboratories since they significantly reduce the complexity of equipment and power requirements. Despite reduced complexity, however, there is still a need for a constant heat source to enable isothermal nucleic acid amplification. This requirement poses significant challenges for laboratories in developing countries where electricity is often unreliable or unavailable. To address this need, we previously developed a low-cost, electricity-free heater using an exothermic reaction thermally coupled with a phase change material. This heater achieved acceptable performance, but exhibited considerable variability. Furthermore, as an enabling technology, the heater was an incomplete diagnostic solution. Here we describe a more precise, affordable, and robust heater design with thermal standard deviation <0.5°C at operating temperature, a cost of approximately US$.06 per test for heater reaction materials, and an ambient temperature operating range from 16°C to 30°C. We also pair the heater with nucleic acid lateral flow (NALF)-detection for a visual readout. To further illustrate the utility of the electricity-free heater and NALF-detection platform, we demonstrate sensitive and repeatable detection of HIV-1 with a ß-actin positive internal amplification control from processed sample to result in less than 80 minutes. Together, these elements are building blocks for an electricity-free platform capable of isothermal amplification and detection of a variety of pathogens.

Electricity-Free Amplification and Detection for Molecular Point-of-Care Diagnosis of HIV-1

PubMed Central

Singleton, Jered; Osborn, Jennifer L.; Lillis, Lorraine; Hawkins, Kenneth; Guelig, Dylan; Price, Will; Johns, Rachel; Ebels, Kelly; Boyle, David; Weigl, Bernhard; LaBarre, Paul

2014-01-01

In resource-limited settings, the lack of decentralized molecular diagnostic testing and sparse access to centralized medical facilities can present a critical barrier to timely diagnosis, treatment, and subsequent control and elimination of infectious diseases. Isothermal nucleic acid amplification methods, including reverse transcription loop-mediated isothermal amplification (RT-LAMP), are well-suited for decentralized point-of-care molecular testing in minimal infrastructure laboratories since they significantly reduce the complexity of equipment and power requirements. Despite reduced complexity, however, there is still a need for a constant heat source to enable isothermal nucleic acid amplification. This requirement poses significant challenges for laboratories in developing countries where electricity is often unreliable or unavailable. To address this need, we previously developed a low-cost, electricity-free heater using an exothermic reaction thermally coupled with a phase change material. This heater achieved acceptable performance, but exhibited considerable variability. Furthermore, as an enabling technology, the heater was an incomplete diagnostic solution. Here we describe a more precise, affordable, and robust heater design with thermal standard deviation <0.5°C at operating temperature, a cost of approximately US$.06 per test for heater reaction materials, and an ambient temperature operating range from 16°C to 30°C. We also pair the heater with nucleic acid lateral flow (NALF)-detection for a visual readout. To further illustrate the utility of the electricity-free heater and NALF-detection platform, we demonstrate sensitive and repeatable detection of HIV-1 with a ß-actin positive internal amplification control from processed sample to result in less than 80 minutes. Together, these elements are building blocks for an electricity-free platform capable of isothermal amplification and detection of a variety of pathogens. PMID:25426953

HPV-18 E6 mutants reveal p53 modulation of viral DNA amplification in organotypic cultures

PubMed Central

Kho, Eun-Young; Wang, Hsu-Kun; Banerjee, N. Sanjib; Broker, Thomas R.; Chow, Louise T.

2013-01-01

Human papillomaviruses (HPVs) amplify in differentiated strata of a squamous epithelium. The HPV E7 protein destabilizes the p130/retinoblastoma susceptibility protein family of tumor suppressors and reactivates S-phase reentry, thereby facilitating viral DNA amplification. The high-risk HPV E6 protein destabilizes the p53 tumor suppressor and many other host proteins. However, the critical E6 targets relevant to viral DNA amplification have not been identified, because functionally significant E6 mutants are not stably maintained in transfected cells. Using Cre-loxP recombination, which efficiently generates HPV genomic plasmids in transfected primary human keratinocytes, we have recapitulated a highly productive infection of HPV-18 in organotypic epithelial cultures. By using this system, we now report the characterization of four HPV-18 E6 mutations. An E6 null mutant accumulated high levels of p53 and amplified very poorly. p53 siRNA or ectopic WT E6 partially restored amplification, whereas three missense E6 mutations that did not effectively destabilize p53 complemented the null mutant poorly. Unexpectedly, in cis, two of the missense mutants amplified, albeit to a lower extent than the WT and only in cells with undetectable p53. These observations and others implicate p53 and additional host proteins in regulating viral DNA amplification and also suggest an inhibitory effect of E6 overexpression. We show that high levels of viral DNA amplification are critical for late protein expression and report several previously undescribed viral RNAs, including bicistronic transcripts predicted to encode E5 and L2 or an alternative form of E1^E4 and L1. PMID:23572574

Molecular Medicine II: Hormone Dependent Cancers

DTIC Science & Technology

2005-04-01

multimode, live-cell videomicroscopy - we are analyzing the cycles of centrosome amplification in living S-phase arrested cells. Finally, we will directly...living cells by time-lapse multi-mode videomicroscopy . The key construct for our work is the generation of a mammalian somatic cell line stably expressing

Non-volatile Clocked Spin Wave Interconnect for Beyond-CMOS Nanomagnet Pipelines

PubMed Central

Dutta, Sourav; Chang, Sou-Chi; Kani, Nickvash; Nikonov, Dmitri E.; Manipatruni, Sasikanth; Young, Ian A.; Naeemi, Azad

2015-01-01

The possibility of using spin waves for information transmission and processing has been an area of active research due to the unique ability to manipulate the amplitude and phase of the spin waves for building complex logic circuits with less physical resources and low power consumption. Previous proposals on spin wave logic circuits have suggested the idea of utilizing the magneto-electric effect for spin wave amplification and amplitude- or phase-dependent switching of magneto-electric cells. Here, we propose a comprehensive scheme for building a clocked non-volatile spin wave device by introducing a charge-to-spin converter that translates information from electrical domain to spin domain, magneto-electric spin wave repeaters that operate in three different regimes - spin wave transmitter, non-volatile memory and spin wave detector, and a novel clocking scheme that ensures sequential transmission of information and non-reciprocity. The proposed device satisfies the five essential requirements for logic application: nonlinearity, amplification, concatenability, feedback prevention, and complete set of Boolean operations. PMID:25955353

140 W peak power laser system tunable in the LWIR.

PubMed

Gutty, François; Grisard, Arnaud; Larat, Christian; Papillon, Dominique; Schwarz, Muriel; Gerard, Bruno; Ostendorf, Ralf; Rattunde, Marcel; Wagner, Joachim; Lallier, Eric

2017-08-07

We present a high peak power rapidly tunable laser system in the long-wave infrared comprising an external-cavity quantum cascade laser (EC-QCL) broadly tunable from 8 to 10 µm and an optical parametric amplifier (OPA) based on quasi phase-matching in orientation-patterned gallium arsenide (OP-GaAs) of fixed grating period. The nonlinear crystal is pumped by a pulsed fiber laser system to achieve efficient amplification in the OPA. Quasi phase-matching remains satisfied when the EC-QCL wavelength is swept from 8 to 10 µm with a crystal of fixed grating period through tuning the pump laser source around 2 µm. The OPA demonstrates parametric amplification from 8 µm to 10 µm and achieves output peak powers up to 140 W with spectral linewidths below 3.5 cm -1 . The beam profile quality (M 2 ) remains below 3.4 in both horizontal and vertical directions. Compared to the EC-QCL, the linewidth broadening is attributed to a coupling with the OPA.

Reverse phase protein microarrays: fluorometric and colorimetric detection.

PubMed

Gallagher, Rosa I; Silvestri, Alessandra; Petricoin, Emanuel F; Liotta, Lance A; Espina, Virginia

2011-01-01

The Reverse Phase Protein Microarray (RPMA) is an array platform used to quantitate proteins and their posttranslationally modified forms. RPMAs are applicable for profiling key cellular signaling pathways and protein networks, allowing direct comparison of the activation state of proteins from multiple samples within the same array. The RPMA format consists of proteins immobilized directly on a nitrocellulose substratum. The analyte is subsequently probed with a primary antibody and a series of reagents for signal amplification and detection. Due to the diversity, low concentration, and large dynamic range of protein analytes, RPMAs require stringent signal amplification methods, high quality image acquisition, and software capable of precisely analyzing spot intensities on an array. Microarray detection strategies can be either fluorescent or colorimetric. The choice of a detection system depends on (a) the expected analyte concentration, (b) type of microarray imaging system, and (c) type of sample. The focus of this chapter is to describe RPMA detection and imaging using fluorescent and colorimetric (diaminobenzidine (DAB)) methods.

Development of microbial genome-probing microarrays using digital multiple displacement amplification of uncultivated microbial single cells.

PubMed

Chang, Ho-Won; Sung, Youlboong; Kim, Kyoung-Ho; Nam, Young-Do; Roh, Seong Woon; Kim, Min-Soo; Jeon, Che Ok; Bae, Jin-Woo

2008-08-15

A crucial problem in the use of previously developed genome-probing microarrays (GPM) has been the inability to use uncultivated bacterial genomes to take advantage of the high sensitivity and specificity of GPM in microbial detection and monitoring. We show here a method, digital multiple displacement amplification (MDA), to amplify and analyze various genomes obtained from single uncultivated bacterial cells. We used 15 genomes from key microbes involved in dichloromethane (DCM)-dechlorinating enrichment as microarray probes to uncover the bacterial population dynamics of samples without PCR amplification. Genomic DNA amplified from single cells originating from uncultured bacteria with 80.3-99.4% similarity to 16S rRNA genes of cultivated bacteria. The digital MDA-GPM method successfully monitored the dynamics of DCM-dechlorinating communities from different phases of enrichment status. Without a priori knowledge of microbial diversity, the digital MDA-GPM method could be designed to monitor most microbial populations in a given environmental sample.

Gain and frequency tuning within the mouse cochlear apex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oghalai, John S.; Raphael, Patrick D.; Gao, Simon

Normal mammalian hearing requires cochlear outer hair cell active processes that amplify the traveling wave with high gain and sharp tuning, termed cochlear amplification. We have used optical coherence tomography to study cochlear amplification within the apical turn of the mouse cochlea. We measured not only classical basilar membrane vibratory tuning curves but also vibratory responses from the rest of the tissues that compose the organ of Corti. Basilar membrane tuning was sharp in live mice and broad in dead mice, whereas other regions of the organ of Corti demonstrated phase shifts consistent with additional filtering beyond that provided bymore » basilar membrane mechanics. We use these experimental data to support a conceptual framework of how cochlear amplification is tuned within the mouse cochlear apex. We will also study transgenic mice with targeted mutations that affect different biomechanical aspects of the organ of Corti in an effort to localize the underlying processes that produce this additional filtering.« less

Enhanced Arctic Amplification Began at the Mid-Brunhes Event ~400,000 years ago.

PubMed

Cronin, T M; Dwyer, G S; Caverly, E K; Farmer, J; DeNinno, L H; Rodriguez-Lazaro, J; Gemery, L

2017-11-03

Arctic Ocean temperatures influence ecosystems, sea ice, species diversity, biogeochemical cycling, seafloor methane stability, deep-sea circulation, and CO 2 cycling. Today's Arctic Ocean and surrounding regions are undergoing climatic changes often attributed to "Arctic amplification" - that is, amplified warming in Arctic regions due to sea-ice loss and other processes, relative to global mean temperature. However, the long-term evolution of Arctic amplification is poorly constrained due to lack of continuous sediment proxy records of Arctic Ocean temperature, sea ice cover and circulation. Here we present reconstructions of Arctic Ocean intermediate depth water (AIW) temperatures and sea-ice cover spanning the last ~ 1.5 million years (Ma) of orbitally-paced glacial/interglacial cycles (GIC). Using Mg/Ca paleothermometry of the ostracode Krithe and sea-ice planktic and benthic indicator species, we suggest that the Mid-Brunhes Event (MBE), a major climate transition ~ 400-350 ka, involved fundamental changes in AIW temperature and sea-ice variability. Enhanced Arctic amplification at the MBE suggests a major climate threshold was reached at ~ 400 ka involving Atlantic Meridional Overturning Circulation (AMOC), inflowing warm Atlantic Layer water, ice sheet, sea-ice and ice-shelf feedbacks, and sensitivity to higher post-MBE interglacial CO 2 concentrations.

Methods and devices based on brillouin selective sideband amplification

NASA Technical Reports Server (NTRS)

Yao, X. Steve (Inventor)

2003-01-01

Opto-electronic devices and techniques using Brillouin scattering to select a sideband in a modulated optical carrier signal for amplification. Two lasers respectively provide a carrier signal beam and a Brillouin pump beam which are fed into an Brillouin optical medium in opposite directions. The relative frequency separation between the lasers is adjusted to align the frequency of the backscattered Brillouin signal with a desired sideband in the carrier signal to effect a Brillouin gain on the sideband. This effect can be used to implement photonic RF signal mixing and conversion with gain, conversion from phase modulation to amplitude modulation, photonic RF frequency multiplication, optical and RF pulse generation and manipulation, and frequency-locking of lasers.

Kinetic characterisation of primer mismatches in allele-specific PCR: a quantitative assessment.

PubMed

Waterfall, Christy M; Eisenthal, Robert; Cobb, Benjamin D

2002-12-20

A novel method of estimating the kinetic parameters of Taq DNA polymerase during rapid cycle PCR is presented. A model was constructed using a simplified sigmoid function to represent substrate accumulation during PCR in combination with the general equation describing high substrate inhibition for Michaelis-Menten enzymes. The PCR progress curve was viewed as a series of independent reactions where initial rates were accurately measured for each cycle. Kinetic parameters were obtained for allele-specific PCR (AS-PCR) amplification to examine the effect of mismatches on amplification. A high degree of correlation was obtained providing evidence of substrate inhibition as a major cause of the plateau phase that occurs in the later cycles of PCR.

Simplifying the circuit of Josephson parametric converters

NASA Astrophysics Data System (ADS)

Abdo, Baleegh; Brink, Markus; Chavez-Garcia, Jose; Keefe, George

Josephson parametric converters (JPCs) are quantum-limited three-wave mixing devices that can play various important roles in quantum information processing in the microwave domain, including amplification of quantum signals, transduction of quantum information, remote entanglement of qubits, nonreciprocal amplification, and circulation of signals. However, the input-output and biasing circuit of a state-of-the-art JPC consists of bulky components, i.e. two commercial off-chip broadband 180-degree hybrids, four phase-matched short coax cables, and one superconducting magnetic coil. Such bulky hardware significantly hinders the integration of JPCs in scalable quantum computing architectures. In my talk, I will present ideas on how to simplify the JPC circuit and show preliminary experimental results

Dynamical mechanisms of Arctic amplification.

PubMed

Dethloff, Klaus; Handorf, Dörthe; Jaiser, Ralf; Rinke, Annette; Klinghammer, Pia

2018-05-12

The Arctic has become a hot spot of climate change, but the nonlinear interactions between regional and global scales in the coupled climate system responsible for Arctic amplification are not well understood and insufficiently described in climate models. Here, we compare reanalysis data with model simulations for low and high Arctic sea ice conditions to identify model biases with respect to atmospheric Arctic-mid-latitude linkages. We show that an appropriate description of Arctic sea ice forcing is able to reproduce the observed winter cooling in mid-latitudes as result of improved tropospheric-stratospheric planetary wave propagation triggering a negative phase of the Arctic Oscillation/North Atlantic Oscillation in late winter. © 2018 New York Academy of Sciences.

Impact of pumping configuration on all-fibered femtosecond chirped pulse amplification

NASA Astrophysics Data System (ADS)

Lecourt, Jean-Bernard; Duterte, Charles; Bertrand, Anthony; Liégeois, Flavien; Hernandez, Yves; Giannone, Domenico

2008-04-01

We experimentally compared the co- and counter-propagative pumping scheme for the amplification of ultra-short optical pulses. According to pumping direction we show that optical pulses with a duration of 75 fs and 100mW of average output power can be obtained for co-propagative pumping, while pulse duration is never shorter than 400 fs for the counter-propagative case. We show that the impact of non-linear effects on pulse propagation is different for the two pumping configurations. We assume that Self Phase Modulation (SPM) is the main effect in the copropagative case, whereas the impact of Stimulated Raman Scattering is bigger for the counter-propagative case.

Molecular MRI in the Earth's Magnetic Field Using Continuous Hyperpolarization of a Biomolecule in Water.

PubMed

Rovedo, Philipp; Knecht, Stephan; Bäumlisberger, Tim; Cremer, Anna Lena; Duckett, Simon B; Mewis, Ryan E; Green, Gary G R; Burns, Michael; Rayner, Peter J; Leibfritz, Dieter; Korvink, Jan G; Hennig, Jürgen; Pütz, Gerhard; von Elverfeldt, Dominik; Hövener, Jan-Bernd

2016-06-30

In this work, we illustrate a method to continuously hyperpolarize a biomolecule, nicotinamide, in water using parahydrogen and signal amplification by reversible exchange (SABRE). Building on the preparation procedure described recently by Truong et al. [ J. Phys. Chem. B , 2014 , 118 , 13882 - 13889 ], aqueous solutions of nicotinamide and an Ir-IMes catalyst were prepared for low-field NMR and MRI. The (1)H-polarization was continuously renewed and monitored by NMR experiments at 5.9 mT for more than 1000 s. The polarization achieved corresponds to that induced by a 46 T magnet (P = 1.6 × 10(-4)) or an enhancement of 10(4). The polarization persisted, although reduced, if cell culture medium (DPBS with Ca(2+) and Mg(2+)) or human cells (HL-60) were added, but was no longer observable after the addition of human blood. Using a portable MRI unit, fast (1)H-MRI was enabled by cycling the magnetic field between 5 mT and the Earth's field for hyperpolarization and imaging, respectively. A model describing the underlying spin physics was developed that revealed a polarization pattern depending on both contact time and magnetic field. Furthermore, the model predicts an opposite phase of the dihydrogen and substrate signal after one exchange, which is likely to result in the cancelation of some signal at low field.

Loss resilience for two-qubit state transmission using distributed phase sensitive amplification

DOE PAGES

Dailey, James; Agarwal, Anjali; Toliver, Paul; ...

2015-11-12

We transmit phase-encoded non-orthogonal quantum states through a 5-km long fibre-based distributed optical phase-sensitive amplifier (OPSA) using telecom-wavelength photonic qubit pairs. The gain is set to equal the transmission loss to probabilistically preserve input states during transmission. While neither state is optimally aligned to the OPSA, each input state is equally amplified with no measurable degradation in state quality. These results promise a new approach to reduce the effects of loss by encoding quantum information in a two-qubit Hilbert space which is designed to benefit from transmission through an OPSA.

Loss resilience for two-qubit state transmission using distributed phase sensitive amplification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dailey, James; Agarwal, Anjali; Toliver, Paul

We transmit phase-encoded non-orthogonal quantum states through a 5-km long fibre-based distributed optical phase-sensitive amplifier (OPSA) using telecom-wavelength photonic qubit pairs. The gain is set to equal the transmission loss to probabilistically preserve input states during transmission. While neither state is optimally aligned to the OPSA, each input state is equally amplified with no measurable degradation in state quality. These results promise a new approach to reduce the effects of loss by encoding quantum information in a two-qubit Hilbert space which is designed to benefit from transmission through an OPSA.

Carrier-envelope phase control using linear electro-optic effect.

PubMed

Gobert, O; Paul, P M; Hergott, J F; Tcherbakoff, O; Lepetit, F; 'Oliveira, P D; Viala, F; Comte, M

2011-03-14

We present a new method to control the Carrier-Envelope Phase of ultra-short laser pulses by using the linear Electro-Optic Effect. Experimental demonstration is carried out on a Chirped Pulse Amplification based laser. Phase shifts greater than π radian can be obtained by applying moderate voltage on a LiNbO3 crystal with practically no changes to all other parameters of the pulse with the exception of its group delay. Time response of the Electro-Optic effect makes possible shaping at a high repetition rate or stabilization of the CEP of ultra short CPA laser systems.

Nuclear localisation of LASP-1 correlates with poor long-term survival in female breast cancer.

PubMed

Frietsch, J J; Grunewald, T G P; Jasper, S; Kammerer, U; Herterich, S; Kapp, M; Honig, A; Butt, E

2010-05-25

LIM and SH3 protein 1 (LASP-1) is a nucleo-cytoplasmatic signalling protein involved in cell proliferation and migration and is upregulated in breast cancer in vitro studies have shown that LASP-1 might be regulated by prostate-derived ETS factor (PDEF), p53 and/or LASP1 gene amplification. This current study analysed the prognostic significance of LASP-1 on overall survival (OS) in 177 breast cancer patients and addressed the suggested mechanisms of LASP-1-regulation. Nucleo-cytoplasmatic LASP-1-positivity of breast carcinoma samples was correlated with long-term survival, clinicopathological parameters, Ki67-positivity and PDEF expression. Rate of LASP1 amplification was determined in micro-dissected primary breast cancer cells using quantitative RT-PCR. Cell-phase dependency of nuclear LASP-1-localisation was studied in synchronised cells. In addition, LASP-1, PDEF and p53 expression was compared in cell lines of different tumour entities to define principles for LASP-1-regulation. We showed that LASP-1 overexpression is not due to LASP1 gene amplification. Moreover, no correlation between p53-mutations or PDEF-expression and LASP-1-status was observed. However, nuclear LASP-1-localisation in breast carcinomas is increased during proliferation with peak in G2/M-phase and correlated significantly with Ki67-positivity and poor OS. Our results provide evidence that nuclear LASP-1-positivity may serve as a negative prognostic indicator for long-term survival of breast cancer patients.

A first-in-human phase I study of SAR125844, a selective MET tyrosine kinase inhibitor, in patients with advanced solid tumours with MET amplification.

PubMed

Angevin, Eric; Spitaleri, Gianluca; Rodon, Jordi; Dotti, Katia; Isambert, Nicolas; Salvagni, Stefania; Moreno, Victor; Assadourian, Sylvie; Gomez, Corinne; Harnois, Marzia; Hollebecque, Antoine; Azaro, Analia; Hervieu, Alice; Rihawi, Karim; De Marinis, Filippo

2017-12-01

Dysregulated MET signalling is implicated in oncogenesis. The safety and preliminary efficacy of a highly selective MET kinase inhibitor (SAR125844) was investigated in patients with advanced solid tumours and MET dysregulation. This was a phase I dose-escalation (3 + 3 design [50-740 mg/m 2 ]) and dose-expansion study. In the dose escalation, patients had high total MET (t-MET) expression by immunohistochemistry (IHC) or MET amplification by fluorescence in situ hybridisation. In the dose expansion, patients had MET amplification (including a subset of patients with non-small cell lung cancer [NSCLC]) or phosphorylated-MET (p-MET) expression (IHC). Objectives were determination of maximum tolerated dose (MTD) of once-weekly intravenous SAR125844 based on dose-limiting toxicities; safety and pharmacokinetic profile; preliminary efficacy of SAR125844 MTD in the expansion cohort. In total, 72 patients were enrolled: dose escalation, N = 33; dose expansion, N = 39; 570 mg/m 2 was established as the MTD. Most frequent treatment-emergent adverse events (AEs) were asthenia/fatigue (58.3%), nausea (31.9%), and abdominal pain, constipation, and dyspnea (27.8% for each); 58.3% of patients reported grade 3 AEs (19.4% were treatment related). Of the 29 evaluable patients with MET amplification treated at 570 mg/m 2 , five achieved a partial response, including four of 22 with NSCLC; 17 patients had stable disease. No response was observed in patients with high p-MET solid tumours. There was no correlation between tumour response and t-MET status or MET gene copy number. The MTD of once-weekly SAR125844 was 570 mg/m 2 ; SAR125844 was well tolerated, with significant antitumour activity in patients with MET-amplified NSCLC. NCT01391533. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Investigation on earthquake ground motions observed along a north-south survey line in the Kumamoto Plain, during the aftershocks of 2016 Kumamoto earthquake

NASA Astrophysics Data System (ADS)

Tsuno, S.; Korenaga, M.; Okamoto, K.; Chimoto, K.; Yamanaka, H.; Yamada, N.; Matsushima, T.

2017-12-01

To evaluate local site effects in the Kumamoto Plain, we installed 15 temporary seismic stations along the north-south survey line, after the 2016 Kumamoto earthquake foreshock (Mj 6.4). In this report, to investigate earthquake ground motions observed along the north-south survey line, we estimated site amplification factors from weak ground motion data and estimated S-wave velocity structures by array microtremor observations at temporary seismic stations. We installed 15 temporary seismic stations at an interval of 300m to 2.5km along the north-south survey line. We estimated site amplification factors, with a station at Mt. Kinbo as a reference. Site amplification factors at the middle part and the southern part along the survey line, located in the alluvial lowland, were dominated in the frequency of 1-2Hz. On the other hand, site amplification factors at the northern part along the survey line were dominated in the frequency of 2-5Hz. It suggests that the ground profiles near the surface are complicate along this north-south survey line in the Kumamoto Plain. Therefore, we performed array microtremor observations at the temporary seismic stations, to estimate S-wave velocity structures along the north-south survey line. We obtained phase velocities of Rayleigh waves by the SPAC method and estimated S-wave velocity structures by applying the Genetic Algorism to those phase velocity. The low velocity layer with a thickness of around 15m was deposited on the surface at sites located in the alluvial lowland. Finally, we compared the distribution of PGAs observed along the north-south survey line to AVs30 estimated by S-wave velocity structures. As a result, PGAs along the survey line were strongly concerned by AVs30. We concluded that earthquake ground motions in the frequency of more than 1Hz observed in this north-south survey line were excited by the low velocity layer near the surface.

Multi-delay, phase coherent pulse pair generation for precision Ramsey-frequency comb spectroscopy.

PubMed

Morgenweg, J; Eikema, K S E

2013-03-11

We demonstrate the generation of phase-stable mJ-pulse pairs at programmable inter-pulse delays up to hundreds of nanoseconds. A detailed investigation of potential sources for phase shifts during the parametric amplification of the selected pulses from a Ti:Sapphire frequency comb is presented, both numerically and experimentally. It is shown that within the statistical error of the phase measurement of 10 mrad, there is no dependence of the differential phase shift over the investigated inter-pulse delay range of more than 300 ns. In combination with nonlinear upconversion of the amplified pulses, the presented system will potentially enable short wavelength (<100 nm), multi-transition Ramsey-frequency comb spectroscopy at the kHz-level.

Phase-I investigation of high-efficiency power amplifiers for 325 and 650 MHz

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raab, Frederick

2018-01-27

This Phase-I SBIR grant investigated techniques for high-efficiency power amplification for DoE particle accelerators such as Project X that operate at 325 and 650 MHz. The recommended system achieves high efficiency, high reliability, and hot-swap capability by integrating class-F power amplifiers, class-S modulators, power combiners, and a digital signal processor. Experimental evaluations demonstrate the production of 120 W per transistor with overall efficiencies from 86 percent at 325 MHz and 80 percent at 650 MHz.

News and views in discontinuous phase transitions

NASA Astrophysics Data System (ADS)

Nagler, Jan

2014-03-01

Recent progress in the theory of discontinuous percolation allow us to better understand the the sudden emergence of large-scale connectedness both in networked systems and on the lattice. We analytically study mechanisms for the amplification of critical fluctuations at the phase transition point, non-self-averaging and power law fluctuations. A single event analysis allow to establish criteria for discontinuous percolation transitions, even on the high-dimensional lattice. Some applications such as salad bowl percolation, and inverse fragmentation are discussed.

Two passive mechanical conditions modulate power generation by the outer hair cells

PubMed Central

Gracewski, Sheryl M.

2017-01-01

In the mammalian cochlea, small vibrations of the sensory epithelium are amplified due to active electro-mechanical feedback of the outer hair cells. The level of amplification is greater in the base than in the apex of the cochlea. Theoretical studies have used longitudinally varying active feedback properties to reproduce the location-dependent amplification. The active feedback force has been considered to be proportional to the basilar membrane displacement or velocity. An underlying assumption was that organ of Corti mechanics are governed by rigid body kinematics. However, recent progress in vibration measurement techniques reveals that organ of Corti mechanics are too complicated to be fully represented with rigid body kinematics. In this study, two components of the active feedback are considered explicitly—organ of Corti mechanics, and outer hair cell electro-mechanics. Physiological properties for the outer hair cells were incorporated, such as the active force gain, mechano-transduction properties, and membrane RC time constant. Instead of a kinematical model, a fully deformable 3D finite element model was used. We show that the organ of Corti mechanics dictate the longitudinal trend of cochlear amplification. Specifically, our results suggest that two mechanical conditions are responsible for location-dependent cochlear amplification. First, the phase of the outer hair cell’s somatic force with respect to its elongation rate varies along the cochlear length. Second, the local stiffness of the organ of Corti complex felt by individual outer hair cells varies along the cochlear length. We describe how these two mechanical conditions result in greater amplification toward the base of the cochlea. PMID:28880884

Low Cost Extraction and Isothermal Amplification of DNA for Infectious Diarrhea Diagnosis

PubMed Central

Huang, Shichu; Do, Jaephil; Mahalanabis, Madhumita; Fan, Andy; Zhao, Lei; Jepeal, Lisa; Singh, Satish K.; Klapperich, Catherine M.

2013-01-01

In order to counter the common perception that molecular diagnostics are too complicated to work in low resource settings, we have performed a difficult sample preparation and DNA amplification protocol using instrumentation designed to be operated without wall or battery power. In this work we have combined a nearly electricity-free nucleic acid extraction process with an electricity-free isothermal amplification assay to detect the presence of Clostridium difficile (C. difficile) DNA in the stool of infected patients. We used helicase-dependent isothermal amplification (HDA) to amplify the DNA in a low-cost, thermoplastic reaction chip heated with a pair of commercially available toe warmers, while using a simple Styrofoam insulator. DNA was extracted from known positive and negative stool samples. The DNA extraction protocol utilized an air pressure driven solid phase extraction device run using a standard bicycle pump. The simple heater setup required no electricity or battery and was capable of maintaining the temperature at 65°C±2°C for 55 min, suitable for repeatable HDA amplification. Experiments were performed to explore the adaptability of the system for use in a range of ambient conditions. When compared to a traditional centrifuge extraction protocol and a laboratory thermocycler, this disposable, no power platform achieved approximately the same lower limit of detection (1.25×10−2 pg of C. difficile DNA) while requiring much less raw material and a fraction of the lab infrastructure and cost. This proof of concept study could greatly impact the accessibility of molecular assays for applications in global health. PMID:23555883

Pathways of Prion Spread during Early Chronic Wasting Disease in Deer

PubMed Central

Hoover, Clare E.; Davenport, Kristen A.; Henderson, Davin M.; Denkers, Nathaniel D.; Mathiason, Candace K.; Soto, Claudio; Zabel, Mark D.

2017-01-01

ABSTRACT Among prion infections, two scenarios of prion spread are generally observed: (i) early lymphoid tissue replication or (ii) direct neuroinvasion without substantial antecedent lymphoid amplification. In nature, cervids are infected with chronic wasting disease (CWD) prions by oral and nasal mucosal exposure, and studies of early CWD pathogenesis have implicated pharyngeal lymphoid tissue as the earliest sites of prion accumulation. However, knowledge of chronological events in prion spread during early infection remains incomplete. To investigate this knowledge gap in early CWD pathogenesis, we exposed white-tailed deer to CWD prions by mucosal routes and performed serial necropsies to assess PrPCWD tissue distribution by real-time quaking-induced conversion (RT-QuIC) and tyramide signal amplification immunohistochemistry (TSA-IHC). Although PrPCWD was not detected by either method in the initial days (1 and 3) postexposure, we observed PrPCWD seeding activity and follicular immunoreactivity in oropharyngeal lymphoid tissues at 1 and 2 months postexposure (MPE). At 3 MPE, PrPCWD replication had expanded to all systemic lymphoid tissues. By 4 MPE, the PrPCWD burden in all lymphoid tissues had increased and approached levels observed in terminal disease, yet there was no evidence of nervous system invasion. These results indicate the first site of CWD prion entry is in the oropharynx, and the initial phase of prion amplification occurs in the oropharyngeal lymphoid tissues followed by rapid dissemination to systemic lymphoid tissues. This lymphoid replication phase appears to precede neuroinvasion. IMPORTANCE Chronic wasting disease (CWD) is a universally fatal transmissible spongiform encephalopathy affecting cervids, and natural infection occurs through oral and nasal mucosal exposure to infectious prions. Terminal disease is characterized by PrPCWD accumulation in the brain and lymphoid tissues of affected animals. However, the initial sites of prion accumulation and pathways of prion spread during early CWD infection remain unknown. To investigate the chronological events of early prion pathogenesis, we exposed deer to CWD prions and monitored the tissue distribution of PrPCWD over the first 4 months of infection. We show CWD uptake occurs in the oropharynx with initial prion replication in the draining oropharyngeal lymphoid tissues, rapidly followed by dissemination to systemic lymphoid tissues without evidence of neuroinvasion. These data highlight the two phases of CWD infection: a robust prion amplification in systemic lymphoid tissues prior to neuroinvasion and establishment of a carrier state. PMID:28250130

Inkjet Printing Based Droplet Generation for Integrated Online Digital Polymerase Chain Reaction.

PubMed

Zhang, Weifei; Li, Nan; Koga, Daisuke; Zhang, Yong; Zeng, Hulie; Nakajima, Hizuru; Lin, Jin-Ming; Uchiyama, Katsumi

2018-04-17

We report on the development of a novel and flexible online digital polymerase chain reaction (dPCR) system. The system was composed of three parts: an inkjet for generating the droplets, a coiled fused-silica capillary for thermal cycling, and a laser-induced fluorescence detector (LIFD) for positive droplet counting. Upon inkjet printing, monodisperse droplets were continuously generated in the oil phase and then introduced into the capillary in the form of a stable dispersion. The droplets containing one or zero molecules of target DNA passed through the helical capillary that was attached to a cylindrical thermal cycler for PCR amplification, resulting in the generation of fluorescence for the DNA-positive droplet. After 36 PCR cycles, the fluorescence signal intensity was detected by laser-induced fluorescence located at the downstream of the capillary, followed by a positive/negative counting. The present system was successfully applied to the absolute quantification of the HPV sequence in Caski cells with dynamic ranges spanning 4 orders of magnitude.

Theory and Modeling of Petawatt Laser Pulse Propagation in Low Density Plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shadwick, Bradley A.; Kalmykov, S. Y.

Report describing accomplishments in all-optical control of self-injection in laser-plasma accelerators and in developing advanced numerical models of laser-plasma interactions. All-optical approaches to controlling electron self-injection and beam formation in laser-plasma accelerators (LPAs) were explored. It was demonstrated that control over the laser pulse evolution is the key ingredient in the generation of low-background, low-phase-space-volume electron beams. To this end, preserving a smooth laser pulse envelope throughout the acceleration process can be achieved through tuning the phase and amplitude of the incident pulse. A negative frequency chirp compensates the frequency red-shift accumulated due to wake excitation, preventing evolution of themore » pulse into a relativistic optical shock. This reduces the ponderomotive force exerted on quiescent plasma electrons, suppressing expansion of the bubble and continuous injection of background electrons, thereby reducing the charge in the low-energy tail by an order of magnitude. Slowly raising the density in the pulse propagation direction locks electrons in the accelerating phase, boosting their energy, keeping continuous injection at a low level, tripling the brightness of the quasi-monoenergetic component. Additionally, propagating the negatively chirped pulse in a plasma channel suppresses diffraction of the pulse leading edge, further reducing continuous injection. As a side effect, oscillations of the pulse tail may be enhanced, leading to production of low-background, polychromatic electron beams. Such beams, consisting of quasi-monoenergetic components with controllable energy and energy separation, may be useful as drivers of polychromatic x-rays based on Thomson backscattering. These all-optical methods of electron beam quality control are critically important for the development of future compact, high-repetition-rate, GeV-scale LPA using 10 TW-class, ultra-high bandwidth pulses and mm-scale, dense plasmas. These results emphasize that investment into new pulse amplification techniques allowing for ultrahigh frequency bandwidth is as important for the design of future LPA as are the current efforts directed to increasing the pulse energy.« less

A Y-chromosome STR marker should be added to commercial multiplex STR kits.

PubMed

Oz, Carla; Zaken, Neomi; Amiel, Merav; Zamir, Ashira

2008-07-01

Autosomal short tandem repeat (STR) analysis has become highly relevant in the identification of victims from mass disasters and terrorist attacks. In such events, gender misidentification can be of grave consequences, yet the list reporting amelogenin amplification failure using STR multiplex kits continues to grow. Presented here are three such examples. In the first case, we present two male suspects who demonstrated amelogenin Y-deficient results using two commercial kit procedures. The presence of their Y chromosomes was proven by obtaining a Y-haplotype. The second case demonstrated a profile from a third male suspect where only the Y homolog of the XY pair was amplified. In events such as mass disasters or terrorist attacks, timely and reliable high throughput DNA typing results are essential. As the number of reported cases of amplification failure at the amelogenin gene continues to grow, we suggest that the incorporation of a better gender identification tool in commercial kits is crucial.

Advanced Concepts in Josephson Junction Reflection Amplifiers

NASA Astrophysics Data System (ADS)

Lähteenmäki, Pasi; Vesterinen, Visa; Hassel, Juha; Paraoanu, G. S.; Seppä, Heikki; Hakonen, Pertti

2014-06-01

Low-noise amplification at microwave frequencies has become increasingly important for the research related to superconducting qubits and nanoelectromechanical systems. The fundamental limit of added noise by a phase-preserving amplifier is the standard quantum limit, often expressed as noise temperature . Towards the goal of the quantum limit, we have developed an amplifier based on intrinsic negative resistance of a selectively damped Josephson junction. Here we present measurement results on previously proposed wide-band microwave amplification and discuss the challenges for improvements on the existing designs. We have also studied flux-pumped metamaterial-based parametric amplifiers, whose operating frequency can be widely tuned by external DC-flux, and demonstrate operation at pumping, in contrast to the typical metamaterial amplifiers pumped via signal lines at.

Transmission function properties for multi-layered structures: application to super-resolution.

PubMed

Mattiucci, N; D'Aguanno, G; Scalora, M; Bloemer, M J; Sibilia, C

2009-09-28

We discuss the properties of the transmission function in the k-space for a generic multi-layered structure. In particular we analytically demonstrate that a transmission greater than one in the evanescent spectrum (amplification of the evanescent modes) can be directly linked to the guided modes supported by the structure. Moreover we show that the slope of the phase of the transmission function in the propagating spectrum is inversely proportional to the ability of the structure to compensate the diffraction of the propagating modes. We apply these findings to discuss several examples where super-resolution is achieved thanks to the simultaneous availability of the amplification of the evanescent modes and the diffraction compensation of the propagating modes.

Optomechanically induced opacity and amplification in a quadratically coupled optomechanical system

NASA Astrophysics Data System (ADS)

Si, Liu-Gang; Xiong, Hao; Zubairy, M. Suhail; Wu, Ying

2017-03-01

We analyze theoretically the features of the output field of a quadratically coupled optomechanical system, which is driven by a strong coupling field and a weak signal field, and in which the membrane (treated as a mechanical resonator) is excited by a weak coherent driving field with two-phonon resonance. We show that the system exhibits complex quantum coherent and interference effects resulting in transmission of the signal field from opacity to remarkable amplification. We also find that the total phase of the applied fields can significantly adjust the signal field's transmission spectrum. The study of the propagation of the signal field in such a quadratically coupled optomechanical system proves that the proposed device can operate as an optical transistor.

Rapid detection of microbial DNA by a novel isothermal genome exponential amplification reaction (GEAR) assay.

PubMed

Prithiviraj, Jothikumar; Hill, Vincent; Jothikumar, Narayanan

2012-04-20

In this study we report the development of a simple target-specific isothermal nucleic acid amplification technique, termed genome exponential amplification reaction (GEAR). Escherichia coli was selected as the microbial target to demonstrate the GEAR technique as a proof of concept. The GEAR technique uses a set of four primers; in the present study these primers targeted 5 regions on the 16S rRNA gene of E. coli. The outer forward and reverse Tab primer sequences are complementary to each other at their 5' end, whereas their 3' end sequences are complementary to their respective target nucleic acid sequences. The GEAR assay was performed at a constant temperature 60 °C and monitored continuously in a real-time PCR instrument in the presence of an intercalating dye (SYTO 9). The GEAR assay enabled amplification of as few as one colony forming units of E. coli per reaction within 30 min. We also evaluated the GEAR assay for rapid identification of bacterial colonies cultured on agar media directly in the reaction without DNA extraction. Cells from E. coli colonies were picked and added directly to GEAR assay mastermix without prior DNA extraction. DNA in the cells could be amplified, yielding positive results within 15 min. Published by Elsevier Inc.

Enhanced Arctic amplification began at the Mid-Brunhes Event 430,000 years ago

USGS Publications Warehouse

Cronin, Thomas M.; Dwyer, Gary S.; Caverly, Emma; Farmer, Jesse; DeNinno, Lauren H.; Rodriguez-Lazaro, Julio; Gemery, Laura

2017-01-01

Arctic Ocean temperatures influence ecosystems, sea ice, species diversity, biogeochemical cycling, seafloor methane stability, deep-sea circulation, and CO2 cycling. Today's Arctic Ocean and surrounding regions are undergoing climatic changes often attributed to "Arctic amplification" - that is, amplified warming in Arctic regions due to sea-ice loss and other processes, relative to global mean temperature. However, the long-term evolution of Arctic amplification is poorly constrained due to lack of continuous sediment proxy records of Arctic Ocean temperature, sea ice cover and circulation. Here we present reconstructions of Arctic Ocean intermediate depth water (AIW) temperatures and sea-ice cover spanning the last ~ 1.5 million years (Ma) of orbitally-paced glacial/interglacial cycles (GIC). Using Mg/Ca paleothermometry of the ostracode Krithe and sea-ice planktic and benthic indicator species, we suggest that the Mid-Brunhes Event (MBE), a major climate transition ~ 400-350 ka, involved fundamental changes in AIW temperature and sea-ice variability. Enhanced Arctic amplification at the MBE suggests a major climate threshold was reached at ~ 400 ka involving Atlantic Meridional Overturning Circulation (AMOC), inflowing warm Atlantic Layer water, ice sheet, sea-ice and ice-shelf feedbacks, and sensitivity to higher post-MBE interglacial CO2 concentrations.

Genome-Wide Stochastic Adaptive DNA Amplification at Direct and Inverted DNA Repeats in the Parasite Leishmania

PubMed Central

Plourde, Marie; Gingras, Hélène; Roy, Gaétan; Lapointe, Andréanne; Leprohon, Philippe; Papadopoulou, Barbara; Corbeil, Jacques; Ouellette, Marc

2014-01-01

Gene amplification of specific loci has been described in all kingdoms of life. In the protozoan parasite Leishmania, the product of amplification is usually part of extrachromosomal circular or linear amplicons that are formed at the level of direct or inverted repeated sequences. A bioinformatics screen revealed that repeated sequences are widely distributed in the Leishmania genome and the repeats are chromosome-specific, conserved among species, and generally present in low copy number. Using sensitive PCR assays, we provide evidence that the Leishmania genome is continuously being rearranged at the level of these repeated sequences, which serve as a functional platform for constitutive and stochastic amplification (and deletion) of genomic segments in the population. This process is adaptive as the copy number of advantageous extrachromosomal circular or linear elements increases upon selective pressure and is reversible when selection is removed. We also provide mechanistic insights on the formation of circular and linear amplicons through RAD51 recombinase-dependent and -independent mechanisms, respectively. The whole genome of Leishmania is thus stochastically rearranged at the level of repeated sequences, and the selection of parasite subpopulations with changes in the copy number of specific loci is used as a strategy to respond to a changing environment. PMID:24844805

Is Polar Amplification Deeper and Stronger than Dynamicists Assume?

NASA Astrophysics Data System (ADS)

Scheff, J.; Maroon, E.

2017-12-01

In the CMIP multi-model mean under strong future warming, Arctic amplification is confined to the lower troposphere, so that the meridional gradient of warming reverses around 500 mb and the upper troposphere is characterized by strong "tropical amplification" in which warming weakens with increasing latitude. This model-derived pattern of warming maxima in the upper-level tropics and lower-level Arctic has become a canonical assumption driving theories of the large-scale circulation response to climate change. Yet, several lines of evidence and reasoning suggest that Arctic amplification may in fact extend through the entire depth of the troposphere, and/or may be stronger than commonly modeled. These include satellite Microwave Sounding Unit (MSU) temperature trends as a function of latitude and vertical level, the recent discovery that the extratropical negative cloud phase feedback in models is largely spurious, and the very strong polar amplification observed in past warm and lukewarm climates. Such a warming pattern, with deep, dominant Arctic amplification, would have very different implications for the circulation than a canonical CMIP-like warming: instead of slightly shifting poleward and strengthening, eddies, jets and cells might shift equatorward and considerably weaken. Indeed, surface winds have been mysteriously weakening ("stilling") at almost all stations over the last half-century or so, there has been no poleward shift in northern hemisphere circulation metrics, and past warm climates' subtropics were apparently quite wet (and their global ocean circulations were weak.) To explore these possibilities more deeply, we examine the y-z structure of warming and circulation changes across a much broader range of models, scenarios and time periods than the CMIP future mean, and use an MSU simulator to compare them to the satellite warming record. Specifically, we examine whether the use of historical (rather than future) forcing, AMIP (rather than CMIP) configuration, individual GCMs, and/or individual ensemble members can better reproduce the structure of the MSU and surface-wind observations. Figure 1 already shows that tropical amplification is absent in the CESM1 historical ensemble (1979-2012). The results of these analyses will guide our future modeling work on these topics.

On the Causes of and Long Term Changes in Eurasian Heat Waves

NASA Technical Reports Server (NTRS)

Schubert, Siegfried; Wang, Hailan; Koster, Randal; Suarez, Max

2012-01-01

The MERRA reanalysis, other observations, and the GEOS-S model have been used to diagnose the causes of Eurasian heat waves including the recent extreme events that occurred in Europe during 2003 and in Russia during 2010. The results show that such extreme events are an amplification of natural patterns of atmospheric variability (in this case a particular large-scale atmospheric planetary wave) that develop over the Eurasian continent as a result of internal atmospheric forcing. The amplification occurs when the wave occasionally becomes locked in place for several weeks to months resulting in extreme heat and drying with the location depending on the phase of the upper atmospheric wave. Model experiments suggest that forcing from both the ocean (SST) and land playa role phase-locking the waves. An ensemble of very long GEOS-S model simulations (spanning the 20th century) forced with observed SST and greenhouse gases show that the model is capable of generating very similar heat waves, and that they have become more extreme in the last thirty years as a result of the overall warming of the Asian continent.

Enhanced traveling wave amplification of co-planar slow wave structure by extended phase-matching

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palm, Andrew; Sirigiri, Jagadishwar; Shin, Young-Min, E-mail: yshin@niu.edu

2015-09-15

The electron beam co-propagating with slow waves in a staggered double grating array (SDGA) efficiently amplifies millimeter and sub-millimeter waves over a wide spectrum. Our theoretical and numerical analyses show that the power amplification in the fundamental passband is enhanced by the extended beam-wave phase-matching. Particle-in-cell simulations on the SDGA slow wave structure, designed with 10.4 keV and 50–100 mA sheet beam, indicate that maintaining beam-wave synchronization along the entire length of the circuit improves the gain by 7.3% leading to a total gain of 28 dB, corresponding to 62 W saturated power at the middle of operating band, and a 3-dB bandwidthmore » of 7 GHz with 10.5% at V-band (73.5 GHz center frequency) with saturated peak power reaching 80 W and 28 dB at 71 GHz. These results also show a reasonably good agreement with analytic calculations based on Pierce small signal gain theory.« less

Phase seeding of a terahertz quantum cascade laser

PubMed Central

Oustinov, Dimitri; Jukam, Nathan; Rungsawang, Rakchanok; Madéo, Julien; Barbieri, Stefano; Filloux, Pascal; Sirtori, Carlo; Marcadet, Xavier; Tignon, Jérôme; Dhillon, Sukhdeep

2010-01-01

The amplification of spontaneous emission is used to initiate laser action. As the phase of spontaneous emission is random, the phase of the coherent laser emission (the carrier phase) will also be random each time laser action begins. This prevents phase-resolved detection of the laser field. Here, we demonstrate how the carrier phase can be fixed in a semiconductor laser: a quantum cascade laser (QCL). This is performed by injection seeding a QCL with coherent terahertz pulses, which forces laser action to start on a fixed phase. This permits the emitted laser field to be synchronously sampled with a femtosecond laser beam, and measured in the time domain. We observe the phase-resolved buildup of the laser field, which can give insights into the laser dynamics. In addition, as the electric field oscillations are directly measured in the time domain, QCLs can now be used as sources for time-domain spectroscopy. PMID:20842195

Local modulation of double optomechanically induced transparency and amplification.

PubMed

Yang, Q; Hou, B P; Lai, D G

2017-05-01

We consider the probe absorption properties in a mechanically coupled optomechanical system in which the two coupled nanomechanical oscillators are driven by the time-dependent forces, respectively. It is found that the mechanical interaction splits the transparency window for a usual single-mode optomechanical system into two parts and then leads to appearance of the double optomechanically induced transparency. The distance between the two transparency positions (the frequency for the maximal transparency) is determined by the mechanical interaction amplitude. This can be explained by using optomechanical dressed-mode picture which is analogue to the interacting dark resonances in coherent atoms. When the mechanical resonators are driven by the external forces, the transparencies in the double-transparency spectrum can be increased into amplifications or be suppressed by tuning the amplitude of the forces. Additionally, it is shown that the double transparencies or the amplifications oscillate with the initial phases of the forces with a period of 2π. These investigations will be useful for more flexible controllability of multi-channel optical communication based on the optomechanical systems.

Respiratory system loop gain in normal men and women measured with proportional-assist ventilation.

PubMed

Wellman, Andrew; Malhotra, Atul; Fogel, Robert B; Edwards, Jill K; Schory, Karen; White, David P

2003-01-01

We hypothesized that increased chemical control instability (CCI) in men could partially explain the male predominance in obstructive sleep apnea (OSA). CCI was assessed by sequentially increasing respiratory control system loop gain (LG) with proportional-assist ventilation (PAV) in 10 men (age 24-48 yr) and 9 women (age 22-36 yr) until periodic breathing or awakening occurred. Women were studied in both the follicular and luteal phases of the menstrual cycle. The amount by which PAV amplified LG was quantified from the tidal volume amplification factor [(VtAF) assisted tidal volume/unassisted tidal volume]. LG was calculated as the inverse of the VtAF occurring at the assist level immediately preceding the emergence of periodic breathing (when LG x VtAF = 1). Only 1 of 10 men and 2 of 9 women developed periodic breathing with PAV. The rest were resistant to periodic breathing despite moderately high levels of PAV amplification. We conclude that LG is low in the majority of normal men and women and that higher volume amplification factors are needed to determine whether gender differences exist in this low range.

Raman Amplification and Tunable Pulse Delays in Silicon Waveguides

NASA Astrophysics Data System (ADS)

Rukhlenko, Ivan D.; Garanovich, Ivan L.; Premaratne, Malin; Sukhorukov, Andrey A.; Agrawal, Govind P.

2010-10-01

The nonlinear process of stimulated Raman scattering is important for silicon photonics as it enables optical amplification and lasing. However, generally employed numerical approaches provide very little insight into the contribution of different silicon Raman amplifier (SRA) parameters. In this paper, we solve the coupled pump-signal equations analytically and derive an exact formula for the envelope of a signal pulse when picosecond optical pulses are amplified inside a SRA pumped by a continuous-wave laser beam. Our solution is valid for an arbitrary pulse shape and fully accounts for the Raman gain-dispersion effects, including temporal broadening and group-velocity reduction. Our results are useful for optimizing the performance of SRAs and for engineering controllable signal delays.

Photovoltaic dependence of photorefractive grating on the externally applied dc electric field

NASA Astrophysics Data System (ADS)

Maurya, M. K.; Yadav, R. A.

2013-04-01

Photovoltaic dependence of photorefractive grating (i.e., space-charge field and phase-shift of the index grating) on the externally applied dc electric field in photovoltaic-photorefractive materials has been investigated. The influence of photovoltaic field (EPhN), diffusion field and carrier concentration ratio r (donor/acceptor impurity concentration ratio) on the space-charge field (SCF) and phase-shift of the index grating in the presence and absence of the externally applied dc electric field have also been studied in details. Our results show that, for a given value of EPhN and r, the magnitude of the SCF and phase-shift of the index grating can be enhanced significantly by employing the lower dc electric field (EON<10) across the photovoltaic-photorefractive crystal and higher value of diffusion field (EDN>40). Such an enhancement in the magnitude of the SCF and phase-shift of the index grating are responsible for the strongest beam coupling in photovoltaic-photorefractive materials. This sufficiently strong beam coupling increases the two-beam coupling gain that may be exceed the absorption and reflection losses of the photovoltaic-photorefractive sample, and optical amplification can occur. The higher value of optical amplification in photovoltaic-photorefractive sample is required for the every applications of photorefractive effect so that technology based on the photorefractive effect such as holographic storage devices, optical information processing, acousto-optic tunable filters, gyro-sensors, optical modulators, optical switches, photorefractive-photovoltaic solitons, biomedical applications, and frequency converters could be improved.

Femtosecond optical parametric amplification in BBO and KTA driven by a Ti:sapphire laser for LIDT testing and diagnostic development

NASA Astrophysics Data System (ADS)

Meadows, Alexander R.; Cupal, Josef; Hříbek, Petr; Durák, Michal; Kramer, Daniel; Rus, Bedřich

2017-05-01

We present the design of a collinear femtosecond optical parametric amplification (OPA) system producing a tunable output at wavelengths between 1030 nm and 1080 nm from a Ti:Sapphire pump laser at a wavelength of 795 nm. Generation of a supercontinuum seed pulse is followed by one stage of amplification in Beta Barium Borate (BBO) and two stages of amplification in Potassium Titanyle Arsenate (KTA), resulting in a 225 μJ output pulse with a duration of 90 fs. The output of the system has been measured by self-referenced spectral interferometry to yield the complete spectrum and spectral phase of the pulse. When compared to KTP, the greater transparency of KTA in the spectral range from 3 - 4 μm allows for reduced idler absorption and enhanced gain from the OPA process when it is pumped by the fundamental frequency of a Ti:sapphire laser. In turn, the use of the Ti:sapphire fundamental at 795 nm as a pump improves the efficiency with which light can be converted to wavelengths between 1030 nm and 1080 nm and subsequently used to test components for Nd-based laser systems. This OPA system is operated at 1 kHz for diagnostic development and laser-induced damage threshold testing of optical components for the ELI-Beamlines project.

humpty dumpty is required for developmental DNA amplification and cell proliferation in Drosophila.

PubMed

Bandura, Jennifer L; Beall, Eileen L; Bell, Maren; Silver, Hannah R; Botchan, Michael R; Calvi, Brian R

2005-04-26

The full complement of proteins required for the proper regulation of genome duplication are yet to be described. We employ a genetic DNA-replication model system based on developmental amplification of Drosophila eggshell (chorion) genes [1]. Hypomorphic mutations in essential DNA replication genes result in a distinct thin-eggshell phenotype owing to reduced amplification [2]. Here, we molecularly identify the gene, which we have named humpty dumpty (hd), corresponding to the thin-eggshell mutant fs(3)272-9 [3]. We confirm that hd is essential for DNA amplification in the ovary and show that it also is required for cell proliferation during development. Mosaic analysis of hd mutant cells during development and RNAi in Kc cells reveal that depletion of Hd protein results in severe defects in genomic replication and DNA damage. Most Hd protein is found in nuclear foci, and some may traverse the nuclear envelope. Consistent with a role in DNA replication, expression of Hd protein peaks during late G1 and S phase, and it responds to the E2F1/Dp transcription factor. Hd protein sequence is conserved from plants to humans, and published microarrays indicate that expression of its putative human ortholog also peaks at G1/S [4]. Our data suggest that hd defines a new gene family likely required for cell proliferation in all multicellular eukaryotes.

Practical implications of erythromycin resistance gene diversity on surveillance and monitoring of resistance

USDA-ARS?s Scientific Manuscript database

Use of antibiotics in human and animal medicine has applied selective pressure for the global dissemination of antibiotic-resistant bacteria. Therefore, it is of interest to develop strategies to mitigate the continued amplification and transmission of resistance genes in environmental reservoirs s...

High-accuracy resolver-to-digital conversion via phase locked loop based on PID controller

NASA Astrophysics Data System (ADS)

Li, Yaoling; Wu, Zhong

2018-03-01

The problem of resolver-to-digital conversion (RDC) is transformed into the problem of angle tracking control, and a phase locked loop (PLL) method based on PID controller is proposed in this paper. This controller comprises a typical PI controller plus an incomplete differential which can avoid the amplification of higher-frequency noise components by filtering the phase detection error with a low-pass filter. Compared with conventional ones, the proposed PLL method makes the converter a system of type III and thus the conversion accuracy can be improved. Experimental results demonstrate the effectiveness of the proposed method.

Squeezing as a route to photonic analogues of topological superconductors

NASA Astrophysics Data System (ADS)

Houde, Martin; Peano, Vittorio; Brendel, Christian; Marquardt, Florian; Clerk, Aashish

There has been considerable recent interest in studying topological phases of photonic systems. In many cases the resulting system is described by a quadratic particle-conserving Hamiltonian which is directly equivalent to its fermionic counterpart. Here, we consider a class of photonic topological phases where this correspondence fails: photonic systems where particle-number non-conserving terms break time-reversal symmetry. We show that these phases support protected edge modes which facilitate chiral inelastic and elastic transport channels. We also discuss the possibility of quantum amplification using these edge states. Our system could be realized in a variety of systems, including nonlinear photonic crystals, superconducting circuits and optomechanical systems.

Relative phase noise induced impairment in M-ary phase-shift-keying coherent optical communication system using distributed fiber Raman amplifier.

PubMed

Cheng, Jingchi; Tang, Ming; Fu, Songnian; Shum, Perry Ping; Liu, Deming

2013-04-01

We show for the first time, to the best of our knowledge, that, in a coherent communication system that employs a phase-shift-keying signal and Raman amplification, besides the pump relative intensity noise (RIN) transfer to the amplitude, the signal's phase will also be affected by pump RIN through the pump-signal cross-phase modulation. Although the average pump power induced linear phase change can be compensated for by the phase-correction algorithm, a relative phase noise (RPN) parameter has been found to characterize pump RIN induced stochastic phase noise. This extra phase noise brings non-negligible system impairments in terms of the Q-factor penalty. The calculation shows that copumping leads to much more stringent requirements to pump RIN, and relatively larger fiber dispersion helps to suppress the RPN induced impairment. A higher-order phase-shift keying (PSK) signal is less tolerant to noise than a lower-order PSK.

A Continuous-Flow Polymerase Chain Reaction Microchip With Regional Velocity Control

PubMed Central

Li, Shifeng; Fozdar, David Y.; Ali, Mehnaaz F.; Li, Hao; Shao, Dongbing; Vykoukal, Daynene M.; Vykoukal, Jody; Floriano, Pierre N.; Olsen, Michael; McDevitt, John T.; Gascoyne, Peter R.C.; Chen, Shaochen

2009-01-01

This paper presents a continuous-flow polymerase chain reaction (PCR) microchip with a serpentine microchannel of varying width for “regional velocity control.” Varying the channel width by incorporating expanding and contracting conduits made it possible to control DNA sample velocities for the optimization of the exposure times of the sample to each temperature phase while minimizing the transitional periods during temperature transitions. A finite element analysis (FEA) and semi-analytical heat transfer model was used to determine the distances between the three heating assemblies that are responsible for creating the denaturation (96 °C), hybridization (60 °C), and extension (72 °C) temperature zones within the microchip. Predictions from the thermal FEA and semi-analytical model were compared with temperature measurements obtained from an infrared (IR) camera. Flow-field FEAs were also performed to predict the velocity distributions in the regions of the expanding and contracting conduits to study the effects of the microchannel geometry on flow recirculation and bubble nucleation. The flow fields were empirically studied using micro particle image velocimetry (μ-PIV) to validate the flow-field FEA’s and to determine experimental velocities in each of the regions of different width. Successful amplification of a 90 base pair (bp) bacillus anthracis DNA fragment was achieved. PMID:19829760

Platinum Nanocatalyst Amplification: Redefining the Gold Standard for Lateral Flow Immunoassays with Ultrabroad Dynamic Range

PubMed Central

2017-01-01

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. PMID:29215864

Comparison of Three Different Sensitive Assays for Hepatitis B Virus DNA in Monitoring of Responses to Antiviral Therapy

PubMed Central

Chan, Henry L. Y.; Leung, Nancy W. Y.; Lau, Tracy C. M.; Wong, May L.; Sung, Joseph J. Y.

2000-01-01

The aim of our study was to compare the performances of two new hepatitis B virus (HBV) DNA assays, a cross-linking assay (NAXCOR) and a hybrid-capture amplification assay (Digene), versus the widely used branched-DNA (bDNA) assay (Chiron) in the monitoring of HBV DNA levels during antiviral treatment. Serial serum samples from 12 chronically HBV infected patients undergoing a phase II trial of an antiviral drug, 2′,3′-dideoxy-5-fluoro-3′-thiacytidine (FTC), were studied. A total of 96 serum samples were tested for HBV DNA using the cross-linking, hybrid-capture amplification, and bDNA assays. In the comparison of the cross-linking and bDNA assays, concordant results were found in 77 (80.3%) samples, no significant difference was found between the median log10 HBV DNA levels (6.66 versus 7.17 meq/ml), and the results of the two assays were closely correlated (r = 0.95). In the comparison of the hybrid-capture amplification and bDNA assays, concordant results were found in 79 (82.3%) samples, no significant difference was found between the median log10 HBV DNA levels (6.98 versus 6.99 meq/ml), and the results of the two assays were closely correlated (r = 0.99). Six (6.3%) samples by the cross-linking assay and 10 (10.4%) samples by the bDNA assay required retesting because of unacceptably high within-run coefficients of variance. No sample required retesting in the hybrid-capture amplification assay according to the internal validation. In conclusion, the cross-linking and hybrid-capture amplification assays were as sensitive as the bDNA assay for HBV DNA detection and can be recommended for monitoring of HBV DNA levels during antiviral treatment. PMID:10970358

CD274/PD-L1 gene amplification and PD-L1 protein expression are common events in squamous cell carcinoma of the oral cavity.

PubMed

Straub, Melanie; Drecoll, Enken; Pfarr, Nicole; Weichert, Wilko; Langer, Rupert; Hapfelmeier, Alexander; Götz, Carolin; Wolff, Klaus-Dietrich; Kolk, Andreas; Specht, Katja

2016-03-15

Immunomodulatory therapies, targeting the immune checkpoint receptor-ligand complex PD-1/PD-L1 have shown promising results in early phase clinical trials in solid malignancies, including carcinomas of the head and neck. In this context, PD-L1 protein expression has been proposed as a potentially valuable predictive marker. In the present study, expression of PD-L1 and PD-1 was evaluated by immunohistochemistry in 80 patients with predominantly HPV-negative oral squamous cell carcinomas and associated nodal metastasis. In addition, CD274/PD-L1 gene copy number status was assessed by fluorescence in situ hybridization analysis. PD-L1 expression was detected in 36/80 (45%) cases and concordance of PD-L1 expression in primary tumor and corresponding nodal metastasis was present in only 20/28 (72%) cases. PD-1 expression was found in tumor-infiltrating lymphocytes (TILs) but not in tumor cells. CD274/PD-L1 gene amplification was detected in 19% of cases, with high level PD-L1 amplification present in 12/80 (15%), and low level amplification in 3/80 (4%). Interestingly, CD274/PD-L1 gene amplification was associated with positive PD-L1 immunostaining in only 73% of cases. PD-L1 copy number status was concordant in primary tumor and associated metastases. Clinically, PD-L1 tumor immunopositivity was associated with a higher risk for nodal metastasis at diagnosis, overall tumor related death und recurrence. Based on our findings we propose to include PD-L1 copy number status in addition to protein status in screening programs for future clinical trials with immunotherapeutic strategies targeting the PD-1/PD-L1 axis.

CD274/PD-L1 gene amplification and PD-L1 protein expression are common events in squamous cell carcinoma of the oral cavity

PubMed Central

Straub, Melanie; Drecoll, Enken; Pfarr, Nicole; Weichert, Wilko; Langer, Rupert; Hapfelmeier, Alexander; Götz, Carolin; Wolff, Klaus-Dietrich; Kolk, Andreas; Specht, Katja

2016-01-01

Immunomodulatory therapies, targeting the immune checkpoint receptor-ligand complex PD-1/PD-L1 have shown promising results in early phase clinical trials in solid malignancies, including carcinomas of the head and neck. In this context, PD-L1 protein expression has been proposed as a potentially valuable predictive marker. In the present study, expression of PD-L1 and PD-1 was evaluated by immunohistochemistry in 80 patients with predominantly HPV-negative oral squamous cell carcinomas and associated nodal metastasis. In addition, CD274/PD-L1 gene copy number status was assessed by fluorescence in situ hybridization analysis. PD-L1 expression was detected in 36/80 (45%) cases and concordance of PD-L1 expression in primary tumor and corresponding nodal metastasis was present in only 20/28 (72%) cases. PD-1 expression was found in tumor-infiltrating lymphocytes (TILs) but not in tumor cells. CD274/PD-L1 gene amplification was detected in 19% of cases, with high level PD-L1 amplification present in 12/80 (15%), and low level amplification in 3/80 (4%). Interestingly, CD274/PD-L1 gene amplification was associated with positive PD-L1 immunostaining in only 73% of cases. PD-L1 copy number status was concordant in primary tumor and associated metastases. Clinically, PD-L1 tumor immunopositivity was associated with a higher risk for nodal metastasis at diagnosis, overall tumor related death und recurrence. Based on our findings we propose to include PD-L1 copy number status in addition to protein status in screening programs for future clinical trials with immunotherapeutic strategies targeting the PD-1/PD-L1 axis. PMID:26918453

Amplification in the rehabilitation of unilateral deafness: speech in noise and directional hearing effects with bone-anchored hearing and contralateral routing of signal amplification.

PubMed

Lin, Li-Mei; Bowditch, Stephen; Anderson, Michael J; May, Bradford; Cox, Kenneth M; Niparko, John K

2006-02-01

Vibromechanical stimulation with a semi-implantable bone conductor (Entific BAHA device) overcomes some of the head-shadow effects in unilateral deafness. What specific rehabilitative benefits are observed when the functional ear exhibits normal hearing versus moderate sensorineural hearing loss (SNHL)? The authors conducted a prospective trial of subjects with unilateral deafness in a tertiary care center. This study comprised adults with unilateral deafness (pure-tone average [PTA] > 90 dB; Sp.D. < 20%) and either normal monaural hearing (n = 18) or moderate SNHL (PTA = 25-50 dB: Sp.D. > 75%) in the contralateral functional ear (n = 5). Subjects were fit with contralateral routing of signal (CROS) devices for 1 month and tested before (mastoid) implantation, fitting, and testing with a bone-anchored hearing aid (BAHA). Outcome measures were: 1) subjective benefit; 2) source localization tests (Source Azimuth Identification in Noise Test [SAINT]); 3) speech discrimination in quiet and in noise assessed with Hearing In Noise Test (HINT) protocols. There was consistent satisfaction with BAHA amplification and poor acceptance of CROS amplification. General directional hearing decreased with CROS use and was unchanged by BAHA and directional microphone aids. Relative to baseline and CROS, BAHA produced significantly better speech recognition in noise. Twenty-two of 23 subjects followed up in this study continue to use their BAHA device over an average follow-up period of 30.24 months (range, 51-12 months). BAHA amplification on the side of a deaf ear yields greater benefit in subjects with monaural hearing than does CROS amplification. Advantages likely related to averting the interference of speech signals delivered to the better ear, as occurs with conventional CROS amplification, while alleviating the negative head-shadow effects of unilateral deafness. The advantages of head-shadow reduction in enhancing speech recognition with noise in the hearing ear outweigh disadvantages inherent in head-shadow reduction that can occur by introducing noise from the deaf side. The level of hearing impairment correlates with incremental benefit provided by the BAHA. Patients with a moderate SNHL in the functioning ear perceived greater increments in benefit, especially in background noise, and demonstrated greater improvements in speech understanding with BAHA amplification.

Conversion from non-orthogonally to orthogonally polarized optical single-sideband modulation using optically injected semiconductor lasers.

PubMed

Hung, Yu-Han; Tseng, Chin-Hao; Hwang, Sheng-Kwang

2018-06-01

This Letter investigates an optically injected semiconductor laser for conversion from non-orthogonally to orthogonally polarized optical single-sideband modulation. The underlying mechanism relies solely on nonlinear laser characteristics and, thus, only a typical semiconductor laser is required as the key conversion unit. This conversion can be achieved for a broadly tunable frequency range up to at least 65 GHz. After conversion, the microwave phase quality, including linewidth and phase noise, is mostly preserved, and simultaneous microwave amplification up to 23 dB is feasible.

Optical parametric amplifiers using chirped quasi-phase-matching gratings I: practical design formulas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Charbonneau-Lefort, Mathieu; Afeyan, Bedros; Fejer, M. M.

Optical parametric amplifiers using chirped quasi-phase-matching (QPM) gratings offer the possibility of engineering the gain and group delay spectra. We give practical formulas for the design of such amplifiers. We consider linearly chirped QPM gratings providing constant gain over a broad bandwidth, sinusoidally modulated profiles for selective frequency amplification and a pair of QPM gratings working in tandem to ensure constant gain and constant group delay at the same time across the spectrum. Finally, the analysis is carried out in the frequency domain using Wentzel–Kramers–Brillouin analysis.

Improving carrier-envelope phase stability in optical parametric chirped-pulse amplifiers by control of timing jitter.

PubMed

Hädrich, S; Rothhardt, J; Krebs, M; Demmler, S; Limpert, J; Tünnermann, A

2012-12-01

It is shown that timing jitter in optical parametric chirped-pulse amplification induces spectral drifts that transfer to carrier-envelope phase (CEP) instabilities via dispersion. Reduction of this effect requires temporal synchronization, which is realized with feedback obtained from the angularly dispersed idler. Furthermore, a novel method to measure the CEP drifts by utilizing parasitic second harmonic generation within parametric amplifiers is presented. Stabilization of the timing allows the obtainment of a CEP stability of 86 mrad over 40 min at 150 kHz repetition rate.

Multiple pass laser amplifier system

DOEpatents

Brueckner, Keith A.; Jorna, Siebe; Moncur, N. Kent

1977-01-01

A laser amplification method for increasing the energy extraction efficiency from laser amplifiers while reducing the energy flux that passes through a flux limited system which includes apparatus for decomposing a linearly polarized light beam into multiple components, passing the components through an amplifier in delayed time sequence and recombining the amplified components into an in phase linearly polarized beam.

Optical Computing, 1991, Technical Digest Series, Vol. 6

DTIC Science & Technology

1992-05-22

lasers). Compound semiconductors may satisfy these requirements. For example, optical signal amplification by two-beam coupling and amplified phase... compound semiconductors can provide this type of implementationi. This paper presents results from a detailed investigation on potentials of the...conductivity to achieve high multichannel cell performance. We describe several high performance Gallium Phosphide multichannel Bragg cells which employ these

Generation of 70 fs broadband pulses in a hybrid nonlinear amplification system with mode-locked Yb:YAG ceramic oscillator

NASA Astrophysics Data System (ADS)

Liu, Yang; Wang, Chao; Luo, Daping; Yang, Chao; Li, Jiang; Ge, Lin; Pan, Yubai; Li, Wenxue

2017-12-01

We demonstrate the passively mode-locked laser performances of bulk Yb:YAG ceramic prepared by non-aqueous tape casting, which generates initial pulses in temporal width of 3 ps and spectrum width of 3 nm without intra-cavity dispersion management. The ceramic laser is further used as seeding oscillator in a fiber nonlinear amplification system, where ultrashort pulses in maximum output power of ˜100 W and pulse duration of 70 fs are achieved. Moreover, the laser spectrum is broadened to be ˜41 nm due to self-phase modulation effects in the gain fiber, overcoming the narrow spectrum limitations of ceramic materials. Our approach opens a new avenue for power-scaling and spectrum-expanding of femtosecond ceramic lasers.

Rolling Circle Amplification For Spatially Directed Synthesis Of A Solid Phase Anchored Single-Stranded DNA Molecule

NASA Astrophysics Data System (ADS)

Reiß, Edda; Hölzel, Ralph; von Nickisch-Rosenegk, Markus; Bier, Frank F.

2006-09-01

In this article the usefulness of the enzyme phi29 DNA polymerase and the principle of rolling circle amplification (RCA) for creating single-stranded DNA (ssDNA) nanostructures is described. Currently we are working on the spatial orientation of a growing ssDNA molecule during its RCA-based synthesis by the application of a hydrodynamic force. Starting at an immobilized primer at single molecule level, the aim is to construct a nanostructure of known location and orientation, providing multiple repeating binding sites that can be addressed via complementary base-pairing. Proof-of-principle experiments demonstrate the potential of the enzymatic reaction. ssDNA molecules of more than 20 μm length were created at an immobilized primer and detected by means of fluorescence microscopy.

Achieving nonlinear optical modulation via four-wave mixing in a four-level atomic system

NASA Astrophysics Data System (ADS)

Li, Hai-Chao; Ge, Guo-Qin; Zubairy, M. Suhail

2018-05-01

We propose an accessible scheme for implementing tunable nonlinear optical amplification and attenuation via a synergetic mechanism of four-wave mixing (FWM) and optical interference in a four-level ladder-type atomic system. By constructing a cyclic atom-field interaction, we show that two reverse FWM processes can coexist via optical transitions in different branches. In the suitable input-field conditions, strong interference effects between the input fields and the generated FWM fields can be induced and result in large amplification and deep attenuation of the output fields. Moreover, such an optical modulation from enhancement to suppression can be controlled by tuning the relative phase. The quantum system can be served as a switchable optical modulator with potential applications in quantum nonlinear optics.

Orbit-based analysis of nonlinear energetic ion dynamics in tokamaks. II. Mechanisms for rapid chirping and convective amplification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bierwage, Andreas; Shinohara, Kouji

2016-04-15

The nonlinear interactions between shear Alfvén modes and tangentially injected beam ions in the 150–400 keV range are studied numerically in realistic geometry for a JT-60U tokamak scenario. In Paper I, which was reported in the companion paper, the recently developed orbit-based resonance analysis method was used to track the resonant frequency of fast ions during their nonlinear evolution subject to large magnetic and electric drifts. Here, that method is applied to map the wave-particle power transfer from the canonical guiding center phase space into the frequency-radius plane, where it can be directly compared with the evolution of the fluctuation spectramore » of fast-ion-driven modes. Using this technique, we study the nonlinear dynamics of strongly driven shear Alfvén modes with low toroidal mode numbers n = 1 and n = 3. In the n = 3 case, both chirping and convective amplification can be attributed to the mode following the resonant frequency of the radially displaced particles, i.e., the usual one-dimensional phase locking process. In the n = 1 case, a new chirping mechanism is found, which involves multiple dimensions, namely, wave-particle trapping in the radial direction and phase mixing across velocity coordinates.« less

Different roles of electron beam in two stream instability in an elliptical waveguide for generation and amplification of THz electromagnetic waves

DOE Office of Scientific and Technical Information (OSTI.GOV)

Safari, S.; Jazi, B., E-mail: jaziada@kashanu.ac.ir; Jahanbakht, S.

2016-08-15

In this work, two stream instability in a metallic waveguide with elliptical cross-section and with a hollow annular dielectric layer is studied for generation and amplification of THz electromagnetic waves. Dispersion relation of waves and their dependents to geometric dimensions and characteristics of the electron beam are analyzed. In continuation, the diagrams of growth rate for some operating frequencies are presented, so that effective factors on the growth rates, such as geometrical dimensions, dielectric constant of dielectric layer, accelerating voltage, and applied current intensity are analyzed. It is shown that while an electron beam is responsible for instability, another electronmore » beam plays a stabilizing role.« less

Adolescents Exiting Homelessness Over Two Years: The Risk Amplification and Abatement Model

PubMed Central

Milburn, Norweeta G.; Rice, Eric; Rotheram-Borus, Mary Jane; Mallett, Shelley; Rosenthal, Doreen; Batterham, Phillip; May, Susanne J.; Witkin, Andrea; Duan, Naihua

2014-01-01

The Risk Amplification and Abatement Model (RAAM), demonstrates that negative contact with socializing agents amplify risk, while positive contact abates risk for homeless adolescents. To test this model, the likelihood of exiting homelessness and returning to familial housing at 2 years and stably exiting over time are examined with longitudinal data collected from 183 newly homeless adolescents followed over 2 years in Los Angeles, CA. In support of RAAM, unadjusted odds of exiting at 2 years and stably exiting over2 years revealed that engagement with pro-social peers, maternal social support, and continued school attendance all promoted exiting behaviors. Simultaneously, exposure to family violence and reliance on shelter services discouraged stably exiting behaviors. Implications for family-based interventions are proposed. PMID:25067896

Neuromotor Noise Is Malleable by Amplifying Perceived Errors

PubMed Central

Zhang, Zhaoran; Abe, Masaki O.; Sternad, Dagmar

2016-01-01

Variability in motor performance results from the interplay of error correction and neuromotor noise. This study examined whether visual amplification of error, previously shown to improve performance, affects not only error correction, but also neuromotor noise, typically regarded as inaccessible to intervention. Seven groups of healthy individuals, with six participants in each group, practiced a virtual throwing task for three days until reaching a performance plateau. Over three more days of practice, six of the groups received different magnitudes of visual error amplification; three of these groups also had noise added. An additional control group was not subjected to any manipulations for all six practice days. The results showed that the control group did not improve further after the first three practice days, but the error amplification groups continued to decrease their error under the manipulations. Analysis of the temporal structure of participants’ corrective actions based on stochastic learning models revealed that these performance gains were attained by reducing neuromotor noise and, to a considerably lesser degree, by increasing the size of corrective actions. Based on these results, error amplification presents a promising intervention to improve motor function by decreasing neuromotor noise after performance has reached an asymptote. These results are relevant for patients with neurological disorders and the elderly. More fundamentally, these results suggest that neuromotor noise may be accessible to practice interventions. PMID:27490197

Random Amplification and Pyrosequencing for Identification of Novel Viral Genome Sequences

PubMed Central

Hang, Jun; Forshey, Brett M.; Kochel, Tadeusz J.; Li, Tao; Solórzano, Víctor Fiestas; Halsey, Eric S.; Kuschner, Robert A.

2012-01-01

ssRNA viruses have high levels of genomic divergence, which can lead to difficulty in genomic characterization of new viruses using traditional PCR amplification and sequencing methods. In this study, random reverse transcription, anchored random PCR amplification, and high-throughput pyrosequencing were used to identify orthobunyavirus sequences from total RNA extracted from viral cultures of acute febrile illness specimens. Draft genome sequence for the orthobunyavirus L segment was assembled and sequentially extended using de novo assembly contigs from pyrosequencing reads and orthobunyavirus sequences in GenBank as guidance. Accuracy and continuous coverage were achieved by mapping all reads to the L segment draft sequence. Subsequently, RT-PCR and Sanger sequencing were used to complete the genome sequence. The complete L segment was found to be 6936 bases in length, encoding a 2248-aa putative RNA polymerase. The identified L segment was distinct from previously published South American orthobunyaviruses, sharing 63% and 54% identity at the nucleotide and amino acid level, respectively, with the complete Oropouche virus L segment and 73% and 81% identity at the nucleotide and amino acid level, respectively, with a partial Caraparu virus L segment. The result demonstrated the effectiveness of a sequence-independent amplification and next-generation sequencing approach for obtaining complete viral genomes from total nucleic acid extracts and its use in pathogen discovery. PMID:22468136

Development of a quantitative fluorescence single primer isothermal amplification-based method for the detection of Salmonella.

PubMed

Wang, Jianchang; Li, Rui; Hu, Lianxia; Sun, Xiaoxia; Wang, Jinfeng; Li, Jing

2016-02-16

Food-borne disease caused by Salmonella has long been, and continues to be, an important global public health problem, necessitating rapid and accurate detection of Salmonella in food. Real time PCR is the most recently developed approach for Salmonella detection. Single primer isothermal amplification (SPIA), a novel gene amplification technique, has emerged as an attractive microbiological testing method. SPIA is performed under a constant temperature, eliminating the need for an expensive thermo-cycler. In addition, SPIA reactions can be accomplished in 30 min, faster than real time PCR that usually takes over 2h. We developed a quantitative fluorescence SPIA-based method for the detection of Salmonella. Using Salmonella Typhimurium genomic DNA as template and a primer targeting Salmonella invA gene, we showed the detection limit of SPIA was 2.0 × 10(1)fg DNA. Its successful amplification of different serotypic Salmonella genomic DNA but not non-Salmonella bacterial DNA demonstrated the specificity of SPIA. Furthermore, this method was validated with artificially contaminated beef. In conclusion, we showed high sensitivity and specificity of SPIA in the detection of Salmonella, comparable to real time PCR. In addition, SPIA is faster and more cost-effective (non-use of expensive cyclers), making it a potential alternative for field detection of Salmonella in resource-limited settings that are commonly encountered in developing countries. Copyright © 2015 Elsevier B.V. All rights reserved.

Target-induced proximity ligation triggers recombinase polymerase amplification and transcription-mediated amplification to detect tumor-derived exosomes in nasopharyngeal carcinoma with high sensitivity.

PubMed

Liu, Wanli; Li, Jianpei; Wu, Yixian; Xing, Shan; Lai, Yanzhen; Zhang, Ge

2018-04-15

Tumor-derived exosomes (TEXs) are extracellular vesicles that are continuously released into the blood by tumor cells and carry specific surface markers of the original tumor cells. Substantial evidence has implicated TEXs as attractive diagnostic markers for cancer. However, the detection of TEXs in blood at an early tumor stage is challenging due to their very low concentration. Here, we established a method called PLA-RPA-TMA assay that allows TEXs to be detected with high sensitivity and specificity. Based on two proximity ligation assay (PLA) probes that recognize a biomarker on a TEX, we generated a unique surrogate DNA signal for the specific biomarker, which was synchronously amplified twice by recombinase polymerase amplification (RPA) coupled with transcription-mediated amplification (TMA), and then the products of the RPA-TMA reaction were quantitatively detected using a gold nanoparticle-based colorimetric assay. We established proof-of-concept evidence for this approach using TEXs from nasopharyngeal carcinoma (NPC) cells, with a detection limit of 10 2 particles/mL, and reported the measurement of plasma Epstein-Barr virus latent membrane protein 1 (LPM1)-positive (LMP1 + , accuracy: 0.956) and epidermal growth factor receptor (EGFR)-positive (EGFR + , accuracy: 0.906) TEXs as potent early diagnostic biomarkers for NPC. Copyright © 2017 Elsevier B.V. All rights reserved.

Linear nicking endonuclease-mediated strand-displacement DNA amplification.

PubMed

Joneja, Aric; Huang, Xiaohua

2011-07-01

We describe a method for linear isothermal DNA amplification using nicking endonuclease-mediated strand displacement by a DNA polymerase. The nicking of one strand of a DNA target by the endonuclease produces a primer for the polymerase to initiate synthesis. As the polymerization proceeds, the downstream strand is displaced into a single-stranded form while the nicking site is also regenerated. The combined continuous repetitive action of nicking by the endonuclease and strand-displacement synthesis by the polymerase results in linear amplification of one strand of the DNA molecule. We demonstrate that DNA templates up to 5000 nucleotides can be linearly amplified using a nicking endonuclease with 7-bp recognition sequence and Sequenase version 2.0 in the presence of single-stranded DNA binding proteins. We also show that a mixture of three templates of 500, 1000, and 5000 nucleotides in length is linearly amplified with the original molar ratios of the templates preserved. Moreover, we demonstrate that a complex library of hydrodynamically sheared genomic DNA from bacteriophage lambda can be amplified linearly. Copyright © 2011 Elsevier Inc. All rights reserved.

Coupling p+n Field-Effect Transistor Circuits for Low Concentration Methane Gas Detection

PubMed Central

Zhou, Xinyuan; Yang, Liping; Bian, Yuzhi; Ma, Xiang; Chen, Yunfa

2018-01-01

Nowadays, the detection of low concentration combustible methane gas has attracted great concern. In this paper, a coupling p+n field effect transistor (FET) amplification circuit is designed to detect methane gas. By optimizing the load resistance (RL), the response to methane of the commercial MP-4 sensor can be magnified ~15 times using this coupling circuit. At the same time, it decreases the limit of detection (LOD) from several hundred ppm to ~10 ppm methane, with the apparent response of 7.0 ± 0.2 and voltage signal of 1.1 ± 0.1 V. This is promising for the detection of trace concentrations of methane gas to avoid an accidental explosion because its lower explosion limit (LEL) is ~5%. The mechanism of this coupling circuit is that the n-type FET firstly generates an output voltage (VOUT) amplification process caused by the gate voltage-induced resistance change of the FET. Then, the p-type FET continues to amplify the signal based on the previous VOUT amplification process. PMID:29509659

Linear nicking endonuclease-mediated strand displacement DNA amplification

PubMed Central

Joneja, Aric; Huang, Xiaohua

2011-01-01

We describe a method for linear isothermal DNA amplification using nicking endonuclease-mediated strand displacement by a DNA polymerase. The nicking of one strand of a DNA target by the endonuclease produces a primer for the polymerase to initiate synthesis. As the polymerization proceeds, the downstream strand is displaced into a single-stranded form while the nicking site is also regenerated. The combined continuous repetitive action of nicking by the endonuclease and strand displacement synthesis by the polymerase results in linear amplification of one strand of the DNA molecule. We demonstrate that DNA templates up to five thousand nucleotides can be linearly amplified using a nicking endonuclease with seven base-pair recognition sequence and Sequenase version 2.0 in the presence of single-stranded DNA binding proteins. We also show that a mixture of three templates of 500, 1000, and 5000 nucleotides in length are linearly amplified with the original molar ratios of the templates preserved. Moreover, we demonstrate that a complex library of hydrodynamically sheared genomic DNA from bacteriophage lambda can be amplified linearly. PMID:21342654

Coupling p+n Field-Effect Transistor Circuits for Low Concentration Methane Gas Detection.

PubMed

Zhou, Xinyuan; Yang, Liping; Bian, Yuzhi; Ma, Xiang; Han, Ning; Chen, Yunfa

2018-03-06

Nowadays, the detection of low concentration combustible methane gas has attracted great concern. In this paper, a coupling p+n field effect transistor (FET) amplification circuit is designed to detect methane gas. By optimizing the load resistance ( R L ), the response to methane of the commercial MP-4 sensor can be magnified ~15 times using this coupling circuit. At the same time, it decreases the limit of detection (LOD) from several hundred ppm to ~10 ppm methane, with the apparent response of 7.0 ± 0.2 and voltage signal of 1.1 ± 0.1 V. This is promising for the detection of trace concentrations of methane gas to avoid an accidental explosion because its lower explosion limit (LEL) is ~5%. The mechanism of this coupling circuit is that the n-type FET firstly generates an output voltage ( V OUT ) amplification process caused by the gate voltage-induced resistance change of the FET. Then, the p-type FET continues to amplify the signal based on the previous V OUT amplification process.

Continuous in vitro evolution of bacteriophage RNA polymerase promoters

NASA Technical Reports Server (NTRS)

Breaker, R. R.; Banerji, A.; Joyce, G. F.

1994-01-01

Rapid in vitro evolution of bacteriophage T7, T3, and SP6 RNA polymerase promoters was achieved by a method that allows continuous enrichment of DNAs that contain functional promoter elements. This method exploits the ability of a special class of nucleic acid molecules to replicate continuously in the presence of both a reverse transcriptase and a DNA-dependent RNA polymerase. Replication involves the synthesis of both RNA and cDNA intermediates. The cDNA strand contains an embedded promoter sequence, which becomes converted to a functional double-stranded promoter element, leading to the production of RNA transcripts. Synthetic cDNAs, including those that contain randomized promoter sequences, can be used to initiate the amplification cycle. However, only those cDNAs that contain functional promoter sequences are able to produce RNA transcripts. Furthermore, each RNA transcript encodes the RNA polymerase promoter sequence that was responsible for initiation of its own transcription. Thus, the population of amplifying molecules quickly becomes enriched for those templates that encode functional promoters. Optimal promoter sequences for phage T7, T3, and SP6 RNA polymerase were identified after a 2-h amplification reaction, initiated in each case with a pool of synthetic cDNAs encoding greater than 10(10) promoter sequence variants.

Pathways of Prion Spread during Early Chronic Wasting Disease in Deer.

PubMed

Hoover, Clare E; Davenport, Kristen A; Henderson, Davin M; Denkers, Nathaniel D; Mathiason, Candace K; Soto, Claudio; Zabel, Mark D; Hoover, Edward A

2017-05-15

Among prion infections, two scenarios of prion spread are generally observed: (i) early lymphoid tissue replication or (ii) direct neuroinvasion without substantial antecedent lymphoid amplification. In nature, cervids are infected with chronic wasting disease (CWD) prions by oral and nasal mucosal exposure, and studies of early CWD pathogenesis have implicated pharyngeal lymphoid tissue as the earliest sites of prion accumulation. However, knowledge of chronological events in prion spread during early infection remains incomplete. To investigate this knowledge gap in early CWD pathogenesis, we exposed white-tailed deer to CWD prions by mucosal routes and performed serial necropsies to assess PrP CWD tissue distribution by real-time quaking-induced conversion (RT-QuIC) and tyramide signal amplification immunohistochemistry (TSA-IHC). Although PrP CWD was not detected by either method in the initial days (1 and 3) postexposure, we observed PrP CWD seeding activity and follicular immunoreactivity in oropharyngeal lymphoid tissues at 1 and 2 months postexposure (MPE). At 3 MPE, PrP CWD replication had expanded to all systemic lymphoid tissues. By 4 MPE, the PrP CWD burden in all lymphoid tissues had increased and approached levels observed in terminal disease, yet there was no evidence of nervous system invasion. These results indicate the first site of CWD prion entry is in the oropharynx, and the initial phase of prion amplification occurs in the oropharyngeal lymphoid tissues followed by rapid dissemination to systemic lymphoid tissues. This lymphoid replication phase appears to precede neuroinvasion. IMPORTANCE Chronic wasting disease (CWD) is a universally fatal transmissible spongiform encephalopathy affecting cervids, and natural infection occurs through oral and nasal mucosal exposure to infectious prions. Terminal disease is characterized by PrP CWD accumulation in the brain and lymphoid tissues of affected animals. However, the initial sites of prion accumulation and pathways of prion spread during early CWD infection remain unknown. To investigate the chronological events of early prion pathogenesis, we exposed deer to CWD prions and monitored the tissue distribution of PrP CWD over the first 4 months of infection. We show CWD uptake occurs in the oropharynx with initial prion replication in the draining oropharyngeal lymphoid tissues, rapidly followed by dissemination to systemic lymphoid tissues without evidence of neuroinvasion. These data highlight the two phases of CWD infection: a robust prion amplification in systemic lymphoid tissues prior to neuroinvasion and establishment of a carrier state. Copyright © 2017 American Society for Microbiology.

The histone acetyltransferases CBP and Chameau integrate developmental and DNA replication programs in Drosophila ovarian follicle cells

PubMed Central

McConnell, Kristopher H.; Dixon, Michael; Calvi, Brian R.

2012-01-01

DNA replication origin activity changes during development. Chromatin modifications are known to influence the genomic location of origins and the time during S phase that they initiate replication in different cells. However, how chromatin regulates origins in concert with cell differentiation remains poorly understood. Here, we use developmental gene amplification in Drosophila ovarian follicle cells as a model to investigate how chromatin modifiers regulate origins in a developmental context. We find that the histone acetyltransferase (HAT) Chameau (Chm) binds to amplicon origins and is partially required for their function. Depletion of Chm had relatively mild effects on origins during gene amplification and genomic replication compared with previous knockdown of its ortholog HBO1 in human cells, which has severe effects on origin function. We show that another HAT, CBP (Nejire), also binds amplicon origins and is partially required for amplification. Knockdown of Chm and CBP together had a more severe effect on nucleosome acetylation and amplicon origin activity than knockdown of either HAT alone, suggesting that these HATs collaborate in origin regulation. In addition to their local function at the origin, we show that Chm and CBP also globally regulate the developmental transition of follicle cells into the amplification stages of oogenesis. Our results reveal a complexity of origin epigenetic regulation by multiple HATs during development and suggest that chromatin modifiers are a nexus that integrates differentiation and DNA replication programs. PMID:22951641

Weak Value Amplification of a Post-Selected Single Photon

NASA Astrophysics Data System (ADS)

Hallaji, Matin

Weak value amplification (WVA) is a measurement technique in which the effect of a pre- and post-selected system on a weakly interacting probe is magnified. In this thesis, I present the first experimental observation of WVA of a single photon. We observed that a signal photon --- sent through a polarization interferometer and post-selected by photodetection in the almost-dark port --- can act like eight photons. The effect of this single photon is measured as a nonlinear phase shift on a separate laser beam. The interaction between the two is mediated by a sample of laser- cooled 85Rb atoms. Electromagnetically induced transparency (EIT) is used to enhance the nonlinearity and overcome resonant absorption. I believe this work to be the first demonstration of WVA where a deterministic interaction is used to entangle two distinct optical systems. In WVA, the amplification is contingent on discarding a large portion of the original data set. While amplification increases measurement sensitivity, discarding data worsens it. Questioning whether these competing effects conspire to improve or diminish measurement accuracy has resulted recently in controversy. I address this question by calculating the maximum amount of information achievable with the WVA technique. By comparing this information to that achievable by the standard technique, where no post-selection is employed, I show that the WVA technique can be advantageous under a certain class of noise models. Finally, I propose a way to optimally apply the WVA technique.

Natural laminar flow flight experiments on a swept wing business jet-boundary layer stability analyses

NASA Technical Reports Server (NTRS)

Rozendaal, R. A.

1986-01-01

The linear boundary layer stability analyses and their correlation with data of 18 cases from a natural laminar flow (NLF) flight test program using a Cessna Citation 3 business jet are described. The transition point varied from 5% to 35% chord for these conditions, and both upper and lower wing surfaces were included. Altitude varied from 10,000 to 43,000 ft and Mach number from 0.3 to 0.8. Four cases were at nonzero sideslip. Although there was much scatter in the results, the analyses of boundary layer stability at the 18 conditions led to the conclusion that crossflow instability was the primary cause of transition. However, the sideslip cases did show some interaction of crossflow and Tollmien-Schlichting disturbances. The lower surface showed much lower Tollmien-Schlichting amplification at transition than the upper surface, but similar crossflow amplifications. No relationship between Mach number and disturbance amplification at transition could be found. The quality of these results is open to question from questionable wing surface quality, inadequate density of transition sensors on the wing upper surface, and an unresolved pressure shift in the wing pressure data. The results of this study show the need for careful preparation for transition experiments. Preparation should include flow analyses of the test surface, boundary layer disturbance amplification analyses, and assurance of adequate surface quality in the test area. The placement of necessary instruments and usefulness of the resulting data could largely be determined during the pretest phase.

SALLY LEVEL II- COMPUTE AND INTEGRATE DISTURBANCE AMPLIFICATION RATES ON SWEPT AND TAPERED LAMINAR FLOW CONTROL WINGS WITH SUCTION

NASA Technical Reports Server (NTRS)

Srokowski, A. J.

1994-01-01

The computer program SALLY was developed to compute the incompressible linear stability characteristics and integrate the amplification rates of boundary layer disturbances on swept and tapered wings. For some wing designs, boundary layer disturbance can significantly alter the wing performance characteristics. This is particularly true for swept and tapered laminar flow control wings which incorporate suction to prevent boundary layer separation. SALLY should prove to be a useful tool in the analysis of these wing performance characteristics. The first step in calculating the disturbance amplification rates is to numerically solve the compressible laminar boundary-layer equation with suction for the swept and tapered wing. A two-point finite-difference method is used to solve the governing continuity, momentum, and energy equations. A similarity transformation is used to remove the wall normal velocity as a boundary condition and place it into the governing equations as a parameter. Thus the awkward nonlinear boundary condition is avoided. The resulting compressible boundary layer data is used by SALLY to compute the incompressible linear stability characteristics. The local disturbance growth is obtained from temporal stability theory and converted into a local growth rate for integration. The direction of the local group velocity is taken as the direction of integration. The amplification rate, or logarithmic disturbance amplitude ratio, is obtained by integration of the local disturbance growth over distance. The amplification rate serves as a measure of the growth of linear disturbances within the boundary layer and can serve as a guide in transition prediction. This program is written in FORTRAN IV and ASSEMBLER for batch execution and has been implemented on a CDC CYBER 70 series computer with a central memory requirement of approximately 67K (octal) of 60 bit words. SALLY was developed in 1979.

HPV16 and 18 genome amplification show different E4-dependence, with 16E4 enhancing E1 nuclear accumulation and replicative efficiency via its cell cycle arrest and kinase activation functions

PubMed Central

Jackson, Deborah; Mahmood, Radma

2017-01-01

To clarify E1^E4’s role during high-risk HPV infection, the E4 proteins of HPV16 and 18 were compared side by side using an isogenic keratinocyte differentiation model. While no effect on cell proliferation or viral genome copy number was observed during the early phase of either virus life cycle, time-course experiments showed that viral genome amplification and L1 expression were differently affected upon differentiation, with HPV16 showing a much clearer E4 dependency. Although E4 loss never completely abolished genome amplification, its more obvious contribution in HPV16 focused our efforts on 16E4. As previously suggested, in the context of the virus life cycle, 16E4s G2-arrest capability was found to contribute to both genome amplification success and L1 accumulation. Loss of 16E4 also lead to a reduced maintenance of ERK, JNK and p38MAPK activity throughout the genome amplifying cell layers, with 16E4 (but not 18E4) co-localizing precisely with activated cytoplasmic JNK in both wild type raft tissue, and HPV16-induced patient biopsy tissue. When 16E1 was co-expressed with E4, as occurs during genome amplification in vivo, the E1 replication helicase accumulated preferentially in the nucleus, and in transient replication assays, E4 stimulated viral genome amplification. Interestingly, a 16E1 mutant deficient in its regulatory phosphorylation sites no longer accumulated in the nucleus following E4 co-expression. E4-mediated stabilisation of 16E2 was also apparent, with E2 levels declining in organotypic raft culture when 16E4 was absent. These results suggest that 16E4-mediated enhancement of genome amplification involves its cell cycle inhibition and cellular kinase activation functions, with E4 modifying the activity and function of viral replication proteins including E1. These activities of 16E4, and the different kinase patterns seen here with HPV18, 31 and 45, may reflect natural differences in the biology and tropisms of these viruses, as well as differences in E4 function. PMID:28306742

Sources of Uncertainty in Modelling mid-Pliocene Arctic Amplification

NASA Astrophysics Data System (ADS)

Dolan, A. M.; Haywood, A.; Howell, F.; Prescott, C.; Pope, J. O.; Hill, D. J.; Voss, J.

2016-12-01

The mid-Pliocene Warm Period (mPWP) is an interval between 3.264 and 3.205 million years ago, which has globally warmer temperatures (Haywood et al., 2013) accompanied by levels of CO2 above pre-Industrial ( 400 ppmv; e.g. Bartoli et al. 2011; Badger et al., 2013). Arctic amplification of temperatures is a major characteristic of all proxy-based reconstructions of the mPWP in terms of both oceanic (Dowsett et al., 2010) and land warming (Salzmann et al., 2013). For example, evidence of fossilised forests in the Canadian high-Arctic show summer temperatures of up to 16°C warmer than present (Csank et al., 2010). Also, summer temperatures estimates based on pollen reconstructions at Lake El'gygytgyn in North East Russia are up to 6°C warmer than present day (Brigham-Grette et al., 2013). Nevertheless, results from the first phase of the Pliocene Model Intercomparison Project (PlioMIP) suggest that climate models may underestimate the degree of Arctic amplification suggested by proxy records (Haywood et al., 2013). Here we use a large ensemble of experiments performed with the HadCM3 climate model to explore relative sources of uncertainty in the simulations of Arctic amplification. Within this suite of over 150 simulations, we consider; (i) a range of mPWP-specific orbital configurations to quantify the influence of temporal variability, (ii) a range of CO2 scenarios to take into account uncertainties in this particular greenhouse gas forcing, (iii) a perturbed physics ensemble to investigate parametric uncertainty within the HadCM3 climate model, and also (iv) a number of experiments with altered palaeogeographies (including changes to topography and ice sheets) to assess the impact of different boundary condition realisations on our simulation of Arctic amplification. We also incorporate results from the PlioMIP project to allude to the effect of structural uncertainty on Arctic warming. Following methods used in Yoshimori et al. (2013) and Laine et al. (2016), we identify the largest sources of uncertainty over both the land and the ocean in simulating the degree of amplification suggested by available proxy data. We also relate predictions of Arctic amplification to key features within the model, for example, sea ice extent and seasonality.

Impact of temporal, spatial and cascaded effects on the pulse formation in ultra-broadband parametric amplifiers.

PubMed

Lang, T; Harth, A; Matyschok, J; Binhammer, T; Schultze, M; Morgner, U

2013-01-14

A 2 + 1 dimensional nonlinear pulse propagation model is presented, illustrating the weighting of different effects for the parametric amplification of ultra-broadband spectra in different regimes of energy scaling. Typical features in the distribution of intensity and phase of state-of-the-art OPA-systems can be understood by cascaded spatial and temporal effects.

Thermal: Differential Scanning Calorimetry (DSC), Thermogravimetric Analysis (TGA), and Polarized Microscopy Instrumentation for the Analysis of Field-Controlled Anisotropic Nanomaterials

DTIC Science & Technology

2014-11-14

figure 1.2.1, right). The discovery TGA furnace design employs a silicon carbide ( SiC ) inner chamber. Four halogen lamps surrounded by a water...amplification,(13, 17) self-phase modulation (18, 19), and new nonlinear phenomena such as the nonlinear optical mirror ,(20) and the mirrorless optical

Advanced Optical Fiber Communication Systems.

DTIC Science & Technology

1993-02-28

feedback (DFB) laser and a fiber Fabry - Perot (FFP) interferometer for optical frequency discrimination. After the photodetector and amplification, a...filter, an envelope detector, and an integrator; these three components function in tandem as a phase demodulator . We have analyzed the nonlinearities...down-converter and FSK demodulator extract the desired video signals. The measured carrier-to-noise ratio (CNR) at the photodiode must be approximately

Principles of quantitation of viral loads using nucleic acid sequence-based amplification in combination with homogeneous detection using molecular beacons.

PubMed

Weusten, Jos J A M; Carpay, Wim M; Oosterlaken, Tom A M; van Zuijlen, Martien C A; van de Wiel, Paul A

2002-03-15

For quantitative NASBA-based viral load assays using homogeneous detection with molecular beacons, such as the NucliSens EasyQ HIV-1 assay, a quantitation algorithm is required. During the amplification process there is a constant growth in the concentration of amplicons to which the beacon can bind while generating a fluorescence signal. The overall fluorescence curve contains kinetic information on both amplicon formation and beacon binding, but only the former is relevant for quantitation. In the current paper, mathematical modeling of the relevant processes is used to develop an equation describing the fluorescence curve as a function of the amplification time and the relevant kinetic parameters. This equation allows reconstruction of RNA formation, which is characterized by an exponential increase in concentrations as long as the primer concentrations are not rate limiting and by linear growth over time after the primer pool is depleted. During the linear growth phase, the actual quantitation is based on assessing the amplicon formation rate from the viral RNA relative to that from a fixed amount of calibrator RNA. The quantitation procedure has been successfully applied in the NucliSens EasyQ HIV-1 assay.

Ultrasensitive and rapid detection of β-conglutin combining aptamers and isothermal recombinase polymerase amplification.

PubMed

Jauset-Rubio, Miriam; Sabaté Del Río, Jonathan; Mairal, Teresa; Svobodová, Markéta; El-Shahawi, Mohammad S; Bashammakh, Abdulaziz S; Alyoubi, Abdulrahman O; O'Sullivan, Ciara K

2017-01-01

Lupin is increasingly being used in a variety of food products due to its nutritional, functional and nutraceutical properties. However, several examples of severe and even fatal food-associated anaphylaxis due to lupin inhalation or ingestion have been reported, resulting in the lupin subunit β-conglutin, being defined as the Lup an 1 allergen by the International Union of Immunological Societies (IUIS) in 2008. Here, we report an innovative method termed aptamer-recombinase polymerase amplification (Apta-RPA) exploiting the affinity and specificity of a DNA aptamer selected against the anaphylactic β-conglutin allergen termed β-conglutin binding aptamer II (β-CBA II), facilitating ultrasensitive detection via isothermal amplification. Combining magnetic beads as the solid phase with Apta-RPA detection, the total assay time was reduced from 210 min to just 25 min, with a limit of detection of 3.5 × 10 -11  M, demonstrating a rapid and ultrasensitive generic methodology that can be used with any aptamer. Future work will focus on further simplification of the assay to a lateral flow format. Graphical Abstract Schematic representation of the rapid and novel bead-based Apta-RPA assay.

An orc1 allele with a mutated APC motif is female sterile with amplification defects.

PubMed

Park, So Young; Asano, Maki

2012-08-01

The origin recognition complex 1 (ORC1) is the largest subunit of the ORC, the heteromeric hexamer. ORC1 is an essential component of the pre-replicative complex (pre-RC) that licenses eukaryote DNA replication origins. The levels of ORC1 fluctuate during the mitotic cell cycle in Drosophila as well as in some human cells. Proteolysis of ORC1 occurs at the end of M phase in Drosophila, which is mediated by the anaphase-promoting complex (APC), and in late S phase in human cells by Skip-Cullin-F box (SCF). Previously we showed that proteolysis of ORC1 by APC is mediated by the ORC1 destruction box (the O-box), an APC motif conserved among species yet distinct from the D-box or KEN-box. Recently we showed that replacing the O-box with the D-box (ORC1O→D) changes the degradation profile of ORC1 during a canonical cell cycle. Here we report further characterization of the ORC1O→D allele that turned out to be a useful tool to examine the function of ORC1 in other modes of DNA replication during oogenesis. In endoreplication stages ORC1O→D does not change any DNA content profiles, consistent with our previous finding that ORC is dispensable for endoreplication. However, in amplification stage replication efficiency of ORC1O→D is drastically reduced, which resulted in amplification defects that led to thin egg shell phenotype. Taken together, our analyses show that orc1 allele newly identified is female sterile and possesses a unique feature of phenotypes that are distinct in different modes of DNA replication.

Generation and Amplification of Tunable Multicolored Femtosecond Laser Pulses by Using Cascaded Four-Wave Mixing in Transparent Bulk Media

PubMed Central

Liu, Jun; Kobayashi, Takayoshi

2010-01-01

We have reviewed the generation and amplification of wavelength-tunable multicolored femtosecond laser pulses using cascaded four-wave mixing (CFWM) in transparent bulk media, mainly concentrating on our recent work. Theoretical analysis and calculations based on the phase-matching condition could explain well the process semi-quantitatively. The experimental studies showed: (1) as many as fifteen spectral up-shifted and two spectral down-shifted sidebands were obtained simultaneously with spectral bandwidth broader than 1.8 octaves from near ultraviolet (360 nm) to near infrared (1.2 μm); (2) the obtained sidebands were spatially separated well and had extremely high beam quality with M2 factor better than 1.1; (3) the wavelengths of the generated multicolor sidebands could be conveniently tuned by changing the crossing angle or simply replacing with different media; (4) as short as 15-fs negatively chirped or nearly transform limited 20-fs multicolored femtosecond pulses were obtained when one of the two input beams was negatively chirped and the other was positively chirped; (5) the pulse energy of the sideband can reach a μJ level with power stability better than 1% RMS; (6) broadband two-dimensional (2-D) multicolored arrays with more than ten periodic columns and more than ten rows were generated in a sapphire plate; (7) the obtained sidebands could be simultaneously spectra broadened and power amplified in another bulk medium by using cross-phase modulation (XPM) in conjunction with four-wave optical parametric amplification (FOPA). The characterization showed that this is interesting and the CFWM sidebands generated by this novel method have good enough qualities in terms of power stability, beam quality, and temporal features suited to various experiments such as ultrafast multicolor time-resolved spectroscopy and multicolor-excitation nonlinear microscopy. PMID:22399882

Generation and subsequent amplification of few-cycle femtosecond pulses from a picosecond pump laser

NASA Astrophysics Data System (ADS)

Mukhin, I. B.; Kuznetsov, I. I.; Palashov, O. V.

2018-04-01

Using a new approach, in which generation of femtosecond pulses as short as a few field cycles is implemented directly from the radiation of a picosecond pump laser, pulses with the microjoule energy, the repetition rate 10 kHz, and the duration less than 26 fs are generated in the spectral range 1.3 ‑ 1.4 μm. In the process of generating this radiation, use was made of a method providing passive phase stabilisation of the carrier oscillation of the electromagnetic field and its slow envelope. The radiation spectrum was converted into the range of parametric amplification in the BBO crystal by the broadband second harmonic generation; the pulse was parametrically amplified up to the microjoule level and compressed by chirped mirrors to a duration of 28 fs.

Resonant interactions between cometary ions and low frequency electromagnetic waves

NASA Technical Reports Server (NTRS)

Thorne, Richard M.; Tsurutani, Bruce T.

1987-01-01

The conditions for resonant wave amplification in a plasma with a ring-beam distribution which is intended to model pick-up ions in a cometary environment are investigated. The inclination between the interplanetary field and the solar wind is found to play a crucial role in governing both the resonant frequency and the growth rate of any unstable mode. It is suggested that the low-frequency MHD mode should experience the most rapid amplification for intermediate inclination. In the frame of the solar wind, such waves should propagate along the field in the direction upstream toward the sun with a phase speed lower than the beaming velocity of the pick-up ions. This mechanism may account for the presence of the interior MHD waves noted by satellites over a region surrounding comets Giacobini-Zinner and Halley.

Resonant interactions between cometary ions and low frequency electromagnetic waves

NASA Astrophysics Data System (ADS)

Thorne, R. M.; Tsurutani, B. T.

1987-12-01

The conditions for resonant wave amplification in a plasma with a ring-beam distribution which is intended to model pick-up ions in a cometary environment are investigated. The inclination between the interplanetary field and the solar wind is found to play a crucial role in governing both the resonant frequency and the growth rate of any unstable mode. It is suggested that the low-frequency MHD mode should experience the most rapid amplification for intermediate inclination. In the frame of the solar wind, such waves should propagate along the field in the direction upstream toward the sun with a phase speed lower than the beaming velocity of the pick-up ions. This mechanism may account for the presence of the interior MHD waves noted by satellites over a region surrounding comets Giacobini-Zinner and Halley.

Magnesium-Assisted Continuous Growth of Strongly Iron-Enriched Incisors.

PubMed

Srot, Vesna; Bussmann, Birgit; Salzberger, Ute; Deuschle, Julia; Watanabe, Masashi; Pokorny, Boštjan; Jelenko Turinek, Ida; Mark, Alison F; van Aken, Peter A

2017-01-24

Teeth are an excellent example where optimally designed nanoarchitectures with precisely constructed components consist of simple compounds. Typically, these simple constituent phases with insignificant properties show mechanical property amplifications when formed into composite architectures. Material properties of functional composites are generally regulated on the nanoscale, which makes their characterization particularly demanding. Using advanced analytical and imaging transmission electron microscopy techniques, we identified innovative microstructural adjustments combined with astonishing compositional adaptations in incisors of coypu. Unique constituents, recognized as an additional amorphous Fe-rich surface layer followed by a transition zone covering pigmented enamel, provide the required structural stability to withstand repeated mechanical load. The chemically diverse Fe-rich surface layer, including ferrihydrite and iron-calcium phosphates, gives the typical orange-brown coloration to the incisors. Within the spaces between elongated hydroxyapatite crystals in the pigmented enamel, only ferrihydrite was found, implying that enamel pigmentation is a very strictly controlled process. Most significantly, an unprecedentedly high amount of Mg was measured in the amorphous flake-like material within the dentinal tubules of the incisors, suggesting the presence of a (Mg,Ca) phosphate phase. This unusually high influx of Mg into the dentin of incisors, but not molars, suggests a substantial functionality of Mg in the initial formation stages and constant growth of incisors. The present results emphasize the strong mutual correlation among the microstructure, chemical composition, and mechanical properties of mineralized dental tissues.

Chromatic characterization of ion-exchanged glass binary phase plates for mode-division multiplexing.

PubMed

Prieto-Blanco, Xesús; Montero-Orille, Carlos; Moreno, Vicente; Mateo, Eduardo F; Liñares, Jesús

2015-04-10

Mode-division multiplexing (MDM) in few-mode fibers is regarded as a promising candidate to increase optical network capacity. A fundamental element for MDM is a modal transformer to LP modes which can be implemented in a free-space basis by using multiregion phase plates, that is, LP plates. Likewise, several wavelengths have to be used due to wavelength multiplexing purposes, optical amplification tasks, and so on. In this work we show that efficient monolithic binary phase plates for different wavelengths can be fabricated by ion-exchange in glass and used for MDM tasks. We introduce an optical characterization method of the chromatic properties of such phase plates which combines the inverse Wentzel-Kramers-Brillouin (IWKB) together with Mach-Zehnder and Michelson-based interferometric techniques. The interferometric method provides a measurement of the phase step for several wavelengths, which characterizes the chromatic properties of the phase plate. Consequently, it is shown that the IWKB method allows us to design and characterize the phase plates in an easy and fast way.

Tailored pump compensation for Brillouin optical time-domain analysis with distributed Brillouin amplification.

PubMed

Kim, Young Hoon; Song, Kwang Yong

2017-06-26

A Brillouin optical time domain analysis (BOTDA) system utilizing tailored compensation for the propagation loss of the pump pulse is demonstrated for long-range and high-resolution distributed sensing. A continuous pump wave for distributed Brillouin amplification (DBA pump) of the pump pulse co-propagates with the probe wave, where gradual variation of the spectral width is additionally introduced to the DBA pump to obtain a uniform Brillouin gain along the position. In the experimental confirmation, a distributed strain measurement along a 51.2 km fiber under test is presented with a spatial resolution of 20 cm, in which the measurement error (σ) of less than 1.45 MHz and the near-constant Brillouin gain of the probe wave are maintained throughout the fiber.

Self-Injurious Behaviour in Intellectual Disability Syndromes: Evidence for Aberrant Pain Signalling as a Contributing Factor

ERIC Educational Resources Information Center

Peebles, K. A.; Price, T. J.

2012-01-01

Background: In most individuals, injury results in activation of peripheral nociceptors (pain-sensing neurons of the peripheral nervous system) and amplification of central nervous system (CNS) pain pathways that serve as a disincentive to continue harmful behaviour; however, this may not be the case in some developmental disorders that cause…

A novel real time PCR assay using melt curve analysis for ivory identification.

PubMed

Kitpipit, Thitika; Penchart, Kitichaya; Ouithavon, Kanita; Satasook, Chutamas; Linacre, Adrian; Thanakiatkrai, Phuvadol

2016-10-01

Demand for ivory and expansion of human settlements have resulted in a rapid decline in the number of elephants. Enforcement of local and international laws and regulations requires identification of the species from which any ivory, or ivory products, originated. Further geographical assignment of the dead elephant from which the ivory was taken can assist in forensic investigations. In this study, a real-time PCR assay using melt curve analysis was developed and fully validated for forensic use. The presence or absence of three Elephantidae-specific and elephant species-specific melting peaks was used to identify the elephant species. Using 141 blood and ivory samples from the three extant elephant species, the assay demonstrated very high reproducibility and accuracy. The limit of detection was as low as 0.031ng of input DNA for conventional amplification and 0.002ng for nested amplification. Both DNA concentrations are typically encountered in forensic casework, especially for degraded samples. No cross-reactivity was observed for non-target species. Evaluation of direct amplification and nested amplification demonstrated the assay's flexibility and capability of analyzing low-template DNA samples and aged samples. Additionally, blind trial testing showed the assay's suitability application in real casework. In conclusion, wildlife forensic laboratories could use this novel, quick, and low-cost assay to help combat the continuing poaching crises leading to the collapse of elephant numbers in the wild. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Miniaturized devices towards an integrated lab-on-a-chip platform for DNA diagnostics

NASA Astrophysics Data System (ADS)

Kaprou, G.; Papadakis, G.; Kokkoris, G.; Papadopoulos, V.; Kefala, I.; Papageorgiou, D.; Gizeli, E.; Tserepi, A.

2015-06-01

Microfluidics is an emerging technology enabling the development of Lab-on-a-chip (LOC) systems for clinical diagnostics, drug discovery and screening, food safety and environmental analysis. LOC systems integrate and scale down one or several laboratory functions on a single chip of a few mm2 to cm2 in size, and account for many advantages on biochemical analyses, such as low sample and reagent consumption, low cost, reduced analysis time, portability and point-of-need compatibility. Currently, available nucleic acid diagnostic tests take advantage of Polymerase Chain Reaction (PCR) that allows exponential amplification of portions of nucleic acid sequences that can be used as indicators for the identification of various diseases. Here, we present a comparison between static chamber and continuous flow miniaturized PCR devices, in terms of energy consumption for devices fabricated on the same material stack, with identical sample volume and channel dimensions. The comparison is implemented by a computational study coupling heat transfer in both solid and fluid, mass conservation of species, and joule heating. Based on the conclusions of this study, we develop low-cost and fast DNA amplification devices for both PCR and isothermal amplification, and we implement them in the detection of mutations related to breast cancer. The devices are fabricated by mass production amenable technologies on printed circuit board (PCB) substrates, where copper facilitates the incorporation of on-chip microheaters, defining the thermal zones necessary for PCR or isothermal amplification methods.

Phase-Noise and Amplitude-Noise Measurement of Low-Power Signals

NASA Technical Reports Server (NTRS)

Rubiola, Enrico; Salik, Ertan; Yu, Nan; Maleki, Lute

2004-01-01

Measuring the phase fluctuation between a pair of low-power microwave signals, the signals must be amplified before detection. In such cases the phase noise of the amplifier pair is the main cause of 1/f background noise of the instrument. this article proposes a scheme that makes amplification possible while rejecting the close in 1/f (flicker) noise of the two amplifiers. Noise rejection, which relies upon the understanding of the amplifier noise mechanism does not require averaging. Therefore, our scheme can also be the detector of a closed loop noise reduction system. the first prototype, compared to a traditional saturated mixer system under the same condition, show a 24 dB noise reduction of the 1/f region.

Towards Terawatt Sub-Cycle Long-Wave Infrared Pulses via Chirped Optical Parametric Amplification and Indirect Pulse Shaping

PubMed Central

Yin, Yanchun; Chew, Andrew; Ren, Xiaoming; Li, Jie; Wang, Yang; Wu, Yi; Chang, Zenghu

2017-01-01

We present an approach for both efficient generation and amplification of 4–12 μm pulses by tailoring the phase matching of the nonlinear crystal Zinc Germanium Phosphide (ZGP) in a narrowband-pumped optical parametric chirped pulse amplifier (OPCPA) and a broadband-pumped dual-chirped optical parametric amplifier (DC-OPA), respectively. Preliminary experimental results are obtained for generating 1.8–4.2 μm super broadband spectra, which can be used to seed both the signal of the OPCPA and the pump of the DC-OPA. The theoretical pump-to-idler conversion efficiency reaches 27% in the DC-OPA pumped by a chirped broadband Cr2+:ZnSe/ZnS laser, enabling the generation of  Terawatt-level 4–12 μm pulses with an available large-aperture ZGP. Furthermore, the 4–12 μm idler pulses can be compressed to sub-cycle pulses by compensating the tailored positive chirp of the idler pulses using the bulk compressor NaCl, and by indirectly controlling the higher-order idler phase through tuning the signal (2.4–4.0 μm) phase with a commercially available acousto-optic programmable dispersive filter (AOPDF). A similar approach is also described for generating high-energy 4–12 μm sub-cycle pulses via OPCPA pumped by a 2 μm Ho:YLF laser. PMID:28367966

Frequency Preference Response to Oscillatory Inputs in Two-dimensional Neural Models: A Geometric Approach to Subthreshold Amplitude and Phase Resonance.

PubMed

Rotstein, Horacio G

2014-01-01

We investigate the dynamic mechanisms of generation of subthreshold and phase resonance in two-dimensional linear and linearized biophysical (conductance-based) models, and we extend our analysis to account for the effect of simple, but not necessarily weak, types of nonlinearities. Subthreshold resonance refers to the ability of neurons to exhibit a peak in their voltage amplitude response to oscillatory input currents at a preferred non-zero (resonant) frequency. Phase-resonance refers to the ability of neurons to exhibit a zero-phase (or zero-phase-shift) response to oscillatory input currents at a non-zero (phase-resonant) frequency. We adapt the classical phase-plane analysis approach to account for the dynamic effects of oscillatory inputs and develop a tool, the envelope-plane diagrams, that captures the role that conductances and time scales play in amplifying the voltage response at the resonant frequency band as compared to smaller and larger frequencies. We use envelope-plane diagrams in our analysis. We explain why the resonance phenomena do not necessarily arise from the presence of imaginary eigenvalues at rest, but rather they emerge from the interplay of the intrinsic and input time scales. We further explain why an increase in the time-scale separation causes an amplification of the voltage response in addition to shifting the resonant and phase-resonant frequencies. This is of fundamental importance for neural models since neurons typically exhibit a strong separation of time scales. We extend this approach to explain the effects of nonlinearities on both resonance and phase-resonance. We demonstrate that nonlinearities in the voltage equation cause amplifications of the voltage response and shifts in the resonant and phase-resonant frequencies that are not predicted by the corresponding linearized model. The differences between the nonlinear response and the linear prediction increase with increasing levels of the time scale separation between the voltage and the gating variable, and they almost disappear when both equations evolve at comparable rates. In contrast, voltage responses are almost insensitive to nonlinearities located in the gating variable equation. The method we develop provides a framework for the investigation of the preferred frequency responses in three-dimensional and nonlinear neuronal models as well as simple models of coupled neurons.

Does the Arctic Amplification peak this decade?

NASA Astrophysics Data System (ADS)

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.

HER2/neu gene amplification determines the sensitivity of uterine serous carcinoma cell lines to AZD8055, a novel dual mTORC1/2 inhibitor.

PubMed

English, Diana P; Roque, Dana M; Carrara, Luisa; Lopez, Salvatore; Bellone, Stefania; Cocco, Emiliano; Bortolomai, Ileana; Schwartz, Peter E; Rutherford, Thomas; Santin, Alessandro D

2013-12-01

To evaluate c-erbB2 gene amplification in a series of primary uterine serous carcinoma (USC) cell lines. To assess the efficacy of AZD8055, a novel dual mTORC1/2 inhibitor against primary HER2/neu amplified vs HER2/neu not amplified USC cell lines. Twenty-two primary USC cell lines were evaluated for c-erbB2 oncogene amplification by FISH assays. In vitro sensitivity to AZD8055 was evaluated by flow-cytometry-based viability and proliferation assays. Cell cycle profile and downstream cellular responses to AZD8055 were assessed by measuring the DNA content of cells and by phosphorylation of the S6 protein by flow-cytometry. Nine of 22 (40.9%) USC cell lines demonstrated c-erbB2 gene amplification by FISH. AZD8055 caused a strong differential growth inhibition in USC cell lines, with high HER-2/neu-expressors demonstrating significantly higher sensitivity when compared to low HER-2/neu-expressors (AZD-8055 IC50 mean±SEM=0.27±0.05μM in c-erbB2 amplified versus 1.67±0.68μM in c-erbB2 not amplified tumors, P=0.03). AZD8055 growth-inhibition was associated with a significant and dose-dependent increase in the percentage of cells blocked in the G0/G1 cell cycle phase and a dose-dependent decline in pS6 levels in both c-erbB2 amplified vs c-erbB2 not amplified USC cell lines. AZD8055 may represent a novel targeted therapeutic agent in patients harboring advanced/recurrent/refractory USC. c-erbB2 gene amplification may represent a biomarker to identify USC patients who may benefit most from the use of AZD8055. © 2013.

Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates.

PubMed

Leung, Kaston; Klaus, Anders; Lin, Bill K; Laks, Emma; Biele, Justina; Lai, Daniel; Bashashati, Ali; Huang, Yi-Fei; Aniba, Radhouane; Moksa, Michelle; Steif, Adi; Mes-Masson, Anne-Marie; Hirst, Martin; Shah, Sohrab P; Aparicio, Samuel; Hansen, Carl L

2016-07-26

The genomes of large numbers of single cells must be sequenced to further understanding of the biological significance of genomic heterogeneity in complex systems. Whole genome amplification (WGA) of single cells is generally the first step in such studies, but is prone to nonuniformity that can compromise genomic measurement accuracy. Despite recent advances, robust performance in high-throughput single-cell WGA remains elusive. Here, we introduce droplet multiple displacement amplification (MDA), a method that uses commercially available liquid dispensing to perform high-throughput single-cell MDA in nanoliter volumes. The performance of droplet MDA is characterized using a large dataset of 129 normal diploid cells, and is shown to exceed previously reported single-cell WGA methods in amplification uniformity, genome coverage, and/or robustness. We achieve up to 80% coverage of a single-cell genome at 5× sequencing depth, and demonstrate excellent single-nucleotide variant (SNV) detection using targeted sequencing of droplet MDA product to achieve a median allelic dropout of 15%, and using whole genome sequencing to achieve false and true positive rates of 9.66 × 10(-6) and 68.8%, respectively, in a G1-phase cell. We further show that droplet MDA allows for the detection of copy number variants (CNVs) as small as 30 kb in single cells of an ovarian cancer cell line and as small as 9 Mb in two high-grade serous ovarian cancer samples using only 0.02× depth. Droplet MDA provides an accessible and scalable method for performing robust and accurate CNV and SNV measurements on large numbers of single cells.

Computational Gene Expression Modeling Identifies Salivary Biomarker Analysis that Predict Oral Feeding Readiness in the Newborn

PubMed Central

Maron, Jill L.; Hwang, Jooyeon S.; Pathak, Subash; Ruthazer, Robin; Russell, Ruby L.; Alterovitz, Gil

2014-01-01

Objective To combine mathematical modeling of salivary gene expression microarray data and systems biology annotation with RT-qPCR amplification to identify (phase I) and validate (phase II) salivary biomarker analysis for the prediction of oral feeding readiness in preterm infants. Study design Comparative whole transcriptome microarray analysis from 12 preterm newborns pre- and post-oral feeding success was used for computational modeling and systems biology analysis to identify potential salivary transcripts associated with oral feeding success (phase I). Selected gene expression biomarkers (15 from computational modeling; 6 evidence-based; and 3 reference) were evaluated by RT-qPCR amplification on 400 salivary samples from successful (n=200) and unsuccessful (n=200) oral feeders (phase II). Genes, alone and in combination, were evaluated by a multivariate analysis controlling for sex and post-conceptional age (PCA) to determine the probability that newborns achieved successful oral feeding. Results Advancing post-conceptional age (p < 0.001) and female sex (p = 0.05) positively predicted an infant’s ability to feed orally. A combination of five genes, NPY2R (hunger signaling), AMPK (energy homeostasis), PLXNA1 (olfactory neurogenesis), NPHP4 (visual behavior) and WNT3 (facial development), in addition to PCA and sex, demonstrated good accuracy for determining feeding success (AUROC = 0.78). Conclusions We have identified objective and biologically relevant salivary biomarkers that noninvasively assess a newborn’s developing brain, sensory and facial development as they relate to oral feeding success. Understanding the mechanisms that underlie the development of oral feeding readiness through translational and computational methods may improve clinical decision making while decreasing morbidities and health care costs. PMID:25620512

The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection.

PubMed

Payen, Celia; Di Rienzi, Sara C; Ong, Giang T; Pogachar, Jamie L; Sanchez, Joseph C; Sunshine, Anna B; Raghuraman, M K; Brewer, Bonita J; Dunham, Maitreya J

2014-03-20

Population adaptation to strong selection can occur through the sequential or parallel accumulation of competing beneficial mutations. The dynamics, diversity, and rate of fixation of beneficial mutations within and between populations are still poorly understood. To study how the mutational landscape varies across populations during adaptation, we performed experimental evolution on seven parallel populations of Saccharomyces cerevisiae continuously cultured in limiting sulfate medium. By combining quantitative polymerase chain reaction, array comparative genomic hybridization, restriction digestion and contour-clamped homogeneous electric field gel electrophoresis, and whole-genome sequencing, we followed the trajectory of evolution to determine the identity and fate of beneficial mutations. During a period of 200 generations, the yeast populations displayed parallel evolutionary dynamics that were driven by the coexistence of independent beneficial mutations. Selective amplifications rapidly evolved under this selection pressure, in particular common inverted amplifications containing the sulfate transporter gene SUL1. Compared with single clones, detailed analysis of the populations uncovers a greater complexity whereby multiple subpopulations arise and compete despite a strong selection. The most common evolutionary adaptation to strong selection in these populations grown in sulfate limitation is determined by clonal interference, with adaptive variants both persisting and replacing one another.

The Dynamics of Diverse Segmental Amplifications in Populations of Saccharomyces cerevisiae Adapting to Strong Selection

PubMed Central

Payen, Celia; Di Rienzi, Sara C.; Ong, Giang T.; Pogachar, Jamie L.; Sanchez, Joseph C.; Sunshine, Anna B.; Raghuraman, M. K.; Brewer, Bonita J.; Dunham, Maitreya J.

2014-01-01

Population adaptation to strong selection can occur through the sequential or parallel accumulation of competing beneficial mutations. The dynamics, diversity, and rate of fixation of beneficial mutations within and between populations are still poorly understood. To study how the mutational landscape varies across populations during adaptation, we performed experimental evolution on seven parallel populations of Saccharomyces cerevisiae continuously cultured in limiting sulfate medium. By combining quantitative polymerase chain reaction, array comparative genomic hybridization, restriction digestion and contour-clamped homogeneous electric field gel electrophoresis, and whole-genome sequencing, we followed the trajectory of evolution to determine the identity and fate of beneficial mutations. During a period of 200 generations, the yeast populations displayed parallel evolutionary dynamics that were driven by the coexistence of independent beneficial mutations. Selective amplifications rapidly evolved under this selection pressure, in particular common inverted amplifications containing the sulfate transporter gene SUL1. Compared with single clones, detailed analysis of the populations uncovers a greater complexity whereby multiple subpopulations arise and compete despite a strong selection. The most common evolutionary adaptation to strong selection in these populations grown in sulfate limitation is determined by clonal interference, with adaptive variants both persisting and replacing one another. PMID:24368781

A large ungated TPC with GEM amplification

NASA Astrophysics Data System (ADS)

Berger, M.; Ball, M.; Fabbietti, L.; Ketzer, B.; Arora, R.; Beck, R.; Böhmer, F. V.; Chen, J.-C.; Cusanno, F.; Dørheim, S.; García, F.; Hehner, J.; Herrmann, N.; Höppner, C.; Kaiser, D.; Kis̆, M.; Kleipa, V.; Konorov, I.; Kunkel, J.; Kurz, N.; Leifels, Y.; Müllner, P.; Münzer, R.; Neubert, S.; Rauch, J.; Schmidt, C. J.; Schmitz, R.; Soyk, D.; Vandenbroucke, M.; Voss, B.; Walther, D.; Zmeskal, J.

2017-10-01

A Time Projection Chamber (TPC) is an ideal device for the detection of charged particle tracks in a large volume covering a solid angle of almost 4 π. The high density of hits on a given particle track facilitates the task of pattern recognition in a high-occupancy environment and in addition provides particle identification by measuring the specific energy loss for each track. For these reasons, TPCs with Multiwire Proportional Chamber (MWPC) amplification have been and are widely used in experiments recording heavy-ion collisions. A significant drawback, however, is the large dead time of the order of 1 ms per event generated by the use of a gating grid, which is mandatory to prevent ions created in the amplification region from drifting back into the drift volume, where they would severely distort the drift path of subsequent tracks. For experiments with higher event rates this concept of a conventional TPC operating with a triggered gating grid can therefore not be applied without a significant loss of data. A continuous readout of the signals is the more appropriate way of operation. This, however, constitutes a change of paradigm with considerable challenges to be met concerning the amplification region, the design and bandwidth of the readout electronics, and the data handling. A mandatory prerequisite for such an operation is a sufficiently good suppression of the ion backflow from the avalanche region, which otherwise limits the tracking and particle identification capabilities of such a detector. Gas Electron Multipliers (GEM) are a promising candidate to combine excellent spatial resolution with an intrinsic suppression of ions. In this paper we describe the design, construction and the commissioning of a large TPC with GEM amplification and without gating grid (GEM-TPC). The design requirements have driven innovations in the construction of a light-weight field-cage, a supporting media flange, the GEM amplification and the readout system, which are presented in this paper. We further describe the support infrastructure such as gas, cooling and slow control. Finally, we report on the operation of the GEM-TPC in the FOPI experiment, and describe the calibration procedures which are applied to achieve the design performance of the device.

Entanglement-seeded, dual, optical parametric amplification: Applications to quantum imaging and metrology

NASA Astrophysics Data System (ADS)

Glasser, Ryan T.; Cable, Hugo; Dowling, Jonathan P.; de Martini, Francesco; Sciarrino, Fabio; Vitelli, Chiara

2008-07-01

The study of optical parametric amplifiers (OPAs) has been successful in describing and creating nonclassical light for use in fields such as quantum metrology and quantum lithography [Agarwal , J. Opt. Soc. Am. B 24, 2 (2007)]. In this paper we present the theory of an OPA scheme utilizing an entangled state input. The scheme involves two identical OPAs seeded with the maximally path-entangled ∣N00N⟩ state (∣2,0⟩+∣0,2⟩)/2 . The stimulated amplification results in output state probability amplitudes that have a dependence on the number of photons in each mode, which differs greatly from two-mode squeezed vacuum. A large family of entangled output states are found. Specific output states allow for the heralded creation of N=4 N00N states, which may be used for quantum lithography, to write sub-Rayleigh fringe patterns, and for quantum interferometry, to achieve Heisenberg-limited phase measurement sensitivity.

Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides.

PubMed

Ducani, Cosimo; Kaul, Corinna; Moche, Martin; Shih, William M; Högberg, Björn

2013-07-01

Single-stranded oligonucleotides are important as research tools, as diagnostic probes, in gene therapy and in DNA nanotechnology. Oligonucleotides are typically produced via solid-phase synthesis, using polymer chemistries that are limited relative to what biological systems produce. The number of errors in synthetic DNA increases with oligonucleotide length, and the resulting diversity of sequences can be a problem. Here we present the 'monoclonal stoichiometric' (MOSIC) method for enzyme-mediated production of DNA oligonucleotides. We amplified oligonucleotides from clonal templates derived from single bacterial colonies and then digested cutter hairpins in the products, which released pools of oligonucleotides with precisely controlled relative stoichiometric ratios. We prepared 14-378-nucleotide MOSIC oligonucleotides either by in vitro rolling-circle amplification or by amplification of phagemid DNA in Escherichia coli. Analyses of the formation of a DNA crystal and folding of DNA nanostructures confirmed the scalability, purity and stoichiometry of the produced oligonucleotides.

Enzymatic Production of Monoclonal Stoichiometric Single-Stranded DNA Oligonucleotides

PubMed Central

Ducani, Cosimo; Kaul, Corinna; Moche, Martin; Shih, William M.; Högberg, Björn

2013-01-01

Single-stranded oligonucleotides are important as research tools as probes for diagnostics and gene therapy. Today, production of oligonucleotides is done via solid-phase synthesis. However, the capabilities of current polymer chemistry are limited in comparison to what can be produced in biological systems. The errors in synthetic DNA increases with oligonucleotide length, and sequence diversity can often be a problem. Here, we present the Monoclonal Stoichiometric (MOSIC) method for enzymatic DNA oligonucleotide production. Using this method, we amplify oligonucleotides from clonal templates followed by digestion of a cutter-hairpin, resulting in pools of monoclonal oligonucleotides with precisely controlled relative stoichiometric ratios. We present data where MOSIC oligonucleotides, 14–378 nt long, were prepared either by in vitro rolling-circle amplification, or by amplification in Escherichia coli in the form of phagemid DNA. The formation of a DNA crystal and folding of DNA nanostructures confirmed the scalability, purity and stoichiometry of the produced oligonucleotides. PMID:23727986

Epstein-Barr Viral Productive Amplification Reprograms Nuclear Architecture, DNA Replication and Histone Deposition

PubMed Central

Chiu, Ya-Fang; Sugden, Arthur U.; Sugden, Bill

2014-01-01

Summary The spontaneous transition of Epstein-Barr Virus (EBV) from latency to productive infection is infrequent, making its analysis in the resulting mixed cell populations difficult. We engineered cells to support this transition efficiently and developed EBV DNA variants that could be visualized and measured as fluorescent signals over multiple cell cycles. This approach revealed that EBV’s productive replication began synchronously for viral DNAs within a cell but asynchronously between cells. EBV DNA amplification was delayed until early S-phase and occurred in factories characterized by the absence of cellular DNA and histones, by a sequential redistribution of PCNA, and by localization away from the nuclear periphery. The earliest amplified DNAs lacked histones accompanying a decline in four histone chaperones. Thus, EBV transitions from being dependent on the cellular replication machinery during latency to commandeering both that machinery and nuclear structure for its own reproductive needs. PMID:24331459

Conceptual design of sub-exa-watt system by using optical parametric chirped pulse amplification

NASA Astrophysics Data System (ADS)

Kawanaka, J.; Tsubakimoto, K.; Yoshida, H.; Fujioka, K.; Fujimoto, Y.; Tokita, S.; Jitsuno, T.; Miyanaga, N.; Gekko-EXA Design Team

2016-03-01

A 50 PW ultrahigh-peak-power laser has been conceptually designed, which is based on optical parametric chirped pulse amplification (OPCPA). A 250 J DPSSL and a flash- lamp-pumped kJ laser are adopted as new repeatable pump source. The existed LFEX-laser with more than ten kilo joules are used in the final amplifier stage and the OPCPA with the 2x2 tiled pump beams in random phase has been proposed with several ten centimeter aperture. A pulse duration of amplified pulses is set at less than 10 fs. A broadband OPCPA with ∼500 nm of the gain spectral width near 1 μm is required. A partially deuterated KDP (p-DKDP) crystal is one of the most promising nonlinear crystals and our numerical calculation ensured such ultra-broad gain width. p-DKDP crystals with several deuteration ratio have been successfully grown.

Identification of a new stem cell population that generates Drosophila flight muscles.

PubMed

Gunage, Rajesh D; Reichert, Heinrich; VijayRaghavan, K

2014-08-18

How myoblast populations are regulated for the formation of muscles of different sizes is an essentially unanswered question. The large flight muscles of Drosophila develop from adult muscle progenitor (AMP) cells set-aside embryonically. The thoracic segments are all allotted the same small AMP number, while those associated with the wing-disc proliferate extensively to give rise to over 2500 myoblasts. An initial amplification occurs through symmetric divisions and is followed by a switch to asymmetric divisions in which the AMPs self-renew and generate post-mitotic myoblasts. Notch signaling controls the initial amplification of AMPs, while the switch to asymmetric division additionally requires Wingless, which regulates Numb expression in the AMP lineage. In both cases, the epidermal tissue of the wing imaginal disc acts as a niche expressing the ligands Serrate and Wingless. The disc-associated AMPs are a novel muscle stem cell population that orchestrates the early phases of adult flight muscle development.

New innovations for contrast enhancement in electron microscopy

NASA Astrophysics Data System (ADS)

Mohan, A.

In this study two techniques for producing and improving contrast in Electron Microscopy are discussed. The first technique deals with the production of secondary contrast in a Variable Pressure SEM under poor vacuum conditions using the specimen current signal. A review of the prior work in this field shows that the presence of the gas ions in the microscope column results in the amplification of the specimen current signal which is enriched in secondary content. The focus of this study is to establish practical conditions for imaging samples in the microscope using specimen current with gas amplification. This is done by understanding the different variables in the microscope which affect the image formation process and then finding out optimum conditions for obtaining the best possible image, i.e., the image most enhanced in secondary contrast. A few 'real life' samples analyzed using this technique show that the gas amplified specimen current images contain secondary information and, in some cases, provide clear advantages to imaging with conventional secondary and backscattered detectors. The second technique dealing with the production of phase contrast in the TEM for extremely thin, electron transparent samples, is analyzed. A review of the literature regarding prior work in the field shows that, while the theoretical aspects of production of phase contrast in the TEM using a phase plate are well understood, there have been problems in practically implementing this in the microscope. One major assumption with most of the studies is that a fiber, partially coated with gold, results in the formation of point charges which is an essential requirement for symmetrically shifting the phase of the electron beam. The focus of this portion of the dissertation is to image the type of fields associated with such a phase plate using the technique of electron holography. It is found that there are two types of fields associated with a phase plate of this sort. One is a cylindrical field which extends along the length of the fiber while the other is a localized spherically symmetric field. A series of simulations show that the spherical field can produce phase contrast in the TEM and also improve the contrast transfer properties of the microscope.

Ultrasonic phased array controller for hyperthermia applications.

PubMed

Benkeser, P J; Pao, T L; Yoon, Y J

1991-01-01

Multiple and mechanically scanned ultrasound transducer systems have demonstrated the efficacy of using ultrasound to produce deep localized hyperthermia. The use of ultrasonic phased arrays has been proposed as an alternative to these systems. A phased array offers a more flexible approach to heating tumours in that the size, shape, and position of its focal region can be altered during the course of treatment in order to achieve the desired temperature distribution. This added flexibility comes at the cost of increased complexity of the hardware necessary to drive the transducer because each element requires its own amplifer with both phase and amplitude control. In order for phased arrays with large numbers of elements to be feasible for hyperthermia applications, the complexity of this circuitry must be minimized. This paper describes a circuit design which simplifies the electronics required to control a phased array transducer system for hyperthermia applications. The design is capable of controlling virtually any type of phased array transducer operating at frequencies less than 2 MHz. The system performance was verified through beam profile measurements using a 48-element tapered phased array transducer.

Self similar solution of superradiant amplification of ultrashort laser pulses in plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moghadasin, H.; Niknam, A. R., E-mail: a-niknam@sbu.ac.ir; Shokri, B.

2015-05-15

Based on the self-similar method, superradiant amplification of ultrashort laser pulses by the counterpropagating pump in a plasma is investigated. Here, we present a governing system of partial differential equations for the signal pulse and the motion of the electrons. These equations are transformed to ordinary differential equations by the self-similar method and numerically solved. It is found that the increase of the signal intensity is proportional to the square of the propagation distance and the signal frequency has a red shift. Also, depending on the pulse width, the signal breaks up into a train of short pulses or itsmore » duration decreases with the inverse square root of the distance. Moreover, we identified two distinct categories of the electrons by the phase space analysis. In the beginning, one of them is trapped in the ponderomotive potential well and oscillates while the other is untrapped. Over time, electrons of the second kind also join to the trapped electrons. In the potential well, the electrons are bunched to form an electron density grating which reflects the pump pulse into the signal pulse. It is shown that the backscattered intensity is enhanced with the increase of the electron bunching parameter which leads to the enhanced efficiency of superradiant amplification.« less

Nonlinear amplification of coherent waves in media with soliton-type refractive index pattern.

PubMed

Bugaychuk, S; Conte, R

2012-08-01

We derive the complex Ginzburg-Landau equation for the dynamical self-diffraction of optical waves in a nonlinear cavity. The case of the reflection geometry of wave interaction as well as a medium that possesses the cubic nonlinearity (including a local and a nonlocal nonlinear responses) and the relaxation is considered. A stable localized spatial structure in the form of a "dark" dissipative soliton is formed in the cavity in the steady state. The envelope of the intensity pattern, as well as of the dynamical grating amplitude, takes the shape of a tanh function. The obtained complex Ginzburg-Landau equation describes the dynamics of this envelope; at the same time, the evolution of this spatial structure changes the parameters of the output waves. New effects are predicted in this system due to the transformation of the dissipative soliton which takes place during the interaction of a pulse with a continuous wave, such as retention of the pulse shape during the transmission of impulses in a long nonlinear cavity, and giant amplification of a seed pulse, which takes energy due to redistribution of the pump continuous energy into the signal.

Titer-plate formatted continuous flow thermal reactors: Design and performance of a nanoliter reactor

PubMed Central

Chen, Pin-Chuan; Park, Daniel S.; You, Byoung-Hee; Kim, Namwon; Park, Taehyun; Soper, Steven A.; Nikitopoulos, Dimitris E.; Murphy, Michael C.

2010-01-01

Arrays of continuous flow thermal reactors were designed, configured, and fabricated in a 96-device (12 × 8) titer-plate format with overall dimensions of 120 mm × 96 mm, with each reactor confined to a 8 mm × 8 mm footprint. To demonstrate the potential, individual 20-cycle (740 nL) and 25-cycle (990 nL) reactors were used to perform the continuous flow polymerase chain reaction (CFPCR) for amplification of DNA fragments of different lengths. Since thermal isolation of the required temperature zones was essential for optimal biochemical reactions, three finite element models, executed with ANSYS (v. 11.0, Canonsburg, PA), were used to characterize the thermal performance and guide system design: (1) a single device to determine the dimensions of the thermal management structures; (2) a single CFPCR device within an 8 mm × 8 mm area to evaluate the integrity of the thermostatic zones; and (3) a single, straight microchannel representing a single loop of the spiral CFPCR device, accounting for all of the heat transfer modes, to determine whether the PCR cocktail was exposed to the proper temperature cycling. In prior work on larger footprint devices, simple grooves between temperature zones provided sufficient thermal resistance between zones. For the small footprint reactor array, 0.4 mm wide and 1.2 mm high fins were necessary within the groove to cool the PCR cocktail efficiently, with a temperature gradient of 15.8°C/mm, as it flowed from the denaturation zone to the renaturation zone. With temperature tolerance bands of ±2°C defined about the nominal temperatures, more than 72.5% of the microchannel length was located within the desired temperature bands. The residence time of the PCR cocktail in each temperature zone decreased and the transition times between zones increased at higher PCR cocktail flow velocities, leading to less time for the amplification reactions. Experiments demonstrated the performance of the CFPCR devices as a function of flow velocity, fragment length, and copy number. A 99 bp DNA fragment was successfully amplified at flow velocities from 1 mm/s to 3 mm/s, requiring from 8.16 minutes for 20 cycles (24.48 s/cycle) to 2.72 minutes for 20 cycles (8.16 s/cycle), respectively. Yield compared to the same amplification sequence performed using a bench top thermal cycler decreased nonlinearly from 73% (at 1 mm/s) to 13% (at 3 mm/s) with shorter residence time at the optimal temperatures for the reactions due to increased flow rate primarily responsible. Six different DNA fragments with lengths between 99 bp and 997 bp were successfully amplified at 1 mm/s. Repeatable, successful amplification of a 99 bp fragment was achieved with a minimum of 8000 copies of the DNA template. This is the first demonstration and characterization of continuous flow thermal reactors within the 8 mm × 8 mm footprint of a 96-well micro-titer plate and is the smallest continuous flow PCR to date. PMID:20871807

A Printed Organic Circuit System for Wearable Amperometric Electrochemical Sensors.

PubMed

Shiwaku, Rei; Matsui, Hiroyuki; Nagamine, Kuniaki; Uematsu, Mayu; Mano, Taisei; Maruyama, Yuki; Nomura, Ayako; Tsuchiya, Kazuhiko; Hayasaka, Kazuma; Takeda, Yasunori; Fukuda, Takashi; Kumaki, Daisuke; Tokito, Shizuo

2018-04-23

Wearable sensor device technologies, which enable continuous monitoring of biological information from the human body, are promising in the fields of sports, healthcare, and medical applications. Further thinness, light weight, flexibility and low-cost are significant requirements for making the devices attachable onto human tissues or clothes like a patch. Here we demonstrate a flexible and printed circuit system consisting of an enzyme-based amperometric sensor, feedback control and amplification circuits based on organic thin-film transistors. The feedback control and amplification circuits based on pseudo-CMOS inverters were successfuly integrated by printing methods on a plastic film. This simple system worked very well like a potentiostat for electrochemical measurements, and enabled the quantitative and real-time measurement of lactate concentration with high sensitivity of 1 V/mM and a short response time of a hundred seconds.

Quasi-Phasematched Nonlinear Optics: Materials and Devices

DTIC Science & Technology

2007-04-16

the soliton energy in pump, signal and idler waves as a function of the final wave- vector mismatch in the chirped QPM gratings. We see good agreement...devices including OP-GaAs devices for broadband optical parametric generation (OPG) at mid-infrared wavelengths, bulk PPLN devices for soliton ...Carrasco, and L. Torner,"Engineering of multi-color spatial solitons with chirped-period quasi-phase-matching gratings in optical parametric amplification

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

PubMed

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.

Parametric generation of high-energy 14.5-fs light pulses at 1.5 mum.

PubMed

Nisoli, M; Stagira, S; De Silvestri, S; Svelto, O; Valiulis, G; Varanavicius, A

1998-04-15

High-energy light pulses that are tunable from 1.1 to 2.6 mum, with a duration as short as 14.5 fs were generated in a type II phase-matching beta-BaB(2)O(4) traveling-wave parametric converter pumped by 18-fs pulses obtained from a Ti:sapphire laser with chirped-pulse amplification, followed by a hollow-fiber compressor.

Exponential isothermal amplification of nucleic acids and amplified assays for proteins, cells, and enzyme activities.

PubMed

Reid, Michael S; Le, X Chris; Zhang, Hongquan

2018-04-27

Isothermal exponential amplification techniques, such as strand-displacement amplification (SDA), rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP), nucleic acid sequence-based amplification (NASBA), helicase-dependent amplification (HDA), and recombinase polymerase amplification (RPA), have great potential for on-site, point-of-care, and in-situ assay applications. These amplification techniques eliminate the need for temperature cycling required for polymerase chain reaction (PCR) while achieving comparable amplification yield. We highlight here recent advances in exponential amplification reaction (EXPAR) for the detection of nucleic acids, proteins, enzyme activities, cells, and metal ions. We discuss design strategies, enzyme reactions, detection techniques, and key features. Incorporation of fluorescence, colorimetric, chemiluminescence, Raman, and electrochemical approaches enables highly sensitive detection of a variety of targets. Remaining issues, such as undesirable background amplification resulting from non-specific template interactions, must be addressed to further improve isothermal and exponential amplification techniques. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vibration Measurement on Reticular Lamina and Basilar Membrane at Multiple Longitudinal Locations

NASA Astrophysics Data System (ADS)

Chen, Fangyi; Zha, Dingjun; Choudhury, Niloy; Fridberger, Anders; Nuttall, Alfred L.

2011-11-01

The longitudinal distribution of the organ of Corti vibration is important for both understanding the energy delivery and the timing of the cochlear amplification. Recent development on low coherence interferomtry technique allows measuring vibration inside the cochlea. The reticular lamina (RL) vibration spectrum demonstrates that RL vibration leads the basilar membrane (BM). This phase lead is consistent with the idea that the active process may lead the BM vibration. In this study, measurements on multiple longitudinal locations demonstrated similar phase lead. Results on this study suggests that there may be another longitudinal coupling mechanism inside the cochlea other than the traveling wave on BM.

Optical Rogue Waves in Vortex Turbulence.

PubMed

Gibson, Christopher J; Yao, Alison M; Oppo, Gian-Luca

2016-01-29

We present a spatiotemporal mechanism for producing 2D optical rogue waves in the presence of a turbulent state with creation, interaction, and annihilation of optical vortices. Spatially periodic structures with bound phase lose stability to phase unbound turbulent states in complex Ginzburg-Landau and Swift-Hohenberg models with external driving. When the pumping is high and the external driving is low, synchronized oscillations are unstable and lead to spatiotemporal vortex-mediated turbulence with high excursions in amplitude. Nonlinear amplification leads to rogue waves close to turbulent optical vortices, where the amplitude tends to zero, and to probability density functions (PDFs) with long tails typical of extreme optical events.

Multistate and phase change selection in constitutional multivalent systems.

PubMed

Barboiu, Mihail

2012-01-01

Molecular architectures and materials can be constitutionally self-sorted in the presence of different biomolecular targets or external physical stimuli or chemical effectors, thus responding to an external selection pressure. The high selectivity and specificity of different bioreceptors or self-correlated internal interactions may be used to describe the complex constitutional behaviors through multistate component selection from a dynamic library. The self-selection may result in the dynamic amplification of self-optimized architectures during the phase change process. The sol-gel resolution of dynamic molecular/supramolecular libraries leads to higher self-organized constitutional hybrid materials, in which organic (supramolecular)/inorganic domains are reversibily connected.

Effect of noise on modulation amplitude and phase in frequency-domain diffusive imaging

PubMed Central

Kupinski, Matthew A.

2012-01-01

Abstract. We theoretically investigate the effect of noise on frequency-domain heterodyne and/or homodyne measurements of intensity-modulated beams propagating through diffusive media, such as a photon density wave. We assumed that the attenuated amplitude and delayed phase are estimated by taking the Fourier transform of the noisy, modulated output data. We show that the estimated amplitude and phase are biased when the number of output photons is small. We also show that the use of image intensifiers for photon amplification in heterodyne or homodyne measurements increases the amount of biases. Especially, it turns out that the biased estimation is independent of AC-dependent noise in sinusoidal heterodyne or homodyne outputs. Finally, the developed theory indicates that the previously known variance model of modulation amplitude and phase is not valid in low light situations. Monte-Carlo simulations with varied numbers of input photons verify our theoretical trends of the bias. PMID:22352660

Thermally controlled femtosecond pulse shaping using metasurface based optical filters

NASA Astrophysics Data System (ADS)

Rahimi, Eesa; Şendur, Kürşat

2018-02-01

Shaping of the temporal distribution of the ultrashort pulses, compensation of pulse deformations due to phase shift in transmission and amplification are of interest in various optical applications. To address these problems, in this study, we have demonstrated an ultra-thin reconfigurable localized surface plasmon (LSP) band-stop optical filter driven by insulator-metal phase transition of vanadium dioxide. A Joule heating mechanism is proposed to control the thermal phase transition of the material. The resulting permittivity variation of vanadium dioxide tailors spectral response of the transmitted pulse from the stack. Depending on how the pulse's spectrum is located with respect to the resonance of the band-stop filter, the thin film stack can dynamically compress/expand the output pulse span up to 20% or shift its phase up to 360°. Multi-stacked filters have shown the ability to dynamically compensate input carrier frequency shifts and pulse span variations besides their higher span expansion rates.

Relative phase noise induced impairment in CO-OFDM optical communication system with distributed fiber Raman amplifier.

PubMed

Wu, Jiadi; Cheng, Jingchi; Tang, Ming; Deng, Lei; Songnian, Fu; Shum, Perry Ping; Liu, Deming

2014-05-15

In this Letter, we demonstrate that the interplay between Raman pump relative intensity noise and cross-phase modulation leads to a relative phase noise (RPN) that brings non-negligible performance degradation to coherent optical orthogonal frequency-division multiplexing (CO-OFDM) transmission systems with co-pumped Raman amplification. By theoretical analysis and numerical simulation, we proved that RPN brings more system impairment in terms of Q-factor penalty than the single carrier system, and relatively larger walk-off between pump and signal helps to suppress the RPN induced impairment. A higher-order modulated signal is less tolerant to RPN than a lower-order signal. With the same spectral efficiency, the quadrature-amplitude modulation format shows better tolerance to RPN than phase-shift keying. The reported findings will be useful for the design and optimization of Raman amplified CO-OFDM multi-carrier transmission systems.

Method and apparatus for controlling carrier envelope phase

DOEpatents

Chang, Zenghu [Manhattan, KS; Li, Chengquan [Sunnyvale, CA; Moon, Eric [Manhattan, KS

2011-12-06

A chirped pulse amplification laser system. The system generally comprises a laser source, a pulse modification apparatus including first and second pulse modification elements separated by a separation distance, a positioning element, a measurement device, and a feedback controller. The laser source is operable to generate a laser pulse and the pulse modification apparatus operable to modify at least a portion of the laser pulse. The positioning element is operable to reposition at least a portion of the pulse modification apparatus to vary the separation distance. The measurement device is operable to measure the carrier envelope phase of the generated laser pulse and the feedback controller is operable to control the positioning element based on the measured carrier envelope phase to vary the separation distance of the pulse modification elements and control the carrier envelope phase of laser pulses generated by the laser source.

Label-free and sensitive detection of T4 polynucleotide kinase activity via coupling DNA strand displacement reaction with enzymatic-aided amplification.

PubMed

Cheng, Rui; Tao, Mangjuan; Shi, Zhilu; Zhang, Xiafei; Jin, Yan; Li, Baoxin

2015-11-15

Several fluorescence signal amplification strategies have been developed for sensitive detection of T4 polynucleotide kinase (T4 PNK) activity, but they need fluorescence dye labeled DNA probe. We have addressed the limitation and report here a label-free strategy for sensitive detection of PNK activity by coupling DNA strand displacement reaction with enzymatic-aided amplification. A hairpin oligonucleotide (hpDNA) with blunt ends was used as the substrate for T4 PNK phosphorylation. In the presence of T4 PNK, the stem of hpDNA was phosphorylated and further degraded by lambda exonuclease (λ exo) from 5' to 3' direction to release a single-stranded DNA as a trigger of DNA strand displacement reaction (SDR). The trigger DNA can continuously displace DNA P2 from P1/P2 hybrid with the help of specific cleavage of nicking endonuclease (Nt.BbvCI). Then, DNA P2 can form G-quadruplex in the presence of potassium ions and quadruplex-selective fluorphore, N-methyl mesoporphyrin IX (NMM), resulting in a significant increase in fluorescence intensity of NMM. Thus, the accumulative release of DNA P2 led to fluorescence signal amplification for determining T4 PNK activity with a detection limit of 6.6×10(-4) U/mL, which is superior or comparative with established approaches. By ingeniously utilizing T4 PNK-triggered DNA SDR, T4 PNK activity can be specifically and facilely studied in homogeneous solution containing complex matrix without any external fluorescence labeling. Moreover, the influence of different inhibitors on the T4 PNK activity revealed that it also can be explored to screen T4 PNK inhibitors. Therefore, this label-free amplification strategy presents a facile and cost-effective approach for nucleic acid phosphorylation related research. Copyright © 2015 Elsevier B.V. All rights reserved.

Preparation of metagenomic libraries from naturally occurring marine viruses.

PubMed

Solonenko, Sergei A; Sullivan, Matthew B

2013-01-01

Microbes are now well recognized as major drivers of the biogeochemical cycling that fuels the Earth, and their viruses (phages) are known to be abundant and important in microbial mortality, horizontal gene transfer, and modulating microbial metabolic output. Investigation of environmental phages has been frustrated by an inability to culture the vast majority of naturally occurring diversity coupled with the lack of robust, quantitative, culture-independent methods for studying this uncultured majority. However, for double-stranded DNA phages, a quantitative viral metagenomic sample-to-sequence workflow now exists. Here, we review these advances with special emphasis on the technical details of preparing DNA sequencing libraries for metagenomic sequencing from environmentally relevant low-input DNA samples. Library preparation steps broadly involve manipulating the sample DNA by fragmentation, end repair and adaptor ligation, size fractionation, and amplification. One critical area of future research and development is parallel advances for alternate nucleic acid types such as single-stranded DNA and RNA viruses that are also abundant in nature. Combinations of recent advances in fragmentation (e.g., acoustic shearing and tagmentation), ligation reactions (adaptor-to-template ratio reference table availability), size fractionation (non-gel-sizing), and amplification (linear amplification for deep sequencing and linker amplification protocols) enhance our ability to generate quantitatively representative metagenomic datasets from low-input DNA samples. Such datasets are already providing new insights into the role of viruses in marine systems and will continue to do so as new environments are explored and synergies and paradigms emerge from large-scale comparative analyses. © 2013 Elsevier Inc. All rights reserved.

Two-octave spanning single pump parametric amplification at 1550 nm in a host lead-silicate binary multi-clad microstructure fiber: Influence of multi-order dispersion engineering

NASA Astrophysics Data System (ADS)

Chatterjee, Sudip K.; Khan, Saba N.; Chaudhuri, Partha Roy

2014-12-01

An ultra-wide 1646 nm (1084-2730 nm), continuous-wave single pump parametric amplification spanning from near-infrared to short-wave infrared band (NIR-SWIR) in a host lead-silicate based binary multi-clad microstructure fiber (BMMF) is analyzed and reported. This ultra-broad band (widest reported to date) parametric amplification with gain more than 10 dB is theoretically achieved by a combination of low input pump power source ~7 W and a short-length of ~70 cm of nonlinear-BMMF through accurately engineered multi-order dispersion coefficients. A highly efficient theoretical formulation based on four-wave-mixing (FWM) is worked out to determine fiber's chromatic dispersion (D) profile which is used to optimise the gain-bandwidth and ripple of the parametric gain profile. It is seen that by appropriately controlling the higher-order dispersion coefficient (up-to sixth order), a great enhancement in the gain-bandwidth (2-3 times) can be achieved when operated very close to zero-dispersion wavelength (ZDW) in the anomalous dispersion regime. Moreover, the proposed theoretical model can predict the maximum realizable spectral width and the required pump-detuning (w.r.t ZDW) of any advanced complex microstructured fiber. Our thorough investigation of the wide variety of broadband gain spectra obtained as an integral part of this research work opens up the way for realizing amplification in the region (SWIR) located far from the pump (NIR) where good amplifiers currently do not exist.

Precision control of carrier-envelope phase in grating based chirped pulse amplifiers.

PubMed

Li, Chengquan; Moon, Eric; Mashiko, Hiroki; Nakamura, Christopher M; Ranitovic, Predrag; Maharjan, Chakra M; Cocke, C Lewis; Chang, Zenghu; Paulus, Gerhard G

2006-11-13

It is demonstrated that the carrier-envelope (CE) phase of pulses from a high power ultrafast laser system with a grating-based stretcher and compressor can be stabilized to a root mean square (rms) value of 180 mrad over almost 2 hours, excluding a brief re-locking period. The stabilization was accomplished via feedback control of the grating separation in the stretcher. It shows that the long term CE phase stability of a grating based chirped pulse amplification system can be as good as that of lasers using a glass-block stretcher and a prism pair compressor. Moreover, by adjusting the grating separation to preset values, the relative CE phase could be locked to an arbitrary value in the range of 2pi. This method is better than using a pair of wedge plates to adjust the phase after the hollow-core fiber compressor. The CE phase stabilization after a hollow-core fiber compressor was confirmed by a CE-phase meter based on the measurement of the left-to-right asymmetry of electrons produced by above-threshold ionization.

Examination of the site amplification factor of OBS and their application to magnitude estimation and ground-motion prediction for EEW

NASA Astrophysics Data System (ADS)

Hayashimoto, N.; Hoshiba, M.

2013-12-01

1. Introduction Ocean bottom seismograph (OBS) is useful for making Earthquake Early Warning (EEW) earlier. However, careful handling of these data is required because the installation environment of OBSs may be different from that of land stations. Site amplification factor is an important factor to estimate the magnitudes, and to predict ground motions (e.g. seismic intensity) in EEW. In this presentation, we discuss the site amplification factor of OBS in the Tonankai area of Japan from these two points of view. 2. Examination of magnitude correction of OBS In the EEW of JMA, the magnitude is estimated from the maximum amplitude of the displacement in real time. To provide the fast magnitude estimation, the magnitude-estimation algorithm switches from the P to S formula (Meew(P) to Meew(S)) depending on the expected S-phase arrival (Kamigaichi,2004). To estimate the magnitude correction for OBS, we determine Meew(P) and Meew(S) at OBSs and compare them with JMA magnitude (Mjma). We find Meew(S) at OBS is generally larger than Mjma by approximately 0.6. The slight differences of spatial distribution of Meew(S) amplification are also found among other OBSs. From the numerical simulations, Nakamura et al. (MGR,submitted) pointed out that the oceanic layer and the low-velocity sediment layers causes the large amplifications in low frequency range (0.1-0.2Hz) at OBSs. We conclude that the site effect of OBS characterized by such a low velocity sediment layers causes those amplification of Magnitude. 3. The frequency-dependent site factor of OBS estimated from Fourier spectrum ratio and their application for prediction of seismic intensity of land station We compare Fourier spectra of S-wave portion on OBSs with those on adjacent land stations. Station pair whose distance is smaller than 50 km is analyzed, and we obtain that spectral ratio of land station (MIEH05 of the KiK-net/NIED) to OBS (KMA01 of the DONET/JAMSTEC) is 5-20 for frequencies 10-20Hz for both horizontal and vertical components, whereas it is approximately 0.2 at less than 2Hz for the horizontal component, which corresponds to the relative site amplification factors in the frequency domain. In addition, we compare the accuracies of expected seismic intensity of land stations using the average of seismic intensity difference with those using the spectral ratio as the empirical amplification factor. In an example of station pair mentioned above, the RMS of the difference between measured and predicted seismic intensity is improved by about 38% by using a spectral ratio as the amplification factor. These results indicate that the frequency-dependent site factor is crucial factor to predict seismic intensity from OBS data, and also show that OBS can be used as front stations in the method for prediction of ground motion based on the real-time monitoring (Hoshiba, 2013). Acknowledgement: Waveform data were obtained from the JMA network, DONET of the JAMSTEC, K-net and KiK-net of the NIED.

Imatinib for melanomas harboring mutationally activated or amplified KIT arising on mucosal, acral, and chronically sun-damaged skin.

PubMed

Hodi, F Stephen; Corless, Christopher L; Giobbie-Hurder, Anita; Fletcher, Jonathan A; Zhu, Meijun; Marino-Enriquez, Adrian; Friedlander, Philip; Gonzalez, Rene; Weber, Jeffrey S; Gajewski, Thomas F; O'Day, Steven J; Kim, Kevin B; Lawrence, Donald; Flaherty, Keith T; Luke, Jason J; Collichio, Frances A; Ernstoff, Marc S; Heinrich, Michael C; Beadling, Carol; Zukotynski, Katherine A; Yap, Jeffrey T; Van den Abbeele, Annick D; Demetri, George D; Fisher, David E

2013-09-10

Amplifications and mutations in the KIT proto-oncogene in subsets of melanomas provide therapeutic opportunities. We conducted a multicenter phase II trial of imatinib in metastatic mucosal, acral, or chronically sun-damaged (CSD) melanoma with KIT amplifications and/or mutations. Patients received imatinib 400 mg once per day or 400 mg twice per day if there was no initial response. Dose reductions were permitted for treatment-related toxicities. Additional oncogene mutation screening was performed by mass spectroscopy. Twenty-five patients were enrolled (24 evaluable). Eight patients (33%) had tumors with KIT mutations, 11 (46%) with KIT amplifications, and five (21%) with both. Median follow-up was 10.6 months (range, 3.7 to 27.1 months). Best overall response rate (BORR) was 29% (21% excluding nonconfirmed responses) with a two-stage 95% CI of 13% to 51%. BORR was significantly greater than the hypothesized null of 5% and statistically significantly different by mutation status (7 of 13 or 54% KIT mutated v 0% KIT amplified only). There were no statistical differences in rates of progression or survival by mutation status or by melanoma site. The overall disease control rate was 50% but varied significantly by KIT mutation status (77% mutated v 18% amplified). Four patients harbored pretreatment NRAS mutations, and one patient acquired increased KIT amplification after treatment. Melanomas that arise on mucosal, acral, or CSD skin should be assessed for KIT mutations. Imatinib can be effective when tumors harbor KIT mutations, but not if KIT is amplified only. NRAS mutations and KIT copy number gain may be mechanisms of therapeutic resistance to imatinib.

Experimental investigation of the Peregrine Breather of gravity waves on finite water depth

NASA Astrophysics Data System (ADS)

Dong, G.; Liao, B.; Ma, Y.; Perlin, M.

2018-06-01

A series of laboratory experiments were performed to study the Peregrine Breather (PB) evolution in a wave flume of finite depth and deep water. Experimental cases were selected with water depths k0h (k0 is the wave number and h is the water depth) varying from 3.11 to 8.17 and initial steepness k0a0 (a0 is the background wave amplitude) in the range 0.06 to 0.12, and the corresponding initial Ursell number in the range 0.03 to 0.061. Experimental results indicate that the water depth plays an important role in the formation of the extreme waves in finite depth; the maximum wave amplification of the PB packets is also strongly dependent on the initial Ursell number. For experimental cases with the initial Ursell number larger than 0.05, the maximum crest amplification can exceed three. If the initial Ursell number is nearly 0.05, a shorter propagation distance is needed for maximum amplification of the height in deeper water. A time-frequency analysis using the wavelet transform reveals that the energy of the higher harmonics is almost in-phase with the carrier wave. The contribution of the higher harmonics to the extreme wave is significant for the cases with initial Ursell number larger than 0.05 in water depth k0h < 5.0. Additionally, the experimental results are compared with computations based on both the nonlinear Schrödinger (NLS) equation and the Dysthe equation, both with a dissipation term. It is found that both models with a dissipation term can predict the maximum amplitude amplification of the primary waves. However, the Dysthe equation also can predict the group horizontal asymmetry.

Enzyme- and label-free electrochemical aptasensor for kanamycin detection based on double stir bar-assisted toehold-mediated strand displacement reaction for dual-signal amplification.

PubMed

Hong, Feng; Chen, Xixue; Cao, Yuting; Dong, Youren; Wu, Dazhen; Hu, Futao; Gan, Ning

2018-07-30

It is critically important to detect antibiotic residues for monitoring food safety. In this study, an enzyme- and label-free electrochemical aptasensor for antibiotics, with kanamycin (Kana) as a typical analyte, was developed based on a double stir bar-assisted toehold-mediated strand displacement reaction (dSB-TMSDR) for dual-signal amplification. First, we modified two gold electrodes (E-1 and E-2) with different DNA probes (S1/S2 hybrid probe in E-1 and DNA fuel strand S3 in E-2). In the presence of Kana, an S1/S2 probe can be disassembled from E-1 to form an S2/Kana complex in supernatant. The S2/Kana could react with S3 on E-2 to form S2/S3 hybrid and release Kana through TMSDR. After then, the target recycling was triggered. Subsequently, the formed S2/S3 hybrid can also trigger a hybridization chain reaction (HCR). Consequently, the dual-signal amplification strategy was established, which resulted in many long dsDNA chains on E-2. The chains can associate with methylene blue (MB) as redox probes to produce a current response for the quantification of Kana. The assay exhibited high sensitivity and specificity with a detection limit at 16 fM Kana due to the dual-signal amplification. The double stir bars system can both increase phase separation and prevent leakage of DNA fuel to reduce background interference. Moreover, it allows flexible sequence design of the TMSDR probes. The assay was successfully employed to detect Kana residues in food and showed potential application value in food safety detection. Copyright © 2018 Elsevier B.V. All rights reserved.

The Effect of Sedimentary Basins on Through-Passing Short-Period Surface Waves

NASA Astrophysics Data System (ADS)

Feng, L.; Ritzwoller, M. H.

2017-12-01

Surface waves propagating through sedimentary basins undergo elastic wave field complications that include multiple scattering, amplification, the formation of secondary wave fronts, and subsequent wave front healing. Unless these effects are accounted for accurately, they may introduce systematic bias to estimates of source characteristics, the inference of the anelastic structure of the Earth, and ground motion predictions for hazard assessment. Most studies of the effects of basins on surface waves have centered on waves inside the basins. In contrast, we investigate wave field effects downstream from sedimentary basins, with particular emphasis on continental basins and propagation paths, elastic structural heterogeneity, and Rayleigh waves at 10 s period. Based on wave field simulations through a recent 3D crustal and upper mantle model of East Asia, we demonstrate significant Rayleigh wave amplification downstream from sedimentary basins in eastern China such that Ms measurements obtained on the simulated wave field vary by more than a magnitude unit. We show that surface wave amplification caused by basins results predominantly from elastic focusing and that amplification effects produced through 3D basin models are reproduced using 2D membrane wave simulations through an appropriately defined phase velocity map. The principal characteristics of elastic focusing in both 2D and 3D simulations include (1) retardation of the wave front inside the basins; (2) deflection of the wave propagation direction; (3) formation of a high amplitude lineation directly downstream from the basin bracketed by two low amplitude zones; and (4) formation of a secondary wave front. Finally, by comparing the impact of elastic focusing with anelastic attenuation, we argue that on-continent sedimentary basins are expected to affect surface wave amplitudes more strongly through elastic focusing than through the anelastic attenuation.

Wavelength-preserving polarization-insensitive all-optical 3R regenerator based on self- and cross-phase modulation and offset filtering utilizing Raman amplification

NASA Astrophysics Data System (ADS)

Chung, Sung Han

Optical regeneration has the potential to significantly increase the reach of long-haul transmission systems. In this thesis, wavelength-preserving polarization-insensitive all-optical 3R regeneration is investigated and demonstrated for 10 and 40 Gb/s signals. The all-optical regenerator utilizes a self-pulsating laser for clock recovery, cross-phase modulation (XPM) based spectral broadening in a highly nonlinear fiber (HNLF) and offset filtering for retiming, and self-phase modulation based spectral broadening in a HNLF and offset filtering for reshaping. Raman amplification is used to increase the XPM-based spectral broadening and thus allow a design that meets the tradeoffs involved in simultaneously achieving good retiming and reshaping performance. The regenerator is shown to reduce amplitude noise and timing jitter while not causing a BER penalty. To fully validate the regeneration scheme, the cascadability is demonstrated using a recirculating loop. For a 10 Gb/s signal, with a regenerator spacing of 240 km, a return-to-zero, on-off-keyed (RZ-OOK) signal was transmitted over 18,000 km (75 loops) with a power penalty of 1.6 dB at a BER of 10 -9 compared to the back-to-back case. For a 40 Gb/s signal, with a regenerator spacing of 80 km, a RZ-OOK signal was transmitted over 8,000 km (100 loops) with a power penalty of 1.2 dB. In addition, all-optical 3R regeneration is demonstrated using a multimode quantum-dot Fabry Perot laser with ultra-low timing jitter.

Coupling and Elastic Loading Affect the Active Response by the Inner Ear Hair Cell Bundles

PubMed Central

Strimbu, Clark Elliott; Fredrickson-Hemsing, Lea; Bozovic, Dolores

2012-01-01

Active hair bundle motility has been proposed to underlie the amplification mechanism in the auditory endorgans of non-mammals and in the vestibular systems of all vertebrates, and to constitute a crucial component of cochlear amplification in mammals. We used semi-intact in vitro preparations of the bullfrog sacculus to study the effects of elastic mechanical loading on both natively coupled and freely oscillating hair bundles. For the latter, we attached glass fibers of different stiffness to the stereocilia and observed the induced changes in the spontaneous bundle movement. When driven with sinusoidal deflections, hair bundles displayed phase-locked response indicative of an Arnold Tongue, with the frequency selectivity highest at low amplitudes and decreasing under stronger stimulation. A striking broadening of the mode-locked response was seen with increasing stiffness of the load, until approximate impedance matching, where the phase-locked response remained flat over the physiological range of frequencies. When the otolithic membrane was left intact atop the preparation, the natural loading of the bundles likewise decreased their frequency selectivity with respect to that observed in freely oscillating bundles. To probe for signatures of the active process under natural loading and coupling conditions, we applied transient mechanical stimuli to the otolithic membrane. Following the pulses, the underlying bundles displayed active movement in the opposite direction, analogous to the twitches observed in individual cells. Tracking features in the otolithic membrane indicated that it moved in phase with the bundles. Hence, synchronous active motility evoked in the system of coupled hair bundles by external input is sufficient to displace large overlying structures. PMID:22479461

Three-Component Integrated Ultrathin Organic Photosensors for Plastic Optoelectronics.

PubMed

Wang, Hanlin; Liu, Hongtao; Zhao, Qiang; Cheng, Cheng; Hu, Wenping; Liu, Yunqi

2016-01-27

By three-component integration, an integrated organic photosensor is presented using common organic dyes as building blocks. Gray-scale photosensing and signal amplification are achieved in the device within a wide range of light intensities. Moreover, with ultrathin film techniques, 470 nm thick devices are realized and continue to work when harshly bent. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Use of sequence-independent-single-primer-amplification (SISPA) for whole genome sequencing using illumina MiSeq platform for avian influenza virus, Newcastle disease virus, and infectious bronchitis virus

USDA-ARS?s Scientific Manuscript database

Over the past decade, Next Generation Sequencing (NGS) technologies, also called deep sequencing, have continued to evolve, increasing capacity and lower the cost necessary for large genome sequencing projects. The one of the advantage of NGS platforms is the possibility to sequence the samples with...

Feasibility of Urban Service Opportunity and Curricular Amplification: "The St. Louis Project." Final Report.

ERIC Educational Resources Information Center

Guthrie, Robert V.; And Others

A study was made to test the feasibility of a small college (located some distance from a city) establishing a residence unit within a slum or transitional area of a city. The purposes of such a program, in which students and faculty live in the city while continuing their normal course work, would be to: (1) enhance the curriculum by broadening…

Selective Entrapment of Extrachromosomally Amplified DNA by Nuclear Budding and Micronucleation during S Phase

PubMed Central

Shimizu, Noriaki; Itoh, Nobuo; Utiyama, Hiroyasu; Wahl, Geoffrey M.

1998-01-01

Acentric, autonomously replicating extrachromosomal structures called double-minute chromosomes (DMs) frequently mediate oncogene amplification in human tumors. We show that DMs can be removed from the nucleus by a novel micronucleation mechanism that is initiated by budding of the nuclear membrane during S phase. DMs containing c-myc oncogenes in a colon cancer cell line localized to and replicated at the nuclear periphery. Replication inhibitors increased micronucleation; cell synchronization and bromodeoxyuridine–pulse labeling demonstrated de novo formation of buds and micronuclei during S phase. The frequencies of S-phase nuclear budding and micronucleation were increased dramatically in normal human cells by inactivating p53, suggesting that an S-phase function of p53 minimizes the probability of producing the broken chromosome fragments that induce budding and micronucleation. These data have implications for understanding the behavior of acentric DNA in interphase nuclei and for developing chemotherapeutic strategies based on this new mechanism for DM elimination. PMID:9508765

Toward continent-scale interferometric recovery of crustal body waves through ambient seismic noise from USArray

NASA Astrophysics Data System (ADS)

Labedz, C. R.

2015-12-01

Cross-correlation of the ambient seismic noise field is now widely applied for imaging and monitoring at many scales, and has been quite successful in retrieving surface wave information useful for estimating three-dimensional shear velocity structure, anisotropy, or wave amplification and attenuation. However, the use of this approach to retrieve crustal body waves has seen less widespread use. While some studies (e.g., Zhan et al. 2010, Poli et al. 2012) have successfully recovered phases over a few hundred kilometers on continental shields, crustal body waves are not yet seen routinely over longer distances and in more structurally complex regions. In this study, we investigate the recovery of crustal body waves in the continental USA using stacked cross-correlations. The data for correlation was gathered over three to five years of continuous recording on an east-to-west line of USArray stations spanning the northern USA. Specifically, we study four parameters to determine which combination of processing produces the most robust crustal body wave estimates in this geologic setting: 1) the role of the total amount of data; 2) the impact of different processes for selecting which correlation traces are to be used or discarded from the final stacks; 3) the recoverability of waves in different directional components of the data; and 4) the geographic region of data collection. We are able to recover short period crustal S-wave phases at as far as 1500 kilometer interstation distances, which will provide unique information for future tomography models.

Experimental and Theoretical Studies of High Power Plasma Filled Backward Wave Oscillators

DTIC Science & Technology

1991-02-01

excitation and amplification plasma may have a phase velocity vph ,, - c, allowing it of electromagnetic waves. This last area has been referred to be more...and (5): e x p lic i t f o r m ir f 12 ( + A f / f , 12 ) ] ( f=f(cosL,G) (2) Vph Cos_ I(B 2 -4C&f) _2-B]I2C), (4) where f is the frequency of the

Multi-Qubit Algorithms in Josephson Phase Qubits

DTIC Science & Technology

2015-12-15

A. Brun. Entanglement -assisted weak value amplification, arXiv:1401.5887 (01 2014) 04/07/2014 05/08/2013 05/15/2014 09/26/2013 11/04/2013 11/07...Motzoi, R. Vijay, A.W. Ediins, A.N. Korotkov, K.B. Whaley, M. Sarovar, I. Siddiqi. Observation of measurement-induced entanglement and quantum...Roushan, Daniel Sank, Amit Vainsencher, Theodore White, Alexander N. Korotkov, Andrew N. Cleland, John M. Martinis. Catching Shaped Microwave Photons with

Shear-wave velocity and site-amplification factors for 50 Australian sites determined by the spectral analysis of surface waves method

USGS Publications Warehouse

Kayen, Robert E.; Carkin, Bradley A.; Allen, Trevor; Collins, Clive; McPherson, Andrew; Minasian, Diane L.

2015-01-01

One-dimensional shear-wave velocity (VS ) profiles are presented at 50 strong motion sites in New South Wales and Victoria, Australia. The VS profiles are estimated with the spectral analysis of surface waves (SASW) method. The SASW method is a noninvasive method that indirectly estimates the VS at depth from variations in the Rayleigh wave phase velocity at the surface.

Rapid detection of infectious bovine Rhinotracheitis virus using recombinase polymerase amplification assays.

PubMed

Hou, Peili; Wang, Hongmei; Zhao, Guimin; He, Chengqiang; He, Hongbin

2017-12-13

Infectious bovine rhinotracheitis virus (IBRV) is a major pathogen in cattle and has led to significant economic losses to the dairy industry worldwide, and therefore a more optimal method for the rapid diagnosis of IBRV infection is highly needed. In this study, we described the development of a lateral flow dipstrip (LFD) of isothermal recombinase polymerase amplification (RPA) method for rapid detection of IBRV. Distinct regions were selected as a candidate target for designing the LFD-RPA primers and probes. The analytical sensitivity of the RPA assay was determined using ten-fold serially diluted IBRV DNA. The specificity of the assay was assessed with other viral pathogens of cattle with similar clinic and other herpesviruses. The clinical performance was evaluated by testing 106 acute-phase high fever clinical specimens. RPA primers and probe were designed to target the specific conserved UL52 region fragment of IBRV. The detection could be completed at a constant temperature of 38 °C for 25 min, and the amplification products were easily visualized on a simple LFD. The detection limit of this assay was 5 copies per reaction of IBRV DNA and there was no cross-reactivity with other viruses causing bovine gastrointestinal and respiratory infections or other herpesviruses. The assay performance on acute-phase high fever clinical samples collected from cattle with no vaccine against IBRV, which were suspected to be infected with IBRV, was validated by detecting 24 fecal, 36 blood, 38 nasal swab and 8 tissue specimens, and compared with SYBR Green I based real-time PCR. The coincidence between IBRV LFD-RPA and real-time PCR was 100%. IBRV LFD-RPA was fast and much easier to serve as an alternative to the common measures used for IBRV diagnosis, as there is reduction in the use of instruments for identification of the infected animals. In addition, this assay may be the potential candidate to be used as point-of-care diagnostics in the field.

Spiral-Based Phononic Plates: From Wave Beaming to Topological Insulators

NASA Astrophysics Data System (ADS)

Foehr, André; Bilal, Osama R.; Huber, Sebastian D.; Daraio, Chiara

2018-05-01

Phononic crystals and metamaterials can sculpt elastic waves, controlling their dispersion using different mechanisms. These mechanisms are mostly Bragg scattering, local resonances, and inertial amplification, derived from ad hoc, often problem-specific geometries of the materials' building blocks. Here, we present a platform that ultilizes a lattice of spiraling unit cells to create phononic materials encompassing Bragg scattering, local resonances, and inertial amplification. We present two examples of phononic materials that can control waves with wavelengths much larger than the lattice's periodicity. (1) A wave beaming plate, which can beam waves at arbitrary angles, independent of the lattice vectors. We show that the beaming trajectory can be continuously tuned, by varying the driving frequency or the spirals' orientation. (2) A topological insulator plate, which derives its properties from a resonance-based Dirac cone below the Bragg limit of the structured lattice of spirals.

Is it time to move to nucleic acid amplification tests screening for pharyngeal and rectal gonorrhoea in men who have sex with men to improve gonorrhoea control?

PubMed

Fairley, Christopher K; Chen, Marcus Y; Bradshaw, Catriona S; Tabrizi, Sepehr N

2011-03-01

The use of nucleic acid amplification tests (NAAT), as well as or in preference to culture for non-genital sites is now recommended both in Australia and overseas because of their greater sensitivity and improved specificity. A survey of 22 Australian sexual health clinics who each year test over 14500 men who have sex with men (MSM) show that culture remains the predominate method for detecting gonorrhoea at pharyngeal (64%) and rectal (73%) sites. This editorial discusses the potential disadvantages of using culture over NAAT in relation to optimal gonorrhoea control among MSM and advocates that significantly improved control would be achieved by moving to NAAT with the proviso that culture samples are taken wherever possible on NAAT-positive samples and from clients with urethritis to ensure continued surveillance for antimicrobial resistance.

Heterogeneous asymmetric recombinase polymerase amplification (haRPA) for rapid hygiene control of large-volume water samples.

PubMed

Elsäßer, Dennis; Ho, Johannes; Niessner, Reinhard; Tiehm, Andreas; Seidel, Michael

2018-04-01

Hygiene of drinking water is periodically controlled by cultivation and enumeration of indicator bacteria. Rapid and comprehensive measurements of emerging pathogens are of increasing interest to improve drinking water safety. In this study, the feasibility to detect bacteriophage PhiX174 as a potential indicator for virus contamination in large volumes of water is demonstrated. Three consecutive concentration methods (continuous ultrafiltration, monolithic adsorption filtration, and centrifugal ultrafiltration) were combined to concentrate phages stepwise from 1250 L drinking water into 1 mL. Heterogeneous asymmetric recombinase polymerase amplification (haRPA) is applied as rapid detection method. Field measurements were conducted to test the developed system for hygiene online monitoring under realistic conditions. We could show that this system allows the detection of artificial contaminations of bacteriophage PhiX174 in drinking water pipelines. Copyright © 2018 Elsevier Inc. All rights reserved.

Selective amyloid β oligomer assay based on abasic site-containing molecular beacon and enzyme-free amplification.

PubMed

Zhu, Linling; Zhang, Junying; Wang, Fengyang; Wang, Ya; Lu, Linlin; Feng, Chongchong; Xu, Zhiai; Zhang, Wen

2016-04-15

Amyloid-beta (Aβ) oligomers are highly toxic species in the process of Aβ aggregation and are regarded as potent therapeutic targets and diagnostic markers for Alzheimer's disease (AD). Herein, a label-free molecular beacon (MB) system integrated with enzyme-free amplification strategy was developed for simple and highly selective assay of Aβ oligomers. The MB system was constructed with abasic site (AP site)-containing stem-loop DNA and a fluorescent ligand 2-amino-5,6,7-trimethyl-1,8-naphyridine (ATMND), of which the fluorescence was quenched upon binding to the AP site in DNA stem. Enzyme-free amplification was realized by target-triggered continuous opening of two delicately designed MBs (MB1 and MB2). Target DNA hybridization with MB1 and then MB2 resulted in the release of two ATMND molecules in one binding event. Subsequent target recycling could greatly amplify the detection sensitivity due to the greatly enhanced turn-on emission of ATMND fluorescence. Combining with Aβ oligomers aptamers, the strategy was applied to analyze Aβ oligomers and the results showed that it could quantify Aβ oligomers with high selectivity and monitor the Aβ aggregation process. This novel method may be conducive to improve the diagnosis and pathogenic study of Alzheimer's disease. Copyright © 2015 Elsevier B.V. All rights reserved.

Synthesis of a fully-integrated digital signal source for communications from chaotic dynamics-based oscillations

NASA Astrophysics Data System (ADS)

Glenn, Chance Michael, Sr.

This work is the conceptualization, derivation, analysis, and fabrication of a fully practical digital signal source designed from a chaotic oscillator. In it we show how a simple electronic circuit based upon the Colpitts oscillator, can be made to produce highly complex signals capable of carrying digital information. We show a direct relationship between the continuous-time chaotic oscillations produced by the circuit and the logistic map, which is discrete-time, one-dimensional map that is a fundamental paradigm for the study of chaotic systems. We demonstrate the direct encoding of binary information into the oscillations of the chaotic circuit. We demonstrate a new concept in power amplification, called syncrodyne amplification , which uses fundamental properties of chaotic oscillators to provide high-efficiency, high gain amplification of standard communication waveforms as well as typical chaotic oscillations. We show modeling results of this system providing nearly 60-dB power gain and 80% PAE for communications waveforms conforming to GMSK modulation. Finally we show results from a fabricated syncrodyne amplifier circuit operating at 2 MHz, providing over 40-dB power gain and 72% PAE, and propose design criteria for an 824--850 MHz circuit utilizing heterojunction bipolar transistors (HBTs), providing the basis for microwave frequency realization.

First-in-human Phase I study of Pictilisib (GDC-0941), a potent pan-class I phosphatidylinositol-3-kinase (PI3K) inhibitor, in patients with advanced solid tumors

PubMed Central

Baird, Richard; Kristeleit, Rebecca; Shah, Krunal; Moreno, Victor; Clarke, Paul A.; Raynaud, Florence I.; Levy, Gallia; Ware, Joseph A; Mazina, Kathryn; Lin, Ray; Wu, Jenny; Fredrickson, Jill; Spoerke, Jill M; Lackner, Mark R; Yan, Yibing; Friedman, Lori S.; Kaye, Stan B.; Derynck, Mika K.; Workman, Paul; de Bono, Johann S.

2014-01-01

Purpose This first-in-human dose-escalation trial evaluated the safety, tolerability, maximal tolerated dose (MTD), dose limiting toxicities (DLTs), pharmacokinetics, pharmacodynamics and preliminary clinical activity of pictilisib (GDC-0941), an oral, potent and selective inhibitor of the Class I phosphatidylinositol-3-kinases (PI3K). Patients and Methods Sixty patients with solid tumors received pictilisib at 14 dose levels from 15 to 450mg once-daily, initially on days 1-21 every 28 days and later, utilizing continuous dosing for selected dose levels. Pharmacodynamic studies incorporated 18F-FDG-PET, and assessment of phosphorylated AKT and S6 ribosomal protein in platelet-rich plasma and tumor tissue. Results Pictilisib was well-tolerated. The most common toxicities were grade 1-2 nausea, rash and fatigue while the DLT was grade 3 maculopapular rash (450mg, 2 of 3 patients; 330mg, 1 of 7 patients). The pharmacokinetic profile was dose-proportional and supported once-daily dosing. Levels of phosphorylated serine-473 AKT were suppressed >90% in platelet rich plasma at 3 hours post-dose at the MTD and in tumor at pictilisib doses associated with AUC >20uM.hr. Significant increase in plasma insulin and glucose levels, and >25% decrease in 18F-FDG uptake by PET in 7 of 32 evaluable patients confirmed target modulation. A patient with V600E BRAF mutant melanoma and another with platinum-refractory epithelial ovarian cancer exhibiting PTEN loss and PIK3CA amplification demonstrated partial response by RECIST and GCIG-CA125 criteria, respectively. Conclusion Pictilisib was safely administered with a dose-proportional pharmacokinetic profile, on-target pharmacodynamic activity at dose levels ≥100mg and signs of antitumor activity. The recommended Phase II dose was continuous dosing at 330mg once-daily. PMID:25370471

First-in-human phase I study of pictilisib (GDC-0941), a potent pan-class I phosphatidylinositol-3-kinase (PI3K) inhibitor, in patients with advanced solid tumors.

PubMed

Sarker, Debashis; Ang, Joo Ern; Baird, Richard; Kristeleit, Rebecca; Shah, Krunal; Moreno, Victor; Clarke, Paul A; Raynaud, Florence I; Levy, Gallia; Ware, Joseph A; Mazina, Kathryn; Lin, Ray; Wu, Jenny; Fredrickson, Jill; Spoerke, Jill M; Lackner, Mark R; Yan, Yibing; Friedman, Lori S; Kaye, Stan B; Derynck, Mika K; Workman, Paul; de Bono, Johann S

2015-01-01

This first-in-human dose-escalation trial evaluated the safety, tolerability, maximal-tolerated dose (MTD), dose-limiting toxicities (DLT), pharmacokinetics, pharmacodynamics, and preliminary clinical activity of pictilisib (GDC-0941), an oral, potent, and selective inhibitor of the class I phosphatidylinositol-3-kinases (PI3K). Sixty patients with solid tumors received pictilisib at 14 dose levels from 15 to 450 mg once-daily, initially on days 1 to 21 every 28 days and later, using continuous dosing for selected dose levels. Pharmacodynamic studies incorporated (18)F-FDG-PET, and assessment of phosphorylated AKT and S6 ribosomal protein in platelet-rich plasma (PRP) and tumor tissue. Pictilisib was well tolerated. The most common toxicities were grade 1-2 nausea, rash, and fatigue, whereas the DLT was grade 3 maculopapular rash (450 mg, 2 of 3 patients; 330 mg, 1 of 7 patients). The pharmacokinetic profile was dose-proportional and supported once-daily dosing. Levels of phosphorylated serine-473 AKT were suppressed >90% in PRP at 3 hours after dose at the MTD and in tumor at pictilisib doses associated with AUC >20 h·μmol/L. Significant increase in plasma insulin and glucose levels, and >25% decrease in (18)F-FDG uptake by PET in 7 of 32 evaluable patients confirmed target modulation. A patient with V600E BRAF-mutant melanoma and another with platinum-refractory epithelial ovarian cancer exhibiting PTEN loss and PIK3CA amplification demonstrated partial response by RECIST and GCIG-CA125 criteria, respectively. Pictilisib was safely administered with a dose-proportional pharmacokinetic profile, on-target pharmacodynamic activity at dose levels ≥100 mg and signs of antitumor activity. The recommended phase II dose was continuous dosing at 330 mg once-daily. ©2014 American Association for Cancer Research.

Stabilization and control of the carrier-envelope phase of high-power femtosecond laser pulses using the direct locking technique.

PubMed

Imran, Tayyab; Lee, Yong S; Nam, Chang H; Hong, Kyung-Han; Yu, Tae J; Sung, Jae H

2007-01-08

We have stabilized and electronically controlled the carrier-envelope phase (CEP) of high-power femtosecond laser pulses, generated in a grating-based chirped-pulse amplification kHz Ti:sapphire laser, using the direct locking technique [Opt. Express 13, 2969 (2005)] combined with a slow feedback loop. An f-2f spectral interferometer has shown the CEP stabilities of 1.2 rad with the direct locking loop applied to the oscillator and of 180 mrad with an additional slow feedback loop, respectively. The electronic CEP modulations that can be easily realized in the direct locking loop are also demonstrated with the amplified pulses.

High-power Yb-fiber comb with feed-forward control of nonlinear-polarization-rotation mode-locking and large-mode-area fiber amplification.

PubMed

Yan, Ming; Li, Wenxue; Yang, Kangwen; Zhou, Hui; Shen, Xuling; Zhou, Qian; Ru, Qitian; Bai, Dongbi; Zeng, Heping

2012-05-01

We report on a simple scheme to precisely control carrier-envelope phase of a nonlinear-polarization-rotation mode-locked self-started Yb-fiber laser system with an average output power of ∼7  W and a pulse width of 130 fs. The offset frequency was locked to the repetition rate of ∼64.5  MHz with a relative linewidth of ∼1.4  MHz by using a self-referenced feed-forward scheme based on an acousto-optic frequency shifter. The phase noise and timing jitter were calculated to be 370 mrad and 120 as, respectively.

The influence of current neutralization and multiple Coulomb scattering on the spatial dynamics of resistive sausage instability of a relativistic electron beam propagating in ohmic plasma

NASA Astrophysics Data System (ADS)

Kolesnikov, E. K.; Manuilov, A. S.; Petrov, V. S.; Klyushnikov, G. N.; Chernov, S. V.

2017-06-01

The influence of the current neutralization process, the phase mixing of the trajectories of electrons and multiple Coulomb scattering of electrons beam on the atoms of the background medium on the spatial increment of the growth of sausage instability of a relativistic electron beam propagating in ohmic plasma channel has been considered. It has been shown that the amplification of the current neutralization leads to a significant increase in this instability, and phase mixing and the process of multiple scattering of electrons beam on the atoms of the background medium are the stabilizing factor.

Femtosecond fiber CPA system based on picosecond master oscillator and power amplifier with CCC fiber.

PubMed

Želudevičius, J; Danilevičius, R; Viskontas, K; Rusteika, N; Regelskis, K

2013-03-11

Results of numerical and experimental investigations of the simple fiber CPA system seeded by nearly bandwidth-limited pulses from the picosecond oscillator are presented. We utilized self-phase modulation in a stretcher fiber to broaden the pulse spectrum and dispersion of the fiber to stretch pulses in time. During amplification in the ytterbium-doped CCC fiber, gain-shaping and self-phase modulation effects were observed, which improved pulse compression with a bulk diffraction grating compressor. After compression with spectral filtering, pulses with the duration of 400 fs and energy as high as 50 µJ were achieved, and the output beam quality was nearly diffraction-limited.

Generation of narrowband, high-intensity, carrier-envelope phase-stable pulses tunable between 4 and 18  THz.

PubMed

Liu, B; Bromberger, H; Cartella, A; Gebert, T; Först, M; Cavalleri, A

2017-01-01

We report on the generation of high-energy (1.9 μJ) far-infrared pulses tunable between 4 and 18 THz frequency. Emphasis is placed on tunability and on minimizing the bandwidth of these pulses to less than 1 THz, as achieved by difference-frequency mixing of two linearly chirped near-infrared pulses in the organic nonlinear crystal DSTMS. As the two near-infrared pulses are derived from amplification of the same white light continuum, their carrier envelope phase fluctuations are mutually correlated, and hence the difference-frequency THz field exhibits absolute phase stability. This source opens up new possibilities for the control of condensed matter and chemical systems by selective excitation of low-energy modes in a frequency range that has, to date, been difficult to access.

Can biological homochirality result from a phase transition?

PubMed

Figureau, A; Duval, E; Boukenter, A

1995-06-01

The problem of chiral purity in living organisms is still one of the prominent difficulties in the study of the origins of life. In particular the parity non-conservation known to occur in weak interactions could not be related to this lack of symmetry: these physical forces, though universal, are very weak and up to now no amplification process had been proposed. In 1991, A. Salam remarked that, due to the attractive character of the parity violating force in electro-weak interactions, a phase transition at low temperature should exist, leading eventually to enantiomeric purity. We undertook then a series of experimental tests, looking for a sizeable change in the optical activity of cystine molecules. We found no evidence for the phase transition down to 0.01 K. The interpretation of these negative results will be discussed, and future experiments proposed.

RESONANT AMPLIFICATION OF TURBULENCE BY THE BLAST WAVES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zankovich, A. M.; Kovalenko, I. G., E-mail: ilya.g.kovalenko@gmail.com

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,more » 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.« less

Quantification of HER2/neu gene amplification by competitive pcr using fluorescent melting curve analysis.

PubMed

Lyon, E; Millson, A; Lowery, M C; Woods, R; Wittwer, C T

2001-05-01

Molecular detection methods for HER2/neu gene amplification include fluorescence in situ hybridization (FISH) and competitive PCR. We designed a quantitative PCR system utilizing fluorescent hybridization probes and a competitor that differed from the HER2/neu sequence by a single base change. Increasing twofold concentrations of competitor were coamplified with DNA from cell lines with various HER2/neu copy numbers at the HER2/neu locus. Competitor DNA was distinguished from the HER2/neu sequence by a fluorescent hybridization probe and melting curve analysis on a fluorescence-monitoring thermal cycler. The percentages of competitor to target peak areas on derivative fluorescence vs temperature curves were used to calculate copy number. Real-time monitoring of the PCR reaction showed comparable relative areas throughout the log phase and during the PCR plateau, indicating that only end-point detection is necessary. The dynamic range was over two logs (2000-250 000 competitor copies) with CVs < 20%. Three cell lines (MRC-5, T-47D, and SK-BR-3) were determined to have gene doses of 1, 3, and 11, respectively. Gene amplification was detected in 3 of 13 tumor samples and was correlated with conventional real-time PCR and FISH analysis. Use of relative peak areas allows gene copy numbers to be quantified against an internal competitive control in < 1 h.

Rapid amplification/detection of nucleic acid targets utilizing a HDA/thin film biosensor.

PubMed

Jenison, Robert; Jaeckel, Heidi; Klonoski, Joshua; Latorra, David; Wiens, Jacinta

2014-08-07

Thin film biosensors exploit a flat, optically coated silicon-based surface whereupon formation of nucleic acid hybrids are enzymatically transduced in a molecular thin film that can be detected by the unaided human eye under white light. While the limit of sensitivity for detection of nucleic acid targets is at sub-attomole levels (60 000 copies) many clinical specimens containing bacterial pathogens have much lower levels of analyte present. Herein, we describe a platform, termed HDA/thin film biosensor, which performs helicase-dependant nucleic acid amplification on a thin film biosensor surface to improve the limit of sensitivity to 10 copies of the mecA gene present in methicillin-resistant strains of Staphylococcus. As double-stranded DNA is unwound by helicase it was either bound by solution-phase DNA primers to be copied by DNA polymerase or hybridized to surface immobilized probe on the thin film biosensor surface to be detected. Herein, we show that amplification reactions on the thin film biosensor are equivalent to in standard thin wall tubes, with detection at the limit of sensitivity of the assay occurring after 30 minutes of incubation time. Further we validate the approach by detecting the presence of the mecA gene in methicillin-resistant Staphylococcus aureus (MRSA) from positive blood culture aliquots with high specificity (signal/noise ratio of 105).

High Phosphohistone H3 Expression Correlates with Adverse Clinical, Biological, and Pathological Factors in Neuroblastomas

PubMed Central

Ramani, Pramila; Taylor, Scott; Miller, Elizabeth; Sowa-Avugrah, Emile; May, Margaret T.

2015-01-01

Phosphohistone H3 (pHH3), a biomarker of the late G2- and M-phase of the cell cycle, provides a powerful indication of the proliferative state of many cancers. We investigated the prognostic significance of pHH3 by immunostaining 80 neuroblastomas and counting the average number of strongly stained nuclei and mitotic figures. The median and 75th percentile pHH3 proliferation indices (PIs) were 0.54% and 1.06% (range, 0.01% to 2.23%) respectively. pHH3 expression was significantly higher in neuroblastomas from patients with adverse clinical characteristics, all unfavorable pathological factors including high mitosis karyorrhexis index (MKI), and adverse biological factors including MYCN oncogene amplification. High pHH3-PIs, at 1% threshold, were significantly associated with a shorter overall survival (OS) and event-free survival (EFS) in the univariable Cox regression analyses. In the multivariable models, high pHH3 counts were significantly associated with worse OS after adjustment for age but were not independent of either high MKI or MYCN amplification. In children less than 18 months of age, high MKIs and high PHH3-PIs were associated with significantly worse OS and EFS. In conclusion, high pHH3 expression correlates strongly with high MKI and MYCN amplification and indicates poor prognosis in neuroblastomas. PMID:25711230

Activation and quenching of the phototransduction cascade in retinal cones as inferred from electrophysiology and mathematical modeling

PubMed Central

Astakhova, Luba; Firsov, Michael

2015-01-01

Purpose To experimentally identify and quantify factors responsible for the lower sensitivity of retinal cones compared to rods. Methods Electrical responses of frog rods and fish (Carassius) cones to short flashes of light were recorded using the suction pipette technique. A fast solution changer was used to apply a solution that fixed intracellular Ca2+ concentration at the prestimulus level, thereby disabling Ca2+ feedback, to the outer segment (OS). The results were analyzed with a specially designed mathematical model of phototransduction. The model included all basic processes of activation and quenching of the phototransduction cascade but omitted unnecessary mechanistic details of each step. Results Judging from the response versus intensity curves, Carassius cones were two to three orders of magnitude less sensitive than frog rods. There was a large scatter in sensitivity among individual cones, with red-sensitive cones being on average approximately two times less sensitive than green-sensitive ones. The scatter was mostly due to different signal amplification, since the kinetic parameters of the responses among cones were far less variable than sensitivity. We argue that the generally accepted definition of the biochemical amplification in phototransduction cannot be used for comparing amplification in rods and cones, since it depends on an irrelevant factor, that is, the cell’s volume. We also show that the routinely used simplified parabolic curve fitting to an initial phase of the response leads to a few-fold underestimate of the amplification. We suggest a new definition of the amplification that only includes molecular parameters of the cascade activation, and show how it can be derived from experimental data. We found that the mathematical model with unrestrained parameters can yield an excellent fit to experimental responses. However, the fits with wildly different sets of parameters can be virtually indistinguishable, and therefore cannot provide meaningful data on underlying mechanisms. Based on results of Ca2+-clamp experiments, we developed an approach to strongly constrain the values of many key parameters that set the time course and sensitivity of the photoresponse (such as the dark turnover rate of cGMP, rates of turnoffs of the photoactivated visual pigment and phosphodiesterase, and kinetics of Ca2+ feedback). We show that applying these constraints to our mathematical model enables accurate determination of the biochemical amplification in phototransduction. It appeared that, contrary to many suggestions, maximum biochemical amplification derived for “best” Carassius cones was as high as in frog rods. On the other hand, all turnoff and recovery reactions in cones proceeded approximately 10 times faster than in rods. Conclusions The main cause of the differing sensitivity of rods and cones is cones’ ability to terminate their photoresponse faster. PMID:25866462

Scheduling Chemotherapy: Catch 22 between Cell Kill and Resistance Evolution

DOE PAGES

Gardner, Shea N.

2000-01-01

Dose response curves show that prolonged drug exposure at a low concentration may kill more cells than short exposures at higher drug concentrations, particularly for cell cycle phase specific drugs. Applying drugs at low concentrations for prolonged periods, however, allows cells with partial resistance to evolve higher levels of resistance through stepwise processes such as gene amplification. Models are developed for cell cycle specific (CS) and cell cycle nonspecific (CNS) drugs to identify the schedule of drug application that balances this tradeoff. The models predict that a CS drug may be applied most effectively by splitting the cumulative dose intomore » many (>40) fractions applied by long-term chemotherapy, while CNS drugs may be better applied in fewer than 10 fractions applied over a shorter term. The model suggests that administering each fraction by continuous infusion may be more effective than giving the drug as a bolus, whether the drug is CS or CNS. In addition, tumors with a low growth fraction or slow rate of cell division are predicted to be controlled more easily with CNS drugs, while those with a high proliferative fraction or fast cell division rate may respond better to CS drugs.« less

Scheduling Chemotherapy: Catch 22 between Cell Kill and Resistance Evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gardner, Shea N.

Dose response curves show that prolonged drug exposure at a low concentration may kill more cells than short exposures at higher drug concentrations, particularly for cell cycle phase specific drugs. Applying drugs at low concentrations for prolonged periods, however, allows cells with partial resistance to evolve higher levels of resistance through stepwise processes such as gene amplification. Models are developed for cell cycle specific (CS) and cell cycle nonspecific (CNS) drugs to identify the schedule of drug application that balances this tradeoff. The models predict that a CS drug may be applied most effectively by splitting the cumulative dose intomore » many (>40) fractions applied by long-term chemotherapy, while CNS drugs may be better applied in fewer than 10 fractions applied over a shorter term. The model suggests that administering each fraction by continuous infusion may be more effective than giving the drug as a bolus, whether the drug is CS or CNS. In addition, tumors with a low growth fraction or slow rate of cell division are predicted to be controlled more easily with CNS drugs, while those with a high proliferative fraction or fast cell division rate may respond better to CS drugs.« less

Amplification of the solar signal in the summer monsoon rainband in China by synergistic actions of different dynamical responses

NASA Astrophysics Data System (ADS)

Zhao, Liang; Wang, Jingsong; Liu, Haiwen; Xiao, Ziniu

2017-02-01

A rainband meridional shift index (RMSI) is defined and used to statistically prove that the East Asian summer monsoon rainband is usually significantly more northward in the early summer of solar maximum years than that of solar minimum years. By applying continuous wavelet transform, cross wavelet transform, and wavelet coherence, it is found that throughout most of the 20th century, the significant decadal oscillations of sunspot number (SSN) and the RMSI are phase-locked and since the 1960s, the SSN has led the RMSI slightly by approximately 1.4 yr. Wind and Eliassen-Palm (EP) flux analysis shows that the decadal meridional oscillation of the June rainband likely results from both a stronger or earlier onset of the tropical monsoon and poleward shift of the subtropical westerly jet in high-solar months of May and June. The dynamical responses of the lower tropical monsoon and the upper subtropical westerly jet to the 11-yr solar cycle transmit bottom-up and top-down solar signals, respectively, and the synergistic actions between the monsoon and the jet likely amplify the solar signal at the northern boundary of the monsoon to some extent.

Miniaturized isothermal nucleic acid amplification, a review.

PubMed

Asiello, Peter J; Baeumner, Antje J

2011-04-21

Micro-Total Analysis Systems (µTAS) for use in on-site rapid detection of DNA or RNA are increasingly being developed. Here, amplification of the target sequence is key to increasing sensitivity, enabling single-cell and few-copy nucleic acid detection. The several advantages to miniaturizing amplification reactions and coupling them with sample preparation and detection on the same chip are well known and include fewer manual steps, preventing contamination, and significantly reducing the volume of expensive reagents. To-date, the majority of miniaturized systems for nucleic acid analysis have used the polymerase chain reaction (PCR) for amplification and those systems are covered in previous reviews. This review provides a thorough overview of miniaturized analysis systems using alternatives to PCR, specifically isothermal amplification reactions. With no need for thermal cycling, isothermal microsystems can be designed to be simple and low-energy consuming and therefore may outperform PCR in portable, battery-operated detection systems in the future. The main isothermal methods as miniaturized systems reviewed here include nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), and strand displacement amplification (SDA). Also, important design criteria for the miniaturized devices are discussed. Finally, the potential of miniaturization of some new isothermal methods such as the exponential amplification reaction (EXPAR), isothermal and chimeric primer-initiated amplification of nucleic acids (ICANs), signal-mediated amplification of RNA technology (SMART) and others is presented.

High-Q Photonic-Crystal Cavities for Light Amplification and Lasing

DTIC Science & Technology

2011-06-10

Neoclassical Theory of Electric Charges", to appear in Discrete and Continuous Dynamical Systems, Vol. 27, Number 4, August 2010. - A. Figotin, I...dynamics of PDE", ICMS, Edinburgh, September, 2010 - A. Figotn and A. Babin, "Some Mathematical Problems in a Neoclassical Theory of Electric Charges...34, Weizmann Institute, Rehovot, Israel, August, 2010. - A. Figotn and A. Babin, "Some Mathematical Problems in a Neoclassical Theory of Electric

Evidence linking rapid Arctic warming to mid-latitude weather patterns.

PubMed

Francis, Jennifer; Skific, Natasa

2015-07-13

The effects of rapid Arctic warming and ice loss on weather patterns in the Northern Hemisphere is a topic of active research, lively scientific debate and high societal impact. The emergence of Arctic amplification--the enhanced sensitivity of high-latitude temperature to global warming--in only the last 10-20 years presents a challenge to identifying statistically robust atmospheric responses using observations. Several recent studies have proposed and demonstrated new mechanisms by which the changing Arctic may be affecting weather patterns in mid-latitudes, and these linkages differ fundamentally from tropics/jet-stream interactions through the transfer of wave energy. In this study, new metrics and evidence are presented that suggest disproportionate Arctic warming-and resulting weakening of the poleward temperature gradient-is causing the Northern Hemisphere circulation to assume a more meridional character (i.e. wavier), although not uniformly in space or by season, and that highly amplified jet-stream patterns are occurring more frequently. Further analysis based on self-organizing maps supports this finding. These changes in circulation are expected to lead to persistent weather patterns that are known to cause extreme weather events. As emissions of greenhouse gases continue unabated, therefore, the continued amplification of Arctic warming should favour an increased occurrence of extreme events caused by prolonged weather conditions.

Integrated Field Scale, Lab Scale, and Modeling Studies for Improving Our Ability to Assess the Groundwater to Indoor Air Pathway at Chlorinated Solvent Impacted Groundwater Sites

DTIC Science & Technology

2016-01-07

clays . The Emean/Estatic values were greater for loam than the other two types of soil – indicating greater amplification of emissions relative to a...ɸT): 0.35 m3-voids/m3- soil Soil permeability to soil gas flow (Kg): 1E-7 cm2 Soil gas phase dynamic viscosity : 1.8E-4 g/cm/s Soil domain

Spectral gain investigation of large size OPCPA based on partially deuterated KDP

NASA Astrophysics Data System (ADS)

Galimberti, Marco; Boyle, Alexis; Musgrave, Ian O.; Oliveira, Pedro; Pepler, Dave; Shaikh, Waseem; Winstone, Trevor B.; Wyatt, Adam; Hernandez-Gomez, Cristina

2018-01-01

The Optical Parametric Chirped Pulse Amplification is one of the most promising techniques to deliver 20PW laser system. The already available KD*P in large size is a good candidate as nonlinear crystal. In this article we report the experimental analysis of the spectral small signal gain for KD*P at 70% deuteration level for different phase matching and non-collinear angle. The data is also compared with a theoretical model.

Optical switching and photoluminescence in erbium-implanted vanadium dioxide thin films

NASA Astrophysics Data System (ADS)

Lim, Herianto; Stavrias, Nikolas; Johnson, Brett C.; Marvel, Robert E.; Haglund, Richard F.; McCallum, Jeffrey C.

2014-03-01

Vanadium dioxide (VO2) is under intensive consideration for optical switching due to its reversible phase transition, which features a drastic and rapid shift in infrared reflectivity. Classified as an insulator-to-metal transition, the phase transition in VO2 can be induced thermally, electrically, and optically. When induced optically, the transition can occur on sub-picosecond time scales. It is interesting to dope VO2 with erbium ions (Er3+) and observe their combined properties. The first excited-state luminescence of Er3+ lies within the wavelength window of minimal transmission-loss in silicon and has been widely utilized for signal amplification and generation in silicon photonics. The incorporation of Er3+ into VO2 could therefore result in a novel photonic material capable of simultaneous optical switching and amplification. In this work, we investigate the optical switching and photoluminescence in Er-implanted VO2 thin films. Thermally driven optical switching is demonstrated in the Er-implanted VO2 by infrared reflectometry. Photoluminescence is observed in the thin films annealed at ˜800 °C or above. In addition, Raman spectroscopy and a statistical analysis of switching hysteresis are carried out to assess the effects of the ion implantation on the VO2 thin films. We conclude that Er-implanted VO2 can function as an optical switch and amplifier, but with reduced switching quality compared to pure VO2.

In vivo measurement of differential motion inside the organ of Corti using a low coherence interferometer system

NASA Astrophysics Data System (ADS)

Chen, Fangyi; Zha, Dingjun; Fridberger, Anders; Zheng, Jiefu; Choudhury, Niloy; Jacques, Steven L.; Wang, Ruikang K.; Nuttall, Alfred L.

2012-02-01

The differential motion of the organ of Corti has been expected as a result of the outer hair cell force, believed to be necessary for the cochlear amplifier. In vitro experiments have been performed to demonstrate this motion but the in vivo data was unavailable due to the technical difficulties. Using a specially-designed time-domain optical coherence tomography system, we performed in vivo imaging and vibration measurement at the sensitive base of the guinea pig cochlea. This technique, for the first time, provides in vivo information about the internal vibration of the organ of Corti. At low sound level, when the cochlea is more sensitive, top surface of the organ of Corti, the reticular lamina (RL) showed tuning at a higher frequency than of the bottom surface, basilar membrane (BM) and its vibration amplitude is 2-3 times of that of the BM. Corresponding to the frequency difference, the phase of RL vibration is lead to that of the BM. Both the amplitude gain and the phase lead on RL is level dependent. This suggests that they are related to the cochlear amplification. The amplitude gain at the RL is an enhancement of the BM motion for stimulating the stereocillia. The advance in time of RL vibration can prepare proper timing of stereocillia stimulation for the cochlear amplification.

Future ocean hypercapnia driven by anthropogenic amplification of the natural CO2 cycle

NASA Astrophysics Data System (ADS)

McNeil, B.

2016-02-01

Elevated carbon dioxide concentrations in seawater (hypercapnia) can induce neurological, physiological and behavioural deficiencies in marine animals. Prediction of the onset and evolution of hypercapnia in the ocean requires a good understanding of annual oceanic carbon dioxide variability, but relevant global observational data are sparse. Here we diagnose global ocean patterns of monthly carbon variability based on observations that allow us to examine the evolution of surface ocean CO2 levels over the entire annual cycle under increasing atmospheric CO2 concentrations. We find that some oceanic regions undergo an up to 10-fold amplification of the natural cycle of CO2 by 2100, if atmospheric carbon dioxide concentrations continue to rise throughout this century (RCP8.5). Projections from a suite of Earth System Climate Models are broadly consistent with the findings from our data based approach. Our predicted amplification in the annual CO2 cycle displays distinct global patterns that may expose major fisheries in the Southern, Pacific and North Atlantic Oceans to high CO2 events many decades earlier than expected from average atmospheric CO2 concentrations. We suggest that these ocean 'CO2 hotspots' evolve as a combination of the strong seasonal dynamics of CO2 and the long-term effective storage of anthropogenic CO2 that lowers the buffer capacity in those regions, causing a non-linear CO2 amplification over the annual cycle. The onset of ocean hypercapnia events (pCO2 >1000 µatm) is forecast for atmospheric CO2 concentrations that exceed 650 ppm, with hypercapnia spreading to up to one half of the surface ocean by the year 2100 under a high-emissions scenario (RCP8.5) with potential implications for fisheries over the coming century.

Human Epidermal Growth Factor Receptor 2 (HER-2/neu)-Directed Therapy for Rare Metastatic Epithelial Tumors with HER-2 Amplification

PubMed Central

Shin, Daniel Sanghoon; Sherry, Timothy; Kallen, Michael E.; Wong, Steven; Drakaki, Alexandra

2016-01-01

Case 1 A 67-year-old Asian female was diagnosed with locally advanced high-grade salivary duct carcinoma in June 2011. Molecular analysis revealed human epidermal growth factor receptor 2 (HER-2) amplification. She received adjuvant therapy with carboplatin/paclitaxel/ trastuzumab and maintenance of trastuzumab. Upon disease progression, trastuzumab could not be continued due to lack of financial coverage. Instead, she was treated with compassionate use of lapatinib from April 2013 and standard 5-fluorouracil. Her disease ultimately progressed and she expired later in 2013. Case 2 A 68-year-old Asian male was diagnosed with extramammary Paget's disease of the scrotum with HER-2 amplification in May 2011. He received 6 cycles of adjuvant trastuzumab/docetaxel/carboplatin followed by maintenance trastuzumab, which was changed to compassionate use of lapatinib as his insurance did not cover further administration of trastuzumab. He showed clinical benefits from single-agent lapatinib and a combination of lapatinib/capecitabine upon progression to the single-agent lapatinib. Ultimately, he was started on ado-trastuzumab emtansine, which was approved at that time by the FDA for HER-2-positive breast cancer progressed on trastuzumab. He is having clinical and radiographic complete response based on current imaging and normalization of his tumor markers. Conclusion HER-2-targeted therapy should be considered for tumors with HER-2 amplification. In our case series, we would like to emphasize this approach in other rare histologies. Specifically, our patient with extramammary Paget's disease of the scrotum represents the first reported case of a non-breast, non-gastric tumor with HER-2 overexpression with complete clinical and radiographic response to HER-2-targeted therapy PMID:27403128

Local seismic hazard assessment in explosive volcanic settings by 3D numerical analyses

NASA Astrophysics Data System (ADS)

Razzano, Roberto; Pagliaroli, Alessandro; Moscatelli, Massimiliano; Gaudiosi, Iolanda; Avalle, Alessandra; Giallini, Silvia; Marcini, Marco; Polpetta, Federica; Simionato, Maurizio; Sirianni, Pietro; Sottili, Gianluca; Vignaroli, Gianluca; Bellanova, Jessica; Calamita, Giuseppe; Perrone, Angela; Piscitelli, Sabatino

2017-04-01

This work deals with the assessment of local seismic response in the explosive volcanic settings by reconstructing the subsoil model of the Stracciacappa maar (Sabatini Volcanic District, central Italy), whose pyroclastic succession records eruptive phases ended about 0.09 Ma ago. Heterogeneous characteristics of the Stracciacappa maar (stratification, structural setting, lithotypes, and thickness variation of depositional units) make it an ideal case history for understanding mechanisms and processes leading to modifications of amplitude-frequency-duration of seismic waves generated at earthquake sources and propagating through volcanic settings. New geological map and cross sections, constrained with recently acquired geotechnical and geophysical data, illustrate the complex geometric relationships among different depositional units forming the maar. A composite interfingering between internal lacustrine sediments and epiclastic debris, sourced from the rim, fills the crater floor; a 45 meters thick continuous coring borehole was drilled in the maar with sampling of undisturbed samples. Electrical Resistivity Tomography surveys and 2D passive seismic arrays were also carried out for constraining the geological model and the velocity profile of the S-waves, respectively. Single station noise measurements were collected in order to define natural amplification frequencies. Finally, the nonlinear cyclic soil behaviour was investigated through simple shear tests on the undisturbed samples. The collected dataset was used to define the subsoil model for 3D finite difference site response numerical analyses by using FLAC 3D software (ITASCA). Moreover, 1D and 2D numerical analyses were carried out for comparison purposes. Two different scenarios were selected as input motions: a moderate magnitude (volcanic event) and a high magnitude (tectonic event). Both earthquake scenarios revealed significant ground motion amplification (up to 15 in terms of spectral acceleration at about 1 s) essentially related to 2D/3D phenomena associated to sharp lateral variations of mechanical properties within the Stracciacappa maar. Our results are relevant to face the assessment of local seismic response in similar volcanic settings in highly urbanised environments elsewhere.

Nonlinear processes associated with the amplification of MHz-linewidth laser pulses in single-mode Tm:fiber

NASA Astrophysics Data System (ADS)

Sincore, Alex; Bodnar, Nathan; Bradford, Joshua; Abdulfattah, Ali; Shah, Lawrence; Richardson, Martin C.

2017-03-01

This work studies the accumulated nonlinearities when amplifying a narrow linewidth 2053 nm seed in a single mode Tm:fiber amplifier. A <2 MHz linewidth CW diode seed is externally modulated using a fiberized acousto-optic modulator. This enables independent control of repetition rate and pulse duration (>30 ns). The pulses are subsequently amplified and the repetition rate is further reduced using a second acousto-optic modulator. It is well known that spectral degradation occurs in such fibers for peak powers over 100's of watts due to self-phase modulation, four-wave mixing, and stimulated Raman scattering. In addition to enabling a thorough test bed to study such spectral broadening, this system will also enable the investigation of stimulated Brillouin scattering thresholds in the same system. This detailed study of the nonlinearities encountered in 2 μm fiber amplifiers is important in a range of applications from telecommunications to the amplification of ultrashort laser pulses.

Graphene Distributed Amplifiers: Generating Desirable Gain for Graphene Field-Effect Transistors

PubMed Central

Lyu, Hongming; Lu, Qi; Huang, Yilin; Ma, Teng; Zhang, Jinyu; Wu, Xiaoming; Yu, Zhiping; Ren, Wencai; Cheng, Hui-Ming; Wu, Huaqiang; Qian, He

2015-01-01

Ever since its discovery, graphene bears great expectations in high frequency electronics due to its irreplaceably high carrier mobility. However, it has long been blamed for the weakness in generating gains, which seriously limits its pace of development. Distributed amplification, on the other hand, has successfully been used in conventional semiconductors to increase the amplifiers’ gain-bandwidth product. In this paper, distributed amplification is first applied to graphene. Transmission lines phase-synchronize paralleled graphene field-effect transistors (GFETs), combining the gain of each stage in an additive manner. Simulations were based on fabricated GFETs whose fT ranged from 8.5 GHz to 10.5 GHz and fmax from 12 GHz to 14 GHz. A simulated four-stage graphene distributed amplifier achieved up to 4 dB gain and 3.5 GHz bandwidth, which could be realized with future IC processes. A PCB level graphene distributed amplifier was fabricated as a proof of circuit concept. PMID:26634442

Ideal plasma response to vacuum magnetic fields with resonant magnetic perturbations in non-axisymmetric tokamaks

DOE PAGES

Kim, Kimin; Ahn, J. -W.; Scotti, F.; ...

2015-09-03

Ideal plasma shielding and amplification of resonant magnetic perturbations in non-axisymmetric tokamak is presented by field line tracing simulation with full ideal plasma response, compared to measurements of divertor lobe structures. Magnetic field line tracing simulations in NSTX with toroidal non-axisymmetry indicate the ideal plasma response can significantly shield/amplify and phase shift the vacuum resonant magnetic perturbations. Ideal plasma shielding for n = 3 mode is found to prevent magnetic islands from opening as consistently shown in the field line connection length profile and magnetic footprints on the divertor target. It is also found that the ideal plasma shielding modifiesmore » the degree of stochasticity but does not change the overall helical lobe structures of the vacuum field for n = 3. Furthermore, amplification of vacuum fields by the ideal plasma response is predicted for low toroidal mode n = 1, better reproducing measurements of strong striation of the field lines on the divertor plate in NSTX.« less

Role of Fanconi Anemia FANCG in Preventing Double-Strand Breakage and Chromosomal Rearrangement during DNA Replication

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tebbs, R S; Hinz, J M; Yamada, N A

The Fanconi anemia (FA) proteins overlap with those of homologous recombination through FANCD1/BRCA2, but the biochemical functions of other FA proteins are unknown. By constructing and characterizing a null fancg mutant of hamster CHO cells, we present several new insights for FA. The fancg cells show a broad sensitivity to genotoxic agents, not supporting the conventional concept of sensitivity to only DNA crosslinking agents. The aprt mutation rate is normal, but hprt mutations are reduced, which we ascribe to the lethality of large deletions. CAD and dhfr gene amplification rates are increased, implying excess chromosomal breakage during DNA replication, andmore » suggesting amplification as a contributing factor to cancer-proneness in FA patients. In S-phase cells, both spontaneous and mutagen-induced Rad51 nuclear foci are elevated. These results support a model in which FancG protein helps to prevent collapse of replication forks by allowing translesion synthesis or lesion bypass through homologous recombination.« less

Peroxy Radical Measurements during PROPHET-AMOS 2016

NASA Astrophysics Data System (ADS)

Wood, E. C. D.; Deming, B.; Rollings, D.

2016-12-01

We present measurements of total peroxy radicals (HO2 + RO2) using the Ethane Chemical Amplifier (ECHAMP) technique during the PROPHET-AMOS project in Pellston, Michigan during July 2016. The C2H6/NO amplification chemistry occurred in FEP reaction chambers at the top of the PROPHET tower at a height of 34 m. The NO2 amplification product was transported through tubing to two cavity attenuated phase shift spectrometers (CAPS) housed inside the PROPHET laboratory. Two calibration sources were used: one based on water photolysis in the presence of isoprene and ozone actinometry, and another based on methyl iodide (CH3I) photolysis. The former was integrated into the inlet system, allowing for daily calibrations, whereas the latter was used twice during the campaign. Peak mixing ratios on warm, sunny days were approximately 40 ppt. Nighttime concentrations varied from below the instrumental detection limit to approximately 5 ppt. The measured peroxy radical concentrations will be compared to HO2 and HO2* mixing ratios measured by the Indiana University LIF-FAGE instrument.

Real-Time PCR Quantification Using A Variable Reaction Efficiency Model

PubMed Central

Platts, Adrian E.; Johnson, Graham D.; Linnemann, Amelia K.; Krawetz, Stephen A.

2008-01-01

Quantitative real-time PCR remains a cornerstone technique in gene expression analysis and sequence characterization. Despite the importance of the approach to experimental biology the confident assignment of reaction efficiency to the early cycles of real-time PCR reactions remains problematic. Considerable noise may be generated where few cycles in the amplification are available to estimate peak efficiency. An alternate approach that uses data from beyond the log-linear amplification phase is explored with the aim of reducing noise and adding confidence to efficiency estimates. PCR reaction efficiency is regressed to estimate the per-cycle profile of an asymptotically departed peak efficiency, even when this is not closely approximated in the measurable cycles. The process can be repeated over replicates to develop a robust estimate of peak reaction efficiency. This leads to an estimate of the maximum reaction efficiency that may be considered primer-design specific. Using a series of biological scenarios we demonstrate that this approach can provide an accurate estimate of initial template concentration. PMID:18570886

Parametric resonance in tunable superconducting cavities

NASA Astrophysics Data System (ADS)

Wustmann, Waltraut; Shumeiko, Vitaly

2013-05-01

We develop a theory of parametric resonance in tunable superconducting cavities. The nonlinearity introduced by the superconducting quantum interference device (SQUID) attached to the cavity and damping due to connection of the cavity to a transmission line are taken into consideration. We study in detail the nonlinear classical dynamics of the cavity field below and above the parametric threshold for the degenerate parametric resonance, featuring regimes of multistability and parametric radiation. We investigate the phase-sensitive amplification of external signals on resonance, as well as amplification of detuned signals, and relate the amplifier performance to that of linear parametric amplifiers. We also discuss applications of the device for dispersive qubit readout. Beyond the classical response of the cavity, we investigate small quantum fluctuations around the amplified classical signals. We evaluate the noise power spectrum both for the internal field in the cavity and the output field. Other quantum-statistical properties of the noise are addressed such as squeezing spectra, second-order coherence, and two-mode entanglement.

DNA Replication Control During Drosophila Development: Insights into the Onset of S Phase, Replication Initiation, and Fork Progression

PubMed Central

Hua, Brian L.; Orr-Weaver, Terry L.

2017-01-01

Proper control of DNA replication is critical to ensure genomic integrity during cell proliferation. In addition, differential regulation of the DNA replication program during development can change gene copy number to influence cell size and gene expression. Drosophila melanogaster serves as a powerful organism to study the developmental control of DNA replication in various cell cycle contexts in a variety of differentiated cell and tissue types. Additionally, Drosophila has provided several developmentally regulated replication models to dissect the molecular mechanisms that underlie replication-based copy number changes in the genome, which include differential underreplication and gene amplification. Here, we review key findings and our current understanding of the developmental control of DNA replication in the contexts of the archetypal replication program as well as of underreplication and differential gene amplification. We focus on the use of these latter two replication systems to delineate many of the molecular mechanisms that underlie the developmental control of replication initiation and fork elongation. PMID:28874453

DNA typing by microbead arrays and PCR-SSP: apparent false-negative or -positive hybridization or amplification signals disclose new HLA-B and -DRB1 alleles.

PubMed

Rahal, M; Kervaire, B; Villard, J; Tiercy, J-M

2008-03-01

Human leukocyte antigen (HLA) typing by polymerase chain reaction-sequence-specific oligonucleotide (PCR-SSO) hybridization on solid phase (microbead assay) or polymerase chain reaction-sequence-specific primers (PCR-SSP) requires interpretation softwares to detect all possible allele combinations. These programs propose allele calls by taking into account false-positive or false-negative signal(s). The laboratory has the option to validate typing results in the presence of strongly cross-reacting or apparent false-negative signals. Alternatively, these seemingly aberrant signals may disclose novel variants. We report here four new HLA-B (B*5620 and B*5716) and HLA-DRB1 alleles (DRB1*110107 and DRB1*1474) that were detected by apparent false-negative or -positive hybridization or amplification patterns, and ultimately resolved by sequencing. To avoid allele misassignments, a comprehensive evaluation of acquired data as documented in a quality assurance system is therefore required to confirm unambiguous typing interpretation.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eagleton, R. T.; Clark, E. L.; Davies, H. M.

2006-10-15

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 60 J on target in a 500 fs pulse, around 100 TW, at the fundamental laser wavelength of 1.054 {mu}m. 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, calibratedmore » 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 10{sup 19} W cm{sup -2} and to underwrite the facility radiological safety system.« less

HER2 and TOP2A amplification in a hospital-based cohort of breast cancer patients: associations with patient and tumor characteristics.

PubMed

Fasching, Peter A; Weihbrecht, Sebastian; Haeberle, Lothar; Gasparyan, Armen; Villalobos, Ivonne E; Ma, Yanling; Ekici, Arif B; Wachter, David L; Hartmann, Arndt; Beckmann, Matthias W; Slamon, Dennis J; Press, Michael F

2014-05-01

Gene amplification is an important factor for altered gene expression in breast cancers. TOP2A-amplification often occurs concomitantly with HER2 amplification, and it has been suggested to be predictive for the response to anthracycline chemotherapy. This study assessed the correlation between HER2 status and TOP2A co-amplification, the possible association of TOP2A single-nucleotide polymorphisms with the frequency of this co-amplification as well as confirmation of association with outcome. HER2 and TOP2A amplification were analyzed in a tissue microarray from a clinical cohort study. Additionally, a common genetic variant (rs13695) in the TOP2A gene was genotyped in germline DNA. HER2 gene amplification was compared with HER2-IHC findings assessed during clinical routine work, and the association between all the biomarkers analyzed and the clinical outcome was determined. As an exploratory aim, rs13695 genotypes were compared with TOP2A amplification status. HER2 amplification was seen in 101 of 628 (16.1 %) and TOP2A amplification in 32 (5.1 %) cancers. No TOP2A amplification occurred without HER2 co-amplification. HER2 amplification was found in 8, 13.6, and 55.1 % of patients with HER2-IHC 0/1+, 2+, and 3+ tumors, respectively. HER2-IHC was not associated with an effect on the prognosis, but HER2-FISH was. There was an association between the rs13695 genotype and TOP2A amplification status (P = 0.03). Although there was a significant correlation between HER2 status determined by IHC and HER2 by FISH, only HER2 gene amplification status by FISH was correlated with outcome indicating greater utility for FISH in routine clinical settings.

Evaluation of microbiological air quality and of microclimate in university classrooms.

PubMed

Grisoli, Pietro; Rodolfi, Marinella; Chiara, Tiziana; Zonta, Laura Attinia; Dacarro, Cesare

2012-07-01

The proliferation of air-diffused microorganisms inside public buildings such as schools, hospitals, and universities, is often indicated as a possible health risk. In this research, we have illustrated the results of an investigation realized to determine the health of the air in some university classrooms, both from a microbiological and a microclimatic viewpoint, during the normal didactic activity of direct lessons. The results obtained have been expressed by means of contamination indices, already used in previous works. Very little contamination was recorded in the different phases of air treatment, which underlines the efficiency of the system and of the maintenance protocols. The Global Index of Microbial Contamination (GIMC per cubic meter) showed a value greater than the mean during the heating period (290), while the highest values (95th percentile 1,138.45) were recorded in the period using air conditioning. The index of mesophilic bacterial contamination, though it did not show any significant differences in the various modes of air treatment, showed a mean value (1.34) and the 95th percentile value (4.14), which was greater in the air-conditioning phase. Finally, the mean value of the amplification index underlined a decrease in the microbial contamination in comparison to the outside, while showing situations of increased microbial amplification during the period of simple ventilation (95th percentile 4.27). The 95th percentile values found for GICM in the three sampling periods, however, permitted us to identify the value of GIMC per cubic meter equal to 1,000 as a guide to provide a means of self-monitoring the quality of the air inside the classrooms. From a microclimatic viewpoint, two periods of the year manifested discomfort situations: during the heating phase (winter) and during the simple ventilation phase (spring). The results obtained indicate, therefore, a need to intervene on the environmental parameters, not being able, in this particular case, to intervene on other aspects that influence the microclimate.

Spatio-temporal distribution of energy radiation from low frequency tremor

NASA Astrophysics Data System (ADS)

Maeda, T.; Obara, K.

2007-12-01

Recent fine-scale hypocenter locations of low frequency tremors (LFTs) estimated by cross-correlation technique (Shelly et al. 2006; Maeda et al. 2006) and new finding of very low frequency earthquake (Ito et al. 2007) suggest that these slow events occur at the plate boundary associated with slow slip events (Obara and Hirose, 2006). However, the number of tremor detected by above technique is limited since continuous tremor waveforms are too complicated. Although an envelope correlation method (ECM) (Obara, 2002) enables us to locate epicenters of LFT without arrival time picks, however, ECM fails to locate LFTs precisely especially on the most active stage of tremor activity because of the low-correlation of envelope amplitude. To reveal total energy release of LFT, here we propose a new method for estimating the location of LFTs together with radiated energy from the tremor source by using envelope amplitude. The tremor amplitude observed at NIED Hi-net stations in western Shikoku simply decays in proportion to the reciprocal of the source-receiver distance after the correction of site- amplification factor even though the phases of the tremor are very complicated. So, we model the observed mean square envelope amplitude by time-dependent energy radiation with geometrical spreading factor. In the model, we do not have origin time of the tremor since we assume that the source of the tremor continuously radiates the energy. Travel-time differences between stations estimated by the ECM technique also incorporated in our locating algorithm together with the amplitude information. Three-component 1-hour Hi-net velocity continuous waveforms with a pass-band of 2-10 Hz are used for the inversion after the correction of site amplification factors at each station estimated by coda normalization method (Takahashi et al. 2005) applied to normal earthquakes in the region. The source location and energy are estimated by applying least square inversion to the 1-min window iteratively. As a first application of our method, we estimated the spatio-temporal distribution of energy radiation for 2006 May episodic tremor and slip event occurred in western Shikoku, Japan, region. Tremor location and their radiated energy are estimated for every 1 minute. We counted the number of located LFTs and summed up their total energy at each grid having 0.05-degree spacing at each day to figure out the spatio-temporal distribution of energy release of tremors. The resultant spatial distribution of radiated energy is concentrated at a specific region. Additionally, we see the daily change of released energy, both of location and amount, which corresponds to the migration of tremor activity. The spatio-temporal distribution of energy radiation of tremors is in good agreement with a spatio-temporal slip distribution of slow slip event estimated from Hi-net tiltmeter record (Hirose et al. 2007). This suggests that small continuous tremors occur associated with a rupture process of slow slip.

Creating biocompatible oil-water interfaces without synthesis: direct interactions between primary amines and carboxylated perfluorocarbon surfactants.

PubMed

DeJournette, Cheryl J; Kim, Joonyul; Medlen, Haley; Li, Xiangpeng; Vincent, Luke J; Easley, Christopher J

2013-11-05

Currently, one of the most prominent methods used to impart biocompatibility to aqueous-in-oil droplets is to synthesize a triblock copolymer surfactant composed of perfluoropolyether and polyether blocks. The resulting surfactants (EA surfactant, KryJeffa, etc.) allow generation of highly biocompatible droplet surfaces while maintaining the heat stability of the starting material. However, production of these surfactants requires expertise in synthetic organic chemistry, creating a barrier to widespread adoption in the field. Herein, we describe a simple alternative to synthetic modification of surfactants to impart biocompatibility. We have observed that aqueous-in-oil droplet surfaces can be made biocompatible and heat stable by merely exploiting binding interactions between polyetherdiamine additives in the aqueous phase and carboxylated perfluorocarbon surfactants in the oil phase. Droplets formed under these conditions are shown to possess biocompatible surfaces capable of supporting picoliter-scale protein assays, droplet polymerase chain reaction (PCR), and droplet DNA amplification with isothermal recombinase polymerase amplification (RPA). Droplets formed with polyetherdiamine aqueous additives are stable enough to withstand temperature cycling during PCR (30-40 cycles at 60-94 °C) while maintaining biocompatibility, and the reaction efficiency of RPA is shown to be similar to that with a covalently modified surfactant (KryJeffa). The binding interaction was confirmed with various methods, including FT-IR spectroscopy, NMR spectroscopy, electrospray ionization mass spectrometry (ESI-MS), and fluorescence microscopy. Overall, our results suggest that, by simply introducing a commercially-available, polyetherdiamine additive (Jeffamine ED-900) to the aqueous phase, researchers can avoid synthetic methods in generating biocompatible droplet surfaces capable of supporting DNA and protein analysis at the subnanoliter scale.

Microtremor exploration for shallow S-wave velocity structure in Bandung Basin, Indonesia

NASA Astrophysics Data System (ADS)

Pramatadie, Andi Muhamad; Yamanaka, Hiroaki; Chimoto, Kosuke; Afnimar Collaboration; Koketsu, Kazuki; Sakaue, Minoru; Miyake, Hiroe; Sengara, I. Wayan; Sadisun, Imam A.

2017-05-01

We have conducted a microtremor survey for shallow S-wave velocity profiles to be used for seismic hazard evaluation in the Bandung Basin, Indonesia. In the survey, two arrays were deployed temporarily at each of 29 sites, by installing seven vertical sensors in triangular configurations with side lengths from 1 to 16 m. Records of vertical microtremors from each array were used to estimate Rayleigh wave phase velocity spectra using the spatial autocorrelation method, as well as the horizontal-to-vertical spectral ratio obtained at the centre of the arrays. Phase velocities at sites on the basin margin exhibit higher values than those obtained in the central part of the basin, in a frequency range of 7 to 30 Hz. The phase velocity data were used to deduce S-wave velocity profiles of shallow soil using a hybrid heuristic inversion method. We validated our inversion models by comparing observed horizontal-to-vertical spectral ratios with ellipticities of the fundamental mode of Rayleigh waves, calculated for the inversion models. The S-wave velocity profiles in the area can be characterised by two soft layers over a firm engineering basement that has an S-wave velocity of 500 m/s. The S-wave velocities of the two layers are 120 and 280 m/s on average. The distribution of the averaged S-wave velocity in the top 30 m clearly indicates low values in the eastern central part and high values in the edge of the basin. The amplification is large in the areas with low velocity layers. In addition, we have proposed an empirical relation between the amplification factor and the topographical slope in the area.

Phase II trial of the CDK4 inhibitor PD0332991 in patients with advanced CDK4-amplified well-differentiated or dedifferentiated liposarcoma.

PubMed

Dickson, Mark A; Tap, William D; Keohan, Mary Louise; D'Angelo, Sandra P; Gounder, Mrinal M; Antonescu, Cristina R; Landa, Jonathan; Qin, Li-Xuan; Rathbone, Dustin D; Condy, Mercedes M; Ustoyev, Yelena; Crago, Aimee M; Singer, Samuel; Schwartz, Gary K

2013-06-01

CDK4 is amplified in > 90% of well-differentiated (WDLS) and dedifferentiated liposarcomas (DDLS). The selective cyclin-dependent kinase 4 (CDK4)/CDK6 inhibitor PD0332991 inhibits growth and induces senescence in cell lines and xenografts. In a phase I trial of PD0332991, several patients with WDLS or DDLS experienced prolonged stable disease. We performed an open-label phase II study to determine the safety and efficacy of PD0332991 in patients with advanced WDLS/DDLS. Patients age ≥ 18 years experiencing disease progression while receiving systemic therapy before enrollment received PD0332991 200 mg orally once per day for 14 consecutive days in 21-day cycles. All were required to have CDK4 amplification by fluorescence in situ hybridization and retinoblastoma protein (RB) expression by immunohistochemistry (≥ 1+). The primary end point was progression-free survival (PFS) at 12 weeks, with 12-week PFS of ≥ 40% considered promising and ≤ 20% not promising. If ≥ nine of 28 patients were progression free at 12 weeks, PD0332991 would be considered active. We screened 48 patients (44 of 48 had CDK4 amplification; 41 of 44 were RB positive). Of those, 30 were enrolled, and 29 were evaluable for the primary end point. Grade 3 to 4 events included anemia (17%), thrombocytopenia (30%), neutropenia (50%), and febrile neutropenia (3%). At 12 weeks, PFS was 66% (90% CI, 51% to 100%), significantly exceeding the primary end point. The median PFS was 18 weeks. There was one partial response. Treatment with the CDK4 inhibitor PD0332991 was associated with a favorable progression-free rate in patients with CDK4-amplified and RB-expressing WDLS/DDLS who had progressive disease despite systemic therapy.

Results of a phase II trial for high-risk neuroblastoma treatment protocol JN-H-07: a report from the Japan Childhood Cancer Group Neuroblastoma Committee (JNBSG).

PubMed

Hishiki, Tomoro; Matsumoto, Kimikazu; Ohira, Miki; Kamijo, Takehiko; Shichino, Hiroyuki; Kuroda, Tatsuo; Yoneda, Akihiro; Soejima, Toshinori; Nakazawa, Atsuko; Takimoto, Tetsuya; Yokota, Isao; Teramukai, Satoshi; Takahashi, Hideto; Fukushima, Takashi; Kaneko, Takashi; Hara, Junichi; Kaneko, Michio; Ikeda, Hitoshi; Tajiri, Tatsuro; Nakagawara, Akira

2018-04-26

The Japanese Children's Cancer Group (JCCG) Neuroblastoma Committee (JNBSG) conducted a phase II clinical trial for high-risk neuroblastoma treatment. We report the result of the protocol treatment and associated genomic aberration studies. JN-H-07 was a single-arm, late phase II trial for high-risk neuroblastoma treatment with open enrollment from June 2007 to February 2009. Eligible patients underwent five courses of induction chemotherapy followed by high-dose chemotherapy with hematopoietic stem cell rescue. Surgery for the primary tumor was scheduled after three or four courses of induction chemotherapy. Radiotherapy was administered to the primary tumor site and to any bone metastases present at the end of induction chemotherapy. The estimated 3-year progression-free and overall survival rates of the 50 patients enrolled were 36.5 ± 7.0 and 69.5 ± 6.6%, respectively. High-dose chemotherapy caused severe toxicity including three treatment-related deaths. In response to this, the high-dose chemotherapy regimen was modified during the trial by infusing melphalan before administering carboplatin and etoposide. The modified high-dose chemotherapy regimen was less toxic. Univariate analysis revealed that patients younger than 547 days and patients whose tumor showed a whole chromosomal gains / losses pattern had a significantly poor prognosis. Notably, the progression-free survival of cases with MYCN amplification were not inferior to those without MYCN amplification. The outcome of patients treated with the JN-H-07 protocol showed improvement over the results reported by previous studies conducted in Japan. Molecular and genetic profiling may enable a more precise stratification of the high-risk cohort.

Dynamics and control of DNA sequence amplification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marimuthu, Karthikeyan; Chakrabarti, Raj, E-mail: raj@pmc-group.com, E-mail: rajc@andrew.cmu.edu; Division of Fundamental Research, PMC Advanced Technology, Mount Laurel, New Jersey 08054

2014-10-28

DNA amplification is the process of replication of a specified DNA sequence 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 as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reactionmore » 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 temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions.« less

Nonlinear Phase Distortion in a Ti:Sapphire Optical Amplifier for Optical Stochastic Cooling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andorf, Matthew; Lebedev, Valeri; Piot, Philippe

2016-06-01

Optical Stochastic Cooling (OSC) has been considered for future high-luminosity colliders as it offers much faster cooling time in comparison to the micro-wave stochastic cooling. The OSC technique relies on collecting and amplifying a broadband optical signal from a pickup undulator and feeding the amplified signal back to the beam. It creates a corrective kick in a kicker undulator. Owing to its superb gain qualities and broadband amplification features, Titanium:Sapphire medium has been considered as a gain medium for the optical amplifier (OA) needed in the OSC*. A limiting factor for any OA used in OSC is the possibility ofmore » nonlinear phase distortions. In this paper we experimentally measure phase distortions by inserting a single-pass OA into one leg of a Mach-Zehnder interferometer. The measurement results are used to estimate the reduction of the corrective kick a particle would receive due to these phase distortions in the kicker undulator.« less

Telomerase Repeated Amplification Protocol (TRAP).

PubMed

Mender, Ilgen; Shay, Jerry W

2015-11-20

Telomeres are found at the end of eukaryotic linear chromosomes, and proteins that bind to telomeres protect DNA from being recognized as double-strand breaks thus preventing end-to-end fusions (Griffith et al. , 1999). However, due to the end replication problem and other factors such as oxidative damage, the limited life span of cultured cells (Hayflick limit) results in progressive shortening of these protective structures (Hayflick and Moorhead, 1961; Olovnikov, 1973). The ribonucleoprotein enzyme complex telomerase-consisting of a protein catalytic component hTERT and a functional RNA component hTR or hTERC - counteracts telomere shortening by adding telomeric repeats to the end of chromosomes in ~90% of primary human tumors and in some transiently proliferating stem-like cells (Shay and Wright, 1996; Shay and Wright, 2001). This results in continuous proliferation of cells which is a hallmark of cancer. Therefore, telomere biology has a central role in aging, cancer progression/metastasis as well as targeted cancer therapies. There are commonly used methods in telomere biology such as Telomere Restriction Fragment (TRF) (Mender and Shay, 2015b), Telomere Repeat Amplification Protocol (TRAP) and Telomere dysfunction Induced Foci (TIF) analysis (Mender and Shay, 2015a). In this detailed protocol we describe Telomere Repeat Amplification Protocol (TRAP). The TRAP assay is a popular method to determine telomerase activity in mammalian cells and tissue samples (Kim et al. , 1994). The TRAP assay includes three steps: extension, amplification, and detection of telomerase products. In the extension step, telomeric repeats are added to the telomerase substrate (which is actually a non telomeric oligonucleotide, TS) by telomerase. In the amplification step, the extension products are amplified by the polymerase chain reaction (PCR) using specific primers (TS upstream primer and ACX downstream primer) and in the detection step, the presence or absence of telomerase is analyzed by electrophoresis. TSNT is, an internal standard control, amplified by TS primer. NT is its own reverse primer, which is not a substrate for telomerase. These primers are used to identify false-negative results by if the gel lacks internal control bands.

Arctic Amplification and Potential Mid-Latitude Weather Linkages

NASA Astrophysics Data System (ADS)

Overland, J. E.

2014-12-01

Increasing temperatures and other changes continued in the Arctic over the last decade, even though the rate of global warming has decreased in part due to a cool Pacific Ocean. Thus Arctic temperatures have increased at least 3 times the rate of mid-latitude temperatures. Credibility for persistent Arctic change comes from multiple indicators which are now available for multiple decades. Further, the spatial pattern of Arctic Amplification differs from patterns of natural variability. The role of the Arctic in the global climate system is based on multiple interacting feedbacks represented by these indicators as a causal basis for Arctic Amplification driven by modest global change. Many of these processes act on a regional basis and their non-linear interactions are not well captured by climate models. For example, future loss of sea ice due to increases in CO2 are demonstrated by these models but the rates of loss appear slow. It is reasonable to suspect that Arctic change which can produce the largest temperature anomalies on the planet and demonstrate recent extremes in the polar vortex could be linked to mid-latitude weather, especially as Arctic change will continue over the next decades. The meteorological community remains skeptical, however, in the sense of "not proven." Natural variability in chaotic atmospheric flow remains the main dynamic process, and it is difficult to determine whether Arctic forcing of a north-south linkage is emerging from the most recent period of Arctic change since 2007. Nonetheless, such a hypothesis is worthy of investigation, given the need to further understand Arctic dynamic atmospheric processes, and the potential for improving mid-latitude seasonal forecasts base on high-latitude forcing. Several AGU sessions and other forums over the next year (WWRP, IASC,CliC) address this issue, but the topic is not ready for a firm answer. The very level of controversy indicates the state of the science.

Standoff detection of trace amounts of solids by nonlinear Raman spectroscopy using shaped femtosecond pulses

NASA Astrophysics Data System (ADS)

Katz, O.; Natan, A.; Silberberg, Y.; Rosenwaks, S.

2008-04-01

We demonstrate a single-beam, standoff (>10m) detection and identification of various materials including minute amounts of explosives under ambient light conditions. This is obtained by multiplex coherent anti-Stokes Raman scattering spectroscopy (CARS) using a single femtosecond phase-shaped laser pulse. We exploit the strong nonresonant background for amplification of the backscattered resonant CARS signals by employing a homodyne detection scheme. The simple and highly sensitive spectroscopic technique has a potential for hazardous materials standoff detection applications.

Phase Noise Squeezing Based Parametric Bifurcation Tracking of MIP-Coated Microbeam MEMS Sensor for TNT Explosive Gas Sensing

DTIC Science & Technology

2014-06-08

actuation. Journal of Micromechanics and Microengineering , 16(5), 890–899. doi:10.1088/0960-1317/16/5/003 [10] Rhoads, J. F., Shaw, S. W., Turner, K. L...Micromechanics and Microengineering , 22(3), 035004. doi:10.1088/0960-1317/22/3/035004 [13] Cleland, A. N. (2005). Thermomechanical noise limits on...Micromechanics and Microengineering , 21(2), 025027. doi:10.1088/0960- 1317/21/2/025027 [15] D. Rugar & P. Grutter. Mechanical Parametric Amplification and

Shock wave interaction with laser-generated single bubbles.

PubMed

Sankin, G N; Simmons, W N; Zhu, S L; Zhong, P

2005-07-15

The interaction of a lithotripter shock wave (LSW) with laser-generated single vapor bubbles in water is investigated using high-speed photography and pressure measurement via a fiber-optic probe hydrophone. The interaction leads to nonspherical collapse of the bubble with secondary shock wave emission and microjet formation along the LSW propagation direction. The maximum pressure amplification is produced during the collapse phase of the bubble oscillation when the compressive pulse duration of the LSW matches with the forced collapse time of the bubble.

Parallel Synthesis and Biocatalytic Amplification of Marine-Inspired Libraries: An Integrated Approach Toward Discovering New Chemotherapeutics

DTIC Science & Technology

2007-09-01

m (Cyt-m). We chose to study the oxidation of camphor to hydroxycamphor (Scheme 1) because it is the natural reaction for P450cam and there was...only one known reaction product. 10 O O HO camphor 5-exo-hydroxycamphor Scheme 1. The hydroxylation of camphor by P450cam, producing...phases, and 250 rpm. The oxidation of camphor to hydroxycamphor is 100% coupled with NADH oxidation, allowing for a direct correlation of NADH

Advanced Sensors Boost Optical Communication, Imaging

NASA Technical Reports Server (NTRS)

2009-01-01

Brooklyn, New York-based Amplification Technologies Inc. (ATI), employed Phase I and II SBIR funding from NASA s Jet Propulsion Laboratory to forward the company's solid-state photomultiplier technology. Under the SBIR, ATI developed a small, energy-efficient, extremely high-gain sensor capable of detecting light down to single photons in the near infrared wavelength range. The company has commercialized this technology in the form of its NIRDAPD photomultiplier, ideal for use in free space optical communications, lidar and ladar, night vision goggles, and other light sensing applications.

Spectral quantum fluctuations in a stimulated Raman generator: a description in terms of temporally coherent modes.

PubMed

Walmsley, I A

1992-03-15

The probability density of the single-shot mean Stokes frequency from a linear Raman generator is calculated. It is shown that the fluctuations in the Stokes pulse energy spectrum that arise from the quantum initiation of the Stokes light are reduced in the transient regime of amplification. Also, it appears that saturation of the Raman gain does not reduce the phase fluctuations of the Stokes light below those present in the unsaturated gain (linear) regime.

Multiple Channel Laser Beam Combination and Phasing Using Stimulated Brillouin Scattering in Optical Fibers

DTIC Science & Technology

2005-12-01

was transmitted through a piece of etched glass into a waveguide containing methane gas (the SBS medium). The experiment compared the reflection from...Wang et. al. first proposed tellurite glass as a candidate for fiber devices.105 Their work has led to the development of a number of rare-earth...amplification near 1500 nm.107,109 Tellurite glasses have also been quite successful as Raman amplifiers110,111 demonstrating over 90 times higher Raman gain

Postselected weak measurement beyond the weak value

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geszti, Tamas

2010-04-15

Closed expressions are derived for the quantum measurement statistics of pre- and postselected Gaussian particle beams. The weakness of the preselection step is shown to compete with the nonorthogonality of postselection in a transparent way. The approach is shown to be useful in analyzing postselection-based signal amplification, allowing measurements to be extended far beyond the range of validity of the well-known Aharonov-Albert-Vaidman limit. Additionally, the present treatment connects postselected weak measurement to the topic of phase-contrast microscopy.

Two-stage Raman compression of laser pulses with controllable phase fronts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balakin, A. A.; Fraiman, G. M.; State University of Nizhny Novgorod, Nizhny Novgorod

2015-05-15

The phase front of an ultrashort laser pulse undergoing Raman amplification and compression in inhomogeneous plasma can be controlled such that it is unaffected by density gradients and thus remains focusable. This is achieved by performing the Raman backscattering in two stages. At the first stage, the standard nonlinear Raman compression of a seed wave takes place and produces a short ultraintense pulse, which yet may be poorly focusable. At the second stage, this amplified pulse is scattered again, now serving as a pump, off a second copy of the initial seed. This stage, which utilizes a denser and shortermore » plasma, is intended not for compression but rather for passing a significant fraction of the energy to the second seed quickly. Then, the output pulse that is produced is not just short and ultraintense, but also has the smooth phase front of the original seed.« less

Detection of ionized gas molecules in air by graphene and carbon nanotube networks

NASA Astrophysics Data System (ADS)

Hao, Ji; Li, Bo; Yung, Hyun Young; Liu, Fangze; Hong, Sanghyung; Jung, Yung Joon; Kar, Swastik

The liquid phase ions sensing by graphene and carbon nanotube has been demonstrated in many publications due to the minimum gate voltage easily shift induced by ionic gating effect, but it is still unclear for vapor phase ions sensing. Here we want to report that the ionized gas molecules in air can be also very sensitively detected by graphene and carbon nanotube networks under very low applied voltage, which shows the very high charge to current amplification factor, the value can be up to 108 A/C, and the direction of current-change can be used to differentiate the positive and negative ions. In further, the field effect of graphene device induced by vapor phase ions was discussed. NSF ECCS 1202376, NSF ECCS CAREER 1351424 and NSF DMREF 1434824, a Northeastern University Provost's Tier-1 seed Grant for interdisciplinary research, Technology Innovation Program (10050481) from Ministry of Trade, Industry & Energy of Republic of Korea.

Stepwise kinetic equilibrium models of quantitative polymerase chain reaction.

PubMed

Cobbs, Gary

2012-08-16

Numerous models for use in interpreting quantitative PCR (qPCR) data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model the annealing phase and does not assume constant efficiency of amplification. Mechanistic models describing the annealing phase with kinetic theory offer the most potential for accurate interpretation of qPCR data. Even so, they have not been thoroughly investigated and are rarely used for interpretation of qPCR data. New results for kinetic modeling of qPCR are presented. Two models are presented in which the efficiency of amplification is based on equilibrium solutions for the annealing phase of the qPCR process. Model 1 assumes annealing of complementary targets strands and annealing of target and primers are both reversible reactions and reach a dynamic equilibrium. Model 2 assumes all annealing reactions are nonreversible and equilibrium is static. Both models include the effect of primer concentration during the annealing phase. Analytic formulae are given for the equilibrium values of all single and double stranded molecules at the end of the annealing step. The equilibrium values are then used in a stepwise method to describe the whole qPCR process. Rate constants of kinetic models are the same for solutions that are identical except for possibly having different initial target concentrations. Analysis of qPCR curves from such solutions are thus analyzed by simultaneous non-linear curve fitting with the same rate constant values applying to all curves and each curve having a unique value for initial target concentration. The models were fit to two data sets for which the true initial target concentrations are known. Both models give better fit to observed qPCR data than other kinetic models present in the literature. They also give better estimates of initial target concentration. Model 1 was found to be slightly more robust than model 2 giving better estimates of initial target concentration when estimation of parameters was done for qPCR curves with very different initial target concentration. Both models may be used to estimate the initial absolute concentration of target sequence when a standard curve is not available. It is argued that the kinetic approach to modeling and interpreting quantitative PCR data has the potential to give more precise estimates of the true initial target concentrations than other methods currently used for analysis of qPCR data. The two models presented here give a unified model of the qPCR process in that they explain the shape of the qPCR curve for a wide variety of initial target concentrations.

Fiber optical parametric amplifiers in optical communication systems

PubMed Central

Marhic (†), Michel E; Andrekson, Peter A; Petropoulos, Periklis; Radic, Stojan; Peucheret, Christophe; Jazayerifar, Mahmoud

2015-01-01

The prospects for using fiber optical parametric amplifiers (OPAs) in optical communication systems are reviewed. Phase-insensitive amplifiers (PIAs) and phase-sensitive amplifiers (PSAs) are considered. Low-penalty amplification at/or near 1 Tb/s has been achieved, for both wavelength- and time-division multiplexed formats. High-quality mid-span spectral inversion has been demonstrated at 0.64 Tb/s, avoiding electronic dispersion compensation. All-optical amplitude regeneration of amplitude-modulated signals has been performed, while PSAs have been used to demonstrate phase regeneration of phase-modulated signals. A PSA with 1.1-dB noise figure has been demonstrated, and preliminary wavelength-division multiplexing experiments have been performed with PSAs. 512 Gb/s have been transmitted over 6,000 km by periodic phase conjugation. Simulations indicate that PIAs could reach data rate x reach products in excess of 14,000 Tb/s × km in realistic wavelength-division multiplexed long-haul networks. Technical challenges remaining to be addressed in order for fiber OPAs to become useful for long-haul communication networks are discussed. PMID:25866588

Successful isolation and PCR amplification of DNA from National Institute of Standards and Technology herbal dietary supplement standard reference material powders and extracts.

PubMed

Cimino, Matthew T

2010-03-01

Twenty-four herbal dietary supplement powder and extract reference standards provided by the National Institute of Standards and Technology (NIST) were investigated using three different commercially available DNA extraction kits to evaluate DNA availability for downstream nucleotide-based applications. The material included samples of Camellia, Citrus, Ephedra, Ginkgo, Hypericum, Serenoa, And Vaccinium. Protocols from Qiagen, MoBio, and Phytopure were used to isolate and purify DNA from the NIST standards. The resulting DNA concentration was quantified using SYBR Green fluorometry. Each of the 24 samples yielded DNA, though the concentration of DNA from each approach was notably different. The Phytopure method consistently yielded more DNA. The average yield ratio was 22 : 3 : 1 (ng/microL; Phytopure : Qiagen : MoBio). Amplification of the internal transcribed spacer II region using PCR was ultimately successful in 22 of the 24 samples. Direct sequencing chromatograms of the amplified material suggested that most of the samples were comprised of mixtures. However, the sequencing chromatograms of 12 of the 24 samples were sufficient to confirm the identity of the target material. The successful extraction, amplification, and sequencing of DNA from these herbal dietary supplement extracts and powders supports a continued effort to explore nucleotide sequence-based tools for the authentication and identification of plants in dietary supplements. (c) Georg Thieme Verlag KG Stuttgart . New York.

Dual-cyclical nucleic acid strand-displacement polymerization based signal amplification system for highly sensitive determination of p53 gene.

PubMed

Xu, Jianguo; Wu, Zai-Sheng; Li, Hongling; Wang, Zhenmeng; Le, Jingqing; Zheng, Tingting; Jia, Lee

2016-12-15

In the present study, we proposed a novel dual-cyclical nucleic acid strand-displacement polymerization (dual-CNDP) based signal amplification system for highly sensitive determination of tumor suppressor genes. The system primarily consisted of a signaling hairpin probe (SHP), a label-free hairpin probe (LHP) and an initiating primer (IP). The presence of target DNA was able to induce one CNDP through continuous process of ligation, polymerization and nicking, leading to extensively accumulation of two nicked triggers (NT1 and NT2). Intriguingly, the NT1 could directly hybridize SHP, while the NT2 could act as the target analog to induce another CNDP. The resulting dual-CNDP contributed the striking signal amplification, and only a very weak blank noise existed since the ligation template of target was not involved. In this case, the target could be detected in a wide linear range (5 orders of magnitude), and a low detection limit (78 fM) was obtained, which is superior to most of the existing fluorescent methods. Moreover, the dual-CNDP sensing system provided a high selectivity towards target DNA against mismatched target and was successfully applied to analysis of target gene extracted from cancer cells or in human serum-contained samples, indicating its great potential for practical applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Optical injection locking-based amplification in phase-coherent transfer of optical frequencies.

PubMed

Kim, Joonyoung; Schnatz, Harald; Wu, David S; Marra, Giuseppe; Richardson, David J; Slavík, Radan

2015-09-15

We demonstrate the use of an optical injection phase locked loop (OIPLL) as a regenerative amplifier for optical frequency transfer applications. The optical injection locking provides high gain within a narrow bandwidth (<100  MHz) and is capable of preserving the fractional frequency stability of the incoming carrier to better than 10(-18) at 1000 s. The OIPLL was tested in the field as a mid-span amplifier for the transfer of an ultrastable optical carrier, stabilized to an optical frequency standard, over a 292 km long installed dark fiber link. The transferred frequency at the remote end reached a fractional frequency instability of less than 1×10(-19) at averaging time of 3200 s.

All-optical switch based on doped graphene quantum dots in a defect layer of a one-dimensional photonic crystal.

PubMed

Sahrai, Mostafa; Abbasabadi, Majid

2018-01-20

We discuss the light pulse propagation in a one-dimensional photonic crystal doped by graphene quantum dots in a defect layer. The graphene quantum dots behave as a three-level quantum system and are driven by three coherent laser fields. It is shown that the group velocity of the transmitted and reflected pulses can be switched from subluminal to superluminal light propagation by adjusting the relative phase of the applied fields. Furthermore, it is found that by proper choice of the phase difference between applied fields, the weak probe field amplification is achieved through a one-dimensional photonic crystal. In this way, the result is simultaneous subluminal transmission and reflection.

Evidence of high-elevation amplification versus Arctic amplification

NASA Astrophysics Data System (ADS)

Wang, Qixiang; Fan, Xiaohui; Wang, Mengben

2016-01-01

Elevation-dependent warming in high-elevation regions and Arctic amplification are of tremendous interest to many scientists who are engaged in studies in climate change. Here, using annual mean temperatures from 2781 global stations for the 1961-2010 period, we find that the warming for the world’s high-elevation stations (>500 m above sea level) is clearly stronger than their low-elevation counterparts; and the high-elevation amplification consists of not only an altitudinal amplification but also a latitudinal amplification. The warming for the high-elevation stations is linearly proportional to the temperature lapse rates along altitudinal and latitudinal gradients, as a result of the functional shape of Stefan-Boltzmann law in both vertical and latitudinal directions. In contrast, neither altitudinal amplification nor latitudinal amplification is found within the Arctic region despite its greater warming than lower latitudes. Further analysis shows that the Arctic amplification is an integrated part of the latitudinal amplification trend for the low-elevation stations (≤500 m above sea level) across the entire low- to high-latitude Northern Hemisphere, also a result of the mathematical shape of Stefan-Boltzmann law but only in latitudinal direction.

Evidence of high-elevation amplification versus Arctic amplification

PubMed Central

Wang, Qixiang; Fan, Xiaohui; Wang, Mengben

2016-01-01

Elevation-dependent warming in high-elevation regions and Arctic amplification are of tremendous interest to many scientists who are engaged in studies in climate change. Here, using annual mean temperatures from 2781 global stations for the 1961–2010 period, we find that the warming for the world’s high-elevation stations (>500 m above sea level) is clearly stronger than their low-elevation counterparts; and the high-elevation amplification consists of not only an altitudinal amplification but also a latitudinal amplification. The warming for the high-elevation stations is linearly proportional to the temperature lapse rates along altitudinal and latitudinal gradients, as a result of the functional shape of Stefan-Boltzmann law in both vertical and latitudinal directions. In contrast, neither altitudinal amplification nor latitudinal amplification is found within the Arctic region despite its greater warming than lower latitudes. Further analysis shows that the Arctic amplification is an integrated part of the latitudinal amplification trend for the low-elevation stations (≤500 m above sea level) across the entire low- to high-latitude Northern Hemisphere, also a result of the mathematical shape of Stefan-Boltzmann law but only in latitudinal direction. PMID:26753547

N-Consecutive-Phase Encoder

NASA Technical Reports Server (NTRS)

Divsalar, Dariush; Lee, Ho-Kyoung; Weber, Charles

1995-01-01

N-consecutive-phase encoder (NCPE) is conceptual encoder for generating alphabet of N consecutive full-response continuous-phase-modulation (CPM) signals. Enables use of binary preencoder of higher rate than used with simple continuous-phase encoder (CPE). NCPE makes possible to achieve power efficiencies and bandwidth efficiencies greater than conventional trellis coders with continuous-phase frequency-shift keying (CPFSK).

Phase plate technology for laser marking of magnetic discs

DOEpatents

Neuman, Bill; Honig, John; Hackel, Lloyd; Dane, C. Brent; Dixit, Shamasundar

1998-01-01

An advanced design for a phase plate enables the distribution of spots in arbitrarily shaped patterns with very high uniformity and with a continuously or near-continuously varying phase pattern. A continuous phase pattern eliminates large phase jumps typically expected in a grating that provides arbitrary shapes. Large phase jumps increase scattered light outside of the desired pattern, reduce efficiency and can make the grating difficult to manufacture. When manufacturing capabilities preclude producing a fully continuous grating, the present design can be easily adapted to minimize manufacturing errors and maintain high efficiencies. This continuous grating is significantly more efficient than previously described Dammann gratings, offers much more flexibility in generating spot patterns and is easier to manufacture and replicate than a multi-level phase grating.

Topoisomerase expression and amplification in solid tumours: Analysis of 24,262 patients

PubMed Central

Heestand, Gregory M.; Schwaederle, Maria; Gatalica, Zoran; Arguello, David; Kurzrock, Razelle

2017-01-01

Background Topoisomerase I (TOPO1) and topoisomerase IIα (TOP2A) are specific targets of multiple chemotherapy drugs. Increased expression of TOPO1 protein and amplification of the TOP2A gene have been associated with treatment response in colorectal and breast cancers, respectively. TOPO1 and TOP2A may be potential therapeutic targets in other malignancies as well. Summary of methods We analysed TOPO1 protein expression and TOP2A gene amplification in patients (n = 24,262 specimens) with diverse cancers. Since HER2 and TOP2A co-amplification have been investigated for predictive value regarding anthracycline benefit, we analysed specimens for HER2 amplification as well. Results Overexpressed TOPO1 protein was present in 51% of the tumours. Four percent of the tumours had TOP2A amplification, with gallbladder tumours and gastroesophageal/oesophageal tumours having rates over 10%. Overall, 4903 specimens were assessed for both TOP2A and HER2 amplification; 129 (2.6%) had co-amplification. High rates (>40%) of HER2 amplification were seen in patients with TOP2A amplification in breast, ovarian, gastroesophageal/oesophageal and pancreatic cancer. Conclusion Our data indicate that increased TOPO1 expression and TOP2A amplification, as well as HER2 co-alterations, are present in multiple malignancies. The implications of these observations regarding sensitivity to chemotherapy not traditionally administered to these tumour types merits investigation. PMID:28728050

Method for in situ characterization of a medium of dispersed matter in a continuous phase

DOEpatents

Kaufman, Eric N.

1995-01-01

A method for in situ characterization of a medium of a dispersed phase in a continuous phase, including the steps of adding a fluorescent dye to one phase capable of producing fluorescence therein when the fluorescent dye is optically excited, optically exciting the fluorescent dye at a wavelength to produce fluorescence in the one phase, and monitoring the fluorescence to distinguish the continuous phase from the dispersed phase.

Turbulent dynamo in a collisionless plasma

NASA Astrophysics Data System (ADS)

Rincon, François; Califano, Francesco; Schekochihin, Alexander A.; Valentini, Francesco

2016-04-01

Magnetic fields pervade the entire universe and affect the formation and evolution of astrophysical systems from cosmological to planetary scales. The generation and dynamical amplification of extragalactic magnetic fields through cosmic times (up to microgauss levels reported in nearby galaxy clusters, near equipartition with kinetic energy of plasma motions, and on scales of at least tens of kiloparsecs) are major puzzles largely unconstrained by observations. A dynamo effect converting kinetic flow energy into magnetic energy is often invoked in that context; however, extragalactic plasmas are weakly collisional (as opposed to magnetohydrodynamic fluids), and whether magnetic field growth and sustainment through an efficient turbulent dynamo instability are possible in such plasmas is not established. Fully kinetic numerical simulations of the Vlasov equation in a 6D-phase space necessary to answer this question have, until recently, remained beyond computational capabilities. Here, we show by means of such simulations that magnetic field amplification by dynamo instability does occur in a stochastically driven, nonrelativistic subsonic flow of initially unmagnetized collisionless plasma. We also find that the dynamo self-accelerates and becomes entangled with kinetic instabilities as magnetization increases. The results suggest that such a plasma dynamo may be realizable in laboratory experiments, support the idea that intracluster medium turbulence may have significantly contributed to the amplification of cluster magnetic fields up to near-equipartition levels on a timescale shorter than the Hubble time, and emphasize the crucial role of multiscale kinetic physics in high-energy astrophysical plasmas.

Turbulent dynamo in a collisionless plasma

PubMed Central

Rincon, François; Califano, Francesco; Schekochihin, Alexander A.; Valentini, Francesco

2016-01-01

Magnetic fields pervade the entire universe and affect the formation and evolution of astrophysical systems from cosmological to planetary scales. The generation and dynamical amplification of extragalactic magnetic fields through cosmic times (up to microgauss levels reported in nearby galaxy clusters, near equipartition with kinetic energy of plasma motions, and on scales of at least tens of kiloparsecs) are major puzzles largely unconstrained by observations. A dynamo effect converting kinetic flow energy into magnetic energy is often invoked in that context; however, extragalactic plasmas are weakly collisional (as opposed to magnetohydrodynamic fluids), and whether magnetic field growth and sustainment through an efficient turbulent dynamo instability are possible in such plasmas is not established. Fully kinetic numerical simulations of the Vlasov equation in a 6D-phase space necessary to answer this question have, until recently, remained beyond computational capabilities. Here, we show by means of such simulations that magnetic field amplification by dynamo instability does occur in a stochastically driven, nonrelativistic subsonic flow of initially unmagnetized collisionless plasma. We also find that the dynamo self-accelerates and becomes entangled with kinetic instabilities as magnetization increases. The results suggest that such a plasma dynamo may be realizable in laboratory experiments, support the idea that intracluster medium turbulence may have significantly contributed to the amplification of cluster magnetic fields up to near-equipartition levels on a timescale shorter than the Hubble time, and emphasize the crucial role of multiscale kinetic physics in high-energy astrophysical plasmas. PMID:27035981

Turbulent dynamo in a collisionless plasma.

PubMed

Rincon, François; Califano, Francesco; Schekochihin, Alexander A; Valentini, Francesco

2016-04-12

Magnetic fields pervade the entire universe and affect the formation and evolution of astrophysical systems from cosmological to planetary scales. The generation and dynamical amplification of extragalactic magnetic fields through cosmic times (up to microgauss levels reported in nearby galaxy clusters, near equipartition with kinetic energy of plasma motions, and on scales of at least tens of kiloparsecs) are major puzzles largely unconstrained by observations. A dynamo effect converting kinetic flow energy into magnetic energy is often invoked in that context; however, extragalactic plasmas are weakly collisional (as opposed to magnetohydrodynamic fluids), and whether magnetic field growth and sustainment through an efficient turbulent dynamo instability are possible in such plasmas is not established. Fully kinetic numerical simulations of the Vlasov equation in a 6D-phase space necessary to answer this question have, until recently, remained beyond computational capabilities. Here, we show by means of such simulations that magnetic field amplification by dynamo instability does occur in a stochastically driven, nonrelativistic subsonic flow of initially unmagnetized collisionless plasma. We also find that the dynamo self-accelerates and becomes entangled with kinetic instabilities as magnetization increases. The results suggest that such a plasma dynamo may be realizable in laboratory experiments, support the idea that intracluster medium turbulence may have significantly contributed to the amplification of cluster magnetic fields up to near-equipartition levels on a timescale shorter than the Hubble time, and emphasize the crucial role of multiscale kinetic physics in high-energy astrophysical plasmas.

Voice amplification versus vocal hygiene instruction for teachers with voice disorders: a treatment outcomes study.

PubMed

Roy, Nelson; Weinrich, Barbara; Gray, Steven D; Tanner, Kristine; Toledo, Sue Walker; Dove, Heather; Corbin-Lewis, Kim; Stemple, Joseph C

2002-08-01

Voice problems are common among schoolteachers. This prospective, randomized clinical trial used patient-based treatment outcomes measures combined with acoustic analysis to evaluate the effectiveness of two treatment programs. Forty-four voice-disordered teachers were randomly assigned to one of three groups: voice amplification using the ChatterVox portable amplifier (VA, n = 15), vocal hygiene (VH, n = 15), and a nontreatment control group (n = 14). Before and after a 6-week treatment phase, all teachers completed: (a) the Voice Handicap Index (VHI), an instrument designed to appraise the self-perceived psychosocial consequences of voice disorders; (b) a voice severity self-rating scale; and (c) an audiorecording for later acoustic analysis. Based on pre- and posttreatment comparisons, only the amplification group experienced significant reductions on mean VHI scores (p = .045), voice severity self-ratings (p = .012), and the acoustic measures of percent jitter (p = .031) and shimmer (p = .008). The nontreatment control group reported a significant increase in level of vocal handicap as assessed by the VHI (p = .012). Although most pre- to posttreatment changes were in the desired direction, no significant improvements were observed within the VH group on any of the dependent measures. Between-group comparisons involving the three possible pairings of the groups revealed a pattern of results to suggest that: (a) compared to the control group, both treatment groups (i.e., VA and VH) experienced significantly more improvement on specific outcomes measures and (b) there were no significant differences between the VA and VH groups to indicate superiority of one treatment over another. Results, however, from a posttreatment questionnaire regarding the perceived benefits of treatment revealed that, compared to the VH group, the VA group reported more clarity of their speaking and singing voice (p = .061), greater ease of voice production (p = .001), and greater compliance with the treatment program (p = .045). These findings clearly support the clinical utility of voice amplification as an alternative for the treatment of voice problems in teachers.

Neratinib shows efficacy in the treatment of HER2/neu amplified uterine serous carcinoma in vitro and in vivo.

PubMed

Schwab, Carlton L; English, Diana P; Roque, Dana M; Bellone, Stefania; Lopez, Salvatore; Cocco, Emiliano; Nicoletti, Roberta; Rutherford, Thomas J; Schwartz, Peter E; Santin, Alessandro D

2014-10-01

Uterine serous carcinoma (USC) represents an aggressive variant of endometrial cancer and accounts for a large proportion of deaths annually. HER2/neu amplification is associated with USC in approximately 30-35% of cases. The objective of this study was to determine the sensitivity of a panel of primary USC cell lines to the small tyrosine kinase inhibitor neratinib, an ErbB1 and HER2 inhibitor, both in vitro and in vivo. HER2/neu amplification was determined by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) in 24 USC cell lines. Flow cytometry was used to determine the effects of neratinib on cell viability, cell cycle distribution and signaling in vitro. Mice harboring HER2/neu amplified xenografts were treated with neratinib to assess the efficacy of the drug in vivo. HER2/neu amplification was noted in 8/24 primary cell lines. Data regarding the efficacy of neratinib was determined using 4 HER2 amplified cell lines and 4 non-amplified cell lines with similar growth rates. Data revealed that cell lines with HER2/neu amplification were exquisitely more sensitive to neratinib compared to non-amplified cell lines (mean ± SEM IC50: 0.011μM ± 0.0008 vs. 0.312μM ± 0.0456 p<0.0001). Neratinib caused arrest in the G0/G1 phase of the cell cycle and resulted in decreased autophosphorylation of HER2 and activation of S6. Neratinib treated mice harboring xenografts of HER2/neu amplified USC showed delayed tumor growth and improved overall survival compared to vehicle (p=0.0019). Neratinib may be a potential treatment option for patients harboring HER2/neu amplified USC. Clinical trials for this subset of endometrial cancer patients are warranted. Copyright © 2014 Elsevier Inc. All rights reserved.

Energy transport, polar amplification, and ITCZ shifts in the GeoMIP G1 ensemble

NASA Astrophysics Data System (ADS)

Russotto, Rick D.; Ackerman, Thomas P.

2018-02-01

The polar amplification of warming and the ability of the Intertropical Convergence Zone (ITCZ) to shift to the north or south are two very important problems in climate science. Examining these behaviors in global climate models (GCMs) running solar geoengineering experiments is helpful not only for predicting the effects of solar geoengineering but also for understanding how these processes work under increased carbon dioxide (CO2). Both polar amplification and ITCZ shifts are closely related to the meridional transport of moist static energy (MSE) by the atmosphere. This study examines changes in MSE transport in 10 fully coupled GCMs in experiment G1 of the Geoengineering Model Intercomparison Project (GeoMIP), in which the solar constant is reduced to compensate for the radiative forcing from abruptly quadrupled CO2 concentrations. In G1, poleward MSE transport decreases relative to preindustrial conditions in all models, in contrast to the Coupled Model Intercomparison Project phase 5 (CMIP5) abrupt4xCO2 experiment, in which poleward MSE transport increases. We show that since poleward energy transport decreases rather than increases, and local feedbacks cannot change the sign of an initial temperature change, the residual polar amplification in the G1 experiment must be due to the net positive forcing in the polar regions and net negative forcing in the tropics, which arise from the different spatial patterns of the simultaneously imposed solar and CO2 forcings. However, the reduction in poleward energy transport likely plays a role in limiting the polar warming in G1. An attribution study with a moist energy balance model shows that cloud feedbacks are the largest source of uncertainty regarding changes in poleward energy transport in midlatitudes in G1, as well as for changes in cross-equatorial energy transport, which are anticorrelated with ITCZ shifts.

Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation

PubMed Central

Kuwahara, Tomomi; Yamashita, Atsushi; Hirakawa, Hideki; Nakayama, Haruyuki; Toh, Hidehiro; Okada, Natsumi; Kuhara, Satoru; Hattori, Masahira; Hayashi, Tetsuya; Ohnishi, Yoshinari

2004-01-01

Bacteroides are predominant human colonic commensals, but the principal pathogenic species, Bacteroides fragilis (BF), lives closely associated with the mucosal surface, whereas a second major species, Bacteroides thetaiotaomicron (BT), concentrates within the colon. We find corresponding differences in their genomes, based on determination of the genome sequence of BF and comparative analysis with BT. Both species have acquired two mechanisms that contribute to their dominance among the colonic microbiota: an exceptional capability to use a wide range of dietary polysaccharides by gene amplification and the capacity to create variable surface antigenicities by multiple DNA inversion systems. However, the gene amplification for polysaccharide assimilation is more developed in BT, in keeping with its internal localization. In contrast, external antigenic structures can be changed more systematically in BF. Thereby, at the mucosal surface, where microbes encounter continuous attack by host defenses, BF evasion of the immune system is favored, and its colonization and infectious potential are increased. PMID:15466707

KSHV cell attachment sites revealed by ultra sensitive tyramide signal amplification (TSA) localize to membrane microdomains that are up-regulated on mitotic cells.

PubMed

Garrigues, H Jacques; Rubinchikova, Yelena E; Rose, Timothy M

2014-03-01

Cell surface structures initiating attachment of Kaposi's sarcoma-associated herpesvirus (KSHV) were characterized using purified hapten-labeled virions visualized by confocal microscopy with a sensitive fluorescent enhancement using tyramide signal amplification (TSA). KSHV attachment sites were present in specific cellular domains, including actin-based filopodia, lamellipodia, ruffled membranes, microvilli and intercellular junctions. Isolated microdomains were identified on the dorsal surface, which were heterogeneous in size with a variable distribution that depended on cellular confluence and cell cycle stage. KSHV binding domains ranged from scarce on interphase cells to dense and continuous on mitotic cells, and quantitation of bound virus revealed a significant increase on mitotic compared to interphase cells. KSHV also bound to a supranuclear domain that was distinct from microdomains in confluent and interphase cells. These results suggest that rearrangement of the cellular membrane during mitosis induces changes in cell surface receptors implicated in the initial attachment stage of KSHV entry. Copyright © 2014 Elsevier Inc. All rights reserved.

Liking, wanting, and the incentive-sensitization theory of addiction.

PubMed

Berridge, Kent C; Robinson, Terry E

2016-11-01

Rewards are both "liked" and "wanted," and those 2 words seem almost interchangeable. However, the brain circuitry that mediates the psychological process of "wanting" a particular reward is dissociable from circuitry that mediates the degree to which it is "liked." Incentive salience or "wanting," a form of motivation, is generated by large and robust neural systems that include mesolimbic dopamine. By comparison, "liking," or the actual pleasurable impact of reward consumption, is mediated by smaller and fragile neural systems, and is not dependent on dopamine. The incentive-sensitization theory posits the essence of drug addiction to be excessive amplification specifically of psychological "wanting," especially triggered by cues, without necessarily an amplification of "liking." This is because of long-lasting changes in dopamine-related motivation systems of susceptible individuals, called "neural sensitization." A quarter-century after its proposal, evidence has continued to grow in support the incentive-sensitization theory. Further, its scope is now expanding to include diverse behavioral addictions and other psychopathologies. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Liking, Wanting and the Incentive-Sensitization Theory of Addiction

PubMed Central

Berridge, Kent C.; Robinson, Terry E.

2016-01-01

Rewards are both ‘liked’ and ‘wanted’, and those two words seem almost interchangeable. However, the brain circuitry that mediates the psychological process of ‘wanting’ a particular reward is dissociable from circuitry that mediates the degree to which it is ‘liked’. Incentive salience or ‘wanting’, a form of motivation, is generated by large and robust neural systems that include mesolimbic dopamine. By comparison, ‘liking’, or the actual pleasurable impact of reward consumption, is mediated by smaller and fragile neural systems, and is not dependent on dopamine. The incentive-sensitization theory posits the essence of drug addiction to be excessive amplification specifically of psychological ‘wanting’, especially triggered by cues, without necessarily an amplification of ‘liking’. This is due to long-lasting changes in dopamine-related motivation systems of susceptible individuals, called neural sensitization. A quarter-century after its proposal, evidence has continued to grow in support the incentive-sensitization theory. Further, its scope is now expanding to include diverse behavioral addictions and other psychopathologies. PMID:27977239

Influence of the pump threshold on the single-frequency output power of singly resonant optical parametric oscillators

NASA Astrophysics Data System (ADS)

Sowade, R.; Breunig, I.; Kiessling, J.; Buse, K.

2009-07-01

We demonstrate that for a given pump source, there is an optimum pump threshold to achieve the maximum single-frequency output power in singly resonant optical parametric oscillators. Therefore, cavity losses and parametric amplification have to be adjusted. In particular, continuous-wave output powers of 1.5 W were achieved with a 2.5 cm lithium niobate crystal in comparison with 0.5 W by a 5 cm long crystal within the same cavity design. This counter-intuitive result of weaker amplification leading to larger powers can be explained using a model from L.B. Kreuzer (Proc. Joint Conf. Lasers and Opt.-Elect., p. 52, 1969). Kreuzer also states that single-mode operation is possible only up to pump powers which are 4.6 times the threshold value. Additionally, implementing an outcoupling mirror to increase losses, single-frequency waves with powers of 3 W at 3.2 µm and 7 W at 1.5 µm could be generated simultaneously.

Phase plate technology for laser marking of magnetic discs

DOEpatents

Neuman, B.; Honig, J.; Hackel, L.; Dane, C.B.; Dixit, S.

1998-10-27

An advanced design for a phase plate enables the distribution of spots in arbitrarily shaped patterns with very high uniformity and with a continuously or near-continuously varying phase pattern. A continuous phase pattern eliminates large phase jumps typically expected in a grating that provides arbitrary shapes. Large phase jumps increase scattered light outside of the desired pattern, reduce efficiency and can make the grating difficult to manufacture. When manufacturing capabilities preclude producing a fully continuous grating, the present design can be easily adapted to minimize manufacturing errors and maintain high efficiencies. This continuous grating is significantly more efficient than previously described Dammann gratings, offers much more flexibility in generating spot patterns and is easier to manufacture and replicate than a multi-level phase grating. 3 figs.

Several hundred kHz repetition rate nanosecond pulses amplification in Er-Yb co-doped fiber amplifier

NASA Astrophysics Data System (ADS)

Yang, Weiqiang; Yin, Ke; Zhang, Bin; Xue, Guanghui; Hou, Jing

2014-07-01

We have experimentally investigated several hundred kHz repetition rate 1,550-nm nanosecond pulses amplification in Er-Yb co-doped fiber amplifier (EYDFA). The experimental setup has three stage fiber amplifiers. At the output of the second stage EYDFA, Yb3+ ions induced amplified spontaneous emission (Yb-ASE) is not observed owing to the low pump power. In the third stage EYDFA, a simultaneously seeded 1,064-nm continuous-wave laser is used to control Yb-ASE. Without any additional 1,064-nm signal, significantly backward Yb-ASE which caused loss-induced heat accumulation at the input port of the pump combiner can be observed. The monitored temperature at the input port of the pump combiner rapidly grows from 30 to 80 °C when the pump power is turned from 20 to 32 W. When a 196-mW forward 1,064-nm laser is added, the monitored backward Yb-ASE power is significantly declined, and the monitored temperature is kept below 35 °C. But, the additional signal caused a large power fraction at 1,064 nm in the output laser. In our experiment at the maximum pump power of 48.5 W, the total output power is 20 W with ~6.4-W 1,550-nm pulsed laser and ~13-W 1,064-nm continuous-wave laser.

Recombinations in Staphylococcal Cassette Chromosome mec Elements Compromise the Molecular Detection of Methicillin Resistance in Staphylococcus aureus

PubMed Central

Hill-Cawthorne, Grant A.; Hudson, Lyndsey O.; El Ghany, Moataz Fouad Abd; Piepenburg, Olaf; Nair, Mridul; Dodgson, Andrew; Forrest, Matthew S.

2014-01-01

Clinical laboratories are increasingly using molecular tests for methicillin-resistant Staphylococcus aureus (MRSA) screening. However, primers have to be targeted to a variable chromosomal region, the staphylococcal cassette chromosome mec (SCCmec). We initially screened 726 MRSA isolates from a single UK hospital trust by recombinase polymerase amplification (RPA), a novel, isothermal alternative to PCR. Undetected isolates were further characterised using multilocus sequence, spa typing and whole genome sequencing. 96% of our tested phenotypically MRSA isolates contained one of the six orfX-SCCmec junctions our RPA test and commercially available molecular tests target. However 30 isolates could not be detected. Sequencing of 24 of these isolates demonstrated recombinations within the SCCmec element with novel insertions that interfered with the RPA, preventing identification as MRSA. This result suggests that clinical laboratories cannot rely solely upon molecular assays to reliably detect all methicillin-resistance. The presence of significant recombinations in the SCCmec element, where the majority of assays target their primers, suggests that there will continue to be isolates that escape identification. We caution that dependence on amplification-based molecular assays will continue to result in failure to diagnose a small proportion (∼4%) of MRSA isolates, unless the true level of SCCmec natural diversity is determined by whole genome sequencing of a large collection of MRSA isolates. PMID:24972080

Switches and latches: a biochemical tug-of-war between the kinases and phosphatases that control mitosis.

PubMed

Domingo-Sananes, Maria Rosa; Kapuy, Orsolya; Hunt, Tim; Novak, Bela

2011-12-27

Activation of the cyclin-dependent kinase (Cdk1) cyclin B (CycB) complex (Cdk1:CycB) in mitosis brings about a remarkable extent of protein phosphorylation. Cdk1:CycB activation is switch-like, controlled by two auto-amplification loops--Cdk1:CycB activates its activating phosphatase, Cdc25, and inhibits its inhibiting kinase, Wee1. Recent experimental evidence suggests that parallel to Cdk1:CycB activation during mitosis, there is inhibition of its counteracting phosphatase activity. We argue that the downregulation of the phosphatase is not just a simple latch that suppresses futile cycles of phosphorylation/dephosphorylation during mitosis. Instead, we propose that phosphatase regulation creates coherent feed-forward loops and adds extra amplification loops to the Cdk1:CycB regulatory network, thus forming an integral part of the mitotic switch. These network motifs further strengthen the bistable characteristic of the mitotic switch, which is based on the antagonistic interaction of two groups of proteins: M-phase promoting factors (Cdk1:CycB, Cdc25, Greatwall and Endosulfine/Arpp19) and interphase promoting factors (Wee1, PP2A-B55 and a Greatwall counteracting phosphatase, probably PP1). The bistable character of the switch implies the existence of a CycB threshold for entry into mitosis. The end of G2 phase is determined by the point where CycB level crosses the CycB threshold for Cdk1 activation.

Clinical Characteristics and Outcome of Patients with Neuroblastoma Presenting Genomic Amplification of Loci Other than MYCN

PubMed Central

Guimier, Anne; Ferrand, Sandrine; Pierron, Gaëlle; Couturier, Jérôme; Janoueix-Lerosey, Isabelle; Combaret, Valérie; Mosseri, Véronique; Thebaud, Estelle; Gambart, Marion; Plantaz, Dominique; Marabelle, Aurélien; Coze, Carole; Rialland, Xavier; Fasola, Sylvie; Lapouble, Eve; Fréneaux, Paul; Peuchmaur, Michel; Michon, Jean; Delattre, Olivier; Schleiermacher, Gudrun

2014-01-01

Background Somatically acquired genomic alterations with MYCN amplification (MNA) are key features of neuroblastoma (NB), the most common extra-cranial malignant tumour of childhood. Little is known about the frequency, clinical characteristics and outcome of NBs harbouring genomic amplification(s) distinct from MYCN. Methods Genomic profiles of 1100 NBs from French centres studied by array-CGH were re-examined specifically to identify regional amplifications. Patients were included if amplifications distinct from the MYCN locus were seen. A subset of NBs treated at Institut Curie and harbouring MNA as determined by array-CGH without other amplification was also studied. Clinical and histology data were retrospectively collected. Results In total, 56 patients were included and categorised into 3 groups. Group 1 (n = 8) presented regional amplification(s) without MNA. Locus 12q13-14 was a recurrent amplified region (4/8 cases). This group was heterogeneous in terms of INSS stages, primary localisations and histology, with atypical clinical features. Group 2 (n = 26) had MNA as well as other regional amplifications. These patients shared clinical features of those of a group of NBs MYCN amplified (Group 3, n = 22). Overall survival for group 1 was better than that of groups 2 and 3 (5 year OS: 87.5%±11% vs 34.9%±7%, log-rank p<0.05). Conclusion NBs harbouring regional amplification(s) without MNA are rare and seem to show atypical features in clinical presentation and genomic profile. Further high resolution genetic explorations are justified in this heterogeneous group, especially when considering these alterations as predictive markers for targeted therapy. PMID:25013904

Method for in situ characterization of a medium of dispersed matter in a continuous phase

DOEpatents

Kaufman, E.N.

1995-03-07

A method is described for the in situ characterization of a medium of a dispersed phase in a continuous phase, including the steps of adding a fluorescent dye to one phase capable of producing fluorescence therein when the fluorescent dye is optically excited, optically exciting the fluorescent dye at a wavelength to produce fluorescence in the one phase, and monitoring the fluorescence to distinguish the continuous phase from the dispersed phase. 2 figs.

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▿

PubMed Central

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

Phase I dose-escalation study of the c-Met tyrosine kinase inhibitor SAR125844 in Asian patients with advanced solid tumors, including patients with MET-amplified gastric cancer.

PubMed

Shitara, Kohei; Kim, Tae Min; Yokota, Tomoya; Goto, Masahiro; Satoh, Taroh; Ahn, Jin-Hee; Kim, Hyo Song; Assadourian, Sylvie; Gomez, Corinne; Harnois, Marzia; Hamauchi, Satoshi; Kudo, Toshihiro; Doi, Toshihido; Bang, Yung-Jue

2017-10-03

SAR125844 is a potent and selective inhibitor of the c-Met kinase receptor. This was an open-label, phase I, multicenter, dose-escalation, and dose-expansion trial of SAR125844 in Asian patients with solid tumors, a subgroup of whom had gastric cancer and MET amplification (NCT01657214). SAR125844 was administered by intravenous infusion (260-570 mg/m 2 ) on days 1, 8, 15, and 22 of each 28-day cycle. Objectives were to determine the maximum tolerated dose (MTD) and to evaluate SAR125844 safety and pharmacokinetic profile. Antitumor activity was also assessed. Of 38 patients enrolled (median age 64.0 years), 22 had gastric cancer, including 14 with MET amplification. In the dose-escalation cohort ( N = 19; unselected population, including three patients with MET -amplification [two with gastric cancer and one with lung cancer]), the MTD was not reached, and the recommended dose was established at 570 mg/m 2 . Most frequent treatment-emergent adverse events (AEs) were nausea (36.8%), vomiting (34.2%), decreased appetite (28.9%), and fatigue or asthenia, constipation, and abdominal pains (each 21.1%); none appeared to be dose-dependent. Grade ≥ 3 AEs were observed in 39.5% of patients and considered drug-related in 7.9%. SAR125844 exposure increased slightly more than expected by dose proportionality; dose had no significant effect on clearance. No objective responses were observed in the dose-escalation cohort, with seven patients (three gastric cancer, two colorectal cancer, one breast cancer, and one with cancer of unknown primary origin) having stable disease. Modest antitumor activity was observed at 570 mg/m 2 in the dose-expansion cohort, comprising patients with MET -amplified tumors ( N = 19). Two gastric cancer patients had partial responses, seven patients had stable disease (six gastric cancer and one kidney cancer), and 10 patients had progressive disease. Single-agent SAR125844 administered up to 570 mg/m 2 has acceptable tolerability and modest antitumor activity in patients with MET -amplified gastric cancer.

Phase II Evaluation of Gefitinib in Patients With Newly Diagnosed Grade 4 Astrocytoma: Mayo/North Central Cancer Treatment Group Study N0074

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uhm, Joon H., E-mail: uhm.joon@mayo.ed; Ballman, Karla V.; Wu Wenting

2011-06-01

Purpose: Amplification of the epidermal growth factor receptor (EGFR) gene represents one of the most frequent gene alterations in glioblastoma (GBM). In the current study, we evaluated gefitinib, a potent EGFR inhibitor, in the treatment of adults with newly diagnosed GBM. Methods and Materials: Ninety-eight patients (96 evaluable) were accrued between May 18, 2001, and August 2, 2002. All were newly diagnosed GBM patients who were clinically and radiographically stable/improved after radiation treatment (enrollment within 5 weeks of radiation completion). No prior chemotherapy was permitted. EGFR amplification/mutation, as assessed by fluorescence in situ hybridization and immunohistochemistry, was not required formore » treatment with gefitinib but was studied when tissues were available. Gefitinib was administered at 500 mg each day; for patients receiving dexamethasone or enzyme-inducing (CYP3A4) agents, dose was escalated to a maximum of 1,000 mg QD. Treatment cycles were repeated at 4-week intervals with brain magnetic resonance imaging at 8-week intervals. Results: Overall survival (OS; calculated from time of initial surgery) at 1 year (primary end point) with gefitinib was 54.2%, which was not statistically different compared with that of historical control population (48.9%, data from three previous Phase III North Central Cancer Treatment Group studies of newly diagnosed GBM patients). Progression-free survival (PFS) at 1 year post-RT (16.7%) was also not significantly different to that of historical controls (30.3%). Clinical outcome was not affected by EGFR status (amplification or vIII mutation). Fatigue (41%), rash (62%), and loose stools (58%) constituted the most frequent adverse events, the majority of these being limited to Grade 1/2. Of note, the occurrence of drug-related adverse effects, such as loose stools was associated with improved OS. Conclusions: In our evaluation of nearly 100 patients with newly diagnosed GBM, treatment with adjuvant gefitinib post-radiation was not associated with significant improvement in OS or PFS. However, patients who experienced gefitinib-associated adverse effects (rash/diarrhea) did demonstrate improved OS.« less

Feedback Augmented Sub-Ranging (FASR) Quantizer

NASA Technical Reports Server (NTRS)

Guilligan, Gerard

2012-01-01

This innovation is intended to reduce the size, power, and complexity of pipeline analog-to-digital converters (ADCs) that require high resolution and speed along with low power. Digitizers are important components in any application where analog signals (such as light, sound, temperature, etc.) need to be digitally processed. The innovation implements amplification of a sampled residual voltage in a switched capacitor amplifier stage that does not depend on charge redistribution. The result is less sensitive to capacitor mismatches that cause gain errors, which are the main limitation of such amplifiers in pipeline ADCs. The residual errors due to mismatch are reduced by at least a factor of 16, which is equivalent to at least 4 bits of improvement. The settling time is also faster because of a higher feedback factor. In traditional switched capacitor residue amplifiers, closed-loop amplification of a sampled and held residue signal is achieved by redistributing sampled charge onto a feedback capacitor around a high-gain transconductance amplifier. The residual charge that was sampled during the acquisition or sampling phase is stored on two or more capacitors, often equal in value or integral multiples of each other. During the hold or amplification phase, all of the charge is redistributed onto one capacitor in the feedback loop of the amplifier to produce an amplified voltage. The key error source is the non-ideal ratios of feedback and input capacitors caused by manufacturing tolerances, called mismatches. The mismatches cause non-ideal closed-loop gain, leading to higher differential non-linearity. Traditional solutions to the mismatch errors are to use larger capacitor values (than dictated by thermal noise requirements) and/or complex calibration schemes, both of which increase the die size and power dissipation. The key features of this innovation are (1) the elimination of the need for charge redistribution to achieve an accurate closed-loop gain of two, (2) a higher feedback factor in the amplifier stage giving a higher closed-loop bandwidth compared to the prior art, and (3) reduced requirement for calibration. The accuracy of the new amplifier is mainly limited by the sampling networks parasitic capacitances, which should be minimized in relation to the sampling capacitors.

Evaluation of BGJ398, a Fibroblast Growth Factor Receptor 1-3 Kinase Inhibitor, in Patients With Advanced Solid Tumors Harboring Genetic Alterations in Fibroblast Growth Factor Receptors: Results of a Global Phase I, Dose-Escalation and Dose-Expansion Study.

PubMed

Nogova, Lucia; Sequist, Lecia V; Perez Garcia, Jose Manuel; Andre, Fabrice; Delord, Jean-Pierre; Hidalgo, Manuel; Schellens, Jan H M; Cassier, Philippe A; Camidge, D Ross; Schuler, Martin; Vaishampayan, Ulka; Burris, Howard; Tian, G Gary; Campone, Mario; Wainberg, Zev A; Lim, Wan-Teck; LoRusso, Patricia; Shapiro, Geoffrey I; Parker, Katie; Chen, Xueying; Choudhury, Somesh; Ringeisen, Francois; Graus-Porta, Diana; Porter, Dale; Isaacs, Randi; Buettner, Reinhard; Wolf, Jürgen

2017-01-10

Purpose This two-part, first-in-human study was initiated in patients with advanced solid tumors harboring genetic alterations in fibroblast growth factor receptors (FGFRs) to determine the maximum tolerated dose (MTD), the recommended phase II dose (RP2D), and the schedule, safety, pharmacokinetics, pharmacodynamics, and antitumor activity of oral BGJ398, a selective FGFR1-3 tyrosine kinase inhibitor. Patients and Methods Adult patients were treated with escalating dosages of BGJ398 5 to 150 mg once daily or 50 mg twice daily continuously in 28-day cycles. During expansion at the MTD, patients with FGFR1-amplified squamous cell non-small-cell lung cancer (sqNSCLC; arm 1) or other solid tumors with FGFR genetic alterations (mutations/amplifications/fusions) received BGJ398 daily on a continuous schedule (arm 2), or on a 3-weeks-on/1-week-off schedule (arm 3). Results Data in 132 patients from the escalation and expansion arms are reported (May 15, 2015, cutoff). The MTD, 125 mg daily, was determined on the basis of dose-limiting toxicities in four patients (100 mg, grade 3 aminotransferase elevations [n = 1]; 125 mg, hyperphosphatemia [n = 1]; 150 mg, grade 1 corneal toxicity [n = 1] and grade 3 aminotransferase elevations [n = 1]). Common adverse events in patients treated at the MTD (n = 57) included hyperphosphatemia (82.5%), constipation (50.9%), decreased appetite (45.6%), and stomatitis (45.6%). A similar safety profile was observed using the 3-weeks-on/1-week-off schedule (RP2D). However, adverse event-related dose adjustments/interruptions were less frequent with the 3-weeks-on/1-week-off (50.0%) versus the continuous (73.7%) schedule. Antitumor activity (seven partial responses [six confirmed]) was demonstrated with BGJ398 doses ≥ 100 mg in patients with FGFR1-amplified sqNSCLC and FGFR3-mutant bladder/urothelial cancer. Conclusion BGJ398 at the MTD/RP2D had a tolerable and manageable safety profile and showed antitumor activity in several tumor types, including FGFR1-amplified sqNSCLC and FGFR3-mutant bladder/urothelial cancers.

HER-2 amplification in tubular carcinoma of the breast.

PubMed

Oakley, Gerard J; Tubbs, Raymond R; Crowe, Joseph; Sebek, Bruce; Budd, G Thomas; Patrick, Rebecca J; Procop, Gary W

2006-07-01

The prognostic and therapeutic implications of HER-2 gene amplification and estrogen and progesterone receptor status in breast cancer are well described. To address the relative paucity of information concerning HER-2 amplification for tubular carcinomas, we assessed the frequency of gene amplification in 55 tubular carcinomas of the breast from 54 patients, 5 of which had axillary node metastases. The HER-2 gene copy number was assessed by fluorescence in situ hybridization for the majority of tumors analyzed, whereas estrogen and progesterone receptor status was achieved by immunohistochemical analysis. HER-2 gene amplification was not observed in any of the tumors examined, and most were estrogen receptor-positive. This HER-2 gene amplification frequency was significantly lower than the frequency of gene amplification previously reported for all invasive ductal carcinoma of no special type (P < .01). HER-2 gene amplification likely occurs infrequently, or not at all, in tubular carcinomas of the breast, whereas most express estrogen receptors.

Investigating mixed phase clouds using a synergy of ground based remote sensing measurements

NASA Astrophysics Data System (ADS)

Gierens, Rosa; Kneifel, Stefan; Löhnert, Ulrich

2017-04-01

Low level mixed phase clouds occur frequently in the Arctic, and can persist from hours to several days. However, the processes that lead to the commonality and persistence of these clouds are not well understood. The aim of our work is to get a more detailed understanding of the dynamics of and the processes in Arctic mixed phase clouds using a combination of instruments operating at the AWIPEV station in Svalbard. In addition, an aircraft campaign collecting in situ measurements inside mixed phase clouds above the station is planned for May-June 2017. The in situ data will be used for developing and validating retrievals for microphysical properties from Doppler cloud radar measurements. Once observational data for cloud properties is obtained, it can be used for evaluating model performance, for studies combining modeling and observational approaches, and eventually lead to developing model parameterizations of mixed phase microphysics. To describe the low-level mixed phase clouds, and the atmospheric conditions in which they occur, we present a case study of a persistent mixed phase cloud observed above the AWIPEV station. In the frame of the Arctic Amplification: Climate Relevant Atmospheric and Surface Processes and Feedback Mechanisms ((AC)3) -project, a millimeter wavelength cloud radar was installed at the site in June 2016. The high vertical (4 m in the lowest layer) and temporal (2.5 sec) resolution allows for a detailed description of the structure of the cloud. In addition to radar reflectivity and mean vertical velocity, we also utilize the higher moments of the Doppler spectra, such as skewness and kurtosis. To supplement the radar measurements, a ceilometer is used to detect liquid layers inside the cloud. Liquid water path and integrated water vapor are estimated using a microwave radiometer, which together with soundings can also provide temperature and humidity profiles in the lower troposphere. Moreover, a three-dimensional wind field is be obtained from a Doppler wind lidar. Furthermore, the Cloudnet scheme (www.cloud-net.org), that combines radar, lidar and microwave radiometer observations with a forecast model to provide a best estimate of cloud properties, is used for identifying mixed phase clouds. The continuous measurements carried out at AWIPEV make it possible to characterize the macro- and micro- physical properties of mixed-phase clouds on a long-term, statistical basis. The Arctic observations are compared to a 5-year observational data set from Jülich Observatory for Cloud Evolution (JOYCE) in Western Germany. The occurrence of different types of clouds (with focus on mixed-phase and super-cooled clouds), the distribution of ice and liquid within the clouds, the turbulent environment as well as the temperatures where the different phases are occurring are investigated.

Gene amplification during myogenic differentiation

PubMed Central

Fischer, Ulrike; Ludwig, Nicole; Raslan, Abdulrahman; Meier, Carola; Meese, Eckart

2016-01-01

Gene amplifications are mostly an attribute of tumor cells and drug resistant cells. Recently, we provided evidence for gene amplifications during differentiation of human and mouse neural progenitor cells. Here, we report gene amplifications in differentiating mouse myoblasts (C2C12 cells) covering a period of 7 days including pre-fusion, fusion and post-fusion stages. After differentiation induction we found an increase in copy numbers of CDK4 gene at day 3, of NUP133 at days 4 and 7, and of MYO18B at day 4. The amplification process was accompanied by gamma-H2AX foci that are indicative of double stand breaks. Amplifications during the differentiating process were also found in primary human myoblasts with the gene CDK4 and NUP133 amplified both in human and mouse myoblasts. Amplifications of NUP133 and CDK4 were also identified in vivo on mouse transversal cryosections at stage E11.5. In the course of myoblast differentiation, we found amplifications in cytoplasm indicative of removal of amplified sequences from the nucleus. The data provide further evidence that amplification is a fundamental mechanism contributing to the differentiation process in mammalians. PMID:26760505

RUNX1 Amplification Increases the Risk for Thrombosis in Children With B-cell Acute Lymphoblastic Leukemia.

PubMed

Boucher, Maria O; Smitherman, Andrew B; Pahl, Kristy S; Rao, Kathleen W; Deal, Allison M; Blatt, Julie

2016-04-01

RUNX1 (AML1) amplification in patients with B-cell acute lymphoblastic leukemia (B-ALL) has been associated with poor survival for unclear reasons. Our anecdotal experience suggests that children with B-ALL and RUNX1 amplification might be predisposed to thrombosis. We performed a retrospective cohort study of children with B-ALL treated from 2008 to 2014 at the North Carolina Children's Hospital. Patient demographics, cytogenetics, and diagnosis of thrombosis were extracted by blinded chart review. Analysis was performed examining the relationship between RUNX1 amplification and thrombosis. We identified 119 patients with B-ALL and a median age of 4.9 years (interquartile range, 2.9 to 8.6 y) at diagnosis. Four patients (3%) had RUNX1 amplification. The average number of RUNX1 copies among those with amplification was 5 (SD 0.81 [range, 4 to 6]). Eighteen thromboses were diagnosed within 6 months of starting treatment. These events were more likely among patients with RUNX1 amplification than in patients without amplification (75% vs. 13%; RR 5.75, 95% confidence interval, 2.75-12.01). RUNX1 amplification may predispose to early thrombotic events in children with B-ALL which could, in part, contribute to their poorer outcomes. Treatment implications, including possible prophylactic anticoagulation of patients with of RUNX1 amplification, justify larger studies to confirm these findings.

An evaluation of direct PCR amplification

PubMed Central

Hall, Daniel E.; Roy, Reena

2014-01-01

Aim To generate complete DNA profiles from blood and saliva samples deposited on FTA® and non-FTA® paper substrates following a direct amplification protocol. Methods Saliva samples from living donors and blood samples from deceased individuals were deposited on ten different FTA® and non-FTA® substrates. These ten paper substrates containing body fluids were kept at room temperature for varying lengths of time ranging from one day to approximately one year. For all assays in this research, 1.2 mm punches were collected from each substrate containing one type of body fluid and amplified with reagents provided in the nine commercial polymerase chain reaction (PCR) amplification kits. The substrates were not subjected to purification reagent or extraction buffer prior to amplification. Results Success rates were calculated for all nine amplification kits and all ten substrates based on their ability to yield complete DNA profiles following a direct amplification protocol. Six out of the nine amplification kits, and four out of the ten paper substrates had the highest success rates overall. Conclusion The data show that it is possible to generate complete DNA profiles following a direct amplification protocol using both standard (non-direct) and direct PCR amplification kits. The generation of complete DNA profiles appears to depend more on the success of the amplification kit rather than the than the FTA®- or non-FTA®-based substrates. PMID:25559837

CDK4 Amplification Predicts Recurrence of Well-Differentiated Liposarcoma of the Abdomen

PubMed Central

Ha, Sang Yun; Paik, Kwang Yeol; Lee, Seung Eun; Kim, Jong Man; Park, Jae Berm; Kwon, Choon Hyuck David; Joh, Jae-Won; Choi, Yoon-La; Kim, Sung Joo

2014-01-01

Background 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. Methods 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). Results 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). Conclusions Level of CDK4 amplification determined by Q-PCR was associated with the recurrence of WD liposarcomas after surgical resection. PMID:25121597

[Investigation of RNA viral genome amplification by multiple displacement amplification technique].

PubMed

Pang, Zheng; Li, Jian-Dong; Li, Chuan; Liang, Mi-Fang; Li, De-Xin

2013-06-01

In order to facilitate the detection of newly emerging or rare viral infectious diseases, a negative-strand RNA virus-severe fever with thrombocytopenia syndrome bunyavirus, and a positive-strand RNA virus-dengue virus, were used to investigate RNA viral genome unspecific amplification by multiple displacement amplification technique from clinical samples. Series of 10-fold diluted purified viral RNA were utilized as analog samples with different pathogen loads, after a series of reactions were sequentially processed, single-strand cDNA, double-strand cDNA, double-strand cDNA treated with ligation without or with supplemental RNA were generated, then a Phi29 DNA polymerase depended isothermal amplification was employed, and finally the target gene copies were detected by real time PCR assays to evaluate the amplification efficiencies of various methods. The results showed that multiple displacement amplification effects of single-strand or double-strand cDNA templates were limited, while the fold increases of double-strand cDNA templates treated with ligation could be up to 6 X 10(3), even 2 X 10(5) when supplemental RNA existed, and better results were obtained when viral RNA loads were lower. A RNA viral genome amplification system using multiple displacement amplification technique was established in this study and effective amplification of RNA viral genome with low load was achieved, which could provide a tool to synthesize adequate viral genome for multiplex pathogens detection.

Beam cleaning of an incoherent laser via plasma Raman amplification

DOE PAGES

Edwards, Matthew R.; Qu, Kenan; Mikhailova, Julia M.; ...

2017-09-25

We show that backward Raman amplification in plasma can efficiently compress a temporally incoherent pump laser into an intense coherent amplified seed pulse, provided that the correlation time of the pump is longer than the inverse plasma frequency. One analytical theory for Raman amplification using pump beams with different correlation functions is developed and compared to numerical calculations and particle-in-cell simulations. Since incoherence on scales shorter than the instability growth time suppresses spontaneous noise amplification, we point out a broad regime where quasi-coherent sources may be used as efficient low-noise Raman amplification pumps. As the amplified seed is coherent, Ramanmore » amplification provides an additional a beam-cleaning mechanism for removing incoherence. At near-infrared wavelengths, finite coherence times as short as 50 fs allow amplification with only minor losses in efficiency.« less

Beam cleaning of an incoherent laser via plasma Raman amplification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edwards, Matthew R.; Qu, Kenan; Mikhailova, Julia M.

We show that backward Raman amplification in plasma can efficiently compress a temporally incoherent pump laser into an intense coherent amplified seed pulse, provided that the correlation time of the pump is longer than the inverse plasma frequency. One analytical theory for Raman amplification using pump beams with different correlation functions is developed and compared to numerical calculations and particle-in-cell simulations. Since incoherence on scales shorter than the instability growth time suppresses spontaneous noise amplification, we point out a broad regime where quasi-coherent sources may be used as efficient low-noise Raman amplification pumps. As the amplified seed is coherent, Ramanmore » amplification provides an additional a beam-cleaning mechanism for removing incoherence. At near-infrared wavelengths, finite coherence times as short as 50 fs allow amplification with only minor losses in efficiency.« less

Flow through PCR module of BioBriefcase

NASA Astrophysics Data System (ADS)

Arroyo, E.; Wheeler, E. K.; Shediac, R.; Hindson, B.; Nasarabadi, S.; Vrankovich, G.; Bell, P.; Bailey, C.; Sheppod, T.; Christian, A. T.

2005-11-01

The BioBriefcase is an integrated briefcase-sized aerosol collection and analysis system for autonomous monitoring of the environment, which is currently being jointly developed by Lawrence Livermore and Sandia National Laboratories. This poster presents results from the polymerase chain reaction (PCR) module of the system. The DNA must be purified after exiting the aerosol collector to prevent inhibition of the enzymatic reaction. Traditional solid-phase extraction results in a large loss of sample. In this flow-through system, we perform sample purification, concentration and amplification in one reactor, which minimizes the loss of material. The sample from the aerosol collector is mixed with a denaturation solution prior to flowing through a capillary packed with silica beads. The DNA adheres to the silica beads allowing the environmental contaminants to be flushed to waste while effectively concentrating the DNA on the silica matrix. The adhered DNA is amplified while on the surface of the silica beads, resulting in a lower limit of detection than an equivalent eluted sample. Thus, this system is beneficial since more DNA is available for amplification, less reagents are utilized, and contamination risks are reduced.

Structural organization and classification of cytochrome P450 genes in flax (Linum usitatissimum L.).

PubMed

Babu, Peram Ravindra; Rao, Khareedu Venkateswara; Reddy, Vudem Dashavantha

2013-01-15

Flax CYPome analysis resulted in the identification of 334 putative cytochrome P450 (CYP450) genes in the cultivated flax genome. Classification of flax CYP450 genes based on the sequence similarity with Arabidopsis orthologs and CYP450 nomenclature, revealed 10 clans representing 44 families and 98 subfamilies. CYP80, CYP83, CYP92, CYP702, CYP705, CYP708, CYP728, CYP729, CYP733 and CYP736 families are absent in the flax genome. The subfamily members exhibited conserved sequences, length of exons and phasing of introns. Similarity search of the genomic resources of wild flax species Linum bienne with CYP450 coding sequences of the cultivated flax, revealed the presence of 127 CYP450 gene orthologs, indicating amplification of novel CYP450 genes in the cultivated flax. Seven families CYP73, 74, 75, 76, 77, 84 and 709, coding for enzymes associated with phenylpropanoid/fatty acid metabolism, showed extensive gene amplification in the flax. About 59% of the flax CYP450 genes were present in the EST libraries. Copyright © 2012 Elsevier B.V. All rights reserved.

A Self-Synchronized Optoelectronic Oscillator based on an RTD Photo-Detector and a Laser Diode

PubMed Central

Romeira, Bruno; Seunarine, Kris; Ironside, Charles N.; Kelly, Anthony E.; Figueiredo, José M. L.

2013-01-01

We propose and demonstrate a simple and stable low-phase noise optoelectronic oscillator (OEO) that uses a laser diode, an optical fiber delay line and a resonant tunneling diode (RTD) free-running oscillator that is monolithic integrated with a waveguide photo-detector. The RTD-OEO exhibits single-side band phase noise power below −100 dBc/Hz with more than 30 dB noise suppression at 10 kHz from the center free-running frequency for fiber loop lengths around 1.2 km. The oscillator power consumption is below 0.55 W, and can be controlled either by the injected optical power or the fiber delay line. The RTD-OEO stability is achieved without using other high-speed optical/optoelectronic components and amplification. PMID:23814452

Information storage and retrieval in a single levitating colloidal particle

NASA Astrophysics Data System (ADS)

Myers, Christopher J.; Celebrano, Michele; Krishnan, Madhavi

2015-10-01

The binary switch is a basic component of digital information. From phase-change alloys to nanomechanical beams, molecules and atoms, new strategies for controlled bistability hold great interest for emerging technologies. We present a generic methodology for precise and parallel spatiotemporal control of nanometre-scale matter in a fluid, and demonstrate the ability to attain digital functionalities such as switching, gating and data storage in a single colloid, with further implications for signal amplification and logic operations. This fluid-phase bit can be arrayed at high densities, manipulated by either electrical or optical fields, supports low-energy, high-speed operation and marks a first step toward ‘colloidal information’. The principle generalizes to any system where spatial perturbation of a particle elicits a differential response amenable to readout.

Information storage and retrieval in a single levitating colloidal particle.

PubMed

Myers, Christopher J; Celebrano, Michele; Krishnan, Madhavi

2015-10-01

The binary switch is a basic component of digital information. From phase-change alloys to nanomechanical beams, molecules and atoms, new strategies for controlled bistability hold great interest for emerging technologies. We present a generic methodology for precise and parallel spatiotemporal control of nanometre-scale matter in a fluid, and demonstrate the ability to attain digital functionalities such as switching, gating and data storage in a single colloid, with further implications for signal amplification and logic operations. This fluid-phase bit can be arrayed at high densities, manipulated by either electrical or optical fields, supports low-energy, high-speed operation and marks a first step toward 'colloidal information'. The principle generalizes to any system where spatial perturbation of a particle elicits a differential response amenable to readout.

Risk factors and timing of default from treatment for non-multidrug-resistant tuberculosis in Moldova.

PubMed

Jenkins, H E; Ciobanu, A; Plesca, V; Crudu, V; Galusca, I; Soltan, V; Cohen, T

2013-03-01

The Republic of Moldova, in Eastern Europe, has among the highest reported nationwide proportions of tuberculosis (TB) patients with multidrug-resistant tuberculosis (MDR-TB) worldwide. Default has been associated with increased mortality and amplification of drug resistance, and may contribute to the high MDR-TB rates in Moldova. To assess risk factors and timing of default from treatment for non-MDR-TB from 2007 to 2010. A retrospective analysis of routine surveillance data on all non-MDR-TB patients reported. A total of 14.7% of non-MDR-TB patients defaulted from treatment during the study period. Independent risk factors for default included sociodemographic factors, such as homelessness, living alone, less formal education and spending substantial time outside Moldova in the year prior to diagnosis; and health-related factors such as human immunodeficiency virus co-infection, greater lung pathology and increasing TB drug resistance. Anti-tuberculosis treatment is usually initiated within an institutional setting in Moldova, and the default risk was highest in the month following the phase of hospitalized treatment (among civilians) and after leaving prison (among those diagnosed while incarcerated). Targeted interventions to increase treatment adherence for patients at highest risk of default, and improving the continuity of care for patients transitioning from institutional to community care may substantially reduce risk of default.

Risk factors and timing of default from treatment for non-multidrug-resistant tuberculosis in Moldova

PubMed Central

Jenkins, Helen E.; Ciobanu, Anisoara; Plesca, Valeriu; Crudu, Valeriu; Galusca, Irina; Soltan, Viorel; Cohen, Ted

2013-01-01

SUMMARY Setting The Republic of Moldova, Eastern Europe, 2007–2010. Moldova has among the highest reported nationwide proportions of TB patients with multidrug-resistant tuberculosis (MDR-TB) worldwide. Objective To assess risk factors and timing of default from treatment for non-MDR-TB. Default has been associated with increased mortality and amplification of drug resistance and may contribute to the high MDR-TB rates in Moldova. Design A retrospective analysis of routine surveillance data on all non-MDR-TB patients reported. Results 14.7% of non-MDR-TB patients defaulted from treatment during the study period. Independent risk factors for default included sociodemographic factors (i.e. homelessness, living alone, less formal education and spending substantial time outside Moldova in the year prior to diagnosis) and health-related factors (i.e. HIV-coinfection, greater lung pathology, and increasing TB drug resistance). TB treatment is usually initiated within an institutional setting in Moldova and the default risk was highest in the month following the hospitalized treatment phase (among civilians) and after leaving prison (among those diagnosed while incarcerated). Conclusions Targeted interventions to increase treatment adherence for patients at highest risk of default and improving the continuity of care for patients transitioning from institutional to community care may substantially reduce the default risk. PMID:23407226

Carbon nanotube enhanced label-free detection of microRNAs based on hairpin probe triggered solid-phase rolling-circle amplification

NASA Astrophysics Data System (ADS)

Tian, Qianqian; Wang, Ying; Deng, Ruijie; Lin, Lei; Liu, Yang; Li, Jinghong

2014-12-01

The detection of microRNAs (miRNAs) is imperative for gaining a better understanding of the functions of these biomarkers and has great potential for the early diagnosis of human disease. High sensitivity and selectivity for miRNA detection brings new challenges. Herein, an ultrasensitive protocol for electrochemical detection of miRNA is designed through carbon nanotube (CNT) enhanced label-free detection based on hairpin probe triggered solid-phase rolling-circle amplification (RCA). Traditionally, RCA, widely applied for signal enhancement in the construction of a variety of biosensors, has an intrinsic limitation of ultrasensitive detection, as it is difficult to separate the enzymes, templates, and padlock DNAs from the RCA products in the homogeneous solution. We purposely designed a solid-phase RCA strategy, using CNTs as the solid substrate, integrated with a hairpin structured probe to recognize target miRNA. In the presence of miRNA the stem-loop structure will be unfolded, triggering the CNT based RCA process. Due to the efficient blocking effect originating from the polymeric RCA products, the label-free assay of miRNA exhibits an ultrasensitive detection limit of 1.2 fM. Furthermore, the protocol possesses excellent specificity for resolving lung cancer-related let-7 family members which have only one-nucleotide variations. The high sensitivity and selectivity give the method great potential for applications in online diagnostics and in situ detection in long-term development.The detection of microRNAs (miRNAs) is imperative for gaining a better understanding of the functions of these biomarkers and has great potential for the early diagnosis of human disease. High sensitivity and selectivity for miRNA detection brings new challenges. Herein, an ultrasensitive protocol for electrochemical detection of miRNA is designed through carbon nanotube (CNT) enhanced label-free detection based on hairpin probe triggered solid-phase rolling-circle amplification (RCA). Traditionally, RCA, widely applied for signal enhancement in the construction of a variety of biosensors, has an intrinsic limitation of ultrasensitive detection, as it is difficult to separate the enzymes, templates, and padlock DNAs from the RCA products in the homogeneous solution. We purposely designed a solid-phase RCA strategy, using CNTs as the solid substrate, integrated with a hairpin structured probe to recognize target miRNA. In the presence of miRNA the stem-loop structure will be unfolded, triggering the CNT based RCA process. Due to the efficient blocking effect originating from the polymeric RCA products, the label-free assay of miRNA exhibits an ultrasensitive detection limit of 1.2 fM. Furthermore, the protocol possesses excellent specificity for resolving lung cancer-related let-7 family members which have only one-nucleotide variations. The high sensitivity and selectivity give the method great potential for applications in online diagnostics and in situ detection in long-term development. Electronic supplementary information (ESI) available: Preparation of the chemically modified multi-walled carbon nanotubes (CNTs), characterization of the CNTs and modified CNTs, preparation of the circular probe, gel electrophoresis of the RCA products, and DNA probes as noted in the text. See DOI: 10.1039/c4nr05243a

Axisymmetric simulations of magnetorotational core collapse: approximate inclusion of general relativistic effects

NASA Astrophysics Data System (ADS)

Obergaulinger, M.; Aloy, M. A.; Dimmelmeier, H.; Müller, E.

2006-10-01

We continue our investigations of the magnetorotational collapse of stellar cores by discussing simulations performed with a modified Newtonian gravitational potential that mimics general relativistic effects. The approximate TOV gravitational potential used in our simulations captures several basic features of fully relativistic simulations quite well. In particular, it is able to correctly reproduce the behavior of models that show a qualitative change both of the dynamics and the gravitational wave signal when switching from Newtonian to fully relativistic simulations. For models where the dynamics and gravitational wave signals are already captured qualitatively correctly by a Newtonian potential, the results of the Newtonian and the approximate TOV models differ quantitatively. The collapse proceeds to higher densities with the approximate TOV potential, allowing for a more efficient amplification of the magnetic field by differential rotation. The strength of the saturation fields (˜ 1015 ~ G at the surface of the inner core) is a factor of two to three higher than in Newtonian gravity. Due to the more efficient field amplification, the influence of magnetic fields is considerably more pronounced than in the Newtonian case for some of the models. As in the Newtonian case, sufficiently strong magnetic fields slow down the core's rotation and trigger a secular contraction phase to higher densities. More clearly than in Newtonian models, the collapsed cores of these models exhibit two different kinds of shock generation. Due to magnetic braking, a first shock wave created during the initial centrifugal bounce at subnuclear densities does not suffice for ejecting any mass, and the temporarily stabilized core continues to collapse to supranuclear densities. Another stronger shock wave is generated during the second bounce as the core exceeds nuclear matter density. The gravitational wave signal of these models does not fit into the standard classification. Therefore, in the first paper of this series we introduced a new type of gravitational wave signal, which we call type IV or “magnetic type”. This signal type is more frequent for the approximate relativistic potential than for the Newtonian one. Most of our weak-field models are marginally detectable with the current LIGO interferometer for a source located at a distance of 10 kpc. Strongly magnetized models emit a substantial fraction of their GW power at very low frequencies. A flat spectrum between 10 Hz and ⪉ 100 kHz denotes the generation of a jet-like hydromagnetic outflow.

Laser light triggers increased Raman amplification in the regime of nonlinear Landau damping

PubMed Central

Depierreux, S.; Yahia, V.; Goyon, C.; Loisel, G.; Masson-Laborde, P. -E.; Borisenko, N.; Orekhov, A.; Rosmej, O.; Rienecker, T.; Labaune, C.

2014-01-01

Stimulated Raman backscattering (SRS) has many unwanted effects in megajoule-scale inertially confined fusion (ICF) plasmas. Moreover, attempts to harness SRS to amplify short laser pulses through backward Raman amplification have achieved limited success. In high-temperature fusion plasmas, SRS usually occurs in a kinetic regime where the nonlinear response of the Langmuir wave to the laser drive and its host of complicating factors make it difficult to predict the degree of amplification that can be achieved under given experimental conditions. Here we present experimental evidence of reduced Landau damping with increasing Langmuir wave amplitude and determine its effects on Raman amplification. The threshold for trapping effects to influence the amplification is shown to be very low. Above threshold, the complex SRS dynamics results in increased amplification factors, which partly explains previous ICF experiments. These insights could aid the development of more efficient backward Raman amplification schemes in this regime. PMID:24938756

Parametric amplification in MoS2 drum resonator.

PubMed

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.

Beyond nonlinear saturation of backward Raman amplifiers

DOE PAGES

Barth, Ido; Toroker, Zeev; Balakin, Alexey A.; ...

2016-06-27

Backward Raman amplification is limited by relativistic nonlinear dephasing resulting in saturation of the leading spike of the amplified pulse. We employed pump detuning in order to mitigate the relativistic phase mismatch and to overcome the associated saturation. In an amplified pulse can then be reshaped into a monospike pulse with little precursory power ahead of it, with the maximum intensity increasing by a factor of two. Finally, this detuning can be employed advantageously both in regimes where the group velocity dispersion is unimportant and where the dispersion is important but small.

Beyond nonlinear saturation of backward Raman amplifiers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barth, Ido; Toroker, Zeev; Balakin, Alexey A.

Backward Raman amplification is limited by relativistic nonlinear dephasing resulting in saturation of the leading spike of the amplified pulse. We employed pump detuning in order to mitigate the relativistic phase mismatch and to overcome the associated saturation. In an amplified pulse can then be reshaped into a monospike pulse with little precursory power ahead of it, with the maximum intensity increasing by a factor of two. Finally, this detuning can be employed advantageously both in regimes where the group velocity dispersion is unimportant and where the dispersion is important but small.

A Two-Stream Plasma Electron Microwave Source for High-Power Millimeter Wave Generation. Phase 1

DTIC Science & Technology

1989-03-29

MIT Press, Cambridge, MA, 1963). these findings that strong amplification is possible for repre- ’See, for example, G. E. Guest and D. J. Sigmar , Nucl...stringency of the stability criteria for electrostatic and whistler modes, as fl(z=O, 6, t=O) = -i/2u,(e/m) discussed by Guest and Sigmar [22], and...therein. Function. Academic Press, New York (1961). 1221 GUEST, G.E., SIGMAR , D.J., Nuci. Fusion It1(1971) [271 ABRAMOWITZ, M., STEGUN. I.A. (Eds

Co-registration of ultrasound and frequency-domain photoacoustic radar images and image improvement for tumor detection

NASA Astrophysics Data System (ADS)

Dovlo, Edem; Lashkari, Bahman; Choi, Sung soo Sean; Mandelis, Andreas

2015-03-01

This paper demonstrates the co-registration of ultrasound (US) and frequency domain photoacoustic radar (FD-PAR) images with significant image improvement from applying image normalization, filtering and amplification techniques. Achieving PA imaging functionality on a commercial Ultrasound instrument could accelerate clinical acceptance and use. Experimental results presented demonstrate live animal testing and show enhancements in signal-to-noise ratio (SNR), contrast and spatial resolution. The co-registered image produced from the US and phase PA images, provides more information than both images independently.

Characterization and application of a broad bandwidth oscillator for the HELEN laser facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andrew, J.E.; Stevenson, R.M.; Bett, T.H.

1995-12-31

Preliminary investigations of a potential broad band oscillator for the HELEN laser facility and its proposed upgrade are described. The reasons for the need of broad bandwidth and the choice of commercial technology to achieve it are discussed. The characterization of the device and the diagnostics used for the investigations are described. Small signal amplification of the bandwidth by a glass amplifier was also performed along with investigations of the effect of various bandwidths on the far field beam quality when using random phase plates.

A Continued Study of Optical Sound Generation and Amplification

DTIC Science & Technology

1987-10-31

compared to the output of a PVDF hydrophone as shown in Figure 1.2. Given the inaccuracies in beam size estimates, the agreement between theory and...on this curve which are separated by two regions of constant acoustic amplitude. The first extends from zero to 75 jiJ. The boiling point of CS2 is...the general shape of the experimental curves . Figure 1.5 shows the magnitude of the probe beam deflection versus time for propanol. Hutchins and Tam

Combined histochemical staining, RNA amplification, regional, and single cell cDNA analysis within the hippocampus.

PubMed

Ginsberg, Stephen D; Che, Shaoli

2004-08-01

The use of five histochemical stains (cresyl violet, thionin, hematoxylin & eosin, silver stain, and acridine orange) was evaluated in combination with an expression profiling paradigm that included regional and single cell analyses within the hippocampus of post-mortem human brains and adult mice. Adjacent serial sections of human and mouse hippocampus were labeled by histochemistry or neurofilament immunocytochemistry. These tissue sections were used as starting material for regional and single cell microdissection followed by a newly developed RNA amplification procedure (terminal continuation (TC) RNA amplification) and subsequent hybridization to custom-designed cDNA arrays. Results indicated equivalent levels of global hybridization signal intensity and relative expression levels for individual genes for hippocampi stained by cresyl violet, thionin, and hematoxylin & eosin, and neurofilament immunocytochemistry. Moreover, no significant differences existed between the Nissl stains and neurofilament immunocytochemistry for individual CA1 neurons obtained via laser capture microdissection. In contrast, a marked decrement was observed in adjacent hippocampal sections stained for silver stain and acridine orange, both at the level of the regional dissection and at the CA1 neuron population level. Observations made on the cDNA array platform were validated by real-time qPCR using primers directed against beta-actin and glyceraldehyde-3 phosphate dehydrogenase. Thus, this report demonstrated the utility of using specific Nissl stains, but not stains that bind RNA species directly, in both human and mouse brain tissues at the regional and cellular level for state-of-the-art molecular fingerprinting studies.

Molecular detection and characterization through analysis of the hexon and fiber genes of Adenoviruses causing conjunctivitis in Tunisia, North Africa.

PubMed

Fedaoui, Nadia; Ben Ayed, Narjess; Ben Yahia, Ahlem; Hammami, Walid; Matri, Leila; Nacef, Leila; Triki, Henda

2017-02-01

Human adenoviruses (HAdVs) are common causes of conjunctivitis. This study describes the epidemiological features and characterizes by phylogenetic analysis HAdVs isolated from patients with conjunctivitis in Tunisia, North Africa. Data on out-patients presenting with conjunctivitis during 2 years (2012-2013) were analyzed. Conjunctival swabs obtained from 240 patients were assessed for the presence of HAdVs by PCR amplification on the fiber and hexon genes. Positive PCR products, together with those of nine viral isolates from previous years, were sequenced and analyzed phylogenetically. Conjunctivitis represented 11.5% of all reasons of consultations with a slight increase between mid-March and mid-June. Sixty-five percent of samples (n = 156) revealed positive by at least one PCR test. PCR amplification in the hexon gene was slightly more sensitive as compared to the fiber gene. Genotyping in the two genomic regions gave concordant results for almost all isolates. HAdV-D8 was the most predominant genotype (87.6%) and was detected continuously from 2000 to 2013. Minor co-circulating genotypes including HAdV-E4, HAdV-B3, HAdV-B55, and HAdV-D37 were identified; most of them were detected by amplification in the hexon gene. In conclusion, this work reports molecular data on adenoviral conjunctivitis from a region where such information is scarce and contributes to a better knowledge of the worldwide distribution of causative genotypes. It revealed a predominance and endemic circulation of HAdV-D8, a genotype that was mainly reported from epidemic keratoconjunctivitis. It shows that PCR amplification in two different genomic regions enhances the sensitivity of HAdV detection in clinical samples and the identification of minor genotypes. J. Med. Virol. 89:304-312, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Approaches to Selection and Fitting of Amplification for Infants and Toddlers.

ERIC Educational Resources Information Center

Beauchaine, Kathryn L.

This paper addresses three areas related to amplification for infants and toddlers with hearing impairments: (1) identification issues as they relate to early amplification; (2) selection of amplification; and (3) assessment of aided function. Identification issues discussed include the goal of early identification of hearing loss and the impact…

Linear and exponential TAIL-PCR: a method for efficient and quick amplification of flanking sequences adjacent to Tn5 transposon insertion sites.

PubMed

Jia, Xianbo; Lin, Xinjian; Chen, Jichen

2017-11-02

Current genome walking methods are very time consuming, and many produce non-specific amplification products. To amplify the flanking sequences that are adjacent to Tn5 transposon insertion sites in Serratia marcescens FZSF02, we developed a genome walking method based on TAIL-PCR. This PCR method added a 20-cycle linear amplification step before the exponential amplification step to increase the concentration of the target sequences. Products of the linear amplification and the exponential amplification were diluted 100-fold to decrease the concentration of the templates that cause non-specific amplification. Fast DNA polymerase with a high extension speed was used in this method, and an amplification program was used to rapidly amplify long specific sequences. With this linear and exponential TAIL-PCR (LETAIL-PCR), we successfully obtained products larger than 2 kb from Tn5 transposon insertion mutant strains within 3 h. This method can be widely used in genome walking studies to amplify unknown sequences that are adjacent to known sequences.

Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices

PubMed Central

Zanoli, Laura Maria; Spoto, Giuseppe

2012-01-01

Diagnostic tools for biomolecular detection need to fulfill specific requirements in terms of sensitivity, selectivity and high-throughput in order to widen their applicability and to minimize the cost of the assay. The nucleic acid amplification is a key step in DNA detection assays. It contributes to improving the assay sensitivity by enabling the detection of a limited number of target molecules. The use of microfluidic devices to miniaturize amplification protocols reduces the required sample volume and the analysis times and offers new possibilities for the process automation and integration in one single device. The vast majority of miniaturized systems for nucleic acid analysis exploit the polymerase chain reaction (PCR) amplification method, which requires repeated cycles of three or two temperature-dependent steps during the amplification of the nucleic acid target sequence. In contrast, low temperature isothermal amplification methods have no need for thermal cycling thus requiring simplified microfluidic device features. Here, the use of miniaturized analysis systems using isothermal amplification reactions for the nucleic acid amplification will be discussed. PMID:25587397

Amplification of seismic waves by the Seattle basin, Washington State

USGS Publications Warehouse

Pratt, T.L.; Brocher, T.M.; Weaver, C.S.; Creager, K.C.; Snelson, C.M.; Crosson, R.S.; Miller, K.C.; Trehu, A.M.

2003-01-01

Recordings of the 1999 Mw 7.6 Chi-Chi (Taiwan) earthquake, two local earthquakes, and five blasts show seismic-wave amplification over a large sedimentary basin in the U.S. Pacific Northwest. For weak ground motions from the Chi-Chi earthquake, the Seattle basin amplified 0.2- to 0.8-Hz waves by factors of 8 to 16 relative to bedrock sites west of the basin. The amplification and peak frequency change during the Chi-Chi coda: the initial S-wave arrivals (0-30 sec) had maximum amplifications of 12 at 0.5-0.8 Hz, whereas later arrivals (35-65 sec) reached amplifications of 16 at 0.3-0.5 Hz. Analysis of local events in the 1.0- to 10.0-Hz frequency range show fourfold amplifications for 1.0-Hz weak ground motion over the Seattle basin. Amplifications decrease as frequencies increase above 1.0 Hz, with frequencies above 7 Hz showing lower amplitudes over the basin than at bedrock sites. Modeling shows that resonance in low-impedance deposits forming the upper 550 m of the basin beneath our profile could cause most of the observed amplification, and the larger amplification at later arrival times suggests surface waves also play a substantial role. These results emphasize the importance of shallow deposits in determining ground motions over large basins.

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

PubMed

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.

Assessment of ERBB2 and EGFR gene amplification and protein expression in gastric carcinoma by immunohistochemistry and fluorescence in situ hybridization

PubMed Central

2011-01-01

Background The goal of this study was to investigate ERBB2(HER2) and EGFR gene amplification and protein expression in gastric cancer. Fluorescence in situ hybridization (FISH) and immunohistochemistry were used to analyze ERBB2 and EGFR gene amplification and protein expression in 69 cases of gastric cancer. Results FISH analysis revealed that 20.3% of the cases exhibited ERBB2 gene amplification. Increases in ERBB2 copy number and gene amplification were present in 52.2% of the samples. Expression of the ERBB2 protein was observed in 42.0% of cases. FISH analysis detected EGFR gene amplification in 29.0% of samples. Increases in EGFR copy number and gene amplification occurred in 57.9% of samples, and EGFR protein expression was present in 52.2% of samples. Both ERBB2 and EGFR gene amplification were 3 cases (4.3%), but abnormalities in both ERBB2 and EGFR gene copy number were present 36.2% of samples. ERBB2 and EGFR gene amplification were significantly associated with the depth of tumor invasion (P < 0.05) and lymph node metastasis (P < 0.05), but not with sex, age, or histological type (P > 0.05). Conclusions Our data indicated that ERBB2 and EGFR genetic abnormalities were associated with the prognosis of gastric cancer. Clinical assessment of ERBB2 and EGFR amplification may represent an important factor for the development of personalized treatment programs for gastic cancer. PMID:21689422

MET amplification as a potential therapeutic target in gastric cancer

PubMed Central

Kawakami, Hisato; Okamoto, Isamu; Arao, Tokuzo; Okamoto, Wataru; Matsumoto, Kazuko; Taniguchi, Hirokazu; Kuwata, Kiyoko; Yamaguchi, Haruka; Nishio, Kazuto; Nakagawa, Kazuhiko; Yamada, Yasuhide

2013-01-01

Our aim was to investigate both the prevalence of MET amplification in gastric cancer as well as the potential of this genetic alteration to serve as a therapeutic target in gastric cancer. MET amplification was assessed by initial screening with a PCR-based copy number assay followed by confirmatory FISH analysis in formalin-fixed, paraffin-embedded specimens of gastric cancer obtained at surgery. The effects of MET tyrosine kinase inhibitors (MET-TKIs) in gastric cancer cells with or without MET amplification were also examined. The median MET copy number in 266 cases of gastric cancer was 1.7, with a range of 0.41 to 21.3. We performed FISH analysis for the 15 cases with the highest MET copy numbers. MET amplification was confirmed in the four assessable cases with a MET copy number of at least 4, whereas MET amplification was not detected in those with a gene copy number of <4. The prevalence of MET amplification was thus 1.5% (4 out of 266 cases). Inhibition of MET by MET-TKIs resulted in the induction of apoptosis accompanied by attenuation of downstream MET signaling in gastric cancer cell lines with MET amplification but not in those without this genetic change. MET amplification identifies a small but clinically important subgroup of gastric cancer patients who are likely to respond to MET-TKIs. Furthermore, screening with a PCR-based copy number assay is an efficient way to reduce the number of patients requiring confirmation of MET amplification by FISH analysis. PMID:23327903

Fibroblast growth factor receptor 1 gene amplification is associated with poor survival in patients with resected esophageal squamous cell carcinoma

PubMed Central

Kim, Dae Joon; Lee, Chang-Geol; Hur, Jin; Chung, Hyunsoo; Park, Jun Chul; Jung, Da Hyun; Shin, Sung Kwan; Lee, Sang Kil; Lee, Yong Chan; Kim, Hye Ryun; Moon, Yong Wha; Kim, Joo Hang; Shim, Young Mog; Jewell, Susan S.; Kim, Hyunki; Choi, Yoon-La; Cho, Byoung Chul

2015-01-01

To investigate the frequency and the prognostic impact of fibroblast growth factor receptor 1 (FGFR1) gene amplification in 526 curatively resected esophageal squamous cell carcinoma (ESCC). Using fluorescent in situ hybridization, high amplification was defined by an FGFR1/centromer 8 ratio is ≥ 2.0, or average number of FGFR1 signals/tumor cell nucleus ≥ 6.0, or percentage of tumor cells containing ≥ 15 FGFR1 signals or large cluster in ≥ 10%. Low amplification was defined by ≥ 5 FGFR1 signals in ≥ 50%. FGFR2 and FGFR3 mutations were assessed by direct sequencing in 388 cases and no mutation was detected. High and low amplification were detected in 8.6% and 1.1%, respectively. High FGFR1 amplification had significantly shorter disease-free survival (34.0 vs 158.5 months P=0.019) and overall survival (52.2 vs not reached P=0.022) than low/no amplification group. After adjusting for sex, smoking, stage, histology, and adjuvant treatment, high FGFR1 amplification had a greater risk of recurrence (adjusted hazard ratio [AHR], 1.6; P=0.029) and death (AHR, 1.53; P=0.050). High amplification was significantly higher in current smokers than former and never-smokers (Ptrend<0.001) and increased proportional to smoking dosage. High FGFR1 amplification is a frequent oncogenic alteration and an independent poor prognostic factor in resected ESCC. PMID:25537505

In-Situ Phase Transition Control in the Supercooled State for Robust Active Glass Fiber.

PubMed

Lv, Shichao; Cao, Maoqing; Li, Chaoyu; Li, Jiang; Qiu, Jianrong; Zhou, Shifeng

2017-06-21

The construction of a dopant-activated photonic composite is of great technological importance for various applications, including smart lighting, optical amplification, laser, and optical detection. The bonding arrangement around the introduced dopants largely determines the properties, yet it remains a daunting challenge to manipulate the local state of the matrix (i.e., phase) inside the transparent composite in a controllable manner. Here we demonstrate that the relaxation of the supercooled state enables in-situ phase transition control in glass. Benefiting from the unique local atom arrangement manner, the strategy offers the possibility for simultaneously tuning the chemical environment of the incorporated dopant and engineering the dopant-host interaction. This allows us to effectively activate the dopant with high efficiency (calculated as ∼100%) and profoundly enhance the dopant-host energy-exchange interaction. Our results highlight that the in-situ phase transition control in glass may provide new opportunities for fabrication of unusual photonic materials with intense broadband emission at ∼1100 nm and development of the robust optical detection unit with high compactness and broadband photon-harvesting capability (from X-ray to ultraviolet light).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strizhkov, B. N.; Drobyshev, A. L.; Mikhailovich, V. M.

PCR amplification on a microarray of gel-immobilized primers (microchip) has been developed. One of a pair of PCR primers was immobilized inside a separate microchip polyacrylamide porous gel pad of 0.1 x 0.1 x 0.02 (or 0.04) micron in size and 0.2 (or 0.4) nL in volume. The amplification was carried out simultaneously both in solution covering the microchip array and inside gel pads. Each gel pad contained the immobilized forward primers, while the fluorescently labeled reverse primers, as well as all components of the amplification reaction, diffused into the gel pads from the solution. To increase the amplification efficiency,more » the forward primers were also added into the solution. The kinetics of amplification was measured in real time in parallel for all gel pads with a fluorescent microscope equipped with a charge-coupled device (CCD) camera. The accuracy of the amplification was assessed by using the melting curves obtained for the duplexes formed by the labeled amplification product and the gel-immobilized primers during the amplification process; alternatively, the duplexes were produced by hybridization of the extended immobilized primers with labeled oligonucleotide probes. The on-chip amplification was applied to detect the anthrax toxin genes and the plasmid-borne beta-lactamase gene responsible for bacterial ampicillin resistance. The allele-specific type of PCR amplification was used to identify the Shiga toxin gene and discriminate it from the Shiga-like one. The genomic mutations responsible for rifampicin resistance of the Mycobacterium tuberculosis strains were detected by the same type of PCR amplification of the rpoB gene fragment isolated from sputum of tuberculosis patients. The on-chip PCR amplification has been shown to be a rapid, inexpensive and powerful tool to test genes responsible for bacterial toxin production and drug resistance, as well as to reveal point nucleotide mutations.« less

Amplification of Genomic DNA for Decoy Receptor 3 Predicts Post-Resection Disease Recurrence in Breast Cancer Patients.

PubMed

Kanbayashi, Chizuko; Koyama, Yu; Ichikawa, Hiroshi; Sakata, Eiko; Hasegawa, Miki; Toshikawa, Chie; Manba, Naoko; Ikarashi, Mayuko; Kobayashi, Takashi; Minagawa, Masahiro; Kosugi, Shin-Ichi; Wakai, Toshifumi

2014-02-01

Decoy receptor 3 (DcR3), a member of the tumor necrosis factor receptor (TNFR) superfamily, shows inhibitory effects on Fas-mediated apoptosis. Currently, data are lacking on the correlation between DcR3 and the recurrence of breast cancer. The authors examined DcR3 mRNA expression and genomic amplification in breast cancer, and investigated the effect of DcR3 gene amplification on prognosis of patients. A total of 95 patients formed the basis of the current retrospective study. DcR3 mRNA expression in breast cancer tissues was examined by RNase protection assay and in situ hybridization. DcR3 gene amplification was examined by quantitative polymerase chain reaction. The correlation between DcR3 gene amplification status and clinicopathological factors was examined and also the relationship between DcR3-Amp and relapse and survival. The relative copy numbers of DcR3 genomic DNA correlated significantly with the levels of DcR3 mRNA expression (ρ = 0.755, P = 0.0067). In addition, lymphatic invasion correlated significantly with DcR3 gene amplification (P = 0.012). However, there was no correlation between the remaining clinicopathological factors and DcR3 gene amplification. In the univariate analysis, the recurrence-free survival (RFS) rate of patients who were positive for DcR3 gene amplification was significantly lower than that of patients who were negative for DcR3 gene amplification (P = 0.0271). Multivariate analysis showed that DcR3 gene amplification (P = 0.028) and disease stage (P < 0.001) remained significant independent predictors of RFS. DcR3 gene amplification was significantly correlated with lymphatic invasion, and also DcR3 gene amplification predicts recurrence after resection, which may be an important prognostic factor in breast cancer patients.

Pre-amplification in the context of high-throughput qPCR gene expression experiment.

PubMed

Korenková, Vlasta; Scott, Justin; Novosadová, Vendula; Jindřichová, Marie; Langerová, Lucie; Švec, David; Šídová, Monika; Sjöback, Robert

2015-03-11

With the introduction of the first high-throughput qPCR instrument on the market it became possible to perform thousands of reactions in a single run compared to the previous hundreds. In the high-throughput reaction, only limited volumes of highly concentrated cDNA or DNA samples can be added. This necessity can be solved by pre-amplification, which became a part of the high-throughput experimental workflow. Here, we focused our attention on the limits of the specific target pre-amplification reaction and propose the optimal, general setup for gene expression experiment using BioMark instrument (Fluidigm). For evaluating different pre-amplification factors following conditions were combined: four human blood samples from healthy donors and five transcripts having high to low expression levels; each cDNA sample was pre-amplified at four cycles (15, 18, 21, and 24) and five concentrations (equivalent to 0.078 ng, 0.32 ng, 1.25 ng, 5 ng, and 20 ng of total RNA). Factors identified as critical for a success of cDNA pre-amplification were cycle of pre-amplification, total RNA concentration, and type of gene. The selected pre-amplification reactions were further tested for optimal Cq distribution in a BioMark Array. The following concentrations combined with pre-amplification cycles were optimal for good quality samples: 20 ng of total RNA with 15 cycles of pre-amplification, 20x and 40x diluted; and 5 ng and 20 ng of total RNA with 18 cycles of pre-amplification, both 20x and 40x diluted. We set up upper limits for the bulk gene expression experiment using gene expression Dynamic Array and provided an easy-to-obtain tool for measuring of pre-amplification success. We also showed that variability of the pre-amplification, introduced into the experimental workflow of reverse transcription-qPCR, is lower than variability caused by the reverse transcription step.

Evaluation of whole genome amplified DNA to decrease material expenditure and increase quality.

PubMed

Bækvad-Hansen, Marie; Bybjerg-Grauholm, Jonas; Poulsen, Jesper B; Hansen, Christine S; Hougaard, David M; Hollegaard, Mads V

2017-06-01

The overall aim of this study is to evaluate whole genome amplification of DNA extracted from dried blood spot samples. We wish to explore ways of optimizing the amplification process, while decreasing the amount of input material and inherently the cost. Our primary focus of optimization is on the amount of input material, the amplification reaction volume, the number of replicates and amplification time and temperature. Increasing the quality of the amplified DNA and the subsequent results of array genotyping is a secondary aim of this project. This study is based on DNA extracted from dried blood spot samples. The extracted DNA was subsequently whole genome amplified using the REPLIg kit and genotyped on the PsychArray BeadChip (assessing > 570,000 SNPs genome wide). We used Genome Studio to evaluate the quality of the genotype data by call rates and log R ratios. The whole genome amplification process is robust and does not vary between replicates. Altering amplification time, temperature or number of replicates did not affect our results. We found that spot size i.e. amount of input material could be reduced without compromising the quality of the array genotyping data. We also showed that whole genome amplification reaction volumes can be reduced by a factor of 4, without compromising the DNA quality. Whole genome amplified DNA samples from dried blood spots is well suited for array genotyping and produces robust and reliable genotype data. However, the amplification process introduces additional noise to the data, making detection of structural variants such as copy number variants difficult. With this study, we explore ways of optimizing the amplification protocol in order to reduce noise and increase data quality. We found, that the amplification process was very robust, and that changes in amplification time or temperature did not alter the genotyping calls or quality of the array data. Adding additional replicates of each sample also lead to insignificant changes in the array data. Thus, the amount of noise introduced by the amplification process was consistent regardless of changes made to the amplification protocol. We also explored ways of decreasing material expenditure by reducing the spot size or the amplification reaction volume. The reduction did not affect the quality of the genotyping data.

High-efficiency tri-band quasi-continuous phase gradient metamaterials based on spoof surface plasmon polaritons

PubMed Central

Li, Yongfeng; Ma, Hua; Wang, Jiafu; Pang, Yongqiang; Zheng, Qiqi; Chen, Hongya; Han, Yajuan; Zhang, Jieqiu; Qu, Shaobo

2017-01-01

A high-efficiency tri-band quasi-continuous phase gradient metamaterial is designed and demonstrated based on spoof surface plasmon polaritons (SSPPs). High-efficiency polarizaiton conversion transmission is firstly achieved via tailoring phase differece between the transmisive SSPP and the space wave in orthogonal directions. As an example, a tri-band circular-to-circular (CTC) polarization conversion metamateiral (PCM) was designed by a nonlinearly dispersive phase difference. Using such PCM unit cell, a tri-band quasi-continuous phase gradient metamaterial (PGM) was then realized by virtue of the Pancharatnam-Berry phase. The distribution of the cross-polarization transmission phase along the x-direction is continuous except for two infinitely small intervals near the phases 0° and 360°, and thus the phase gradient has definition at any point along the x-direction. The simulated normalized polarization conversion transmission spectrums together with the electric field distributions for circularly polarized wave and linearly polarized wave demonstrated the high-efficiency anomalous refraction of the quasi-continuous PGM. The experimental verification for the linearly polarized incidence was also provided. PMID:28079185

Intermodulation and harmonic distortion in slow light Microwave Photonic phase shifters based on Coherent Population Oscillations in SOAs.

PubMed

Gasulla, Ivana; Sancho, Juan; Capmany, José; Lloret, Juan; Sales, Salvador

2010-12-06

We theoretically and experimentally evaluate the propagation, generation and amplification of signal, harmonic and intermodulation distortion terms inside a Semiconductor Optical Amplifier (SOA) under Coherent Population Oscillation (CPO) regime. For that purpose, we present a general optical field model, valid for any arbitrarily-spaced radiofrequency tones, which is necessary to correctly describe the operation of CPO based slow light Microwave Photonic phase shifters which comprise an electrooptic modulator and a SOA followed by an optical filter and supplements another recently published for true time delay operation based on the propagation of optical intensities. The phase shifter performance has been evaluated in terms of the nonlinear distortion up to 3rd order, for a modulating signal constituted of two tones, in function of the electrooptic modulator input RF power and the SOA input optical power, obtaining a very good agreement between theoretical and experimental results. A complete theoretical spectral analysis is also presented which shows that under small signal operation conditions, the 3rd order intermodulation products at 2Ω1 + Ω2 and 2Ω2 + Ω1 experience a power dip/phase transition characteristic of the fundamental tones phase shifting operation.

Monolithic Microwave Integrated Circuit (MMIC) Phased Array Demonstrated With ACTS

NASA Technical Reports Server (NTRS)

1996-01-01

Monolithic Microwave Integrated Circuit (MMIC) arrays developed by the NASA Lewis Research Center and the Air Force Rome Laboratory were demonstrated in aeronautical terminals and in mobile or fixed Earth terminals linked with NASA's Advanced Communications Technology Satellite (ACTS). Four K/Ka-band experimental arrays were demonstrated between May 1994 and May 1995. Each array had GaAs MMIC devices at each radiating element for electronic beam steering and distributed power amplification. The 30-GHz transmit array used in uplinks to ACTS was developed by Lewis and Texas Instruments. The three 20-GHz receive arrays used in downlinks from ACTS were developed in cooperation with the Air Force Rome Laboratory, taking advantage of existing Air Force integrated-circuit, active-phased-array development contracts with the Boeing Company and Lockheed Martin Corporation. Four demonstrations, each related to an application of high interest to both commercial and Department of Defense organizations, were conducted. The location, type of link, and the data rate achieved for each of the applications is shown. In one demonstration-- an aeronautical terminal experiment called AERO-X--a duplex voice link between an aeronautical terminal on the Lewis Learjet and ACTS was achieved. Two others demonstrated duplex voice links (and in one case, interactive video links as well) between ACTS and an Army high-mobility, multipurpose wheeled vehicle (HMMWV, or "humvee"). In the fourth demonstration, the array was on a fixed mount and was electronically steered toward ACTS. Lewis served as project manager for all demonstrations and as overall system integrator. Lewis engineers developed the array system including a controller for open-loop tracking of ACTS during flight and HMMWV motion, as well as a laptop data display and recording system used in all demonstrations. The Jet Propulsion Laboratory supported the AERO-X program, providing elements of the ACTS Mobile Terminal. The successful performance of experimental, proof-of-concept MMIC K/Ka-band arrays developed with U.S. industry in field demonstrations with ACTS indicates that high density MMIC integration at 20 and 30 GHz is indeed feasible. The successful development and demonstration of the MMIC array systems was possible only because of significant intergovernmental and Government/industry cooperation and the high level of teamwork within Lewis. The results provide a strong incentive for continuing the focused development of MMIC-array technology for satellite communications applications, with emphasis on packaging and cost issues, and for continuing the planning and conducting of other appropriate demonstrations or experiments of phased-array technology with ACTS. Given the present pressures on reducing funding for research and development in Government and industry, the extent to which this can be continued in a cooperative manner will determine whether MMIC array technology will make the transition from the proof-of-concept level to the operational system level.

40 CFR 86.1915 - What are the requirements for Phase 1 and Phase 2 testing?

Code of Federal Regulations, 2011 CFR

2011-07-01

... (CONTINUED) AIR PROGRAMS (CONTINUED) CONTROL OF EMISSIONS FROM NEW AND IN-USE HIGHWAY VEHICLES AND ENGINES (CONTINUED) Manufacturer-Run In-Use Testing Program for Heavy-Duty Diesel Engines § 86.1915 What are the requirements for Phase 1 and Phase 2 testing? For all selected engine families, you must do the following: (a...

40 CFR 86.1915 - What are the requirements for Phase 1 and Phase 2 testing?

Code of Federal Regulations, 2013 CFR

2013-07-01

... (CONTINUED) AIR PROGRAMS (CONTINUED) CONTROL OF EMISSIONS FROM NEW AND IN-USE HIGHWAY VEHICLES AND ENGINES (CONTINUED) Manufacturer-Run In-Use Testing Program for Heavy-Duty Diesel Engines § 86.1915 What are the requirements for Phase 1 and Phase 2 testing? For all selected engine families, you must do the following: (a...

40 CFR 86.1915 - What are the requirements for Phase 1 and Phase 2 testing?

Code of Federal Regulations, 2012 CFR

2012-07-01

... (CONTINUED) AIR PROGRAMS (CONTINUED) CONTROL OF EMISSIONS FROM NEW AND IN-USE HIGHWAY VEHICLES AND ENGINES (CONTINUED) Manufacturer-Run In-Use Testing Program for Heavy-Duty Diesel Engines § 86.1915 What are the requirements for Phase 1 and Phase 2 testing? For all selected engine families, you must do the following: (a...

40 CFR 86.1915 - What are the requirements for Phase 1 and Phase 2 testing?

Code of Federal Regulations, 2010 CFR

2010-07-01

... (CONTINUED) AIR PROGRAMS (CONTINUED) CONTROL OF EMISSIONS FROM NEW AND IN-USE HIGHWAY VEHICLES AND ENGINES (CONTINUED) Manufacturer-Run In-Use Testing Program for Heavy-Duty Diesel Engines § 86.1915 What are the requirements for Phase 1 and Phase 2 testing? For all selected engine families, you must do the following: (a...

Effects of local geology on ground motion in the San Francisco Bay region, California—A continued study

USGS Publications Warehouse

Gibbs, James F.; Borcherdt, Roger D.

1974-01-01

Measurements of ground motion generated by nuclear explosions in Nevada have been completed for 99 locations in the San Francisco Bay region, California. The seismograms, Fourier amplitude spectra, spectral amplification curves for the signal, and the Fourier amplitude spectra of the seismic noise are presented for 60 locations. Analog amplifications, based on the maximum signal amplitude, are computed for an additional 39 locations. The recordings of the nuclear explosions show marked amplitude variations which are consistently related to the local geologic conditions of the recording site. The average spectral amplifications observed for vertical and horizontal ground motions are, respectively: (1, 1) for granite, (1.5, 1.6) for the Franciscan Formation, (2.3, 2.3), for other pre-Tertiary and Tertiary rocks, (3.0, 2.7) for the Santa Clara Formation, (3.3, 4.4) for older bay sediments, and (3.7, 11.3) for younger bay mud. Spectral amplification curves define predominant ground frequencies for younger bay mud sites and for some older bay sediment sites. The predominant frequencies for most sites were not clearly defined by the amplitude spectra computed from the seismic background noise. The intensities ascribed to various sites in the San Francisco Bay region for the California earthquake of April 18, 1906, are strongly dependent on distance from the zone of surface faulting and the geological character of the ground. Considering only those sites (approximately one square city block in size) for which there is good evidence for the degree of ascribed intensity, the intensities for 917 sites on Franciscan rocks generally decrease with the logarithm of distance as Intensity = 2.69 - 1.90 log (Distance Km). For sites on other geologic units, intensity increments, derived from this empirical rela.tion, correlate strongly with the Average Horizontal Spectral Amplifications (MISA) according to the empirical relation Intensity Increment= 0.27 + 2.70 log(AHSA). Average intensity increments predicted for various geologic units are -0.3 for granite, 0.2 for Franciscan Formation, 0.6 for other pre-Tertiary, Tertiary bedrock, 0.8 for Santa Clara Formation, 1 .3 for older bay sediments, 2.4 for younger bay mud. These empirical relations, together with detailed geologic maps, delineate areas in the San Francisco Bay region of potentially high intensity from future earthquakes on either the San Andreas fault or the Hayward fault.

Dual Coding Theory Explains Biphasic Collective Computation in Neural Decision-Making.

PubMed

Daniels, Bryan C; Flack, Jessica C; Krakauer, David C

2017-01-01

A central question in cognitive neuroscience is how unitary, coherent decisions at the whole organism level can arise from the distributed behavior of a large population of neurons with only partially overlapping information. We address this issue by studying neural spiking behavior recorded from a multielectrode array with 169 channels during a visual motion direction discrimination task. It is well known that in this task there are two distinct phases in neural spiking behavior. Here we show Phase I is a distributed or incompressible phase in which uncertainty about the decision is substantially reduced by pooling information from many cells. Phase II is a redundant or compressible phase in which numerous single cells contain all the information present at the population level in Phase I, such that the firing behavior of a single cell is enough to predict the subject's decision. Using an empirically grounded dynamical modeling framework, we show that in Phase I large cell populations with low redundancy produce a slow timescale of information aggregation through critical slowing down near a symmetry-breaking transition. Our model indicates that increasing collective amplification in Phase II leads naturally to a faster timescale of information pooling and consensus formation. Based on our results and others in the literature, we propose that a general feature of collective computation is a "coding duality" in which there are accumulation and consensus formation processes distinguished by different timescales.

Dual Coding Theory Explains Biphasic Collective Computation in Neural Decision-Making

PubMed Central

Daniels, Bryan C.; Flack, Jessica C.; Krakauer, David C.

2017-01-01

A central question in cognitive neuroscience is how unitary, coherent decisions at the whole organism level can arise from the distributed behavior of a large population of neurons with only partially overlapping information. We address this issue by studying neural spiking behavior recorded from a multielectrode array with 169 channels during a visual motion direction discrimination task. It is well known that in this task there are two distinct phases in neural spiking behavior. Here we show Phase I is a distributed or incompressible phase in which uncertainty about the decision is substantially reduced by pooling information from many cells. Phase II is a redundant or compressible phase in which numerous single cells contain all the information present at the population level in Phase I, such that the firing behavior of a single cell is enough to predict the subject's decision. Using an empirically grounded dynamical modeling framework, we show that in Phase I large cell populations with low redundancy produce a slow timescale of information aggregation through critical slowing down near a symmetry-breaking transition. Our model indicates that increasing collective amplification in Phase II leads naturally to a faster timescale of information pooling and consensus formation. Based on our results and others in the literature, we propose that a general feature of collective computation is a “coding duality” in which there are accumulation and consensus formation processes distinguished by different timescales. PMID:28634436

EGFR Gene Amplification and KRAS Mutation Predict Response to Combination Targeted Therapy in Metastatic Colorectal Cancer.

PubMed

Khan, Sajid A; Zeng, Zhaoshi; Shia, Jinru; Paty, Philip B

2017-07-01

Genetic variability in KRAS and EGFR predicts response to cetuximab in irinotecan refractory colorectal cancer. Whether these markers or others remain predictive in combination biologic therapies including bevacizumab is unknown. We identified predictive biomarkers from patients with irinotecan refractory metastatic colorectal cancer treated with cetuximab plus bevacizumab. Patients who received cetuximab plus bevacizumab for irinotecan refractory colorectal cancer in either of two Phase II trials conducted were identified. Tumor tissue was available for 33 patients. Genomic DNA was extracted and used for mutational analysis of KRAS, BRAF, and p53 genes. Fluorescence in situ hybridization was performed to assess EGFR copy number. The status of single genes and various combinations were tested for association with response. Seven of 33 patients responded to treatment. KRAS mutations were found in 14/33 cases, and 0 responded to treatment (p = 0.01). EGFR gene amplification was seen in 3/33 of tumors and in every case was associated with response to treatment (p < 0.001). TP53 and BRAF mutations were found in 18/33 and 0/33 tumors, respectively, and there were no associations with response to either gene. EGFR gene amplification and KRAS mutations are predictive markers for patients receiving combination biologic therapy of cetuximab plus bevacizumab for metastatic colorectal cancer. One marker or the other is present in the tumor of half of all patients allowing treatment response to be predicted with a high degree of certainty. The role for molecular markers in combination biologic therapy seems promising.

Distortion of liquid film discharging from twin-fluid atomizer

NASA Astrophysics Data System (ADS)

Mehring, C.; Sirignano, W. A.

2001-11-01

The nonlinear distortion and disintegration of a thin liquid film exiting from a two-dimensional twin-fluid atomizer is analyzed numerically. Pulsed gas jets impacting on both sides of the discharging liquid film at the atomizer exit generate dilational and/or sinuous deformations of the film. Both liquid phase and gas phase are inviscid and incompressible. For the liquid phase the so-called long-wavelength approximation is employed yielding a system of unsteady one-dimensional equations for the planar film. Solution of Laplace's equation for the velocity potential yields the gas-phase velocity field on both sides of the liquid stream. Coupling between both phases is described through kinematic and dynamic boundary conditions at the phase interfaces, and includes the solution of the unsteady Bernoulli equation to determine the gas-phase pressure along the interfaces. Both gas- and liquid-phase equations are solved simultaneously. Solution of Laplace's equation for the gas streams is obtained by means of a boundary-element method. Numerical solutions for the liquid phase use the Lax-Wendroff method with Richtmyer splitting. Sheet distortion resulting from the stagnation pressure of the impacting gas jets and subsequent disturbance amplification due to Kelvin-Helmholtz effects are studied for various combinations of gas-pulse timing, gas-jet impact angles, gas-to-liquid-density ratio, liquid-phase Weber number and gas-jet-to-liquid-jet-momentum ratio. Dilational and sinuous oscillations of the liquid are examined and film pinch-off is predicted.

New Mexico Liquid Metal αω -dynamo experiment: Most Recent Progress

NASA Astrophysics Data System (ADS)

Si, Jiahe; Sonnenfeld, Richard; Colgate, Art; Li, Hui

2017-10-01

The goal of the New Mexico Liquid Metal αω -dynamo experiment is to demonstrate a galactic dynamo can be generated through two phases, the ω-phase and α-phase by two semi-coherent flows in laboratory. We have demonstrated an 8-fold poloidal-to-toroidal flux amplification from differential rotation (the ω-effect) by minimizing turbulence in our apparatus. To demonstrate the α-effect, major upgrades are needed. The upgrades include building a helicity injection facility, mounting new 100hp motors and new sensors, designing a new data acquisition system capable of transmitting data from about 80 sensors in a high speed rotating frame with an overall 200kS/sec sampling rate. We hope the upgrade can be utilized to answer the question of whether a self-sustaining αω -dynamo can be implemented with a realistic lab fluid flow field, as well as to obtain more details to understand dynamo action in highly turbulent Couette flow.

Light-melt adhesive based on dynamic carbon frameworks in a columnar liquid-crystal phase

NASA Astrophysics Data System (ADS)

Saito, Shohei; Nobusue, Shunpei; Tsuzaka, Eri; Yuan, Chunxue; Mori, Chigusa; Hara, Mitsuo; Seki, Takahiro; Camacho, Cristopher; Irle, Stephan; Yamaguchi, Shigehiro

2016-07-01

Liquid crystal (LC) provides a suitable platform to exploit structural motions of molecules in a condensed phase. Amplification of the structural changes enables a variety of technologies not only in LC displays but also in other applications. Until very recently, however, a practical use of LCs for removable adhesives has not been explored, although a spontaneous disorganization of LC materials can be easily triggered by light-induced isomerization of photoactive components. The difficulty of such application derives from the requirements for simultaneous implementation of sufficient bonding strength and its rapid disappearance by photoirradiation. Here we report a dynamic molecular LC material that meets these requirements. Columnar-stacked V-shaped carbon frameworks display sufficient bonding strength even during heating conditions, while its bonding ability is immediately lost by a light-induced self-melting function. The light-melt adhesive is reusable and its fluorescence colour reversibly changes during the cycle, visualizing the bonding/nonbonding phases of the adhesive.

Experimental observation of the luminescence flash at the collapse phase of a bubble produced by pulsed discharge in water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Yifan; Zhang, Liancheng; Zhu, Xinlei

2015-11-02

This letter presents an experimental observation of luminescence flash at the collapse phase of an oscillating bubble produced by a pulsed discharge in water. According to the high speed records, the flash lasts around tens of microseconds, which is much longer than the lifetime of laser and ultrasound induced luminescence flashes in nanoseconds and picoseconds, respectively. The pulse width of temperature waveform and minimum radius calculated at the collapse phase also show that the thermodynamic and dynamic signatures of the bubbles in this work are much larger than those of ultrasound and laser induced bubbles both in time and spacemore » scales. However, the peak temperature at the point of collapse is close to the results of ultrasound and laser induced bubbles. This result provides another possibility for accurate emission spectrum measurement other than amplification of the emitted light, such as increasing laser energy or sound energy or substituting water with sulphuric acid.« less

Amplification of a bi-phase shift-key modulated signal by a mm-wave FEL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prosnitz, D.; Scharlemann, E.T.; Sheaffer, M.K.

Bi-phase shift keying (BPSK) is a modulation scheme used in communications and radar in which the phase of a transmitted rf signal is switched in a coded pattern between discrete values differing by {pi} radians. The transmitted information rate (in communications) or resolution (in imaging radar) depends on the rate at which the transmitted signal can be modulated. Modulation rates of greater than 1 GHz are generally desired. Although the instantaneous gain bandwidth of a mm-wave FEL amplifier can be much greater than 10 GHz, slippage may limit the BPSK modulation rate that can be amplified. Qualitative slippage arguments wouldmore » limit the modulation rate to relatively low values; nevertheless, simulations with a time-dependent FEL code (GINGER) indicate that rates of 2 GHz or more are amplified without much loss in modulation integrity. In this paper we describe the effects of slippage in the simulations and discuss the limits of simple arguments.« less