An entangled-light-emitting diode.

PubMed

Salter, C L; Stevenson, R M; Farrer, I; Nicoll, C A; Ritchie, D A; Shields, A J

2010-06-03

An optical quantum computer, powerful enough to solve problems so far intractable using conventional digital logic, requires a large number of entangled photons. At present, entangled-light sources are optically driven with lasers, which are impractical for quantum computing owing to the bulk and complexity of the optics required for large-scale applications. Parametric down-conversion is the most widely used source of entangled light, and has been used to implement non-destructive quantum logic gates. However, these sources are Poissonian and probabilistically emit zero or multiple entangled photon pairs in most cycles, fundamentally limiting the success probability of quantum computational operations. These complications can be overcome by using an electrically driven on-demand source of entangled photon pairs, but so far such a source has not been produced. Here we report the realization of an electrically driven source of entangled photon pairs, consisting of a quantum dot embedded in a semiconductor light-emitting diode (LED) structure. We show that the device emits entangled photon pairs under d.c. and a.c. injection, the latter achieving an entanglement fidelity of up to 0.82. Entangled light with such high fidelity is sufficient for application in quantum relays, in core components of quantum computing such as teleportation, and in entanglement swapping. The a.c. operation of the entangled-light-emitting diode (ELED) indicates its potential function as an on-demand source without the need for a complicated laser driving system; consequently, the ELED is at present the best source on which to base future scalable quantum information applications.

Weak nanoscale chaos and anomalous relaxation in DNA

NASA Astrophysics Data System (ADS)

Mazur, Alexey K.

2017-06-01

Anomalous nonexponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA base pairs exhibits a slow power-law relaxation attributable to weak Hamiltonian chaos, with parameters similar to experimental data. Here, the relationship is studied between this motion and spectroscopic signals measured in DNA with a small molecular photoprobe inserted into the base-pair stack. To this end, the earlier computational approach in combination with an analytical theory is applied to the experimental DNA fragment. It is found that the intensity of breathing dynamics is strongly increased in the internal base pairs that flank the photoprobe, with anomalous relaxation quantitatively close to that in terminal base pairs. A physical mechanism is proposed to explain the coupling between the relaxation of base-pair breathing and the experimental response signal. It is concluded that the algebraic relaxation observed experimentally is very likely a manifestation of weakly chaotic dynamics of hydrogen-bond breathing in the base pairs stacked to the photoprobe and that the weak nanoscale chaos can represent an ubiquitous hidden source of nonexponential relaxation in ultrafast spectroscopy.

Weak nanoscale chaos and anomalous relaxation in DNA.

PubMed

Mazur, Alexey K

2017-06-01

Anomalous nonexponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA base pairs exhibits a slow power-law relaxation attributable to weak Hamiltonian chaos, with parameters similar to experimental data. Here, the relationship is studied between this motion and spectroscopic signals measured in DNA with a small molecular photoprobe inserted into the base-pair stack. To this end, the earlier computational approach in combination with an analytical theory is applied to the experimental DNA fragment. It is found that the intensity of breathing dynamics is strongly increased in the internal base pairs that flank the photoprobe, with anomalous relaxation quantitatively close to that in terminal base pairs. A physical mechanism is proposed to explain the coupling between the relaxation of base-pair breathing and the experimental response signal. It is concluded that the algebraic relaxation observed experimentally is very likely a manifestation of weakly chaotic dynamics of hydrogen-bond breathing in the base pairs stacked to the photoprobe and that the weak nanoscale chaos can represent an ubiquitous hidden source of nonexponential relaxation in ultrafast spectroscopy.

Joint spectral characterization of photon-pair sources

NASA Astrophysics Data System (ADS)

Zielnicki, Kevin; Garay-Palmett, Karina; Cruz-Delgado, Daniel; Cruz-Ramirez, Hector; O'Boyle, Michael F.; Fang, Bin; Lorenz, Virginia O.; U'Ren, Alfred B.; Kwiat, Paul G.

2018-06-01

The ability to determine the joint spectral properties of photon pairs produced by the processes of spontaneous parametric downconversion (SPDC) and spontaneous four-wave mixing (SFWM) is crucial for guaranteeing the usability of heralded single photons and polarization-entangled pairs for multi-photon protocols. In this paper, we compare six different techniques that yield either a characterization of the joint spectral intensity or of the closely related purity of heralded single photons. These six techniques include: (i) scanning monochromator measurements, (ii) a variant of Fourier transform spectroscopy designed to extract the desired information exploiting a resource-optimized technique, (iii) dispersive fibre spectroscopy, (iv) stimulated-emission-based measurement, (v) measurement of the second-order correlation function ? for one of the two photons, and (vi) two-source Hong-Ou-Mandel interferometry. We discuss the relative performance of these techniques for the specific cases of a SPDC source designed to be factorable and SFWM sources of varying purity, and compare the techniques' relative advantages and disadvantages.

Real-time spectral characterization of a photon pair source using a chirped supercontinuum seed.

PubMed

Erskine, Jennifer; England, Duncan; Kupchak, Connor; Sussman, Benjamin

2018-02-15

Photon pair sources have wide ranging applications in a variety of quantum photonic experiments and protocols. Many of these protocols require well controlled spectral correlations between the two output photons. However, due to low cross-sections, measuring the joint spectral properties of photon pair sources has historically been a challenging and time-consuming task. Here, we present an approach for the real-time measurement of the joint spectral properties of a fiber-based four wave mixing source. We seed the four wave mixing process using a broadband chirped pulse, studying the stimulated process to extract information regarding the spontaneous process. In addition, we compare stimulated emission measurements with the spontaneous process to confirm the technique's validity. Joint spectral measurements have taken many hours historically and several minutes with recent techniques. Here, measurements have been demonstrated in 5-30 s depending on resolution, offering substantial improvement. Additional benefits of this approach include flexible resolution, large measurement bandwidth, and reduced experimental overhead.

Generation and analysis of correlated pairs of photons on board a nanosatellite

NASA Astrophysics Data System (ADS)

Chandrasekara, R.; Tang, Z.; Tan, Y. C.; Cheng, C.; Sha, L.; Hiang, G. C.; Oi, D.; Ling, A.

2016-10-01

Progress in quantum computers and their threat to conventional public key infrastructure is driving new forms of encryption. Quantum Key Distribution (QKD) using entangled photons is a promising approach. A global QKD network can be achieved using satellites equipped with optical links. Despite numerous proposals, actual experimental work demonstrating relevant entanglement technology in space is limited due to the prohibitive cost of traditional satellite development. To make progress, we have designed a photon pair source that can operate on modular spacecraft called CubeSats. We report the in-orbit operation of the photon pair source on board an orbiting CubeSat and demonstrate pair generation and polarisation correlation under space conditions. The in-orbit polarisation correlations are compatible with ground-based tests, validating our design. This successful demonstration is a major experimental milestone towards a space-based quantum network. Our approach provides a cost-effective method for proving the space-worthiness of critical components used in entangled photon technology. We expect that it will also accelerate efforts to probe the overlap between quantum and relativistic models of physics.

The analysis of photon pair source at telecom wavelength based on the BBO crystal (Conference Presentation)

NASA Astrophysics Data System (ADS)

Gajewski, Andrzej; Kolenderski, Piotr L.

2016-10-01

There are several problems that must be solved in order to increase the distance of quantum communication protocols based on photons as an information carriers. One of them is the dispersion, whose effects can be minimized by engineering spectral properties of transmitted photons. In particular, it is expected that positively correlated photon pairs can be very useful. We present the full characterization of a source of single photon pairs at a telecom wavelength based on type II spontaneous parametric down conversion (SPDC) process in a beta-barium borate (BBO) crystal. In the type II process, a pump photon, which is polarized extraordinarily, splits in a nonlinear medium into signal and idler photons, which are polarized perpendicularly to each other. In order for the process to be efficient a phase matching condition must be fulfilled. These conditions originate from momentum and energy conservation rules and put severe restrictions on source parameters. Seemingly, these conditions force the photon pair to be negatively correlated in their spectral domain. However, it is possible to achieve positive correlation for pulsed pumping. The experimentally available degrees of freedom of a source are the width of the pumping beam, the collected modes' widths, the length of the nonlinear crystal and the duration of the pumping pulse. In our numerical model we use the following figures of merit: the pair production rate, the efficiency of photon coupling into a single mode fiber, the spectral correlation of the coupled photon pair. The last one is defined as the Pearson correlation parameter for a joint spectral distribution. The aim here is to find the largest positive spectral correlation and the highest coupling efficiency. By resorting to the numerical model Ref. [1] we showed in Ref. [2], that by careful adjustment of the pump's and the collected modes' characteristics, one can optimize any of the source's parameters. Our numerical outcomes conform to the experimental results presented in Refs [3,4]. Here we investigate typical, experimentally available source parameters: the widths of the pump beam and collected modes ranging from 20μm to 500m, the crystal length ranging from 1mm to 7.5mm while the pulse duration is set to 50fs, 100fs or 150fs. We achieve the correlation coefficient value as high as approximately 0.8, or - for different values of parameters - coupling efficiency equal to 0.76.

Qubit entanglement between ring-resonator photon-pair sources on a silicon chip

PubMed Central

Silverstone, J. W.; Santagati, R.; Bonneau, D.; Strain, M. J.; Sorel, M.; O'Brien, J. L.; Thompson, M. G.

2015-01-01

Entanglement—one of the most delicate phenomena in nature—is an essential resource for quantum information applications. Scalable photonic quantum devices must generate and control qubit entanglement on-chip, where quantum information is naturally encoded in photon path. Here we report a silicon photonic chip that uses resonant-enhanced photon-pair sources, spectral demultiplexers and reconfigurable optics to generate a path-entangled two-qubit state and analyse its entanglement. We show that ring-resonator-based spontaneous four-wave mixing photon-pair sources can be made highly indistinguishable and that their spectral correlations are small. We use on-chip frequency demultiplexers and reconfigurable optics to perform both quantum state tomography and the strict Bell-CHSH test, both of which confirm a high level of on-chip entanglement. This work demonstrates the integration of high-performance components that will be essential for building quantum devices and systems to harness photonic entanglement on the large scale. PMID:26245267

SeaQuaKE: Sea-optimized Quantum Key Exchange

DTIC Science & Technology

2015-01-01

of photon pairs in both polarization [3] and time-bin [4] degrees of freedom simultaneously. Entanglement analysis components in both the...greater throughput per entangled photon pair compared to alternative sources that encode in only a Photon -pair source Time-bin entanglement ...Polarization Entanglement & Pair Generation Hyperentangled Photon Pair Source •Wavelength availability • Power • Pulse rate Time-bin Mux • Waveguide vs

Studies of Positron Generation from Ultraintense Laser-Matter Interactions

NASA Astrophysics Data System (ADS)

Williams, Gerald Jackson

Laser-produced pair jets possess unique characteristics that offer great potential for their use in laboratory-astrophysics experiments to study energetic phenomenon such as relativistic shock accelerations. High-flux, high-energy positron sources may also be used to study relativistic pair plasmas and useful as novel diagnostic tools for high energy density conditions. Copious amounts of positrons are produced with MeV energies from directly irradiating targets with ultraintense lasers where relativistic electrons, accelerated by the laser field, drive positron-electron pair production. Alternatively, laser wakefield accelerated electrons can produce pairs by the same mechanisms inside a secondary converter target. This dissertation describes a series of novel experiments that investigate the characteristics and scaling of pair production from ultraintense lasers, which are designed to establish a robust platform for laboratory-based relativistic pair plasmas. Results include a simple power-law scaling to estimate the effective positron yield for elemental targets for any Maxwellian electron source, typical of direct laser-target interactions. To facilitate these measurements, a solenoid electromagnetic coil was constructed to focus emitted particles, increasing the effective collection angle of the detector and enabling the investigation of pair production from thin targets and low-Z materials. Laser wakefield electron sources were also explored as a compact, high repetition rate platform for the production of high energy pairs with potential applications to the creation of charge-neutral relativistic pair plasmas. Plasma accelerators can produce low-divergence electron beams with energies approaching a GeV at Hz frequencies. It was found that, even for high-energy positrons, energy loss and scattering mechanisms in the target create a fundamental limit to the divergence and energy spectrum of the emitted positrons. The potential future application of laser-generated pairs was considered by exploring the feasibility of radiographing an imploding inertial confinement fusion capsule at ignition- relevant conditions. For an in-flight areal density of 0.02-0.2 g/cm2, currently available positron sources can make density and spatial measurements of deuterium-tritium fuel cores where additional complications of full-scale experiments are expected to reduce the measurement sensitivity.

Highly efficient heralded single-photon source for telecom wavelengths based on a PPLN waveguide.

PubMed

Bock, Matthias; Lenhard, Andreas; Chunnilall, Christopher; Becher, Christoph

2016-10-17

We present the realization of a highly efficient photon pair source based on spontaneous parametric downconversion (SPDC) in a periodically poled lithium niobate (PPLN) ridge waveguide. The source is suitable for long distance quantum communication applications as the photon pairs are located at the centers of the telecommunication O- and C- band at 1312 nm and 1557 nm. The high efficiency is confirmed by a conversion efficiency of 4 × 10^-6 - which is to our knowledge among the highest conversion efficiencies reported so far - and a heralding efficiency of 64.1 ± 2.1%. The heralded single-photon properties are confirmed by the measurement of the photon statistics with a Click/No-Click method as well as the heralded g⁽²⁾-function. A minimum value for g⁽²⁾(0) of 0.001 ± 0.0003 indicating clear antibunching has been observed.

High yield and ultrafast sources of electrically triggered entangled-photon pairs based on strain-tunable quantum dots.

PubMed

Zhang, Jiaxiang; Wildmann, Johannes S; Ding, Fei; Trotta, Rinaldo; Huo, Yongheng; Zallo, Eugenio; Huber, Daniel; Rastelli, Armando; Schmidt, Oliver G

2015-12-01

Triggered sources of entangled photon pairs are key components in most quantum communication protocols. For practical quantum applications, electrical triggering would allow the realization of compact and deterministic sources of entangled photons. Entangled-light-emitting-diodes based on semiconductor quantum dots are among the most promising sources that can potentially address this task. However, entangled-light-emitting-diodes are plagued by a source of randomness, which results in a very low probability of finding quantum dots with sufficiently small fine structure splitting for entangled-photon generation (∼10(-2)). Here we introduce strain-tunable entangled-light-emitting-diodes that exploit piezoelectric-induced strains to tune quantum dots for entangled-photon generation. We demonstrate that up to 30% of the quantum dots in strain-tunable entangled-light-emitting-diodes emit polarization-entangled photons. An entanglement fidelity as high as 0.83 is achieved with fast temporal post selection. Driven at high speed, that is 400 MHz, strain-tunable entangled-light-emitting-diodes emerge as promising devices for high data-rate quantum applications.

Paired Learners' Verbalised Strategies for Determining Grammatical Correctness: A Turn-Based System for Coding Metatalk

ERIC Educational Resources Information Center

Ishii, David N.

2011-01-01

The purpose of this paper is to explore the use of a new coding system that incorporates the various types of metatalk that occurred during paired learners' engagement in a consciousness-raising task. On the basis of previous studies, metalanguage (e.g. with or without terminology), knowledge sources (e.g. intuition), and verbalisation strategies…

Free-space quantum key distribution with a high generation rate potassium titanyl phosphate waveguide photon-pair source

NASA Astrophysics Data System (ADS)

Wilson, Jeffrey D.; Chaffee, Dalton W.; Wilson, Nathaniel C.; Lekki, John D.; Tokars, Roger P.; Pouch, John J.; Roberts, Tony D.; Battle, Philip R.; Floyd, Bertram; Lind, Alexander J.; Cavin, John D.; Helmick, Spencer R.

2016-09-01

A high generation rate photon-pair source using a dual element periodically-poled potassium titanyl phosphate (PP KTP) waveguide is described. The fully integrated photon-pair source consists of a 1064-nm pump diode laser, fiber-coupled to a dual element waveguide within which a pair of 1064-nm photons are up-converted to a single 532-nm photon in the first stage. In the second stage, the 532-nm photon is down-converted to an entangled photon-pair at 800 nm and 1600 nm which are fiber-coupled at the waveguide output. The photon-pair source features a high pair generation rate, a compact power-efficient package, and continuous wave (CW) or pulsed operation. This is a significant step towards the long term goal of developing sources for high-rate Quantum Key Distribution (QKD) to enable Earth-space secure communications. Characterization and test results are presented. Details and preliminary results of a laboratory free space QKD experiment with the B92 protocol are also presented.

Free-Space Quantum Key Distribution with a High Generation Rate Potassium Titanyl Phosphate Waveguide Photon-Pair Source

NASA Technical Reports Server (NTRS)

Wilson, Jeffrey D.; Chaffee, Dalton W.; Wilson, Nathaniel C.; Lekki, John D.; Tokars, Roger P.; Pouch, John J.; Roberts, Tony D.; Battle, Philip; Floyd, Bertram M.; Lind, Alexander J.;

High-Efficiency Plug-and-Play Source of Heralded Single Photons

NASA Astrophysics Data System (ADS)

Montaut, Nicola; Sansoni, Linda; Meyer-Scott, Evan; Ricken, Raimund; Quiring, Viktor; Herrmann, Harald; Silberhorn, Christine

2017-08-01

Reliable generation of single photons is of key importance for fundamental physical experiments and to demonstrate quantum protocols. Waveguide-based photon-pair sources have shown great promise in this regard due to their large spectral tunability, high generation rates, and long temporal coherence of the photon wave packet. However, integrating such sources with fiber-optic networks often results in a strong degradation of performance. We answer this challenge by presenting an alignment-free source of photon pairs in the telecommunications band that maintains heralding efficiency >50 % even after fiber pigtailing, photon separation, and pump suppression. The source combines this outstanding performance in heralding efficiency with a compact, stable, and easy-to-use "plug-and-play" package: one simply connects a laser to the input and detectors to the output, and the source is ready to use. This high performance can be achieved even outside the lab without the need for alignment which makes the source extremely useful for any experiment or demonstration needing heralded single photons.

The use of a multidimensional space for fusion candidate representation in a maritime domain awareness application

NASA Astrophysics Data System (ADS)

Lefebvre, Eric; Helleur, Christopher; Kashyap, Nathan

2008-03-01

Maritime surveillance of coastal regions requires operational staff to integrate a large amount of information from a variety of military and civilian sources. The diverse nature of the information sources makes complete automation difficult. The volume of vessels tracked and the number of sources makes it difficult for the limited operation centre staff to fuse all the information manually within a reasonable timeframe. In this paper, a conceptual decision space is proposed to provide a framework for automating the process of operators integrating the sources needed to maintain Maritime Domain Awareness. The decision space contains all potential pairs of ship tracks that are candidates for fusion. The location of the candidate pairs in this defined space depends on the value of the parameters used to make a decision. In the application presented, three independent parameters are used: the source detection efficiency, the geo-feasibility, and the track quality. One of three decisions is applied to each candidate track pair based on these three parameters: 1. to accept the fusion, in which case tracks are fused in one track, 2. to reject the fusion, in which case the candidate track pair is removed from the list of potential fusion, and 3. to defer the fusion, in which case no fusion occurs but the candidate track pair remains in the list of potential fusion until sufficient information is provided. This paper demonstrates in an operational setting how a proposed conceptual space is used to optimize the different thresholds for automatic fusion decision while minimizing the list of unresolved cases when the decision is left to the operator.

Photonic Crystal Fiber Based Entangled Photon Sources

DTIC Science & Technology

2014-03-01

5 Figure 2: The diagram of the counter- propagating scheme. FP: fiber port ( free - space to fiber). PBS: polarization beam splitter. LP: Linear... entangled photon -pairs using the highly nonlinear fiber in a counter- propagating scheme (CPS). With the HNLF at room temperature, we obtain a... propagating scheme for generating polarization entangled photon pairs at telecom wavelengths. We use 10 m of highly nonlinear fiber. We measure a

Integrable optical-fiber source of polarization-entangled photon pairs in the telecom band

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

Li Xiaoying; Liang Chuang; Fook Lee, Kim

We demonstrate an optical-fiber-based source of polarization-entangled photon pairs with improved quality and efficiency, which has been integrated with off-the-shelf telecom components and is, therefore, well suited for quantum communication applications in the 1550-nm telecom band. Polarization entanglement is produced by simultaneously pumping a loop of standard dispersion-shifted fiber with two orthogonally polarized pump pulses, one propagating in the clockwise and the other in the counterclockwise direction. We characterize this source by investigating two-photon interference between the generated signal-idler photon pairs under various conditions. The experimental parameters are carefully optimized to maximize the generated photon-pair correlation and to minimize contaminationmore » of the entangled photon pairs from extraneously scattered background photons that are produced by the pump pulses for two reasons: (i) spontaneous Raman scattering causes uncorrelated photons to be emitted in the signal and idler bands and (ii) broadening of the pump-pulse spectrum due to self-phase modulation causes pump photons to leak into the signal and idler bands. We obtain two-photon interference with visibility >90% without subtracting counts caused by the background photons (only dark counts of the detectors are subtracted), when the mean photon number in the signal (idler) channel is about 0.02/pulse, while no interference is observed in direct detection of either the signal or idler photons.« less

Optical flashes from internal pairs formed in gamma-ray burst afterglows

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

Panaitescu, A.

We develop a numerical formalism for calculating the distribution with energy of the (internal) pairs formed in a relativistic source from unscattered MeV–TeV photons. For gamma-ray burst (GRB) afterglows, this formalism is more suitable if the relativistic reverse shock that energizes the ejecta is the source of the GeV photons. The number of pairs formed is set by the source GeV output (calculated from the Fermi-LAT fluence), the unknown source Lorentz factor, and the unmeasured peak energy of the LAT spectral component. We show synchrotron and inverse-Compton light curves expected from pairs formed in the shocked medium and identify some criteria for testing a pair origin of GRB optical counterparts. Pairs formed in bright LAT afterglows with a Lorentz factor in the few hundreds may produce bright optical counterparts (more » $$R\\lt 10$$) lasting for up to one hundred seconds. As a result, the number of internal pairs formed from unscattered seed photons decreases very strongly with the source Lorentz factor, thus bright GRB optical counterparts cannot arise from internal pairs if the afterglow Lorentz factor is above several hundreds.« less

Optical flashes from internal pairs formed in gamma-ray burst afterglows

DOE PAGES

Panaitescu, A.

2015-06-09

We develop a numerical formalism for calculating the distribution with energy of the (internal) pairs formed in a relativistic source from unscattered MeV–TeV photons. For gamma-ray burst (GRB) afterglows, this formalism is more suitable if the relativistic reverse shock that energizes the ejecta is the source of the GeV photons. The number of pairs formed is set by the source GeV output (calculated from the Fermi-LAT fluence), the unknown source Lorentz factor, and the unmeasured peak energy of the LAT spectral component. We show synchrotron and inverse-Compton light curves expected from pairs formed in the shocked medium and identify some criteria for testing a pair origin of GRB optical counterparts. Pairs formed in bright LAT afterglows with a Lorentz factor in the few hundreds may produce bright optical counterparts (more » $$R\\lt 10$$) lasting for up to one hundred seconds. As a result, the number of internal pairs formed from unscattered seed photons decreases very strongly with the source Lorentz factor, thus bright GRB optical counterparts cannot arise from internal pairs if the afterglow Lorentz factor is above several hundreds.« less

Switch wear leveling

DOEpatents

Wu, Hunter; Sealy, Kylee; Gilchrist, Aaron

2015-09-01

An apparatus for switch wear leveling includes a switching module that controls switching for two or more pairs of switches in a switching power converter. The switching module controls switches based on a duty cycle control technique and closes and opens each switch in a switching sequence. The pairs of switches connect to a positive and negative terminal of a DC voltage source. For a first switching sequence a first switch of a pair of switches has a higher switching power loss than a second switch of the pair of switches. The apparatus includes a switch rotation module that changes the switching sequence of the two or more pairs of switches from the first switching sequence to a second switching sequence. The second switch of a pair of switches has a higher switching power loss than the first switch of the pair of switches during the second switching sequence.

A Comparison of Source Code Plagiarism Detection Engines

NASA Astrophysics Data System (ADS)

Lancaster, Thomas; Culwin, Fintan

2004-06-01

Automated techniques for finding plagiarism in student source code submissions have been in use for over 20 years and there are many available engines and services. This paper reviews the literature on the major modern detection engines, providing a comparison of them based upon the metrics and techniques they deploy. Generally the most common and effective techniques are seen to involve tokenising student submissions then searching pairs of submissions for long common substrings, an example of what is defined to be a paired structural metric. Computing academics are recommended to use one of the two Web-based detection engines, MOSS and JPlag. It is shown that whilst detection is well established there are still places where further research would be useful, particularly where visual support of the investigation process is possible.

Effects of Sleep on Word Pair Memory in Children - Separating Item and Source Memory Aspects.

PubMed

Wang, Jing-Yi; Weber, Frederik D; Zinke, Katharina; Noack, Hannes; Born, Jan

2017-01-01

Word paired-associate learning is a well-established task to demonstrate sleep-dependent memory consolidation in adults as well as children. Sleep has also been proposed to benefit episodic features of memory, i.e., a memory for an event (item) bound into the spatiotemporal context it has been experienced in (source). We aimed to explore if sleep enhances word pair memory in children by strengthening the episodic features of the memory, in particular. Sixty-one children (8-12 years) studied two lists of word pairs with 1 h in between. Retrieval testing comprised cued recall of the target word of each word pair (item memory) and recalling in which list the word pair had appeared in (source memory). Retrieval was tested either after 1 h (short retention interval) or after 11 h, with this long retention interval covering either nocturnal sleep or daytime wakefulness. Compared with the wake interval, sleep enhanced separate recall of both word pairs and the lists per se , while recall of the combination of the word pair and the list it had appeared in remained unaffected by sleep. An additional comparison with adult controls ( n = 37) suggested that item-source bound memory (combined recall of word pair and list) is generally diminished in children. Our results argue against the view that the sleep-induced enhancement in paired-associate learning in children is a consequence of sleep specifically enhancing the episodic features of the memory representation. On the contrary, sleep in children might strengthen item and source representations in isolation, while leaving the episodic memory representations (item-source binding) unaffected.

How Different EEG References Influence Sensor Level Functional Connectivity Graphs

PubMed Central

Huang, Yunzhi; Zhang, Junpeng; Cui, Yuan; Yang, Gang; He, Ling; Liu, Qi; Yin, Guangfu

2017-01-01

Highlights: Hamming Distance is applied to distinguish the difference of functional connectivity networkThe orientations of sources are testified to influence the scalp Functional Connectivity Graph (FCG) from different references significantlyREST, the reference electrode standardization technique, is proved to have an overall stable and excellent performance in variable situations. The choice of an electroencephalograph (EEG) reference is a practical issue for the study of brain functional connectivity. To study how EEG reference influence functional connectivity estimation (FCE), this study compares the differences of FCE resulting from the different references such as REST (the reference electrode standardization technique), average reference (AR), linked mastoids (LM), and left mastoid references (LR). Simulations involve two parts. One is based on 300 dipolar pairs, which are located on the superficial cortex with a radial source direction. The other part is based on 20 dipolar pairs. In each pair, the dipoles have various orientation combinations. The relative error (RE) and Hamming distance (HD) between functional connectivity matrices of ideal recordings and that of recordings obtained with different references, are metrics to compare the differences of the scalp functional connectivity graph (FCG) derived from those two kinds of recordings. Lower RE and HD values imply more similarity between the two FCGs. Using the ideal recording (IR) as a standard, the results show that AR, LM and LR perform well only in specific conditions, i.e., AR performs stable when there is no upward component in sources' orientation. LR achieves desirable results when the sources' locations are away from left ear. LM achieves an indistinct difference with IR, i.e., when the distribution of source locations is symmetric along the line linking the two ears. However, REST not only achieves excellent performance for superficial and radial dipolar sources, but also achieves a stable and robust performance with variable source locations and orientations. Benefitting from the stable and robust performance of REST vs. other reference methods, REST might best recover the real FCG of EEG. Thus, REST based FCG may be a good candidate to compare the FCG of EEG based on different references from different labs. PMID:28725175

Photon pair source via two coupling single quantum emitters

NASA Astrophysics Data System (ADS)

Peng, Yong-Gang; Zheng, Yu-Jun

2015-10-01

We study the two coupling two-level single molecules driven by an external field as a photon pair source. The probability of emitting two photons, P2, is employed to describe the photon pair source quality in a short time, and the correlation coefficient RAB is employed to describe the photon pair source quality in a long time limit. The results demonstrate that the coupling single quantum emitters can be considered as a stable photon pair source. Project supported by the National Natural Science Foundation of China (Grand Nos. 91021009, 21073110, and 11374191), the Natural Science Foundation of Shandong Province, China (Grant No. ZR2013AQ020), the Postdoctoral Science Foundation of China (Grant No. 2013M531584), the Doctoral Program of Higher Education of China (Grant Nos. 20130131110005 and 20130131120006), and the Taishan Scholarship Project of Shandong Province, China.

Pulsed source of spectrally uncorrelated and indistinguishable photons at telecom wavelengths.

PubMed

Bruno, N; Martin, A; Guerreiro, T; Sanguinetti, B; Thew, R T

2014-07-14

We report on the generation of indistinguishable photon pairs at telecom wavelengths based on a type-II parametric down conversion process in a periodically poled potassium titanyl phosphate (PPKTP) crystal. The phase matching, pump laser characteristics and coupling geometry are optimised to obtain spectrally uncorrelated photons with high coupling efficiencies. Four photons are generated by a counter-propagating pump in the same crystal and anlysed via two photon interference experiments between photons from each pair source as well as joint spectral and g((2)) measurements. We obtain a spectral purity of 0.91 and coupling efficiencies around 90% for all four photons without any filtering. These pure indistinguishable photon sources at telecom wavelengths are perfectly adapted for quantum network demonstrations and other multi-photon protocols.

A Silicon-Chip Source of Bright Photon-Pair Comb

DTIC Science & Technology

2012-10-16

A silicon -chip source of bright photon-pair comb Wei C. Jiang,1, ∗ Xiyuan Lu,2, ∗ Jidong Zhang,3 Oskar Painter,4 and Qiang Lin1, 3, † 1Institute of...efficient monolithic photon-pair source for on-chip application. Here we report a device on the silicon -on-insulator platform that utilizes dramatic cavity...enhanced four-wave mixing in a high-Q silicon microdisk resonator. The device is able to produce high-purity photon pairs in a comb fashion, with an

Quantum State Tomography of a Fiber-Based Source of Polarization-Entangled Photon Pairs

DTIC Science & Technology

2007-12-20

Processing 175−179 (IEEE, Bangalore, 1984). 4. A. K. Ekert, “ Quantum cryptography based on Bell’s theorem ,” Phys. Rev. Lett. 67, 661–663 (1991). 5...NUMBERS Quantum State Tomography of a Fiber- Based Source of MURI Center for Photonic Quantum Information Systems: AROIARDA Program Polarization...Computer Society Press, Los Alamitos, 1996). 7. N. Gisin, G. Ribordy, W. Tittel, and H. Zbinden, “ Quantum cryptography ,” Rev. Mod. Phys. 74, 145

SQUID (superconducting quantum interference device) arrays for simultaneous magnetic measurements: Calibration and source localization performance

NASA Astrophysics Data System (ADS)

Kaufman, Lloyd; Williamson, Samuel J.; Costaribeiro, P.

1988-02-01

Recently developed small arrays of SQUID-based magnetic sensors can, if appropriately placed, locate the position of a confined biomagnetic source without moving the array. The authors present a technique with a relative accuracy of about 2 percent for calibrating such sensors having detection coils with the geometry of a second-order gradiometer. The effects of calibration error and magnetic noise on the accuracy of locating an equivalent current dipole source in the human brain are investigated for 5- and 7-sensor probes and for a pair of 7-sensor probes. With a noise level of 5 percent of peak signal, uncertainties of about 20 percent in source strength and depth for a 5-sensor probe are reduced to 8 percent for a pair of 7-sensor probes, and uncertainties of about 15 mm in lateral position are reduced to 1 mm, for the configuration considered.

High-gain AlGaAs/GaAs double heterojunction Darlington phototransistors for optical neural networks

NASA Technical Reports Server (NTRS)

Kim, Jae H. (Inventor); Lin, Steven H. (Inventor)

1991-01-01

High-gain MOCVD-grown (metal-organic chemical vapor deposition) AlGaAs/GaAs/AlGaAs n-p-n double heterojunction bipolar transistors (DHBTs) and Darlington phototransistor pairs are provided for use in optical neural networks and other optoelectronic integrated circuit applications. The reduced base doping level used results in effective blockage of Zn out-diffusion, enabling a current gain of 500, higher than most previously reported values for Zn-diffused-base DHBTs. Darlington phototransitor pairs of this material can achieve a current gain of over 6000, which satisfies the gain requirement for optical neural network designs, which advantageously may employ neurons comprising the Darlington phototransistor pairs in series with a light source.

High-fidelity entanglement swapping and generation of three-qubit GHZ state using asynchronous telecom photon pair sources.

PubMed

Tsujimoto, Yoshiaki; Tanaka, Motoki; Iwasaki, Nobuo; Ikuta, Rikizo; Miki, Shigehito; Yamashita, Taro; Terai, Hirotaka; Yamamoto, Takashi; Koashi, Masato; Imoto, Nobuyuki

2018-01-23

We experimentally demonstrate a high-fidelity entanglement swapping and a generation of the Greenberger-Horne-Zeilinger (GHZ) state using polarization-entangled photon pairs at telecommunication wavelength produced by spontaneous parametric down conversion with continuous-wave pump light. While spatially separated sources asynchronously emit photon pairs, the time-resolved photon detection guarantees the temporal indistinguishability of photons without active timing synchronizations of pump lasers and/or adjustment of optical paths. In the experiment, photons are sufficiently narrowed by fiber-based Bragg gratings with the central wavelengths of 1541 nm & 1580 nm, and detected by superconducting nanowire single-photon detectors with low timing jitters. The observed fidelities of the final states for entanglement swapping and the generated three-qubit state were 0.84 ± 0.04 and 0.70 ± 0.05, respectively.

Producing data-based sensitivity kernels from convolution and correlation in exploration geophysics.

NASA Astrophysics Data System (ADS)

Chmiel, M. J.; Roux, P.; Herrmann, P.; Rondeleux, B.

2016-12-01

Many studies have shown that seismic interferometry can be used to estimate surface wave arrivals by correlation of seismic signals recorded at a pair of locations. In the case of ambient noise sources, the convergence towards the surface wave Green's functions is obtained with the criterion of equipartitioned energy. However, seismic acquisition with active, controlled sources gives more possibilities when it comes to interferometry. The use of controlled sources makes it possible to recover the surface wave Green's function between two points using either correlation or convolution. We investigate the convolutional and correlational approaches using land active-seismic data from exploration geophysics. The data were recorded on 10,710 vertical receivers using 51,808 sources (seismic vibrator trucks). The sources spacing is the same in both X and Y directions (30 m) which is known as a "carpet shooting". The receivers are placed in parallel lines with a spacing 150 m in the X direction and 30 m in the Y direction. Invoking spatial reciprocity between sources and receivers, correlation and convolution functions can thus be constructed between either pairs of receivers or pairs of sources. Benefiting from the dense acquisition, we extract sensitivity kernels from correlation and convolution measurements of the seismic data. These sensitivity kernels are subsequently used to produce phase-velocity dispersion curves between two points and to separate the higher mode from the fundamental mode for surface waves. Potential application to surface wave cancellation is also envisaged.

A monolithically integrated polarization entangled photon pair source on a silicon chip

PubMed Central

Matsuda, Nobuyuki; Le Jeannic, Hanna; Fukuda, Hiroshi; Tsuchizawa, Tai; Munro, William John; Shimizu, Kaoru; Yamada, Koji; Tokura, Yasuhiro; Takesue, Hiroki

2012-01-01

Integrated photonic circuits are one of the most promising platforms for large-scale photonic quantum information systems due to their small physical size and stable interferometers with near-perfect lateral-mode overlaps. Since many quantum information protocols are based on qubits defined by the polarization of photons, we must develop integrated building blocks to generate, manipulate, and measure the polarization-encoded quantum state on a chip. The generation unit is particularly important. Here we show the first integrated polarization-entangled photon pair source on a chip. We have implemented the source as a simple and stable silicon-on-insulator photonic circuit that generates an entangled state with 91 ± 2% fidelity. The source is equipped with versatile interfaces for silica-on-silicon or other types of waveguide platforms that accommodate the polarization manipulation and projection devices as well as pump light sources. Therefore, we are ready for the full-scale implementation of photonic quantum information systems on a chip. PMID:23150781

Fiber-Optic Linear Displacement Sensor Based On Matched Interference Filters

NASA Astrophysics Data System (ADS)

Fuhr, Peter L.; Feener, Heidi C.; Spillman, William B.

1990-02-01

A fiber optic linear displacement sensor has been developed in which a pair of matched interference filters are used to encode linear position on a broadband optical signal as relative intensity variations. As the filters are displaced, the optical beam illuminates varying amounts of each filter. Determination of the relative intensities at each filter pairs' passband is based on measurements acquired with matching filters and photodetectors. Source power variation induced errors are minimized by basing determination of linear position on signal Visibility. A theoretical prediction of the sensor's performance is developed and compared with experiments performed in the near IR spectral region using large core multimode optical fiber.

Towards next generation time-domain diffuse optics devices

NASA Astrophysics Data System (ADS)

Dalla Mora, Alberto; Contini, Davide; Arridge, Simon R.; Martelli, Fabrizio; Tosi, Alberto; Boso, Gianluca; Farina, Andrea; Durduran, Turgut; Martinenghi, Edoardo; Torricelli, Alessandro; Pifferi, Antonio

2015-03-01

Diffuse Optics is growing in terms of applications ranging from e.g. oximetry, to mammography, molecular imaging, quality assessment of food and pharmaceuticals, wood optics, physics of random media. Time-domain (TD) approaches, although appealing in terms of quantitation and depth sensibility, are presently limited to large fiber-based systems, with limited number of source-detector pairs. We present a miniaturized TD source-detector probe embedding integrated laser sources and single-photon detectors. Some electronics are still external (e.g. power supply, pulse generators, timing electronics), yet full integration on-board using already proven technologies is feasible. The novel devices were successfully validated on heterogeneous phantoms showing performances comparable to large state-of-the-art TD rack-based systems. With an investigation based on simulations we provide numerical evidence that the possibility to stack many TD compact source-detector pairs in a dense, null source-detector distance arrangement could yield on the brain cortex about 1 decade higher contrast as compared to a continuous wave (CW) approach. Further, a 3-fold increase in the maximum depth (down to 6 cm) is estimated, opening accessibility to new organs such as the lung or the heart. Finally, these new technologies show the way towards compact and wearable TD probes with orders of magnitude reduction in size and cost, for a widespread use of TD devices in real life.

PAIRS, The GIS-Based Incident Response System for Pennsylvania, and NASA

NASA Technical Reports Server (NTRS)

Conrad, Eric; Arbegast, Daniel; Maynard, Nancy; Vicente, Gilberto

2003-01-01

Over the past several years the Pennsylvania Departments of Environmental Protection (DEP), Health (DOH), and Agriculture (PDA) built the GIs-based Pennsylvania West Nile Surveillance System. That system has become a model for collecting data that has a field component, laboratory component, reporting and mapping component, and a public information component. Given the success of the West Nile Virus System and the events of September 11, 2001, DEP then embarked on the development of the Pennsylvania Incident Response System, or PAIRS. PAIRS is an effective GIs-based approach to providing a system for response to incidents of any kind, including terrorism because it is building upon the existing experience, infrastructure and databases that were successfully developed to respond to the West Nile Virus by DEP, DOH, and PDA. The proposed system can be described as one that supports data acquisition, laboratory forensics, decision making/response, and communications. Decision makers will have tools to view and analyze data from various sources and, at the same time, to communicate with the large numbers of people responding to the same incident. Recent collaborations with NASA partners are creating mechanisms for the PAIRS system to incorporate space-based and other remote sensing geophysical parameters relevant to public health assessment and management, such as surface temperatures, precipitation, land cover/land use change, and humidity. This presentation will describe the PAIRS system and outline the Pennsylvania-NASA collaboration for integration of space-based data into the PAIRS system.

High-visibility two-photon interference at a telecom wavelength using picosecond-regime separated sources

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

Aboussouan, Pierre; Alibart, Olivier; Ostrowsky, Daniel B.

We report on a two-photon interference experiment in a quantum relay configuration using two picosecond regime periodically poled lithium niobate (PPLN) waveguide based sources emitting paired photons at 1550 nm. The results show that the picosecond regime associated with a guided-wave scheme should have important repercussions for quantum relay implementations in real conditions, essential for improving both the working distance and the efficiency of quantum cryptography and networking systems. In contrast to already reported regimes, namely, femtosecond and CW, it allows achieving a 99% net visibility two-photon interference while maintaining a high effective photon pair rate using only standard telecommore » components and detectors.« less

Multipli-Entangled Photons from a Spontaneous Parametric Down-Conversion Source

DTIC Science & Technology

2011-01-01

Alsing, Corey J. Peters (AFRL/RITA); Enrique J. Galvez ( Colgate University, Hamilton, NY) 5d. PROJECT NUMBER QIS0 5e. TASK NUMBER PR 5f...and Enrique J. Galvez Colgate University, Hamilton, NY (USA) 1. ABSTRACT In this work, we discuss a novel compact source that generates six...single pair of entangled photons per pass in conventional SPDC-based sources. We first describe the experimental testbed used for evaluation and

Towards Scalable Entangled Photon Sources with Self-Assembled InAs /GaAs Quantum Dots

NASA Astrophysics Data System (ADS)

Wang, Jianping; Gong, Ming; Guo, G.-C.; He, Lixin

2015-08-01

The biexciton cascade process in self-assembled quantum dots (QDs) provides an ideal system for realizing deterministic entangled photon-pair sources, which are essential to quantum information science. The entangled photon pairs have recently been generated in experiments after eliminating the fine-structure splitting (FSS) of excitons using a number of different methods. Thus far, however, QD-based sources of entangled photons have not been scalable because the wavelengths of QDs differ from dot to dot. Here, we propose a wavelength-tunable entangled photon emitter mounted on a three-dimensional stressor, in which the FSS and exciton energy can be tuned independently, thereby enabling photon entanglement between dissimilar QDs. We confirm these results via atomistic pseudopotential calculations. This provides a first step towards future realization of scalable entangled photon generators for quantum information applications.

Ion funnel device

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

Ibrahim, Yehia M.; Chen, Tsung-Chi; Harrer, Marques B.

2017-11-21

An ion funnel device is disclosed. A first pair of electrodes is positioned in a first direction. A second pair of electrodes is positioned in a second direction. The device includes an RF voltage source and a DC voltage source. A RF voltage with a superimposed DC voltage gradient is applied to the first pair of electrodes, and a DC voltage gradient is applied to the second pair of electrodes.

Quantum Communication with a High-Rate Entangled Photon Source

NASA Technical Reports Server (NTRS)

Wilson, Nathaniel C.; Chaffee, Dalton W.; Lekki, John D.; Wilson, Jeffrey D.

2016-01-01

A high generation rate photon-pair source using a dual element periodically-poled potassium titanyl phosphate (PP KTP) waveguide is described. The photon-pair source features a high pair generation rate, a compact power-efficient package, and continuous wave (CW) or pulsed operation. Characterization and test results are presented. Details and preliminary results of a laboratory free-space QKD experiment with the B92 protocol are also presented.

Characterization of the LCLS “nanosecond two-bunch” mode for x-ray speckle visibility spectroscopy experiments

DOE PAGES

Sun, Yanwen; Zhu, Diling; Song, Sanghoon; ...

2017-05-23

The generation of two X-ray pulses with tunable nanosecond scale time separations has recently been demonstrated at the Linac Coherent Light Source using an accelerator based technique. This approach offers the opportunity to extend X-ray Photon Correlation Spectroscopy techniques to the yet unexplored regime of nanosecond timescales by means of X-ray Speckle Visibility Spectroscopy. As the two pulses originate from two independent Spontaneous Amplified Stimulated Emission processes, the beam properties fluctuate from pulse pair to pulse pair, but as well between the individual pulses within a pair. However, two-pulse XSVS experiments require the intensity of the individual pulses to bemore » either identical in the ideal case, or with a accurately known intensity ratio. We present the design and performances of a non-destructive intensity diagnostic based on measurement of scattering from a transparent target using a high-speed photo-detector. Individual pulses within a pulse pair with time delays as short as 0.7 ns can be resolved. Moreover, using small angle coherent scattering, we characterize the averaged spatial overlap of the focused pulse pairs. Furthermore, the multi-shot average-speckle contrasts from individual pulses and pulse pairs are compared.« less

Progress towards the development of a source of entangled photons for Space

NASA Astrophysics Data System (ADS)

Fedrizzi, Alessandro; Jennewein, Thomas; Ursin, Rupert; Zeilinger, Anton

2007-03-01

Quantum entanglement offers exciting applications like quantum computing, quantum teleportation and quantum cryptography. Ground based quantum communication schemes in optical fibres however are limited to a distance of the order of ˜100 km. In order to extend this limit to a global scale we are working on the realization of an entanglement-based quantum communication transceiver for space deployment. Here we report on a compact, extremely bright source for polarization entangled photons meeting the scientific requirements for a potential space to ground optical link. The pair production rate exceeds 4*10̂6 pairs/s at just 20mW of laser diode pump power. Furthermore, we will present the results of various experiments proving the feasibility of quantum information in space, including a weak coherent pulse single-photon downlink from a LEO satellite and the distribution of entanglement over a 144km free space link, using ESAs optical ground station.

Accurate quantification of magnetic particle properties by intra-pair magnetophoresis for nanobiotechnology

NASA Astrophysics Data System (ADS)

van Reenen, Alexander; Gao, Yang; Bos, Arjen H.; de Jong, Arthur M.; Hulsen, Martien A.; den Toonder, Jaap M. J.; Prins, Menno W. J.

2013-07-01

The application of magnetic particles in biomedical research and in-vitro diagnostics requires accurate characterization of their magnetic properties, with single-particle resolution and good statistics. Here, we report intra-pair magnetophoresis as a method to accurately quantify the field-dependent magnetic moments of magnetic particles and to rapidly generate histograms of the magnetic moments with good statistics. We demonstrate our method with particles of different sizes and from different sources, with a measurement precision of a few percent. We expect that intra-pair magnetophoresis will be a powerful tool for the characterization and improvement of particles for the upcoming field of particle-based nanobiotechnology.

Partial hyperbolicity and attracting regions in 3-dimensional manifolds

NASA Astrophysics Data System (ADS)

Potrie, Rafael

The need for reliable, fiber-based sources of entangled and paired photons has intensified in recent years because of potential uses in optical quantum communication and computing. In particular, indistinguishable photon sources are an inherent part of several quantum communication protocols and are needed to establish the viability of quantum communication networks. This thesis is centered around the development of such sources at telecommunication-band wavelengths. In this thesis, we describe experiments on entangled photon generation and the creation of quantum logic gates in the C-band, and on photon indistinguishability in the O-band. These experiments utilize the four-wave mixing process in fiber which occurs as a result of the Kerr nonlinearity, to create paired photons. To begin, we report the development of a source of 1550-nm polarization entangled photons in fiber. We then interface this source with a quantum Controlled-NOT gate, which is a universal quantum logic gate. We set experimental bounds on the process fidelity of the Controlled-NOT gate. Next, we report a demonstration of quantum interference between 1310-nm photons produced in independent sources. We demonstrate high quantum interference visibility, a signature of quantum indistinguishability, while using distinguishable pump photons. Together, these efforts constitute preliminary steps toward establishing the viability of fiber-based quantum communication, which will allow us to utilize existing infrastructure for implementing quantum communication protocols.

Conceptual design of an intense positron source based on an LIA

NASA Astrophysics Data System (ADS)

Long, Ji-Dong; Yang, Zhen; Dong, Pan; Shi, Jin-Shui

2012-04-01

Accelerator based positron sources are widely used due to their high intensity. Most of these accelerators are RF accelerators. An LIA (linear induction accelerator) is a kind of high current pulsed accelerator used for radiography. A conceptual design of an intense pulsed positron source based on an LIA is presented in the paper. One advantage of an LIA is its pulsed power being higher than conventional accelerators, which means a higher amount of primary electrons for positron generations per pulse. Another advantage of an LIA is that it is very suitable to decelerate the positron bunch generated by bremsstrahlung pair process due to its ability to adjustably shape the voltage pulse. By implementing LIA cavities to decelerate the positron bunch before it is moderated, the positron yield could be greatly increased. These features may make the LIA based positron source become a high intensity pulsed positron source.

Three-photon N00N states generated by photon subtraction from double photon pairs.

PubMed

Kim, Heonoh; Park, Hee Su; Choi, Sang-Kyung

2009-10-26

We describe an experimental demonstration of a novel three-photon N00N state generation scheme using a single source of photons based on spontaneous parametric down-conversion (SPDC). The three-photon entangled state is generated when a photon is subtracted from a double pair of photons and detected by a heralding counter. Interference fringes measured with an emulated three-photon detector reveal the three-photon de Broglie wavelength and exhibit visibility > 70% without background subtraction.

Modeling and experimental validation of angular radiance and distance-dependent radiance in a turbid medium

NASA Astrophysics Data System (ADS)

Liu, Lingling; Li, Chenxi; Zhao, Huijuan; Yi, Xi; Gao, Feng; Meng, Wei; Lu, Yiming

2014-03-01

Radiance is sensitive to the variations of tissue optical parameters, such as absorption coefficient μa, scattering coefficient μs, and anisotropy factor g. Therefore, similar to fluence, radiance can be used for tissue characterization. Compared with fluence, radiance has the advantage of offering the direction information of light intensity. Taking such advantage, the optical parameters can be determined by rotating the detector through 360 deg with only a single optode pair. Instead of the translation mode used in the fluence-based technologies, the Rotation mode has less invasiveness in the clinical diagnosis. This paper explores a new method to obtain the optical properties by measuring the distribution of light intensity in liquid phantom with only a single optode pair and the detector rotation through 360 deg. The angular radiance and distance-dependent radiance are verified by comparing experimental measurement data with Monte Carlo (MC) simulation for the short source-detector separations and diffusion approximation for the large source-detector separations. Detecting angular radiance with only a single optode pair under a certain source-detection separation will present a way for prostate diagnose and light dose calculation during the photon dynamic therapy (PDT).

Wedge MUSIC: a novel approach to examine experimental differences of brain source connectivity patterns from EEG/MEG data.

PubMed

Ewald, Arne; Avarvand, Forooz Shahbazi; Nolte, Guido

2014-11-01

We introduce a novel method to estimate bivariate synchronization, i.e. interacting brain sources at a specific frequency or band, from MEG or EEG data robust to artifacts of volume conduction. The data driven calculation is solely based on the imaginary part of the cross-spectrum as opposed to the imaginary part of coherency. In principle, the method quantifies how strong a synchronization between a distinct pair of brain sources is present in the data. As an input of the method all pairs of pre-defined locations inside the brain can be used which is computationally exhaustive. In contrast to that, reference sources can be used that have been identified by any source reconstruction technique in a prior analysis step. We introduce different variants of the method and evaluate the performance in simulations. As a particular advantage of the proposed methodology, we demonstrate that the novel approach is capable of investigating differences in brain source interactions between experimental conditions or with respect to a certain baseline. For measured data, we first show the application on resting state MEG data where we find locally synchronized sources in the motor-cortex based on the sensorimotor idle rhythms. Finally, we show an example on EEG motor imagery data where we contrast hand and foot movements. Here, we also find local interactions in the expected brain areas. Copyright © 2014. Published by Elsevier Inc.

Selective Listening Point Audio Based on Blind Signal Separation and Stereophonic Technology

NASA Astrophysics Data System (ADS)

Niwa, Kenta; Nishino, Takanori; Takeda, Kazuya

A sound field reproduction method is proposed that uses blind source separation and a head-related transfer function. In the proposed system, multichannel acoustic signals captured at distant microphones are decomposed to a set of location/signal pairs of virtual sound sources based on frequency-domain independent component analysis. After estimating the locations and the signals of the virtual sources by convolving the controlled acoustic transfer functions with each signal, the spatial sound is constructed at the selected point. In experiments, a sound field made by six sound sources is captured using 48 distant microphones and decomposed into sets of virtual sound sources. Since subjective evaluation shows no significant difference between natural and reconstructed sound when six virtual sources and are used, the effectiveness of the decomposing algorithm as well as the virtual source representation are confirmed.

Experimental many-pairs nonlocality

NASA Astrophysics Data System (ADS)

Poh, Hou Shun; Cerè, Alessandro; Bancal, Jean-Daniel; Cai, Yu; Sangouard, Nicolas; Scarani, Valerio; Kurtsiefer, Christian

2017-08-01

Collective measurements on large quantum systems together with a majority voting strategy can lead to a violation of the Clauser-Horne-Shimony-Holt Bell inequality. In the presence of many entangled pairs, this violation decreases quickly with the number of pairs and vanishes for some critical pair number that is a function of the noise present in the system. Here we show that a different binning strategy can lead to a more substantial Bell violation when the noise is sufficiently small. Given the relation between the critical pair number and the source noise, we then present an experiment where the critical pair number is used to quantify the quality of a high visibility photon pair source. Our results demonstrate nonlocal correlations using collective measurements operating on clusters of more than 40 photon pairs.

Coding Instead of Splitting - Algebraic Combinations in Time and Space

DTIC Science & Technology

2016-06-09

sources message. For certain classes of two-unicast-Z networks, we show that the rate-tuple ( N ,1) is achievable as long as the individual source...destination cuts for the two source-destination pairs are respectively at least as large as N and 1, and the generalized network sharing cut - a bound...previously defined by Kamath et. al. - is at least as large as N + 1. We show this through a novel achievable scheme which is based on random linear coding at

A stable wavelength-tunable triggered source of single photons and cascaded photon pairs at the telecom C-band

NASA Astrophysics Data System (ADS)

Zeuner, Katharina D.; Paul, Matthias; Lettner, Thomas; Reuterskiöld Hedlund, Carl; Schweickert, Lucas; Steinhauer, Stephan; Yang, Lily; Zichi, Julien; Hammar, Mattias; Jöns, Klaus D.; Zwiller, Val

2018-04-01

The implementation of fiber-based long-range quantum communication requires tunable sources of single photons at the telecom C-band. Stable and easy-to-implement wavelength-tunability of individual sources is crucial to (i) bring remote sources into resonance, (ii) define a wavelength standard, and (iii) ensure scalability to operate a quantum repeater. So far, the most promising sources for true, telecom single photons are semiconductor quantum dots, due to their ability to deterministically and reliably emit single and entangled photons. However, the required wavelength-tunability is hard to attain. Here, we show a stable wavelength-tunable quantum light source by integrating strain-released InAs quantum dots on piezoelectric substrates. We present triggered single-photon emission at 1.55 μm with a multi-photon emission probability as low as 0.097, as well as photon pair emission from the radiative biexciton-exciton cascade. We achieve a tuning range of 0.25 nm which will allow us to spectrally overlap remote quantum dots or tuning distant quantum dots into resonance with quantum memories. This opens up realistic avenues for the implementation of photonic quantum information processing applications at telecom wavelengths.

[Pharmacokinetic research strategies of compatibilities and synergistic effects of classical Danshen herb pairs based on pharmacokinetics of "Danshen-Bingpian" and "Danshen-Honghua"].

PubMed

Zhang, Cui-Ying; Ren, Wei-Guang

2017-06-01

Herb pairs are usual clinical compatibility forms and one of compound prescription sources in Chinese medicine. Pharmacokinetic research in vivo is one of the important items in elucidating the mechanism for synergistic and attenuated mechanisms of herb pairs. The paper comprehensively summarized and systemized the pharmacokinetic researches of marker-ingredients about Danshen-Honghua and Danshen-Bingpian in order to elucidate the rationality and scientificity of herb pairs and provide some feasible suggestions on the pharmacokinetics of drugs in the future. In view of complicated system of Traditional Chinese medicines and a chemical system that is not separated from its natural state, comparative pharmacokinetic researches on marker-ingredients from the herb pairs are reasonable to elucidate the synergistic and attenuated mechanisms of monarch-subjects compatible herbs and monarch-guide compatible herbs. Such pharmacokinetic research can better explain the mechanism of drug compatibility, while the pharmacokinetic researches based on the monomer chemical compositions and marker-ingredients that have been separated from complex chemical environment of traditional Chinese Medicine are still unreasonable and should be discussed deeply. Copyright© by the Chinese Pharmaceutical Association.

A femtoscopic correlation analysis tool using the Schrödinger equation (CATS)

NASA Astrophysics Data System (ADS)

Mihaylov, D. L.; Mantovani Sarti, V.; Arnold, O. W.; Fabbietti, L.; Hohlweger, B.; Mathis, A. M.

2018-05-01

We present a new analysis framework called "Correlation Analysis Tool using the Schrödinger equation" (CATS) which computes the two-particle femtoscopy correlation function C( k), with k being the relative momentum for the particle pair. Any local interaction potential and emission source function can be used as an input and the wave function is evaluated exactly. In this paper we present a study on the sensitivity of C( k) to the interaction potential for different particle pairs: p-p, p-Λ, K^-p, K^+-p, p-Ξ ^- and Λ- Λ. For the p-p Argonne v_{18} and Reid Soft-Core potentials have been tested. For the other pair systems we present results based on strong potentials obtained from effective Lagrangians such as χ EFT for p-Λ, Jülich models for K(\\bar{K})-N and Nijmegen models for Λ-Λ. For the p-Ξ^- pairs we employ the latest lattice results from the HAL QCD collaboration. Our detailed study of different interacting particle pairs as a function of the source size and different potentials shows that femtoscopic measurements can be exploited in order to constrain the final state interactions among hadrons. In particular, small collision systems of the order of 1 fm, as produced in pp collisions at the LHC, seem to provide a suitable environment for quantitative studies of this kind.

Fingerprints of Both Watson-Crick and Hoogsteen Isomers of the Isolated (Cytosine-Guanine)H+ Pair.

PubMed

Cruz-Ortiz, Andrés F; Rossa, Maximiliano; Berthias, Francis; Berdakin, Matías; Maitre, Philippe; Pino, Gustavo A

2017-11-16

 Gas phase protonated guanine-cytosine (CGH + ) pair was generated using an electrospray ionization source from solutions at two different pH (5.8 and 3.2). Consistent evidence from MS/MS fragmentation patterns and differential ion mobility spectra (DIMS) point toward the presence of two isomers of the CGH + pair, whose relative populations depend strongly on the pH of the solution. Gas phase infrared multiphoton dissociation (IRMPD) spectroscopy in the 900-1900 cm -1 spectral range further confirms that the Watson-Crick isomer is preferentially produced (91%) at pH = 5.8, while the Hoogsteen isomer predominates (66%) at pH = 3.2). These fingerprint signatures are expected to be useful for the development of new analytical methodologies and to trigger isomer selective photochemical studies of protonated DNA base pairs.

Statistical use of argonaute expression and RISC assembly in microRNA target identification.

PubMed

Stanhope, Stephen A; Sengupta, Srikumar; den Boon, Johan; Ahlquist, Paul; Newton, Michael A

2009-09-01

MicroRNAs (miRNAs) posttranscriptionally regulate targeted messenger RNAs (mRNAs) by inducing cleavage or otherwise repressing their translation. We address the problem of detecting m/miRNA targeting relationships in homo sapiens from microarray data by developing statistical models that are motivated by the biological mechanisms used by miRNAs. The focus of our modeling is the construction, activity, and mediation of RNA-induced silencing complexes (RISCs) competent for targeted mRNA cleavage. We demonstrate that regression models accommodating RISC abundance and controlling for other mediating factors fit the expression profiles of known target pairs substantially better than models based on m/miRNA expressions alone, and lead to verifications of computational target pair predictions that are more sensitive than those based on marginal expression levels. Because our models are fully independent of exogenous results from sequence-based computational methods, they are appropriate for use as either a primary or secondary source of information regarding m/miRNA target pair relationships, especially in conjunction with high-throughput expression studies.

Reference set for performance testing of pediatric vaccine safety signal detection methods and systems.

PubMed

Brauchli Pernus, Yolanda; Nan, Cassandra; Verstraeten, Thomas; Pedenko, Mariia; Osokogu, Osemeke U; Weibel, Daniel; Sturkenboom, Miriam; Bonhoeffer, Jan

2016-12-12

Safety signal detection in spontaneous reporting system databases and electronic healthcare records is key to detection of previously unknown adverse events following immunization. Various statistical methods for signal detection in these different datasources have been developed, however none are geared to the pediatric population and none specifically to vaccines. A reference set comprising pediatric vaccine-adverse event pairs is required for reliable performance testing of statistical methods within and across data sources. The study was conducted within the context of the Global Research in Paediatrics (GRiP) project, as part of the seventh framework programme (FP7) of the European Commission. Criteria for the selection of vaccines considered in the reference set were routine and global use in the pediatric population. Adverse events were primarily selected based on importance. Outcome based systematic literature searches were performed for all identified vaccine-adverse event pairs and complemented by expert committee reports, evidence based decision support systems (e.g. Micromedex), and summaries of product characteristics. Classification into positive (PC) and negative control (NC) pairs was performed by two independent reviewers according to a pre-defined algorithm and discussed for consensus in case of disagreement. We selected 13 vaccines and 14 adverse events to be included in the reference set. From a total of 182 vaccine-adverse event pairs, we classified 18 as PC, 113 as NC and 51 as unclassifiable. Most classifications (91) were based on literature review, 45 were based on expert committee reports, and for 46 vaccine-adverse event pairs, an underlying pathomechanism was not plausible classifying the association as NC. A reference set of vaccine-adverse event pairs was developed. We propose its use for comparing signal detection methods and systems in the pediatric population. Published by Elsevier Ltd.

Integrated model of multiple kernel learning and differential evolution for EUR/USD trading.

PubMed

Deng, Shangkun; Sakurai, Akito

2014-01-01

Currency trading is an important area for individual investors, government policy decisions, and organization investments. In this study, we propose a hybrid approach referred to as MKL-DE, which combines multiple kernel learning (MKL) with differential evolution (DE) for trading a currency pair. MKL is used to learn a model that predicts changes in the target currency pair, whereas DE is used to generate the buy and sell signals for the target currency pair based on the relative strength index (RSI), while it is also combined with MKL as a trading signal. The new hybrid implementation is applied to EUR/USD trading, which is the most traded foreign exchange (FX) currency pair. MKL is essential for utilizing information from multiple information sources and DE is essential for formulating a trading rule based on a mixture of discrete structures and continuous parameters. Initially, the prediction model optimized by MKL predicts the returns based on a technical indicator called the moving average convergence and divergence. Next, a combined trading signal is optimized by DE using the inputs from the prediction model and technical indicator RSI obtained from multiple timeframes. The experimental results showed that trading using the prediction learned by MKL yielded consistent profits.

Remote sensing of a NTC radio source from a Cluster tilted spacecraft pair

NASA Astrophysics Data System (ADS)

Décréau, P. M. E.; Kougblénou, S.; Lointier, G.; Rauch, J.-L.; Trotignon, J.-G.; Vallières, X.; Canu, P.; Rochel Grimald, S.; El-Lemdani Mazouz, F.; Darrouzet, F.

2013-11-01

The Cluster mission operated a "tilt campaign" during the month of May 2008. Two of the four identical Cluster spacecraft were placed at a close distance (~50 km) from each other and the spin axis of one of the spacecraft pair was tilted by an angle of ~46°. This gave the opportunity, for the first time in space, to measure global characteristics of AC electric field, at the sensitivity available with long boom (88 m) antennas, simultaneously from the specific configuration of the tilted pair of satellites and from the available base of three satellites placed at a large characteristic separation (~1 RE). This paper describes how global characteristics of radio waves, in this case the configuration of the electric field polarization ellipse in 3-D-space, are identified from in situ measurements of spin modulation features by the tilted pair, validating a novel experimental concept. In the event selected for analysis, non-thermal continuum (NTC) waves in the 15-25 kHz frequency range are observed from the Cluster constellation placed above the polar cap. The observed intensity variations with spin angle are those of plane waves, with an electric field polarization close to circular, at an ellipticity ratio e = 0.87. We derive the source position in 3-D by two different methods. The first one uses ray path orientation (measured by the tilted pair) combined with spectral signature of magnetic field magnitude at source. The second one is obtained via triangulation from the three spacecraft baseline, using estimation of directivity angles under assumption of circular polarization. The two results are not compatible, placing sources widely apart. We present a general study of the level of systematic errors due to the assumption of circular polarization, linked to the second approach, and show how this approach can lead to poor triangulation and wrong source positioning. The estimation derived from the first method places the NTC source region in the dawn sector, at a large L value (L ~ 10) and a medium geomagnetic latitude (35° S). We discuss these untypical results within the frame of the geophysical conditions prevailing that day, i.e. a particularly quiet long time interval, followed by a short increase of magnetic activity.

Discriminating tastes

PubMed Central

Storz, Gisela

2011-01-01

Hfq-binding small RNAs (sRNAs) are critical regulators that form limited base-pairing interactions with target mRNAs in bacteria. These sRNAs have been linked to diverse environmental responses, yet little is known how Hfq-binding sRNAs participate in the regulatory networks associated with each response. We recently described how the Hfq-binding sRNA Spot 42 in Escherichia coli contributes to catabolite repression, a regulatory phenomenon that allows bacteria to consume some carbon sources over others. Spot 42 base pairs with numerous mRNAs encoding enzymes in central and secondary metabolism, redox balancing, and the uptake and consumption of non-preferred carbon sources. Many of the corresponding genes are transcriptionally activated by the Spot 42-repressor CRP, forming a regulatory circuit called a multi-output feedforward loop. We found that this loop influences both the steady-state levels and dynamics of gene regulation. In this article, we discuss how the CRP-Spot 42 feedforward loop is integrated into encompassing networks and how this loop may benefit enteric bacteria facing uncertain and changing nutrient conditions. PMID:21788732

Hybrid TLC-pair meter for the Sphinx Project

NASA Technical Reports Server (NTRS)

Wada, T.; Yamamoto, I.; Takahashi, N.; Misaki, A.

1985-01-01

The chief aims in THE SPHINX PROJECT are research of super lepton physics and new detector experiments. At the second phase of THE SPHINX PROJECT, a hybrid TLC-PAIR METER was designed for measuring high energy neutrino sources (E upsilon * TeV), searching high energy muon sources (E mu TeV) and measuring muon group (E mu 1 TeV). The principle of PAIR METER has been already proposed. In this TLC-PAIR METER, electromagnetic shower induced by cosmic ray muons are detected using TL (Thermoluminescence) sheets with position counters.

Time-domain diffuse optics: towards next generation devices

NASA Astrophysics Data System (ADS)

Contini, Davide; Dalla Mora, Alberto; Arridge, Simon; Martelli, Fabrizio; Tosi, Alberto; Boso, Gianluca; Farina, Andrea; Durduran, Turgut; Martinenghi, Edoardo; Torricelli, Alessandro; Pifferi, Antonio

2015-07-01

Diffuse optics is a powerful tool for clinical applications ranging from oncology to neurology, but also for molecular imaging, and quality assessment of food, wood and pharmaceuticals. We show that ideally time-domain diffuse optics can give higher contrast and a higher penetration depth with respect to standard technology. In order to completely exploit the advantages of a time-domain system a distribution of sources and detectors with fast gating capabilities covering all the sample surface is needed. Here, we present the building block to build up such system. This basic component is made of a miniaturised source-detector pair embedded into the probe based on pulsed Vertical-Cavity Surface-Emitting Lasers (VCSEL) as sources and Single-Photon Avalanche Diodes (SPAD) or Silicon Photomultipliers (SiPM) as detectors. The possibility to miniaturized and dramatically increase the number of source detectors pairs open the way to an advancement of diffuse optics in terms of improvement of performances and exploration of new applications. Furthermore, availability of compact devices with reduction in size and cost can boost the application of this technique.

Interdisciplinary Education and Critical Thinking in Religion and History: The Delivery of Two "Content-Based" Linked Courses

ERIC Educational Resources Information Center

McDougall, Roseanne; LaMonica, Jeffrey

2007-01-01

Primary sources in religion and history enable first year university students to connect "content-based" linked courses in the core curriculum. Fifty-four first year university students in three separate pairs of courses worked in teams to present oral critical reports on texts related to the Reformation, the Enlightenment, and the…

A big data geospatial analytics platform - Physical Analytics Integrated Repository and Services (PAIRS)

NASA Astrophysics Data System (ADS)

Hamann, H.; Jimenez Marianno, F.; Klein, L.; Albrecht, C.; Freitag, M.; Hinds, N.; Lu, S.

2015-12-01

A big data geospatial analytics platform:Physical Analytics Information Repository and Services (PAIRS)Fernando Marianno, Levente Klein, Siyuan Lu, Conrad Albrecht, Marcus Freitag, Nigel Hinds, Hendrik HamannIBM TJ Watson Research Center, Yorktown Heights, NY 10598A major challenge in leveraging big geospatial data sets is the ability to quickly integrate multiple data sources into physical and statistical models and be run these models in real time. A geospatial data platform called Physical Analytics Information and Services (PAIRS) is developed on top of open source hardware and software stack to manage Terabyte of data. A new data interpolation and re gridding is implemented where any geospatial data layers can be associated with a set of global grid where the grid resolutions is doubling for consecutive layers. Each pixel on the PAIRS grid have an index that is a combination of locations and time stamp. The indexing allow quick access to data sets that are part of a global data layers and allowing to retrieve only the data of interest. PAIRS takes advantages of parallel processing framework (Hadoop) in a cloud environment to digest, curate, and analyze the data sets while being very robust and stable. The data is stored on a distributed no-SQL database (Hbase) across multiple server, data upload and retrieval is parallelized where the original analytics task is broken up is smaller areas/volume, analyzed independently, and then reassembled for the original geographical area. The differentiating aspect of PAIRS is the ability to accelerate model development across large geographical regions and spatial resolution ranging from 0.1 m up to hundreds of kilometer. System performance is benchmarked on real time automated data ingestion and retrieval of Modis and Landsat data layers. The data layers are curated for sensor error, verified for correctness, and analyzed statistically to detect local anomalies. Multi-layer query enable PAIRS to filter different data layers based on specific conditions (e.g analyze flooding risk of a property based on topography, soil ability to hold water, and forecasted precipitation) or retrieve information about locations that share similar weather and vegetation patterns during extreme weather events like heat wave.

Observations on Rupture Behaviour of Fluid Induced Events at the Basel EGS Based on Empirical Green's Function Analysis

NASA Astrophysics Data System (ADS)

Folesky, J.; Kummerow, J.; Shapiro, S. A.; Asanuma, H.; Häring, M. O.

2015-12-01

The Emprirical Green's Function (EGF) method uses pairs of events of high wave form similarity and adjacent hypocenters to decompose the influences of source time function, ray path, instrument site, and instrument response. The seismogram of the smaller event is considered as the Green's Function which then can be deconvolved from the other seismogram. The result provides a reconstructed relative source time function (RSTF) of the larger event of that event pair. The comparison of the RSTFs at different stations of the observation systems produces information on the rupture process of the larger event based on the observation of the directivity effect and on changing RSTFs complexities.The Basel EGS dataset of 2006-2007 consists of about 2800 localized events of magnitudes between 0.0

Risk assessment of water pollution sources based on an integrated k-means clustering and set pair analysis method in the region of Shiyan, China.

PubMed

Li, Chunhui; Sun, Lian; Jia, Junxiang; Cai, Yanpeng; Wang, Xuan

2016-07-01

Source water areas are facing many potential water pollution risks. Risk assessment is an effective method to evaluate such risks. In this paper an integrated model based on k-means clustering analysis and set pair analysis was established aiming at evaluating the risks associated with water pollution in source water areas, in which the weights of indicators were determined through the entropy weight method. Then the proposed model was applied to assess water pollution risks in the region of Shiyan in which China's key source water area Danjiangkou Reservoir for the water source of the middle route of South-to-North Water Diversion Project is located. The results showed that eleven sources with relative high risk value were identified. At the regional scale, Shiyan City and Danjiangkou City would have a high risk value in term of the industrial discharge. Comparatively, Danjiangkou City and Yunxian County would have a high risk value in terms of agricultural pollution. Overall, the risk values of north regions close to the main stream and reservoir of the region of Shiyan were higher than that in the south. The results of risk level indicated that five sources were in lower risk level (i.e., level II), two in moderate risk level (i.e., level III), one in higher risk level (i.e., level IV) and three in highest risk level (i.e., level V). Also risks of industrial discharge are higher than that of the agricultural sector. It is thus essential to manage the pillar industry of the region of Shiyan and certain agricultural companies in the vicinity of the reservoir to reduce water pollution risks of source water areas. Copyright © 2016 Elsevier B.V. All rights reserved.

Investigation of focused and unfocused transducer beam patterns in moderately nonlinear absorbing media

NASA Astrophysics Data System (ADS)

Kharin, Nikolay A.

2001-05-01

The novel solution of the KZK equation for acoustic pressure of the second harmonic in slightly focused beam of a circular transducer was obtained in a closed form for moderately nonlinear absorbing media (Gol'dberg numbers ~ 1). The solution is based on the method of slowly changing wave profile in combination with the method of successive approximations. Two pairs of transducers (Valpey-Fisher Corp.) Were compared to investigate the influence of focusing on the applicability of the moderate nonlinearity approach. The first pair was of 0.25' diameter and the second was of 0.5' diameter. Both pairs has one transducer with flat surface and the other geometrically focused at 4'. The central frequency for all transducers was 5 MHz. Measurements were undertaken in the blood-mimicking solution of water and glycerine. The results demonstrated that for slightly focused transducers with circular apertures, the moderate nonlinearity approach is still valid, as it was proved for flat sources with the same source level, despite the higher pressures in the focal region. The peak pressure for the weakly focused system occurs at a shorter range than focal length.

Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing

PubMed Central

2013-01-01

Background A large-scale, highly accurate, machine-understandable drug-disease treatment relationship knowledge base is important for computational approaches to drug repurposing. The large body of published biomedical research articles and clinical case reports available on MEDLINE is a rich source of FDA-approved drug-disease indication as well as drug-repurposing knowledge that is crucial for applying FDA-approved drugs for new diseases. However, much of this information is buried in free text and not captured in any existing databases. The goal of this study is to extract a large number of accurate drug-disease treatment pairs from published literature. Results In this study, we developed a simple but highly accurate pattern-learning approach to extract treatment-specific drug-disease pairs from 20 million biomedical abstracts available on MEDLINE. We extracted a total of 34,305 unique drug-disease treatment pairs, the majority of which are not included in existing structured databases. Our algorithm achieved a precision of 0.904 and a recall of 0.131 in extracting all pairs, and a precision of 0.904 and a recall of 0.842 in extracting frequent pairs. In addition, we have shown that the extracted pairs strongly correlate with both drug target genes and therapeutic classes, therefore may have high potential in drug discovery. Conclusions We demonstrated that our simple pattern-learning relationship extraction algorithm is able to accurately extract many drug-disease pairs from the free text of biomedical literature that are not captured in structured databases. The large-scale, accurate, machine-understandable drug-disease treatment knowledge base that is resultant of our study, in combination with pairs from structured databases, will have high potential in computational drug repurposing tasks. PMID:23742147

Ultrabright, narrow-band photon-pair source for atomic quantum memories

NASA Astrophysics Data System (ADS)

Tsai, Pin-Ju; Chen, Ying-Cheng

2018-06-01

We demonstrate an ultrabright, narrow-band and frequency-tunable photon-pair source based on cavity-enhanced spontaneous parametric down conversion (SPDC) which is compatible with atomic transition of rubidium D 2-line (780 nm) or cesium D 2-line (852 nm). With the pump beam alternating between a high and a low power phase, the output is switching between the optical parametric oscillator (OPO) and photon-pair generation mode. We utilize the OPO output light to lock the cavity length to maintain the double resonances of signal and idler, as well as to lock the signal frequency to cesium atomic transition. With a type-II phase matching and a double-passed pump scheme such that the cluster frequency spacing is larger than the SPDC bandwidth, the photon-pair output is in a nearly single-mode operation as confirmed by a scanning Fabry–Perot interferometer with its output detected by a photomultiplier. The achieved generation and detection rates are 7.24× {10}5 and 6142 s‑1 mW‑1, respectively. The correlation time of the photon pair is 21.6(2.2) ns, corresponding to a bandwidth of 2π × 6.6(6) MHz. The spectral brightness is 1.06× {10}5 s‑1 mW‑1 MHz‑1. This is a relatively high value under a single-mode operation with the cavity-SPDC scheme. The generated single photons can be readily used in experiments related to atomic quantum memories.

Quantum Theory of Three-Dimensional Superresolution Using Rotating-PSF Imagery

NASA Astrophysics Data System (ADS)

Prasad, S.; Yu, Z.

The inverse of the quantum Fisher information (QFI) matrix (and extensions thereof) provides the ultimate lower bound on the variance of any unbiased estimation of a parameter from statistical data, whether of intrinsically quantum mechanical or classical character. We calculate the QFI for Poisson-shot-noise-limited imagery using the rotating PSF that can localize and resolve point sources fully in all three dimensions. We also propose an experimental approach based on the use of computer generated hologram and projective measurements to realize the QFI-limited variance for the problem of super-resolving a closely spaced pair of point sources at a highly reduced photon cost. The paper presents a preliminary analysis of quantum-limited three-dimensional (3D) pair optical super-resolution (OSR) problem with potential applications to astronomical imaging and 3D space-debris localization.

Ultrabright femtosecond source of biphotons based on a spatial mode inverter.

PubMed

Jarutis, Vygandas; Juodkazis, Saulius; Mizeikis, Vygantas; Sasaki, Keiji; Misawa, Hiroaki

2005-02-01

A method of enhancing the efficiency of entangled biphoton sources based on a type II femtosecond spontaneous parametric downconversion (SPDC) process is proposed and implemented experimentally. Enhancement is obtained by mode inversion of one of the SPDC output beams, which allows the beams to overlap completely, thus maximizing the number of SPDC photon pairs with optimum spatiotemporal overlap. By use of this method, biphoton count rates as high as 16 kHz from a single 0.5-mm-long beta-barium borate crystal pumped by second-harmonic radiation from a Ti:sapphire laser were obtained.

Whole-genome sequencing of Salmonella enterica subsp. enterica serovar Cubana strains isolated from agricultural sources

USDA-ARS?s Scientific Manuscript database

We report draft genomes of Salmonella enterica subsp. enterica Serovar Cubana strain CVM42234 isolated from chick feed in 2012 and Salmonella Cubana strain 76814 isolated from swine in 2004. The genome sizes are 4,975,046 and 4,936,251 base pairs, respectively....

Intense source of slow positrons

NASA Astrophysics Data System (ADS)

Perez, P.; Rosowsky, A.

2004-10-01

We describe a novel design for an intense source of slow positrons based on pair production with a beam of electrons from a 10 MeV accelerator hitting a thin target at a low incidence angle. The positrons are collected with a set of coils adapted to the large production angle. The collection system is designed to inject the positrons into a Greaves-Surko trap (Phys. Rev. A 46 (1992) 5696). Such a source could be the basis for a series of experiments in fundamental and applied research and would also be a prototype source for industrial applications, which concern the field of defect characterization in the nanometer scale.

Integrated Model of Multiple Kernel Learning and Differential Evolution for EUR/USD Trading

PubMed Central

Deng, Shangkun; Sakurai, Akito

2014-01-01

Currency trading is an important area for individual investors, government policy decisions, and organization investments. In this study, we propose a hybrid approach referred to as MKL-DE, which combines multiple kernel learning (MKL) with differential evolution (DE) for trading a currency pair. MKL is used to learn a model that predicts changes in the target currency pair, whereas DE is used to generate the buy and sell signals for the target currency pair based on the relative strength index (RSI), while it is also combined with MKL as a trading signal. The new hybrid implementation is applied to EUR/USD trading, which is the most traded foreign exchange (FX) currency pair. MKL is essential for utilizing information from multiple information sources and DE is essential for formulating a trading rule based on a mixture of discrete structures and continuous parameters. Initially, the prediction model optimized by MKL predicts the returns based on a technical indicator called the moving average convergence and divergence. Next, a combined trading signal is optimized by DE using the inputs from the prediction model and technical indicator RSI obtained from multiple timeframes. The experimental results showed that trading using the prediction learned by MKL yielded consistent profits. PMID:25097891

Sequence-similar, structure-dissimilar protein pairs in the PDB.

PubMed

Kosloff, Mickey; Kolodny, Rachel

2008-05-01

It is often assumed that in the Protein Data Bank (PDB), two proteins with similar sequences will also have similar structures. Accordingly, it has proved useful to develop subsets of the PDB from which "redundant" structures have been removed, based on a sequence-based criterion for similarity. Similarly, when predicting protein structure using homology modeling, if a template structure for modeling a target sequence is selected by sequence alone, this implicitly assumes that all sequence-similar templates are equivalent. Here, we show that this assumption is often not correct and that standard approaches to create subsets of the PDB can lead to the loss of structurally and functionally important information. We have carried out sequence-based structural superpositions and geometry-based structural alignments of a large number of protein pairs to determine the extent to which sequence similarity ensures structural similarity. We find many examples where two proteins that are similar in sequence have structures that differ significantly from one another. The source of the structural differences usually has a functional basis. The number of such proteins pairs that are identified and the magnitude of the dissimilarity depend on the approach that is used to calculate the differences; in particular sequence-based structure superpositioning will identify a larger number of structurally dissimilar pairs than geometry-based structural alignments. When two sequences can be aligned in a statistically meaningful way, sequence-based structural superpositioning provides a meaningful measure of structural differences. This approach and geometry-based structure alignments reveal somewhat different information and one or the other might be preferable in a given application. Our results suggest that in some cases, notably homology modeling, the common use of nonredundant datasets, culled from the PDB based on sequence, may mask important structural and functional information. We have established a data base of sequence-similar, structurally dissimilar protein pairs that will help address this problem (http://luna.bioc.columbia.edu/rachel/seqsimstrdiff.htm).

A selection of giant radio sources from NVSS

DOE PAGES

Proctor, D. D.

2016-06-01

Results of the application of pattern-recognition techniques to the problem of identifying giant radio sources (GRSs) from the data in the NVSS catalog are presented, and issues affecting the process are explored. Decision-tree pattern-recognition software was applied to training-set source pairs developed from known NVSS large-angular-size radio galaxies. The full training set consisted of 51,195 source pairs, 48 of which were known GRSs for which each lobe was primarily represented by a single catalog component. The source pairs had a maximum separation ofmore » $$20^{\\prime} $$ and a minimum component area of 1.87 square arcmin at the 1.4 mJy level. The importance of comparing the resulting probability distributions of the training and application sets for cases of unknown class ratio is demonstrated. The probability of correctly ranking a randomly selected (GRS, non-GRS) pair from the best of the tested classifiers was determined to be 97.8 ± 1.5%. The best classifiers were applied to the over 870,000 candidate pairs from the entire catalog. Images of higher-ranked sources were visually screened, and a table of over 1600 candidates, including morphological annotation, is presented. These systems include doubles and triples, wide-angle tail and narrow-angle tail, S- or Z-shaped systems, and core-jets and resolved cores. In conclusion, while some resolved-lobe systems are recovered with this technique, generally it is expected that such systems would require a different approach.« less

X-ray flares from runaway pair production in active galactic nuclei

NASA Technical Reports Server (NTRS)

Kirk, J. G.; Mastichiadis, A.

1992-01-01

The hard X-ray spectrum of AGNs is nonthermal, probably arising from an electron-positron pair cascade, with some emission reflected off relatively cold matter. There has been interest in models on which protons are accelerated and create relativistic electrons on interaction with a local radiation field. It is shown here that a sufficient column density of protons can lead to runaway pair production: photons generated by the relativistic pairs are the targets for the protons to produce more pairs. This can produce X-ray fluxes with the characteristics observed in AGN. The model predicts the maximum ratio of luminosity to source size as well as their spectrum in the early phases. The same mechanism may also be able to create the knots of synchrotron-radiating pair plasma seen in sources such as 3C273.

Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification

PubMed Central

Stanhope, Stephen A.; Sengupta, Srikumar; den Boon, Johan; Ahlquist, Paul; Newton, Michael A.

2009-01-01

MicroRNAs (miRNAs) posttranscriptionally regulate targeted messenger RNAs (mRNAs) by inducing cleavage or otherwise repressing their translation. We address the problem of detecting m/miRNA targeting relationships in homo sapiens from microarray data by developing statistical models that are motivated by the biological mechanisms used by miRNAs. The focus of our modeling is the construction, activity, and mediation of RNA-induced silencing complexes (RISCs) competent for targeted mRNA cleavage. We demonstrate that regression models accommodating RISC abundance and controlling for other mediating factors fit the expression profiles of known target pairs substantially better than models based on m/miRNA expressions alone, and lead to verifications of computational target pair predictions that are more sensitive than those based on marginal expression levels. Because our models are fully independent of exogenous results from sequence-based computational methods, they are appropriate for use as either a primary or secondary source of information regarding m/miRNA target pair relationships, especially in conjunction with high-throughput expression studies. PMID:19779550

Integrated radiotherapy imaging system (IRIS): design considerations of tumour tracking with linac gantry-mounted diagnostic x-ray systems with flat-panel detectors

NASA Astrophysics Data System (ADS)

Berbeco, Ross I.; Jiang, Steve B.; Sharp, Gregory C.; Chen, George T. Y.; Mostafavi, Hassan; Shirato, Hiroki

2004-01-01

The design of an integrated radiotherapy imaging system (IRIS), consisting of gantry mounted diagnostic (kV) x-ray tubes and fast read-out flat-panel amorphous-silicon detectors, has been studied. The system is meant to be capable of three main functions: radiographs for three-dimensional (3D) patient set-up, cone-beam CT and real-time tumour/marker tracking. The goal of the current study is to determine whether one source/panel pair is sufficient for real-time tumour/marker tracking and, if two are needed, the optimal position of each relative to other components and the isocentre. A single gantry-mounted source/imager pair is certainly capable of the first two of the three functions listed above and may also be useful for the third, if combined with prior knowledge of the target's trajectory. This would be necessary because only motion in two dimensions is visible with a single imager/source system. However, with previously collected information about the trajectory, the third coordinate may be derived from the other two with sufficient accuracy to facilitate tracking. This deduction of the third coordinate can only be made if the 3D tumour/marker trajectory is consistent from fraction to fraction. The feasibility of tumour tracking with one source/imager pair has been theoretically examined here using measured lung marker trajectory data for seven patients from multiple treatment fractions. The patients' selection criteria include minimum mean amplitudes of the tumour motions greater than 1 cm peak-to-peak. The marker trajectory for each patient was modelled using the first fraction data. Then for the rest of the data, marker positions were derived from the imager projections at various gantry angles and compared with the measured tumour positions. Our results show that, due to the three dimensionality and irregular trajectory characteristics of tumour motion, on a fraction-to-fraction basis, a 'monoscopic' system (single source/imager) is inadequate for consistent real-time tumour tracking, even with prior knowledge. We found that, among the seven patients studied with peak-to-peak marker motion greater than 1 cm, five cases have mean localization errors greater than 2 mm and two have mean errors greater than 3 mm. Because of this uncertainty associated with a monoscopic system, two source/imager pairs are necessary for robust 3D target localization. Dual orthogonal x-ray source/imager pairs mounted on the linac gantry are chosen for the IRIS. We further studied the placement of the x-ray sources/panel based on the geometric specifications of the Varian 21EX Clinac. The best configuration minimizes the localization error while maintaining a large field of view and avoiding collisions with the floor/ceiling or couch.

A terrain-based paired-site sampling design to assess biodiversity losses from eastern hemlock decline

USGS Publications Warehouse

Young, J.A.; Smith, D.R.; Snyder, C.D.; Lemarie, D.P.

2002-01-01

Biodiversity surveys are often hampered by the inability to control extraneous sources of variability introduced into comparisons of populations across a heterogenous landscape. If not specifically accounted for a priori, this noise can weaken comparisons between sites, and can make it difficult to draw inferences about specific ecological processes. We developed a terrain-based, paired-site sampling design to analyze differences in aquatic biodiversity between streams draining eastern hemlock (Tsuga canadensis) forests, and those draining mixed hardwood forests in Delaware Water Gap National Recreation Area (USA). The goal of this design was to minimize variance due to terrain influences on stream communities, while representing the range of hemlock dominated stream environments present in the park. We used geographic information systems (GIS) and cluster analysis to define and partition hemlock dominated streams into terrain types based on topographic variables and stream order. We computed similarity of forest stands within terrain types and used this information to pair hemlock-dominated streams with hardwood counterparts prior to sampling. We evaluated the effectiveness of the design through power analysis and found that power to detect differences in aquatic invertebrate taxa richness was highest when sites were paired and terrain type was included as a factor in the analysis. Precision of the estimated difference in mean richness was nearly doubled using the terrain-based, paired site design in comparison to other evaluated designs. Use of this method allowed us to sample stream communities representative of park-wide forest conditions while effectively controlling for landscape variability.

Optical sensing system based on wireless paired emitter detector diode device and ionogels for lab-on-a-disc water quality analysis.

PubMed

Czugala, Monika; Gorkin, Robert; Phelan, Thomas; Gaughran, Jennifer; Curto, Vincenzo Fabio; Ducrée, Jens; Diamond, Dermot; Benito-Lopez, Fernando

2012-12-07

This work describes the first use of a wireless paired emitter detector diode device (PEDD) as an optical sensor for water quality monitoring in a lab-on-a-disc device. The microfluidic platform, based on an ionogel sensing area combined with a low-cost optical sensor, is applied for quantitative pH and qualitative turbidity monitoring of water samples at point-of-need. The autonomous capabilities of the PEDD system, combined with the portability and wireless communication of the full device, provide the flexibility needed for on-site water testing. Water samples from local fresh and brackish sources were successfully analysed using the device, showing very good correlation with standard bench-top systems.

VizieR Online Data Catalog: NIR proper motion catalogue from UKIDSS-LAS (Smith+, 2014)

NASA Astrophysics Data System (ADS)

Smith, L.; Lucas, P. W.; Burningham, B.; Jones, H. R. A.; Smart, R. L.; Andrei, A. H.; Catalan, S.; Pinfield, D. J.

2015-07-01

We constructed two epoch catalogues for each pointing by matching sources within the pairs of multiframes using the Starlink Tables Infrastructure Library Tool Set (STILTS; Taylor 2006, ASP conf. Ser. 351, 666). We required pairs of sources to be uniquely paired to their closest match within 6-arcsec, and we required the J band magnitudes for the two epochs to agree within 0.5mag, to minimize mismatches. (1 data file).

Methylene blue, curcumin and ion pairing nanoparticles effects on photodynamic therapy of MDA-MB-231 breast cancer cell.

PubMed

Hosseinzadeh, Reza; Khorsandi, Khatereh

2017-06-01

The aim of current study was to use methylene blue-curcumin ion pair nanoparticles and single dyes as photosensitizer for comparison of photodynamic therapy (PDT) efficacy on MDA-MB-231 cancer cells, also various light sources effect on activation of photosensitizer (PS) was considered. Ion pair nanoparticles were synthesized using opposite charge ions precipitation and lyophilized. The PDT experiments were designed and the effect of PSs and light sources (Red LED (630nm; power density: 30mWcm -2 ) and blue LED (465nm; power density: 34mWcm -2 )) on the human breast cancer cell line were examined. The effect of PS concentration (0-75μg.mL -1 ), incubation time, irradiation time and light sources, and priority in irradiation of blue or red lights were determined. The results show that the ion pairing of methylene blue and curcumin enhance the photodynamic activity of both dyes and the cytotoxicity of ion pair nanoparticles on the MDA-231 breast cancer cell line. Blue and red LED light sources were used for photo activation of photosensitizers. The results demonstrated that both dyes can activate using red light LED better than blue light LED for singlet oxygen producing. Nano scale ion pair precipitating of methylene blue-curcumin enhanced the cell penetrating and subsequently cytotoxicity of both dyes together. Copyright © 2017 Elsevier B.V. All rights reserved.

The Kadomtsev{endash}Petviashvili equation as a source of integrable model equations

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

Maccari, A.

1996-12-01

A new integrable and nonlinear partial differential equation (PDE) in 2+1 dimensions is obtained, by an asymptotically exact reduction method based on Fourier expansion and spatiotemporal rescaling, from the Kadomtsev{endash}Petviashvili equation. The integrability property is explicitly demonstrated, by exhibiting the corresponding Lax pair, that is obtained by applying the reduction technique to the Lax pair of the Kadomtsev{endash}Petviashvili equation. This model equation is likely to be of applicative relevance, because it may be considered a consistent approximation of a large class of nonlinear evolution PDEs. {copyright} {ital 1996 American Institute of Physics.}

Diffractive shear interferometry for extreme ultraviolet high-resolution lensless imaging

NASA Astrophysics Data System (ADS)

Jansen, G. S. M.; de Beurs, A.; Liu, X.; Eikema, K. S. E.; Witte, S.

2018-05-01

We demonstrate a novel imaging approach and associated reconstruction algorithm for far-field coherent diffractive imaging, based on the measurement of a pair of laterally sheared diffraction patterns. The differential phase profile retrieved from such a measurement leads to improved reconstruction accuracy, increased robustness against noise, and faster convergence compared to traditional coherent diffractive imaging methods. We measure laterally sheared diffraction patterns using Fourier-transform spectroscopy with two phase-locked pulse pairs from a high harmonic source. Using this approach, we demonstrate spectrally resolved imaging at extreme ultraviolet wavelengths between 28 and 35 nm.

Robust transcriptional tumor signatures applicable to both formalin-fixed paraffin-embedded and fresh-frozen samples

PubMed Central

Cheng, Jun; He, Jun; Liu, Huaping; Cai, Hao; Hong, Guini; Zhang, Jiahui; Li, Na; Ao, Lu; Guo, Zheng

2017-01-01

Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable resource for clinical researches. However, FFPE samples are usually considered an unreliable source for gene expression analysis due to the partial RNA degradation. In this study, through comparing gene expression profiles between FFPE samples and paired fresh-frozen (FF) samples for three cancer types, we firstly showed that expression measurements of thousands of genes had at least two-fold change in FFPE samples compared with paired FF samples. Therefore, for a transcriptional signature based on risk scores summarized from the expression levels of the signature genes, the risk score thresholds trained from FFPE (or FF) samples could not be applied to FF (or FFPE) samples. On the other hand, we found that more than 90% of the relative expression orderings (REOs) of gene pairs in the FF samples were maintained in their paired FFPE samples and largely unaffected by the storage time. The result suggested that the REOs of gene pairs were highly robust against partial RNA degradation in FFPE samples. Finally, as a case study, we developed a REOs-based signature to distinguish liver cirrhosis from hepatocellular carcinoma (HCC) using FFPE samples. The signature was validated in four datasets of FFPE samples and eight datasets of FF samples. In conclusion, the valuable FFPE samples can be fully exploited to identify REOs-based diagnostic and prognostic signatures which could be robustly applicable to both FF samples and FFPE samples with degraded RNA. PMID:28036264

Towards building a disease-phenotype knowledge base: extracting disease-manifestation relationship from literature

PubMed Central

Xu, Rong; Li, Li; Wang, QuanQiu

2013-01-01

Motivation: Systems approaches to studying phenotypic relationships among diseases are emerging as an active area of research for both novel disease gene discovery and drug repurposing. Currently, systematic study of disease phenotypic relationships on a phenome-wide scale is limited because large-scale machine-understandable disease–phenotype relationship knowledge bases are often unavailable. Here, we present an automatic approach to extract disease–manifestation (D-M) pairs (one specific type of disease–phenotype relationship) from the wide body of published biomedical literature. Data and Methods: Our method leverages external knowledge and limits the amount of human effort required. For the text corpus, we used 119 085 682 MEDLINE sentences (21 354 075 citations). First, we used D-M pairs from existing biomedical ontologies as prior knowledge to automatically discover D-M–specific syntactic patterns. We then extracted additional pairs from MEDLINE using the learned patterns. Finally, we analysed correlations between disease manifestations and disease-associated genes and drugs to demonstrate the potential of this newly created knowledge base in disease gene discovery and drug repurposing. Results: In total, we extracted 121 359 unique D-M pairs with a high precision of 0.924. Among the extracted pairs, 120 419 (99.2%) have not been captured in existing structured knowledge sources. We have shown that disease manifestations correlate positively with both disease-associated genes and drug treatments. Conclusions: The main contribution of our study is the creation of a large-scale and accurate D-M phenotype relationship knowledge base. This unique knowledge base, when combined with existing phenotypic, genetic and proteomic datasets, can have profound implications in our deeper understanding of disease etiology and in rapid drug repurposing. Availability: http://nlp.case.edu/public/data/DMPatternUMLS/ Contact: rxx@case.edu PMID:23828786

Accelerating calculations of RNA secondary structure partition functions using GPUs

PubMed Central

2013-01-01

Background RNA performs many diverse functions in the cell in addition to its role as a messenger of genetic information. These functions depend on its ability to fold to a unique three-dimensional structure determined by the sequence. The conformation of RNA is in part determined by its secondary structure, or the particular set of contacts between pairs of complementary bases. Prediction of the secondary structure of RNA from its sequence is therefore of great interest, but can be computationally expensive. In this work we accelerate computations of base-pair probababilities using parallel graphics processing units (GPUs). Results Calculation of the probabilities of base pairs in RNA secondary structures using nearest-neighbor standard free energy change parameters has been implemented using CUDA to run on hardware with multiprocessor GPUs. A modified set of recursions was introduced, which reduces memory usage by about 25%. GPUs are fastest in single precision, and for some hardware, restricted to single precision. This may introduce significant roundoff error. However, deviations in base-pair probabilities calculated using single precision were found to be negligible compared to those resulting from shifting the nearest-neighbor parameters by a random amount of magnitude similar to their experimental uncertainties. For large sequences running on our particular hardware, the GPU implementation reduces execution time by a factor of close to 60 compared with an optimized serial implementation, and by a factor of 116 compared with the original code. Conclusions Using GPUs can greatly accelerate computation of RNA secondary structure partition functions, allowing calculation of base-pair probabilities for large sequences in a reasonable amount of time, with a negligible compromise in accuracy due to working in single precision. The source code is integrated into the RNAstructure software package and available for download at http://rna.urmc.rochester.edu. PMID:24180434

Can tautomerization of the A·T Watson-Crick base pair via double proton transfer provoke point mutations during DNA replication? A comprehensive QM and QTAIM analysis.

PubMed

Brovarets, Ol'ha O; Hovorun, Dmytro M

2014-01-01

Trying to answer the question posed in the title, we have carried out a detailed theoretical investigation of the biologically important mechanism of the tautomerization of the A·T Watson-Crick DNA base pair, information that is hard to establish experimentally. By combining theoretical investigations at the MP2 and density functional theory levels of QM theory with quantum theory of atoms in molecules analysis, the tautomerization of the A·T Watson-Crick base pair by the double proton transfer (DPT) was comprehensively studied in vacuo and in the continuum with a low dielectric constant (ϵ = 4) corresponding to a hydrophobic interfaces of protein-nucleic acid interactions. Based on the sweeps of the electron-topological, geometric, and energetic parameters, which describe the course of the tautomerization along its intrinsic reaction coordinate (IRC), it was proved that the A·T → A(∗)·T(∗) tautomerization through the DPT is a concerted (i.e. the pathway without an intermediate) and asynchronous (i.e. protons move with a time gap) process. The limiting stage of this phenomenon is the final PT along the N6H⋯O4 hydrogen bond (H-bond). The continuum with ϵ = 4 does not affect qualitatively the course of the tautomerization reaction: similar to that observed in vacuo, it proceeds via a concerted asynchronous process with the same structure of the transition state (TS). For the first time, the nine key points along the IRC of the A·T base pair tautomerization, which could be considered as electron-topological "fingerprints" of a concerted asynchronous process of the tautomerization via the DPT, have been identified and fully characterized. These nine key points have been used to define the reactant, TS, and product regions of the DPT in the A·T base pair. Considering the energy dependence of each of the three H-bonds, which stabilize the Watson-Crick and Löwdin's base pairs, along the IRC of the tautomerization, it was found that all these H-bonds in the А·Т base pair are cooperative, reinforcing each other, whereas the C2H⋯O2 H-bond in the А(∗)·Т(∗) base pair behaves anticooperatively, in other words it gets weakened while two others get strengthened. From a quantum-mechanical point of view, the A(∗)·T(∗) Löwdin's base pair appeared to be dynamically unstable because the electronic energy of the back-reaction barrier of the A·T → A(∗)·T(∗) tautomerization does not exceed zero-point vibrational energy associated with the mode for which vibrational frequency becomes imaginary in the TS of tautomerization. Additionally, it was demonstrated using the conductor-like polarizable continuum model that the effects of biomolecular environment (ϵ = 4) cannot ensure dynamic stabilization of the A(∗)·T(∗) Löwdin's base pair. These findings, together with data available from the literature, indicate that the tautomerization of the A·T Watson-Crick base pair to the A(∗)·T(∗) Löwdin's base pair through the DPT cannot be a source of spontaneous point errors that occur during DNA replication.

Modeling of light distribution in the brain for topographical imaging

NASA Astrophysics Data System (ADS)

Okada, Eiji; Hayashi, Toshiyuki; Kawaguchi, Hiroshi

2004-07-01

Multi-channel optical imaging system can obtain a topographical distribution of the activated region in the brain cortex by a simple mapping algorithm. Near-infrared light is strongly scattered in the head and the volume of tissue that contributes to the change in the optical signal detected with source-detector pair on the head surface is broadly distributed in the brain. This scattering effect results in poor resolution and contrast in the topographic image of the brain activity. We report theoretical investigations on the spatial resolution of the topographic imaging of the brain activity. The head model for the theoretical study consists of five layers that imitate the scalp, skull, subarachnoid space, gray matter and white matter. The light propagation in the head model is predicted by Monte Carlo simulation to obtain the spatial sensitivity profile for a source-detector pair. The source-detector pairs are one dimensionally arranged on the surface of the model and the distance between the adjoining source-detector pairs are varied from 4 mm to 32 mm. The change in detected intensity caused by the absorption change is obtained by Monte Carlo simulation. The position of absorption change is reconstructed by the conventional mapping algorithm and the reconstruction algorithm using the spatial sensitivity profiles. We discuss the effective interval between the source-detector pairs and the choice of reconstruction algorithms to improve the topographic images of brain activity.

Ross filter pairs for metal artefact reduction in x-ray tomography: a case study based on imaging and segmentation of metallic implants

NASA Astrophysics Data System (ADS)

Arhatari, Benedicta D.; Abbey, Brian

2018-01-01

Ross filter pairs have recently been demonstrated as a highly effective means of producing quasi-monoenergetic beams from polychromatic X-ray sources. They have found applications in both X-ray spectroscopy and for elemental separation in X-ray computed tomography (XCT). Here we explore whether they could be applied to the problem of metal artefact reduction (MAR) for applications in medical imaging. Metal artefacts are a common problem in X-ray imaging of metal implants embedded in bone and soft tissue. A number of data post-processing approaches to MAR have been proposed in the literature, however these can be time-consuming and sometimes have limited efficacy. Here we describe and demonstrate an alternative approach based on beam conditioning using Ross filter pairs. This approach obviates the need for any complex post-processing of the data and enables MAR and segmentation from the surrounding tissue by exploiting the absorption edge contrast of the implant.

Auction-based Security Game for Multiuser Cooperative Networks

NASA Astrophysics Data System (ADS)

Wang, An; Cai, Yueming; Yang, Wendong; Cheng, Yunpeng

2013-04-01

In this paper, we develop an auction-based algorithm to allocate the relay power efficiently to improve the system secrecy rate in a cooperative network, where several source-destination pairs and one cooperative relay are involved. On the one hand, the cooperative relay assists these pairs to transmit under a peak power constraint. On the other hand, the relay is untrusty and is also a passive eavesdropper. The whole auction process is completely distributed and no instantaneous channel state information exchange is needed. We also prove the existence and uniqueness of the Nash Equilibrium (NE) for the proposed power auction game. Moreover, the Pareto optimality is also validated. Simulation results show that our proposed auction-based algorithm can effectively improve the system secrecy rate. Besides, the proposed auction-based algorithm can converge to the unique NE point within a finite number of iterations. More interestingly, we also find that the proposed power auction mechanism is cheat-proof.

Near-Field Source Localization by Using Focusing Technique

NASA Astrophysics Data System (ADS)

He, Hongyang; Wang, Yide; Saillard, Joseph

2008-12-01

We discuss two fast algorithms to localize multiple sources in near field. The symmetry-based method proposed by Zhi and Chia (2007) is first improved by implementing a search-free procedure for the reduction of computation cost. We present then a focusing-based method which does not require symmetric array configuration. By using focusing technique, the near-field signal model is transformed into a model possessing the same structure as in the far-field situation, which allows the bearing estimation with the well-studied far-field methods. With the estimated bearing, the range estimation of each source is consequently obtained by using 1D MUSIC method without parameter pairing. The performance of the improved symmetry-based method and the proposed focusing-based method is compared by Monte Carlo simulations and with Crammer-Rao bound as well. Unlike other near-field algorithms, these two approaches require neither high-computation cost nor high-order statistics.

CALUTRON ION SOURCE

DOEpatents

Lofgren, E.J.

1959-02-17

An improvement is described in ion source mechanisms whereby the source structure is better adapted to withstanid the ravages of heat, erosion, and deterioration concomitant with operation of an ion source of the calutron type. A pair of molybdenum plates define the exit opening of the arc chamber and are in thermal contact with the walls of the chamber. These plates are maintained at a reduced temperature by a pair of copper blocks in thermal conducting contact therewith to form subsequent diverging margins for the exit opening.

Attenuation Tomography of Northern California and the Yellow Sea/Korean Peninsula from Coda-Source Normalized and Direct LG Amplitudes

DTIC Science & Technology

2008-09-01

method correlate slightly with global Vs30 measurements . While the coda-source and amplitude ratio methods do not correlate with Vs30 measurements ...Ford et al., 2008), we compared 1-D methods to measure QLg and attempted to assess the error associated with the results. The assessment showed the...reverse two-station (RTS), source-pair/receiver-pair (SPRP), and the new coda-source normalization (CS) methods to measure Q of the regional phase, Lg

Energy-tunable sources of entangled photons: a viable concept for solid-state-based quantum relays.

PubMed

Trotta, Rinaldo; Martín-Sánchez, Javier; Daruka, Istvan; Ortix, Carmine; Rastelli, Armando

2015-04-17

We propose a new method of generating triggered entangled photon pairs with wavelength on demand. The method uses a microstructured semiconductor-piezoelectric device capable of dynamically reshaping the electronic properties of self-assembled quantum dots (QDs) via anisotropic strain engineering. Theoretical models based on k·p theory in combination with finite-element calculations show that the energy of the polarization-entangled photons emitted by QDs can be tuned in a range larger than 100 meV without affecting the degree of entanglement of the quantum source. These results pave the way towards the deterministic implementation of QD entanglement resources in all-electrically-controlled solid-state-based quantum relays.

Energy-Tunable Sources of Entangled Photons: A Viable Concept for Solid-State-Based Quantum Relays

NASA Astrophysics Data System (ADS)

Trotta, Rinaldo; Martín-Sánchez, Javier; Daruka, Istvan; Ortix, Carmine; Rastelli, Armando

2015-04-01

We propose a new method of generating triggered entangled photon pairs with wavelength on demand. The method uses a microstructured semiconductor-piezoelectric device capable of dynamically reshaping the electronic properties of self-assembled quantum dots (QDs) via anisotropic strain engineering. Theoretical models based on k .p theory in combination with finite-element calculations show that the energy of the polarization-entangled photons emitted by QDs can be tuned in a range larger than 100 meV without affecting the degree of entanglement of the quantum source. These results pave the way towards the deterministic implementation of QD entanglement resources in all-electrically-controlled solid-state-based quantum relays.

Heterospecific pairing and hybridization between Nasutitermes corniger and N. ephratae

NASA Astrophysics Data System (ADS)

Hartke, Tamara R.; Rosengaus, Rebeca B.

2011-09-01

The sympatric neotropical termites Nasutitermes corniger and Nasutitermes ephratae are clearly distinguishable based on morphology, nest architecture, defensive secretion composition, and molecular markers. However, given the extensive ecological, geographical, and behavioral overlap of these closely related species, the potential for interbreeding may exist. To explore this possibility, heterospecific pairs were formed experimentally to examine courtship and colony-establishment behaviors, and reproductive potential. Courtship and nest construction behavior occurred in heterospecific pairs in a similar manner to that of conspecific pairs. Survival of pairs depended upon the species of the female partner. N. ephratae females paired with N. corniger males produced as many offspring as conspecific pairs. N. corniger females mated to N. ephratae males, however, produced significantly fewer offspring at 60 days post-establishment than the reciprocal cross or conspecific N. ephratae or N. corniger pairs. This was also the only pairing in which any aggression was observed. Heterospecific pairs and groups formed in mate choice mesocosms, suggesting that species recognition between these two termites is not an important aspect of mate choice. Overall, species mismatch tolerance and hybrid offspring viability are high. The present data, together with previous evidence from defensive secretions and isozyme analysis, suggest that hybridization may periodically occur in nature, and that reproductive barriers between these two species may be incomplete. Hybridization could provide a rare but important source of genetic diversity and may ensure mating opportunities for the more abundant sex of alates in each species.

Past, present and future of kidney paired donation transplantation in India

PubMed Central

Kute, Vivek B; Patel, Himanshu V; Shah, Pankaj R; Modi, Pranjal R; Shah, Veena R; Rizvi, Sayyed J; Pal, Bipin C; Modi, Manisha P; Shah, Priya S; Varyani, Umesh T; Wakhare, Pavan S; Shinde, Saiprasad G; Ghodela, Vijay A; Patel, Minaxi H; Trivedi, Varsha B; Trivedi, Hargovind L

2017-01-01

One third of healthy willing living kidney donors are rejected due to ABO blood group incompatibility and donor specific antibody. This increases pre-transplant dialysis duration leading to increased morbidity and mortality on the kidney transplantation waiting list. Over the last decade kidney paired donation is most rapidly increased source of living kidney donors. In a kidney transplantation program dominated by living donor kidney transplantation, kidney paired donation is a legal and valid alternative strategy to increase living donor kidney transplantation. This is more useful in countries with limited resources where ABO incompatible kidney transplantation or desensitization protocol is not feasible because of costs/infectious complications and deceased donor kidney transplantation is in initial stages. The matching allocation, ABO blood type imbalance, reciprocity, simultaneity, geography were the limitation for the expansion of kidney paired donation. Here we describe different successful ways to increase living donor kidney transplantation through kidney paired donation. Compatible pairs, domino chain, combination of kidney paired donation with desensitization or ABO incompatible transplantation, international kidney paired donation, non-simultaneous, extended, altruistic donor chain and list exchange are different ways to expand the donor pool. In absence of national kidney paired donation program, a dedicated kidney paired donation team will increase access to living donor kidney transplantation in individual centres with team work. Use of social networking sites to expand donor pool, HLA based national kidney paired donation program will increase quality and quantity of kidney paired donation transplantation. Transplant centres should remove the barriers to a broader implementation of multicentre, national kidney paired donation program to further optimize potential of kidney paired donation to increase transplantation of O group and sensitized patients. This review assists in the development of similar programs in other developing countries. PMID:28507916

Past, present and future of kidney paired donation transplantation in India.

PubMed

Kute, Vivek B; Patel, Himanshu V; Shah, Pankaj R; Modi, Pranjal R; Shah, Veena R; Rizvi, Sayyed J; Pal, Bipin C; Modi, Manisha P; Shah, Priya S; Varyani, Umesh T; Wakhare, Pavan S; Shinde, Saiprasad G; Ghodela, Vijay A; Patel, Minaxi H; Trivedi, Varsha B; Trivedi, Hargovind L

2017-04-24

One third of healthy willing living kidney donors are rejected due to ABO blood group incompatibility and donor specific antibody. This increases pre-transplant dialysis duration leading to increased morbidity and mortality on the kidney transplantation waiting list. Over the last decade kidney paired donation is most rapidly increased source of living kidney donors. In a kidney transplantation program dominated by living donor kidney transplantation, kidney paired donation is a legal and valid alternative strategy to increase living donor kidney transplantation. This is more useful in countries with limited resources where ABO incompatible kidney transplantation or desensitization protocol is not feasible because of costs/infectious complications and deceased donor kidney transplantation is in initial stages. The matching allocation, ABO blood type imbalance, reciprocity, simultaneity, geography were the limitation for the expansion of kidney paired donation. Here we describe different successful ways to increase living donor kidney transplantation through kidney paired donation. Compatible pairs, domino chain, combination of kidney paired donation with desensitization or ABO incompatible transplantation, international kidney paired donation, non-simultaneous, extended, altruistic donor chain and list exchange are different ways to expand the donor pool. In absence of national kidney paired donation program, a dedicated kidney paired donation team will increase access to living donor kidney transplantation in individual centres with team work. Use of social networking sites to expand donor pool, HLA based national kidney paired donation program will increase quality and quantity of kidney paired donation transplantation. Transplant centres should remove the barriers to a broader implementation of multicentre, national kidney paired donation program to further optimize potential of kidney paired donation to increase transplantation of O group and sensitized patients. This review assists in the development of similar programs in other developing countries.

PPLN-waveguide-based polarization entangled QKD simulator

NASA Astrophysics Data System (ADS)

Gariano, John; Djordjevic, Ivan B.

2017-08-01

We have developed a comprehensive simulator to study the polarization entangled quantum key distribution (QKD) system, which takes various imperfections into account. We assume that a type-II SPDC source using a PPLN-based nonlinear optical waveguide is used to generate entangled photon pairs and implements the BB84 protocol, using two mutually unbiased basis with two orthogonal polarizations in each basis. The entangled photon pairs are then simulated to be transmitted to both parties; Alice and Bob, through the optical channel, imperfect optical elements and onto the imperfect detector. It is assumed that Eve has no control over the detectors, and can only gain information from the public channel and the intercept resend attack. The secure key rate (SKR) is calculated using an upper bound and by using actual code rates of LDPC codes implementable in FPGA hardware. After the verification of the simulation results, such as the pair generation rate and the number of error due to multiple pairs, for the ideal scenario, available in the literature, we then introduce various imperfections. Then, the results are compared to previously reported experimental results where a BBO nonlinear crystal is used, and the improvements in SKRs are determined for when a PPLN-waveguide is used instead.

Bright nanoscale source of deterministic entangled photon pairs violating Bell's inequality.

PubMed

Jöns, Klaus D; Schweickert, Lucas; Versteegh, Marijn A M; Dalacu, Dan; Poole, Philip J; Gulinatti, Angelo; Giudice, Andrea; Zwiller, Val; Reimer, Michael E

2017-05-10

Global, secure quantum channels will require efficient distribution of entangled photons. Long distance, low-loss interconnects can only be realized using photons as quantum information carriers. However, a quantum light source combining both high qubit fidelity and on-demand bright emission has proven elusive. Here, we show a bright photonic nanostructure generating polarization-entangled photon pairs that strongly violates Bell's inequality. A highly symmetric InAsP quantum dot generating entangled photons is encapsulated in a tapered nanowire waveguide to ensure directional emission and efficient light extraction. We collect ~200 kHz entangled photon pairs at the first lens under 80 MHz pulsed excitation, which is a 20 times enhancement as compared to a bare quantum dot without a photonic nanostructure. The performed Bell test using the Clauser-Horne-Shimony-Holt inequality reveals a clear violation (S CHSH  > 2) by up to 9.3 standard deviations. By using a novel quasi-resonant excitation scheme at the wurtzite InP nanowire resonance to reduce multi-photon emission, the entanglement fidelity (F = 0.817 ± 0.002) is further enhanced without temporal post-selection, allowing for the violation of Bell's inequality in the rectilinear-circular basis by 25 standard deviations. Our results on nanowire-based quantum light sources highlight their potential application in secure data communication utilizing measurement-device-independent quantum key distribution and quantum repeater protocols.

A resolution measure for three-dimensional microscopy

PubMed Central

Chao, Jerry; Ram, Sripad; Abraham, Anish V.; Ward, E. Sally; Ober, Raimund J.

2009-01-01

A three-dimensional (3D) resolution measure for the conventional optical microscope is introduced which overcomes the drawbacks of the classical 3D (axial) resolution limit. Formulated within the context of a parameter estimation problem and based on the Cramer-Rao lower bound, this 3D resolution measure indicates the accuracy with which a given distance between two objects in 3D space can be determined from the acquired image. It predicts that, given enough photons from the objects of interest, arbitrarily small distances of separation can be estimated with prespecified accuracy. Using simulated images of point source pairs, we show that the maximum likelihood estimator is capable of attaining the accuracy predicted by the resolution measure. We also demonstrate how different factors, such as extraneous noise sources and the spatial orientation of the imaged object pair, can affect the accuracy with which a given distance of separation can be determined. PMID:20161040

Integrated resonant micro-optical gyroscope and method of fabrication

DOEpatents

Vawter, G Allen [Albuquerque, NM; Zubrzycki, Walter J [Sandia Park, NM; Guo, Junpeng [Albuquerque, NM; Sullivan, Charles T [Albuquerque, NM

2006-09-12

An integrated optic gyroscope is disclosed which is based on a photonic integrated circuit (PIC) having a bidirectional laser source, a pair of optical waveguide phase modulators and a pair of waveguide photodetectors. The PIC can be connected to a passive ring resonator formed either as a coil of optical fiber or as a coiled optical waveguide. The lasing output from each end of the bidirectional laser source is phase modulated and directed around the passive ring resonator in two counterpropagating directions, with a portion of the lasing output then being detected to determine a rotation rate for the integrated optical gyroscope. The coiled optical waveguide can be formed on a silicon, glass or quartz substrate with a silicon nitride core and a silica cladding, while the PIC includes a plurality of III V compound semiconductor layers including one or more quantum well layers which are disordered in the phase modulators and to form passive optical waveguides.

Hybrid microfiber-lithium-niobate nanowaveguide structures as high-purity heralded single-photon sources

NASA Astrophysics Data System (ADS)

Main, Philip; Mosley, Peter J.; Ding, Wei; Zhang, Lijian; Gorbach, Andrey V.

2016-12-01

We propose a compact, fiber-integrated architecture for photon-pair generation by parametric downconversion with unprecedented flexibility in the properties of the photons produced. Our approach is based on a thin-film lithium niobate nanowaveguide, evanescently coupled to a tapered silica microfiber. We demonstrate how controllable mode hybridization between the fiber and waveguide yields control over the joint spectrum of the photon pairs. We also investigate how independent engineering of the linear and nonlinear properties of the structure can be achieved through the addition of a tapered, proton-exchanged layer to the waveguide. This allows further refinement of the joint spectrum through custom profiling of the effective nonlinearity, drastically improving the purity of the heralded photons. We give details of a source design capable of generating heralded single photons in the telecom wavelength range with purity of at least 0.95, and we provide a feasible fabrication methodology.

Development of double-pair double difference location algorithm and its application to the regular earthquakes and non-volcanic tremors

NASA Astrophysics Data System (ADS)

Guo, H.; Zhang, H.

2016-12-01

Relocating high-precision earthquakes is a central task for monitoring earthquakes and studying the structure of earth's interior. The most popular location method is the event-pair double-difference (DD) relative location method, which uses the catalog and/or more accurate waveform cross-correlation (WCC) differential times from event pairs with small inter-event separations to the common stations to reduce the effect of the velocity uncertainties outside the source region. Similarly, Zhang et al. [2010] developed a station-pair DD location method which uses the differential times from common events to pairs of stations to reduce the effect of the velocity uncertainties near the source region, to relocate the non-volcanic tremors (NVT) beneath the San Andreas Fault (SAF). To utilize advantages of both DD location methods, we have proposed and developed a new double-pair DD location method to use the differential times from pairs of events to pairs of stations. The new method can remove the event origin time and station correction terms from the inversion system and cancel out the effects of the velocity uncertainties near and outside the source region simultaneously. We tested and applied the new method on the northern California regular earthquakes to validate its performance. In comparison, among three DD location methods, the new double-pair DD method can determine more accurate relative locations and the station-pair DD method can better improve the absolute locations. Thus, we further proposed a new location strategy combining station-pair and double-pair differential times to determine accurate absolute and relative locations at the same time. For NVTs, it is difficult to pick the first arrivals and derive the WCC event-pair differential times, thus the general practice is to measure station-pair envelope WCC differential times. However, station-pair tremor locations are scattered due to the low-precision relative locations. The ability that double-pair data can be directly constructed from the station-pair data means that double-pair DD method can be used for improving NVT locations. We have applied the new method to the NVTs beneath the SAF near Cholame, California. Compared to the previous results, the new double-pair DD tremor locations are more concentrated and show more detailed structures.

ADEpedia 2.0: Integration of Normalized Adverse Drug Events (ADEs) Knowledge from the UMLS.

PubMed

Jiang, Guoqian; Liu, Hongfang; Solbrig, Harold R; Chute, Christopher G

2013-01-01

A standardized Adverse Drug Events (ADEs) knowledge base that encodes known ADE knowledge can be very useful in improving ADE detection for drug safety surveillance. In our previous study, we developed the ADEpedia that is a standardized knowledge base of ADEs based on drug product labels. The objectives of the present study are 1) to integrate normalized ADE knowledge from the Unified Medical Language System (UMLS) into the ADEpedia; and 2) to enrich the knowledge base with the drug-disorder co-occurrence data from a 51-million-document electronic medical records (EMRs) system. We extracted 266,832 drug-disorder concept pairs from the UMLS, covering 14,256 (1.69%) distinct drug concepts and 19,006 (3.53%) distinct disorder concepts. Of them, 71,626 (26.8%) concept pairs from UMLS co-occurred in the EMRs. We performed a preliminary evaluation on the utility of the UMLS ADE data. In conclusion, we have built an ADEpedia 2.0 framework that intends to integrate known ADE knowledge from disparate sources. The UMLS is a useful source for providing standardized ADE knowledge relevant to indications, contraindications and adverse effects, and complementary to the ADE data from drug product labels. The statistics from EMRs would enable the meaningful use of ADE data for drug safety surveillance.

Source Characterization of Microseismic Events using Empirical Green's Functions at the Basel EGS Project

NASA Astrophysics Data System (ADS)

Folesky, Jonas; Kummerow, Jörn

2015-04-01

The Empirical Green's Function (EGF) method uses pairs of events of high wave form similarity and adjacent hypocenters to decompose the influences of source time function, ray path, instrument site, and instrument response. The seismogram of the smaller event is considered as the Green's function which then can be deconvolved from the other seismogram. The result provides a reconstructed relative source time function (RSTF) of the larger event of that event pair. The comparison of the RSTFs at all stations of the observation systems produces information on the rupture process of the event based on an apparent directivity effect and possible changes in the RSTFs complexities. The Basel EGS dataset of 2006-2007 consists of about 2800 localized events of magnitudes between 0.0 < ML < 3.5 with event pairs of adequate magnitude difference for EGF analysis. The data has sufficient quality to analyse events with magnitudes down to ML = 0.0 for an apparent directivity effect although the approximate rupture duration for those events is of only a few milliseconds. The dataset shows a number of multiplets where fault plane solutions are known from earlier studies. Using the EGF method we compute rupture orientations for about 190 event pairs and compare them to the fault plane solutions of the multiplets. For the majority of events we observe a good consistency between the rupture direction found there and one of the previously determined nodal planes from fault plane solutions. In combination this resolves the fault plane ambiguity. Furthermore the rupture direction fitting yields estimates for projections of the rupture velocity on the horizontal plane. They seem to vary between the multiplets in the reservoir from 0.3 to 0.7 times the S-wave velocity. To our knowledge source characterization by EGF analysis has not yet been introduced to microseismic reservoirs with the data quality found in Basel. Our results show that EGF analysis can provide valuable additional insights on the distribution of rupture properties within the reservoir.

Mismatch and G-Stack Modulated Probe Signals on SNP Microarrays

PubMed Central

Binder, Hans; Fasold, Mario; Glomb, Torsten

2009-01-01

Background Single nucleotide polymorphism (SNP) arrays are important tools widely used for genotyping and copy number estimation. This technology utilizes the specific affinity of fragmented DNA for binding to surface-attached oligonucleotide DNA probes. We analyze the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the probe sequence to identify relevant sequence motifs which potentially cause systematic biases of genotyping and copy number estimates. Methodology/Principal Findings The probe design of GeneChip SNP arrays enables us to disentangle different sources of intensity modulations such as the number of mismatches per duplex, matched and mismatched base pairings including nearest and next-nearest neighbors and their position along the probe sequence. The effect of probe sequence was estimated in terms of triple-motifs with central matches and mismatches which include all 256 combinations of possible base pairings. The probe/target interactions on the chip can be decomposed into nearest neighbor contributions which correlate well with free energy terms of DNA/DNA-interactions in solution. The effect of mismatches is about twice as large as that of canonical pairings. Runs of guanines (G) and the particular type of mismatched pairings formed in cross-allelic probe/target duplexes constitute sources of systematic biases of the probe signals with consequences for genotyping and copy number estimates. The poly-G effect seems to be related to the crowded arrangement of probes which facilitates complex formation of neighboring probes with at minimum three adjacent G's in their sequence. Conclusions The applied method of “triple-averaging” represents a model-free approach to estimate the mean intensity contributions of different sequence motifs which can be applied in calibration algorithms to correct signal values for sequence effects. Rules for appropriate sequence corrections are suggested. PMID:19924253

Nonlinear Optical Properties of Traditional and Novel Materials

NASA Astrophysics Data System (ADS)

Krupa, Sean J.

Nonlinear optical processes are an excellent candidate to provide the heralded, indistinguishable, or entangled photons necessary for development of quantum mechanics based technology which currently lack bright sources of these photons. In order to support these technologies, and others, two classes of materials: traditional and novel, were investigated via optical characterization methods with goal of gaining insight into which materials and experimental conditions yield the greatest nonlinear optical effects. Optical characterization of periodically poled lithium niobate (PPLN) helped support the development of a simple, efficient photon pair source that could be easily integrated into optical networks. Additionally, an in-situ measurement of the 2nd order nonlinear optical coefficient was developed to aid in the characterization of PPLN pair sources. Lastly, an undergraduate demonstration of quantum key distribution was constructed such that students could see the primary application for PPLN photon pair sources in an affordable, approachable demonstration. A class of novel optical materials known as 2D materials has been identified as potential replacements to the traditional nonlinear optical materials discussed in Part I. Through optical characterization of second harmonic generation (SHG) the ideal conditions for spontaneous parametric downconversion were established as well as signal thresholds for successful detection. Attempts to observe SPDC produces hints that weak generate SPDC may be present in WS2 samples however this is incredibly difficult to confirm. As growth techniques of 2D materials improve, a photonic device constructed from these materials may be possible, however it will need some mechanism e.g. stacking, a cavity, etc. to help enhance the SPDC signal.

Effect of chromatic-dispersion-induced chirp on the temporal coherence properties of individual beams from spontaneous four-wave mixing

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

Ma Xiaoxin; Li Xiaoying; Cui Liang

2011-08-15

Temporal coherence of individual signal or idler beam, determined by the spectral correlation property of photon pairs, is important for realizing quantum interference among independent sources. Based on spontaneous four-wave mixing in optical fibers, we study the effect of chirp on the temporal coherence property by introducing a different amount of chirp into either the pulsed pump or individual signal (idler) beam. The investigation shows that the pump chirp induces additional frequency correlation into photon pairs; the mutual spectral correlation of photon pairs and the coherence of individual beam can be characterized by measuring the intensity correlation function g{sup (2)}more » of the individual beam. To improve the coherence degree, the pump chirp should be minimized. Moreover, a Hong-Ou-Mandel-type two-photon interference experiment with the signal beams generated in two different fibers illustrates that the chirp of the individual signal (idler) beam does not change the temporal coherence degree, but affects the temporal mode matching. To achieve high visibility among multiple sources, apart from improving the coherence degree, mode matching should be optimized by managing the chirps of individual beams.« less

Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants

PubMed Central

Bagley, Steven C.; Sirota, Marina; Chen, Richard; Butte, Atul J.; Altman, Russ B.

2016-01-01

Patterns of disease co-occurrence that deviate from statistical independence may represent important constraints on biological mechanism, which sometimes can be explained by shared genetics. In this work we study the relationship between disease co-occurrence and commonly shared genetic architecture of disease. Records of pairs of diseases were combined from two different electronic medical systems (Columbia, Stanford), and compared to a large database of published disease-associated genetic variants (VARIMED); data on 35 disorders were available across all three sources, which include medical records for over 1.2 million patients and variants from over 17,000 publications. Based on the sources in which they appeared, disease pairs were categorized as having predominant clinical, genetic, or both kinds of manifestations. Confounding effects of age on disease incidence were controlled for by only comparing diseases when they fall in the same cluster of similarly shaped incidence patterns. We find that disease pairs that are overrepresented in both electronic medical record systems and in VARIMED come from two main disease classes, autoimmune and neuropsychiatric. We furthermore identify specific genes that are shared within these disease groups. PMID:27115429

Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants.

PubMed

Bagley, Steven C; Sirota, Marina; Chen, Richard; Butte, Atul J; Altman, Russ B

2016-04-01

Patterns of disease co-occurrence that deviate from statistical independence may represent important constraints on biological mechanism, which sometimes can be explained by shared genetics. In this work we study the relationship between disease co-occurrence and commonly shared genetic architecture of disease. Records of pairs of diseases were combined from two different electronic medical systems (Columbia, Stanford), and compared to a large database of published disease-associated genetic variants (VARIMED); data on 35 disorders were available across all three sources, which include medical records for over 1.2 million patients and variants from over 17,000 publications. Based on the sources in which they appeared, disease pairs were categorized as having predominant clinical, genetic, or both kinds of manifestations. Confounding effects of age on disease incidence were controlled for by only comparing diseases when they fall in the same cluster of similarly shaped incidence patterns. We find that disease pairs that are overrepresented in both electronic medical record systems and in VARIMED come from two main disease classes, autoimmune and neuropsychiatric. We furthermore identify specific genes that are shared within these disease groups.

A fast method for searching for repeating earthquakes, applied to the northern San Francisco Bay area

NASA Astrophysics Data System (ADS)

Shakibay Senobari, N.; Funning, G.

2016-12-01

Repeating earthquakes (REs) are the regular or semi-regular failures of the same patch on a fault, producing near-identical waveforms at a given station. Sequences of REs are commonly interpreted as slip on small locked patches surrounded by large areas of fault that are creeping (Nadeau and McEvilly, 1999). Detecting them, therefore, places important constraints on the extent of fault creep at depth. In addition, the magnitude and recurrence interval of these RE sequences can be related to the creep rate and used as constraints on slip models. In this study we search for REs in northern California fault systems upon which creep is suspected, but not well constrained, including the Rodgers Creek, Maacama, Bartlett Springs, Concord-Green Valley, West Napa and Greenville faults, targeting events recorded at stations where the instrument was not changed for 10 years or more. A pair of events can be identified as REs based on a high cross-correlation coefficient (CCC) between their waveforms. Thus a fundamental step in RE searches is calculating the CCC for all event waveform pairs recorded at common stations. This becomes computationally expensive for large data sets. To expedite our search, we use a fast and accurate similarity search algorithm developed by the computer science community (Mueen et al., 2015; Zhu et al., 2016). Our initial tests on a data set including 1500 waveforms suggest it is around 40 times faster than the algorithm that we used previously (Shakibay Senobari and Funning, AGU Fall Meeting 2014). We search for event pairs with CCC>0.85 and cluster them based on their similarity. A second, location based filter, based on the differential S-P times for each event pair at 5 or more stations, is used as an independent check. We consider a cluster of events a RE sequence if the source location separation distance for each pair is less than the estimated circular size of the source (e.g. Chen et al., 2008); these are gathered into an RE catalogue. In future, we plan to use this information in combination with geodetic data to produce a robust creep distribution model for all of the faults in this region.

A sensitivity analysis for missing outcomes due to truncation by death under the matched-pairs design.

PubMed

Imai, Kosuke; Jiang, Zhichao

2018-04-29

The matched-pairs design enables researchers to efficiently infer causal effects from randomized experiments. In this paper, we exploit the key feature of the matched-pairs design and develop a sensitivity analysis for missing outcomes due to truncation by death, in which the outcomes of interest (e.g., quality of life measures) are not even well defined for some units (e.g., deceased patients). Our key idea is that if 2 nearly identical observations are paired prior to the randomization of the treatment, the missingness of one unit's outcome is informative about the potential missingness of the other unit's outcome under an alternative treatment condition. We consider the average treatment effect among always-observed pairs (ATOP) whose units exhibit no missing outcome regardless of their treatment status. The naive estimator based on available pairs is unbiased for the ATOP if 2 units of the same pair are identical in terms of their missingness patterns. The proposed sensitivity analysis characterizes how the bounds of the ATOP widen as the degree of the within-pair similarity decreases. We further extend the methodology to the matched-pairs design in observational studies. Our simulation studies show that informative bounds can be obtained under some scenarios when the proportion of missing data is not too large. The proposed methodology is also applied to the randomized evaluation of the Mexican universal health insurance program. An open-source software package is available for implementing the proposed research. Copyright © 2018 John Wiley & Sons, Ltd.

Properties of entangled photon pairs generated in one-dimensional nonlinear photonic-band-gap structures

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

Perina, Jan Jr.; Centini, Marco; Sibilia, Concita

We have developed a rigorous quantum model of spontaneous parametric down-conversion in a nonlinear 1D photonic-band-gap structure based upon expansion of the field into monochromatic plane waves. The model provides a two-photon amplitude of a created photon pair. The spectra of the signal and idler fields, their intensity profiles in the time domain, as well as the coincidence-count interference pattern in a Hong-Ou-Mandel interferometer are determined both for cw and pulsed pumping regimes in terms of the two-photon amplitude. A broad range of parameters characterizing the emitted down-converted fields can be used. As an example, a structure composed of 49more » layers of GaN/AlN is analyzed as a suitable source of photon pairs having high efficiency.« less

Tailoring entanglement through domain engineering in a lithium niobate waveguide

PubMed Central

Ming, Yang; Tan, Ai-Hong; Wu, Zi-Jian; Chen, Zhao-Xian; Xu, Fei; Lu, Yan-Qing

2014-01-01

We propose to integrate the electro-optic (EO) tuning function into on-chip domain engineered lithium niobate (LN) waveguide. Due to the versatility of LN, both the spontaneously parametric down conversion (SPDC) and EO interaction could be realized simultaneously. Photon pairs are generated through SPDC, and the formation of entangled state is modulated by EO processes. An EO tunable polarization-entangled photon state is proposed. Orthogonally-polarized and parallel-polarized entanglements of photon pairs are instantly switchable by tuning the applied field. The characteristics of the source are theoretically investigated showing adjustable bandwidths and high entanglement degrees. Moreover, other kinds of reconfigurable entanglement are also achievable based on suitable domain-design. We believe tailoring entanglement based on domain engineering is a very promising solution for next generation function-integrated quantum circuits. PMID:24770555

Free-Space Quantum Key Distribution with a High Generation Rate KTP Waveguide Photon-Pair Source

NASA Technical Reports Server (NTRS)

Wilson, J.; Chaffee, D.; Wilson, N.; Lekki, J.; Tokars, R.; Pouch, J.; Lind, A.; Cavin, J.; Helmick, S.; Roberts, T.;

Hubble Source Catalog

NASA Astrophysics Data System (ADS)

Lubow, S.; Budavári, T.

2013-10-01

We have created an initial catalog of objects observed by the WFPC2 and ACS instruments on the Hubble Space Telescope (HST). The catalog is based on observations taken on more than 6000 visits (telescope pointings) of ACS/WFC and more than 25000 visits of WFPC2. The catalog is obtained by cross matching by position in the sky all Hubble Legacy Archive (HLA) Source Extractor source lists for these instruments. The source lists describe properties of source detections within a visit. The calculations are performed on a SQL Server database system. First we collect overlapping images into groups, e.g., Eta Car, and determine nearby (approximately matching) pairs of sources from different images within each group. We then apply a novel algorithm for improving the cross matching of pairs of sources by adjusting the astrometry of the images. Next, we combine pairwise matches into maximal sets of possible multi-source matches. We apply a greedy Bayesian method to split the maximal matches into more reliable matches. We test the accuracy of the matches by comparing the fluxes of the matched sources. The result is a set of information that ties together multiple observations of the same object. A byproduct of the catalog is greatly improved relative astrometry for many of the HST images. We also provide information on nondetections that can be used to determine dropouts. With the catalog, for the first time, one can carry out time domain, multi-wavelength studies across a large set of HST data. The catalog is publicly available. Much more can be done to expand the catalog capabilities.

A fast and fully automatic registration approach based on point features for multi-source remote-sensing images

NASA Astrophysics Data System (ADS)

Yu, Le; Zhang, Dengrong; Holden, Eun-Jung

2008-07-01

Automatic registration of multi-source remote-sensing images is a difficult task as it must deal with the varying illuminations and resolutions of the images, different perspectives and the local deformations within the images. This paper proposes a fully automatic and fast non-rigid image registration technique that addresses those issues. The proposed technique performs a pre-registration process that coarsely aligns the input image to the reference image by automatically detecting their matching points by using the scale invariant feature transform (SIFT) method and an affine transformation model. Once the coarse registration is completed, it performs a fine-scale registration process based on a piecewise linear transformation technique using feature points that are detected by the Harris corner detector. The registration process firstly finds in succession, tie point pairs between the input and the reference image by detecting Harris corners and applying a cross-matching strategy based on a wavelet pyramid for a fast search speed. Tie point pairs with large errors are pruned by an error-checking step. The input image is then rectified by using triangulated irregular networks (TINs) to deal with irregular local deformations caused by the fluctuation of the terrain. For each triangular facet of the TIN, affine transformations are estimated and applied for rectification. Experiments with Quickbird, SPOT5, SPOT4, TM remote-sensing images of the Hangzhou area in China demonstrate the efficiency and the accuracy of the proposed technique for multi-source remote-sensing image registration.

A convergence algorithm for correlation of breech face images based on the congruent matching cells (CMC) method.

PubMed

Chen, Zhe; Song, John; Chu, Wei; Soons, Johannes A; Zhao, Xuezeng

2017-11-01

The Congruent Matching Cells (CMC) method was invented at the National Institute of Standards and Technology (NIST) for accurate firearm evidence identification and error rate estimation. The CMC method is based on the principle of discretization. The toolmark image of the reference sample is divided into correlation cells. Each cell is registered to the cell-sized area of the compared image that has maximum surface topography similarity. For each resulting cell pair, one parameter quantifies the similarity of the cell surface topography and three parameters quantify the pattern congruency of the registration position and orientation. An identification (declared match) requires a significant number of CMCs, that is, cell pairs that meet both similarity and pattern congruency requirements. The use of cell correlations reduces the effects of "invalid regions" in the compared image pairs and increases the correlation accuracy. The identification accuracy of the CMC method can be further improved by considering a feature named "convergence," that is, the tendency of the x-y registration positions of the correlated cell pairs to converge at the correct registration angle when comparing same-source samples at different relative orientations. In this paper, the difference of the convergence feature between known matching (KM) and known non-matching (KNM) image pairs is characterized, based on which an improved algorithm is developed for breech face image correlations using the CMC method. Its advantage is demonstrated by comparison with three existing CMC algorithms using four datasets. The datasets address three different brands of consecutively manufactured pistol slides, with significant differences in the distribution overlap of cell pair topography similarity for KM and KNM image pairs. For the same CMC threshold values, the convergence algorithm demonstrates noticeably improved results by reducing the number of false-positive or false-negative CMCs in a comparison. Published by Elsevier B.V.

High spectral purity silicon ring resonator photon-pair source

NASA Astrophysics Data System (ADS)

Steidle, Jeffrey A.; Fanto, Michael L.; Tison, Christopher C.; Wang, Zihao; Preble, Stefan F.; Alsing, Paul M.

2015-05-01

Here we present the experimental demonstration of a Silicon ring resonator photon-pair source. The crystalline Silicon ring resonator (radius of 18.5μm) was designed to realize low dispersion across multiple resonances, which allows for operation with a high quality factor of Q~50k. In turn, the source exhibits very high brightness of >3x105 photons/s/mW2/GHz since the produced photon pairs have a very narrow bandwidth. Furthermore, the waveguidefiber coupling loss was minimized to <1.5dB using an inverse tapered waveguide (tip width of ~150nm over a 300μm length) that is butt-coupled to a high-NA fiber (Nufern UHNA-7). This ensured minimal loss of photon pairs to the detectors, which enabled very high purity photon pairs with minimal noise, as exhibited by a very high Coincidental-Accidental Ratio of >1900. The low coupling loss (3dB fiber-fiber) also allowed for operation with very low off-chip pump power of <200μW. In addition, the zero dispersion of the ring resonator resulted in the production of a photon-pair comb across multiple resonances symmetric about the pump resonance (every ~5nm spanning >20nm), which could be used in future wavelength division multiplexed quantum networks.

Long-distance entanglement-based quantum key distribution experiment using practical detectors.

PubMed

Takesue, Hiroki; Harada, Ken-Ichi; Tamaki, Kiyoshi; Fukuda, Hiroshi; Tsuchizawa, Tai; Watanabe, Toshifumi; Yamada, Koji; Itabashi, Sei-Ichi

2010-08-02

We report an entanglement-based quantum key distribution experiment that we performed over 100 km of optical fiber using a practical source and detectors. We used a silicon-based photon-pair source that generated high-purity time-bin entangled photons, and high-speed single photon detectors based on InGaAs/InP avalanche photodiodes with the sinusoidal gating technique. To calculate the secure key rate, we employed a security proof that validated the use of practical detectors. As a result, we confirmed the successful generation of sifted keys over 100 km of optical fiber with a key rate of 4.8 bit/s and an error rate of 9.1%, with which we can distill secure keys with a key rate of 0.15 bit/s.

Intrication temporelle et communication quantique

NASA Astrophysics Data System (ADS)

Bussieres, Felix

Quantum communication is the art of transferring a quantum state from one place to another and the study of tasks that can be accomplished with it. This thesis is devoted to the development of tools and tasks for quantum communication in a real-world setting. These were implemented using an underground optical fibre link deployed in an urban environment. The technological and theoretical innovations presented here broaden the range of applications of time-bin entanglement through new methods of manipulating time-bin qubits, a novel model for characterizing sources of photon pairs, new ways of testing non-locality and the design and the first implementation of a new loss-tolerant quantum coin-flipping protocol. Manipulating time-bin qubits. A single photon is an excellent vehicle in which a qubit, the fundamental unit of quantum information, can be encoded. In particular, the time-bin encoding of photonic qubits is well suited for optical fibre transmission. Before this thesis, the applications of quantum communication based on the time-bin encoding were limited due to the lack of methods to implement arbitrary operations and measurements. We have removed this restriction by proposing the first methods to realize arbitrary deterministic operations on time-bin qubits as well as single qubit measurements in an arbitrary basis. We applied these propositions to the specific case of optical measurement-based quantum computing and showed how to implement the feedforward operations, which are essential to this model. This therefore opens new possibilities for creating an optical quantum computer, but also for other quantum communication tasks. Characterizing sources of photon pairs. Experimental quantum communication requires the creation of single photons and entangled photons. These two ingredients can be obtained from a source of photon pairs based on non-linear spontaneous processes. Several tasks in quantum communication require a precise knowledge of the properties of the source being used. We developed and implemented a fast and simple method to characterize a source of photon pairs. This method is well suited for a realistic setting where experimental conditions, such as channel transmittance, may fluctuate, and for which the characterization of the source has to be done in real time. Testing the non-locality of time-bin entanglement. Entanglement is a resource needed for the realization of many important tasks in quantum communication. It also allows two physical systems to be correlated in a way that cannot be explained by classical physics; this manifestation of entanglement is called non-locality. We built a source of time-bin entangled photonic qubits and characterized it with the new methods implementing arbitrary single qubit measurements that we developed. This allowed us to reveal the non-local nature of our source of entanglement in ways that were never implemented before. It also opens the door to study previously untested features of non-locality using this source. Theses experiments were performed in a realistic setting where quantum (non-local) correlations were observed even after transmission of one of the entangled qubits over 12.4 km of an underground optical fibre. Flipping quantum coins. Quantum coin-flipping is a quantum cryptographic primitive proposed in 1984, that is when the very first steps of quantum communication were being taken, where two players alternate in sending classical and quantum information in order to generate a shared random bit. The use of quantum information is such that a potential cheater cannot force the outcome to his choice with certainty. Classically, however, one of the players can always deterministically choose the outcome. Unfortunately, the security of all previous quantum coin-flipping protocols is seriously compromised in the presence of losses on the transmission channel, thereby making this task impractical. We found a solution to this problem and obtained the first loss-tolerant quantum coin-flipping protocol whose security is independent of the amount of the losses. We have also experimentally demonstrated our loss-tolerant protocol using our source of time-bin entanglement combined with our arbitrary single qubit measurement methods. This experiment took place in a realistic setting where qubits travelled over an underground optical fibre link. This new task thus joins quantum key distribution as a practical application of quantum communication. Keywords. quantum communication, photonics, time-bin encoding, source of photon pairs, heralded single photon source, entanglement, non-locality, time-bin entanglement, hybrid entanglement, quantum network, quantum cryptography, quantum coin-flipping, measurement-based quantum computation, telecommunication, optical fibre, nonlinear optics.

Sources of Stress among Parents of Children with Intellectual Disabilities: A Preliminary Investigation in Saudi Arabia

ERIC Educational Resources Information Center

Aldosari, Mubarak S.; Pufpaff, Lisa A.

2014-01-01

This study identified differences in sources of stress between parents of male children with intellectual disabilities in Saudi Arabia. Seventeen pairs of parents completed the Parent Stress Index (Abidin, 1995). Each pair of parents had a male child diagnosed with intellectual disability who either attended an institute for male children with…

Source Memory in the Absence of Successful Cued Recall

ERIC Educational Resources Information Center

Cook, Gabriel I.; Marsh, Richard L.; Hicks, Jason L.

2006-01-01

Five experiments were conducted to address the question of whether source information could be accessed in the absence of being able to recall an item. The authors used a paired-associate learning paradigm in which cue-target word pairs were studied, and target recall was requested in the presence of the cue. When target recall failed,…

Four-gate transistor analog multiplier circuit

NASA Technical Reports Server (NTRS)

Mojarradi, Mohammad M. (Inventor); Blalock, Benjamin (Inventor); Cristoloveanu, Sorin (Inventor); Chen, Suheng (Inventor); Akarvardar, Kerem (Inventor)

2011-01-01

A differential output analog multiplier circuit utilizing four G.sup.4-FETs, each source connected to a current source. The four G.sup.4-FETs may be grouped into two pairs of two G.sup.4-FETs each, where one pair has its drains connected to a load, and the other par has its drains connected to another load. The differential output voltage is taken at the two loads. In one embodiment, for each G.sup.4-FET, the first and second junction gates are each connected together, where a first input voltage is applied to the front gates of each pair, and a second input voltage is applied to the first junction gates of each pair. Other embodiments are described and claimed.

Ant Lion Optimization algorithm for kidney exchanges.

PubMed

Hamouda, Eslam; El-Metwally, Sara; Tarek, Mayada

2018-01-01

The kidney exchange programs bring new insights in the field of organ transplantation. They make the previously not allowed surgery of incompatible patient-donor pairs easier to be performed on a large scale. Mathematically, the kidney exchange is an optimization problem for the number of possible exchanges among the incompatible pairs in a given pool. Also, the optimization modeling should consider the expected quality-adjusted life of transplant candidates and the shortage of computational and operational hospital resources. In this article, we introduce a bio-inspired stochastic-based Ant Lion Optimization, ALO, algorithm to the kidney exchange space to maximize the number of feasible cycles and chains among the pool pairs. Ant Lion Optimizer-based program achieves comparable kidney exchange results to the deterministic-based approaches like integer programming. Also, ALO outperforms other stochastic-based methods such as Genetic Algorithm in terms of the efficient usage of computational resources and the quantity of resulting exchanges. Ant Lion Optimization algorithm can be adopted easily for on-line exchanges and the integration of weights for hard-to-match patients, which will improve the future decisions of kidney exchange programs. A reference implementation for ALO algorithm for kidney exchanges is written in MATLAB and is GPL licensed. It is available as free open-source software from: https://github.com/SaraEl-Metwally/ALO_algorithm_for_Kidney_Exchanges.

Self-organization of quantum-dot pairs by high-temperature droplet epitaxy

PubMed Central

Holmes, Kyland; Mazur, Yuriy I; Ramsey, Kimberly A; Salamo, Gregory J

2006-01-01

The spontaneously formation of epitaxial GaAs quantum-dot pairs was demonstrated on an AlGaAs surface using Ga droplets as a Ga nano-source. The dot pair formation was attributed to the anisotropy of surface diffusion during high-temperature droplet epitaxy.

Ion pair reinforced semi-interpenetrating polymer network for direct methanol fuel cell applications.

PubMed

Fang, Chunliu; Julius, David; Tay, Siok Wei; Hong, Liang; Lee, Jim Yang

2012-06-07

This paper describes the synthesis of ion-pair-reinforced semi-interpenetrating polymer networks (SIPNs) as proton exchange membranes (PEMs) for the direct methanol fuel cells (DMFCs). Specifically, sulfonated poly(2,6-dimethyl-1,4-phenylene oxide) (SPPO), a linear polymer proton source, was immobilized in a brominated PPO (BPPO) network covalently cross-linked by ethylenediamine (EDA). The immobilization of SPPO in the SIPN network was accomplished not only by the usual means of mechanical interlocking but also by ion pair formation between the sulfonic acid groups of SPPO and the amine moieties formed during the cross-linking reaction of BPPO with EDA. Through the ion pair interactions, the immobilization of SPPO polymer in the BPPO network was made more effective, resulting in a greater uniformity of sulfonic acid cluster distribution in the membrane. The hydrophilic amine-containing cross-links also compensated for some of the decrease in proton conductivity caused by ion pair formation. The SIPN membranes prepared as such showed good proton conductivity, low methanol permeability, good mechanical properties, and dimensional stability. Consequently, the PPO based SIPN membranes were able to deliver a higher maximum power density than Nafion, demonstrating the potential of the SIPN structure for PEM designs.

Coherence properties of spontaneous parametric down-conversion pumped by a multi-mode cw diode laser.

PubMed

Kwon, Osung; Ra, Young-Sik; Kim, Yoon-Ho

2009-07-20

Coherence properties of the photon pair generated via spontaneous parametric down-conversion pumped by a multi-mode cw diode laser are studied with a Mach-Zehnder interferometer. Each photon of the pair enters a different input port of the interferometer and the biphoton coherence properties are studied with a two-photon detector placed at one output port. When the photon pair simultaneously enters the interferometer, periodic recurrence of the biphoton de Broglie wave packet is observed, closely resembling the coherence properties of the pump diode laser. With non-zero delays between the photons at the input ports, biphoton interference exhibits the same periodic recurrence but the wave packet shapes are shown to be dependent on both the input delay as well as the interferometer delay. These properties could be useful for building engineered entangled photon sources based on diode laser-pumped spontaneous parametric down-conversion.

A single chip 2 Gbit/s clock recovery subsystem for digital communications

NASA Astrophysics Data System (ADS)

Hickling, Ronald M.

A self-contained clock recovery/data resynchronizer phase locked loop (PLL) for use in microwave and fiber optic digital communications has been fabricated using GaAs integrated circuit technology. The IC contains the analog and digital components for the PLL: an edge-triggered phase detector based on a 1.2 GHz phase/frequency comparator, an op amp for creating the loop filter, and a VCO based on a differential source-coupled pair amplifier.

Why the tautomerization of the G·C Watson-Crick base pair via the DPT does not cause point mutations during DNA replication? QM and QTAIM comprehensive analysis.

PubMed

Brovarets', Ol'ha O; Hovorun, Dmytro M

2014-01-01

The ground-state tautomerization of the G·C Watson-Crick base pair by the double proton transfer (DPT) was comprehensively studied in vacuo and in the continuum with a low dielectric constant (ϵ = 4), corresponding to a hydrophobic interface of protein-nucleic acid interactions, using DFT and MP2 levels of quantum-mechanical (QM) theory and quantum theory "Atoms in molecules" (QTAIM). Based on the sweeps of the electron-topological, geometric, polar, and energetic parameters, which describe the course of the G·C ↔ G*·C* tautomerization (mutagenic tautomers of the G and C bases are marked with an asterisk) through the DPT along the intrinsic reaction coordinate (IRC), it was proved that it is, strictly speaking, a concerted asynchronous process both at the DFT and MP2 levels of theory, in which protons move with a small time gap in vacuum, while this time delay noticeably increases in the continuum with ϵ = 4. It was demonstrated using the conductor-like polarizable continuum model (CPCM) that the continuum with ϵ = 4 does not qualitatively affect the course of the tautomerization reaction. The DPT in the G·C Watson-Crick base pair occurs without any intermediates both in vacuum and in the continuum with ϵ = 4 at the DFT/MP2 levels of theory. The nine key points along the IRC of the G·C base pair tautomerization, which could be considered as electron-topological "fingerprints" of a concerted asynchronous process of the tautomerization via the DPT, have been identified and fully characterized. These key points have been used to define the reactant, transition state, and product regions of the DPT reaction in the G·C base pair. Analysis of the energetic characteristics of the H-bonds allows us to arrive at a definite conclusion that the middle N1H⋯N3/N3H⋯N1 and the lower N2H⋯O2/N2H⋯O2 parallel H-bonds in the G·C/G*·C* base pairs, respectively, are anticooperative, that is, the strengthening of the middle H-bond is accompanied by the weakening of the lower H-bond. At that point, the upper N4H⋯O6 and O6H⋯N4 H-bonds in the G·C and G*·C* base pairs, respectively, remain constant at the changes of the middle and the lower H-bonds at the beginning and at the ending of the G·C ↔ G*·C* tautomerization. Aiming to answer the question posed in the title of the article, we established that the G*·C* Löwdin's base pair satisfies all the requirements necessary to cause point mutations in DNA except its lifetime, which is much less than the period of time required for the replication machinery to forcibly dissociate a base pair into the monomers (several ns) during DNA replication. So, from the physicochemical point of view, the G*·C* Löwdin's base pair cannot be considered as a source of point mutations arising during DNA replication.

Special Component Designs for Differential-Amplifier MMICs

NASA Technical Reports Server (NTRS)

Kangaslahti, Pekka

2010-01-01

Special designs of two types of electronic components transistors and transmission lines have been conceived to optimize the performances of these components as parts of waveguide-embedded differential-amplifier monolithic microwave integrated circuits (MMICs) of the type described in the immediately preceding article. These designs address the following two issues, the combination of which is unique to these particular MMICs: Each MMIC includes a differential double-strip transmission line that typically has an impedance between 60 and 100 W. However, for purposes of matching of impedances, transmission lines having lower impedances are also needed. The transistors in each MMIC are, more specifically, one or more pair(s) of InP-based high-electron-mobility transistors (HEMTs). Heretofore, it has been common practice to fabricate each such pair as a single device configured in the side-to-side electrode sequence source/gate/drain/gate/source. This configuration enables low-inductance source grounding from the sides of the device. However, this configuration is not suitable for differential operation, in which it is necessary to drive the gates differentially and to feed the output from the drain electrodes differentially. The special transmission-line design provides for three conductors, instead of two, in places where lower impedance is needed. The third conductor is a metal strip placed underneath the differential double-strip transmission line. The third conductor increases the capacitance per unit length of the transmission line by such an amount as to reduce the impedance to between 5 and 15 W. In the special HEMT-pair design, the side-to-side electrode sequence is changed to drain/gate/source/gate/ drain. In addition, the size of the source is reduced significantly, relative to corresponding sizes in prior designs. This reduction is justified by the fact that, by virtue of the differential configuration, the device has an internal virtual ground, and therefore there is no need for a low-resistance contact between the source and the radio-frequency circuitry. The source contact is needed only for DC biasing. These designs were implemented in a single-stage-amplifier MMIC. In a test at a frequency of 305 GHz, the amplifier embedded in a waveguide exhibited a gain of 0 dB; after correcting for the loss in the waveguide, the amplifier was found to afford a gain of 0.9 dB. In a test at 220 GHz, the overall gain of the amplifier- and-waveguide assembly was found to be 3.5 dB.

Math expression retrieval using an inverted index over symbol pairs

NASA Astrophysics Data System (ADS)

Stalnaker, David; Zanibbi, Richard

2015-01-01

We introduce a new method for indexing and retrieving mathematical expressions, and a new protocol for evaluating math formula retrieval systems. The Tangent search engine uses an inverted index over pairs of symbols in math expressions. Each key in the index is a pair of symbols along with their relative distance and vertical displacement within an expression. Matched expressions are ranked by the harmonic mean of the percentage of symbol pairs matched in the query, and the percentage of symbol pairs matched in the candidate expression. We have found that our method is fast enough for use in real time and finds partial matches well, such as when subexpressions are re-arranged (e.g. expressions moved from the left to the right of an equals sign) or when individual symbols (e.g. variables) differ from a query expression. In an experiment using expressions from English Wikipedia, student and faculty participants (N=20) found expressions returned by Tangent significantly more similar than those from a text-based retrieval system (Lucene) adapted for mathematical expressions. Participants provided similarity ratings using a 5-point Likert scale, evaluating expressions from both algorithms one-at-a-time in a randomized order to avoid bias from the position of hits in search result lists. For the Lucene-based system, precision for the top 1 and 10 hits averaged 60% and 39% across queries respectively, while for Tangent mean precision at 1 and 10 were 99% and 60%. A demonstration and source code are publicly available.

Implementing Diffie-Hellman key exchange using quantum EPR pairs

NASA Astrophysics Data System (ADS)

Mandal, Sayonnha; Parakh, Abhishek

2015-05-01

This paper implements the concepts of perfect forward secrecy and the Diffie-Hellman key exchange using EPR pairs to establish and share a secret key between two non-authenticated parties and transfer messages between them without the risk of compromise. Current implementations of quantum cryptography are based on the BB84 protocol, which is susceptible to siphoning attacks on the multiple photons emitted by practical laser sources. This makes BB84-based quantum cryptography protocol unsuitable for network computing environments. Diffie-Hellman does not require the two parties to be mutually authenticated to each other, yet it can provide a basis for a number of authenticated protocols, most notably the concept of perfect forward secrecy. The work proposed in this paper provides a new direction in utilizing quantum EPR pairs in quantum key exchange. Although, classical cryptography boasts of efficient and robust protocols like the Diffie-Hellman key exchange, in the current times, with the advent of quantum computing they are very much vulnerable to eavesdropping and cryptanalytic attacks. Using quantum cryptographic principles, however, these classical encryption algorithms show more promise and a more robust and secure structure for applications. The unique properties of quantum EPR pairs also, on the other hand, go a long way in removing attacks like eavesdropping by their inherent nature of one particle of the pair losing its state if a measurement occurs on the other. The concept of perfect forward secrecy is revisited in this paper to attribute tighter security to the proposed protocol.

Bispectral pairwise interacting source analysis for identifying systems of cross-frequency interacting brain sources from electroencephalographic or magnetoencephalographic signals

NASA Astrophysics Data System (ADS)

Chella, Federico; Pizzella, Vittorio; Zappasodi, Filippo; Nolte, Guido; Marzetti, Laura

2016-05-01

Brain cognitive functions arise through the coordinated activity of several brain regions, which actually form complex dynamical systems operating at multiple frequencies. These systems often consist of interacting subsystems, whose characterization is of importance for a complete understanding of the brain interaction processes. To address this issue, we present a technique, namely the bispectral pairwise interacting source analysis (biPISA), for analyzing systems of cross-frequency interacting brain sources when multichannel electroencephalographic (EEG) or magnetoencephalographic (MEG) data are available. Specifically, the biPISA makes it possible to identify one or many subsystems of cross-frequency interacting sources by decomposing the antisymmetric components of the cross-bispectra between EEG or MEG signals, based on the assumption that interactions are pairwise. Thanks to the properties of the antisymmetric components of the cross-bispectra, biPISA is also robust to spurious interactions arising from mixing artifacts, i.e., volume conduction or field spread, which always affect EEG or MEG functional connectivity estimates. This method is an extension of the pairwise interacting source analysis (PISA), which was originally introduced for investigating interactions at the same frequency, to the study of cross-frequency interactions. The effectiveness of this approach is demonstrated in simulations for up to three interacting source pairs and for real MEG recordings of spontaneous brain activity. Simulations show that the performances of biPISA in estimating the phase difference between the interacting sources are affected by the increasing level of noise rather than by the number of the interacting subsystems. The analysis of real MEG data reveals an interaction between two pairs of sources of central mu and beta rhythms, localizing in the proximity of the left and right central sulci.

First operation and effect of a new tandem-type ion source based on electron cyclotron resonance

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

Kato, Yushi, E-mail: kato@eei.eng.osaka-u.ac.jp; Kimura, Daiju; Yano, Keisuke

A new tandem type source has been constructed on the basis of electron cyclotron resonance plasma for producing synthesized ion beams in Osaka University. Magnetic field in the first stage consists of all permanent magnets, i.e., cylindrically comb shaped one, and that of the second stage consists of a pair of mirror coil, a supplemental coil and the octupole magnets. Both stage plasmas can be individually operated, and produced ions in which is energy controlled by large bore extractor also can be transported from the first to the second stage. We investigate the basic operation and effects of the tandemmore » type electron cyclotron resonance ion source (ECRIS). Analysis of ion beams and investigation of plasma parameters are conducted on produced plasmas in dual plasmas operation as well as each single operation. We describe construction and initial experimental results of the new tandem type ion source based on ECRIS with wide operation window for aiming at producing synthesized ion beams as this new source can be a universal source in future.« less

PAIRED-CITY STUDY TO DETERMINE THE CONTRIBUTION OF SOURCE WATER TYPE TO THE ENDEMIC LEVEL OF MICROBIAL DISEASE

EPA Science Inventory

Paired-City Study to Determine the Contribution of Source Water Type to the Endemic Level of Microbial Disease

F Frost PhD, T Kunde MPH, L Harter PhD, T Muller MS, GF Craun PE MPH, RL Calderon MPH PhD

ABSTRACT

Context: The effectiveness of current drinking...

Joint subchannel pairing and power control for cognitive radio networks with amplify-and-forward relaying.

PubMed

Shen, Yanyan; Wang, Shuqiang; Wei, Zhiming

2014-01-01

Dynamic spectrum sharing has drawn intensive attention in cognitive radio networks. The secondary users are allowed to use the available spectrum to transmit data if the interference to the primary users is maintained at a low level. Cooperative transmission for secondary users can reduce the transmission power and thus improve the performance further. We study the joint subchannel pairing and power allocation problem in relay-based cognitive radio networks. The objective is to maximize the sum rate of the secondary user that is helped by an amplify-and-forward relay. The individual power constraints at the source and the relay, the subchannel pairing constraints, and the interference power constraints are considered. The problem under consideration is formulated as a mixed integer programming problem. By the dual decomposition method, a joint optimal subchannel pairing and power allocation algorithm is proposed. To reduce the computational complexity, two suboptimal algorithms are developed. Simulations have been conducted to verify the performance of the proposed algorithms in terms of sum rate and average running time under different conditions.

Secure quantum key distribution using continuous variables of single photons.

PubMed

Zhang, Lijian; Silberhorn, Christine; Walmsley, Ian A

2008-03-21

We analyze the distribution of secure keys using quantum cryptography based on the continuous variable degree of freedom of entangled photon pairs. We derive the information capacity of a scheme based on the spatial entanglement of photons from a realistic source, and show that the standard measures of security known for quadrature-based continuous variable quantum cryptography (CV-QKD) are inadequate. A specific simple eavesdropping attack is analyzed to illuminate how secret information may be distilled well beyond the bounds of the usual CV-QKD measures.

Deterministic quantum splitter based on time-reversed Hong-Ou-Mandel interference

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

Chen, Jun; Lee, Kim Fook; Kumar, Prem

2007-09-15

By utilizing a fiber-based indistinguishable photon-pair source in the 1.55 {mu}m telecommunications band [J. Chen et al., Opt. Lett. 31, 2798 (2006)], we present the first, to the best of our knowledge, deterministic quantum splitter based on the principle of time-reversed Hong-Ou-Mandel quantum interference. The deterministically separated identical photons' indistinguishability is then verified by using a conventional Hong-Ou-Mandel quantum interference, which exhibits a near-unity dip visibility of 94{+-}1%, making this quantum splitter useful for various quantum information processing applications.

Storage and long-distance distribution of telecommunications-band polarization entanglement generated in an optical fiber.

PubMed

Li, Xiaoying; Voss, Paul L; Chen, Jun; Sharping, Jay E; Kumar, Prem

2005-05-15

We demonstrate storage of polarization-entangled photons for 125 micros, a record storage time to date, in a 25-km-long fiber spool, using a telecommunications-band fiber-based source of entanglement. With this source we also demonstrate distribution of polarization entanglement over 50 km by separating the two photons of an entangled pair and transmitting them individually over separate 25-km fibers. The measured two-photon fringe visibilities were 82% in the storage experiment and 86% in the distribution experiment. Preservation of polarization entanglement over such long-distance transmission demonstrates the viability of all-fiber sources for use in quantum memories and quantum logic gates.

Source memory in the absence of successful cued recall.

PubMed

Cook, Gabriel I; Marsh, Richard L; Hicks, Jason L

2006-07-01

Five experiments were conducted to address the question of whether source information could be accessed in the absence of being able to recall an item. The authors used a paired-associate learning paradigm in which cue-target word pairs were studied, and target recall was requested in the presence of the cue. When target recall failed, participants were asked to make a source judgment of whether a man or woman spoke the unrecalled item. In 3 of the 5 experiments, source accuracy was at or very close to chance. By contrast, if cue-target pairs were studied multiple times or participants knew in advance of learning that a predictive judgment would be required, then predictive source accuracy was well above chance. These data are suggestive that context information may not play a very large role in metacognitive judgments such as feeling-of-knowing ratings or putting one into a tip-of-the-tongue state without strong and specific encoding procedures. These same results also highlight the important role that item memory plays in retrieving information about the context in which an item was experienced. Copyright 2006 APA, all rights reserved.

High heralding-efficiency of near-IR fiber coupled photon pairs for quantum technologies

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

Dixon, P. Ben; Murphy, Ryan; Rosenberg, Danna

We report on the development and use of a high heralding-efficiency, single-mode-fiber coupled telecom-band source of entangled photons for quantum technology applications. The source development efforts consisted of theoretical and experimental efforts and we demonstrated a correlated-mode coupling efficiency of 97% 2%, the highest efficiency yet achieved for this type of system. We then incorporated these beneficial source development techniques in a Sagnac configured telecom-band entangled photon source that generates photon pairs entangled in both time/energy and polarization degrees of freedom. We made use of these highly desirable entangled states to investigate several promising quantum technologies.

Combining automatic table classification and relationship extraction in extracting anticancer drug-side effect pairs from full-text articles.

PubMed

Xu, Rong; Wang, QuanQiu

2015-02-01

Anticancer drug-associated side effect knowledge often exists in multiple heterogeneous and complementary data sources. A comprehensive anticancer drug-side effect (drug-SE) relationship knowledge base is important for computation-based drug target discovery, drug toxicity predication and drug repositioning. In this study, we present a two-step approach by combining table classification and relationship extraction to extract drug-SE pairs from a large number of high-profile oncological full-text articles. The data consists of 31,255 tables downloaded from the Journal of Oncology (JCO). We first trained a statistical classifier to classify tables into SE-related and -unrelated categories. We then extracted drug-SE pairs from SE-related tables. We compared drug side effect knowledge extracted from JCO tables to that derived from FDA drug labels. Finally, we systematically analyzed relationships between anti-cancer drug-associated side effects and drug-associated gene targets, metabolism genes, and disease indications. The statistical table classifier is effective in classifying tables into SE-related and -unrelated (precision: 0.711; recall: 0.941; F1: 0.810). We extracted a total of 26,918 drug-SE pairs from SE-related tables with a precision of 0.605, a recall of 0.460, and a F1 of 0.520. Drug-SE pairs extracted from JCO tables is largely complementary to those derived from FDA drug labels; as many as 84.7% of the pairs extracted from JCO tables have not been included a side effect database constructed from FDA drug labels. Side effects associated with anticancer drugs positively correlate with drug target genes, drug metabolism genes, and disease indications. Copyright © 2014 Elsevier Inc. All rights reserved.

Report on Pairing-based Cryptography.

PubMed

Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

2015-01-01

This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST's position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed.

Report on Pairing-based Cryptography

PubMed Central

Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

2015-01-01

This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST’s position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed. PMID:26958435

CPM Pairs from LSPM so Far Not WDS Listed – Part IV

NASA Astrophysics Data System (ADS)

Knapp, Wilfried; Nanson, John

2018-04-01

The LSPM catalog (Lepine and Shara 2005) is a rich source for CPM pairs we thought already exhausted – but as we found during research for our report "A New Concept for Counter-Checking of Assumed CPM Pairs" (Knapp and Nanson 2017), there are still many potential CPM pairs indicated in LSPM not listed in the WDS catalog. After our first three reports on about 100 such objects (Knapp and Nanson 2017 - CPM pairs from LSPM so far not WDS listed – Part I/II/III), this report with 30 additional potential common proper motion pairs is presented here.

Technical Report on Modeling for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

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

McLoughlin, K.

2016-01-11

The overall aim of this project is to develop a software package, called MetaQuant, that can determine the constituents of a complex microbial sample and estimate their relative abundances by analysis of metagenomic sequencing data. The goal for Task 1 is to create a generative model describing the stochastic process underlying the creation of sequence read pairs in the data set. The stages in this generative process include the selection of a source genome sequence for each read pair, with probability dependent on its abundance in the sample. The other stages describe the evolution of the source genome from itsmore » nearest common ancestor with a reference genome, breakage of the source DNA into short fragments, and the errors in sequencing the ends of the fragments to produce read pairs.« less

Widespread Transient Hoogsteen Base-Pairs in Canonical Duplex DNA with Variable Energetics

PubMed Central

Alvey, Heidi S.; Gottardo, Federico L.; Nikolova, Evgenia N.; Al-Hashimi, Hashim M.

2015-01-01

Hoogsteen base-pairing involves a 180 degree rotation of the purine base relative to Watson-Crick base-pairing within DNA duplexes, creating alternative DNA conformations that can play roles in recognition, damage induction, and replication. Here, using Nuclear Magnetic Resonance R1ρ relaxation dispersion, we show that transient Hoogsteen base-pairs occur across more diverse sequence and positional contexts than previously anticipated. We observe sequence-specific variations in Hoogsteen base-pair energetic stabilities that are comparable to variations in Watson-Crick base-pair stability, with Hoogsteen base-pairs being more abundant for energetically less favorable Watson-Crick base-pairs. Our results suggest that the variations in Hoogsteen stabilities and rates of formation are dominated by variations in Watson-Crick base pair stability, suggesting a late transition state for the Watson-Crick to Hoogsteen conformational switch. The occurrence of sequence and position-dependent Hoogsteen base-pairs provide a new potential mechanism for achieving sequence-dependent DNA transactions. PMID:25185517

The photon pair source that survived a rocket explosion

PubMed Central

Tang, Zhongkan; Chandrasekara, Rakhitha; Tan, Yue Chuan; Cheng, Cliff; Durak, Kadir; Ling, Alexander

2016-01-01

We report on the performance of a compact photon pair source that was recovered intact from a failed space launch. The source had been embedded in a nanosatellite and was designed to perform pathfinder experiments leading to global quantum communication networks using spacecraft. Despite the launch vehicle explosion soon after takeoff, the nanosatellite was successfully retrieved from the accident site and the source within it was found to be fully operational. We describe the assembly technique for the rugged source. Post-recovery data is compared to baseline measurements collected before the launch attempt and no degradation in brightness or polarization correlation was observed. The survival of the source through an extreme environment provides strong evidence that it is possible to engineer rugged quantum optical systems. PMID:27161541

Power-law X-ray and gamma-ray emission from relativistic thermal plasmas

NASA Technical Reports Server (NTRS)

Zdziarski, A. A.

1985-01-01

A common characteristic of cosmic sources is power-law X-ray emission. Extragalactic sources of this type include compact components of active galactic nuclei (AGN). The present study is concerned with a theoretical model of such sources, taking into account the assumption that the power-law spectra are produced by repeated Compton scatterings of soft photons by relativistic thermal electrons. This is one of several possible physical mechanisms leading to the formation of a power-law spectrum. Attention is given to the Comptonization of soft photon sources, the rates of pair processes, the solution of the pair equilibrium equation, and the constraints on a soft photon source and an energy source. It is concluded that the compactness parameters L/R of most of the cosmic sources observed to date lie below the maximum luminosity curves considered.

Origins of coevolution between residues distant in protein 3D structures

PubMed Central

Ovchinnikov, Sergey; Kamisetty, Hetunandan; Baker, David

2017-01-01

Residue pairs that directly coevolve in protein families are generally close in protein 3D structures. Here we study the exceptions to this general trend—directly coevolving residue pairs that are distant in protein structures—to determine the origins of evolutionary pressure on spatially distant residues and to understand the sources of error in contact-based structure prediction. Over a set of 4,000 protein families, we find that 25% of directly coevolving residue pairs are separated by more than 5 Å in protein structures and 3% by more than 15 Å. The majority (91%) of directly coevolving residue pairs in the 5–15 Å range are found to be in contact in at least one homologous structure—these exceptions arise from structural variation in the family in the region containing the residues. Thirty-five percent of the exceptions greater than 15 Å are at homo-oligomeric interfaces, 19% arise from family structural variation, and 27% are in repeat proteins likely reflecting alignment errors. Of the remaining long-range exceptions (<1% of the total number of coupled pairs), many can be attributed to close interactions in an oligomeric state. Overall, the results suggest that directly coevolving residue pairs not in repeat proteins are spatially proximal in at least one biologically relevant protein conformation within the family; we find little evidence for direct coupling between residues at spatially separated allosteric and functional sites or for increased direct coupling between residue pairs on putative allosteric pathways connecting them. PMID:28784799

Ultra-intense Pair Creation using the Texas Petawatt Laser and Applications

NASA Astrophysics Data System (ADS)

Liang, Edison; Henderson, Alexander; Clarke, Taylor; Lo, Willie; Chaguine, Petr; Dyer, Gilliss; Riley, Nathan; Serratto, Kristina; Donovan, Michael; Ditmire, Todd

2014-10-01

Pair plasmas and intense gamma-ray sources are ubiquitous in the high-energy universe, from pulser winds to gamma-ray bursts (GRB). Their study can be greatly enhanced if such sources can be recreated in the laboratory under controlled conditions. In 2012 and 2013, a joint Rice-University of Texas team performed over 130 laser shots on thick gold and platinum targets using the 100 Joule Texas Petawatt Laser in Austin. The laser intensity of many shots exceeded 1021 W.cm-2 with pulses as short as 130 fs. These experiments probe a new extreme regime of ultra-intense laser - high-Z solid target interactions never achieved before. In addition to creating copious pairs with the highest density (>1015/cc) and emergent e +/e- ratio exceeding 20% in many shots, these experiments also created the highest density multi-MeV gamma-rays, comparable in absolute numbers to those found inside a gamma-ray burst (GRB). Potential applications of such intense pair and gamma-ray sources to laboratory astrophysics and innovative technologies will be discussed. Work supported by DOE HEDLP program.

Identification of repeating earthquakes and spatio-temporal variations of fault zone properties around the Parkfield section of the San Andreas fault and the central Calaveras fault

NASA Astrophysics Data System (ADS)

Zhao, P.; Peng, Z.

2008-12-01

We systemically identify repeating earthquakes and investigate spatio-temporal variations of fault zone properties associated with the 2004 Mw6.0 Parkfield earthquake along the Parkfield section of the San Andreas fault, and the 1984 Mw6.2 Morgan Hill earthquake along the central Calaveras fault. The procedure for identifying repeating earthquakes is based on overlapping of the source regions and the waveform similarity, and is briefly described as follows. First, we estimate the source radius of each event based on a circular crack model and a normal stress drop of 3 MPa. Next, we compute inter-hypocentral distance for events listed in the relocated catalog of Thurber et al. (2006) around Parkfield, and Schaff et al. (2002) along the Calaveras fault. Then, we group all events into 'initial' clusters by requiring the separation distance between each event pair to be less than the source radius of larger event, and their magnitude difference to be less than 1. Next, we calculate the correlation coefficients between every event pair within each 'initial' cluster using a 3-s time window around the direct P waves for all available stations. The median value of the correlation coefficients is used as a measure of similarity between each event pair. We drop an event if the median similarity to the rest events in that cluster is less than 0.9. After identifying repeating clusters in both regions, our next step is to apply a sliding window waveform cross-correlation technique (Niu et al., 2003; Peng and Ben-Zion, 2006) to calculate the delay time and decorrelation index for each repeating cluster. By measuring temporal changes in waveforms of repeating clusters at different locations and depth, we hope to obtain a better constraint on spatio-temporal variations of fault zone properties and near-surface layers associated with the occurrence of major earthquakes.

Automating Performance Measures and Clinical Practice Guidelines: Differences and Complementarities.

PubMed

Tu, Samson W; Martins, Susana; Oshiro, Connie; Yuen, Kaeli; Wang, Dan; Robinson, Amy; Ashcraft, Michael; Heidenreich, Paul A; Goldstein, Mary K

2016-01-01

Through close analysis of two pairs of systems that implement the automated evaluation of performance measures (PMs) and guideline-based clinical decision support (CDS), we contrast differences in their knowledge encoding and necessary changes to a CDS system that provides management recommendations for patients failing performance measures. We trace the sources of differences to the implementation environments and goals of PMs and CDS.

High-fidelity transmission of polarization encoded qubits from an entangled source over 100 km of fiber.

PubMed

Hübel, Hannes; Vanner, Michael R; Lederer, Thomas; Blauensteiner, Bibiane; Lorünser, Thomas; Poppe, Andreas; Zeilinger, Anton

2007-06-11

We demonstrate non-degenerate down-conversion at 810 and 1550 nm for long-distance fiber based quantum communication using polarization entangled photon pairs. Measurements of the two-photon visibility, without dark count subtraction, have shown that the quantum correlations (raw visibility 89%) allow secure quantum cryptography after 100 km of non-zero dispersion shifted fiber using commercially available single photon detectors. In addition, quantum state tomography has revealed little degradation of state negativity, decreasing from 0.99 at the source to 0.93 after 100 km, indicating minimal loss in fidelity during the transmission.

Electrically actuatable temporal tristimulus-color device

DOEpatents

Koehler, Dale R.

1992-01-01

The electrically actuated light filter operates in a cyclical temporal mode to effect a tristimulus-color light analyzer. Construction is based on a Fabry-Perot interferometer comprised of a high-speed movable mirror pair and cyclically powered electrical actuators. When combined with a single vidicon tube or a monochrome solid state image sensor, a temporally operated tristimulus-color video camera is effected. A color-generated is accomplished when constructed with a companion light source and is a flicker-free colored-light source for transmission type display systems. Advantages of low cost and small physical size result from photolithographic batch-processing manufacturability.

High-speed true random number generation based on paired memristors for security electronics

NASA Astrophysics Data System (ADS)

Zhang, Teng; Yin, Minghui; Xu, Changmin; Lu, Xiayan; Sun, Xinhao; Yang, Yuchao; Huang, Ru

2017-11-01

True random number generator (TRNG) is a critical component in hardware security that is increasingly important in the era of mobile computing and internet of things. Here we demonstrate a TRNG using intrinsic variation of memristors as a natural source of entropy that is otherwise undesirable in most applications. The random bits were produced by cyclically switching a pair of tantalum oxide based memristors and comparing their resistance values in the off state, taking advantage of the more pronounced resistance variation compared with that in the on state. Using an alternating read scheme in the designed TRNG circuit, the unbiasedness of the random numbers was significantly improved, and the bitstream passed standard randomness tests. The Pt/TaO x /Ta memristors fabricated in this work have fast programming/erasing speeds of ˜30 ns, suggesting a high random number throughput. The approach proposed here thus holds great promise for physically-implemented random number generation.

High-speed true random number generation based on paired memristors for security electronics.

PubMed

Zhang, Teng; Yin, Minghui; Xu, Changmin; Lu, Xiayan; Sun, Xinhao; Yang, Yuchao; Huang, Ru

2017-11-10

True random number generator (TRNG) is a critical component in hardware security that is increasingly important in the era of mobile computing and internet of things. Here we demonstrate a TRNG using intrinsic variation of memristors as a natural source of entropy that is otherwise undesirable in most applications. The random bits were produced by cyclically switching a pair of tantalum oxide based memristors and comparing their resistance values in the off state, taking advantage of the more pronounced resistance variation compared with that in the on state. Using an alternating read scheme in the designed TRNG circuit, the unbiasedness of the random numbers was significantly improved, and the bitstream passed standard randomness tests. The Pt/TaO x /Ta memristors fabricated in this work have fast programming/erasing speeds of ∼30 ns, suggesting a high random number throughput. The approach proposed here thus holds great promise for physically-implemented random number generation.

Development of mini linac-based positron source and an efficient positronium convertor for positively charged antihydrogen production

NASA Astrophysics Data System (ADS)

Muranaka, T.; Debu, P.; Dupré, P.; Liszkay, L.; Mansoulie, B.; Pérez, P.; Rey, J. M.; Ruiz, N.; Sacquin, Y.; Crivelli, P.; Gendotti, U.; Rubbia, A.

2010-04-01

We have installed in Saclay a facility for an intense positron source in November 2008. It is based on a compact 5.5 MeV electron linac connected to a reaction chamber with a tungsten target inside to produce positrons via pair production. The expected production rate for fast positrons is 5·1011 per second. The study of moderation of fast positrons and the construction of a slow positron trap are underway. In parallel, we have investigated an efficient positron-positronium convertor using porous silica materials. These studies are parts of a project to produce positively charged antihydrogen ions aiming to demonstrate the feasibility of a free fall antigravity measurement of neutral antihydrogen.

Semantic Entity Pairing for Improved Data Validation and Discovery

NASA Astrophysics Data System (ADS)

Shepherd, Adam; Chandler, Cyndy; Arko, Robert; Chen, Yanning; Krisnadhi, Adila; Hitzler, Pascal; Narock, Tom; Groman, Robert; Rauch, Shannon

2014-05-01

One of the central incentives for linked data implementations is the opportunity to leverage the rich logic inherent in structured data. The logic embedded in semantic models can strengthen capabilities for data discovery and data validation when pairing entities from distinct, contextually-related datasets. The creation of links between the two datasets broadens data discovery by using the semantic logic to help machines compare similar entities and properties that exist on different levels of granularity. This semantic capability enables appropriate entity pairing without making inaccurate assertions as to the nature of the relationship. Entity pairing also provides a context to accurately validate the correctness of an entity's property values - an exercise highly valued by data management practices who seek to ensure the quality and correctness of their data. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) semantically models metadata surrounding oceanographic researchcruises, but other sources outside of BCO-DMO exist that also model metadata about these same cruises. For BCO-DMO, the process of successfully pairing its entities to these sources begins by selecting sources that are decidedly trustworthy and authoritative for the modeled concepts. In this case, the Rolling Deck to Repository (R2R) program has a well-respected reputation among the oceanographic research community, presents a data context that is uniquely different and valuable, and semantically models its cruise metadata. Where BCO-DMO exposes the processed, analyzed data products generated by researchers, R2R exposes the raw shipboard data that was collected on the same research cruises. Interlinking these cruise entities expands data discovery capabilities but also allows for validating the contextual correctness of both BCO-DMO's and R2R's cruise metadata. Assessing the potential for a link between two datasets for a similar entity consists of aligning like properties and deciding on the appropriate semantic markup to describe the link. This highlights the desire for research organizations like BCO-DMO and R2R to ensure the complete accuracy of their exposed metadata, as it directly reflects on their reputations as successful and trustworthy source of research data. Therefore, data validation reaches beyond simple syntax of property values into contextual correctness. As a human process, this is a time-intensive task that does not scale well for finite human and funding resources. Therefore, to assess contextual correctness across datasets at different levels of granularity, BCO-DMO is developing a system that employs semantic technologies to aid the human process by organizing potential links and calculating a confidence coefficient as to the correctness of the potential pairing based on the distance between certain entity property values. The system allows humans to quickly scan potential links and their confidence coefficients for asserting persistence and correcting and investigating misaligned entity property values.

A quantum light-emitting diode for the standard telecom window around 1,550 nm.

PubMed

Müller, T; Skiba-Szymanska, J; Krysa, A B; Huwer, J; Felle, M; Anderson, M; Stevenson, R M; Heffernan, J; Ritchie, D A; Shields, A J

2018-02-28

Single photons and entangled photon pairs are a key resource of many quantum secure communication and quantum computation protocols, and non-Poissonian sources emitting in the low-loss wavelength region around 1,550 nm are essential for the development of fibre-based quantum network infrastructure. However, reaching this wavelength window has been challenging for semiconductor-based quantum light sources. Here we show that quantum dot devices based on indium phosphide are capable of electrically injected single photon emission in this wavelength region. Using the biexciton cascade mechanism, they also produce entangled photons with a fidelity of 87 ± 4%, sufficient for the application of one-way error correction protocols. The material system further allows for entangled photon generation up to an operating temperature of 93 K. Our quantum photon source can be directly integrated with existing long distance quantum communication and cryptography systems, and provides a promising material platform for developing future quantum network hardware.

Multimodal Medical Image Fusion by Adaptive Manifold Filter.

PubMed

Geng, Peng; Liu, Shuaiqi; Zhuang, Shanna

2015-01-01

Medical image fusion plays an important role in diagnosis and treatment of diseases such as image-guided radiotherapy and surgery. The modified local contrast information is proposed to fuse multimodal medical images. Firstly, the adaptive manifold filter is introduced into filtering source images as the low-frequency part in the modified local contrast. Secondly, the modified spatial frequency of the source images is adopted as the high-frequency part in the modified local contrast. Finally, the pixel with larger modified local contrast is selected into the fused image. The presented scheme outperforms the guided filter method in spatial domain, the dual-tree complex wavelet transform-based method, nonsubsampled contourlet transform-based method, and four classic fusion methods in terms of visual quality. Furthermore, the mutual information values by the presented method are averagely 55%, 41%, and 62% higher than the three methods and those values of edge based similarity measure by the presented method are averagely 13%, 33%, and 14% higher than the three methods for the six pairs of source images.

Acoustic source localization in mixed field using spherical microphone arrays

NASA Astrophysics Data System (ADS)

Huang, Qinghua; Wang, Tong

2014-12-01

Spherical microphone arrays have been used for source localization in three-dimensional space recently. In this paper, a two-stage algorithm is developed to localize mixed far-field and near-field acoustic sources in free-field environment. In the first stage, an array signal model is constructed in the spherical harmonics domain. The recurrent relation of spherical harmonics is independent of far-field and near-field mode strengths. Therefore, it is used to develop spherical estimating signal parameter via rotational invariance technique (ESPRIT)-like approach to estimate directions of arrival (DOAs) for both far-field and near-field sources. In the second stage, based on the estimated DOAs, simple one-dimensional MUSIC spectrum is exploited to distinguish far-field and near-field sources and estimate the ranges of near-field sources. The proposed algorithm can avoid multidimensional search and parameter pairing. Simulation results demonstrate the good performance for localizing far-field sources, or near-field ones, or mixed field sources.

Nucleic acid duplexes incorporating a dissociable covalent base pair

NASA Technical Reports Server (NTRS)

Gao, K.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1999-01-01

We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

SU-E-T-46: Application of a Twin-Detector Method for the Determination of the Mean Photon Energy Em at Points of Measurement in a Water Phantom Surrounding a GammaMed HDR 192Ir Brachytherapy Source

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

Chofor, N; Poppe, B; Nebah, F

Purpose: In a brachytherapy photon field in water the fluence-averaged mean photon energy Em at the point of measurement correlates with the radiation quality correction factor kQ of a non water-equivalent detector. To support the experimental assessment of Em, we show that the normalized signal ratio NSR of a pair of radiation detectors, an unshielded silicon diode and a diamond detector can serve to measure quantity Em in a water phantom at a Ir-192 unit. Methods: Photon fluence spectra were computed in EGSnrc based on a detailed model of the GammaMed source. Factor kQ was calculated as the ratio ofmore » the detector's spectrum-weighted responses under calibration conditions at a 60Co unit and under brachytherapy conditions at various radial distances from the source. The NSR was investigated for a pair of a p-type unshielded silicon diode 60012 and a synthetic single crystal diamond detector 60019 (both PTW Freiburg). Each detector was positioned according to its effective point of measurement, with its axis facing the source. Lateral signal profiles were scanned under complete scatter conditions, and the NSR was determined as the quotient of the signal ratio under application conditions x and that at position r-ref = 1 cm. Results: The radiation quality correction factor kQ shows a close correlation with the mean photon energy Em. The NSR of the diode/diamond pair changes by a factor of two from 0–18 cm from the source, while Em drops from 350 to 150 keV. Theoretical and measured NSR profiles agree by ± 2 % for points within 5 cm from the source. Conclusion: In the presence of the close correlation between radiation quality correction factor kQ and photon mean energy Em, the NSR provides a practical means of assessing Em under clinical conditions. Precise detector positioning is the major challenge.« less

A three-wavelength multi-channel brain functional imager based on digital lock-in photon-counting technique

NASA Astrophysics Data System (ADS)

Ding, Xuemei; Wang, Bingyuan; Liu, Dongyuan; Zhang, Yao; He, Jie; Zhao, Huijuan; Gao, Feng

2018-02-01

During the past two decades there has been a dramatic rise in the use of functional near-infrared spectroscopy (fNIRS) as a neuroimaging technique in cognitive neuroscience research. Diffuse optical tomography (DOT) and optical topography (OT) can be employed as the optical imaging techniques for brain activity investigation. However, most current imagers with analogue detection are limited by sensitivity and dynamic range. Although photon-counting detection can significantly improve detection sensitivity, the intrinsic nature of sequential excitations reduces temporal resolution. To improve temporal resolution, sensitivity and dynamic range, we develop a multi-channel continuous-wave (CW) system for brain functional imaging based on a novel lock-in photon-counting technique. The system consists of 60 Light-emitting device (LED) sources at three wavelengths of 660nm, 780nm and 830nm, which are modulated by current-stabilized square-wave signals at different frequencies, and 12 photomultiplier tubes (PMT) based on lock-in photon-counting technique. This design combines the ultra-high sensitivity of the photon-counting technique with the parallelism of the digital lock-in technique. We can therefore acquire the diffused light intensity for all the source-detector pairs (SD-pairs) in parallel. The performance assessments of the system are conducted using phantom experiments, and demonstrate its excellent measurement linearity, negligible inter-channel crosstalk, strong noise robustness and high temporal resolution.

Broadband continuous wave source localization via pair-wise, cochleagram processing

NASA Astrophysics Data System (ADS)

Nosal, Eva-Marie; Frazer, L. Neil

2005-04-01

A pair-wise processor has been developed for the passive localization of broadband continuous-wave underwater sources. The algorithm uses sparse hydrophone arrays and does not require previous knowledge of the source signature. It is applicable in multiple source situations. A spectrogram/cochleagram version of the algorithm has been developed in order to utilize higher frequencies at longer ranges where signal incoherence, and limited computational resources, preclude the use of full waveforms. Simulations demonstrating the robustness of the algorithm with respect to noise and environmental mismatch will be presented, together with initial results from the analysis of humpback whale song recorded at the Pacific Missile Range Facility off Kauai. [Work supported by MHPCC and ONR.

Generation of Single Photons and Entangled Photon Pairs from a Quantum Dot

NASA Astrophysics Data System (ADS)

Yamamoto, Y.; Pelton, M.; Santori, C.; Solomon, G. S.

2002-10-01

Current quantum cryptography systems are limited by the Poissonian photon statistics of a standard light source: a security loophole is opened up by the possibility of multiple-photon pulses. By replacing the source with a single-photon emitter, transmission rates of secure information can be improved. A single photon source is also essential to implement a linear optics quantum computer. We have investigated the use of single self-assembled InAs/GaAs quantum dots as such single-photon sources, and have seen a hundred-fold reduction in the multi-photon probability as compared to Poissonian pulses. An extension of our experiment should also allow for the generation of triggered, polarizationentangled photon pairs.

Complementary b/y fragment ion pairs from post-source decay of metastable YahO for calibration of MALDI-TOF-TOF-MS/MS

USDA-ARS?s Scientific Manuscript database

Complementary b/y fragment ion pairs from post-source decay (PSD) of metastable YahO protein ion were evaluated for use in the calibration of MALDI-TOF-TOF for tandem mass spectrometry (MS/MS). The yahO gene from pathogenic Escherichia coli O157:H7 strain EDL933 was cloned into a pBAD18 plasmid vect...

Bridging visible and telecom wavelengths with a single-mode broadband photon pair source

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

Soeller, C.; Brecht, B.; Mosley, P. J.

We present a spectrally decorrelated photon pair source bridging the visible and telecom wavelength regions. Tailored design and fabrication of a solid-core photonic crystal fiber (PCF) lead to the emission of signal and idler photons into only a single spectral and spatial mode. Thus no narrowband filtering is necessary and the heralded generation of pure photon number states in ultrafast wave packets at telecom wavelengths becomes possible.

Frequency-bin entanglement of ultra-narrow band non-degenerate photon pairs

NASA Astrophysics Data System (ADS)

Rieländer, Daniel; Lenhard, Andreas; Jime`nez Farìas, Osvaldo; Máttar, Alejandro; Cavalcanti, Daniel; Mazzera, Margherita; Acín, Antonio; de Riedmatten, Hugues

2018-01-01

We demonstrate frequency-bin entanglement between ultra-narrowband photons generated by cavity enhanced spontaneous parametric down conversion. Our source generates photon pairs in widely non-degenerate discrete frequency modes, with one photon resonant with a quantum memory material based on praseodymium doped crystals and the other photon at telecom wavelengths. Correlations between the frequency modes are analyzed using phase modulators and narrowband filters before detection. We show high-visibility two photon interference between the frequency modes, allowing us to infer a coherent superposition of the modes. We develop a model describing the state that we create and use it to estimate optimal measurements to achieve a violation of the Clauser-Horne (CH) Bell inequality under realistic assumptions. With these settings we perform a Bell test and show a significant violation of the CH inequality, thus proving the entanglement of the photons. Finally we demonstrate the compatibility with a quantum memory material by using a spectral hole in the praseodymium (Pr) doped crystal as spectral filter for measuring high-visibility two-photon interference. This demonstrates the feasibility of combining frequency-bin entangled photon pairs with Pr-based solid state quantum memories.

The nearest neighbor and next nearest neighbor effects on the thermodynamic and kinetic properties of RNA base pair

NASA Astrophysics Data System (ADS)

Wang, Yujie; Wang, Zhen; Wang, Yanli; Liu, Taigang; Zhang, Wenbing

2018-01-01

The thermodynamic and kinetic parameters of an RNA base pair with different nearest and next nearest neighbors were obtained through long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The results indicate that thermodynamic parameters of GC base pair are dependent on the nearest neighbor base pair, and the next nearest neighbor base pair has little effect, which validated the nearest-neighbor model. The closing and opening rates of the GC base pair also showed nearest neighbor dependences. At certain temperature, the closing and opening rates of the GC pair with nearest neighbor AU is larger than that with the nearest neighbor GC, and the next nearest neighbor plays little role. The free energy landscape of the GC base pair with the nearest neighbor GC is rougher than that with nearest neighbor AU.

[Structural and Dipole Structure Peculiarities of Hoogsteen Base Pairs Formed in Complementary Nucleobases according to ab initio Quantum Mechanics Studies].

PubMed

Petrenko, Y M

2015-01-01

Ab initio quantum mechanics studies for the detection of structure and dipole structure peculiarities of Hoogsteen base pairs relative to Watson-Crick base pairs, were performed during our work. These base pairs are formed as a result of complementary interactions. It was revealed, that adenine-thymine Hoogsteen base pair and adenine-thymine Watson-Crick base pairs can be formed depending on initial configuration. Cytosine-guanine Hoogsteen pairs are formed only when cytosine was originally protonated. Both types of Hoogsteen pairs have noticeable difference in the bond distances and angles. These differences appeared in purine as well as in pyrimidine parts of the pairs. Hoogsteen pairs have mostly shorter hydrogen bond lengths and significantly larger angles of hydrogen bonds and larger angles between the hydrogen bonds than Watson-Crick base pairs. Notable differences are also observed with respect to charge distribution and dipole moment. Quantitative data on these differences are shown in our work. It is also reported that the values of local parameters (according to Cambridge classification of the parameters which determine DNA properties) in Hoogsteen base pairs, are greatly different from Watson-Crick ones.

Experimental demonstration of entanglement-enhanced classical communication over a quantum channel with correlated noise.

PubMed

Banaszek, Konrad; Dragan, Andrzej; Wasilewski, Wojciech; Radzewicz, Czesław

2004-06-25

We present an experiment demonstrating the entanglement enhanced capacity of a quantum channel with correlated noise, modeled by a fiber optic link exhibiting fluctuating birefringence. In this setting, introducing entanglement between two photons is required to maximize the amount of information that can be encoded into their joint polarization degree of freedom. We demonstrated this effect using a fiber-coupled source of entangled photon pairs based on spontaneous parametric down-conversion, and a linear-optics Bell state measurement. The obtained experimental classical capacity with entangled states is equal to 0.82+/-0.04 per a photon pair, and it exceeds approximately 2.5 times the theoretical upper limit when no quantum correlations are allowed.

Nucleic acid duplexes incorporating a dissociable covalent base pair

PubMed Central

Gao, Kui; Orgel, Leslie E.

1999-01-01

We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure. PMID:10611299

Robust prediction of consensus secondary structures using averaged base pairing probability matrices.

PubMed

Kiryu, Hisanori; Kin, Taishin; Asai, Kiyoshi

2007-02-15

Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic cells. To investigate the functional roles of these transcripts, it is of great interest to find conserved secondary structures from multiple alignments on a genomic scale. Since multiple alignments are often created using alignment programs that neglect the special conservation patterns of RNA secondary structures for computational efficiency, alignment failures can cause potential risks of overlooking conserved stem structures. We investigated the dependence of the accuracy of secondary structure prediction on the quality of alignments. We compared three algorithms that maximize the expected accuracy of secondary structures as well as other frequently used algorithms. We found that one of our algorithms, called McCaskill-MEA, was more robust against alignment failures than others. The McCaskill-MEA method first computes the base pairing probability matrices for all the sequences in the alignment and then obtains the base pairing probability matrix of the alignment by averaging over these matrices. The consensus secondary structure is predicted from this matrix such that the expected accuracy of the prediction is maximized. We show that the McCaskill-MEA method performs better than other methods, particularly when the alignment quality is low and when the alignment consists of many sequences. Our model has a parameter that controls the sensitivity and specificity of predictions. We discussed the uses of that parameter for multi-step screening procedures to search for conserved secondary structures and for assigning confidence values to the predicted base pairs. The C++ source code that implements the McCaskill-MEA algorithm and the test dataset used in this paper are available at http://www.ncrna.org/papers/McCaskillMEA/. Supplementary data are available at Bioinformatics online.

Bose-Einstein correlation of kaons in Si + Au collisions at 14.6 A GeV/c

NASA Technical Reports Server (NTRS)

Akiba, Y.; Beavis, D.; Beery, P.; Britt, H. C.; Budick, B.; Chasman, C.; Chen, Z.; Chi, C. Y.; Chu, Y. Y.; Cianciolo, V.

1993-01-01

The E-802 spectrometer at the Brookhaven Alternating Gradient Synchrotron, enhanced by a trigger for selection of events with one or more specified particles, has been used to measure the momentum-space correlation between pairs of K(+)s emitted in central Si + Au collisions at 14.6 A GeV/c. This correlation has been projected onto the Lorentz-invariant relative four-momentum axis. Fits to this correlation function yield a size for the kaon source that is comparable to that found using pi(+) pairs from a similar rapidity range, once a transformation from the particle-pair frames to a single source frame is made.

Photon pair generation with tailored frequency correlations in graded-index multimode fibers.

PubMed

Pourbeyram, Hamed; Mafi, Arash

2018-05-01

We study theoretically the generation of photon pairs with controlled spectral correlations via the four-wave mixing process in graded-index multimode optical fibers (GIMFs). We show that the quantum correlations of the generated photons in GIMFs can be preserved over a wide spectral range for a tunable pump source. Therefore, GIMFs can be utilized as quantum-state-preserving tunable sources of photons. In particular, we have shown that it is possible to generate factorable two-photon states, which allow for heralding of pure-state single photons without the need for narrowband spectral post filtering. We also elaborate on the possibility of simultaneously generating correlated and uncorrelated photon pairs in the same optical fiber.

Validation of a PCR-based method for the detection of various rendered materials in feedstuffs using a forensic DNA extraction kit.

PubMed

Myers, Michael J; Yancy, Haile F; Araneta, Michael; Armour, Jennifer; Derr, Janice; Hoostelaere, Lawrence A D; Farmer, Doris; Jackson, Falana; Kiessling, William M; Koch, Henry; Lin, Huahua; Liu, Yan; Mowlds, Gabrielle; Pinero, David; Riter, Ken L; Sedwick, John; Shen, Yuelian; Wetherington, June; Younkins, Ronsha

2006-01-01

A method trial was initiated to validate the use of a commercial DNA forensic kit to extract DNA from animal feed as part of a PCR-based method. Four different PCR primer pairs (one bovine pair, one porcine pair, one ovine primer pair, and one multispecies pair) were also evaluated. Each laboratory was required to analyze a total of 120 dairy feed samples either not fortified (control, true negative) or fortified with bovine meat and bone meal, porcine meat and bone meal (PMBM), or lamb meal. Feeds were fortified with the animal meals at a concentration of 0.1% (wt/wt). Ten laboratories participated in this trial, and each laboratory was required to evaluate two different primer pairs, i.e., each PCR primer pair was evaluated by five different laboratories. The method was considered to be validated for a given animal source when three or more laboratories achieved at least 97% accuracy (29 correct of 30 samples for 96.7% accuracy, rounded up to 97%) in detecting the fortified samples for that source. Using this criterion, the method was validated for the bovine primer because three laboratories met the criterion, with an average accuracy of 98.9%. The average false-positive rate was 3.0% in these laboratories. A fourth laboratory was 80% accurate in identifying the samples fortified with bovine meat and bone meal. A fifth laboratory was not able to consistently extract the DNA from the feed samples and did not achieve the criterion for accuracy for either the bovine or multispecies PCR primers. For the porcine primers, the method was validated, with four laboratories meeting the criterion for accuracy with an average accuracy of 99.2%. The fifth laboratory had a 93.3% accuracy outcome for the porcine primer. Collectively, these five laboratories had a 1.3% false-positive rate for the porcine primer. No laboratory was able to meet the criterion for accuracy with the ovine primers, most likely because of problems with the synthesis of the primer pair; none of the positive control DNA samples could be detected with the ovine primers. The multispecies primer pair was validated in three laboratories for use with bovine meat and bone meal and lamb meal but not with PMBM. The three laboratories had an average accuracy of 98.9% for bovine meat and bone meal, 97.8% for lamb meal, and 63.3% for PMBM. When examined on an individual laboratory basis, one of these four laboratories could not identify a single feed sample containing PMBM by using the multispecies primer, whereas the other laboratory identified only one PMBM-fortified sample, suggesting that the limit of detection for PMBM with this primer pair is around 0.1% (wt/wt). The results of this study demonstrated that the DNA forensic kit can be used to extract DNA from animal feed, which can then be used for PCR analysis to detect animal-derived protein present in the feed sample.

Integrated spatial multiplexing of heralded single-photon sources

PubMed Central

Collins, M.J.; Xiong, C.; Rey, I.H.; Vo, T.D.; He, J.; Shahnia, S.; Reardon, C.; Krauss, T.F.; Steel, M.J.; Clark, A.S.; Eggleton, B.J.

2013-01-01

The non-deterministic nature of photon sources is a key limitation for single-photon quantum processors. Spatial multiplexing overcomes this by enhancing the heralded single-photon yield without enhancing the output noise. Here the intrinsic statistical limit of an individual source is surpassed by spatially multiplexing two monolithic silicon-based correlated photon pair sources in the telecommunications band, demonstrating a 62.4% increase in the heralded single-photon output without an increase in unwanted multipair generation. We further demonstrate the scalability of this scheme by multiplexing photons generated in two waveguides pumped via an integrated coupler with a 63.1% increase in the heralded photon rate. This demonstration paves the way for a scalable architecture for multiplexing many photon sources in a compact integrated platform and achieving efficient two-photon interference, required at the core of optical quantum computing and quantum communication protocols. PMID:24107840

MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments.

PubMed

Martin, Daniel B; Holzman, Ted; May, Damon; Peterson, Amelia; Eastham, Ashley; Eng, Jimmy; McIntosh, Martin

2008-11-01

Multiple reaction monitoring (MRM) mass spectrometry identifies and quantifies specific peptides in a complex mixture with very high sensitivity and speed and thus has promise for the high throughput screening of clinical samples for candidate biomarkers. We have developed an interactive software platform, called MRMer, for managing highly complex MRM-MS experiments, including quantitative analyses using heavy/light isotopic peptide pairs. MRMer parses and extracts information from MS files encoded in the platform-independent mzXML data format. It extracts and infers precursor-product ion transition pairings, computes integrated ion intensities, and permits rapid visual curation for analyses exceeding 1000 precursor-product pairs. Results can be easily output for quantitative comparison of consecutive runs. Additionally MRMer incorporates features that permit the quantitative analysis experiments including heavy and light isotopic peptide pairs. MRMer is open source and provided under the Apache 2.0 license.

Nonlinear characterization of a silicon integrated Bragg waveguide filter.

PubMed

Massara, Micol Previde; Menotti, Matteo; Bergamasco, Nicola; Harris, Nicholas C; Baehr-Jones, Tom; Hochberg, Michael; Galland, Christophe; Liscidini, Marco; Galli, Matteo; Bajoni, Daniele

2018-03-01

Bragg waveguides are promising optical filters for pump suppression in spontaneous four-wave mixing (FWM) photon sources. In this work, we investigate the generation of unwanted photon pairs in the filter itself. We do this by taking advantage of the relation between spontaneous and classical FWM, which allows for the precise characterization of the nonlinear response of the device. The pair generation rate estimated from the classical measurement is compared with the theoretical value calculated by means of a full quantum model of the filter, which also allows investigation of the spectral properties of the generated pairs. We find a good agreement between theory and experiment, confirming that stimulated FWM is a valuable approach to characterize the nonlinear response of an integrated filter, and that the pairs generated in a Bragg waveguide are not a serious issue for the operation of a fully integrated nonclassical source.

Seismic reflection study of Flathead Lake, Montana

USGS Publications Warehouse

Wold, Richard J.

1982-01-01

A seismic reflection survey of Flathead Lake, Montana, was carried out in 1970 to study the geologic structure underlying the lake. Approximately 200 km of track lines were surveyed resulting in about 140 km of useable data (Fig. 1). A one cu. in. air gun was used as the energy source. Navigation was by a series of theodolite sitings of the boat from pairs of shore-based control points. 

A study of atmospheric mixing of trace gases by aerial sampling with a multi-rotor drone

NASA Astrophysics Data System (ADS)

Chang, Chih-Chung; Chang, Chih-Yuan; Wang, Jia-Lin; Lin, Ming-Ren; Ou-Yang, Chang-Feng; Pan, Hsiang-Hsu; Chen, Yen-Chen

2018-07-01

We exploited a novel sampling vehicle, a multi-rotor drone carrying a remote-controlled whole air sampling device, to collect aerial samples with high sample integrity and preservation conditions. An array of 106 volatile organic compounds (VOCs), CO, CH4, and CO2 were analyzed and compared between the aerial samples (300-m height) and the ground-level samples in pairs to inspect for vertical mixing of the trace gases at a coastal site under three different meteorological conditions of local circulation, frontal passage, and high-pressure peripheral circulation. A rather homogeneous composition was observed for the sample pairs immediately after the frontal passage, indicating a well-mixed condition below 300 m. In contrast, inhomogeneous mixing was observed for the sample pairs under the other two conditions (local circulation and high-pressure peripheral circulation), suggesting different layers of air masses. Furthermore, information of unique source markers, composition profiles, and lifetimes of compounds were used to differentiate the origins of the air masses aloft and at the surface to substantiate the observed inhomogeneity. The study demonstrates that, with the availability of the near-surface aerial sampling coupling with in-laboratory analysis, detailed compositions of trace gases can now be readily obtained with superior data quality. Based on the distinctive chemical compositions, the sources, transport, and atmospheric mixing of the airborne pollutants in the near-surface atmosphere can be better studied and understood.

Fluctuations in the electron system of a superconductor exposed to a photon flux

PubMed Central

de Visser, P. J.; Baselmans, J. J. A.; Bueno, J.; Llombart, N.; Klapwijk, T. M.

2014-01-01

In a superconductor, in which electrons are paired, the density of unpaired electrons should become zero when approaching zero temperature. Therefore, radiation detectors based on breaking of pairs promise supreme sensitivity, which we demonstrate using an aluminium superconducting microwave resonator. Here we show that the resonator also enables the study of the response of the electron system of the superconductor to pair-breaking photons, microwave photons and varying temperatures. A large range in radiation power (at 1.54 THz) can be chosen by carefully filtering the radiation from a blackbody source. We identify two regimes. At high radiation power, fluctuations in the electron system caused by the random arrival rate of the photons are resolved, giving a straightforward measure of the optical efficiency (48±8%) and showing an unprecedented detector sensitivity. At low radiation power, fluctuations are dominated by excess quasiparticles, the number of which is measured through their recombination lifetime. PMID:24496036

Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides.

PubMed

Buchmueller, Karen L; Staples, Andrew M; Uthe, Peter B; Howard, Cameron M; Pacheco, Kimberly A O; Cox, Kari K; Henry, James A; Bailey, Suzanna L; Horick, Sarah M; Nguyen, Binh; Wilson, W David; Lee, Moses

2005-01-01

Polyamides containing an N-terminal formamido (f) group bind to the minor groove of DNA as staggered, antiparallel dimers in a sequence-specific manner. The formamido group increases the affinity and binding site size, and it promotes the molecules to stack in a staggered fashion thereby pairing itself with either a pyrrole (Py) or an imidazole (Im). There has not been a systematic study on the DNA recognition properties of the f/Py and f/Im terminal pairings. These pairings were analyzed here in the context of f-ImPyPy, f-ImPyIm, f-PyPyPy and f-PyPyIm, which contain the central pairing modes, -ImPy- and -PyPy-. The specificity of these triamides towards symmetrical recognition sites allowed for the f/Py and f/Im terminal pairings to be directly compared by SPR, CD and DeltaT (M) experiments. The f/Py pairing, when placed next to the -ImPy- or -PyPy- central pairings, prefers A/T and T/A base pairs to G/C base pairs, suggesting that f/Py has similar DNA recognition specificity to Py/Py. With -ImPy- central pairings, f/Im prefers C/G base pairs (>10 times) to the other Watson-Crick base pairs; therefore, f/Im behaves like the Py/Im pair. However, the f/Im pairing is not selective for the C/G base pair when placed next to the -PyPy- central pairings.

1.5-μm band polarization entangled photon-pair source with variable Bell states.

PubMed

Arahira, Shin; Kishimoto, Tadashi; Murai, Hitoshi

2012-04-23

In this paper we report a polarization-entangled photon-pair source in a 1.5-μm band which can generate arbitrary entangled states including four maximum entangled states (Bell states) by using cascaded optical second nonlinearities (second-harmonic generation and the following spontaneous parametric down conversion) in a periodically poled LiNbO(3) (PPLN) ridge-waveguide device. Exchange among the Bell states was achieved by using an optical phase bias compensator (OPBC) in a Sagnac loop interferometer and a half-wave plate outside the loop for polarization conversion. Quantitative evaluation was made on the performance of the photon-pair source through the experiments of two-photon interferences, quantum state tomography, and test of violation of Bell inequality. We observed high visibilities of 96%, fidelities of 97%, and 2.71 of the S parameter in inequality of Clauser, Horne, Shimony, and Holt (CHSH). The experimental values, including peak coincidence counts in the two-photon interference (approximately 170 counts per second), remained almost unchanged in despite of the exchange among the Bell states. They were also in good agreement with the theoretical assumption from the mean number of the photon-pairs under the test (0.04 per pulse). More detailed experimental studies on the dependence of the mean number of the photon-pairs revealed that the quantum states were well understood as the Werner state. © 2012 Optical Society of America

Measures and Relative Motions of Some Mostly F. G. W. Struve Doubles

NASA Astrophysics Data System (ADS)

Wiley, E. O.

2012-04-01

Measures of 59 pairs of double stars with long observational histories using "lucky imaging" techniques are reported. Relative motions of 59 pairs are investigated using histories of observation, scatter plots of relative motion, ordinary least-squares (OLS) and total proper motion analyses performed in "R," an open source programming language. A scatter plot of the coefficient of determinations derived from the OLS y|epoch and OLS x|epoch clearly separates common proper motion pairs from optical pairs and what are termed "long-period binary candidates." Differences in proper motion separate optical pairs from long-term binary candidates. An Appendix is provided that details how to use known rectilinear pairs as calibration pairs for the program REDUC.

Unique Thermal Stability of Unnatural Hydrophobic Ds Bases in Double-Stranded DNAs.

PubMed

Kimoto, Michiko; Hirao, Ichiro

2017-10-20

Genetic alphabet expansion technology, the introduction of unnatural bases or base pairs into replicable DNA, has rapidly advanced as a new synthetic biology area. A hydrophobic unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px) exhibited high fidelity as a third base pair in PCR. SELEX methods using the Ds-Px pair enabled high-affinity DNA aptamer generation, and introducing a few Ds bases into DNA aptamers extremely augmented their affinities and selectivities to target proteins. Here, to further scrutinize the functions of this highly hydrophobic Ds base, the thermal stabilities of double-stranded DNAs (dsDNA) containing a noncognate Ds-Ds or G-Ds pair were examined. The thermal stability of the Ds-Ds self-pair was as high as that of the natural G-C pair, and apart from the generally higher stability of the G-C pair than that of the A-T pair, most of the 5'-pyrimidine-Ds-purine-3' sequences, such as CDsA and TDsA, exhibited higher stability than the 5'-purine-Ds-pyrimidine-3' sequences, such as GDsC and ADsC, in dsDNAs. This trait enabled the GC-content-independent control of the thermal stability of the designed dsDNA fragments. The melting temperatures of dsDNA fragments containing the Ds-Ds pair can be predicted from the nearest-neighbor parameters including the Ds base. In addition, the noncognate G-Ds pair can efficiently distinguish its neighboring cognate natural base pairs from noncognate pairs. We demonstrated that real-time PCR using primers containing Ds accurately detected a single-nucleotide mismatch in target DNAs. These unique properties of the Ds base that affect the stabilities of the neighboring base pairs could impart new functions to DNA molecules and technologies.

Convex Hull Aided Registration Method (CHARM).

PubMed

Fan, Jingfan; Yang, Jian; Zhao, Yitian; Ai, Danni; Liu, Yonghuai; Wang, Ge; Wang, Yongtian

2017-09-01

Non-rigid registration finds many applications such as photogrammetry, motion tracking, model retrieval, and object recognition. In this paper we propose a novel convex hull aided registration method (CHARM) to match two point sets subject to a non-rigid transformation. First, two convex hulls are extracted from the source and target respectively. Then, all points of the point sets are projected onto the reference plane through each triangular facet of the hulls. From these projections, invariant features are extracted and matched optimally. The matched feature point pairs are mapped back onto the triangular facets of the convex hulls to remove outliers that are outside any relevant triangular facet. The rigid transformation from the source to the target is robustly estimated by the random sample consensus (RANSAC) scheme through minimizing the distance between the matched feature point pairs. Finally, these feature points are utilized as the control points to achieve non-rigid deformation in the form of thin-plate spline of the entire source point set towards the target one. The experimental results based on both synthetic and real data show that the proposed algorithm outperforms several state-of-the-art ones with respect to sampling, rotational angle, and data noise. In addition, the proposed CHARM algorithm also shows higher computational efficiency compared to these methods.

Independent EEG Sources Are Dipolar

PubMed Central

Delorme, Arnaud; Palmer, Jason; Onton, Julie; Oostenveld, Robert; Makeig, Scott

2012-01-01

Independent component analysis (ICA) and blind source separation (BSS) methods are increasingly used to separate individual brain and non-brain source signals mixed by volume conduction in electroencephalographic (EEG) and other electrophysiological recordings. We compared results of decomposing thirteen 71-channel human scalp EEG datasets by 22 ICA and BSS algorithms, assessing the pairwise mutual information (PMI) in scalp channel pairs, the remaining PMI in component pairs, the overall mutual information reduction (MIR) effected by each decomposition, and decomposition ‘dipolarity’ defined as the number of component scalp maps matching the projection of a single equivalent dipole with less than a given residual variance. The least well-performing algorithm was principal component analysis (PCA); best performing were AMICA and other likelihood/mutual information based ICA methods. Though these and other commonly-used decomposition methods returned many similar components, across 18 ICA/BSS algorithms mean dipolarity varied linearly with both MIR and with PMI remaining between the resulting component time courses, a result compatible with an interpretation of many maximally independent EEG components as being volume-conducted projections of partially-synchronous local cortical field activity within single compact cortical domains. To encourage further method comparisons, the data and software used to prepare the results have been made available (http://sccn.ucsd.edu/wiki/BSSComparison). PMID:22355308

Intramolecular CH···O hydrogen bonds in the AI and BI DNA-like conformers of canonical nucleosides and their Watson-Crick pairs. Quantum chemical and AIM analysis.

PubMed

Yurenko, Yevgen P; Zhurakivsky, Roman O; Samijlenko, Svitlana P; Hovorun, Dmytro M

2011-08-01

The aim of this work is to cast some light on the H-bonds in double-stranded DNA in its AI and BI forms. For this purpose, we have performed the MP2 and DFT quantum chemical calculations of the canonical nucleoside conformers, relative to the AI and BI DNA forms, and their Watson-Crick pairs, which were regarded as the simplest models of the double-stranded DNA. Based on the atoms-in-molecules analysis (AIM), five types of the CH···O hydrogen bonds, involving bases and sugar, were detected numerically from 1 to 3 per a conformer: C2'H···O5', C1'H···O2, C6H···O5', C8H···O5', and C6H···O4'. The energy values of H-bonds occupy the range of 2.3-5.6 kcal/mol, surely exceeding the kT value (0.62 kcal/mol). The nucleoside CH···O hydrogen bonds appeared to "survive" turns of bases against the sugar, sometimes in rather large ranges of the angle values, pertinent to certain conformations, which points out to the source of the DNA lability, necessary for the conformational adaptation in processes of its functioning. The calculation of the interactions in the dA·T nucleoside pair gives evidence, that additionally to the N6H···O4 and N1···N3H canonical H-bonds, between the bases adenine and thymine the third one (C2H···O2) is formed, which, though being rather weak (about 1 kcal/mol), satisfies the AIM criteria of H-bonding and may be classified as a true H-bond. The total energy of all the CH···O nontraditional intramolecular H-bonds in DNA nucleoside pairs appeared to be commensurable with the energy of H-bonds between the bases in Watson-Crick pairs, which implies their possible important role in the DNA shaping.

Surface finish quality of the outer AXAF mirror pair based on x ray measurements of the VETA-I

NASA Technical Reports Server (NTRS)

Hughes, John P.; Schwartz, Daniel A.; Szentgyorgyi, Andrew; Vanspeybroeck, Leon; Zhao, Ping

1992-01-01

We employ the X-ray measurements of the VETA-I taken at the X-Ray Calibration Facility (XRCF) of the Marshall Space Flight Center (MSFC) to extract information about the surface finish quality of the outermost pair of AXAF mirrors. The particular measurements we consider are one dimensional scans of the core of the point response function (PRF) (full width half maximum (FWHM) scans), the encircled energy as a function of radius, and one dimensional scans of the wings of the PRF. We discuss briefly our ray trace model which incorporates the numerous effects present in the VETA-I test, such as the finite source distance, the size and shape of the X-ray source, the residual gravitational distortions of the optic, the despace of the VETA-I, and particulate contamination. We show how the data constrain the amplitude of mirror surface deviations for spatial frequencies greater than about 0.1 mm(exp -1). Constraints on the average amplitude of circumferential slope errors are derived as well.

KIC 4150611: a rare multi-eclipsing quintuple with a hybrid pulsator

NASA Astrophysics Data System (ADS)

Hełminiak, K. G.; Ukita, N.; Kambe, E.; Kozłowski, S. K.; Pawłaszek, R.; Maehara, H.; Baranec, C.; Konacki, M.

2017-06-01

Aims: We aim to analyse KIC 4150611 (HD 181469) - an interesting, bright quintuple system that includes a hybrid δ Sct/γ Dor pulsator. Four periods of eclipses - 94.2, 8.65, 1.52 and 1.43 d - have been observed by the Kepler satellite, and three point sources (A, B, and C) are seen in high angular resolution images. Methods: From spectroscopic observations made with the HIDES spectrograph attached to the 1.88-m telescope of the Okayama Astrophysical Observatory (OAO), we have calculated for the first time radial velocities (RVs) of the component B - a pair of G-type stars - and combined them with Kepler photometry in order to obtain absolute physical parameters of this pair. We also managed to directly measure RVs of the pulsator, for the first time. Additionally, we modelled the light curves of the 1.52 and 1.43-day pairs, and measured their eclipse timing variations (ETVs). We also performed relative astrometry and photometry of three sources seen on the images taken with the NIRC2 camera of the Keck II telescope. Finally, we compared our results with theoretical isochrones. Results: The brightest component Aa is the hybrid pulsator, transited every 94.2 days by a pair of K/M-type stars (Ab1+Ab2), which themselves form a 1.52-day eclipsing binary. The components Ba and Bb are late G-type stars, forming another eclipsing pair with a 8.65 day period. Their masses and radii are MBa = 0.894 ± 0.010 M⊙, RBa = 0.802 ± 0.044 R⊙ for the primary, and MBb = 0.888 ± 0.010 M⊙, RBb = 0.856 ± 0.038 R⊙ for the secondary. The remaining period of 1.43 days is possibly related to a faint third star C, which itself is most likely a background object. The system's properties are well-represented by a 35 Myr isochrone, basing on which the masses of the pulsator and the 1.52-day pair are MAa = 1.64(6) M⊙, and MAb,tot = 0.90(13) M⊙, respectively. There are also suggestions of additional bodies in the system.

Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides

PubMed Central

Buchmueller, Karen L.; Staples, Andrew M.; Uthe, Peter B.; Howard, Cameron M.; Pacheco, Kimberly A. O.; Cox, Kari K.; Henry, James A.; Bailey, Suzanna L.; Horick, Sarah M.; Nguyen, Binh; Wilson, W. David; Lee, Moses

2005-01-01

Polyamides containing an N-terminal formamido (f) group bind to the minor groove of DNA as staggered, antiparallel dimers in a sequence-specific manner. The formamido group increases the affinity and binding site size, and it promotes the molecules to stack in a staggered fashion thereby pairing itself with either a pyrrole (Py) or an imidazole (Im). There has not been a systematic study on the DNA recognition properties of the f/Py and f/Im terminal pairings. These pairings were analyzed here in the context of f-ImPyPy, f-ImPyIm, f-PyPyPy and f-PyPyIm, which contain the central pairing modes, –ImPy– and –PyPy–. The specificity of these triamides towards symmetrical recognition sites allowed for the f/Py and f/Im terminal pairings to be directly compared by SPR, CD and ΔTM experiments. The f/Py pairing, when placed next to the –ImPy– or –PyPy– central pairings, prefers A/T and T/A base pairs to G/C base pairs, suggesting that f/Py has similar DNA recognition specificity to Py/Py. With –ImPy– central pairings, f/Im prefers C/G base pairs (>10 times) to the other Watson–Crick base pairs; therefore, f/Im behaves like the Py/Im pair. However, the f/Im pairing is not selective for the C/G base pair when placed next to the –PyPy– central pairings. PMID:15703305

Cooper pair splitter realized in a two-quantum-dot Y-junction.

PubMed

Hofstetter, L; Csonka, S; Nygård, J; Schönenberger, C

2009-10-15

Non-locality is a fundamental property of quantum mechanics that manifests itself as correlations between spatially separated parts of a quantum system. A fundamental route for the exploration of such phenomena is the generation of Einstein-Podolsky-Rosen (EPR) pairs of quantum-entangled objects for the test of so-called Bell inequalities. Whereas such experimental tests of non-locality have been successfully conducted with pairwise entangled photons, it has not yet been possible to realize an electronic analogue of it in the solid state, where spin-1/2 mobile electrons are the natural quantum objects. The difficulty stems from the fact that electrons are immersed in a macroscopic ground state-the Fermi sea-which prevents the straightforward generation and splitting of entangled pairs of electrons on demand. A superconductor, however, could act as a source of EPR pairs of electrons, because its ground-state is composed of Cooper pairs in a spin-singlet state. These Cooper pairs can be extracted from a superconductor by tunnelling, but, to obtain an efficient EPR source of entangled electrons, the splitting of the Cooper pairs into separate electrons has to be enforced. This can be achieved by having the electrons 'repel' each other by Coulomb interaction. Controlled Cooper pair splitting can thereby be realized by coupling of the superconductor to two normal metal drain contacts by means of individually tunable quantum dots. Here we demonstrate the first experimental realization of such a tunable Cooper pair splitter, which shows a surprisingly high efficiency. Our findings open a route towards a first test of the EPR paradox and Bell inequalities in the solid state.

Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m5dCyd: Implications for the Stability of DNA i-Motif Conformations

NASA Astrophysics Data System (ADS)

Yang, Bo; Rodgers, M. T.

2015-08-01

Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m5dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m5dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m5dCyd)H+(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.

Fecal indicator organism modeling and microbial source tracking in environmental waters: Chapter 3.4.6

USGS Publications Warehouse

Nevers, Meredith; Byappanahalli, Muruleedhara; Phanikumar, Mantha S.; Whitman, Richard L.

2016-01-01

Mathematical models have been widely applied to surface waters to estimate rates of settling, resuspension, flow, dispersion, and advection in order to calculate movement of particles that influence water quality. Of particular interest are the movement, survival, and persistence of microbial pathogens or their surrogates, which may contaminate recreational water, drinking water, or shellfish. Most models devoted to microbial water quality have been focused on fecal indicator organisms (FIO), which act as a surrogate for pathogens and viruses. Process-based modeling and statistical modeling have been used to track contamination events to source and to predict future events. The use of these two types of models require different levels of expertise and input; process-based models rely on theoretical physical constructs to explain present conditions and biological distribution while data-based, statistical models use extant paired data to do the same. The selection of the appropriate model and interpretation of results is critical to proper use of these tools in microbial source tracking. Integration of the modeling approaches could provide insight for tracking and predicting contamination events in real time. A review of modeling efforts reveals that process-based modeling has great promise for microbial source tracking efforts; further, combining the understanding of physical processes influencing FIO contamination developed with process-based models and molecular characterization of the population by gene-based (i.e., biological) or chemical markers may be an effective approach for locating sources and remediating contamination in order to protect human health better.

To pair or not to pair: Sources of social variability with white-faced saki monkeys (Pithecia pithecia) as a case study.

PubMed

Thompson, Cynthia L

2016-05-01

Intraspecific variability in social systems is gaining increased recognition in primatology. Many primate species display variability in pair-living social organizations through incorporating extra adults into the group. While numerous models exist to explain primate pair-living, our tools to assess how and why variation in this trait occurs are currently limited. Here I outline an approach which: (i) utilizes conceptual models to identify the selective forces driving pair-living; (ii) outlines novel possible causes for variability in social organization; and (iii) conducts a holistic species-level analysis of social behavior to determine the factors contributing to variation in pair-living. A case study on white-faced sakis (Pithecia pithecia) is used to exemplify this approach. This species lives in either male-female pairs or groups incorporating "extra" adult males and/or females. Various conceptual models of pair-living suggest that high same-sex aggression toward extra-group individuals is a key component of the white-faced saki social system. Variable pair-living in white-faced sakis likely represents alternative strategies to achieve competency in this competition, in which animals experience conflicting selection pressures between achieving successful group defense and maintaining sole reproductive access to mates. Additionally, independent decisions by individuals may generate social variation by preventing other animals from adopting a social organization that maximizes fitness. White-faced saki inter-individual relationships and demographic patterns also lend conciliatory support to this conclusion. By utilizing both model-level and species-level approaches, with a consideration for potential sources of variation, researchers can gain insight into the factors generating variation in pair-living social organizations. © 2014 The Authors. American Journal of Primatology published by Wiley Periodicals, Inc.

Beamlike photon pairs entangled by a 2x2 fiber

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

Lo, Hsin-Pin; Department of Electrophysics, National Chiao-Tung University, Hsinchu, 300, Taiwan; Yabushita, Atsushi

Polarization-entangled photon pairs have been widely used as a light source of quantum communication. The polarization-entangled photon pairs are generally obtained at the crossing points of the light cones that are generated from a type-II nonlinear crystal. However, it is hard to pick up the photon pairs coming out from the crossing points because of their invisible wavelength and low intensity. In our previous work, we succeeded in generating polarization-entangled photon pairs by overlapping two light paths for the photon-pair generation. The photon pairs could be entangled in all of the generated photon pairs without clipping the crossing points, evenmore » with some difficulty in its alignment to overlap the two light paths. In this paper, we have developed an optical system which generates polarization-entangled photon pairs using a beamlike photon pair, without the difficulty in alignment. The measured results show that the photon pairs generated in the system are entangled in their polarizations.« less

Metal-mediated DNA base pairing: alternatives to hydrogen-bonded Watson-Crick base pairs.

PubMed

Takezawa, Yusuke; Shionoya, Mitsuhiko

2012-12-18

With its capacity to store and transfer the genetic information within a sequence of monomers, DNA forms its central role in chemical evolution through replication and amplification. This elegant behavior is largely based on highly specific molecular recognition between nucleobases through the specific hydrogen bonds in the Watson-Crick base pairing system. While the native base pairs have been amazingly sophisticated through the long history of evolution, synthetic chemists have devoted considerable efforts to create alternative base pairing systems in recent decades. Most of these new systems were designed based on the shape complementarity of the pairs or the rearrangement of hydrogen-bonding patterns. We wondered whether metal coordination could serve as an alternative driving force for DNA base pairing and why hydrogen bonding was selected on Earth in the course of molecular evolution. Therefore, we envisioned an alternative design strategy: we replaced hydrogen bonding with another important scheme in biological systems, metal-coordination bonding. In this Account, we provide an overview of the chemistry of metal-mediated base pairing including basic concepts, molecular design, characteristic structures and properties, and possible applications of DNA-based molecular systems. We describe several examples of artificial metal-mediated base pairs, such as Cu(2+)-mediated hydroxypyridone base pair, H-Cu(2+)-H (where H denotes a hydroxypyridone-bearing nucleoside), developed by us and other researchers. To design the metallo-base pairs we carefully chose appropriate combinations of ligand-bearing nucleosides and metal ions. As expected from their stronger bonding through metal coordination, DNA duplexes possessing metallo-base pairs exhibited higher thermal stability than natural hydrogen-bonded DNAs. Furthermore, we could also use metal-mediated base pairs to construct or induce other high-order structures. These features could lead to metal-responsive functional DNA molecules such as artificial DNAzymes and DNA machines. In addition, the metallo-base pairing system is a powerful tool for the construction of homogeneous and heterogeneous metal arrays, which can lead to DNA-based nanomaterials such as electronic wires and magnetic devices. Recently researchers have investigated these systems as enzyme replacements, which may offer an additional contribution to chemical biology and synthetic biology through the expansion of the genetic alphabet.

Theoretical determination of one-electron redox potentials for DNA bases, base pairs, and stacks.

PubMed

Paukku, Y; Hill, G

2011-05-12

Electron affinities, ionization potentials, and redox potentials for DNA bases, base pairs, and N-methylated derivatives are computed at the DFT/M06-2X/6-31++G(d,p) level of theory. Redox properties of a guanine-guanine stack model are explored as well. Reduction and oxidation potentials are in good agreement with the experimental ones. Electron affinities of base pairs were found to be negative. Methylation of canonical bases affects the ionization potentials the most. Base pair formation and base stacking lower ionization potentials by 0.3 eV. Pairing of guanine with the 5-methylcytosine does not seem to influence the redox properties of this base pair much.

Power law X- and gamma-ray emission from relativistic thermal plasmas

NASA Technical Reports Server (NTRS)

Zdziarski, A. A.

1984-01-01

Pair equilibrium in thermal plasmas emitting power law photon spectra by repeated Compton scatterings of a soft photon source active galactic nuclei was studied. Dependence of the spectral index on optical thickness and on temperature of the plasma is discussed. The equation for pair equilibrium is solved for the maximum steady luminosity. Analytical solutions for the subrelativistic region, and for the ultrarelativistic region are found. In the transrelativistic region the solutions are expressed by single integrals over the pair production cross sections, performed numerically. The constraints on soft photon source imposed by the condition that the soft photon flux cannot exceed the black-body flux are considered. For the Comptonized synchrotron radiation model a relation between magnetic field strength and output luminosity is found.

Base pairing and base mis-pairing in nucleic acids

NASA Technical Reports Server (NTRS)

Wang, A. H. J.; Rich, A.

1986-01-01

In recent years we have learned that DNA is conformationally active. It can exist in a number of different stable conformations including both right-handed and left-handed forms. Using single crystal X-ray diffraction analysis we are able to discover not only additional conformations of the nucleic acids but also different types of hydrogen bonded base-base interactions. Although Watson-Crick base pairings are the predominant type of interaction in double helical DNA, they are not the only types. Recently, we have been able to examine mismatching of guanine-thymine base pairs in left-handed Z-DNA at atomic resolution (1A). A minimum amount of distortion of the sugar phosphate backbone is found in the G x T pairing in which the bases are held together by two hydrogen bonds in the wobble pairing interaction. Because of the high resolution of the analysis we can visualize water molecules which fill in to accommodate the other hydrogen bonding positions in the bases which are not used in the base-base interactions. Studies on other DNA oligomers have revealed that other types of non-Watson-Crick hydrogen bonding interactions can occur. In the structure of a DNA octamer with the sequence d(GCGTACGC) complexed to an antibiotic triostin A, it was found that the two central AT base pairs are held together by Hoogsteen rather than Watson-Crick base pairs. Similarly, the G x C base pairs at the ends are also Hoogsteen rather than Watson-Crick pairing. Hoogsteen base pairs make a modified helix which is distinct from the Watson-Crick double helix.

Hidden in Plain Sight: Subtle Effects of the 8-Oxoguanine Lesion on the Structure, Dynamics, and Thermodynamics of a 15-Base-Pair Oligodeoxynucleotide Duplex†

PubMed Central

Crenshaw, Charisse M.; Wade, Jacqueline E.; Arthanari, Haribabu; Frueh, Dominique; Lane, Benjamin F.; Núñez, Megan E.

2011-01-01

The base lesion 8-oxoguanine is formed readily by oxidation of DNA, potentially leading to G→T transversion mutations. Despite the apparent similarity of 8-oxoguanine-cytosine base pairs to normal guanine-cytosine base pairs, cellular base excision repair systems effectively recognize the lesion base. Here we apply several techniques to examine a single 8-oxoguanine lesion at the center of a nonpalindromic 15-mer duplex oligonucleotide in an effort to determine what, if anything, distinguishes an 8-oxoguanine-cytosine base pair from a normal base pair. The lesion duplex is globally almost indistinguishable from the unmodified parent duplex using CD spectroscopy and UV melting thermodynamics. The DNA mismatch-detecting photocleavage agent Rh(bpy)2chrysi3+ cleaves only weakly and nonspecifically, revealing that the 8oxoG-C pair is locally stable at the level of the individual base pairs. NMR spectra are also consistent with a well-conserved B-form duplex structure. In the 2D NOESY spectra, base-sugar and imino-imino crosspeaks are strikingly similar between parent and lesion duplexes. Changes in chemical shift due to the 8oxoG lesion are localized to its complementary cytosine and to the 2–3 base pairs immediately flanking the lesion on the lesion strand. Residues further removed from the lesion are shown to be unperturbed by its presence. Notably, imino exchange experiments indicate that the 8-oxoguanine-cytosine pair is strong and stable, with an apparent equilibrium constant for opening equal to that of other internal guanine-cytosine base pairs, on the order of 10−6. This collection of experiments shows that the 8-oxoguanine-cytosine base pair is incredibly stable and similar to the native pair. PMID:21902242

A PCR-based tool for the cultivation-independent monitoring of Pandora neoaphidis.

PubMed

Fournier, A; Enkerli, J; Keller, S; Widmer, F

2008-09-01

Pandora neoaphidis is one of the most important fungal pathogens of aphids and has a great potential for use in biocontrol. Little is known on how this fungus persists in an area and in particular on its overwintering strategies. It is hypothesized that natural areas play an important role for survival and that soil may serve as a source of inoculum for new aphid populations in spring. To test these hypotheses, a cultivation-independent PCR-based diagnostic tool was developed, that allows the detection of P. neoaphidis in the environment. Two P. neoaphidis specific PCR primer pairs were designed, targeting sequences in the ribosomal RNA gene cluster. Specificity of both primer pairs was demonstrated with P. neoaphidis and non-target close entomophthoralean relatives. Moreover, single amplicons of expected sizes were obtained with both primer pairs from various environmental sample types, including aphid cadavers, plant material, and soil. The PCR-based diagnostic tool was applied to investigate the persistence of P. neoaphidis in soil samples obtained in 2004/2005 from a nettle field harboring infected aphids in fall 2004. P. neoaphidis was detected in every sample collected in November 2004 and March 2005, suggesting an overwintering stage of P. neoaphidis in top soil layers. The developed cultivation-independent PCR-based tool will be valuable for further investigation of the ecology of P. neoaphidis and for the development and future implementation of management strategies against aphids involving conservation biocontrol.

Structural landscape of base pairs containing post-transcriptional modifications in RNA

PubMed Central

Seelam, Preethi P.; Sharma, Purshotam

2017-01-01

Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts toward understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures and most commonly involve guanine or uridine modifications. Further, analysis of tRNA sequences reveals additional examples of modified base pairs at structurally conserved tRNA regions and highlights the conservation patterns of these base pairs in three domains of life. Comparison of structures and binding energies of modified base pairs with their unmodified counterparts, using quantum chemical methods, allowed us to classify the base modifications in terms of the nature of their electronic structure effects on base-pairing. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding sites on the ribosome, and the three-way junctions within tRNA. These scenarios, when analyzed in the context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with their specific functional roles. Overall, our study highlights the structural importance of modified base pairs in RNA and points toward the need for greater appreciation of the role of modified bases and their interactions, in the context of many biological processes involving RNA. PMID:28341704

Stability of non-Watson-Crick G-A/A-G base pair in synthetic DNA and RNA oligonucleotides.

PubMed

Ito, Yuko; Sone, Yumiko; Mizutani, Takaharu

2004-03-01

A non-Watson-Crick G-A/A-G base pair is found in SECIS (selenocysteine-insertion sequence) element in the 3'-untranslated region of Se-protein mRNAs and in the functional site of the hammerhead ribozyme. We studied the stability of G-A/A-G base pair (bold) in 17mer GT(U)GACGGAAACCGGAAC synthetic DNA and RNA oligonucleotides by thermal melting experiments and gel electrophoresis. The measured Tm value of DNA oligonucleotide having G-A/A-G pair showed an intermediate value (58 degrees C) between that of Watson-Crick G-C/C-G base pair (75 degrees C) and that of G-G/A-A of non-base-pair (40 degrees C). Similar thermal melting patterns were obtained with RNA oligonucleotides. This result indicates that the secondary structure of oligonucleotide having G-A/A-G base pair is looser than that of the G-C type Watson-Crick base pair. In the comparison between RNA and DNA having G-A/A-G base pair, the Tm value of the RNA oligonucleotide was 11 degrees C lower than that of DNA, indicating that DNA has a more rigid structure than RNA. The stained pattern of oligonucleotide on polyacrylamide gel clarified that the mobility of the DNA oligonucleotide G-A/A-G base pair changed according to the urea concentration from the rigid state (near the mobility of G-C/C-G oligonucleotide) in the absence of urea to the random state (near the mobility of G-G/A-A oligonucleotide) in 7 M urea. However, the RNA oligonucleotide with G-A/A-G pair moved at an intermediate mobility between that of oligonucleotide with G-C/C-G and of the oligonucleotide with G-G/A-A, and the mobility pattern did not depend on urea concentration. Thus, DNA and RNA oligonucleotides with the G-A/A-G base pair showed a pattern indicating an intermediate structure between the rigid Watson-Crick base pair and the random structure of non-base pair. RNA with G-A/A-G base pair has the intermediate structure not influenced by urea concentration. Finally, this study indicated that the intermediate rigidity imparted by Non-Watson-Crick base pair in SECIS element plays an important role in the selenocysteine expression by UGA codon.

Introducing a model of pairing based on base pair specific interactions between identical DNA sequences

NASA Astrophysics Data System (ADS)

(O' Lee, Dominic J.

2018-02-01

At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One mechanism solely relies on base pair specific patterns of helix distortion being the same on the two molecules, discussed extensively in the past. The other mechanism proposes that there are preferential interactions between base pairs of the same composition. We introduce a model, built on this second mechanism, where both thermal stretching and twisting fluctuations are included, as well as the base pair specific helix distortions. Firstly, we consider an approximation for weak pairing interactions, or short molecules. This yields a dependence of the energy on the square root of the molecular length, which could explain recent experimental data. However, analysis suggests that this approximation is no longer valid at large DNA lengths. In a second approximation, for long molecules, we define two adaptation lengths for twisting and stretching, over which the pairing interaction can limit the accumulation of helix disorder. When the pairing interaction is sufficiently strong, both adaptation lengths are finite; however, as we reduce pairing strength, the stretching adaptation length remains finite but the torsional one becomes infinite. This second state persists to arbitrarily weak values of the pairing strength; suggesting that, if the molecules are long enough, the pairing energy scales as length. To probe differences between the two pairing mechanisms, we also construct a model of similar form. However, now, pairing between identical sequences solely relies on the intrinsic helix distortion patterns. Between the two models, we see interesting qualitative differences. We discuss our findings, and suggest new work to distinguish between the two mechanisms.

High intensity positron source at HFR: Basic concept, scoring and design optimisation

NASA Astrophysics Data System (ADS)

Zeman, A.; Tuček, K.; Debarberis, L.; Hogenbirk, A.

2012-01-01

Recent applications of positron beam techniques in various fields of research have led to an increasing demand for high intensity positron sources required for advanced applications, particularly in materials science. Considerable efforts are being made worldwide to design and set-up high intensity positron sources and beam systems that are based on several principles. Such positron sources could be used in fundamental and applied research experiments, as well as in industrial applications, especially in the field of condensed matter characterisation at the nanometre scale. Phenomena involving positrons are also important in other applied science fields such as medicine, biology, physics, energy, etc. However, such studies are often limited due to the relative lack of suitable positron sources. Results from the recently completed Exploratory Research Project called "HIPOS" are discussed in this paper, which describes the principles behind such a powerful very high intensity positron beam experimental facility that is based on a reactor source. Details of a proposed concept that uses nuclear reactions [(n, γ) and (γ, pair)] within a designed positron generator at the High Flux Reactor (HFR) in Petten are also discussed. The HIPOS source has been designed to produce slow positrons with intensity of the order of 10 10 e +/s.

TeV-photon paradox and space with SU(2) fuzziness

NASA Astrophysics Data System (ADS)

Shariati, A.; Khorrami, M.; Fatollahi, A. H.

2008-02-01

The possibility is examined that a model based on space noncommutativity of linear type can explain why photons from distant sources with multi-TeV energies can reach the Earth. In particular within a model in which space coordinates satisfy the algebra of the SU(2) Lie group, it is shown that there is a possibility that the pair production through the reaction of CMB and energetic photons be forbidden kinematically.

Satellite-based quantum communication terminal employing state-of-the-art technology

NASA Astrophysics Data System (ADS)

Pfennigbauer, Martin; Aspelmeyer, Markus; Leeb, Walter R.; Baister, Guy; Dreischer, Thomas; Jennewein, Thomas; Neckamm, Gregor; Perdigues, Josep M.; Weinfurter, Harald; Zeilinger, Anton

2005-09-01

Feature Issue on Optical Wireless Communications (OWC) We investigate the design and the accommodation of a quantum communication transceiver in an existing classical optical communication terminal on board a satellite. Operation from a low earth orbit (LEO) platform (e.g., the International Space Station) would allow transmission of single photons and pairs of entangled photons to ground stations and hence permit quantum communication applications such as quantum cryptography on a global scale. Integration of a source generating entangled photon pairs and single-photon detection into existing optical terminal designs is feasible. Even more, major subunits of the classical terminals such as those for pointing, acquisition, and tracking as well as those providing the required electronic, thermal, and structural backbone can be adapted so as to meet the quantum communication terminal needs.

CPM Pairs from LSPM so far not WDS Listed – Part II

NASA Astrophysics Data System (ADS)

Knapp, Wilfried; Nanson, John

2017-10-01

The LSPM catalog (Lepine and Shara 2005) is a rich source for CPM pairs we thought already exhausted – but as we found during research for our report “A new concept for counter-checking of assumed CPM pairs” (Knapp and Nanson 2017) there are still many poten-tial CPM pairs indicated in LSPM which as of the end of 2016 are not listed in the WDS cata-log. After our first part on about 40 such objects (Knapp and Nanson 2017) the next report with about 30 additional common proper motion pairs is presented here.

A Common Calibration Source Framework for Fully-Polarimetric and Interferometric Radiometers

NASA Technical Reports Server (NTRS)

Kim, Edward J.; Davis, Brynmor; Piepmeier, Jeff; Zukor, Dorothy J. (Technical Monitor)

2000-01-01

Two types of microwave radiometry--synthetic thinned array radiometry (STAR) and fully-polarimetric (FP) radiometry--have received increasing attention during the last several years. STAR radiometers offer a technological solution to achieving high spatial resolution imaging from orbit without requiring a filled aperture or a moving antenna, and FP radiometers measure extra polarization state information upon which entirely new or more robust geophysical retrieval algorithms can be based. Radiometer configurations used for both STAR and FP instruments share one fundamental feature that distinguishes them from more 'standard' radiometers, namely, they measure correlations between pairs of microwave signals. The calibration requirements for correlation radiometers are broader than those for standard radiometers. Quantities of interest include total powers, complex correlation coefficients, various offsets, and possible nonlinearities. A candidate for an ideal calibration source would be one that injects test signals with precisely controllable correlation coefficients and absolute powers simultaneously into a pair of receivers, permitting all of these calibration quantities to be measured. The complex nature of correlation radiometer calibration, coupled with certain inherent similarities between STAR and FP instruments, suggests significant leverage in addressing both problems together. Recognizing this, a project was recently begun at NASA Goddard Space Flight Center to develop a compact low-power subsystem for spaceflight STAR or FP receiver calibration. We present a common theoretical framework for the design of signals for a controlled correlation calibration source. A statistical model is described, along with temporal and spectral constraints on such signals. Finally, a method for realizing these signals is demonstrated using a Matlab-based implementation.

Anisotropy of thermal dileptons

NASA Astrophysics Data System (ADS)

Goloviznin, V. V.; Snigirev, A. M.; Zinovjev, G. M.

2018-05-01

The meaningful specific anisotropy in the angle distribution of leptons with respect to the three-momentum of pair is predicted as a feasibility signature of synchrotron-like mechanism resulting from the quarks interacting with a collective confining color field in the heavy ion collisions. The lepton pair production rate and the spectrum of pair invariant mass are presented for this new dilepton source that is apparently not taken into consideration in the available phenomenological estimates.

Correspondence of electroencephalography and near-infrared spectroscopy sensitivities to the cerebral cortex using a high-density layout

PubMed Central

Giacometti, Paolo; Diamond, Solomon G.

2014-01-01

Abstract. This study investigates the correspondence of the cortical sensitivity of electroencephalography (EEG) and near-infrared spectroscopy (NIRS). EEG forward model sensitivity to the cerebral cortex was calculated for 329 EEG electrodes following the 10-5 EEG positioning system using a segmented structural magnetic resonance imaging scan of a human subject. NIRS forward model sensitivity was calculated for the same subject using 156 NIRS source-detector pairs selected from 32 source and 32 detector optodes positioned on the scalp using a subset of the 10-5 EEG positioning system. Sensitivity correlations between colocalized NIRS source-detector pair groups and EEG channels yielded R=0.46±0.08. Groups of NIRS source-detector pairs with maximum correlations to EEG electrode sensitivities are tabulated. The mean correlation between the point spread functions for EEG and NIRS regions of interest (ROI) was R=0.43±0.07. Spherical ROIs with radii of 26 mm yielded the maximum correlation between EEG and NIRS averaged across all cortical mesh nodes. These sensitivity correlations between EEG and NIRS should be taken into account when designing multimodal studies of neurovascular coupling and when using NIRS as a statistical prior for EEG source localization. PMID:25558462

Sensitivity of the Cherenkov Telescope Array to the Detection of Intergalactic Magnetic Fields

NASA Astrophysics Data System (ADS)

Meyer, Manuel; Conrad, Jan; Dickinson, Hugh

2016-08-01

Very high energy (VHE; energy E ≳ 100 GeV) γ-rays originating from extragalactic sources undergo pair production with low-energy photons of background radiation fields. These pairs can inverse-Compton-scatter background photons, initiating an electromagnetic cascade. The spatial and temporal structure of this secondary γ-ray signal is altered as the {e}+{e}- pairs are deflected in an intergalactic magnetic field (IGMF). We investigate how VHE observations with the future Cherenkov Telescope Array, with its high angular resolution and broad energy range, can potentially probe the IGMF. We identify promising sources and simulate γ-ray spectra over a wide range of values of the IGMF strength and coherence length using the publicly available ELMAG Monte Carlo code. Combining simulated observations in a joint likelihood approach, we find that current limits on the IGMF can be significantly improved. The projected sensitivity depends strongly on the time a source has been γ-ray active and on the emitted maximum γ-ray energy.

Controlling the spectrum of photons generated on a silicon nanophotonic chip

PubMed Central

Kumar, Ranjeet; Ong, Jun Rong; Savanier, Marc; Mookherjea, Shayan

2014-01-01

Directly modulated semiconductor lasers are widely used, compact light sources in optical communications. Semiconductors can also be used to generate nonclassical light; in fact, CMOS-compatible silicon chips can be used to generate pairs of single photons at room temperature. Unlike the classical laser, the photon-pair source requires control over a two-dimensional joint spectral intensity (JSI) and it is not possible to process the photons separately, as this could destroy the entanglement. Here we design a photon-pair source, consisting of planar lightwave components fabricated using CMOS-compatible lithography in silicon, which has the capability to vary the JSI. By controlling either the optical pump wavelength, or the temperature of the chip, we demonstrate the ability to select different JSIs, with a large variation in the Schmidt number. Such control can benefit high-dimensional communications where detector-timing constraints can be relaxed by realizing a large Schmidt number in a small frequency range. PMID:25410792

Drop-in compatible entanglement for optical-fiber networks.

PubMed

Hall, Matthew A; Altepeter, Joseph B; Kumar, Prem

2009-08-17

A growing number of quantum communication protocols require entanglement distribution among remote parties, which is best accomplished by exploiting the mature technology and extensive infrastructure of low-loss optical fiber. For this reason, a practical source of entangled photons must be drop-in compatible with optical fiber networks. Here we demonstrate such a source for the first time, in which the nonlinearity of standard single-mode fiber is utilized to yield entangled photon pairs in the 1310-nm O-band. Using an ultra-stable design, we produce polarization entanglement with 98.0% +/- 0.5% fidelity to a maximally entangled state as characterized via coincidence-basis tomography. To demonstrate the source's drop-in capability, we transmit one photon from each entangled pair through a telecommunications-grade optical amplifier set to boost classical 1550-nm (C-band) communication signals. We verify that the photon pairs experience no measurable decoherence upon passing through the active amplifier (the output state's fidelity with a maximally entangled state is 98.4% +/- 1.4%). (c) 2009 Optical Society of America

pKa shifting in double-stranded RNA is highly dependent upon nearest neighbors and bulge positioning.

PubMed

Wilcox, Jennifer L; Bevilacqua, Philip C

2013-10-22

Shifting of pKa's in RNA is important for many biological processes; however, the driving forces responsible for shifting are not well understood. Herein, we determine how structural environments surrounding protonated bases affect pKa shifting in double-stranded RNA (dsRNA). Using (31)P NMR, we determined the pKa of the adenine in an A(+)·C base pair in various sequence and structural environments. We found a significant dependence of pKa on the base pairing strength of nearest neighbors and the location of a nearby bulge. Increasing nearest neighbor base pairing strength shifted the pKa of the adenine in an A(+)·C base pair higher by an additional 1.6 pKa units, from 6.5 to 8.1, which is well above neutrality. The addition of a bulge two base pairs away from a protonated A(+)·C base pair shifted the pKa by only ~0.5 units less than a perfectly base paired hairpin; however, positioning the bulge just one base pair away from the A(+)·C base pair prohibited formation of the protonated base pair as well as several flanking base pairs. Comparison of data collected at 25 °C and 100 mM KCl to biological temperature and Mg(2+) concentration revealed only slight pKa changes, suggesting that similar sequence contexts in biological systems have the potential to be protonated at biological pH. We present a general model to aid in the determination of the roles protonated bases may play in various dsRNA-mediated processes including ADAR editing, miRNA processing, programmed ribosomal frameshifting, and general acid-base catalysis in ribozymes.

Database of non-canonical base pairs found in known RNA structures

NASA Technical Reports Server (NTRS)

Nagaswamy, U.; Voss, N.; Zhang, Z.; Fox, G. E.

2000-01-01

Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson-Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/, contains information such as sequence context, sugar pucker conformation, anti / syn base conformations, chemical shift, p K (a)values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.

Memory and disgust: Effects of appearance-congruent and appearance-incongruent information on source memory for food.

PubMed

Mieth, Laura; Bell, Raoul; Buchner, Axel

2016-01-01

The present study was stimulated by previous findings showing that people preferentially remember person descriptions that violate appearance-based first impressions. Given that until now all studies used faces as stimuli, these findings can be explained by referring to a content-specific module for social information processing that facilitates social orientation within groups via stereotyping and counter-stereotyping. The present study tests whether the same results can be obtained with fitness-relevant stimuli from another domain--pictures of disgusting-looking or tasty-looking food, paired with tasty and disgusting descriptions. A multinomial model was used to disentangle item memory, guessing and source memory. There was an old-new recognition advantage for disgusting-looking food. People had a strong tendency towards guessing that disgusting-looking food had been previously associated with a disgusting description. Source memory was enhanced for descriptions that disconfirmed these negative, appearance-based impressions. These findings parallel the results from the social domain. Heuristic processing of stimuli based on visual appearance may be complemented by intensified processing of incongruent information that invalidates these first impressions.

Predicting drug-disease interactions by semi-supervised graph cut algorithm and three-layer data integration.

PubMed

Wu, Guangsheng; Liu, Juan; Wang, Caihua

2017-12-28

Prediction of drug-disease interactions is promising for either drug repositioning or disease treatment fields. The discovery of novel drug-disease interactions, on one hand can help to find novel indictions for the approved drugs; on the other hand can provide new therapeutic approaches for the diseases. Recently, computational methods for finding drug-disease interactions have attracted lots of attention because of their far more higher efficiency and lower cost than the traditional wet experiment methods. However, they still face several challenges, such as the organization of the heterogeneous data, the performance of the model, and so on. In this work, we present to hierarchically integrate the heterogeneous data into three layers. The drug-drug and disease-disease similarities are first calculated separately in each layer, and then the similarities from three layers are linearly fused into comprehensive drug similarities and disease similarities, which can then be used to measure the similarities between two drug-disease pairs. We construct a novel weighted drug-disease pair network, where a node is a drug-disease pair with known or unknown treatment relation, an edge represents the node-node relation which is weighted with the similarity score between two pairs. Now that similar drug-disease pairs are supposed to show similar treatment patterns, we can find the optimal graph cut of the network. The drug-disease pair with unknown relation can then be considered to have similar treatment relation with that within the same cut. Therefore, we develop a semi-supervised graph cut algorithm, SSGC, to find the optimal graph cut, based on which we can identify the potential drug-disease treatment interactions. By comparing with three representative network-based methods, SSGC achieves the highest performances, in terms of both AUC score and the identification rates of true drug-disease pairs. The experiments with different integration strategies also demonstrate that considering several sources of data can improve the performances of the predictors. Further case studies on four diseases, the top-ranked drug-disease associations have been confirmed by KEGG, CTD database and the literature, illustrating the usefulness of SSGC. The proposed comprehensive similarity scores from multi-views and multiple layers and the graph-cut based algorithm can greatly improve the prediction performances of drug-disease associations.

WebGIVI: a web-based gene enrichment analysis and visualization tool.

PubMed

Sun, Liang; Zhu, Yongnan; Mahmood, A S M Ashique; Tudor, Catalina O; Ren, Jia; Vijay-Shanker, K; Chen, Jian; Schmidt, Carl J

2017-05-04

A major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined for enriched biological concepts. One approach to help the researcher interpret large gene datasets is to associate genes and informative terms (iTerm) that are obtained from the biomedical literature using the eGIFT text-mining system. However, examining large lists of iTerm and gene pairs is a daunting task. We have developed WebGIVI, an interactive web-based visualization tool ( http://raven.anr.udel.edu/webgivi/ ) to explore gene:iTerm pairs. WebGIVI was built via Cytoscape and Data Driven Document JavaScript libraries and can be used to relate genes to iTerms and then visualize gene and iTerm pairs. WebGIVI can accept a gene list that is used to retrieve the gene symbols and corresponding iTerm list. This list can be submitted to visualize the gene iTerm pairs using two distinct methods: a Concept Map or a Cytoscape Network Map. In addition, WebGIVI also supports uploading and visualization of any two-column tab separated data. WebGIVI provides an interactive and integrated network graph of gene and iTerms that allows filtering, sorting, and grouping, which can aid biologists in developing hypothesis based on the input gene lists. In addition, WebGIVI can visualize hundreds of nodes and generate a high-resolution image that is important for most of research publications. The source code can be freely downloaded at https://github.com/sunliang3361/WebGIVI . The WebGIVI tutorial is available at http://raven.anr.udel.edu/webgivi/tutorial.php .

High-speed volume measurement system and method

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

Lane, Michael H.; Doyle, Jr., James L.; Brinkman, Michael J.

2017-12-12

Disclosed is a volume sensor having first, second, and third laser sources emitting first, second, and third laser beams; first, second, and third beam splitters splitting the first, second, and third laser beams into first, second, and third beam pairs; first, second, and third optical assemblies expanding the first, second, and third beam pairs into first, second, and third pairs of parallel beam sheets; fourth, fifth, and sixth optical assemblies focusing the first, second, and third beam sheet pairs into fourth, fifth, and sixth beam pairs; and first, second, and third detector pairs receiving the fourth, fifth, and sixth beammore » pairs and converting a change in intensity of at least one of the beam pairs resulting from an object passing through at least one of the first, second, and third parallel beam sheets into at least one electrical signal proportional to a three-dimensional representation of the object.« less

Thermodynamic Signature of DNA Damage: Characterization of DNA with a 5-Hydroxy-2'-deoxycytidine•2'-Deoxyguanosine Base Pair

PubMed Central

Ganguly, Manjori; Szulik, Marta W.; Donahue, Patrick S.; Clancy, Kate; Stone, Michael P.; Gold, Barry

2012-01-01

Oxidation of DNA due to exposure to reactive oxygen species is a major source of DNA damage. One of the oxidation lesions formed, 5-hydroxy-2'-deoxycytidine, has been shown to miscode by some replicative DNA polymerases but not by error prone polymerases capable of translesion synthesis. The 5-hydroxy-2'-deoxycytidine lesion is repaired by DNA glycosylases that require the 5-hydroxycytidine base to be extrahelical so it can enter into the enzyme's active site where it is excised off the DNA backbone to afford an abasic site. The thermodynamic and NMR results presented herein, describe the effect of a 5-hydroxy-2'-deoxycytidine•2'-deoxyguanosine base pair on the stability of two different DNA duplexes. The results demonstrate that the lesion is highly destabilizing and that the energy barrier for the unstacking of 5-hydroxy-2'-deoxycytidine from the DNA duplex may be low. This could provide a thermodynamic mode of adduct identification by DNA glycosylases that require the lesion to be extrahelical. PMID:22332945

Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs

PubMed Central

2017-01-01

Prediction of RNA tertiary structure from sequence is an important problem, but generating accurate structure models for even short sequences remains difficult. Predictions of RNA tertiary structure tend to be least accurate in loop regions, where non-canonical pairs are important for determining the details of structure. Non-canonical pairs can be predicted using a knowledge-based model of structure that scores nucleotide cyclic motifs, or NCMs. In this work, a partition function algorithm is introduced that allows the estimation of base pairing probabilities for both canonical and non-canonical interactions. Pairs that are predicted to be probable are more likely to be found in the true structure than pairs of lower probability. Pair probability estimates can be further improved by predicting the structure conserved across multiple homologous sequences using the TurboFold algorithm. These pairing probabilities, used in concert with prior knowledge of the canonical secondary structure, allow accurate inference of non-canonical pairs, an important step towards accurate prediction of the full tertiary structure. Software to predict non-canonical base pairs and pairing probabilities is now provided as part of the RNAstructure software package. PMID:29107980

Photoproduction of lepton pairs in proton-nucleus and nucleus-nucleus collisions at RHIC and LHC energies

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

Moreira, B. D.; Goncalves, V. P.; De Santana Amaral, J. T.

2013-03-25

In this contribution we study coherent interactions as a probe of the nonlinear effects in the Quantum Electrodynamics (QED). In particular, we study the multiphoton effects in the production of leptons pairs for proton-nucleus and nucleus-nucleus collisions for heavy nuclei. In the proton-nucleus we assume the ultrarelativistic proton as a source of photons and estimate the photoproduction of lepton pairs on nuclei at RHIC and LHC energies considering the multiphoton effects associated to multiple rescattering of the projectile photon on the proton of the nucleus. In nucleus - nucleus colllisions we consider the two nuclei as a source of photons.more » As each scattering contributes with a factor {alpha}Z to the cross section, this contribution must be taken into account for heavy nuclei. We consider the Coulomb corrections to calculate themultiple scatterings and estimate the total cross section for muon and tau pair production in proton-nucleus and nucleus-nucleus collisions at RHIC and LHC energies.« less

Toolbox for the design of LiNbO3-based passive and active integrated quantum circuits

NASA Astrophysics Data System (ADS)

Sharapova, P. R.; Luo, K. H.; Herrmann, H.; Reichelt, M.; Meier, T.; Silberhorn, C.

2017-12-01

We present and discuss perspectives of current developments on advanced quantum optical circuits monolithically integrated in the lithium niobate platform. A set of basic components comprising photon pair sources based on parametric down conversion (PDC), passive routing elements and active electro-optically controllable switches and polarisation converters are building blocks of a toolbox which is the basis for a broad range of diverse quantum circuits. We review the state-of-the-art of these components and provide models that properly describe their performance in quantum circuits. As an example for applications of these models we discuss design issues for a circuit providing on-chip two-photon interference. The circuit comprises a PDC section for photon pair generation followed by an actively controllable modified mach-Zehnder structure for observing Hong-Ou-Mandel interference. The performance of such a chip is simulated theoretically by taking even imperfections of the properties of the individual components into account.

Facial appearance affects science communication.

PubMed

Gheorghiu, Ana I; Callan, Mitchell J; Skylark, William J

2017-06-06

First impressions based on facial appearance predict many important social outcomes. We investigated whether such impressions also influence the communication of scientific findings to lay audiences, a process that shapes public beliefs, opinion, and policy. First, we investigated the traits that engender interest in a scientist's work, and those that create the impression of a "good scientist" who does high-quality research. Apparent competence and morality were positively related to both interest and quality judgments, whereas attractiveness boosted interest but decreased perceived quality. Next, we had members of the public choose real science news stories to read or watch and found that people were more likely to choose items that were paired with "interesting-looking" scientists, especially when selecting video-based communications. Finally, we had people read real science news items and found that the research was judged to be of higher quality when paired with researchers who look like "good scientists." Our findings offer insights into the social psychology of science, and indicate a source of bias in the dissemination of scientific findings to broader society.

The constitutional t(11;22): implications for a novel mechanism responsible for gross chromosomal rearrangements

PubMed Central

Kurahashi, H; Inagaki, H; Ohye, T; Kogo, H; Tsutsumi, M; Kato, T; Tong, M; Emanuel, BS

2012-01-01

The constitutional t(11;22)(q23;q11) is the most common recurrent non-Robertsonian translocation in humans. The breakpoint sequences of both chromosomes are characterized by several hundred base pairs of palindromic AT-rich repeats (PATRRs). Similar PATRRs have also been identified at the breakpoints of other nonrecurrent translocations, suggesting that PATRR-mediated chromosomal translocation represents one of the universal pathways for gross chromosomal rearrangement in the human genome. We propose that PATRRs have the potential to form cruciform structures through intrastrand-base pairing in single-stranded DNA, creating a source of genomic instability and leading to translocations. Indeed, de novo examples of the t(11;22) are detected at a high frequency in sperm from normal healthy males. This review synthesizes recent data illustrating a novel paradigm for an apparent spermatogenesis-specific translocation mechanism. This observation has important implications pertaining to the predominantly paternal origin of de novo gross chromosomal rearrangements in humans. PMID:20507342

High-Resolution Melting (HRM) of the Cytochrome B Gene: A Powerful Approach to Identify Blood-Meal Sources in Chagas Disease Vectors

PubMed Central

Peña, Victor H.; Fernández, Geysson J.; Gómez-Palacio, Andrés M.; Mejía-Jaramillo, Ana M.; Cantillo, Omar; Triana-Chávez, Omar

2012-01-01

Methods to determine blood-meal sources of hematophagous Triatominae bugs (Chagas disease vectors) are serological or based on PCR employing species-specific primers or heteroduplex analysis, but these are expensive, inaccurate, or problematic when the insect has fed on more than one species. To solve those problems, we developed a technique based on HRM analysis of the mitochondrial gene cytochrome B (Cyt b). This technique recognized 14 species involved in several ecoepidemiological cycles of the transmission of Trypanosoma cruzi and it was suitable with DNA extracted from intestinal content and feces 30 days after feeding, revealing a resolution power that can display mixed feedings. Field samples were analyzed showing blood meal sources corresponding to domestic, peridomiciliary and sylvatic cycles. The technique only requires a single pair of primers that amplify the Cyt b gene in vertebrates and no other standardization, making it quick, easy, relatively inexpensive, and highly accurate. PMID:22389739

DNA base dimers are stabilized by hydrogen-bonding interactions including non-Watson-Crick pairing near graphite surfaces.

PubMed

Shankar, Akshaya; Jagota, Anand; Mittal, Jeetain

2012-10-11

Single- and double-stranded DNA are increasingly being paired with surfaces and nanoparticles for numerous applications, such as sensing, imaging, and drug delivery. Unlike the majority of DNA structures in bulk that are stabilized by canonical Watson-Crick pairing between Ade-Thy and Gua-Cyt, those adsorbed on surfaces are often stabilized by noncanonical base pairing, quartet formation, and base-surface stacking. Not much is known about these kinds of interactions. To build an understanding of the role of non-Watson-Crick pairing on DNA behavior near surfaces, one requires basic information on DNA base pair stacking and hydrogen-bonding interactions. All-atom molecular simulations of DNA bases in two cases--in bulk water and strongly adsorbed on a graphite surface--are conducted to study the relative strengths of stacking and hydrogen bond interactions for each of the 10 possible combinations of base pairs. The key information obtained from these simulations is the free energy as a function of distance between two bases in a pair. We find that stacking interactions exert the dominant influence on the stability of DNA base pairs in bulk water as expected. The strength of stability for these stacking interactions is found to decrease in the order Gua-Gua > Ade-Gua > Ade-Ade > Gua-Thy > Gua-Cyt > Ade-Thy > Ade-Cyt > Thy-Thy > Cyt-Thy > Cyt-Cyt. On the other hand, mutual interactions of surface-adsorbed base pairs are stabilized mostly by hydrogen-bonding interactions in the order Gua-Cyt > Ade-Gua > Ade-Thy > Ade-Ade > Cyt-Thy > Gua-Gua > Cyt-Cyt > Ade-Cyt > Thy-Thy > Gua-Thy. Interestingly, several non-Watson-Crick base pairings, which are commonly ignored, have similar stabilization free energies due to interbase hydrogen bonding as Watson-Crick pairs. This clearly highlights the importance of non-Watson-Crick base pairing in the development of secondary structures of oligonucleotides near surfaces.

Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction.

PubMed

Sadowski, Peter; Fooshee, David; Subrahmanya, Niranjan; Baldi, Pierre

2016-11-28

Machine learning (ML) and quantum mechanical (QM) methods can be used in two-way synergy to build chemical reaction expert systems. The proposed ML approach identifies electron sources and sinks among reactants and then ranks all source-sink pairs. This addresses a bottleneck of QM calculations by providing a prioritized list of mechanistic reaction steps. QM modeling can then be used to compute the transition states and activation energies of the top-ranked reactions, providing additional or improved examples of ranked source-sink pairs. Retraining the ML model closes the loop, producing more accurate predictions from a larger training set. The approach is demonstrated in detail using a small set of organic radical reactions.

A reference skeletal dosimetry model for an adult male radionuclide therapy patient based on three-dimensional imaging and paired-image radiation transport

NASA Astrophysics Data System (ADS)

Shah, Amish P.

The need for improved patient-specificity of skeletal dose estimates is widely recognized in radionuclide therapy. Current clinical models for marrow dose are based on skeletal mass estimates from a variety of sources and linear chord-length distributions that do not account for particle escape into cortical bone. To predict marrow dose, these clinical models use a scheme that requires separate calculations of cumulated activity and radionuclide S values. Selection of an appropriate S value is generally limited to one of only three sources, all of which use as input the trabecular microstructure of an individual measured 25 years ago, and the tissue mass derived from different individuals measured 75 years ago. Our study proposed a new modeling approach to marrow dosimetry---the Paired Image Radiation Transport (PIRT) model---that properly accounts for both the trabecular microstructure and the cortical macrostructure of each skeletal site in a reference male radionuclide patient. The PIRT model, as applied within EGSnrc, requires two sets of input geometry: (1) an infinite voxel array of segmented microimages of the spongiosa acquired via microCT; and (2) a segmented ex-vivo CT image of the bone site macrostructure defining both the spongiosa (marrow, endosteum, and trabeculae) and the cortical bone cortex. Our study also proposed revising reference skeletal dosimetry models for the adult male cancer patient. Skeletal site-specific radionuclide S values were obtained for a 66-year-old male reference patient. The derivation for total skeletal S values were unique in that the necessary skeletal mass and electron dosimetry calculations were formulated from the same source bone site over the entire skeleton. We conclude that paired-image radiation-transport techniques provide an adoptable method by which the intricate, anisotropic trabecular microstructure of the skeletal site; and the physical size and shape of the bone can be handled together, for improved compilation of reference radionuclide S values. We also conclude that this comprehensive model for the adult male cancer patient should be implemented for use in patient-specific calculations for radionuclide dosimetry of the skeleton.

Design Considerations for a Dedicated Gravity Recovery Satellite Mission Consisting of Two Pairs of Satellites

NASA Technical Reports Server (NTRS)

Wiese, D. N.; Nerem, R. S.; Lemoine, F. G.

2011-01-01

Future satellite missions dedicated to measuring time-variable gravity will need to address the concern of temporal aliasing errors; i.e., errors due to high-frequency mass variations. These errors have been shown to be a limiting error source for future missions with improved sensors. One method of reducing them is to fly multiple satellite pairs, thus increasing the sampling frequency of the mission. While one could imagine a system architecture consisting of dozens of satellite pairs, this paper explores the more economically feasible option of optimizing the orbits of two pairs of satellites. While the search space for this problem is infinite by nature, steps have been made to reduce it via proper assumptions regarding some parameters and a large number of numerical simulations exploring appropriate ranges for other parameters. A search space originally consisting of 15 variables is reduced to two variables with the utmost impact on mission performance: the repeat period of both pairs of satellites (shown to be near-optimal when they are equal to each other), as well as the inclination of one of the satellite pairs (the other pair is assumed to be in a polar orbit). To arrive at this conclusion, we assume circular orbits, repeat groundtracks for both pairs of satellites, a 100-km inter-satellite separation distance, and a minimum allowable operational satellite altitude of 290 km based on a projected 10-year mission lifetime. Given the scientific objectives of determining time-variable hydrology, ice mass variations, and ocean bottom pressure signals with higher spatial resolution, we find that an optimal architecture consists of a polar pair of satellites coupled with a pair inclined at 72deg, both in 13-day repeating orbits. This architecture provides a 67% reduction in error over one pair of satellites, in addition to reducing the longitudinal striping to such a level that minimal post-processing is required, permitting a substantial increase in the spatial resolution of the gravity field products. It should be emphasized that given different sets of scientific objectives for the mission, or a different minimum allowable satellite altitude, different architectures might be selected.

Assessing race and ethnicity data quality across cancer registries and EMRs in two hospitals.

PubMed

Lee, Simon J Craddock; Grobe, James E; Tiro, Jasmin A

2016-05-01

Measurement of patient race/ethnicity in electronic health records is mandated and important for tracking health disparities. Characterize the quality of race/ethnicity data collection efforts. For all cancer patients diagnosed (2007-2010) at two hospitals, we extracted demographic data from five sources: 1) a university hospital cancer registry, 2) a university electronic medical record (EMR), 3) a community hospital cancer registry, 4) a community EMR, and 5) a joint clinical research registry. The patients whose data we examined (N = 17 834) contributed 41 025 entries (range: 2-5 per patient across sources), and the source comparisons generated 1-10 unique pairs per patient. We used generalized estimating equations, chi-squares tests, and kappas estimates to assess data availability and agreement. Compared to sex and insurance status, race/ethnicity information was significantly less likely to be available (χ(2 )> 8043, P < .001), with variation across sources (χ(2 )> 10 589, P < .001). The university EMR had a high prevalence of "Unknown" values. Aggregate kappa estimates across the sources was 0.45 (95% confidence interval, 0.45-0.45; N = 31 276 unique pairs), but improved in sensitivity analyses that excluded the university EMR source (κ = 0.89). Race/ethnicity data were in complete agreement for only 6988 patients (39.2%). Pairs with a "Black" data value in one of the sources had the highest agreement (95.3%), whereas pairs with an "Other" value exhibited the lowest agreement across sources (11.1%). Our findings suggest that high-quality race/ethnicity data are attainable. Many of the "errors" in race/ethnicity data are caused by missing or "Unknown" data values. To facilitate transparent reporting of healthcare delivery outcomes by race/ethnicity, healthcare systems need to monitor and enforce race/ethnicity data collection standards. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Neuromorphic audio-visual sensor fusion on a sound-localizing robot.

PubMed

Chan, Vincent Yue-Sek; Jin, Craig T; van Schaik, André

2012-01-01

This paper presents the first robotic system featuring audio-visual (AV) sensor fusion with neuromorphic sensors. We combine a pair of silicon cochleae and a silicon retina on a robotic platform to allow the robot to learn sound localization through self motion and visual feedback, using an adaptive ITD-based sound localization algorithm. After training, the robot can localize sound sources (white or pink noise) in a reverberant environment with an RMS error of 4-5° in azimuth. We also investigate the AV source binding problem and an experiment is conducted to test the effectiveness of matching an audio event with a corresponding visual event based on their onset time. Despite the simplicity of this method and a large number of false visual events in the background, a correct match can be made 75% of the time during the experiment.

Killed by Police: Validity of Media-Based Data and Misclassification of Death Certificates in Massachusetts, 2004-2016.

PubMed

Feldman, Justin M; Gruskin, Sofia; Coull, Brent A; Krieger, Nancy

2017-10-01

To assess the validity of demographic data reported in news media-based data sets for persons killed by police in Massachusetts (2004-2016) and to evaluate misclassification of these deaths in vital statistics mortality data. We identified 84 deaths resulting from police intervention in 4 news media-based data sources (WGBH News, Fatal Encounters, The Guardian, and The Washington Post) and, via record linkage, conducted matched-pair analyses with the Massachusetts mortality data. Compared with death certificates, there was near-perfect correlation for age in all sources (Pearson r > 0.99) and perfect concordance for gender. Agreement for race/ethnicity ranged from perfect (The Counted and The Washington Post) to high (Fatal Encounters Cohen's κ = 0.92). Among the 78 decedents for whom finalized International Classification of Diseases, 10th Revision (ICD-10), codes were available, 59 (75.6%) were properly classified as "deaths due to legal intervention." In Massachusetts, the 4 media-based sources on persons killed by police provide valid demographic data. Misclassification of deaths due to legal intervention in the mortality data does, however, remain a problem. Replication of the study in other states and nationally is warranted.

On the Feasibility of a Pulsed 14 TeV C.M.E. Muon Collider in the LHC Tunnel

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

Shiltsev, Vladimir; Neuffer, D.

We discuss the technical feasibility, key machine pa-rameters and major challenges of a 14 TeV c.m.e. muon-muon collider in the LHC tunnel [1]. The luminosity of the collider is evaluated for three alternative muon sources – the PS synchrotron, one of a type developed by the US Muon Accelerator Program (MAP) and a low-emittance option based on resonant μ-pair production.

Using the global positioning satellite system to determine attitude rates using doppler effects

NASA Technical Reports Server (NTRS)

Campbell, Charles E. (Inventor)

2003-01-01

In the absence of a gyroscope, the attitude and attitude rate of a receiver can be determined using signals received by antennae on the receiver. Based on the signals received by the antennae, the Doppler difference between the signals is calculated. The Doppler difference may then be used to determine the attitude rate. With signals received from two signal sources by three antennae pairs, the three-dimensional attitude rate is determined.

The Telecommunications and Data Acquisition

NASA Technical Reports Server (NTRS)

Renzetti, N. A. (Editor)

1981-01-01

Progress in the development and operations of the Deep Space Network is reported including developments in Earth based radio technology as applied to other research programs. These programs include application of radio interferometry at microwave frequencies to geodetic measurements and geodynamics, use of deep space stations individually and in pairs as an interferometer by radio astronomers for astrophysics research by direct observations of radio sources, and radio search for extraterrestrial intelligence in the microwave region of the electromagnetic spectrum.

The Roles of Similarity in Transfer: Determinants of Similarity-Based Reminding and Mapping

DTIC Science & Technology

1991-06-02

Psychology , Northwestern University, 2029 Sheridan Road, Evanston, IL 60208. Reproduction in whole or part is permitted for any purpose of the United...ADDRESS (City, State, and ZIPCode) 10 SOURCE OF FUNDING NUMBERS Department of Psychology PROGRAM PROJECT TASK WORK UNIT 603 E. Daniel ELEMENT NO NO NO...according to 3 whether the stimuli (in an S-R pair) or the responses are similar from training to test . Ellis (1965), while agreeing that similarity is

Complementary metal-oxide semiconductor compatible source of single photons at near-visible wavelengths

NASA Astrophysics Data System (ADS)

Cernansky, Robert; Martini, Francesco; Politi, Alberto

2018-02-01

We demonstrate on chip generation of correlated pairs of photons in the near-visible spectrum using a CMOS compatible PECVD Silicon Nitride photonic device. Photons are generated via spontaneous four wave mixing enhanced by a ring resonator with high quality Q-factor of 320,000 resulting in a generation rate of 950,000 $\\frac{pairs}{mW}$. The high brightness of this source offers the opportunity to expand photonic quantum technologies over a broad wavelength range and provides a path to develop fully integrated quantum chips working at room temperature.

Turboprop and rotary-wing aircraft flight parameter estimation using both narrow-band and broadband passive acoustic signal-processing methods.

PubMed

Ferguson, B G; Lo, K W

2000-10-01

Flight parameter estimation methods for an airborne acoustic source can be divided into two categories, depending on whether the narrow-band lines or the broadband component of the received signal spectrum is processed to estimate the flight parameters. This paper provides a common framework for the formulation and test of two flight parameter estimation methods: one narrow band, the other broadband. The performances of the two methods are evaluated by applying them to the same acoustic data set, which is recorded by a planar array of passive acoustic sensors during multiple transits of a turboprop fixed-wing aircraft and two types of rotary-wing aircraft. The narrow-band method, which is based on a kinematic model that assumes the source travels in a straight line at constant speed and altitude, requires time-frequency analysis of the acoustic signal received by a single sensor during each aircraft transit. The broadband method is based on the same kinematic model, but requires observing the temporal variation of the differential time of arrival of the acoustic signal at each pair of sensors that comprises the planar array. Generalized cross correlation of each pair of sensor outputs using a cross-spectral phase transform prefilter provides instantaneous estimates of the differential times of arrival of the signal as the acoustic wavefront traverses the array.

CPM Pairs from LSPM so far not WDS Listed – Part III

NASA Astrophysics Data System (ADS)

Knapp, Wilfried; Nanson, John

2017-10-01

The LSPM catalog (Lepine and Shara 2005) is a rich source for CPM pairs we thought already exhausted – but as we found during research for our report “A new concept for counter-checking of assumed CPM pairs” (Knapp and Nanson 2017) there are still many poten-tial CPM pairs indicated in LSPM which as of the end of 2016 are not listed in the WDS cata-log. After our first two reports on in total about 70 such objects (Knapp and Nanson 2017) the next paper with about 25 additional potential common proper motion pairs is presented here.

ENHANCED AIR POLLUTION EPIDEMIOLOGY USING A SOURCE-ORIENTED CHEMICAL TRANSPORT MODEL

EPA Science Inventory

Air quality model predictions describing source-oriented PM component concentrations in multiple size cuts will provide new inputs to examine the effects of acute and chronic PM exposure on mortality and morbidity. Associations between adverse health effects and PM sources/com...

Using distances between Top-n-gram and residue pairs for protein remote homology detection.

PubMed

Liu, Bin; Xu, Jinghao; Zou, Quan; Xu, Ruifeng; Wang, Xiaolong; Chen, Qingcai

2014-01-01

Protein remote homology detection is one of the central problems in bioinformatics, which is important for both basic research and practical application. Currently, discriminative methods based on Support Vector Machines (SVMs) achieve the state-of-the-art performance. Exploring feature vectors incorporating the position information of amino acids or other protein building blocks is a key step to improve the performance of the SVM-based methods. Two new methods for protein remote homology detection were proposed, called SVM-DR and SVM-DT. SVM-DR is a sequence-based method, in which the feature vector representation for protein is based on the distances between residue pairs. SVM-DT is a profile-based method, which considers the distances between Top-n-gram pairs. Top-n-gram can be viewed as a profile-based building block of proteins, which is calculated from the frequency profiles. These two methods are position dependent approaches incorporating the sequence-order information of protein sequences. Various experiments were conducted on a benchmark dataset containing 54 families and 23 superfamilies. Experimental results showed that these two new methods are very promising. Compared with the position independent methods, the performance improvement is obvious. Furthermore, the proposed methods can also provide useful insights for studying the features of protein families. The better performance of the proposed methods demonstrates that the position dependant approaches are efficient for protein remote homology detection. Another advantage of our methods arises from the explicit feature space representation, which can be used to analyze the characteristic features of protein families. The source code of SVM-DT and SVM-DR is available at http://bioinformatics.hitsz.edu.cn/DistanceSVM/index.jsp.

Long-distance practical quantum key distribution by entanglement swapping.

PubMed

Scherer, Artur; Sanders, Barry C; Tittel, Wolfgang

2011-02-14

We develop a model for practical, entanglement-based long-distance quantum key distribution employing entanglement swapping as a key building block. Relying only on existing off-the-shelf technology, we show how to optimize resources so as to maximize secret key distribution rates. The tools comprise lossy transmission links, such as telecom optical fibers or free space, parametric down-conversion sources of entangled photon pairs, and threshold detectors that are inefficient and have dark counts. Our analysis provides the optimal trade-off between detector efficiency and dark counts, which are usually competing, as well as the optimal source brightness that maximizes the secret key rate for specified distances (i.e. loss) between sender and receiver.

Rotational-translational fourier imaging system

NASA Technical Reports Server (NTRS)

Campbell, Jonathan W. (Inventor)

2004-01-01

This invention has the ability to create Fourier-based images with only two grid pairs. The two grid pairs are manipulated in a manner that allows (1) a first grid pair to provide multiple real components of the Fourier-based image and (2) a second grid pair to provide multiple imaginary components of the Fourier-based image. The novelty of this invention resides in the use of only two grid pairs to provide the same imaging information that has been traditionally collected with multiple grid pairs.

CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways.

PubMed

Abaka, Gamze; Bıyıkoğlu, Türker; Erten, Cesim

2013-07-01

Given a pair of metabolic pathways, an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction, drug design and overall may enhance our understanding of cellular metabolism. We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable, which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database, we demonstrate that when compared with a state-of-the-art alternative, the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms. Open source codes, executable binary, useful scripts, all the experimental data and the results are freely available as part of the Supplementary Material at http://code.google.com/p/campways/. Supplementary data are available at Bioinformatics online.

Magnetic Pair Creation Attenuation Altitude Constraints in Gamma-Ray Pulsars

NASA Astrophysics Data System (ADS)

Baring, Matthew; Story, Sarah

The Fermi gamma-ray pulsar database now exceeds 150 sources and has defined an important part of Fermi's science legacy, providing rich information for the interpretation of young energetic pulsars and old millisecond pulsars. Among the well established population characteristics is the common occurrence of exponential turnovers in the 1-10 GeV range. These turnovers are too gradual to arise from magnetic pair creation in the strong magnetic fields of pulsar inner magnetospheres, so their energy can be used to provide lower bounds to the typical altitude of GeV band emission. We explore such constraints due to single-photon pair creation transparency at and below the turnover energy. Our updated computations span both domains when general relativistic influences are important and locales where flat spacetime photon propagation is modified by rotational aberration effects. The altitude bounds, typically in the range of 2-5 stellar radii, provide key information on the emission altitude in radio quiet pulsars that do not possess double-peaked pulse profiles. However, the exceptional case of the Crab pulsar provides an altitude bound of around 20% of the light cylinder radius if pair transparency persists out to 350 GeV, the maximum energy detected by MAGIC. This is an impressive new physics-based constraint on the Crab's gamma-ray emission locale.

Thermodynamic stability of Hoogsteen and Watson-Crick base pairs in the presence of histone H3-mimicking peptide.

PubMed

Pramanik, Smritimoy; Nakamura, Kaori; Usui, Kenji; Nakano, Shu-ichi; Saxena, Sarika; Matsui, Jun; Miyoshi, Daisuke; Sugimoto, Naoki

2011-03-14

We found that Hoogsteen base pairs were stabilized by molecular crowding and a histone H3-mimicking peptide, which was not observed for Watson-Crick base pairs. Our findings demonstrate that the type of DNA base pair is critical for the interaction between DNA and histones.

Asynchronous Replication and Autosome-Pair Non-Equivalence in Human Embryonic Stem Cells

PubMed Central

Dutta, Devkanya; Ensminger, Alexander W.; Zucker, Jacob P.; Chess, Andrew

2009-01-01

A number of mammalian genes exhibit the unusual properties of random monoallelic expression and random asynchronous replication. Such exceptional genes include genes subject to X inactivation and autosomal genes including odorant receptors, immunoglobulins, interleukins, pheromone receptors, and p120 catenin. In differentiated cells, random asynchronous replication of interspersed autosomal genes is coordinated at the whole chromosome level, indicative of chromosome-pair non-equivalence. Here we have investigated the replication pattern of the random asynchronously replicating genes in undifferentiated human embryonic stem cells, using fluorescence in situ hybridization based assay. We show that allele-specific replication of X-linked genes and random monoallelic autosomal genes occur in human embryonic stem cells. The direction of replication is coordinated at the whole chromosome level and can cross the centromere, indicating the existence of autosome-pair non-equivalence in human embryonic stem cells. These results suggest that epigenetic mechanism(s) that randomly distinguish between two parental alleles are emerging in the cells of the inner cell mass, the source of human embryonic stem cells. PMID:19325893

A new fundamental bioheat equation for muscle tissue--part II: Temperature of SAV vessels.

PubMed

Zhu, Liang; Xu, Lisa X; He, Qinghong; Weinbaum, Sheldon

2002-02-01

In this study, a new theoretical framework was developed to investigate temperature variations along countercurrent SAV blood vessels from 300 to 1000 microm diameter in skeletal muscle. Vessels of this size lie outside the range of validity of the Weinbaum-Jiji bioheat equation and, heretofore, have been treated using discrete numerical methods. A new tissue cylinder surrounding these vessel pairs is defined based on vascular anatomy, Murray's law, and the assumption of uniform perfusion. The thermal interaction between the blood vessel pair and surrounding tissue is investigated for two vascular branching patterns, pure branching and pure perfusion. It is shown that temperature variations along these large vessel pairs strongly depend on the branching pattern and the local blood perfusion rate. The arterial supply temperature in different vessel generations was evaluated to estimate the arterial inlet temperature in the modified perfusion source term for the s vessels in Part I of this study. In addition, results from the current research enable one to explore the relative contribution of the SAV vessels and the s vessels to the overall thermal equilibration between blood and tissue.

Coherence of beam arrays propagating in the turbulent atmosphere

NASA Astrophysics Data System (ADS)

Charnotskii, Mikhail

2010-04-01

We analyze some recent publications addressing propagation of the partially coherent polarized beams and beam arrays in the turbulent atmosphere. We show that the published results are limited to the scalar propagation model, and are not particular to the beam polarization. Therefore these results are equally relevant for the scalar beam pairs and arrays discriminated by some parameters such as small frequency shift, time delay or geometry, but not necessary the polarization. We use the virtual incoherent source model to derive the general form of the mutual coherence function of the two Schell-type beams. We discuss some physical stochastic models that result in the creation of the Schell-type beams and beam arrays. New classes of the uniformly, nonuniformly and nonlocally coherent beam pairs emerge naturally from this analysis. Rigorous, Markov approximation-based, propagation model provides relatively simple analytic results for the second-order moments of the optical field of the partially-coherent individual beams and beam pairs. We examine the changes of the beam mutual coherence in the process of the free-space propagation and propagation through the turbulent atmosphere.

Soil organic matter fractions in experimental forested watersheds

Treesearch

Jennifer L. Parker; Ivan J. Fernandez; Lindsey E. Rustad; Stephen A. Norton

2002-01-01

Recent concerns about climate change and atmospheric greenhouse gas concentrations have demonstrated the importance of understanding ecosystem C source/sink relationships. Soil organic matter fractionation was carried out in three paired, forested watershed sites where one of each watershed pair represented a different ecosystem perturbation. The perturbations were 8...

A Systematic Evaluation of Analogs for the Read-across ...

EPA Pesticide Factsheets

Read-across is a data gap filling technique widely used within category and analog approaches to predict a biological property for a target data-poor chemical using known information from similar (source analog) chemical(s). Potential source analogs are typically identified based on structural similarity. Although much guidance has been published for read-across, practical guiding principles for the identification and evaluation of the scientific validity of source analogs, which is a critical step in deriving a robust read-across prediction, remains largely lacking.This case study explores the extent to which 3 structure descriptor sets (Pubchem, Chemotyper and MoSS) and their combinations are able to identify valid analogs for reading across Estrogen Receptor (ER) activity for a specific class of chemicals: hindered phenols. For each target chemical, two sets of analogs (hindered and non-hindered phenols) were selected using each descriptor set with two cut-offs: (1). Minimum Tanimoto similarity (range 0.1 - 0.9), and (2). Closest N analogs (range 1 - 10). Each target-analog pair was then evaluated for its agreement with measured ER binding and agonism. Subsequently, the analogs were filtered using physchem properties (LogKow & Molecular Volume) and the resultant agreement between each target-analog pair was evaluated. The data set comprised 462 hindered phenols and 296 non-hindered phenols. The results demonstrate that: (1). The concordance in ER activity r

Efficient Implementation of the Pairing on Mobilephones Using BREW

NASA Astrophysics Data System (ADS)

Yoshitomi, Motoi; Takagi, Tsuyoshi; Kiyomoto, Shinsaku; Tanaka, Toshiaki

Pairing based cryptosystems can accomplish novel security applications such as ID-based cryptosystems, which have not been constructed efficiently without the pairing. The processing speed of the pairing based cryptosystems is relatively slow compared with the other conventional public key cryptosystems. However, several efficient algorithms for computing the pairing have been proposed, namely Duursma-Lee algorithm and its variant ηT pairing. In this paper, we present an efficient implementation of the pairing over some mobilephones. Moreover, we compare the processing speed of the pairing with that of the other standard public key cryptosystems, i. e. RSA cryptosystem and elliptic curve cryptosystem. Indeed the processing speed of our implementation in ARM9 processors on BREW achieves under 100 milliseconds using the supersingular curve over F397. In addition, the pairing is more efficient than the other public key cryptosystems, and the pairing can be achieved enough also on BREW mobilephones. It has become efficient enough to implement security applications, such as short signature, ID-based cryptosystems or broadcast encryption, using the pairing on BREW mobilephones.

CPM Pairs from LSPM so far not WDS Listed

NASA Astrophysics Data System (ADS)

Knapp, Wilfried; Nanson, John

2017-04-01

The LSPM catalog (Lepine and Shara 2005) is a rich source for CPM pairs we thought already exhausted - but as we found during research for our report “A new concept for counter-checking of assumed CPM pairs” (Knapp and Nanson 2016) there are still many potential CPM pairs indicated in LSPM which as of the beginning of 2016 are not listed in the WDS catalog. A first part of about 40 such objects is presented here.

Simulations of Ar gas-puff Z-pinch radiation sources with double shells and central jets on the Z generator

DOE PAGES

Tangri, V.; Harvey-Thompson, Adam James; Giuliani, J. L.; ...

2016-10-19

Radiation-magnetohydrodynamic simulations using the non-LTE Mach2-TCRE code in (r,z) geometry are performed for two pairs of recent Ar gas-puff Z-pinch experiments on the refurbished Z generator with an 8 cm diameter nozzle. One pair of shots had an outer-to-inner shell mass ratio of 1:1.6 and a second pair had a ratio of 1:1.

Gastric cancer mortality and nitrate levels in Wisconsin drinking water.

PubMed

Rademacher, J J; Young, T B; Kanarek, M S

1992-01-01

The association between nitrate levels in public and private sources of drinking water and gastric cancer mortality in Wisconsin was investigated in a case-control study. All gastric cancer deaths of Wisconsin residents from 1982 through 1985 were compared with deaths from other causes (controls), and nitrate levels in the home drinking water of these residents were determined. Nitrate measures for public sources were obtained from historic nitrate data from municipal sources that existed in 1970. Nitrate measures for private water sources were obtained by testing the wells individually at the existing residences. Controls were matched individually to gastric cancer cases with respect to sex, year of birth, year of death, Wisconsin birth, and Wisconsin residency at the time of death. Matched-pair analyses were performed on the paired data, and the following levels of nitrate-nitrogen exposure were used as indicators of exposure: 0.5, 2.5, 5.0, and 10.0 mg/l. Matched-pair analysis was also performed for which private water supply constituted exposure. Odds ratios and 95% confidence intervals were, respectively, 0.92 (0.75, 1.12); 0.97 (0.74, 1.35); 0.86 (0.69, 1.08); 1.50 (0.12, 18.25); and 1.09 (0.82, 1.47) for exposure to private well-water sources. These results did not indicate an increased risk of gastric cancer at any level.

An ensemble of SVM classifiers based on gene pairs.

PubMed

Tong, Muchenxuan; Liu, Kun-Hong; Xu, Chungui; Ju, Wenbin

2013-07-01

In this paper, a genetic algorithm (GA) based ensemble support vector machine (SVM) classifier built on gene pairs (GA-ESP) is proposed. The SVMs (base classifiers of the ensemble system) are trained on different informative gene pairs. These gene pairs are selected by the top scoring pair (TSP) criterion. Each of these pairs projects the original microarray expression onto a 2-D space. Extensive permutation of gene pairs may reveal more useful information and potentially lead to an ensemble classifier with satisfactory accuracy and interpretability. GA is further applied to select an optimized combination of base classifiers. The effectiveness of the GA-ESP classifier is evaluated on both binary-class and multi-class datasets. Copyright © 2013 Elsevier Ltd. All rights reserved.

Appearance-Based Inferences Bias Source Memory

PubMed Central

Cassidy, Brittany S.; Zebrowitz, Leslie A.; Gutchess, Angela H.

2012-01-01

Previous research varying the trustworthiness of appearance has demonstrated that facial characteristics contribute to source memory. Two studies extended this work by investigating the contribution to source memory of babyfaceness, a facial quality known to elicit strong spontaneous trait inferences. Young adult participants viewed younger and older babyfaced and mature-faced individuals paired with sentences that were either congruent or incongruent with the target's facial characteristics. Identifying a source as dominant or submissive was least accurate when participants chose between a target whose behavior was incongruent with facial characteristics and a lure whose face mismatched the target in appearance, but matched the source memory question. In Study 1, this effect held true when identifying older sources, but not own-age, younger sources. When task difficulty was increased in Study 2, the relationship between face-behavior congruence and lure facial characteristics persisted, but it was not moderated by target age even though participants continued to correctly identify fewer older than younger sources. Taken together, these results indicate that trait expectations associated with variations in facial maturity can bias source memory for both own- and other-age faces, although own-age faces are less vulnerable to this bias, as shown in the moderation by task difficulty. PMID:22806429

Envisaging quantum transport phenomenon in a muddled base pair of DNA

NASA Astrophysics Data System (ADS)

Vohra, Rajan; Sawhney, Ravinder Singh

2018-05-01

The effect of muddled base pair on electron transfer through a deoxyribonucleic acid (DNA) molecule connected to the gold electrodes has been elucidated using tight binding model. The effect of hydrogen and nitrogen bonds on the resistance of the base pair has been minutely observed. Using the semiempirical extended Huckel approach within NEGF regime, we have determined the current and conductance vs. bias voltage for disordered base pairs of DNA made of thymine (T) and adenine (A). The asymmetrical behaviour amid five times depreciation in the current characteristics has been observed for deviated Au-AT base pair-Au devices. An interesting revelation is that the conductance of the intrinsic AT base pair configuration attains dramatically high values with the symmetrical zig-zag pattern of current, which clearly indicates the transformation of the bond length within the strands of base pair when compared with other samples. A thorough investigation of the transmission coefficients T( E) and HOMO-LUMO gap reveals the misalignment of the strands in base pairs of DNA. The observed results present an insight to extend this work to build biosensing devices to predict the abnormality with the DNA.

Higher order structural effects stabilizing the reverse Watson–Crick Guanine-Cytosine base pair in functional RNAs

PubMed Central

Chawla, Mohit; Abdel-Azeim, Safwat; Oliva, Romina; Cavallo, Luigi

2014-01-01

The G:C reverse Watson–Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. PMID:24121683

Kinetic selection vs. free energy of DNA base pairing in control of polymerase fidelity.

PubMed

Oertell, Keriann; Harcourt, Emily M; Mohsen, Michael G; Petruska, John; Kool, Eric T; Goodman, Myron F

2016-04-19

What is the free energy source enabling high-fidelity DNA polymerases (pols) to favor incorporation of correct over incorrect base pairs by 10(3)- to 10(4)-fold, corresponding to free energy differences of ΔΔGinc∼ 5.5-7 kcal/mol? Standard ΔΔG° values (∼0.3 kcal/mol) calculated from melting temperature measurements comparing matched vs. mismatched base pairs at duplex DNA termini are far too low to explain pol accuracy. Earlier analyses suggested that pol active-site steric constraints can amplify DNA free energy differences at the transition state (kinetic selection). A recent paper [Olson et al. (2013)J Am Chem Soc135:1205-1208] used Vent pol to catalyze incorporations in the presence of inorganic pyrophosphate intended to equilibrate forward (polymerization) and backward (pyrophosphorolysis) reactions. A steady-state leveling off of incorporation profiles at long reaction times was interpreted as reaching equilibrium between polymerization and pyrophosphorolysis, yielding apparent ΔG° = -RTlnKeq, indicating ΔΔG° of 3.5-7 kcal/mol, sufficient to account for pol accuracy without need of kinetic selection. Here we perform experiments to measure and account for pyrophosphorolysis explicitly. We show that forward and reverse reactions attain steady states far from equilibrium for wrong incorporations such as G opposite T. Therefore,[Formula: see text]values obtained from such steady-state evaluations ofKeqare not dependent on DNA properties alone, but depend largely on constraints imposed on right and wrong substrates in the polymerase active site.

Bifacial Base-Pairing Behaviors of 5-Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination.

PubMed

Takezawa, Yusuke; Nishiyama, Kotaro; Mashima, Tsukasa; Katahira, Masato; Shionoya, Mitsuhiko

2015-10-12

A novel bifacial ligand-bearing nucleobase, 5-hydroxyuracil (U(OH) ), which forms both a hydrogen-bonded base pair (U(OH) -A) and a metal-mediated base pair (U(OH) -M-U(OH) ) has been developed. The U(OH) -M-U(OH) base pairs were quantitatively formed in the presence of lanthanide ions such as Gd(III) when U(OH) -U(OH) pairs were consecutively incorporated into DNA duplexes. This result established metal-assisted duplex stabilization as well as DNA-templated assembly of lanthanide ions. Notably, a duplex possessing U(OH) -A base pairs was destabilized by addition of Gd(III) ions. This observation suggests that the hybridization behaviors of the U(OH) -containing DNA strands are altered by metal complexation. Thus, the U(OH) nucleobase with a bifacial base-pairing property holds great promise as a component for metal-responsive DNA materials. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular switching behavior in isosteric DNA base pairs.

PubMed

Jissy, A K; Konar, Sukanya; Datta, Ayan

2013-04-15

The structures and proton-coupled behavior of adenine-thymine (A-T) and a modified base pair containing a thymine isostere, adenine-difluorotoluene (A-F), are studied in different solvents by dispersion-corrected density functional theory. The stability of the canonical Watson-Crick base pair and the mismatched pair in various solvents with low and high dielectric constants is analyzed. It is demonstrated that A-F base pairing is favored in solvents with low dielectric constant. The stabilization and conformational changes induced by protonation are also analyzed for the natural as well as the mismatched base pair. DNA sequences capable of changing their sequence conformation on protonation are used in the construction of pH-based molecular switches. An acidic medium has a profound influence in stabilizing the isostere base pair. Such a large gain in stability on protonation leads to an interesting pH-controlled molecular switch, which can be incorporated in a natural DNA tract. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Time-bin entangled photons from a quantum dot

PubMed Central

Jayakumar, Harishankar; Predojević, Ana; Kauten, Thomas; Huber, Tobias; Solomon, Glenn S.; Weihs, Gregor

2014-01-01

Long distance quantum communication is one of the prime goals in the field of quantum information science. With information encoded in the quantum state of photons, existing telecommunication fibre networks can be effectively used as a transport medium. To achieve this goal, a source of robust entangled single photon pairs is required. Here, we report the realization of a source of time-bin entangled photon pairs utilizing the biexciton-exciton cascade in a III/V self-assembled quantum dot. We analyse the generated photon pairs by an inherently phase-stable interferometry technique, facilitating uninterrupted long integration times. We confirm the entanglement by performing quantum state tomography of the emitted photons, which yields a fidelity of 0.69(3) and a concurrence of 0.41(6) for our realization of time-energy entanglement from a single quantum emitter. PMID:24968024

Time-bin entangled photons from a quantum dot.

PubMed

Jayakumar, Harishankar; Predojević, Ana; Kauten, Thomas; Huber, Tobias; Solomon, Glenn S; Weihs, Gregor

2014-06-26

Long-distance quantum communication is one of the prime goals in the field of quantum information science. With information encoded in the quantum state of photons, existing telecommunication fibre networks can be effectively used as a transport medium. To achieve this goal, a source of robust entangled single-photon pairs is required. Here we report the realization of a source of time-bin entangled photon pairs utilizing the biexciton-exciton cascade in a III/V self-assembled quantum dot. We analyse the generated photon pairs by an inherently phase-stable interferometry technique, facilitating uninterrupted long integration times. We confirm the entanglement by performing quantum state tomography of the emitted photons, which yields a fidelity of 0.69(3) and a concurrence of 0.41(6) for our realization of time-energy entanglement from a single quantum emitter.

Genetically improved BarraCUDA.

PubMed

Langdon, W B; Lam, Brian Yee Hong

2017-01-01

BarraCUDA is an open source C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. Recently its source code was optimised using "Genetic Improvement". The genetically improved (GI) code is up to three times faster on short paired end reads from The 1000 Genomes Project and 60% more accurate on a short BioPlanet.com GCAT alignment benchmark. GPGPU BarraCUDA running on a single K80 Tesla GPU can align short paired end nextGen sequences up to ten times faster than bwa on a 12 core server. The speed up was such that the GI version was adopted and has been regularly downloaded from SourceForge for more than 12 months.

Automatic signal extraction, prioritizing and filtering approaches in detecting post-marketing cardiovascular events associated with targeted cancer drugs from the FDA Adverse Event Reporting System (FAERS).

PubMed

Xu, Rong; Wang, Quanqiu

2014-02-01

Targeted drugs dramatically improve the treatment outcomes in cancer patients; however, these innovative drugs are often associated with unexpectedly high cardiovascular toxicity. Currently, cardiovascular safety represents both a challenging issue for drug developers, regulators, researchers, and clinicians and a concern for patients. While FDA drug labels have captured many of these events, spontaneous reporting systems are a main source for post-marketing drug safety surveillance in 'real-world' (outside of clinical trials) cancer patients. In this study, we present approaches to extracting, prioritizing, filtering, and confirming cardiovascular events associated with targeted cancer drugs from the FDA Adverse Event Reporting System (FAERS). The dataset includes records of 4,285,097 patients from FAERS. We first extracted drug-cardiovascular event (drug-CV) pairs from FAERS through named entity recognition and mapping processes. We then compared six ranking algorithms in prioritizing true positive signals among extracted pairs using known drug-CV pairs derived from FDA drug labels. We also developed three filtering algorithms to further improve precision. Finally, we manually validated extracted drug-CV pairs using 21 million published MEDLINE records. We extracted a total of 11,173 drug-CV pairs from FAERS. We showed that ranking by frequency is significantly more effective than by the five standard signal detection methods (246% improvement in precision for top-ranked pairs). The filtering algorithm we developed further improved overall precision by 91.3%. By manual curation using literature evidence, we show that about 51.9% of the 617 drug-CV pairs that appeared in both FAERS and MEDLINE sentences are true positives. In addition, 80.6% of these positive pairs have not been captured by FDA drug labeling. The unique drug-CV association dataset that we created based on FAERS could facilitate our understanding and prediction of cardiotoxic events associated with targeted cancer drugs. Copyright © 2013 Elsevier Inc. All rights reserved.

It Depends on the Partner: Person-Related Sources of Efficacy Beliefs and Performance for Athlete Pairs.

PubMed

Habeeb, Christine M; Eklund, Robert C; Coffee, Pete

2017-06-01

This study explored person-related sources of variance in athletes' efficacy beliefs and performances when performing in pairs with distinguishable roles differing in partner dependence. College cheerleaders (n = 102) performed their role in repeated performance trials of two low- and two high-difficulty paired-stunt tasks with three different partners. Data were obtained on self-, other-, and collective efficacy beliefs and subjective performances, and objective performance assessments were obtained from digital recordings. Using the social relations model framework, total variance in each belief/assessment was partitioned, for each role, into numerical components of person-related variance relative to the self, the other, and the collective. Variance component by performance role by task-difficulty repeated-measures analysis of variances revealed that the largest person-related variance component differed by athlete role and increased in size in high-difficulty tasks. Results suggest that the extent the athlete's performance depends on a partner relates to the extent the partner is a source of self-, other-, and collective efficacy beliefs.

Asymmetrically cut crystal pair as x-ray magnifier for imaging at high intensity laser facilitiesa)

NASA Astrophysics Data System (ADS)

Szabo, C. I.; Feldman, U.; Seely, J. F.; Curry, J. J.; Hudson, L. T.; Henins, A.

2010-10-01

The potential of an x-ray magnifier prepared from a pair of asymmetrically cut crystals is studied to explore high energy x-ray imaging capabilities at high intensity laser facilities. OMEGA-EP and NIF when irradiating mid and high Z targets can be a source of high-energy x-rays whose production mechanisms and use as backlighters are a subject of active research. This paper studies the properties and potential of existing asymmetric cut crystal pairs from the National Institute of Standards and Technology (NIST) built in a new enclosure for imaging x-ray sources. The technique of the x-ray magnifier has been described previously. This new approach is aimed to find a design that could be used at laser facilities by magnifying the x-ray source into a screen far away from the target chamber center, with fixed magnification defined by the crystals' lattice spacing and the asymmetry angles. The magnified image is monochromatic and the imaging wavelength is set by crystal asymmetry and incidence angles. First laboratory results are presented and discussed.

1,8-Naphthyridine-2,7-diamine: a potential universal reader of Watson-Crick base pairs for DNA sequencing by electron tunneling.

PubMed

Liang, Feng; Lindsay, Stuart; Zhang, Peiming

2012-11-21

With the aid of Density Functional Theory (DFT), we designed 1,8-naphthyridine-2,7-diamine as a recognition molecule to read DNA base pairs for genomic sequencing by electron tunneling. NMR studies show that it can form stable triplets with both A : T and G : C base pairs through hydrogen bonding. Our results suggest that the naphthyridine molecule should be able to function as a universal base pair reader in a tunneling gap, generating distinguishable signatures under electrical bias for each of DNA base pairs.

1,8-Naphthyridine-2,7-diamine: A Potential Universal Reader of the Watson-Crick Base Pairs for DNA Sequencing by Electron Tunneling

PubMed Central

Liang, Feng; Lindsay, Stuart; Zhang, Peiming

2013-01-01

With the aid of Density Functional Theory (DFT), we designed 1,8-naphthyridine-2,7-diamine as a recognition molecule to read the DNA base pairs for genomic sequencing by electron tunneling. NMR studies show that it can form stable triplets with both A:T and G:C base pairs through hydrogen bonding. Our results suggest that the naphthyridine molecule should be able to function as a universal base pair reader in a tunneling gap, generating distinguishable signatures under electrical bias for each of DNA base pairs. PMID:23038027

Quantum Information Science

DTIC Science & Technology

2012-02-01

group velocity matched temporal compensator crystal assembly to increase the usable range of entangled photon sources, and (vi) the development and...characterization of a new multipli- entangled photon source that increased the usable number of photon pairs by a factor of six. 15. SUBJECT TERMS...compensated crystal assembly ....................................................................................... 17 3.7 Entangled photon sources

The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone.

PubMed

Kumar, Pawan; Sharma, Pawan K; Madsen, Charlotte S; Petersen, Michael; Nielsen, Poul

2013-06-17

Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantum cryptography with entangled photons

PubMed

Jennewein; Simon; Weihs; Weinfurter; Zeilinger

2000-05-15

By realizing a quantum cryptography system based on polarization entangled photon pairs we establish highly secure keys, because a single photon source is approximated and the inherent randomness of quantum measurements is exploited. We implement a novel key distribution scheme using Wigner's inequality to test the security of the quantum channel, and, alternatively, realize a variant of the BB84 protocol. Our system has two completely independent users separated by 360 m, and generates raw keys at rates of 400-800 bits/s with bit error rates around 3%.

Co-Prime Frequency and Aperture Design for HF Surveillance, Wideband Radar Imaging, and Nonstationary Array Processing

DTIC Science & Technology

2018-03-10

can be generated using only two sensors in the physical array. In case ofredundancy in the difference coarray, there is more than one antenna pair that...estimation results based on the MUSIC algorithm using multi- frequency co-prime arrays. Both proportional and nonproportional source spectra cases are...be made in this case as well. However, two differences can be noticed by comparing the RMSE plots in Figs. 11 and 13. First, the RMSE takes on lower

Demonstration of a quantum controlled-NOT gate in the telecommunications band.

PubMed

Chen, Jun; Altepeter, Joseph B; Medic, Milja; Lee, Kim Fook; Gokden, Burc; Hadfield, Robert H; Nam, Sae Woo; Kumar, Prem

2008-04-04

We present the first quantum controlled-not (cnot) gate realized using a fiber-based indistinguishable photon-pair source in the 1.55 microm telecommunications band. Using this free-space cnot gate, all four Bell states are produced and fully characterized by performing quantum-state tomography, demonstrating the gate's unambiguous entangling capability and high fidelity. Telecom-band operation makes this cnot gate particularly suitable for quantum-information-processing tasks that are at the interface of quantum communication and linear optical quantum computing.

Spatial and Temporal Stress Drop Variations of the 2011 Tohoku Earthquake Sequence

NASA Astrophysics Data System (ADS)

Miyake, H.

2013-12-01

The 2011 Tohoku earthquake sequence consists of foreshocks, mainshock, aftershocks, and repeating earthquakes. To quantify spatial and temporal stress drop variations is important for understanding M9-class megathrust earthquakes. Variability and spatial and temporal pattern of stress drop is a basic information for rupture dynamics as well as useful to source modeling. As pointed in the ground motion prediction equations by Campbell and Bozorgnia [2008, Earthquake Spectra], mainshock-aftershock pairs often provide significant decrease of stress drop. We here focus strong motion records before and after the Tohoku earthquake, and analyze source spectral ratios considering azimuth- and distance dependency [Miyake et al., 2001, GRL]. Due to the limitation of station locations on land, spatial and temporal stress drop variations are estimated by adjusting shifts from the omega-squared source spectral model. The adjustment is based on the stochastic Green's function simulations of source spectra considering azimuth- and distance dependency. We assumed the same Green's functions for event pairs for each station, both the propagation path and site amplification effects are cancelled out. Precise studies of spatial and temporal stress drop variations have been performed [e.g., Allmann and Shearer, 2007, JGR], this study targets the relations between stress drop vs. progression of slow slip prior to the Tohoku earthquake by Kato et al. [2012, Science] and plate structures. Acknowledgement: This study is partly supported by ERI Joint Research (2013-B-05). We used the JMA unified earthquake catalogue and K-NET, KiK-net, and F-net data provided by NIED.

Robot and robot system

NASA Technical Reports Server (NTRS)

Behar, Alberto E. (Inventor); Marzwell, Neville I. (Inventor); Wall, Jonathan N. (Inventor); Poole, Michael D. (Inventor)

2011-01-01

A robot and robot system that are capable of functioning in a zero-gravity environment are provided. The robot can include a body having a longitudinal axis and having a control unit and a power source. The robot can include a first leg pair including a first leg and a second leg. Each leg of the first leg pair can be pivotally attached to the body and constrained to pivot in a first leg pair plane that is substantially perpendicular to the longitudinal axis of the body.

Quasiparticle pair creation in unstable superflow

NASA Astrophysics Data System (ADS)

Elser, Veit

1995-06-01

Landau's instability mechanism in superflow is considered with special attention given to the role of nonuniformity in the flow. Linear stability analysis applied to the first in a series of approximate microscopic equations for the superfluid reveals a growth rate for Landau's instability proportional to the shear in the flow. In a quasiparticle description, the shear acts as a source of particle pair creation. The observation of roton-pair creation in experiments with electron bubbles in helium is offered as evidence of this phenomenon.

Molecular and morphological differentiation between the crop and weedy types in velvetleaf (Abutilon theophrasti Medik.) using a chloroplast DNA marker: seed source of the present invasive velvetleaf in Japan.

PubMed

Kurokawa, S; Shibaike, H; Akiyama, H; Yoshimura, Y

2004-12-01

A comparison of chloroplast DNA (cpDNA) sequences was carried out between the crop and weed types of Abutilon theophrasti to clarify the seed source of the present weedy velvetleaf in Japan. A sequencing analysis of approx. 6% of the chloroplast genome (ca 10 kbp) detected three nucleotide substitutions, one six-base-pair insertion/deletion (indel) and one 30-base pair inversion, which distinguish two haplotypes of cpDNA. A PCR-based survey of the indel and the inversion revealed that the 93 accessions of velvetleaf collected from the world could be divided into two groups. A morphological marker (capsule color) could be used to discriminate the crop type and the weed type, and hence, along with cpDNA haplotype, to distinguish three genotypes (Type I, II, and III). All Japanese cultivars and crop accessions from other countries were Type I. Weed types were divided into Type II and III. All of the samples from the USA, and the samples taken from grain imports to Japan were Type III. Since most of the weedy types distributed in Japan were of Type III, it is argued that they were introduced as seeds in the imported grain. We also found that the Type II plants sporadically occurred in Japan. It is suggested that they originated as hybrids, with indigenous cultivars as the maternal ancestor. Such hybrids must have survived since the cessation of velvetleaf cultivation about a century ago.

Human milk is a source of lactic acid bacteria for the infant gut.

PubMed

Martín, Rocío; Langa, Susana; Reviriego, Carlota; Jimínez, Esther; Marín, María L; Xaus, Jordi; Fernández, Leonides; Rodríguez, Juan M

2003-12-01

To investigate whether human breast milk contains potentially probiotic lactic acid bacteria, and therefore, whether it can be considered a synbiotic food. Study design Lactic acid bacteria were isolated from milk, mammary areola, and breast skin of eight healthy mothers and oral swabs and feces of their respective breast-fed infants. Some isolates (178 from each mother and newborn pair) were randomly selected and submitted to randomly amplified polymorphic DNA (RAPD) polymerase chain reaction analysis, and those that displayed identical RAPD patterns were identified by 16S rDNA sequencing. Within each mother and newborn pair, some rod-shaped lactic acid bacteria isolated from mammary areola, breast milk, and infant oral swabs and feces displayed identical RAPD profiles. All of them, independently from the mother and child pair, were identified as Lactobacillus gasseri. Similarly, among coccoid lactic acid bacteria from these different sources, some shared an identical RAPD pattern and were identified as Enterococcus faecium. In contrast, none of the lactic acid bacteria isolated from breast skin shared RAPD profiles with lactic acid bacteria of the other sources. Breast-feeding can be a significant source of lactic acid bacteria to the infant gut. Lactic acid bacteria present in milk may have an endogenous origin and may not be the result of contamination from the surrounding breast skin.

The ALHAMBRA survey: accurate merger fractions derived by PDF analysis of photometrically close pairs

NASA Astrophysics Data System (ADS)

López-Sanjuan, C.; Cenarro, A. J.; Varela, J.; Viironen, K.; Molino, A.; Benítez, N.; Arnalte-Mur, P.; Ascaso, B.; Díaz-García, L. A.; Fernández-Soto, A.; Jiménez-Teja, Y.; Márquez, I.; Masegosa, J.; Moles, M.; Pović, M.; Aguerri, J. A. L.; Alfaro, E.; Aparicio-Villegas, T.; Broadhurst, T.; Cabrera-Caño, J.; Castander, F. J.; Cepa, J.; Cerviño, M.; Cristóbal-Hornillos, D.; Del Olmo, A.; González Delgado, R. M.; Husillos, C.; Infante, L.; Martínez, V. J.; Perea, J.; Prada, F.; Quintana, J. M.

2015-04-01

Aims: Our goal is to develop and test a novel methodology to compute accurate close-pair fractions with photometric redshifts. Methods: We improved the currently used methodologies to estimate the merger fraction fm from photometric redshifts by (i) using the full probability distribution functions (PDFs) of the sources in redshift space; (ii) including the variation in the luminosity of the sources with z in both the sample selection and the luminosity ratio constrain; and (iii) splitting individual PDFs into red and blue spectral templates to reliably work with colour selections. We tested the performance of our new methodology with the PDFs provided by the ALHAMBRA photometric survey. Results: The merger fractions and rates from the ALHAMBRA survey agree excellently well with those from spectroscopic work for both the general population and red and blue galaxies. With the merger rate of bright (MB ≤ -20-1.1z) galaxies evolving as (1 + z)n, the power-law index n is higher for blue galaxies (n = 2.7 ± 0.5) than for red galaxies (n = 1.3 ± 0.4), confirming previous results. Integrating the merger rate over cosmic time, we find that the average number of mergers per galaxy since z = 1 is Nmred = 0.57 ± 0.05 for red galaxies and Nmblue = 0.26 ± 0.02 for blue galaxies. Conclusions: Our new methodology statistically exploits all the available information provided by photometric redshift codes and yields accurate measurements of the merger fraction by close pairs from using photometric redshifts alone. Current and future photometric surveys will benefit from this new methodology. Based on observations collected at the German-Spanish Astronomical Center, Calar Alto, jointly operated by the Max-Planck-Institut für Astronomie (MPIA) at Heidelberg and the Instituto de Astrofísica de Andalucía (CSIC).The catalogues, probabilities, and figures of the ALHAMBRA close pairs detected in Sect. 5.1 are available at http://https://cloud.iaa.csic.es/alhambra/catalogues/ClosePairs

Presenting International Literature through Author Studies and Author Pairings.

ERIC Educational Resources Information Center

Lynch-Brown, Carol; Tomlinson, Carl M.

1997-01-01

Discusses the value of international books as a source of literature for middle school students. Considers the benefits of international books, and instructional strategies including focusing on an international author and author pairings. Provides an annotated list of works by Robin Klein, John Marsden, Uri Orlev, Anthony Browne, and Jorg Muller.…

The transverse momentum dependence of charged kaon Bose–Einstein correlations in the SELEX experiment

DOE PAGES

Nigmatkulov, G. A.; et al.

2015-12-18

We report the measurement of the one-dimensional charged kaon correlation functions using 600 GeV/c Σ –, π – and 540 GeV/C ρ beams from the SELEX (E781) experiment at the Fermilab Tevatron. K ±K ± correlation functions are studied for three transverse pair momentum, kT, ranges and parameterized by a Gaussian form. The emission source radii, R, and the correlation strength, λ, are extracted. Furthermore, the analysis shows a decrease of the source radii with increasing kaon transverse pair momentum for all beam types.

The origin of infrasonic ionosphere oscillations over tropospheric thunderstorms

NASA Astrophysics Data System (ADS)

Shao, Xuan-Min; Lay, Erin H.

2016-07-01

Thunderstorms have been observed to introduce infrasonic oscillations in the ionosphere, but it is not clear what processes or which parts of the thunderstorm generate the oscillations. In this paper, we present a new technique that uses an array of ground-based GPS total electron content (TEC) measurements to locate the source of the infrasonic oscillations and compare the source locations with thunderstorm features to understand the possible source mechanisms. The location technique utilizes instantaneous phase differences between pairs of GPS-TEC measurements and an algorithm to best fit the measured and the expected phase differences for assumed source positions and other related parameters. In this preliminary study, the infrasound waves are assumed to propagate along simple geometric raypaths from the source to the measurement locations to avoid extensive computations. The located sources are compared in time and space with thunderstorm development and lightning activity. Sources are often found near the main storm cells, but they are more likely related to the downdraft process than to the updraft process. The sources are also commonly found in the convectively quiet stratiform regions behind active cells and are in good coincidence with extensive lightning discharges and inferred high-altitude sprites discharges.

A squeezed light source operated under high vacuum

PubMed Central

Wade, Andrew R.; Mansell, Georgia L.; Chua, Sheon S. Y.; Ward, Robert L.; Slagmolen, Bram J. J.; Shaddock, Daniel A.; McClelland, David E.

2015-01-01

Non-classical squeezed states of light are becoming increasingly important to a range of metrology and other quantum optics applications in cryptography, quantum computation and biophysics. Applications such as improving the sensitivity of advanced gravitational wave detectors and the development of space-based metrology and quantum networks will require robust deployable vacuum-compatible sources. To date non-linear photonics devices operated under high vacuum have been simple single pass systems, testing harmonic generation and the production of classically correlated photon pairs for space-based applications. Here we demonstrate the production under high-vacuum conditions of non-classical squeezed light with an observed 8.6 dB of quantum noise reduction down to 10 Hz. Demonstration of a resonant non-linear optical device, for the generation of squeezed light under vacuum, paves the way to fully exploit the advantages of in-vacuum operations, adapting this technology for deployment into new extreme environments. PMID:26657616

A squeezed light source operated under high vacuum

NASA Astrophysics Data System (ADS)

Wade, Andrew R.; Mansell, Georgia L.; Chua, Sheon S. Y.; Ward, Robert L.; Slagmolen, Bram J. J.; Shaddock, Daniel A.; McClelland, David E.

2015-12-01

Non-classical squeezed states of light are becoming increasingly important to a range of metrology and other quantum optics applications in cryptography, quantum computation and biophysics. Applications such as improving the sensitivity of advanced gravitational wave detectors and the development of space-based metrology and quantum networks will require robust deployable vacuum-compatible sources. To date non-linear photonics devices operated under high vacuum have been simple single pass systems, testing harmonic generation and the production of classically correlated photon pairs for space-based applications. Here we demonstrate the production under high-vacuum conditions of non-classical squeezed light with an observed 8.6 dB of quantum noise reduction down to 10 Hz. Demonstration of a resonant non-linear optical device, for the generation of squeezed light under vacuum, paves the way to fully exploit the advantages of in-vacuum operations, adapting this technology for deployment into new extreme environments.

Rapidity and kT dependence of HBT correlations in Au+Au collisions at 200 GeV with PHOBOS

NASA Astrophysics Data System (ADS)

Holzman, Burt; PHOBOS Collaboration; Back, B. B.; Baker, M. D.; Ballintijn, M.; Barton, D. S.; Betts, R. R.; Bickley, A. A.; Bindel, R.; Budzanowski, A.; Busza, W.; Carroll, A.; Decowski, M. P.; García, E.; George, N.; Gulbrandsen, K.; Gushue, S.; Halliwell, C.; Hamblen, J.; Heintzelman, G. A.; Henderson, C.; Hofman, D. J.; Hollis, R. S.; Holynski, R.; Holzman, B.; Iordanova, A.; Johnson, E.; Kane, J. L.; Katzy, J.; Khan, N.; Kucewicz, W.; Kulinich, P.; Kuo, C. M.; Lin, W. T.; Manly, S.; McLeod, D.; Mignerey, A. C.; Nouicer, R.; Olszewski, A.; Pak, R.; Park, I. C.; Pernegger, H.; Reed, C.; Remsberg, L. P.; Reuter, M.; Roland, C.; Roland, G.; Rosenberg, L.; Sagerer, J.; Sarin, P.; Sawicki, P.; Skulski, W.; Steinberg, P.; Stephans, G. S. F.; Sukhanov, A.; Tang, J.-L.; Tonjes, M. B.; Trzupek, A.; Vale, C.; van Nieuwenhuizen, G. J.; Verdier, R.; Wolfs, F. L. H.; Wosiek, B.; Wozniak, K.; Wuosmaa, A. H.; Wyslouch, B.

2004-08-01

Two-particle correlations of identical charged pion pairs from Au+Au collisions at \\sqrt{s_{\\rm NN}} = 200 GeV were measured by the PHOBOS experiment at RHIC. Data for the most central (0 15%) events were analysed with Bertsch Pratt (BP) and Yano Koonin Podgoretskii (YKP) parametrizations using pairs with rapidities of 0.4 < y < 1.3 and transverse momenta 0.1 < kT < 1.4 GeV/c. The Bertsch Pratt radii decrease as a function of pair transverse momentum. The pair rapidity Ypgrpgr roughly scales with the source rapidity YYKP, indicating strong dynamical correlations.

Rapidity and kT dependence of HBT correlations in Au+Au collisions at 200 GeV with PHOBOS

NASA Astrophysics Data System (ADS)

Holzman, Burt; the PHOBOS Collaboration; Back, B. B.; Baker, M. D.; Ballintijn, M.; Barton, D. S.; Betts, R. R.; Bickley, A. A.; Bindel, R.; Budzanowski, A.; Busza, W.; Carroll, A.; Decowski, M. P.; García, E.; George, N.; Gulbrandsen, K.; Gushue, S.; Halliwell, C.; Hamblen, J.; Heintzelman, G. A.; Henderson, C.; Hofman, D. J.; Hollis, R. S.; Hołyński, R.; Holzman, B.; Iordanova, A.; Johnson, E.; Kane, J. L.; Katzy, J.; Khan, N.; Kucewicz, W.; Kulinich, P.; Kuo, C. M.; Lin, W. T.; Manly, S.; McLeod, D.; Mignerey, A. C.; Nouicer, R.; Olszewski, A.; Pak, R.; Park, I. C.; Pernegger, H.; Reed, C.; Remsberg, L. P.; Reuter, M.; Roland, C.; Roland, G.; Rosenberg, L.; Sagerer, J.; Sarin, P.; Sawicki, P.; Skulski, W.; Steinberg, P.; Stephans, G. S. F.; Sukhanov, A.; Tang, J.-L.; Tonjes, M. B.; Trzupek, A.; Vale, C.; van Nieuwenhuizen, G. J.; Verdier, R.; Wolfs, F. L. H.; Wosiek, B.; Wozniak, K.; Wuosmaa, A. H.; Wysłouch, B.

2004-08-01

Two-particle correlations of identical charged pion pairs from Au+Au collisions at \\sqrt{s_NN} = 200 GeV were measured by the PHOBOS experiment at RHIC. Data for the most central (0-15%) events were analysed with Bertsch-Pratt (BP) and Yano-Koonin-Podgoretskii (YKP) parametrizations using pairs with rapidities of 0.4 < y < 1.3 and transverse momenta 0.1 < kT < 1.4 GeV/c. The Bertsch-Pratt radii decrease as a function of pair transverse momentum. The pair rapidity Yππ roughly scales with the source rapidity YYKP, indicating strong dynamical correlations.

Preliminary Assessment of Detection Efficiency for the Geostationary Lightning Mapper Using Intercomparisons with Ground-Based Systems

NASA Technical Reports Server (NTRS)

Bateman, Monte; Mach, Douglas; Blakeslee, Richard J.; Koshak, William

2018-01-01

As part of the calibration/validation (cal/val) effort for the Geostationary Lightning Mapper (GLM) on GOES-16, we need to assess instrument performance (detection efficiency and accuracy). One major effort is to calculate the detection efficiency of GLM by comparing to multiple ground-based systems. These comparisons will be done pair-wise between GLM and each other source. A complication in this process is that the ground-based systems sense different properties of the lightning signal than does GLM (e.g., RF vs. optical). Also, each system has a different time and space resolution and accuracy. Preliminary results indicate that GLM is performing at or above its specification.

Compact Tunable Narrowband Terahertz-Wave Source Based on Difference Frequency Generation Pumped by Dual Fiber Lasers in MgO:LiNbO3

NASA Astrophysics Data System (ADS)

Wada, Yoshio; Satoh, Takumi; Higashi, Yasuhiro; Urata, Yoshiharu

2017-12-01

We demonstrate a high-average-power, single longitudinal-mode, and tunable terahertz (THz)-wave source based on difference frequency generation (DFG) in a MgO:LiNbO3 (MgO:LN) crystal. The waves for DFG are generated using a pair of Yb-doped pulsed fiber lasers with a master oscillator power fiber amplifier configuration. The average power of the THz-wave output reaches 450 μW at 1.07 THz (280 μm) at a linewidth of 7.2 GHz, and the tunability ranges from 0.35 to 1.07 THz under the pulse repetition frequency of 500 kHz. A short burn-in test of the THz wave is also carried out, and the output power stability is within ± 5% of the averaged power without any active stabilizing technique. The combination of MgO:LN-DFG and stable and robust fiber laser sources is highly promising for the development of high-average-power THz-wave sources, particularly in the high transmission sub-THz region. This approach may enable new applications of THz-wave spectroscopy in imaging and remote sensing.

Simultaneous deblurring and iterative reconstruction of CBCT for image guided brain radiosurgery.

PubMed

Hashemi, SayedMasoud; Song, William Y; Sahgal, Arjun; Lee, Young; Huynh, Christopher; Grouza, Vladimir; Nordström, Håkan; Eriksson, Markus; Dorenlot, Antoine; Régis, Jean Marie; Mainprize, James G; Ruschin, Mark

2017-04-07

One of the limiting factors in cone-beam CT (CBCT) image quality is system blur, caused by detector response, x-ray source focal spot size, azimuthal blurring, and reconstruction algorithm. In this work, we develop a novel iterative reconstruction algorithm that improves spatial resolution by explicitly accounting for image unsharpness caused by different factors in the reconstruction formulation. While the model-based iterative reconstruction techniques use prior information about the detector response and x-ray source, our proposed technique uses a simple measurable blurring model. In our reconstruction algorithm, denoted as simultaneous deblurring and iterative reconstruction (SDIR), the blur kernel can be estimated using the modulation transfer function (MTF) slice of the CatPhan phantom or any other MTF phantom, such as wire phantoms. The proposed image reconstruction formulation includes two regularization terms: (1) total variation (TV) and (2) nonlocal regularization, solved with a split Bregman augmented Lagrangian iterative method. The SDIR formulation preserves edges, eases the parameter adjustments to achieve both high spatial resolution and low noise variances, and reduces the staircase effect caused by regular TV-penalized iterative algorithms. The proposed algorithm is optimized for a point-of-care head CBCT unit for image-guided radiosurgery and is tested with CatPhan phantom, an anthropomorphic head phantom, and 6 clinical brain stereotactic radiosurgery cases. Our experiments indicate that SDIR outperforms the conventional filtered back projection and TV penalized simultaneous algebraic reconstruction technique methods (represented by adaptive steepest-descent POCS algorithm, ASD-POCS) in terms of MTF and line pair resolution, and retains the favorable properties of the standard TV-based iterative reconstruction algorithms in improving the contrast and reducing the reconstruction artifacts. It improves the visibility of the high contrast details in bony areas and the brain soft-tissue. For example, the results show the ventricles and some brain folds become visible in SDIR reconstructed images and the contrast of the visible lesions is effectively improved. The line-pair resolution was improved from 12 line-pair/cm in FBP to 14 line-pair/cm in SDIR. Adjusting the parameters of the ASD-POCS to achieve 14 line-pair/cm caused the noise variance to be higher than the SDIR. Using these parameters for ASD-POCS, the MTF of FBP and ASD-POCS were very close and equal to 0.7 mm -1 which was increased to 1.2 mm -1 by SDIR, at half maximum.

Simultaneous deblurring and iterative reconstruction of CBCT for image guided brain radiosurgery

NASA Astrophysics Data System (ADS)

Hashemi, SayedMasoud; Song, William Y.; Sahgal, Arjun; Lee, Young; Huynh, Christopher; Grouza, Vladimir; Nordström, Håkan; Eriksson, Markus; Dorenlot, Antoine; Régis, Jean Marie; Mainprize, James G.; Ruschin, Mark

2017-04-01

One of the limiting factors in cone-beam CT (CBCT) image quality is system blur, caused by detector response, x-ray source focal spot size, azimuthal blurring, and reconstruction algorithm. In this work, we develop a novel iterative reconstruction algorithm that improves spatial resolution by explicitly accounting for image unsharpness caused by different factors in the reconstruction formulation. While the model-based iterative reconstruction techniques use prior information about the detector response and x-ray source, our proposed technique uses a simple measurable blurring model. In our reconstruction algorithm, denoted as simultaneous deblurring and iterative reconstruction (SDIR), the blur kernel can be estimated using the modulation transfer function (MTF) slice of the CatPhan phantom or any other MTF phantom, such as wire phantoms. The proposed image reconstruction formulation includes two regularization terms: (1) total variation (TV) and (2) nonlocal regularization, solved with a split Bregman augmented Lagrangian iterative method. The SDIR formulation preserves edges, eases the parameter adjustments to achieve both high spatial resolution and low noise variances, and reduces the staircase effect caused by regular TV-penalized iterative algorithms. The proposed algorithm is optimized for a point-of-care head CBCT unit for image-guided radiosurgery and is tested with CatPhan phantom, an anthropomorphic head phantom, and 6 clinical brain stereotactic radiosurgery cases. Our experiments indicate that SDIR outperforms the conventional filtered back projection and TV penalized simultaneous algebraic reconstruction technique methods (represented by adaptive steepest-descent POCS algorithm, ASD-POCS) in terms of MTF and line pair resolution, and retains the favorable properties of the standard TV-based iterative reconstruction algorithms in improving the contrast and reducing the reconstruction artifacts. It improves the visibility of the high contrast details in bony areas and the brain soft-tissue. For example, the results show the ventricles and some brain folds become visible in SDIR reconstructed images and the contrast of the visible lesions is effectively improved. The line-pair resolution was improved from 12 line-pair/cm in FBP to 14 line-pair/cm in SDIR. Adjusting the parameters of the ASD-POCS to achieve 14 line-pair/cm caused the noise variance to be higher than the SDIR. Using these parameters for ASD-POCS, the MTF of FBP and ASD-POCS were very close and equal to 0.7 mm-1 which was increased to 1.2 mm-1 by SDIR, at half maximum.

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

Okutsu, N.; Shimamura, K.; Shimizu, E.

To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approximated by the continuum solvation model. The DFT calculations revealed that the OH radical abstracts the hydrogen atom of a NH{sub 2} group of G or A base and induces a tautomeric reaction for an A-T base pair more significantly than for a G-C base pair. On the other hand, the H radical prefers to bind to the Cytosine NH{sub 2} group of G-Cmore » base pair and induce a tautomeric reaction from G-C to G*-C*, whose activation free energy is considerably small (−0.1 kcal/mol) in comparison with that (42.9 kcal/mol) for the reaction of an A-T base pair. Accordingly, our DFT calculations elucidated that OH and H radicals have a significant effect on A-T and G-C base pairs, respectively. This finding will be useful for predicting the effect of radiation on the genetic information recorded in the base sequences of DNA duplexes.« less

A versatile design for resonant guided-wave parametric down-conversion sources for quantum repeaters

NASA Astrophysics Data System (ADS)

Brecht, Benjamin; Luo, Kai-Hong; Herrmann, Harald; Silberhorn, Christine

2016-05-01

Quantum repeaters—fundamental building blocks for long-distance quantum communication—are based on the interaction between photons and quantum memories. The photons must fulfil stringent requirements on central frequency, spectral bandwidth and purity in order for this interaction to be efficient. We present a design scheme for monolithically integrated resonant photon-pair sources based on parametric down-conversion in nonlinear waveguides, which facilitate the generation of such photons. We investigate the impact of different design parameters on the performance of our source. The generated photon spectral bandwidths can be varied between several tens of MHz up to around 1 GHz, facilitating an efficient coupling to different memories. The central frequency of the generated photons can be coarsely tuned by adjusting the pump frequency, poling period and sample temperature, and we identify stability requirements on the pump laser and sample temperature that can be readily fulfilled with off-the-shelf components. We find that our source is capable of generating high-purity photons over a wide range of photon bandwidths. Finally, the PDC emission can be frequency fine-tuned over several GHz by simultaneously adjusting the sample temperature and pump frequency. We conclude our study with demonstrating the adaptability of our source to different quantum memories.

Changes in latent fingerprint examiners' markup between analysis and comparison.

PubMed

Ulery, Bradford T; Hicklin, R Austin; Roberts, Maria Antonia; Buscaglia, JoAnn

2015-02-01

After the initial analysis of a latent print, an examiner will sometimes revise the assessment during comparison with an exemplar. Changes between analysis and comparison may indicate that the initial analysis of the latent was inadequate, or that confirmation bias may have affected the comparison. 170 volunteer latent print examiners, each randomly assigned 22 pairs of prints from a pool of 320 total pairs, provided detailed markup documenting their interpretations of the prints and the bases for their comparison conclusions. We describe changes in value assessments and markup of features and clarity. When examiners individualized, they almost always added or deleted minutiae (90.3% of individualizations); every examiner revised at least some markups. For inconclusive and exclusion determinations, changes were less common, and features were added more frequently when the image pair was mated (same source). Even when individualizations were based on eight or fewer corresponding minutiae, in most cases some of those minutiae had been added during comparison. One erroneous individualization was observed: the markup changes were notably extreme, and almost all of the corresponding minutiae had been added during comparison. Latents assessed to be of value for exclusion only (VEO) during analysis were often individualized when compared to a mated exemplar (26%); in our previous work, where examiners were not required to provide markup of features, VEO individualizations were much less common (1.8%). Published by Elsevier Ireland Ltd.

Generalized quantum interference of correlated photon pairs.

PubMed

Kim, Heonoh; Lee, Sang Min; Moon, Han Seb

2015-05-07

Superposition and indistinguishablility between probability amplitudes have played an essential role in observing quantum interference effects of correlated photons. The Hong-Ou-Mandel interference and interferences of the path-entangled photon number state are of special interest in the field of quantum information technologies. However, a fully generalized two-photon quantum interferometric scheme accounting for the Hong-Ou-Mandel scheme and path-entangled photon number states has not yet been proposed. Here we report the experimental demonstrations of the generalized two-photon interferometry with both the interferometric properties of the Hong-Ou-Mandel effect and the fully unfolded version of the path-entangled photon number state using photon-pair sources, which are independently generated by spontaneous parametric down-conversion. Our experimental scheme explains two-photon interference fringes revealing single- and two-photon coherence properties in a single interferometer setup. Using the proposed interferometric measurement, it is possible to directly estimate the joint spectral intensity of a photon pair source.

Recognition of Watson-Crick base pairs: constraints and limits due to geometric selection and tautomerism

PubMed Central

Yusupov, Marat; Yusupova, Gulnara

2014-01-01

The natural bases of nucleic acids have a strong preference for one tautomer form, guaranteeing fidelity in their hydrogen bonding potential. However, base pairs observed in recent crystal structures of polymerases and ribosomes are best explained by an alternative base tautomer, leading to the formation of base pairs with Watson-Crick-like geometries. These observations set limits to geometric selection in molecular recognition of complementary Watson-Crick pairs for fidelity in replication and translation processes. PMID:24765524

Large-scale combining signals from both biomedical literature and the FDA Adverse Event Reporting System (FAERS) to improve post-marketing drug safety signal detection

PubMed Central

2014-01-01

Background Independent data sources can be used to augment post-marketing drug safety signal detection. The vast amount of publicly available biomedical literature contains rich side effect information for drugs at all clinical stages. In this study, we present a large-scale signal boosting approach that combines over 4 million records in the US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) and over 21 million biomedical articles. Results The datasets are comprised of 4,285,097 records from FAERS and 21,354,075 MEDLINE articles. We first extracted all drug-side effect (SE) pairs from FAERS. Our study implemented a total of seven signal ranking algorithms. We then compared these different ranking algorithms before and after they were boosted with signals from MEDLINE sentences or abstracts. Finally, we manually curated all drug-cardiovascular (CV) pairs that appeared in both data sources and investigated whether our approach can detect many true signals that have not been included in FDA drug labels. We extracted a total of 2,787,797 drug-SE pairs from FAERS with a low initial precision of 0.025. The ranking algorithm combined signals from both FAERS and MEDLINE, significantly improving the precision from 0.025 to 0.371 for top-ranked pairs, representing a 13.8 fold elevation in precision. We showed by manual curation that drug-SE pairs that appeared in both data sources were highly enriched with true signals, many of which have not yet been included in FDA drug labels. Conclusions We have developed an efficient and effective drug safety signal ranking and strengthening approach We demonstrate that large-scale combining information from FAERS and biomedical literature can significantly contribute to drug safety surveillance. PMID:24428898

Large-scale combining signals from both biomedical literature and the FDA Adverse Event Reporting System (FAERS) to improve post-marketing drug safety signal detection.

PubMed

Xu, Rong; Wang, QuanQiu

2014-01-15

Independent data sources can be used to augment post-marketing drug safety signal detection. The vast amount of publicly available biomedical literature contains rich side effect information for drugs at all clinical stages. In this study, we present a large-scale signal boosting approach that combines over 4 million records in the US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) and over 21 million biomedical articles. The datasets are comprised of 4,285,097 records from FAERS and 21,354,075 MEDLINE articles. We first extracted all drug-side effect (SE) pairs from FAERS. Our study implemented a total of seven signal ranking algorithms. We then compared these different ranking algorithms before and after they were boosted with signals from MEDLINE sentences or abstracts. Finally, we manually curated all drug-cardiovascular (CV) pairs that appeared in both data sources and investigated whether our approach can detect many true signals that have not been included in FDA drug labels. We extracted a total of 2,787,797 drug-SE pairs from FAERS with a low initial precision of 0.025. The ranking algorithm combined signals from both FAERS and MEDLINE, significantly improving the precision from 0.025 to 0.371 for top-ranked pairs, representing a 13.8 fold elevation in precision. We showed by manual curation that drug-SE pairs that appeared in both data sources were highly enriched with true signals, many of which have not yet been included in FDA drug labels. We have developed an efficient and effective drug safety signal ranking and strengthening approach We demonstrate that large-scale combining information from FAERS and biomedical literature can significantly contribute to drug safety surveillance.

Mismatch cleavage by single-strand specific nucleases

PubMed Central

Till, Bradley J.; Burtner, Chris; Comai, Luca; Henikoff, Steven

2004-01-01

We have investigated the ability of single-strand specific (sss) nucleases from different sources to cleave single base pair mismatches in heteroduplex DNA templates used for mutation and single-nucleotide polymorphism analysis. The TILLING (Targeting Induced Local Lesions IN Genomes) mismatch cleavage protocol was used with the LI-COR gel detection system to assay cleavage of amplified heteroduplexes derived from a variety of induced mutations and naturally occurring polymorphisms. We found that purified nucleases derived from celery (CEL I), mung bean sprouts and Aspergillus (S1) were able to specifically cleave nearly all single base pair mismatches tested. Optimal nicking of heteroduplexes for mismatch detection was achieved using higher pH, temperature and divalent cation conditions than are routinely used for digestion of single-stranded DNA. Surprisingly, crude plant extracts performed as well as the highly purified preparations for this application. These observations suggest that diverse members of the S1 family of sss nucleases act similarly in cleaving non-specifically at bulges in heteroduplexes, and single-base mismatches are the least accessible because they present the smallest single-stranded region for enzyme binding. We conclude that a variety of sss nucleases and extracts can be effectively used for high-throughput mutation and polymorphism discovery. PMID:15141034

Silicon Carbide Mixers Demonstrated to Improve the Interference Immunity of Radio-Based Aircraft Avionics

NASA Technical Reports Server (NTRS)

Neudeck, Philip G.

1998-01-01

Concern over the interference of stray radiofrequency (RF) emissions with key aircraft avionics is evident during takeoff and landing of every commercial flight when the flight attendant requests that all portable electronics be switched off. The operation of key radio-based avionics (such as glide-slope and localizer approach instruments) depends on the ability of front-end RF receivers to detect and amplify desired information signals while rejecting interference from undesired RF sources both inside and outside the aircraft. Incidents where key navigation and approach avionics malfunction because of RF interference clearly represent an increasing threat to flight safety as the radio spectrum becomes more crowded. In an initial feasibility experiment, the U.S. Army Research Laboratory and the NASA Lewis Research Center recently demonstrated the strategic use of silicon carbide (SiC) semiconductor components to significantly reduce the susceptibility of an RF receiver circuit to undesired RF interference. A pair of silicon carbide mixer diodes successfully reduced RF interference (intermodulation distortion) in a prototype receiver circuit by a factor of 10 (20 dB) in comparison to a pair of commercial silicon-based mixer diodes.

Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation.

PubMed

Szatkiewicz, Jin P; Wang, WeiBo; Sullivan, Patrick F; Wang, Wei; Sun, Wei

2013-02-01

Structural variation is an important class of genetic variation in mammals. High-throughput sequencing (HTS) technologies promise to revolutionize copy-number variation (CNV) detection but present substantial analytic challenges. Converging evidence suggests that multiple types of CNV-informative data (e.g. read-depth, read-pair, split-read) need be considered, and that sophisticated methods are needed for more accurate CNV detection. We observed that various sources of experimental biases in HTS confound read-depth estimation, and note that bias correction has not been adequately addressed by existing methods. We present a novel read-depth-based method, GENSENG, which uses a hidden Markov model and negative binomial regression framework to identify regions of discrete copy-number changes while simultaneously accounting for the effects of multiple confounders. Based on extensive calibration using multiple HTS data sets, we conclude that our method outperforms existing read-depth-based CNV detection algorithms. The concept of simultaneous bias correction and CNV detection can serve as a basis for combining read-depth with other types of information such as read-pair or split-read in a single analysis. A user-friendly and computationally efficient implementation of our method is freely available.

A Subcarrier-Pair Based Resource Allocation Scheme Using Proportional Fairness for Cooperative OFDM-Based Cognitive Radio Networks

PubMed Central

Ma, Yongtao; Zhou, Liuji; Liu, Kaihua

2013-01-01

The paper presents a joint subcarrier-pair based resource allocation algorithm in order to improve the efficiency and fairness of cooperative multiuser orthogonal frequency division multiplexing (MU-OFDM) cognitive radio (CR) systems. A communication model where one source node communicates with one destination node assisted by one half-duplex decode-and-forward (DF) relay is considered in the paper. An interference-limited environment is considered, with the constraint of transmitted sum-power over all channels and aggregate average interference towards multiple primary users (PUs). The proposed resource allocation algorithm is capable of maximizing both the system transmission efficiency and fairness among secondary users (SUs). Besides, the proposed algorithm can also keep the interference introduced to the PU bands below a threshold. A proportional fairness constraint is used to assure that each SU can achieve a required data rate, with quality of service guarantees. Moreover, we extend the analysis to the scenario where each cooperative SU has no channel state information (CSI) about non-adjacent links. We analyzed the throughput and fairness tradeoff in CR system. A detailed analysis of the performance of the proposed algorithm is presented with the simulation results. PMID:23939586

Phonon cross-plane transport and thermal boundary resistance: effect of heat source size and thermal boundary resistance on phonon characteristics

NASA Astrophysics Data System (ADS)

Ali, H.; Yilbas, B. S.

2016-09-01

Phonon cross-plane transport across silicon and diamond thin films pair is considered, and thermal boundary resistance across the films pair interface is examined incorporating the cut-off mismatch and diffusive mismatch models. In the cut-off mismatch model, phonon frequency mismatch for each acoustic branch is incorporated across the interface of the silicon and diamond films pair in line with the dispersion relations of both films. The frequency-dependent and transient solution of the Boltzmann transport equation is presented, and the equilibrium phonon intensity ratios at the silicon and diamond film edges are predicted across the interface for each phonon acoustic branch. Temperature disturbance across the edges of the films pair is incorporated to assess the phonon transport characteristics due to cut-off and diffusive mismatch models across the interface. The effect of heat source size, which is allocated at high-temperature (301 K) edge of the silicon film, on the phonon transport characteristics at the films pair interface is also investigated. It is found that cut-off mismatch model predicts higher values of the thermal boundary resistance across the films pair interface as compared to that of the diffusive mismatch model. The ratio of equilibrium phonon intensity due to the cut-off mismatch over the diffusive mismatch models remains >1 at the silicon edge, while it becomes <1 at the diamond edge for all acoustic branches.

Gamma rays from pulsar wind shock acceleration

NASA Technical Reports Server (NTRS)

Harding, Alice K.

1990-01-01

A shock forming in the wind of relativistic electron-positron pairs from a pulsar, as a result of confinement by surrounding material, could convert part of the pulsar spin-down luminosity to high energy particles through first order Fermi acceleration. High energy protons could be produced by this mechanism both in supernova remnants and in binary systems containing pulsars. The pion-decay gamma-rays resulting from interaction of accelerated protons with surrounding target material in such sources might be observable above 70 MeV with EGRET (Energetic Gamma-Ray Experimental Telescope) and above 100 GeV with ground-based detectors. Acceleration of protons and expected gamma-ray fluxes from SN1987A, Cyg X-3 type sources and binary pulsars are discussed.

e(sup +/-) Pair Loading and the Origin of the Upstream Magnetic Field in GRB Shocks

NASA Technical Reports Server (NTRS)

Ramirez-Ruiz, Enrico; Nishikawa, Ken-Ichi; Hededal, Christian B.

2006-01-01

We investigate here the effects of plasma instabilities driven by rapid e(sup +/-) pair cascades, which arise in the environment of GRB sources as a result of back-scattering of a seed fraction of their original spectrum. The injection of e(sup +/-) pairs induces strong streaming motions in the ambient medium. One therefore expects the pair-enriched medium ahead of the forward shock to be strongly sheared on length scales comparable to the radiation front thickness. Using three-dimensional particle-in-cell simulations, we show that plasma instabilities driven by these streaming e(sup +/-) pairs are responsible for the excitation of near-equipartition, turbulent magnetic fields. Our results reveal the importance of the electromagnetic filamentation instability in ensuring an effective coupling between e(sup +/-) pairs and ions, and may help explain the origin of large upstream fields in GRB shocks.

e+/- Pair Loading and the Origin of the Upstream Field in GRB Shocks

NASA Technical Reports Server (NTRS)

Ramirez-Ruiz, Enrico; Nishikawa, Ken-Ichi; Hededal, Christian B.

2006-01-01

We investigate here the effects of plasma instabilities driven by rapid e(sup plus or minus) pair cascades, which arise in the environment of GRB sources as a result of back-scattering of a seed fraction of their original spectrum. The injection of e(sup plus or minus) pairs induces strong streaming motions in the ambient medium. One therefore expects the pair-enriched medium ahead of the forward shock to be strongly sheared on length scales comparable to the radiation front thickness. Using three-dimensional particle-in-cell simulations, we show that plasma instabilities driven by these streaming e(sup plus or minus) pairs are responsible for the excitation of near-equipartition, turbulent magnetic fields. Our results reveal the importance of the electromagnetic filamentation instability in ensuring an effective coupling between e(sup plus or minus) pairs and ions, and may help explain the origin of large upstream fields in GRB shocks.

Rotary electrical contact device and method for providing current to and/or from a rotating member

DOEpatents

Koplow, Jeffrey P

2013-11-19

Examples of rotary electrical connectors include a first pair and a second pair of opposing sheaves coupled together by intersecting first shaft connecting the first pair of opposing sheaves and a second shaft connecting the second pair of opposing sheaves, and at least partially electrically conductive belt disposed about respective perimeters of the first pair and second pair of opposing sheaves and adapted to remain in contact with at least a portion of the respective perimeters of the sheaves during motion of said sheaves. In example devices, one of the plurality of sheaves may remain stationary during operation of the device while the remaining sheaves rotate and/or orbit around a center axis of the stationary sheave, the device being configured to couple current between a stationary power source and a rotating member through the electrically conductive belt.

Proof-of-principle experiment of measurement-device-independent quantum key distribution with vector vortex beams

NASA Astrophysics Data System (ADS)

Dong, Chen; Zhao, Shang-Hong; Li, Wei; Yang, Jian

2018-03-01

In this paper, by combining measurement-device-independent quantum key distribution (MDI-QKD) scheme with entangled photon sources, we present a modified MDI-QKD scheme with pairs of vector vortex(VV) beams, which shows a structure of hybrid entangled entanglement corresponding to intrasystem entanglement and intersystem entanglement. The former entanglement, which is entangled between polarization and orbit angular momentum within each VV beam, is adopted to overcome the polarization misalignment associated with random rotations in quantum key distribution. The latter entanglement, which is entangled between the two VV beams, is used to perform entangled-based MDI-QKD protocol with pair of VV beams to inherit the merit of long distance. The numerical simulations show that our modified scheme can tolerate 97dB with practical detectors. Furthermore, our modified protocol only needs to insert q-plates in practical experiment.

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

PubMed

Mallick, Swapan; Li, Heng; Lipson, Mark; Mathieson, Iain; Gymrek, Melissa; Racimo, Fernando; Zhao, Mengyao; Chennagiri, Niru; Nordenfelt, Susanne; Tandon, Arti; Skoglund, Pontus; Lazaridis, Iosif; Sankararaman, Sriram; Fu, Qiaomei; Rohland, Nadin; Renaud, Gabriel; Erlich, Yaniv; Willems, Thomas; Gallo, Carla; Spence, Jeffrey P; Song, Yun S; Poletti, Giovanni; Balloux, Francois; van Driem, George; de Knijff, Peter; Romero, Irene Gallego; Jha, Aashish R; Behar, Doron M; Bravi, Claudio M; Capelli, Cristian; Hervig, Tor; Moreno-Estrada, Andres; Posukh, Olga L; Balanovska, Elena; Balanovsky, Oleg; Karachanak-Yankova, Sena; Sahakyan, Hovhannes; Toncheva, Draga; Yepiskoposyan, Levon; Tyler-Smith, Chris; Xue, Yali; Abdullah, M Syafiq; Ruiz-Linares, Andres; Beall, Cynthia M; Di Rienzo, Anna; Jeong, Choongwon; Starikovskaya, Elena B; Metspalu, Ene; Parik, Jüri; Villems, Richard; Henn, Brenna M; Hodoglugil, Ugur; Mahley, Robert; Sajantila, Antti; Stamatoyannopoulos, George; Wee, Joseph T S; Khusainova, Rita; Khusnutdinova, Elza; Litvinov, Sergey; Ayodo, George; Comas, David; Hammer, Michael F; Kivisild, Toomas; Klitz, William; Winkler, Cheryl A; Labuda, Damian; Bamshad, Michael; Jorde, Lynn B; Tishkoff, Sarah A; Watkins, W Scott; Metspalu, Mait; Dryomov, Stanislav; Sukernik, Rem; Singh, Lalji; Thangaraj, Kumarasamy; Pääbo, Svante; Kelso, Janet; Patterson, Nick; Reich, David

2016-10-13

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

PubMed Central

Mallick, Swapan; Li, Heng; Lipson, Mark; Mathieson, Iain; Gymrek, Melissa; Racimo, Fernando; Zhao, Mengyao; Chennagiri, Niru; Nordenfelt, Susanne; Tandon, Arti; Skoglund, Pontus; Lazaridis, Iosif; Sankararaman, Sriram; Fu, Qiaomei; Rohland, Nadin; Renaud, Gabriel; Erlich, Yaniv; Willems, Thomas; Gallo, Carla; Spence, Jeffrey P.; Song, Yun S.; Poletti, Giovanni; Balloux, Francois; van Driem, George; de Knijff, Peter; Romero, Irene Gallego; Jha, Aashish R.; Behar, Doron M.; Bravi, Claudio M.; Capelli, Cristian; Hervig, Tor; Moreno-Estrada, Andres; Posukh, Olga L.; Balanovska, Elena; Balanovsky, Oleg; Karachanak-Yankova, Sena; Sahakyan, Hovhannes; Toncheva, Draga; Yepiskoposyan, Levon; Tyler-Smith, Chris; Xue, Yali; Abdullah, M. Syafiq; Ruiz-Linares, Andres; Beall, Cynthia M.; Di Rienzo, Anna; Jeong, Choongwon; Starikovskaya, Elena B.; Metspalu, Ene; Parik, Jüri; Villems, Richard; Henn, Brenna M.; Hodoglugil, Ugur; Mahley, Robert; Sajantila, Antti; Stamatoyannopoulos, George; Wee, Joseph T. S.; Khusainova, Rita; Khusnutdinova, Elza; Litvinov, Sergey; Ayodo, George; Comas, David; Hammer, Michael; Kivisild, Toomas; Klitz, William; Winkler, Cheryl; Labuda, Damian; Bamshad, Michael; Jorde, Lynn B.; Tishkoff, Sarah A.; Watkins, W. Scott; Metspalu, Mait; Dryomov, Stanislav; Sukernik, Rem; Singh, Lalji; Thangaraj, Kumarasamy; Pääbo, Svante; Kelso, Janet; Patterson, Nick; Reich, David

2016-01-01

We report the Simons Genome Diversity Project (SGDP) dataset: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioral modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that in other non-Africans. PMID:27654912

Controlled dipole-dipole interactions between K Rydberg atoms in a laser-chopped effusive beam

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

Kutteruf, M. R.; Jones, R. R.

2010-12-15

We explore pulsed-field control of resonant dipole-dipole interactions between K Rydberg atoms. A laser-based atomic beam chopper is used to reduce the relative velocities of Rydberg atoms excited from an effusive thermal source. Resonant energy transfer (RET) between pairs of atoms is controlled via Stark tuning of the relevant Rydberg energy levels. Resonance line shapes in the electric field dependence of the RET probability are used to determine the effective temperature of the sample. We demonstrate that the relative atom velocities can be reduced to the point where the duration of the electric-field tuning pulses, and not the motion ofmore » neighboring atoms, defines the interaction time for each pair within the ensemble. Coherent, transform-limited broadening of the resonance line shape is observed as the tuning pulse duration is reduced below the natural time scale for collisions.« less

Local structure analysis on (La,Ba)(Ga,Mg)O3-δ by the pair distribution function method using a neutron source and density functional theory calculations

NASA Astrophysics Data System (ADS)

Kitamura, Naoto; Vogel, Sven C.; Idemoto, Yasushi

2013-06-01

In this work, we focused on La0.95Ba0.05Ga0.8Mg0.2O3-δ with the perovskite structure, and investigated the local structure around the oxygen vacancy by pair distribution function (PDF) method and density functional theory (DFT) calculation. By comparing the G(r) simulated based on the DFT calculation and the experimentally-observed G(r), it was suggested that the oxygen vacancy was trapped by Ba2+ at the La3+ site at least at room temperature. Such a defect association may be one of the reasons why the La0.95Ba0.05Ga0.8Mg0.2O3-δ showed lower oxide-ion conductivity than (La,Sr)(Ga,Mg)O3-δ which was widely-used as an electrolyte of the solid oxide fuel cell.

Multihop teleportation of two-qubit state via the composite GHZ-Bell channel

NASA Astrophysics Data System (ADS)

Zou, Zhen-Zhen; Yu, Xu-Tao; Gong, Yan-Xiao; Zhang, Zai-Chen

2017-01-01

A multihop teleportation protocol in quantum communication network is introduced to teleport an arbitrary two-qubit state, between two nodes without directly sharing entanglement pairs. Quantum channels are built among neighbor nodes based on a five-qubit entangled system composed of GHZ and Bell pairs. The von Neumann measurements in all intermediate nodes and the source node are implemented, and then the measurement outcomes are sent to the destination node independently. After collecting all the measurement outcomes at the destination node, an efficient method is proposed to calculate the unitary operations for transforming the receiver's states to the state teleported. Therefore, only adopting the proper unitary operations at the destination node, the desired quantum state can be recovered perfectly. The transmission flexibility and efficiency of quantum network with composite GHZ-Bell channel are improved by transmitting measurement outcomes of all nodes in parallelism and reducing hop-by-hop teleportation delay.

Uncoupling of sgRNAs from their associated barcodes during PCR amplification of combinatorial CRISPR screens

PubMed Central

2018-01-01

Many implementations of pooled screens in mammalian cells rely on linking an element of interest to a barcode, with the latter subsequently quantitated by next generation sequencing. However, substantial uncoupling between these paired elements during lentiviral production has been reported, especially as the distance between elements increases. We detail that PCR amplification is another major source of uncoupling, and becomes more pronounced with increased amounts of DNA template molecules and PCR cycles. To lessen uncoupling in systems that use paired elements for detection, we recommend minimizing the distance between elements, using low and equal template DNA inputs for plasmid and genomic DNA during PCR, and minimizing the number of PCR cycles. We also present a vector design for conducting combinatorial CRISPR screens that enables accurate barcode-based detection with a single short sequencing read and minimal uncoupling. PMID:29799876

Multi-scale comparison of source parameter estimation using empirical Green's function approach

NASA Astrophysics Data System (ADS)

Chen, X.; Cheng, Y.

2015-12-01

Analysis of earthquake source parameters requires correction of path effect, site response, and instrument responses. Empirical Green's function (EGF) method is one of the most effective methods in removing path effects and station responses by taking the spectral ratio between a larger and smaller event. Traditional EGF method requires identifying suitable event pairs, and analyze each event individually. This allows high quality estimations for strictly selected events, however, the quantity of resolvable source parameters is limited, which challenges the interpretation of spatial-temporal coherency. On the other hand, methods that exploit the redundancy of event-station pairs are proposed, which utilize the stacking technique to obtain systematic source parameter estimations for a large quantity of events at the same time. This allows us to examine large quantity of events systematically, facilitating analysis of spatial-temporal patterns, and scaling relationship. However, it is unclear how much resolution is scarified during this process. In addition to the empirical Green's function calculation, choice of model parameters and fitting methods also lead to biases. Here, using two regional focused arrays, the OBS array in the Mendocino region, and the borehole array in the Salton Sea geothermal field, I compare the results from the large scale stacking analysis, small-scale cluster analysis, and single event-pair analysis with different fitting methods to systematically compare the results within completely different tectonic environment, in order to quantify the consistency and inconsistency in source parameter estimations, and the associated problems.

Directly Phase-Modulated Light Source

NASA Astrophysics Data System (ADS)

Yuan, Z. L.; Fröhlich, B.; Lucamarini, M.; Roberts, G. L.; Dynes, J. F.; Shields, A. J.

2016-07-01

The art of imparting information onto a light wave by optical signal modulation is fundamental to all forms of optical communication. Among many schemes, direct modulation of laser diodes stands out as a simple, robust, and cost-effective method. However, the simultaneous changes in intensity, frequency, and phase have prevented its application in the field of secure quantum communication. Here, we propose and experimentally demonstrate a directly phase-modulated light source which overcomes the main disadvantages associated with direct modulation and is suitable for diverse applications such as coherent communications and quantum cryptography. The source separates the tasks of phase preparation and pulse generation between a pair of semiconductor lasers leading to very pure phase states. Moreover, the cavity-enhanced electro-optic effect enables the first example of subvolt half-wave phase modulation at high signal rates. The source is compact, stable, and versatile, and we show its potential to become the standard transmitter for future quantum communication networks based on attenuated laser pulses.

Effectively identifying compound-protein interactions by learning from positive and unlabeled examples.

PubMed

Cheng, Zhanzhan; Zhou, Shuigeng; Wang, Yang; Liu, Hui; Guan, Jihong; Chen, Yi-Ping Phoebe

2016-05-18

Prediction of compound-protein interactions (CPIs) is to find new compound-protein pairs where a protein is targeted by at least a compound, which is a crucial step in new drug design. Currently, a number of machine learning based methods have been developed to predict new CPIs in the literature. However, as there is not yet any publicly available set of validated negative CPIs, most existing machine learning based approaches use the unknown interactions (not validated CPIs) selected randomly as the negative examples to train classifiers for predicting new CPIs. Obviously, this is not quite reasonable and unavoidably impacts the CPI prediction performance. In this paper, we simply take the unknown CPIs as unlabeled examples, and propose a new method called PUCPI (the abbreviation of PU learning for Compound-Protein Interaction identification) that employs biased-SVM (Support Vector Machine) to predict CPIs using only positive and unlabeled examples. PU learning is a class of learning methods that leans from positive and unlabeled (PU) samples. To the best of our knowledge, this is the first work that identifies CPIs using only positive and unlabeled examples. We first collect known CPIs as positive examples and then randomly select compound-protein pairs not in the positive set as unlabeled examples. For each CPI/compound-protein pair, we extract protein domains as protein features and compound substructures as chemical features, then take the tensor product of the corresponding compound features and protein features as the feature vector of the CPI/compound-protein pair. After that, biased-SVM is employed to train classifiers on different datasets of CPIs and compound-protein pairs. Experiments over various datasets show that our method outperforms six typical classifiers, including random forest, L1- and L2-regularized logistic regression, naive Bayes, SVM and k-nearest neighbor (kNN), and three types of existing CPI prediction models. Source code, datasets and related documents of PUCPI are available at: http://admis.fudan.edu.cn/projects/pucpi.html.

Development of a MeV proton beam irradiation system.

PubMed

Park, Bum-Sik; Cho, Yong-Sub; Hong, In-Seok

2008-02-01

A proton beam irradiation system for the application of the MeV class proton beam, such as an implantation for a power semiconductor device and a smart-cut technology for a semiconductor production process, has been developed. This system consists of a negative ion source, an Einzel lens for a low energy beam transport, accelerating tubes, a gas stripper, a Cockroft-Walton high voltage power supply with 1 MV, a vacuum pumping system, and a high pressure insulating gas system. The negative hydrogen ion source is based on TRIUMF's design. Following the tandem accelerator, a pair of magnets is installed for raster scanning of the MeV proton beam to obtain a uniform irradiation pattern on the target. The system is 7 m long from the ion source to the target and is optimized for the proton beam irradiation. The details of the system development will be described.

Metacognitive Control over the Distribution of Practice: When Is Spacing Preferred?

ERIC Educational Resources Information Center

Toppino, Thomas C.; Cohen, Michael S.; Davis, Meghan L.; Moors, Amy C.

2009-01-01

The authors clarify the source of a conflict between previous findings related to metacognitive control over the distribution of practice. In a study by L. Son (2004), learners were initially presented pairs of Graduate Record Examination (GRE) vocabulary words and their common synonyms for 1 s, after which they chose to study the pair again…

Generating photon pairs from a silicon microring resonator using an electronic step recovery diode for pump pulse generation

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

Savanier, Marc, E-mail: msavanier@eng.ucsd.edu; Mookherjea, Shayan, E-mail: smookherjea@eng.ucsd.edu

Generation of photon pairs from compact, manufacturable, and inexpensive silicon (Si) photonic devices at room temperature may help develop practical applications of quantum photonics. An important characteristic of photon-pair generation is the two-photon joint spectral intensity, which describes the frequency correlations of the photon pair. Recent attempts to generate a factorizable photon-pair state suitable for heralding have used short optical pump pulses from mode-locked lasers, which are much more expensive and bigger table-top or rack-sized instruments compared with the Si microchip used for generating photon pairs, and thus dominate the cost and inhibit the miniaturization of the source. Here, wemore » generate photon pairs from an Si microring resonator by using an electronic step-recovery diode to drive an electro-optic modulator which carves the pump light from a continuous-wave laser diode into pulses of the appropriate width, thus potentially eliminating the need for optical mode-locked lasers.« less

Generating photon pairs from a silicon microring resonator using an electronic step recovery diode for pump pulse generation

NASA Astrophysics Data System (ADS)

Savanier, Marc; Mookherjea, Shayan

2016-06-01

Generation of photon pairs from compact, manufacturable, and inexpensive silicon (Si) photonic devices at room temperature may help develop practical applications of quantum photonics. An important characteristic of photon-pair generation is the two-photon joint spectral intensity, which describes the frequency correlations of the photon pair. Recent attempts to generate a factorizable photon-pair state suitable for heralding have used short optical pump pulses from mode-locked lasers, which are much more expensive and bigger table-top or rack-sized instruments compared with the Si microchip used for generating photon pairs, and thus dominate the cost and inhibit the miniaturization of the source. Here, we generate photon pairs from an Si microring resonator by using an electronic step-recovery diode to drive an electro-optic modulator which carves the pump light from a continuous-wave laser diode into pulses of the appropriate width, thus potentially eliminating the need for optical mode-locked lasers.

Interactions in ion pairs of protic ionic liquids: Comparison with aprotic ionic liquids

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

Tsuzuki, Seiji, E-mail: s.tsuzuki@aist.go.jp; Shinoda, Wataru; Miran, Md. Shah

2013-11-07

The stabilization energies for the formation (E{sub form}) of 11 ion pairs of protic and aprotic ionic liquids were studied by MP2/6-311G{sup **} level ab initio calculations to elucidate the difference between the interactions of ions in protic ionic liquids and those in aprotic ionic liquids. The interactions in the ion pairs of protic ionic liquids (diethylmethylammonium [dema] and dimethylpropylammonium [dmpa] based ionic liquids) are stronger than those of aprotic ionic liquids (ethyltrimethylammonium [etma] based ionic liquids). The E{sub form} for the [dema][CF{sub 3}SO{sub 3}] and [dmpa][CF{sub 3}SO{sub 3}] complexes (−95.6 and −96.4 kcal/mol, respectively) are significantly larger (more negative)more » than that for the [etma][CF{sub 3}SO{sub 3}] complex (−81.0 kcal/mol). The same trend was observed for the calculations of ion pairs of the three cations with the Cl{sup −}, BF{sub 4}{sup −}, TFSA{sup −} anions. The anion has contact with the N–H bond of the dema{sup +} or dmpa{sup +} cations in the most stable geometries of the dema{sup +} and dmpa{sup +} complexes. The optimized geometries, in which the anions locate on the counter side of the cations, are 11.0–18.0 kcal/mol less stable, which shows that the interactions in the ions pairs of protic ionic liquids have strong directionality. The E{sub form} for the less stable geometries for the dema{sup +} and dmpa{sup +} complexes are close to those for the most stable etma{sup +} complexes. The electrostatic interaction, which is the major source of the attraction in the ion pairs, is responsible for the directionality of the interactions and determining the magnitude of the interaction energy. Molecular dynamic simulations of the [dema][TFSA] and [dmpa][TFSA] ionic liquids show that the N–H bonds of the cations have contact with the negatively charged (oxygen and nitrogen) atoms of TFSA{sup −} anion, while the strong directionality of the interactions was not suggested from the simulation of the [etma][CF{sub 3}SO{sub 3}] ionic liquid.« less

Structure based alignment and clustering of proteins (STRALCP)

DOEpatents

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

2013-06-18

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

Leveraging gigawatt potentials by smart heat-pump technologies using ionic liquids.

PubMed

Wasserscheid, Peter; Seiler, Matthias

2011-04-18

One of the greatest challenges to science in the 21 st century is the development of efficient energy production, storage, and transformation systems with minimal ecological footprints. Due to the lack of efficient heat-transformation technologies, industries around the world currently waste energy in the gigawatt range at low temperatures (40-80 °C). These energy potentials can be unlocked or used more efficiently through a new generation of smart heat pumps operating with novel ionic liquid (IL)-based working pairs. The new technology is expected to allow revolutionary technical progress in heat-transformation devices, for example, significantly higher potential efficiencies, lower specific investments, and broader possibilities to incorporate waste energy from renewable sources. Furthermore, due to drastically reduced corrosion rates and excellent thermal stabilities of the new, IL-based working pairs, the high driving temperatures necessary for multi-effect cycles such as double- or triple-effect absorption chillers, can also be realized. The details of this novel and innovative heat-transformation technology are described. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Facial appearance affects science communication

PubMed Central

Gheorghiu, Ana I.; Callan, Mitchell J.; Skylark, William J.

2017-01-01

First impressions based on facial appearance predict many important social outcomes. We investigated whether such impressions also influence the communication of scientific findings to lay audiences, a process that shapes public beliefs, opinion, and policy. First, we investigated the traits that engender interest in a scientist’s work, and those that create the impression of a “good scientist” who does high-quality research. Apparent competence and morality were positively related to both interest and quality judgments, whereas attractiveness boosted interest but decreased perceived quality. Next, we had members of the public choose real science news stories to read or watch and found that people were more likely to choose items that were paired with “interesting-looking” scientists, especially when selecting video-based communications. Finally, we had people read real science news items and found that the research was judged to be of higher quality when paired with researchers who look like “good scientists.” Our findings offer insights into the social psychology of science, and indicate a source of bias in the dissemination of scientific findings to broader society. PMID:28533389

Sequence dependency of canonical base pair opening in the DNA double helix

PubMed Central

Villa, Alessandra

2017-01-01

The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair. PMID:28369121

A novel craniotomy simulation system for evaluation of stereo-pair reconstruction fidelity and tracking

NASA Astrophysics Data System (ADS)

Yang, Xiaochen; Clements, Logan W.; Conley, Rebekah H.; Thompson, Reid C.; Dawant, Benoit M.; Miga, Michael I.

2016-03-01

Brain shift compensation using computer modeling strategies is an important research area in the field of image-guided neurosurgery (IGNS). One important source of available sparse data during surgery to drive these frameworks is deformation tracking of the visible cortical surface. Possible methods to measure intra-operative cortical displacement include laser range scanners (LRS), which typically complicate the clinical workflow, and reconstruction of cortical surfaces from stereo pairs acquired with the operating microscopes. In this work, we propose and demonstrate a craniotomy simulation device that permits simulating realistic cortical displacements designed to measure and validate the proposed intra-operative cortical shift measurement systems. The device permits 3D deformations of a mock cortical surface which consists of a membrane made of a Dragon Skin® high performance silicone rubber on which vascular patterns are drawn. We then use this device to validate our stereo pair-based surface reconstruction system by comparing landmark positions and displacements measured with our systems to those positions and displacements as measured by a stylus tracked by a commercial optical system. Our results show a 1mm average difference in localization error and a 1.2mm average difference in displacement measurement. These results suggest that our stereo-pair technique is accurate enough for estimating intra-operative displacements in near real-time without affecting the surgical workflow.

Household transmission of invasive group A Streptococcus infections in England: a population-based study, 2009, 2011 to 2013

PubMed Central

Mearkle, Rachel; Saavedra-Campos, Maria; Lamagni, Theresa; Usdin, Martine; Coelho, Juliana; Chalker, Vicki; Sriskandan, Shiranee; Cordery, Rebecca; Rawlings, Chas; Balasegaram, Sooria

2017-01-01

Invasive group A streptococcal infection has a 15% case fatality rate and a risk of secondary transmission. This retrospective study used two national data sources from England; enhanced surveillance (2009) and a case management system (2011–2013) to identify clusters of severe group A streptococcal disease. Twenty-four household pairs were identified. The median onset interval between cases was 2 days (range 0–28) with simultaneous onset in eight pairs. The attack rate during the 30 days after first exposure to a primary case was 4,520 per 100,000 person-years at risk (95% confidence interval (CI): 2,900–6,730) a 1,940 (95% CI: 1,240–2,880) fold elevation over the background incidence. The theoretical number needed to treat to prevent one secondary case using antibiotic prophylaxis was 271 overall (95% CI: 194–454), 50 for mother-neonate pairs (95% CI: 27–393) and 82 for couples aged 75 years and over (95% CI: 46–417). While a dramatically increased risk of infection was noted in all household contacts, increased risk was greatest for mother-neonate pairs and couples aged 75 and over, suggesting targeted prophylaxis could be considered. Offering prophylaxis is challenging due to the short time interval between cases emphasising the importance of immediate notification and assessment of contacts. PMID:28537550

Household transmission of invasive group A Streptococcus infections in England: a population-based study, 2009, 2011 to 2013.

PubMed

Mearkle, Rachel; Saavedra-Campos, Maria; Lamagni, Theresa; Usdin, Martine; Coelho, Juliana; Chalker, Vicki; Sriskandan, Shiranee; Cordery, Rebecca; Rawlings, Chas; Balasegaram, Sooria

2017-05-11

Invasive group A streptococcal infection has a 15% case fatality rate and a risk of secondary transmission. This retrospective study used two national data sources from England; enhanced surveillance (2009) and a case management system (2011-2013) to identify clusters of severe group A streptococcal disease. Twenty-four household pairs were identified. The median onset interval between cases was 2 days (range 0-28) with simultaneous onset in eight pairs. The attack rate during the 30 days after first exposure to a primary case was 4,520 per 100,000 person-years at risk (95% confidence interval (CI): 2,900-6,730) a 1,940 (95% CI: 1,240-2,880) fold elevation over the background incidence. The theoretical number needed to treat to prevent one secondary case using antibiotic prophylaxis was 271 overall (95% CI: 194-454), 50 for mother-neonate pairs (95% CI: 27-393) and 82 for couples aged 75 years and over (95% CI: 46-417). While a dramatically increased risk of infection was noted in all household contacts, increased risk was greatest for mother-neonate pairs and couples aged 75 and over, suggesting targeted prophylaxis could be considered. Offering prophylaxis is challenging due to the short time interval between cases emphasising the importance of immediate notification and assessment of contacts. This article is copyright of The Authors, 2017.

Theoretical study on the binding mechanism between N6-methyladenine and natural DNA bases.

PubMed

Song, Qi-Xia; Ding, Zhen-Dong; Liu, Jian-Hua; Li, Yan; Wang, Hai-Jun

2013-03-01

N6-methyladenine (m(6)A) is a rare base naturally occurring in DNA. It is different from the base adenine due to its N-CH(3). Therefore, the base not only pairs with thymine, but also with other DNA bases (cytosine, adenine and guanine). In this work, Møller-Plesset second-order (MP2) method has been used to investigate the binding mechanism between m(6)A and natural DNA bases in gas phase and in aqueous solution. The results show that N-CH(3) changed the way of N6-methyladenine binding to natural DNA bases. The binding style significantly influences the stability of base pairs. The trans-m(6)A:G and trans-m(6)A:C conformers are the most stable among all the base pairs. The existence of solvent can remarkably reduce the stability of the base pairs, and the DNA bases prefer pairing with trans-m(6)A to cis-m(6)A. Besides, the properties of these hydrogen bonds have been analyzed by atom in molecules (AIM) theory, natural bond orbital (NBO) analysis and Wiberg bond indexes (WBI). In addition, pairing with m(6)A decreases the binding energies compared to the normal Watson-Crick base pairs, it may explain the instability of the N6 site methylated DNA in theory.

Validation of a Crowdsourcing Methodology for Developing a Knowledge Base of Related Problem-Medication Pairs.

PubMed

McCoy, A B; Wright, A; Krousel-Wood, M; Thomas, E J; McCoy, J A; Sittig, D F

2015-01-01

Clinical knowledge bases of problem-medication pairs are necessary for many informatics solutions that improve patient safety, such as clinical summarization. However, developing these knowledge bases can be challenging. We sought to validate a previously developed crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large, non-university health care system with a widely used, commercially available electronic health record. We first retrieved medications and problems entered in the electronic health record by clinicians during routine care during a six month study period. Following the previously published approach, we calculated the link frequency and link ratio for each pair then identified a threshold cutoff for estimated problem-medication pair appropriateness through clinician review; problem-medication pairs meeting the threshold were included in the resulting knowledge base. We selected 50 medications and their gold standard indications to compare the resulting knowledge base to the pilot knowledge base developed previously and determine its recall and precision. The resulting knowledge base contained 26,912 pairs, had a recall of 62.3% and a precision of 87.5%, and outperformed the pilot knowledge base containing 11,167 pairs from the previous study, which had a recall of 46.9% and a precision of 83.3%. We validated the crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large non-university health care system with a widely used, commercially available electronic health record, indicating that the approach may be generalizable across healthcare settings and clinical systems. Further research is necessary to better evaluate the knowledge, to compare crowdsourcing with other approaches, and to evaluate if incorporating the knowledge into electronic health records improves patient outcomes.

Validation of a Crowdsourcing Methodology for Developing a Knowledge Base of Related Problem-Medication Pairs

PubMed Central

Wright, A.; Krousel-Wood, M.; Thomas, E. J.; McCoy, J. A.; Sittig, D. F.

2015-01-01

Summary Background Clinical knowledge bases of problem-medication pairs are necessary for many informatics solutions that improve patient safety, such as clinical summarization. However, developing these knowledge bases can be challenging. Objective We sought to validate a previously developed crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large, non-university health care system with a widely used, commercially available electronic health record. Methods We first retrieved medications and problems entered in the electronic health record by clinicians during routine care during a six month study period. Following the previously published approach, we calculated the link frequency and link ratio for each pair then identified a threshold cutoff for estimated problem-medication pair appropriateness through clinician review; problem-medication pairs meeting the threshold were included in the resulting knowledge base. We selected 50 medications and their gold standard indications to compare the resulting knowledge base to the pilot knowledge base developed previously and determine its recall and precision. Results The resulting knowledge base contained 26,912 pairs, had a recall of 62.3% and a precision of 87.5%, and outperformed the pilot knowledge base containing 11,167 pairs from the previous study, which had a recall of 46.9% and a precision of 83.3%. Conclusions We validated the crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large non-university health care system with a widely used, commercially available electronic health record, indicating that the approach may be generalizable across healthcare settings and clinical systems. Further research is necessary to better evaluate the knowledge, to compare crowdsourcing with other approaches, and to evaluate if incorporating the knowledge into electronic health records improves patient outcomes. PMID:26171079

A new light emitting diode-light emitting diode portable carbon dioxide gas sensor based on an interchangeable membrane system for industrial applications.

PubMed

de Vargas-Sansalvador, I M Pérez; Fay, C; Phelan, T; Fernández-Ramos, M D; Capitán-Vallvey, L F; Diamond, D; Benito-Lopez, F

2011-08-12

A new system for CO(2) measurement (0-100%) based on a paired emitter-detector diode arrangement as a colorimetric detection system is described. Two different configurations were tested: configuration 1 (an opposite side configuration) where a secondary inner-filter effect accounts for CO(2) sensitivity. This configuration involves the absorption of the phosphorescence emitted from a CO(2)-insensitive luminophore by an acid-base indicator and configuration 2 wherein the membrane containing the luminophore is removed, simplifying the sensing membrane that now only contains the acid-base indicator. In addition, two different instrumental configurations have been studied, using a paired emitter-detector diode system, consisting of two LEDs wherein one is used as the light source (emitter) and the other is used in reverse bias mode as the light detector. The first configuration uses a green LED as emitter and a red LED as detector, whereas in the second case two identical red LEDs are used as emitter and detector. The system was characterised in terms of sensitivity, dynamic response, reproducibility, stability and temperature influence. We found that configuration 2 presented a better CO(2) response in terms of sensitivity. Copyright © 2011 Elsevier B.V. All rights reserved.

A Registration Method Based on Contour Point Cloud for 3D Whole-Body PET and CT Images

PubMed Central

Yang, Qiyao; Wang, Zhiguo; Zhang, Guoxu

2017-01-01

The PET and CT fusion image, combining the anatomical and functional information, has important clinical meaning. An effective registration of PET and CT images is the basis of image fusion. This paper presents a multithread registration method based on contour point cloud for 3D whole-body PET and CT images. Firstly, a geometric feature-based segmentation (GFS) method and a dynamic threshold denoising (DTD) method are creatively proposed to preprocess CT and PET images, respectively. Next, a new automated trunk slices extraction method is presented for extracting feature point clouds. Finally, the multithread Iterative Closet Point is adopted to drive an affine transform. We compare our method with a multiresolution registration method based on Mattes Mutual Information on 13 pairs (246~286 slices per pair) of 3D whole-body PET and CT data. Experimental results demonstrate the registration effectiveness of our method with lower negative normalization correlation (NC = −0.933) on feature images and less Euclidean distance error (ED = 2.826) on landmark points, outperforming the source data (NC = −0.496, ED = 25.847) and the compared method (NC = −0.614, ED = 16.085). Moreover, our method is about ten times faster than the compared one. PMID:28316979

Evaluating a Pivot-Based Approach for Bilingual Lexicon Extraction

PubMed Central

Kim, Jae-Hoon; Kwon, Hong-Seok; Seo, Hyeong-Won

2015-01-01

A pivot-based approach for bilingual lexicon extraction is based on the similarity of context vectors represented by words in a pivot language like English. In this paper, in order to show validity and usability of the pivot-based approach, we evaluate the approach in company with two different methods for estimating context vectors: one estimates them from two parallel corpora based on word association between source words (resp., target words) and pivot words and the other estimates them from two parallel corpora based on word alignment tools for statistical machine translation. Empirical results on two language pairs (e.g., Korean-Spanish and Korean-French) have shown that the pivot-based approach is very promising for resource-poor languages and this approach observes its validity and usability. Furthermore, for words with low frequency, our method is also well performed. PMID:25983745

Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes.

PubMed

Kondo, Jiro; Westhof, Eric

2011-10-01

Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide-protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson-Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson-Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues.

Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide–protein complexes

PubMed Central

Kondo, Jiro; Westhof, Eric

2011-01-01

Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide–protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson–Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson–Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues. PMID:21737431

Simultaneous determination of five characteristic stilbene glycosides in root bark of Morus albus L. (Cortex Mori) using high-performance liquid chromatography.

PubMed

Piao, Shu-juan; Chen, Li-xia; Kang, Ning; Qiu, Feng

2011-01-01

Cortex Mori, one of the well-known traditional Chinese herbal medicines, is derived from the root bark of Morus alba L. according to the China Pharmacopeia. Stilbene glycosides are the main components isolated from aqueous extracts of Morus alba and their content varies depending on where Cortex Mori was collected. We have established a qualitative and quantitative method based on the bioactive stilbene glycosides for control of the quality of Cortex Mori from different sources. To develop a high-performance liquid chromatography coupled with ultraviolet absorption detection for simultaneous quantitative determination of five major characteristic stilbene glycosides in 34 samples of the root bark of Morus alba L. (Cortex Mori) from different sources. The analysis was performed on an ODS column using methanol-water-acetic acid (18: 82: 0.1, v/v/v) as the mobile phase and the peaks were monitored at 320 nm. All calibration curves showed good linearity (r ≥ 0.9991) within test ranges. This method showed good repeatability for the quantification of these five components in Cortex Mori with intra- and inter-day standard deviations less than 2.19% and 1.45%, respectively. The validated method was successfully applied to quantify the five investigated components, including a pair of cis-trans-isomers 1 and 2 and a pair of isomers 4 and 5 in 34 samples of Cortex Mori from different sources. Copyright © 2010 John Wiley & Sons, Ltd.

Gamma oscillation maintains stimulus structure-dependent synchronization in cat visual cortex.

PubMed

Samonds, Jason M; Bonds, A B

2005-01-01

Visual cortical cells demonstrate both oscillation and synchronization, although the underlying causes and functional significance of these behaviors remain uncertain. We simultaneously recorded single-unit activity with microelectrode arrays in supragranular layers of area 17 of cats paralyzed and anesthetized with propofol and N(2)O. Rate-normalized autocorrelograms of 24 cells reveal bursting (100%) and gamma oscillation (63%). Renewal density analysis, used to explore the source of oscillation, suggests a contribution from extrinsic influences such as feedback. However, a bursting refractory period, presumably membrane-based, could also encourage oscillatory firing. When we investigated the source of synchronization for 60 cell pairs we found only moderate correlation of synchrony with bursts and oscillation. We did, nonetheless, discover a possible functional role for oscillation. In all cases of cross-correlograms that exhibited oscillation, the strength of the synchrony was maintained throughout the stimulation period. When no oscillation was apparent, 75% of the cell pairs showed decay in their synchronization. The synchrony between cells is strongly dependent on similar response onset latencies. We therefore propose that structured input, which yields tight organization of latency, is a more likely candidate for the source of synchronization than oscillation. The reliable synchrony at response onset could be driven by spatial and temporal correlation of the stimulus that is preserved through the earlier stages of the visual system. Oscillation then contributes to maintenance of the synchrony to enhance reliable transmission of the information for higher cognitive processing.

Performing monkeys of Bangladesh: characterizing their source and genetic variation.

PubMed

Hasan, M Kamrul; Feeroz, M Mostafa; Jones-Engel, Lisa; Engel, Gregory A; Akhtar, Sharmin; Kanthaswamy, Sree; Smith, David Glenn

2016-04-01

The acquisition and training of monkeys to perform is a centuries-old tradition in South Asia, resulting in a large number of rhesus macaques kept in captivity for this purpose. The performing monkeys are reportedly collected from free-ranging populations, and may escape from their owners or may be released into other populations. In order to determine whether this tradition involving the acquisition and movement of animals has influenced the population structure of free-ranging rhesus macaques in Bangladesh, we first characterized the source of these monkeys. Biological samples from 65 performing macaques collected between January 2010 and August 2013 were analyzed for genetic variation using 716 base pairs of mitochondrial DNA. Performing monkey sequences were compared with those of free-ranging rhesus macaque populations in Bangladesh, India and Myanmar. Forty-five haplotypes with 116 (16 %) polymorphic nucleotide sites were detected among the performing monkeys. As for the free-ranging rhesus population, most of the substitutions (89 %) were transitions, and no indels (insertion/deletion) were observed. The estimate of the mean number of pair-wise differences for the performing monkey population was 10.1264 ± 4.686, compared to 14.076 ± 6.363 for the free-ranging population. Fifteen free-ranging rhesus macaque populations were identified as the source of performing monkeys in Bangladesh; several of these populations were from areas where active provisioning has resulted in a large number of macaques. The collection of performing monkeys from India was also evident.

Performing monkeys of Bangladesh: characterizing their source and genetic variation

PubMed Central

Hasan, M Kamrul; Feeroz, M Mostafa; Jones-Engel, Lisa; Engel, Gregory A; Akhtar, Sharmin; Kanthaswamy, Sree; Smith, David Glenn

2016-01-01

The acquisition and training of monkeys to perform is a century's old tradition in South Asia, resulting in a large number of rhesus macaques kept in captivity for this purpose. The performing monkeys are reportedly collected from free-ranging populations and may escape from their owners or be released into other populations. In order to determine whether this tradition, that involves the acquisition and movement of animals, has influenced the population structure of free-ranging rhesus macaques in Bangladesh we first characterized the source of these monkeys. Biological samples from 65 performing macaques, collected between January 2010 and August 2013 were analyzed for genetic variation using 716 base pairs of mitochondrial DNA. Performing monkey sequences were compared with those of free-ranging rhesus macaque populations in Bangladesh, India and Myanmar. Forty-five haplotypes with 116 (16%) polymorphic nucleotide sites were detected among the performing monkeys. As for the free-ranging rhesus population, most of the substitutions (89%) were transitions and no indels (insertion/deletion) were observed. The estimate of the mean number of pair-wise difference for the performing monkey population was 10.1264 ± 4.686, compared to 14.076 ± 6.363 for the free-ranging population. Fifteen free-ranging rhesus macaque populations were identified as the source of performing monkeys in Bangladesh; several of these populations were from areas where active provisioning has resulted in a large number of macaques. Collection of performing monkeys from India was also evident. PMID:26758818

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

PubMed Central

Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H.

2008-01-01

A novel method is presented for joint prediction of alignment and common secondary structures of two RNA sequences. The joint consideration of common secondary structures and alignment is accomplished by structural alignment over a search space defined by the newly introduced motif called matched helical regions. The matched helical region formulation generalizes previously employed constraints for structural alignment and thereby better accommodates the structural variability within RNA families. A probabilistic model based on pseudo free energies obtained from precomputed base pairing and alignment probabilities is utilized for scoring structural alignments. Maximum a posteriori (MAP) common secondary structures, sequence alignment and joint posterior probabilities of base pairing are obtained from the model via a dynamic programming algorithm called PARTS. The advantage of the more general structural alignment of PARTS is seen in secondary structure predictions for the RNase P family. For this family, the PARTS MAP predictions of secondary structures and alignment perform significantly better than prior methods that utilize a more restrictive structural alignment model. For the tRNA and 5S rRNA families, the richer structural alignment model of PARTS does not offer a benefit and the method therefore performs comparably with existing alternatives. For all RNA families studied, the posterior probability estimates obtained from PARTS offer an improvement over posterior probability estimates from a single sequence prediction. When considering the base pairings predicted over a threshold value of confidence, the combination of sensitivity and positive predictive value is superior for PARTS than for the single sequence prediction. PARTS source code is available for download under the GNU public license at http://rna.urmc.rochester.edu. PMID:18304945

Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

PubMed

Golebiowski, Jérôme; Antonczak, Serge; Fernandez-Carmona, Juan; Condom, Roger; Cabrol-Bass, Daniel

2004-12-01

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal that the mismatch GA base, mediated by a water molecule, leads to a complex that presents the best compromise between flexibility and energetic contributions. The mismatch CU base pair, in spite of the presence of an inserted water molecule, is too short to achieve a tight interaction at the closing-loop junction and seems to force TAR to reorganize upon binding. An energetic analysis has allowed us to quantify the strength of the interactions of the closing and the loop-loop pairs throughout the simulations. Although the water-mediated GA closing base pair presents an interaction energy similar to that found on fully geometry-optimized structure, the water-mediated CU closing base pair energy interaction reaches less than half the optimal value.

Positive emotion can protect against source memory impairment.

PubMed

MacKenzie, Graham; Powell, Tim F; Donaldson, David I

2015-01-01

Despite widespread belief that memory is enhanced by emotion, evidence also suggests that emotion can impair memory. Here we test predictions inspired by object-based binding theory, which states that memory enhancement or impairment depends on the nature of the information to be retrieved. We investigated emotional memory in the context of source retrieval, using images of scenes that were negative, neutral or positive in valence. At study each scene was paired with a colour and during retrieval participants reported the source colour for recognised scenes. Critically, we isolated effects of valence by equating stimulus arousal across conditions. In Experiment 1 colour borders surrounded scenes at study: memory impairment was found for both negative and positive scenes. Experiment 2 used colours superimposed over scenes at study: valence affected source retrieval, with memory impairment for negative scenes only. These findings challenge current theories of emotional memory by showing that emotion can impair memory for both intrinsic and extrinsic source information, even when arousal is equated between emotional and neutral stimuli, and by dissociating the effects of positive and negative emotion on episodic memory retrieval.

Non-Poissonian Distribution of Tsunami Waiting Times

NASA Astrophysics Data System (ADS)

Geist, E. L.; Parsons, T.

2007-12-01

Analysis of the global tsunami catalog indicates that tsunami waiting times deviate from an exponential distribution one would expect from a Poisson process. Empirical density distributions of tsunami waiting times were determined using both global tsunami origin times and tsunami arrival times at a particular site with a sufficient catalog: Hilo, Hawai'i. Most sources for the tsunamis in the catalog are earthquakes; other sources include landslides and volcanogenic processes. Both datasets indicate an over-abundance of short waiting times in comparison to an exponential distribution. Two types of probability models are investigated to explain this observation. Model (1) is a universal scaling law that describes long-term clustering of sources with a gamma distribution. The shape parameter (γ) for the global tsunami distribution is similar to that of the global earthquake catalog γ=0.63-0.67 [Corral, 2004]. For the Hilo catalog, γ is slightly greater (0.75-0.82) and closer to an exponential distribution. This is explained by the fact that tsunamis from smaller triggered earthquakes or landslides are less likely to be recorded at a far-field station such as Hilo in comparison to the global catalog, which includes a greater proportion of local tsunamis. Model (2) is based on two distributions derived from Omori's law for the temporal decay of triggered sources (aftershocks). The first is the ETAS distribution derived by Saichev and Sornette [2007], which is shown to fit the distribution of observed tsunami waiting times. The second is a simpler two-parameter distribution that is the exponential distribution augmented by a linear decay in aftershocks multiplied by a time constant Ta. Examination of the sources associated with short tsunami waiting times indicate that triggered events include both earthquake and landslide tsunamis that begin in the vicinity of the primary source. Triggered seismogenic tsunamis do not necessarily originate from the same fault zone, however. For example, subduction-thrust and outer-rise earthquake pairs are evident, such as the November 2006 and January 2007 Kuril Islands tsunamigenic pair. Because of variations in tsunami source parameters, such as water depth above the source, triggered tsunami events with short waiting times are not systematically smaller than the primary tsunami.

Search for top-squark pairs decaying into Higgs or Z bosons in pp collisions at √s=8 TeV

DOE PAGES

Khachatryan, Vardan

2014-08-01

Our search for supersymmetry through the direct pair production of top squarks, with Higgs (H) or Z bosons in the decay chain, is performed using a data sample of proton–proton collisions at √s= 8TeV collected in 2012 with the CMS detector at the LHC. The sample corresponds to an integrated luminosity of 19.5 fb -1. The search is performed using a selection of events containing leptons and bottom-quark jets. No evidence for a significant excess of events over the standard model background prediction is observed. The results are interpreted in the context of simplified supersymmetric models with pair production ofmore » a heavier top-squark mass eigenstate t ~ 2 source decaying to a lighter top-squark mass eigenstate t ~ 2 via either t ~ 2 → Ht ~ 1 or t ~ 2 →Zt ~ 1, followed in both cases by t ~ 1→ tχ ~0 1, where χ ~0 1 source is an undetected, stable, lightest supersymmetric particle. The interpretation is performed in the region where the mass difference between the t ~ 1 and χ ~0 1 states is approximately equal to the top-quark mass (m t1-m χ0 1≃m t), which is not probed by searches for direct t ~ 1 squark pair production. This analysis excludes top squarks with mass m t1 <575 GeVand m t2 <400 GeV source at a 95% confidence level.« less

[Under what conditions does G.C Watson-Crick DNA base pair acquire all four configurations characteristic for A.T Watson-Crick DNA base pair?].

PubMed

Brovarets', O O

2013-01-01

At the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory it was established for the first time, that the Löwdin's G*.C* DNA base pair formed by the mutagenic tautomers can acquire, as the A-T Watson-Crick DNA base pair, four biologically important configurations, namely: Watson-Crick, reverse Watson-Crick, Hoogsteen and reverse Hoogsteen. This fact demonstrates rather unexpected role of the tautomerisation of the one of the Watson-Crick DNA base pairs, in particular, via double proton transfer: exactly the G.C-->G*.C* tautomerisation allows to overcome steric hindrances for the implementation of the above mentioned configurations. Geometric, electron-topological and energetic properties of the H-bonds that stabilise the studied pairs, as well as the energetic characteristics of the latters are presented.

Approximation for the Rayleigh Resolution of a Circular Aperture

ERIC Educational Resources Information Center

Mungan, Carl E.

2009-01-01

Rayleigh's criterion states that a pair of point sources are barely resolved by an optical instrument when the central maximum of the diffraction pattern due to one source coincides with the first minimum of the pattern of the other source. As derived in standard introductory physics textbooks, the first minimum for a rectangular slit of width "a"…

Two-photon x-ray diffraction

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

Stohr, J.

The interference pattern of a circular photon source has long been used to define the optical diffraction limit. Here we show the breakdown of conventional x-ray diffraction theory for the fundamental case of a “source”, consisting of a back-illuminated thin film in a circular aperture. When the conventional spontaneous x-ray scattering by atoms in the film is replaced at high incident intensity by stimulated resonant scattering, the film becomes the source of cloned photon twins and the diffraction pattern becomes self-focused beyond the diffraction limit. Furthermore, the case of cloned photon pairs is compared to and distinguished from entangled photonmore » pairs or biphotons.« less

A Benes-like theorem for the shuffle-exchange graph

NASA Technical Reports Server (NTRS)

Schwabe, Eric J.

1992-01-01

One of the first theorems on permutation routing, proved by V. E. Beness (1965), shows that given a set of source-destination pairs in an N-node butterfly network with at most a constant number of sources or destinations in each column of the butterfly, there exists a set of paths of lengths O(log N) connecting each pair such that the total congestion is constant. An analogous theorem yielding constant-congestion paths for off-line routing in the shuffle-exchange graph is proved here. The necklaces of the shuffle-exchange graph play the same structural role as the columns of the butterfly in Beness' theorem.

Two-photon x-ray diffraction

DOE PAGES

Stohr, J.

2017-01-11

The interference pattern of a circular photon source has long been used to define the optical diffraction limit. Here we show the breakdown of conventional x-ray diffraction theory for the fundamental case of a “source”, consisting of a back-illuminated thin film in a circular aperture. When the conventional spontaneous x-ray scattering by atoms in the film is replaced at high incident intensity by stimulated resonant scattering, the film becomes the source of cloned photon twins and the diffraction pattern becomes self-focused beyond the diffraction limit. Furthermore, the case of cloned photon pairs is compared to and distinguished from entangled photonmore » pairs or biphotons.« less

Multi-user quantum key distribution with entangled photons from an AlGaAs chip

NASA Astrophysics Data System (ADS)

Autebert, C.; Trapateau, J.; Orieux, A.; Lemaître, A.; Gomez-Carbonell, C.; Diamanti, E.; Zaquine, I.; Ducci, S.

2016-12-01

In view of real-world applications of quantum information technologies, the combination of miniature quantum resources with existing fibre networks is a crucial issue. Among such resources, on-chip entangled photon sources play a central role for applications spanning quantum communications, computing and metrology. Here, we use a semiconductor source of entangled photons operating at room temperature in conjunction with standard telecom components to demonstrate multi-user quantum key distribution, a core protocol for securing communications in quantum networks. The source consists of an AlGaAs chip-emitting polarisation entangled photon pairs over a large bandwidth in the main telecom band around 1550 nm without the use of any off-chip compensation or interferometric scheme; the photon pairs are directly launched into a dense wavelength division multiplexer (DWDM) and secret keys are distributed between several pairs of users communicating through different channels. We achieve a visibility measured after the DWDM of 87% and show long-distance key distribution using a 50-km standard telecom fibre link between two network users. These results illustrate a promising route to practical, resource-efficient implementations adapted to quantum network infrastructures.

Assessment of the significance of patent-derived information for the early identification of compound-target interaction hypotheses.

PubMed

Senger, Stefan

2017-04-21

Patents are an important source of information for effective decision making in drug discovery. Encouragingly, freely accessible patent-chemistry databases are now in the public domain. However, at present there is still a wide gap between relatively low coverage-high quality manually-curated data sources and high coverage data sources that use text mining and automated extraction of chemical structures. To secure much needed funding for further research and an improved infrastructure, hard evidence is required to demonstrate the significance of patent-derived information in drug discovery. Surprisingly little such evidence has been reported so far. To address this, the present study attempts to quantify the relevance of patents for formulating and substantiating hypotheses for compound-target interactions. A manually-curated set of 130 compound-target interaction pairs annotated with what are considered to be the earliest patent and publication has been produced. The analysis of this set revealed that in stark contrast to what has been reported for novel chemical structures, only about 10% of the compound-target interaction pairs could be found in publications in the scientific literature within one year of being reported in patents. The average delay across all interaction pairs is close to 4 years. In an attempt to benchmark current capabilities, it was also examined how much of the benefit of using patent-derived information can be retained when a bioannotated version of SureChEMBL is used as secondary source for the patent literature. Encouragingly, this approach found the patents in the annotated set for 72% of the compound-target interaction pairs. Similarly, the effect of using the bioactivity database ChEMBL as secondary source for the scientific literature was studied. Here, the publications from the annotated set were only found for 46% of the compound-target interaction pairs. Patent-derived information is a significant enabler for formulating compound-target interaction hypotheses even in cases where the respective interaction is later reported in the scientific literature. The findings of this study clearly highlight the significance of future investments in the development and provision of databases and tools that will allow scientists to search patent information in a comprehensive, reliable, and efficient manner.

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

Leszczynski, Jerzy; Sponer, Judit; Sponer, Jiri

Recent experimental studies on the Watson Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two NH O hydrogen bonds separated by one NH N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the basesmore » and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.« less

Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs.

PubMed

Saunders, Christopher T; Wong, Wendy S W; Swamy, Sajani; Becq, Jennifer; Murray, Lisa J; Cheetham, R Keira

2012-07-15

Whole genome and exome sequencing of matched tumor-normal sample pairs is becoming routine in cancer research. The consequent increased demand for somatic variant analysis of paired samples requires methods specialized to model this problem so as to sensitively call variants at any practical level of tumor impurity. We describe Strelka, a method for somatic SNV and small indel detection from sequencing data of matched tumor-normal samples. The method uses a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. We demonstrate that the method has superior accuracy and sensitivity on impure samples compared with approaches based on either diploid genotype likelihoods or general allele-frequency tests. The Strelka workflow source code is available at ftp://strelka@ftp.illumina.com/. csaunders@illumina.com

Thermal transport in topological-insulator-based superconducting hybrid structures with mixed singlet and triplet pairing states.

PubMed

Li, Hai; Zhao, Yuan Yuan

2017-11-22

In the framework of the Bogoliubov-de Gennes equation, we investigate the thermal transport properties in topological-insulator-based superconducting hybrid structures with mixed spin-singlet and spin-triplet pairing states, and emphasize the different manifestations of the spin-singlet and spin-triplet pairing states in the thermal transport signatures. It is revealed that the temperature-dependent differential thermal conductance strongly depends on the components of the pairing state, and the negative differential thermal conductance only occurs in the spin-singlet pairing state dominated regime. It is also found that the thermal conductance is profoundly sensitive to the components of the pairing state. In the spin-singlet pairing state controlled regime, the thermal conductance obviously oscillates with the phase difference and junction length. With increasing the proportion of the spin-triplet pairing state, the oscillating characteristic of the thermal conductance fades out distinctly. These results suggest an alternative route for distinguishing the components of pairing states in topological-insulator-based superconducting hybrid structures.

Genetic and DNA sequence analysis of the kanamycin resistance transposon Tn903.

PubMed Central

Grindley, N D; Joyce, C M

1980-01-01

The kanamycin resistance transposon Tn903 consists of a unique region of about 1000 base pairs bounded by a pair of 1050-base-pair inverted repeat sequences. Each repeat contains two Pvu II endonuclease cleavage sites separated by 520 base pairs. We have constructed derivatives of Tn903 in which this 520-base-pair fragment is deleted from one or both repeats. Those derivatives that lack both 520-base-pair fragments cannot transpose, whereas those that lack just one remain transposition proficient. One such transposable derivative, Tn903 delta I, has been selected for further study. We have determined the sequence of the intact inverted repeat. The 18 base pairs at each end are identical and inverted relative to one another, a structure characteristic of insertion sequences. Additional experiments indicate that a single inverted repeat from Tn903 can, in fact, transpose; we propose that this element be called IS903. To correlate the DNA sequence with genetic activities, we have created mutations by inserting a 10-base-pair DNA fragment at several sites within the intact repeat of Tn903 delta 1, and we have examined the effect of such insertions on transposability. The results suggest that IS903 encodes a 307-amino-acid polypeptide (a "transposase") that is absolutely required for transposition of IS903 or Tn903. Images PMID:6261245

Silver(I)-Mediated Base Pairs in DNA Sequences Containing 7-Deazaguanine/Cytosine: towards DNA with Entirely Metallated Watson-Crick Base Pairs.

PubMed

Méndez-Arriaga, José M; Maldonado, Carmen R; Dobado, José A; Galindo, Miguel A

2018-03-26

DNA sequences comprising noncanonical 7-deazaguanine ( 7C G) and canonical cytosine (C) are capable of forming Watson-Crick base pairs via hydrogen bonds as well as silver(I)-mediated base pairs by coordination to central silver(I) ions. Duplexes I and II containing 7C G and C have been synthesized and characterized. The incorporation of silver(I) ions into these duplexes has been studied by means of temperature-dependent UV spectroscopy, circular dichroism, and DFT calculations. The results suggest the formation of DNA molecules comprising contiguous metallated 7C G-Ag I -C Watson-Crick base pairs that preserve the original B-type conformation. Furthermore, additional studies performed on duplex III indicated that, in the presence of Ag I ions, 7C G-C and 7C A-T Watson-Crick base pairs ( 7C A, 7-deazadenine; T, thymine) can be converted to metallated 7C G-Ag I -C and 7C A-Ag I -T base pairs inside the same DNA molecule whilst maintaining its initial double helix conformation. These findings are very important for the development of customized silver-DNA nanostructures based on a Watson-Crick complementarity pattern. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparable stability of Hoogsteen and Watson-Crick base pairs in ionic liquid choline dihydrogen phosphate.

PubMed

Tateishi-Karimata, Hisae; Nakano, Miki; Sugimoto, Naoki

2014-01-08

The instability of Hoogsteen base pairs relative to Watson-Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson-Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson-Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo.

Comparable Stability of Hoogsteen and Watson–Crick Base Pairs in Ionic Liquid Choline Dihydrogen Phosphate

PubMed Central

Tateishi-Karimata, Hisae; Nakano, Miki; Sugimoto, Naoki

2014-01-01

The instability of Hoogsteen base pairs relative to Watson–Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson–Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson–Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo. PMID:24399194

m1A and m1G Potently Disrupt A-RNA Structure Due to the Intrinsic Instability of Hoogsteen Base Pairs

PubMed Central

Zhou, Huiqing; Kimsey, Isaac J.; Nikolova, Evgenia N.; Sathyamoorthy, Bharathwaj; Grazioli, Gianmarc; McSally, James; Bai, Tianyu; Wunderlich, Christoph H.; Kreutz, Christoph; Andricioaei, Ioan; Al-Hashimi, Hashim M.

2016-01-01

The B-DNA double helix can dynamically accommodate G–C and A–T base pairs in either Watson-Crick or Hoogsteen configurations. Here, we show that G–C+ and A–U Hoogsteen base pairs are strongly disfavored in A-RNA. As a result, N1-methyl adenosine and N1-methyl guanosine, which occur in DNA as a form of alkylation damage, and in RNA as a posttranscriptional modification, have dramatically different consequences. They create G–C+ and A–U Hoogsteen base pairs in duplex DNA that maintain the structural integrity of the double helix, but block base pairing all together and induce local duplex melting in RNA, providing a mechanism for potently disrupting RNA structure through posttranscriptional modifications. The markedly different propensities to form Hoogsteen base pairs in B-DNA and A-RNA may help meet the opposing requirements of maintaining genome stability on one hand, and dynamically modulating the structure of the epitranscriptome on the other. PMID:27478929

Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data.

PubMed

Greenwald, William W; Li, He; Smith, Erin N; Benaglio, Paola; Nariai, Naoki; Frazer, Kelly A

2017-04-07

Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, and merging of data from multiple experiments. While many file types and analysis tools exist for storing and manipulating single locus NGS data, there is currently no file standard or analysis tool suite for manipulating and storing paired-genomic-loci: the data type resulting from "genomic interaction" studies. As genomic interaction sequencing data are becoming prevalent, a standard file format and tools for working with these data conveniently and efficiently are needed. This article details a file standard and novel software tool suite for working with paired-genomic-loci data. We present the paired-genomic-loci (PGL) file standard for genomic-interactions data, and the accompanying analysis tool suite "pgltools": a cross platform, pypy compatible python package available both as an easy-to-use UNIX package, and as a python module, for integration into pipelines of paired-genomic-loci analyses. Pgltools is a freely available, open source tool suite for manipulating paired-genomic-loci data. Source code, an in-depth manual, and a tutorial are available publicly at www.github.com/billgreenwald/pgltools , and a python module of the operations can be installed from PyPI via the PyGLtools module.

Analysis of different adsorption heat transformation applications and working pairs for climatic regions of Russia

NASA Astrophysics Data System (ADS)

Grekova, A. D.; Gordeeva, L. G.

2018-04-01

Adsorption heat transformation is an energy and environment saving technology for cooling/heating driven by renewable energy sources. Each specific cycle of adsorption heat transformer (AHT) makes particular requirements to the properties of the sorption material, depending on the climatic zone in which the AHT is used, the type of application (cooling, heating and heat storage), and energy source used for regenerating the sorbent. Therefore, the effective operation of AHT can be realized only if the working pair "adsorbent-adsorbate" is intelligently selected in accordance with the requirements of a particular working cycle. One of the most important factors influencing the choice of a working pair is the climatic conditions in which the AHT will operate. In this paper, the climatic conditions of various regions of Russian Federation (RF) were analyzed. For each considered zone, the boundary potentials of Polanyi corresponding to different AHT cycles are calculated. The sorption equilibrium data of various sorbents with water and methanol presented in the literature are summarized, and characteristic sorption curves are plotted in coordinates "sorption - the Polanyi potential". The characteristic adsorption curves found are approximated by analytic expressions, which allow the analysis of working pairs applicability for different AHT cycles. The recommendations of using the discussed sorption pairs under conditions of determined climatic zones are given for the AHT applications.

Nanoeletromechanical switch and logic circuits formed therefrom

DOEpatents

Nordquist, Christopher D [Albuquerque, NM; Czaplewski, David A [Albuquerque, NM

2010-05-18

A nanoelectromechanical (NEM) switch is formed on a substrate with a source electrode containing a suspended electrically-conductive beam which is anchored to the substrate at each end. This beam, which can be formed of ruthenium, bows laterally in response to a voltage applied between a pair of gate electrodes and the source electrode to form an electrical connection between the source electrode and a drain electrode located near a midpoint of the beam. Another pair of gate electrodes and another drain electrode can be located on an opposite side of the beam to allow for switching in an opposite direction. The NEM switch can be used to form digital logic circuits including NAND gates, NOR gates, programmable logic gates, and SRAM and DRAM memory cells which can be used in place of conventional CMOS circuits, or in combination therewith.

Model of Ni-63 battery with realistic PIN structure

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

Munson, Charles E.; Voss, Paul L.; Ougazzaden, Abdallah, E-mail: aougazza@georgiatech-metz.fr

2015-09-14

GaN, with its wide bandgap of 3.4 eV, has emerged as an efficient material for designing high-efficiency betavoltaic batteries. An important part of designing efficient betavoltaic batteries involves a good understanding of the full process, from the behavior of the nuclear material and the creation of electron-hole pairs all the way through the collection of photo-generated carriers. This paper presents a detailed model based on Monte Carlo and Silvaco for a GaN-based betavoltaic battery device, modeled after Ni-63 as an energy source. The accuracy of the model is verified by comparing it with experimental values obtained for a GaN-based p-i-nmore » structure under scanning electron microscope illumination.« less

Model of Ni-63 battery with realistic PIN structure

NASA Astrophysics Data System (ADS)

Munson, Charles E.; Arif, Muhammad; Streque, Jeremy; Belahsene, Sofiane; Martinez, Anthony; Ramdane, Abderrahim; El Gmili, Youssef; Salvestrini, Jean-Paul; Voss, Paul L.; Ougazzaden, Abdallah

2015-09-01

GaN, with its wide bandgap of 3.4 eV, has emerged as an efficient material for designing high-efficiency betavoltaic batteries. An important part of designing efficient betavoltaic batteries involves a good understanding of the full process, from the behavior of the nuclear material and the creation of electron-hole pairs all the way through the collection of photo-generated carriers. This paper presents a detailed model based on Monte Carlo and Silvaco for a GaN-based betavoltaic battery device, modeled after Ni-63 as an energy source. The accuracy of the model is verified by comparing it with experimental values obtained for a GaN-based p-i-n structure under scanning electron microscope illumination.

Development and evaluation of geochemical methods for the sourcing of archaeological maize

USGS Publications Warehouse

Benson, L.V.; Taylor, Howard E.; Peterson, K.A.; Shattuck, B.D.; Ramotnik, C.A.; Stein, J.R.

2008-01-01

Strontium (Sr)-isotope values on bone from deer mice pairs from 12 field sites in the Chaco Canyon area, New Mexico, were compared with isotope values of synthetic soil waters from the same fields. The data indicate that mice obtain Sr from near-surface sources and that soil samples collected at depths ranging from 25 to 95 cm contain Sr that is more accessible to the deep roots of maize; thus, synthetic soil solutions provide better data for the sourcing of archaeological maize. However, the Sr-isotope composition of mice may be more valuable in sourcing archaeological remains of animals such as rabbit, turkey, and deer. In a separate study, five Native American maize (Zea mays L. ssp. mays) accessions grown out at New Mexico State University Agricultural Science Center, Farmington, New Mexico were used to determine if soil-water metal pairs partition systematically into cobs and kernels. The sampled maize included landraces from three Native American groups (Acoma, Hopi, Zuni) that still occupy the Four Corners area. Two cobs each were picked from 10 plants of each landrace. Partitioning of the Ba/Mn, Ba/Sr, Ca/Sr, and K/Rb metal pairs from the soil water to the cob appears to behave in a systematic fashion. In addition, 51 rare earth element (REE) pairs also appear to systematically partition from the soil water into cobs; however, the ratios of the REE dissolved in the soil waters are relatively invariant; therefore, the distribution coefficients that describe the partitioning of REE from the soil water to the cob may not apply to archeological cobs grown under chemically heterogeneous conditions. Partitioning of Ba/Rb, Ba/Sr, Mg/P, and Mn/P metal pairs from the soil water to kernels also behaves in a systematic fashion. Given that modern Native American landraces were grown under optimal environmental conditions that may not have been duplicated by prehistoric Native Americans, the distribution coefficients obtained in this study should be used with caution. ?? 2007 Elsevier Ltd. All rights reserved.

The Importance of Water for Life

NASA Astrophysics Data System (ADS)

Westall, Frances; Brack, André

2018-03-01

Liquid water is essential for life as we know it, i.e. carbon-based life. Although other compound-solvent pairs that could exist in very specific physical environments could be envisaged, the elements essential to carbon and water-based life are among the most common in the universe. Carbon molecules and liquid water have physical and chemical properties that make them optimised compound-solvent pairs. Liquid water is essential for important prebiotic reactions. But equally important for the emergence of life is the contact of carbon molecules in liquid water with hot rocks and minerals. We here review the environmental conditions of the early Earth, as soon as it had liquid water at its surface and was habitable. Basing our approach to life as a "cosmic phenomenon" (de Duve 1995), i.e. a chemical continuum, we briefly address the various hypotheses for the origin of life, noting their relevance with respect to early environmental conditions. It appears that hydrothermal environments were important in this respect. We continue with the record of early life noting that, by 3.5 Ga, when the sedimentary environment started being well-preserved, anaerobic life forms had colonised all habitable microenvironments from the sea floor to exposed beach environments and, possibly, in the photic planktonic zone of the sea. Life on Earth had also evolved to the relatively sophisticated stage of anoxygenic photosynthesis. We conclude with an evaluation of the potential for habitability and colonisation of other planets and satellites in the Solar System, noting that the most common life forms in the Solar System and probably in the Universe would be similar to terrestrial chemotrophs whose carbon source is either reduced carbon or CO2 dissolved in water and whose energy would be sourced from oxidized carbon, H2, or other transition elements.

COSMIC-RAY POSITRONS FROM MILLISECOND PULSARS

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

Venter, C.; Kopp, A.; Büsching, I.

2015-07-10

Observations by the Fermi Large Area Telescope of γ-ray millisecond pulsar (MSP) light curves imply copious pair production in their magnetospheres, and not exclusively in those of younger pulsars. Such pair cascades may be a primary source of Galactic electrons and positrons, contributing to the observed enhancement in positron flux above ∼10 GeV. Fermi has also uncovered many new MSPs, impacting Galactic stellar population models. We investigate the contribution of Galactic MSPs to the flux of terrestrial cosmic-ray electrons and positrons. Our population synthesis code predicts the source properties of present-day MSPs. We simulate their pair spectra invoking an offset-dipolemore » magnetic field. We also consider positrons and electrons that have been further accelerated to energies of several TeV by strong intrabinary shocks in black widow (BW) and redback (RB) systems. Since MSPs are not surrounded by pulsar wind nebulae or supernova shells, we assume that the pairs freely escape and undergo losses only in the intergalactic medium. We compute the transported pair spectra at Earth, following their diffusion and energy loss through the Galaxy. The predicted particle flux increases for non-zero offsets of the magnetic polar caps. Pair cascades from the magnetospheres of MSPs are only modest contributors around a few tens of GeV to the lepton fluxes measured by the Alpha Magnetic Spectrometer, PAMELA, and Fermi, after which this component cuts off. The contribution by BWs and RBs may, however, reach levels of a few tens of percent at tens of TeV, depending on model parameters.« less

Micro-unmanned aerodynamic vehicle

DOEpatents

Reuel, Nigel [Rio Rancho, NM; Lionberger, Troy A [Ann Arbor, MI; Galambos, Paul C [Albuquerque, NM; Okandan, Murat [Albuquerque, NM; Baker, Michael S [Albuquerque, NM

2008-03-11

A MEMS-based micro-unmanned vehicle includes at least a pair of wings having leading wing beams and trailing wing beams, at least two actuators, a leading actuator beam coupled to the leading wing beams, a trailing actuator beam coupled to the trailing wing beams, a vehicle body having a plurality of fulcrums pivotally securing the leading wing beams, the trailing wing beams, the leading actuator beam and the trailing actuator beam and having at least one anisotropically etched recess to accommodate a lever-fulcrum motion of the coupled beams, and a power source.

Selective Excitation of Lamb-Waves for Damage Detection in Composites

NASA Astrophysics Data System (ADS)

Petculescu, G.; Krishnaswamy, S.; Achenbach, J. D.

2006-03-01

Sensors based on periodic arrays of coherent piezoelectric sources (comb design) are used to selectively excite and detect Lamb waves in aluminum and AS4/3601 unidirectional carbon-epoxy plates. 110 μm PVDF film poled in the thickness direction is used as piezoelectric material. An algorithm to eliminate the effect of coupling in amplitude measurements, using individual Lamb modes excited/detected by the same transducer pair, is described. A multiple-impact test showing a decrease in amplitude and group velocity as damage progresses is used as an example.

Local Sampling of the Wigner Function at Telecom Wavelength with Loss-Tolerant Detection of Photon Statistics.

PubMed

Harder, G; Silberhorn, Ch; Rehacek, J; Hradil, Z; Motka, L; Stoklasa, B; Sánchez-Soto, L L

2016-04-01

We report the experimental point-by-point sampling of the Wigner function for nonclassical states created in an ultrafast pulsed type-II parametric down-conversion source. We use a loss-tolerant time-multiplexed detector based on a fiber-optical setup and a pair of photon-number-resolving avalanche photodiodes. By capitalizing on an expedient data-pattern tomography, we assess the properties of the light states with outstanding accuracy. The method allows us to reliably infer the squeezing of genuine two-mode states without any phase reference.

Empirical study of fuzzy compatibility measures and aggregation operators

NASA Astrophysics Data System (ADS)

Cross, Valerie V.; Sudkamp, Thomas A.

1992-02-01

Two fundamental requirements for the generation of support using incomplete and imprecise information are the ability to measure the compatibility of discriminatory information with domain knowledge and the ability to fuse information obtained from disparate sources. A generic architecture utilizing the generalized fuzzy relational database model has been developed to empirically investigate the support generation capabilities of various compatibility measures and aggregation operators. This paper examines the effectiveness of combinations of compatibility measures from the set-theoretic, geometric distance, and logic- based classes paired with t-norm and generalized mean families of aggregation operators.

Tunable optical coherence tomography in the infrared range using visible photons

NASA Astrophysics Data System (ADS)

Paterova, Anna V.; Yang, Hongzhi; An, Chengwu; Kalashnikov, Dmitry A.; Krivitsky, Leonid A.

2018-04-01

Optical coherence tomography (OCT) is an appealing technique for bio-imaging, medicine, and material analysis. For many applications, OCT in mid- and far-infrared (IR) leads to significantly more accurate results. Reported mid-IR OCT systems require light sources and photodetectors which operate in mid-IR range. These devices are expensive and need cryogenic cooling. Here, we report a proof-of-concept demonstration of a wavelength tunable IR OCT technique with detection of only visible range photons. Our method is based on the nonlinear interference of frequency correlated photon pairs. The nonlinear crystal, introduced in the Michelson-type interferometer, generates photon pairs with one photon in the visible and another in the IR range. The intensity of detected visible photons depends on the phase and loss of IR photons, which interact with the sample under study. This enables us to characterize sample properties and perform imaging in the IR range by detecting visible photons. The technique possesses broad wavelength tunability and yields a fair axial and lateral resolution, which can be tailored to the specific application. The work contributes to the development of versatile 3D imaging and material characterization systems working in a broad range of IR wavelengths, which do not require the use of IR-range light sources and photodetectors.

detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation.

PubMed

Ye, Congting; Ji, Guoli; Li, Lei; Liang, Chun

2014-01-01

Inverted repeats are present in abundance in both prokaryotic and eukaryotic genomes and can form DNA secondary structures--hairpins and cruciforms that are involved in many important biological processes. Bioinformatics tools for efficient and accurate detection of inverted repeats are desirable, because existing tools are often less accurate and time consuming, sometimes incapable of dealing with genome-scale input data. Here, we present a MATLAB-based program called detectIR for the perfect and imperfect inverted repeat detection that utilizes complex numbers and vector calculation and allows genome-scale data inputs. A novel algorithm is adopted in detectIR to convert the conventional sequence string comparison in inverted repeat detection into vector calculation of complex numbers, allowing non-complementary pairs (mismatches) in the pairing stem and a non-palindromic spacer (loop or gaps) in the middle of inverted repeats. Compared with existing popular tools, our program performs with significantly higher accuracy and efficiency. Using genome sequence data from HIV-1, Arabidopsis thaliana, Homo sapiens and Zea mays for comparison, detectIR can find lots of inverted repeats missed by existing tools whose outputs often contain many invalid cases. detectIR is open source and its source code is freely available at: https://sourceforge.net/projects/detectir.

pgRNAFinder: a web-based tool to design distance independent paired-gRNA.

PubMed

Xiong, Yuanyan; Xie, Xiaowei; Wang, Yanzhi; Ma, Wenbing; Liang, Puping; Songyang, Zhou; Dai, Zhiming

2017-11-15

The CRISPR/Cas System has been shown to be an efficient and accurate genome-editing technique. There exist a number of tools to design the guide RNA sequences and predict potential off-target sites. However, most of the existing computational tools on gRNA design are restricted to small deletions. To address this issue, we present pgRNAFinder, with an easy-to-use web interface, which enables researchers to design single or distance-free paired-gRNA sequences. The web interface of pgRNAFinder contains both gRNA search and scoring system. After users input query sequences, it searches gRNA by 3' protospacer-adjacent motif (PAM), and possible off-targets, and scores the conservation of the deleted sequences rapidly. Filters can be applied to identify high-quality CRISPR sites. PgRNAFinder offers gRNA design functionality for 8 vertebrate genomes. Furthermore, to keep pgRNAFinder open, extensible to any organism, we provide the source package for local use. The pgRNAFinder is freely available at http://songyanglab.sysu.edu.cn/wangwebs/pgRNAFinder/, and the source code and user manual can be obtained from https://github.com/xiexiaowei/pgRNAFinder. songyang@bcm.edu or daizhim@mail.sysu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Repeating aftershocks of the great 2004 Sumatra and 2005 Nias earthquakes

NASA Astrophysics Data System (ADS)

Yu, Wen-che; Song, Teh-Ru Alex; Silver, Paul G.

2013-05-01

We investigate repeating aftershocks associated with the great 2004 Sumatra-Andaman (Mw 9.2) and 2005 Nias-Simeulue (Mw 8.6) earthquakes by cross-correlating waveforms recorded by the regional seismographic station PSI and teleseismic stations. We identify 10 and 18 correlated aftershock sequences associated with the great 2004 Sumatra and 2005 Nias earthquakes, respectively. The majority of the correlated aftershock sequences are located near the down-dip end of a large afterslip patch. We determine the precise relative locations of event pairs among these sequences and estimate the source rupture areas. The correlated event pairs identified are appropriately referred to as repeating aftershocks, in that the source rupture areas are comparable and significantly overlap within a sequence. We use the repeating aftershocks to estimate afterslip based on the slip-seismic moment scaling relationship and to infer the temporal decay rate of the recurrence interval. The estimated afterslip resembles that measured from the near-field geodetic data to the first order. The decay rate of repeating aftershocks as a function of lapse time t follows a power-law decay 1/tp with the exponent p in the range 0.8-1.1. Both types of observations indicate that repeating aftershocks are governed by post-seismic afterslip.

Base Pair Opening in a Deoxynucleotide Duplex Containing a cis-syn Thymine Cyclobutane Dimer Lesion

PubMed Central

Wenke, Belinda B.; Huiting, Leah N.; Frankel, Elisa B.; Lane, Benjamin F.; Núñez, Megan E.

2014-01-01

The cis-syn thymine cyclobutane dimer is a DNA photoproduct implicated in skin cancer. We compared the stability of individual base pairs in thymine dimer-containing duplexes to undamaged parent 10-mer duplexes. UV melting thermodynamic measurements, CD spectroscopy, and 2D NOESY NMR spectroscopy confirm that the thymine dimer lesion is locally and moderately destabilizing within an overall B-form duplex conformation. We measured the rates of exchange of individual imino protons by NMR using magnetization transfer from water and determined the equilibrium constant for the opening of each base pair Kop. In the normal duplex Kop decreases from the frayed ends of the duplex toward the center, such that the central TA pair is the most stable with a Kop of 8×10−7. In contrast, base pair opening at the 5’T of the thymine dimer is facile. The 5’T of the dimer has the largest equilibrium constant (Kop =3×10−4) in its duplex, considerably larger than even the frayed penultimate base pairs. Notably, base pairing by the 3’T of the dimer is much more stable than by the 5’T, indicating that the predominant opening mechanism for the thymine dimer lesion is not likely to be flipping out into solution as a single unit. The dimer asymmetrically affects the stability of the duplex in its vicinity, destabilizing base pairing on its 5’ side more than on the 3’ side. The striking differences in base pair opening between parent and dimer duplexes occur independently of the duplex-single strand melting transitions. PMID:24328089

Preceding Vehicle Detection and Tracking Adaptive to Illumination Variation in Night Traffic Scenes Based on Relevance Analysis

PubMed Central

Guo, Junbin; Wang, Jianqiang; Guo, Xiaosong; Yu, Chuanqiang; Sun, Xiaoyan

2014-01-01

Preceding vehicle detection and tracking at nighttime are challenging problems due to the disturbance of other extraneous illuminant sources coexisting with the vehicle lights. To improve the detection accuracy and robustness of vehicle detection, a novel method for vehicle detection and tracking at nighttime is proposed in this paper. The characteristics of taillights in the gray level are applied to determine the lower boundary of the threshold for taillights segmentation, and the optimal threshold for taillight segmentation is calculated using the OTSU algorithm between the lower boundary and the highest grayscale of the region of interest. The candidate taillight pairs are extracted based on the similarity between left and right taillights, and the non-vehicle taillight pairs are removed based on the relevance analysis of vehicle location between frames. To reduce the false negative rate of vehicle detection, a vehicle tracking method based on taillights estimation is applied. The taillight spot candidate is sought in the region predicted by Kalman filtering, and the disturbed taillight is estimated based on the symmetry and location of the other taillight of the same vehicle. Vehicle tracking is completed after estimating its location according to the two taillight spots. The results of experiments on a vehicle platform indicate that the proposed method could detect vehicles quickly, correctly and robustly in the actual traffic environments with illumination variation. PMID:25195855

Preceding vehicle detection and tracking adaptive to illumination variation in night traffic scenes based on relevance analysis.

PubMed

Guo, Junbin; Wang, Jianqiang; Guo, Xiaosong; Yu, Chuanqiang; Sun, Xiaoyan

2014-08-19

Preceding vehicle detection and tracking at nighttime are challenging problems due to the disturbance of other extraneous illuminant sources coexisting with the vehicle lights. To improve the detection accuracy and robustness of vehicle detection, a novel method for vehicle detection and tracking at nighttime is proposed in this paper. The characteristics of taillights in the gray level are applied to determine the lower boundary of the threshold for taillights segmentation, and the optimal threshold for taillight segmentation is calculated using the OTSU algorithm between the lower boundary and the highest grayscale of the region of interest. The candidate taillight pairs are extracted based on the similarity between left and right taillights, and the non-vehicle taillight pairs are removed based on the relevance analysis of vehicle location between frames. To reduce the false negative rate of vehicle detection, a vehicle tracking method based on taillights estimation is applied. The taillight spot candidate is sought in the region predicted by Kalman filtering, and the disturbed taillight is estimated based on the symmetry and location of the other taillight of the same vehicle. Vehicle tracking is completed after estimating its location according to the two taillight spots. The results of experiments on a vehicle platform indicate that the proposed method could detect vehicles quickly, correctly and robustly in the actual traffic environments with illumination variation.

Vfold: a web server for RNA structure and folding thermodynamics prediction.

PubMed

Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2014-01-01

The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

Imidazopyridine/Pyrrole and hydroxybenzimidazole/pyrrole pairs for DNA minor groove recognition.

PubMed

Renneberg, Dorte; Dervan, Peter B

2003-05-14

The DNA binding properties of fused heterocycles imidazo[4,5-b]pyridine (Ip) and hydroxybenzimidazole (Hz) paired with pyrrole (Py) in eight-ring hairpin polyamides are reported. The recognition profile of Ip/Py and Hz/Py pairs were compared to the five-membered ring pairs Im/Py and Hp/Py on a DNA restriction fragment at four 6-base pair recognition sites which vary at a single position 5'-TGTNTA-3', where N = G, C, T, A. The Ip/Py pair distinguishes G.C from C.G, T.A, and A.T, and the Hz/Py pair distinguishes T.A from A.T, G.C, and C.G, affording a new set of heterocycle pairs to target the four Watson-Crick base pairs in the minor groove of DNA.

A bright triggered twin-photon source in the solid state

PubMed Central

Heindel, T.; Thoma, A.; von Helversen, M.; Schmidt, M.; Schlehahn, A.; Gschrey, M.; Schnauber, P.; Schulze, J. -H.; Strittmatter, A.; Beyer, J.; Rodt, S.; Carmele, A.; Knorr, A.; Reitzenstein, S.

2017-01-01

A non-classical light source emitting pairs of identical photons represents a versatile resource of interdisciplinary importance with applications in quantum optics and quantum biology. To date, photon twins have mostly been generated using parametric downconversion sources, relying on Poissonian number distributions, or atoms, exhibiting low emission rates. Here we propose and experimentally demonstrate the efficient, triggered generation of photon twins using the energy-degenerate biexciton–exciton radiative cascade of a single semiconductor quantum dot. Deterministically integrated within a microlens, this nanostructure emits highly correlated photon pairs, degenerate in energy and polarization, at a rate of up to (234±4) kHz. Furthermore, we verify a significant degree of photon indistinguishability and directly observe twin-photon emission by employing photon-number-resolving detectors, which enables the reconstruction of the emitted photon number distribution. Our work represents an important step towards the realization of efficient sources of twin-photon states on a fully scalable technology platform. PMID:28367950

Sound source localization method in an environment with flow based on Amiet-IMACS

NASA Astrophysics Data System (ADS)

Wei, Long; Li, Min; Qin, Sheng; Fu, Qiang; Yang, Debin

2017-05-01

A sound source localization method is proposed to localize and analyze the sound source in an environment with airflow. It combines the improved mapping of acoustic correlated sources (IMACS) method and Amiet's method, and is called Amiet-IMACS. It can localize uncorrelated and correlated sound sources with airflow. To implement this approach, Amiet's method is used to correct the sound propagation path in 3D, which improves the accuracy of the array manifold matrix and decreases the position error of the localized source. Then, the mapping of acoustic correlated sources (MACS) method, which is as a high-resolution sound source localization algorithm, is improved by self-adjusting the constraint parameter at each irritation process to increase convergence speed. A sound source localization experiment using a pair of loud speakers in an anechoic wind tunnel under different flow speeds is conducted. The experiment exhibits the advantage of Amiet-IMACS in localizing a more accurate sound source position compared with implementing IMACS alone in an environment with flow. Moreover, the aerodynamic noise produced by a NASA EPPLER 862 STRUT airfoil model in airflow with a velocity of 80 m/s is localized using the proposed method, which further proves its effectiveness in a flow environment. Finally, the relationship between the source position of this airfoil model and its frequency, along with its generation mechanism, is determined and interpreted.

The origin of infrasonic ionosphere oscillations over tropospheric thunderstorms

DOE PAGES

Shao, Xuan -Min; Lay, Erin Hoffmann

2016-07-01

Thunderstorms have been observed to introduce infrasonic oscillations in the ionosphere, but it is not clear what processes or which parts of the thunderstorm generate the oscillations. In this paper, we present a new technique that uses an array of ground-based GPS total electron content (TEC) measurements to locate the source of the infrasonic oscillations and compare the source locations with thunderstorm features to understand the possible source mechanisms. The location technique utilizes instantaneous phase differences between pairs of GPS-TEC measurements and an algorithm to best fit the measured and the expected phase differences for assumed source positions and othermore » related parameters. In this preliminary study, the infrasound waves are assumed to propagate along simple geometric raypaths from the source to the measurement locations to avoid extensive computations. The located sources are compared in time and space with thunderstorm development and lightning activity. Sources are often found near the main storm cells, but they are more likely related to the downdraft process than to the updraft process. As a result, the sources are also commonly found in the convectively quiet stratiform regions behind active cells and are in good coincidence with extensive lightning discharges and inferred high-altitude sprites discharges.« less

The origin of infrasonic ionosphere oscillations over tropospheric thunderstorms

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

Shao, Xuan -Min; Lay, Erin Hoffmann

Thunderstorms have been observed to introduce infrasonic oscillations in the ionosphere, but it is not clear what processes or which parts of the thunderstorm generate the oscillations. In this paper, we present a new technique that uses an array of ground-based GPS total electron content (TEC) measurements to locate the source of the infrasonic oscillations and compare the source locations with thunderstorm features to understand the possible source mechanisms. The location technique utilizes instantaneous phase differences between pairs of GPS-TEC measurements and an algorithm to best fit the measured and the expected phase differences for assumed source positions and othermore » related parameters. In this preliminary study, the infrasound waves are assumed to propagate along simple geometric raypaths from the source to the measurement locations to avoid extensive computations. The located sources are compared in time and space with thunderstorm development and lightning activity. Sources are often found near the main storm cells, but they are more likely related to the downdraft process than to the updraft process. As a result, the sources are also commonly found in the convectively quiet stratiform regions behind active cells and are in good coincidence with extensive lightning discharges and inferred high-altitude sprites discharges.« less

Stacking interactions and DNA intercalation

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

Li, Dr. Shen; Cooper, Valentino R; Thonhauser, Prof. Timo

2009-01-01

The relationship between stacking interactions and the intercalation of proflavine and ellipticine within DNA is investigated using a nonempirical van der Waals density functional for the correlation energy. Our results, employing a binary stack model, highlight fundamental, qualitative differences between base-pair base-pair interactions and that of the stacked intercalator base pair system. Most notable result is the paucity of torque which so distinctively defines the Twist of DNA. Surprisingly, this model, when combined with a constraint on the twist of the surrounding base-pair steps to match the observed unwinding of the sugar-phosphate backbone, was sufficient for explaining the experimentally observedmore » proflavine intercalator configuration. Our extensive mapping of the potential energy surface of base-pair intercalator interactions can provide valuable information for future nonempirical studies of DNA intercalation dynamics.« less

IIPImage: Large-image visualization

NASA Astrophysics Data System (ADS)

Pillay, Ruven

2014-08-01

IIPImage is an advanced high-performance feature-rich image server system that enables online access to full resolution floating point (as well as other bit depth) images at terabyte scales. Paired with the VisiOmatic (ascl:1408.010) celestial image viewer, the system can comfortably handle gigapixel size images as well as advanced image features such as both 8, 16 and 32 bit depths, CIELAB colorimetric images and scientific imagery such as multispectral images. Streaming is tile-based, which enables viewing, navigating and zooming in real-time around gigapixel size images. Source images can be in either TIFF or JPEG2000 format. Whole images or regions within images can also be rapidly and dynamically resized and exported by the server from a single source image without the need to store multiple files in various sizes.

50-GHz-spaced comb of high-dimensional frequency-bin entangled photons from an on-chip silicon nitride microresonator

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

Imany, Poolad; Jaramillo-Villegas, Jose A.; Odele, Ogaga D.

Quantum frequency combs from chip-scale integrated sources are promising candidates for scalable and robust quantum information processing (QIP). However, to use these quantum combs for frequency domain QIP, demonstration of entanglement in the frequency basis, showing that the entangled photons are in a coherent superposition of multiple frequency bins, is required. We present a verification of qubit and qutrit frequency-bin entanglement using an on-chip quantum frequency comb with 40 mode pairs, through a two-photon interference measurement that is based on electro-optic phase modulation. Our demonstrations provide an important contribution in establishing integrated optical microresonators as a source for high-dimensional frequency-binmore » encoded quantum computing, as well as dense quantum key distribution.« less

50-GHz-spaced comb of high-dimensional frequency-bin entangled photons from an on-chip silicon nitride microresonator

DOE PAGES

Imany, Poolad; Jaramillo-Villegas, Jose A.; Odele, Ogaga D.; ...

2018-01-18

Quantum frequency combs from chip-scale integrated sources are promising candidates for scalable and robust quantum information processing (QIP). However, to use these quantum combs for frequency domain QIP, demonstration of entanglement in the frequency basis, showing that the entangled photons are in a coherent superposition of multiple frequency bins, is required. We present a verification of qubit and qutrit frequency-bin entanglement using an on-chip quantum frequency comb with 40 mode pairs, through a two-photon interference measurement that is based on electro-optic phase modulation. Our demonstrations provide an important contribution in establishing integrated optical microresonators as a source for high-dimensional frequency-binmore » encoded quantum computing, as well as dense quantum key distribution.« less

Development and evaluation of a crowdsourcing methodology for knowledge base construction: identifying relationships between clinical problems and medications

PubMed Central

Wright, Adam; Laxmisan, Archana; Ottosen, Madelene J; McCoy, Jacob A; Butten, David; Sittig, Dean F

2012-01-01

Objective We describe a novel, crowdsourcing method for generating a knowledge base of problem–medication pairs that takes advantage of manually asserted links between medications and problems. Methods Through iterative review, we developed metrics to estimate the appropriateness of manually entered problem–medication links for inclusion in a knowledge base that can be used to infer previously unasserted links between problems and medications. Results Clinicians manually linked 231 223 medications (55.30% of prescribed medications) to problems within the electronic health record, generating 41 203 distinct problem–medication pairs, although not all were accurate. We developed methods to evaluate the accuracy of the pairs, and after limiting the pairs to those meeting an estimated 95% appropriateness threshold, 11 166 pairs remained. The pairs in the knowledge base accounted for 183 127 total links asserted (76.47% of all links). Retrospective application of the knowledge base linked 68 316 medications not previously linked by a clinician to an indicated problem (36.53% of unlinked medications). Expert review of the combined knowledge base, including inferred and manually linked problem–medication pairs, found a sensitivity of 65.8% and a specificity of 97.9%. Conclusion Crowdsourcing is an effective, inexpensive method for generating a knowledge base of problem–medication pairs that is automatically mapped to local terminologies, up-to-date, and reflective of local prescribing practices and trends. PMID:22582202

A Pair Production Telescope for Medium-Energy Gamma-Ray Polarimetry

NASA Technical Reports Server (NTRS)

Hunter, Stanley D.; Bloser, Peter F.; Depaola, Gerardo; Dion, Michael P.; DeNolfo, Georgia A.; Hanu, Andrei; Iparraguirre, Marcos; Legere, Jason; Longo, Francesco; McConnell, Mark L.;

Electromagnetic attachment mechanism

NASA Technical Reports Server (NTRS)

Monford, Leo G., Jr. (Inventor)

1992-01-01

An electromagnetic attachment mechanism is disclosed for use as an end effector of a remote manipulator system. A pair of electromagnets, each with a U-shaped magnetic core with a pull-in coil and two holding coils, are mounted by a spring suspension system on a base plate of the mechanism housing with end pole pieces adapted to move through openings in the base plate when the attractive force of the electromagnets is exerted on a strike plate of a grapple fixture affixed to a target object. The pole pieces are spaced by an air gap from the strike plate when the mechanism first contacts the grapple fixture. An individual control circuit and power source is provided for the pull-in coil and one holding coil of each electromagnet. A back-up control circuit connected to the two power sources and a third power source is provided for the remaining holding coils. When energized, the pull-in coils overcome the suspension system and air gap and are automatically de-energized when the pole pieces move to grapple and impose a preload force across the grapple interface. A battery backup is a redundant power source for each electromagnet in each individual control circuit and is automatically connected upon failure of the primary source. A centerline mounted camera and video monitor are used in cooperation with a target pattern on the reflective surface of the strike plate to effect targeting and alignment.

Acuity of a Cryptochrome and Vision-Based Magnetoreception System in Birds

PubMed Central

Solov'yov, Ilia A.; Mouritsen, Henrik; Schulten, Klaus

2010-01-01

Abstract The magnetic compass of birds is embedded in the visual system and it has been hypothesized that the primary sensory mechanism is based on a radical pair reaction. Previous models of magnetoreception have assumed that the radical pair-forming molecules are rigidly fixed in space, and this assumption has been a major objection to the suggested hypothesis. In this article, we investigate theoretically how much disorder is permitted for the radical pair-forming, protein-based magnetic compass in the eye to remain functional. Our study shows that only one rotational degree of freedom of the radical pair-forming protein needs to be partially constrained, while the other two rotational degrees of freedom do not impact the magnetoreceptive properties of the protein. The result implies that any membrane-associated protein is sufficiently restricted in its motion to function as a radical pair-based magnetoreceptor. We relate our theoretical findings to the cryptochromes, currently considered the likeliest candidate to furnish radical pair-based magnetoreception. PMID:20655831

Inhomogeneous ensembles of radical pairs in chemical compasses

PubMed Central

Procopio, Maria; Ritz, Thorsten

2016-01-01

The biophysical basis for the ability of animals to detect the geomagnetic field and to use it for finding directions remains a mystery of sensory biology. One much debated hypothesis suggests that an ensemble of specialized light-induced radical pair reactions can provide the primary signal for a magnetic compass sensor. The question arises what features of such a radical pair ensemble could be optimized by evolution so as to improve the detection of the direction of weak magnetic fields. Here, we focus on the overlooked aspect of the noise arising from inhomogeneity of copies of biomolecules in a realistic biological environment. Such inhomogeneity leads to variations of the radical pair parameters, thereby deteriorating the signal arising from an ensemble and providing a source of noise. We investigate the effect of variations in hyperfine interactions between different copies of simple radical pairs on the directional response of a compass system. We find that the choice of radical pair parameters greatly influences how strongly the directional response of an ensemble is affected by inhomogeneity. PMID:27804956

Inhomogeneous ensembles of radical pairs in chemical compasses

NASA Astrophysics Data System (ADS)

Procopio, Maria; Ritz, Thorsten

2016-11-01

The biophysical basis for the ability of animals to detect the geomagnetic field and to use it for finding directions remains a mystery of sensory biology. One much debated hypothesis suggests that an ensemble of specialized light-induced radical pair reactions can provide the primary signal for a magnetic compass sensor. The question arises what features of such a radical pair ensemble could be optimized by evolution so as to improve the detection of the direction of weak magnetic fields. Here, we focus on the overlooked aspect of the noise arising from inhomogeneity of copies of biomolecules in a realistic biological environment. Such inhomogeneity leads to variations of the radical pair parameters, thereby deteriorating the signal arising from an ensemble and providing a source of noise. We investigate the effect of variations in hyperfine interactions between different copies of simple radical pairs on the directional response of a compass system. We find that the choice of radical pair parameters greatly influences how strongly the directional response of an ensemble is affected by inhomogeneity.

A structural determinant in the uracil DNA glycosylase superfamily for the removal of uracil from adenine/uracil base pairs

PubMed Central

Lee, Dong-Hoon; Liu, Yinling; Lee, Hyun-Wook; Xia, Bo; Brice, Allyn R.; Park, Sung-Hyun; Balduf, Hunter; Dominy, Brian N.; Cao, Weiguo

2015-01-01

The uracil DNA glycosylase superfamily consists of several distinct families. Family 2 mismatch-specific uracil DNA glycosylase (MUG) from Escherichia coli is known to exhibit glycosylase activity on three mismatched base pairs, T/U, G/U and C/U. Family 1 uracil N-glycosylase (UNG) from E. coli is an extremely efficient enzyme that can remove uracil from any uracil-containing base pairs including the A/U base pair. Here, we report the identification of an important structural determinant that underlies the functional difference between MUG and UNG. Substitution of a Lys residue at position 68 with Asn in MUG not only accelerates the removal of uracil from mismatched base pairs but also enables the enzyme to gain catalytic activity on A/U base pairs. Binding and kinetic analysis demonstrate that the MUG-K68N substitution results in enhanced ground state binding and transition state interactions. Molecular modeling reveals that MUG-K68N, UNG-N123 and family 5 Thermus thermophiles UDGb-A111N can form bidentate hydrogen bonds with the N3 and O4 moieties of the uracil base. Genetic analysis indicates the gain of function for A/U base pairs allows the MUG-K68N mutant to remove uracil incorporated into the genome during DNA replication. The implications of this study in the origin of life are discussed. PMID:25550433

Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop.

PubMed Central

van Dongen, M J; Mooren, M M; Willems, E F; van der Marel, G A; van Boom, J H; Wijmenga, S S; Hilbers, C W

1997-01-01

The three-dimensional structure of the hairpin formed by d(ATCCTA-GTTA-TAGGAT) has been determined by means of two-dimensional NMR studies, distance geometry and molecular dynamics calculations. The first and the last residues of the tetraloop of this hairpin form a sheared G-A base pair on top of the six Watson-Crick base pairs in the stem. The glycosidic torsion angles of the guanine and adenine residues in the G-A base pair reside in the anti and high- anti domain ( approximately -60 degrees ) respectively. Several dihedral angles in the loop adopt non-standard values to accommodate this base pair. The first and second residue in the loop are stacked in a more or less normal helical fashion; the fourth loop residue also stacks upon the stem, while the third residue is directed away from the loop region. The loop structure can be classified as a so-called type-I loop, in which the bases at the 5'-end of the loop stack in a continuous fashion. In this situation, loop stability is unlikely to depend heavily on the nature of the unpaired bases in the loop. Moreover, the present study indicates that the influence of the polarity of a closing A.T pair is much less significant than that of a closing C.G base pair. PMID:9092659

Chromatographic and computational assessment of lipophilicity using sum of ranking differences and generalized pair-correlation.

PubMed

Andrić, Filip; Héberger, Károly

2015-02-06

Lipophilicity (logP) represents one of the most studied and most frequently used fundamental physicochemical properties. At present there are several possibilities for its quantitative expression and many of them stems from chromatographic experiments. Numerous attempts have been made to compare different computational methods, chromatographic methods vs. computational approaches, as well as chromatographic methods and direct shake-flask procedure without definite results or these findings are not accepted generally. In the present work numerous chromatographically derived lipophilicity measures in combination with diverse computational methods were ranked and clustered using the novel variable discrimination and ranking approaches based on the sum of ranking differences and the generalized pair correlation method. Available literature logP data measured on HILIC, and classical reversed-phase combining different classes of compounds have been compared with most frequently used multivariate data analysis techniques (principal component and hierarchical cluster analysis) as well as with the conclusions in the original sources. Chromatographic lipophilicity measures obtained under typical reversed-phase conditions outperform the majority of computationally estimated logPs. Oppositely, in the case of HILIC none of the many proposed chromatographic indices overcomes any of the computationally assessed logPs. Only two of them (logkmin and kmin) may be selected as recommended chromatographic lipophilicity measures. Both ranking approaches, sum of ranking differences and generalized pair correlation method, although based on different backgrounds, provides highly similar variable ordering and grouping leading to the same conclusions. Copyright © 2015. Published by Elsevier B.V.

Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions.

PubMed

Miyoshi, Daisuke; Nakamura, Kaori; Tateishi-Karimata, Hisae; Ohmichi, Tatsuo; Sugimoto, Naoki

2009-03-18

It has been revealed recently that molecular crowding, which is one of the largest differences between in vivo and in vitro conditions, is a critical factor determining the structure, stability, and function of nucleic acids. However, the effects of molecular crowding on Watson-Crick and Hoogsteen base pairs remain unclear. In order to investigate directly and quantitatively the molecular crowding effects on base pair types in nucleic acids, we designed intramolecular parallel- and antiparallel-stranded DNA duplexes consisting of Hoogsteen and Watson-Crick base pairs, respectively, as well as an intramolecular parallel-stranded triplex containing both types of base pairs. Thermodynamic analyses demonstrated that the values of free energy change at 25 degrees C for Hoogsteen base-pair formations decreased from +1.45 +/- 0.15 to +1.09 +/- 0.13 kcal mol(-1), and from -1.89 +/- 0.13 to -2.71 +/- 0.11 kcal mol(-1) in the intramolecular duplex and triplex, respectively, when the concentration of PEG 200 (polyethylene glycol with average molecular weight 200) increased from 0 to 20 wt %. However, corresponding values for Watson-Crick formation in the duplex and triplex increased from -10.2 +/- 0.2 to -8.7 +/- 0.1 kcal mol(-1), and from -10.8 +/- 0.2 to -9.2 +/- 0.2 kcal mol(-1), respectively. Furthermore, it was revealed that the opposing effects of molecular crowding on the Hoogsteen and Watson-Crick base pairs were due to different behaviors of water molecules binding to the DNA strands.

Generalized quantum interference of correlated photon pairs

PubMed Central

Kim, Heonoh; Lee, Sang Min; Moon, Han Seb

2015-01-01

Superposition and indistinguishablility between probability amplitudes have played an essential role in observing quantum interference effects of correlated photons. The Hong-Ou-Mandel interference and interferences of the path-entangled photon number state are of special interest in the field of quantum information technologies. However, a fully generalized two-photon quantum interferometric scheme accounting for the Hong-Ou-Mandel scheme and path-entangled photon number states has not yet been proposed. Here we report the experimental demonstrations of the generalized two-photon interferometry with both the interferometric properties of the Hong-Ou-Mandel effect and the fully unfolded version of the path-entangled photon number state using photon-pair sources, which are independently generated by spontaneous parametric down-conversion. Our experimental scheme explains two-photon interference fringes revealing single- and two-photon coherence properties in a single interferometer setup. Using the proposed interferometric measurement, it is possible to directly estimate the joint spectral intensity of a photon pair source. PMID:25951143

The effects of rice canopy on the air-soil exchange of polycyclic aromatic hydrocarbons and organochlorine pesticides using paired passive air samplers.

PubMed

Wang, Yan; Wang, Shaorui; Luo, Chunling; Li, Jun; Ming, Lili; Zhang, Gan; Li, Xiangdong

2015-05-01

The rice canopy in paddy fields can influence the air-soil exchange of organic chemicals. We used paired passive air samplers to assess the exchange of polycyclic aromatic hydrocarbons (PAHs) and organochlorine pesticides (OCPs) in a paddy field, South China. Levels of OCPs and light PAHs were generally higher under the canopy than above it. We found that the rice canopy can physically obstruct the evaporation of most OCPs and light PAHs, and can also act as a barrier to the gaseous deposition of p,p'-DDT and heavy PAHs. Paddy fields can behave as a secondary source of OCPs and light PAHs. The homolog patterns of these two types of chemical varied slightly between the air below and above the rice canopy, implying contributions of different sources. Paired passive air samplers can be used effectively to assess the in situ air-soil exchange of PAHs and OCPs in subtropical paddy fields. Copyright © 2015 Elsevier Ltd. All rights reserved.

Matter-wave entanglement and teleportation by molecular dissociation and collisions.

PubMed

Opatrný, T; Kurizki, G

2001-04-02

We propose dissociation of cold diatomic molecules as a source of atom pairs with highly correlated (entangled) positions and momenta, approximating the original quantum state introduced by Einstein, Podolsky, and Rosen (EPR) [Phys. Rev. 47, 777 (1935)]. Wave packet teleportation is shown to be achievable by its collision with one of the EPR correlated atoms and manipulation of the other atom in the pair.

Matter-Wave Entanglement and Teleportation by Molecular Dissociation and Collisions

NASA Astrophysics Data System (ADS)

Opatrný, T.; Kurizki, G.

2001-04-01

We propose dissociation of cold diatomic molecules as a source of atom pairs with highly correlated (entangled) positions and momenta, approximating the original quantum state introduced by Einstein, Podolsky, and Rosen (EPR) [Phys. Rev. 47, 777 (1935)]. Wave packet teleportation is shown to be achievable by its collision with one of the EPR correlated atoms and manipulation of the other atom in the pair.

Penrose pair production as a power source of quasars and active galactic nuclei. [black hole mechanisms

NASA Technical Reports Server (NTRS)

Kafatos, M.; Leiter, D.

1979-01-01

Penrose pair production in massive canonical Kerr black holes (those with a/M equal to 0.998) is proposed as a way to explain the nature of the vast fluctuating energy production associated with active galactic nuclei and quasars. It is assumed that a Kerr black hole with a mass of the order of 100 million solar masses lies at the center of an active nucleus and that an accretion disk is formed. Penrose pair production in the inner ergosphere of such a massive canonical Kerr black hole is analyzed. The results indicate that: (1) particle pairs are ejected within a 40 deg angle relative to the equator; (2) the particle energy is of the order of 1 GeV per pair; (3) the pressure of the electron-positron relativistic gas is proportional to the electron-positron number density; (4) pair production may occur in bursts; and (5) the overall lifetime of an active nucleus would depend on the time required to exhaust the disk of its matter content. A test of the theory is suggested which involves observation of the 0.5-MeV pair-annihilation gamma rays that would be generated by annihilating particle pairs.

Mid-infrared coincidence measurements based on intracavity frequency conversion

NASA Astrophysics Data System (ADS)

Piccione, S.; Mancinelli, M.; Trenti, A.; Fontana, G.; Dam, J.; Tidemand-Lichtenberg, P.; Pedersen, C.; Pavesi, L.

2018-02-01

In the last years, the Mid Infrared (MIR) spectral region has attracted the attention of many areas of science and technology, opening the way to important applications, such as molecular imaging, remote sensing, free- space communication and environmental monitoring. However, the development of new sources of light, such as quantum cascade laser, was not followed by an adequate improvement in the MIR detection system, able to exceed the current challenges. Here we demonstrate the single-photon counting capability of a new detection system, based on efficient up-converter modules, by proving the correlated nature of twin photons pairs at about 3.1μm, opening the way to the extension of quantum optics experiments in the MIR.

Three-dimensional axisymmetric sources for Majumdar-Papapetrou type spacetimes

NASA Astrophysics Data System (ADS)

García-Reyes, Gonzalo; Hernández-Gómez, Kevin A.

From Newtonian potential-density pairs, we construct three-dimensional axisymmetric relativistic sources for a Majumdar-Papapetrou type conformastatic spacetime. As simple examples, we build two families of relativistic thick disks from the first two Miyamoto-Nagai potential-density pairs used in Newtonian gravity to model flat galaxies, and a three-component relativistic model of galaxy (bulge, disk and dark matter halo). We study the equatorial circular motion of test particles around such structures. Also the stability of the orbits is analyzed for radial perturbation using an extension of the Rayleigh criterion. In all examples, the relativistic effects are analyzed and compared with the Newtonian approximation. The models are considered satisfying all the energy conditions.

Method and an apparatus for non-invasively determining the quantity of an element in a body organ

DOEpatents

Vartsky, D.; Ellis, K.J.; Cohn, S.H.

1980-06-27

An apparatus and a method for determining in a body organ the amount of an element with the aid of a gaseous gamma ray source, where the element and the source are paired in predetermined pairs, and with the aid of at least one detector selected from the group consisting of Ge(Li) and NaI(Tl). Gamma rays are directed towards the organ, thereby resonantly scattering the gamma rays from nuclei of the element in the organ; the intensity of the gamma rays is detected by the detector; and the amount of the element in the organ is then substantially proportional to the detected intensity of the gamma rays.

Theory of nodal s ±-wave pairing symmetry in the Pu-based 115 superconductor family

DOE PAGES

Das, Tanmoy; Zhu, Jian -Xin; Graf, Matthias J.

2015-02-27

The spin-fluctuation mechanism of superconductivity usually results in the presence of gapless or nodal quasiparticle states in the excitation spectrum. Nodal quasiparticle states are well established in copper-oxide, and heavy-fermion superconductors, but not in iron-based superconductors. Here, we study the pairing symmetry and mechanism of a new class of plutonium-based high-T c superconductors and predict the presence of a nodal s⁺⁻ wave pairing symmetry in this family. Starting from a density-functional theory (DFT) based electronic structure calculation we predict several three-dimensional (3D) Fermi surfaces in this 115 superconductor family. We identify the dominant Fermi surface “hot-spots” in the inter-band scatteringmore » channel, which are aligned along the wavevector Q = (π, π, π), where degeneracy could induce sign-reversal of the pairing symmetry. Our calculation demonstrates that the s⁺⁻ wave pairing strength is stronger than the previously thought d-wave pairing; and more importantly, this pairing state allows for the existence of nodal quasiparticles. Finally, we predict the shape of the momentum- and energy-dependent magnetic resonance spectrum for the identification of this pairing symmetry.« less

A NEW METHOD FOR FINDING POINT SOURCES IN HIGH-ENERGY NEUTRINO DATA

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

Fang, Ke; Miller, M. Coleman

The IceCube collaboration has reported the first detection of high-energy astrophysical neutrinos, including ∼50 high-energy starting events, but no individual sources have been identified. It is therefore important to develop the most sensitive and efficient possible algorithms to identify the point sources of these neutrinos. The most popular current method works by exploring a dense grid of possible directions to individual sources, and identifying the single direction with the maximum probability of having produced multiple detected neutrinos. This method has numerous strengths, but it is computationally intensive and because it focuses on the single best location for a point source,more » additional point sources are not included in the evidence. We propose a new maximum likelihood method that uses the angular separations between all pairs of neutrinos in the data. Unlike existing autocorrelation methods for this type of analysis, which also use angular separations between neutrino pairs, our method incorporates information about the point-spread function and can identify individual point sources. We find that if the angular resolution is a few degrees or better, then this approach reduces both false positive and false negative errors compared to the current method, and is also more computationally efficient up to, potentially, hundreds of thousands of detected neutrinos.« less

Rotational-translational fourier imaging system requiring only one grid pair

NASA Technical Reports Server (NTRS)

Campbell, Jonathan W. (Inventor)

2006-01-01

The sky contains many active sources that emit X-rays, gamma rays, and neutrons. Unfortunately hard X-rays, gamma rays, and neutrons cannot be imaged by conventional optics. This obstacle led to the development of Fourier imaging systems. In early approaches, multiple grid pairs were necessary in order to create rudimentary Fourier imaging systems. At least one set of grid pairs was required to provide multiple real components of a Fourier derived image, and another set was required to provide multiple imaginary components of the image. It has long been recognized that the expense associated with the physical production of the numerous grid pairs required for Fourier imaging was a drawback. Herein one grid pair (two grids), with accompanying rotation and translation, can be used if one grid has one more slit than the other grid, and if the detector is modified.

Simulation Study of Magnetic Fields Generated by the Electromagnetic Filamentation Instability

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Ramirez-Ruiz, E.; Hardee, P.; Hededal, C. B.; Mizuno, Y.; Fishman, G. J.

2007-01-01

We have investigated the effects of plasma instabilities driven by rapid e(sup plus or minus) pair cascades, which arise in the environment of GRB sources as a result of back-scattering of a seed fraction of the original spectrum. The injection of e(sup plus or minus) pairs induces strong streaming motions in the ambient medium. One therefore expects the pair-enriched medium ahead of the forward shock to be strongly sheared on length scales comparable to the radiation front thickness. Using three-dimensional particle-in-cell simulations, we show that plasma instabilities driven by these streaming e(sup plus or minus) pairs are responsible for the excitation of near-equipartition, turbulent magnetic fields. Our results reveal the importance of the electromagnetic filamentation instability in ensuring an effective coupling between e(sup plus or minus) pairs and ions, and may help explain the origin of large upstream fields in GRB shocks.

Growth properties associated with A-U replacement of specific G-C base pairs in 16S rRNA from Escherichia coli.

PubMed Central

Triman, K L

1995-01-01

Mutations that disrupt each of seven specific G-C base pairs in 16S rRNA from Escherichia coli confer loss of expression of a plasmid-encoded 16S rRNA selectable marker (spectinomycin resistance). However, A-U replacement of G-C base pairs at nucleotides 359/52 or 1292/1245 in 16S rRNA permits normal expression of the marker. By contrast, A-U replacements at 146/176, 153/168, 350/339, or 1293/1244 are associated with loss of expression of the marker. These genetic studies are designed to determine the importance of specific base pairs by assessment of the structural and functional impairments of 16S rRNA molecules resulting from expression of base pair substitutions at these positions. PMID:7543481

Experimental demonstration of wavelength domain rogue-free ONU based on wavelength-pairing for TDM/WDM optical access networks.

PubMed

Lee, Jie Hyun; Park, Heuk; Kang, Sae-Kyoung; Lee, Joon Ki; Chung, Hwan Seok

2015-11-30

In this study, we propose and experimentally demonstrate a wavelength domain rogue-free ONU based on wavelength-pairing of downstream and upstream signals for time/wavelength division-multiplexed optical access networks. The wavelength-pairing tunable filter is aligned to the upstream wavelength channel by aligning it to one of the downstream wavelength channels. Wavelength-pairing is implemented with a compact and cyclic Si-AWG integrated with a Ge-PD. The pairing filter covered four 100 GHz-spaced wavelength channels. The feasibility of the wavelength domain rogue-free operation is investigated by emulating malfunction of the misaligned laser. The wavelength-pairing tunable filter based on the Si-AWG blocks the upstream signal in the non-assigned wavelength channel before data collision with other ONUs.

Orbital selective pairing and gap structures of iron-based superconductors

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

Kreisel, Andreas; Andersen, Brian M.; Sprau, P. O.

We discuss the in uence on spin-fluctuation pairing theory of orbital selective strong correlation effects in Fe-based superconductors, particularly Fe chalcogenide systems. We propose that a key ingredient for an improved itinerant pairing theory is orbital selectivity, i.e., incorporating the reduced coherence of quasiparticles occupying specific orbital states. This modifies the usual spin-fluctuation via suppression of pair scattering processes involving those less coherent states and results in orbital selective Cooper pairing of electrons in the remaining states. We show that this paradigm yields remarkably good agreement with the experimentally observed anisotropic gap structures in both bulk and monolayer FeSe, asmore » well as LiFeAs, indicating that orbital selective Cooper pairing plays a key role in the more strongly correlated iron-based superconductors.« less

Orbital selective pairing and gap structures of iron-based superconductors

DOE PAGES

Kreisel, Andreas; Andersen, Brian M.; Sprau, P. O.; ...

2017-05-08

We discuss the in uence on spin-fluctuation pairing theory of orbital selective strong correlation effects in Fe-based superconductors, particularly Fe chalcogenide systems. We propose that a key ingredient for an improved itinerant pairing theory is orbital selectivity, i.e., incorporating the reduced coherence of quasiparticles occupying specific orbital states. This modifies the usual spin-fluctuation via suppression of pair scattering processes involving those less coherent states and results in orbital selective Cooper pairing of electrons in the remaining states. We show that this paradigm yields remarkably good agreement with the experimentally observed anisotropic gap structures in both bulk and monolayer FeSe, asmore » well as LiFeAs, indicating that orbital selective Cooper pairing plays a key role in the more strongly correlated iron-based superconductors.« less

Acid-induced exchange of the imino proton in G.C pairs.

PubMed Central

Nonin, S; Leroy, J L; Gueron, M

1996-01-01

Acid-induced catalysis of imino proton exchange in G.C pairs of DNA duplexes is surprisingly fast, being nearly as fast as for the isolated nucleoside, despite base-pair dissociation constants in the range of 10(-5) at neutral or basic pH. It is also observed in terminal G.C pairs of duplexes and in base pairs of drug-DNA complexes. We have measured imino proton exchange in deoxyguanosine and in the duplex (ATATAGATCTATAT) as a function of pH. We show that acid-induced exchange can be assigned to proton transfer from N7-protonated guanosine to cytidine in the open state of the pair. This is faster than transfer from neutral guanosine (the process of intrinsic catalysis previously characterized at neutral ph) due to the lower imino proton pK of the protonated form, 7.2 instead of 9.4. Other interpretations are excluded by a study of exchange catalysis by formiate and cytidine as exchange catalysts. The cross-over pH between the regimes of pH-independent and acid-induced exchange rates is more basic in the case of base pairs than in the mononucleoside, suggestive of an increase by one to two decades in the dissociation constant of the base pair upon N7 protonation of G. Acid-induced catalysis is much weaker in A.T base pairs, as expected in view of the low pK for protonation of thymidine. PMID:8604298

Acid-induced exchange of the imino proton in G.C pairs.

PubMed

Nonin, S; Leroy, J L; Gueron, M

1996-02-15

Acid-induced catalysis of imino proton exchange in G.C pairs of DNA duplexes is surprisingly fast, being nearly as fast as for the isolated nucleoside, despite base-pair dissociation constants in the range of 10(-5) at neutral or basic pH. It is also observed in terminal G.C pairs of duplexes and in base pairs of drug-DNA complexes. We have measured imino proton exchange in deoxyguanosine and in the duplex (ATATAGATCTATAT) as a function of pH. We show that acid-induced exchange can be assigned to proton transfer from N7-protonated guanosine to cytidine in the open state of the pair. This is faster than transfer from neutral guanosine (the process of intrinsic catalysis previously characterized at neutral ph) due to the lower imino proton pK of the protonated form, 7.2 instead of 9.4. Other interpretations are excluded by a study of exchange catalysis by formiate and cytidine as exchange catalysts. The cross-over pH between the regimes of pH-independent and acid-induced exchange rates is more basic in the case of base pairs than in the mononucleoside, suggestive of an increase by one to two decades in the dissociation constant of the base pair upon N7 protonation of G. Acid-induced catalysis is much weaker in A.T base pairs, as expected in view of the low pK for protonation of thymidine.

Methods, systems, and apparatus for storage, transfer and/or control of information via matter wave dynamics

NASA Technical Reports Server (NTRS)

Vestergaard Hau, Lene (Inventor)

2012-01-01

Methods, systems and apparatus for generating atomic traps, and for storing, controlling and transferring information between first and second spatially separated phase-coherent objects, or using a single phase-coherent object. For plural objects, both phase-coherent objects have a macroscopic occupation of a particular quantum state by identical bosons or identical BCS-paired fermions. The information may be optical information, and the phase-coherent object(s) may be Bose-Einstein condensates, superfluids, or superconductors. The information is stored in the first phase-coherent object at a first storage time and recovered from the second phase-coherent object, or the same first phase-coherent object, at a second revival time. In one example, an integrated silicon wafer-based optical buffer includes an electrolytic atom source to provide the phase-coherent object(s), a nanoscale atomic trap for the phase-coherent object(s), and semiconductor-based optical sources to cool the phase-coherent object(s) and provide coupling fields for storage and transfer of optical information.

MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud.

PubMed

Expósito, Roberto R; Veiga, Jorge; González-Domínguez, Jorge; Touriño, Juan

2017-09-01

This article presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single- and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted MapReduce programming model to fully exploit Big Data technologies on cloud-based infrastructures. Written in Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for scalable Big Data processing. On a 16-node cluster deployed on the Amazon EC2 cloud platform, MarDRe is up to 8.52 times faster than a representative state-of-the-art tool. Source code in Java and Hadoop as well as a user's guide are freely available under the GNU GPLv3 license at http://mardre.des.udc.es . rreye@udc.es. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Photochemical grid model performance with varying horizontal grid resolution and sub-grid plume treatment for the Martins Creek near-field SO2 study

NASA Astrophysics Data System (ADS)

Baker, Kirk R.; Hawkins, Andy; Kelly, James T.

2014-12-01

Near source modeling is needed to assess primary and secondary pollutant impacts from single sources and single source complexes. Source-receptor relationships need to be resolved from tens of meters to tens of kilometers. Dispersion models are typically applied for near-source primary pollutant impacts but lack complex photochemistry. Photochemical models provide a realistic chemical environment but are typically applied using grid cell sizes that may be larger than the distance between sources and receptors. It is important to understand the impacts of grid resolution and sub-grid plume treatments on photochemical modeling of near-source primary pollution gradients. Here, the CAMx photochemical grid model is applied using multiple grid resolutions and sub-grid plume treatment for SO2 and compared with a receptor mesonet largely impacted by nearby sources approximately 3-17 km away in a complex terrain environment. Measurements are compared with model estimates of SO2 at 4- and 1-km resolution, both with and without sub-grid plume treatment and inclusion of finer two-way grid nests. Annual average estimated SO2 mixing ratios are highest nearest the sources and decrease as distance from the sources increase. In general, CAMx estimates of SO2 do not compare well with the near-source observations when paired in space and time. Given the proximity of these sources and receptors, accuracy in wind vector estimation is critical for applications that pair pollutant predictions and observations in time and space. In typical permit applications, predictions and observations are not paired in time and space and the entire distributions of each are directly compared. Using this approach, model estimates using 1-km grid resolution best match the distribution of observations and are most comparable to similar studies that used dispersion and Lagrangian modeling systems. Model-estimated SO2 increases as grid cell size decreases from 4 km to 250 m. However, it is notable that the 1-km model estimates using 1-km meteorological model input are higher than the 1-km model simulation that used interpolated 4-km meteorology. The inclusion of sub-grid plume treatment did not improve model skill in predicting SO2 in time and space and generally acts to keep emitted mass aloft.

Maser mechanism of optical pulsations from anomalous X-ray pulsar 4U 0142+61

NASA Astrophysics Data System (ADS)

Lu, Y.; Zhang, S. N.

2004-11-01

Based on the work of Luo & Melrose from the early 1990s, a maser curvature emission mechanism in the presence of curvature drift is used to explain the optical pulsations from anomalous X-ray pulsars (AXPs). The model comprises a rotating neutron star with a strong surface magnetic field, i.e. a magnetar. Assuming the space-charge-limited flow acceleration mechanism, in which the strongly magnetized neutron star induces strong electric fields that pull the charges from its surface and flow along the open field lines, the neutron star generates a dense flow of electrons and positrons (relativistic pair plasma) by either two-photon pair production or one-photon pair creation resulting from inverse Compton scattering of the thermal photons above the pulsar polar cap (PC). The motion of the pair plasma is essentially one-dimensional along the field lines. We propose that optical pulsations from AXPs are generated by a curvature-drift-induced maser developing in the PC of magnetars. Pair plasma is considered as an active medium that can amplify its normal modes. The curvature drift, which is energy-dependent, is another essential ingredient in allowing negative absorption (maser action) to occur. For the source AXP 4U 0142+61, we find that the optical pulsation triggered by curvature-drift maser radiation occurs at the radial distance R(νM) ~ 4.75 × 109 cm to the neutron star. The corresponding curvature maser frequency is about νM~ 1.39 × 1014 Hz, and the pulse component from the maser amplification is about 27 per cent. The result is consistent with the observation of the optical pulsations from AXP 4U 0142+61.

A sibling based design to quantify genetic and shared environmental effects of venous thromboembolism in Sweden.

PubMed

Zöller, Bengt; Ohlsson, Henrik; Sundquist, Jan; Sundquist, Kristina

2017-01-01

Few large studies have examined the heritability of venous thromboembolism (VTE). Moreover, twin studies have been suggested to overestimate heritability. The aim of the present study was to determine the heritability nationwide in the general Swedish population using full siblings and half-siblings. VTE was defined using the Swedish patient register. Full sibling (FS) and half-sibling (HS) pairs born 1950-1990 were obtained from the Swedish Multi-generation Register. A maximum of 5years age difference was allowed. We also required that the individuals within the pair should reside in the same household for at least 8years or not at all (0years) before the youngest turned 16. Information about sibling pair residence within the same household, small residential area, and municipality was obtained from Statistics Sweden. We assumed three potential sources of liability to VTE: additive genetic (A), shared (or common/familial) environment (C), and unique environment (E) components. Totally 881,206 FS pairs and 95,198 HS pairs were included. The full model predicted heritability for VTE with 47% for males and 40% for females. Environmental factors shared by siblings contributed to 0% of the variance in liability for both sexes, and unique environment (E) components accounted for 53% in males and 60% in females. The high heritability of VTE risk indicates that genetic susceptibility plays a substantial role for VTE in the Swedish general population. Overestimation of heritability from twin studies is not likely. The proportion of the variance attributable to shared familial environment factors is small. Subject codes: Genetics, epidemiology, thrombosis, cardiovascular disease, embolism. Copyright © 2016 Elsevier Ltd. All rights reserved.

Base pairing among three cis-acting sequences contributes to template switching during hepadnavirus reverse transcription.

PubMed

Liu, Ning; Tian, Ru; Loeb, Daniel D

2003-02-18

Synthesis of the relaxed-circular (RC) DNA genome of hepadnaviruses requires two template switches during plus-strand DNA synthesis: primer translocation and circularization. Although primer translocation and circularization use different donor and acceptor sequences, and are distinct temporally, they share the common theme of switching from one end of the minus-strand template to the other end. Studies of duck hepatitis B virus have indicated that, in addition to the donor and acceptor sequences, three other cis-acting sequences, named 3E, M, and 5E, are required for the synthesis of RC DNA by contributing to primer translocation and circularization. The mechanism by which 3E, M, and 5E act was not known. We present evidence that these sequences function by base pairing with each other within the minus-strand template. 3E base-pairs with one portion of M (M3) and 5E base-pairs with an adjacent portion of M (M5). We found that disrupting base pairing between 3E and M3 and between 5E and M5 inhibited primer translocation and circularization. More importantly, restoring base pairing with mutant sequences restored the production of RC DNA. These results are consistent with the model that, within duck hepatitis B virus capsids, the ends of the minus-strand template are juxtaposed via base pairing to facilitate the two template switches during plus-strand DNA synthesis.

Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif.

PubMed

Cojocaru, Vlad; Klement, Reinhard; Jovin, Thomas M

2005-01-01

Upon binding to the 15.5K protein, two tandem-sheared G-A base pairs are formed in the internal loop of the kink-turn motif of U4 snRNA (Kt-U4). We have reported that the folding of Kt-U4 is assisted by protein binding. Unstable interactions that contribute to a large opening of the free RNA ('k-e motion') were identified using locally enhanced sampling molecular dynamics simulations, results that agree with experiments. A detailed analysis of the simulations reveals that the k-e motion in Kt-U4 is triggered both by loss of G-A base pairs in the internal loop and backbone flexibility in the stems. Essential dynamics show that the loss of G-A base pairs is correlated along the first mode but anti-correlated along the third mode with the k-e motion. Moreover, when enhanced sampling was confined to the internal loop, the RNA adopted an alternative conformation characterized by a sharper kink, opening of G-A base pairs and modified stacking interactions. Thus, loss of G-A base pairs is insufficient for achieving a large opening of the free RNA. These findings, supported by previously published RNA structure probing experiments, suggest that G-A base pair formation occurs upon protein binding, thereby stabilizing a selective orientation of the stems.

Semivolatile Endocrine-Disrupting Compounds in Paired Indoor and Outdoor Air in Two Northern California Communities

PubMed Central

2010-01-01

Interest in the health effects of potential endocrine-disrupting compounds (EDCs) that are high production volume chemicals used in consumer products has made exposure assessment and source identification a priority. We collected paired indoor and outdoor air samples in 40 nonsmoking homes in urban, industrial Richmond, CA, and 10 in rural Bolinas, CA. Samples were analyzed by GC-MS for 104 analytes, including phthalates (11), alkylphenols (3), parabens (3), polybrominated diphenyl ether (PBDE) flame retardants (3), polychlorinated biphenyls (PCBs) (3), polycyclic aromatic hydrocarbons (PAHs) (24), pesticides (38), and phenolic compounds (19). We detected 39 analytes in outdoor air and 63 in indoor air. For many of the phenolic compounds, alkylphenols, phthalates, and PBDEs, these represent some of the first outdoor measures and the first analysis of the relative importance of indoor and outdoor sources in paired samples. Data demonstrate higher indoor concentrations for 32 analytes, suggesting primarily indoor sources, as compared with only 2 that were higher outdoors. Outdoor air concentrations were higher in Richmond than Bolinas for 3 phthalates, 10 PAHs, and o-phenylphenol, while indoor air levels were more similar between communities, except that differences observed outdoors were also seen indoors. Indoor concentrations of the most ubiquitous chemicals were generally correlated with each other (4-t-butylphenol, o-phenylphenol, nonylphenol, several phthalates, and methyl phenanthrenes; Kendall correlation coefficients 0.2−0.6, p < 0.05), indicating possible shared sources and highlighting the importance of considering mixtures in health studies. PMID:20681565

A plausible energy source and structure for quasi-stellar objects

NASA Technical Reports Server (NTRS)

Daltabuit, E.; Cox, D.

1972-01-01

If a collision of two large, massive, fast gas clouds occurs, their kinetic energy is converted to radiation in a pair of shock fronts at their interface. The resulting structure is described, and the relevance of this as a radiation source for quasi-stellar objects is considered.

Hydride heat pump

DOEpatents

Cottingham, James G.

1977-01-01

Method and apparatus for the use of hydrides to exhaust heat from one temperature source and deliver the thermal energy extracted for use at a higher temperature, thereby acting as a heat pump. For this purpose there are employed a pair of hydridable metal compounds having different characteristics working together in a closed pressure system employing a high temperature source to upgrade the heat supplied from a low temperature source.

Quasars Probing Quasars. X. The Quasar Pair Spectral Database

NASA Astrophysics Data System (ADS)

Findlay, Joseph R.; Prochaska, J. Xavier; Hennawi, Joseph F.; Fumagalli, Michele; Myers, Adam D.; Bartle, Stephanie; Chehade, Ben; DiPompeo, Michael A.; Shanks, Tom; Lau, Marie Wingyee; Rubin, Kate H. R.

2018-06-01

The rare close projection of two quasars on the sky provides the opportunity to study the host galaxy environment of a foreground quasar in absorption against the continuum emission of a background quasar. For over a decade the “Quasars probing quasars” series has utilized this technique to further the understanding of galaxy formation and evolution in the presence of a quasar at z > 2, resolving scales as small as a galactic disk and from bound gas in the circumgalactic medium to the diffuse environs of intergalactic space. Presented here is the public release of the quasar pair spectral database utilized in these studies. In addition to projected pairs at z > 2, the database also includes quasar pair members at z < 2, gravitational lens candidates, and quasars closely separated in redshift that are useful for small-scale clustering studies. In total, the database catalogs 5627 distinct objects, with 4083 lying within 5‧ of at least one other source. A spectral library contains 3582 optical and near-infrared spectra for 3028 of the cataloged sources. As well as reporting on 54 newly discovered quasar pairs, we outline the key contributions made by this series over the last 10 years, summarize the imaging and spectroscopic data used for target selection, discuss the target selection methodologies, describe the database content, and explore some avenues for future work. Full documentation for the spectral database, including download instructions, is supplied at http://specdb.readthedocs.io/en/latest/.

Discrimination among individual Watson–Crick base pairs at the termini of single DNA hairpin molecules

PubMed Central

Vercoutere, Wenonah A.; Winters-Hilt, Stephen; DeGuzman, Veronica S.; Deamer, David; Ridino, Sam E.; Rodgers, Joseph T.; Olsen, Hugh E.; Marziali, Andre; Akeson, Mark

2003-01-01

Nanoscale α-hemolysin pores can be used to analyze individual DNA or RNA molecules. Serial examination of hundreds to thousands of molecules per minute is possible using ionic current impedance as the measured property. In a recent report, we showed that a nanopore device coupled with machine learning algorithms could automatically discriminate among the four combinations of Watson–Crick base pairs and their orientations at the ends of individual DNA hairpin molecules. Here we use kinetic analysis to demonstrate that ionic current signatures caused by these hairpin molecules depend on the number of hydrogen bonds within the terminal base pair, stacking between the terminal base pair and its nearest neighbor, and 5′ versus 3′ orientation of the terminal bases independent of their nearest neighbors. This report constitutes evidence that single Watson–Crick base pairs can be identified within individual unmodified DNA hairpin molecules based on their dynamic behavior in a nanoscale pore. PMID:12582251

[Mass spectrometric and quantum chemical study of dimeric associates of nucleosides].

PubMed

Sukhodub, L F; Aksenov, S A; Boldeskul, A I

1995-01-01

Deoxyribonucleosides H-bonded pairs were investigated using fast atom bombardment mass spectrometry and MNDO/H quantum chemistry method. It was shown that "rare" (enol or imin) forms of the nitrogen bases could form pairs with energy comparable with "canonical" base pair energy. It was shown that pair stability rows, which are measured using different experimental techniques, were in conformity each with other.

Hippocampus is required for paired associate memory with neither delay nor trial uniqueness

PubMed Central

Yoon, Jinah; Seo, Yeran; Kim, Jangjin; Lee, Inah

2012-01-01

Cued retrieval of memory is typically examined with delay when testing hippocampal functions, as in delayed matching-to-sample tasks. Equally emphasized in the literature, on the other hand, is the hippocampal involvement in making arbitrary associations. Paired associate memory tasks are widely used for examining this function. However, the two variables (i.e., delay and paired association) were often mixed in paired associate tasks, and this makes it difficult to localize the cognitive source of deficits with hippocampal perturbation. Specifically, a few studies have recently shown that rats can learn arbitrary paired associations between certain locations and nonspatial items (e.g., object or flavor) and later can retrieve the paired location when cued by the item remotely. Such tasks involve both (1) delay between sampling the cue and retrieving the target location and (2) arbitrary association between the cueing object and its paired location. Here, we tested whether delay was necessary in a cued paired associate task by using a task in which no delay existed between object cueing and the choice of its paired associate. Moreover, fixed associative relationships between the cueing objects and their paired locations were repeatedly used, thus involving no trial-unique association. Nevertheless, inactivations of the dorsal hippocampus with muscimol severely disrupted retrieval of paired associates, whereas the same manipulations did not affect discriminating individual objects or locations. The results powerfully demonstrate that the hippocampus is inherently required for retrieving paired associations between objects and places, and that delay and trial uniqueness of the paired associates are not necessarily required. PMID:22174309

Rate-loss analysis of an efficient quantum repeater architecture

NASA Astrophysics Data System (ADS)

Guha, Saikat; Krovi, Hari; Fuchs, Christopher A.; Dutton, Zachary; Slater, Joshua A.; Simon, Christoph; Tittel, Wolfgang

2015-08-01

We analyze an entanglement-based quantum key distribution (QKD) architecture that uses a linear chain of quantum repeaters employing photon-pair sources, spectral-multiplexing, linear-optic Bell-state measurements, multimode quantum memories, and classical-only error correction. Assuming perfect sources, we find an exact expression for the secret-key rate, and an analytical description of how errors propagate through the repeater chain, as a function of various loss-and-noise parameters of the devices. We show via an explicit analytical calculation, which separately addresses the effects of the principle nonidealities, that this scheme achieves a secret-key rate that surpasses the Takeoka-Guha-Wilde bound—a recently found fundamental limit to the rate-vs-loss scaling achievable by any QKD protocol over a direct optical link—thereby providing one of the first rigorous proofs of the efficacy of a repeater protocol. We explicitly calculate the end-to-end shared noisy quantum state generated by the repeater chain, which could be useful for analyzing the performance of other non-QKD quantum protocols that require establishing long-distance entanglement. We evaluate that shared state's fidelity and the achievable entanglement-distillation rate, as a function of the number of repeater nodes, total range, and various loss-and-noise parameters of the system. We extend our theoretical analysis to encompass sources with nonzero two-pair-emission probability, using an efficient exact numerical evaluation of the quantum state propagation and measurements. We expect our results to spur formal rate-loss analysis of other repeater protocols and also to provide useful abstractions to seed analyses of quantum networks of complex topologies.

Twin hydroxymethyluracil-A base pair steps define the binding site for the DNA-binding protein TF1.

PubMed

Grove, A; Figueiredo, M L; Galeone, A; Mayol, L; Geiduschek, E P

1997-05-16

The DNA-bending protein TF1 is the Bacillus subtilis bacteriophage SPO1-encoded homolog of the bacterial HU proteins and the Escherichia coli integration host factor. We recently proposed that TF1, which binds with high affinity (Kd was approximately 3 nM) to preferred sites within the hydroxymethyluracil (hmU)-containing phage genome, identifies its binding sites based on sequence-dependent DNA flexibility. Here, we show that two hmU-A base pair steps coinciding with two previously proposed sites of DNA distortion are critical for complex formation. The affinity of TF1 is reduced 10-fold when both of these hmU-A base pair steps are replaced with A-hmU, G-C, or C-G steps; only modest changes in affinity result when substitutions are made at other base pairs of the TF1 binding site. Replacement of all hmU residues with thymine decreases the affinity of TF1 greatly; remarkably, the high affinity is restored when the two hmU-A base pair steps corresponding to previously suggested sites of distortion are reintroduced into otherwise T-containing DNA. T-DNA constructs with 3-base bulges spaced apart by 9 base pairs of duplex also generate nM affinity of TF1. We suggest that twin hmU-A base pair steps located at the proposed sites of distortion are key to target site selection by TF1 and that recognition is based largely, if not entirely, on sequence-dependent DNA flexibility.

Statistical analysis of aerosol species, trace gasses, and meteorology in Chicago.

PubMed

Binaku, Katrina; O'Brien, Timothy; Schmeling, Martina; Fosco, Tinamarie

2013-09-01

Both canonical correlation analysis (CCA) and principal component analysis (PCA) were applied to atmospheric aerosol and trace gas concentrations and meteorological data collected in Chicago during the summer months of 2002, 2003, and 2004. Concentrations of ammonium, calcium, nitrate, sulfate, and oxalate particulate matter, as well as, meteorological parameters temperature, wind speed, wind direction, and humidity were subjected to CCA and PCA. Ozone and nitrogen oxide mixing ratios were also included in the data set. The purpose of statistical analysis was to determine the extent of existing linear relationship(s), or lack thereof, between meteorological parameters and pollutant concentrations in addition to reducing dimensionality of the original data to determine sources of pollutants. In CCA, the first three canonical variate pairs derived were statistically significant at the 0.05 level. Canonical correlation between the first canonical variate pair was 0.821, while correlations of the second and third canonical variate pairs were 0.562 and 0.461, respectively. The first canonical variate pair indicated that increasing temperatures resulted in high ozone mixing ratios, while the second canonical variate pair showed wind speed and humidity's influence on local ammonium concentrations. No new information was uncovered in the third variate pair. Canonical loadings were also interpreted for information regarding relationships between data sets. Four principal components (PCs), expressing 77.0 % of original data variance, were derived in PCA. Interpretation of PCs suggested significant production and/or transport of secondary aerosols in the region (PC1). Furthermore, photochemical production of ozone and wind speed's influence on pollutants were expressed (PC2) along with overall measure of local meteorology (PC3). In summary, CCA and PCA results combined were successful in uncovering linear relationships between meteorology and air pollutants in Chicago and aided in determining possible pollutant sources.

Free-Space Quantum Key Distribution using Polarization Entangled Photons

NASA Astrophysics Data System (ADS)

Kurtsiefer, Christian

2007-06-01

We report on a complete experimental implementation of a quantum key distribution protocol through a free space link using polarization-entangled photon pairs from a compact parametric down-conversion source [1]. Based on a BB84-equivalent protocol, we generated without interruption over 10 hours a secret key free-space optical link distance of 1.5 km with a rate up to 950 bits per second after error correction and privacy amplification. Our system is based on two time stamp units and relies on no specific hardware channel for coincidence identification besides an IP link. For that, initial clock synchronization with an accuracy of better than 2 ns is achieved, based on a conventional NTP protocol and a tiered cross correlation of time tags on both sides. Time tags are used to servo a local clock, allowing a streamed measurement on correctly identified photon pairs. Contrary to the majority of quantum key distribution systems, this approach does not require a trusted large-bandwidth random number generator, but integrates that into the physical key generation process. We discuss our current progress of implementing a key distribution via an atmospherical link during daylight conditions, and possible attack scenarios on a physical timing information side channel to a entanglement-based key distribution system. [1] I. Marcikic, A. Lamas-Linares, C. Kurtsiefer, Appl. Phys. Lett. 89, 101122 (2006).

Packet based serial link realized in FPGA dedicated for high resolution infrared image transmission

NASA Astrophysics Data System (ADS)

Bieszczad, Grzegorz

2015-05-01

In article the external digital interface specially designed for thermographic camera built in Military University of Technology is described. The aim of article is to illustrate challenges encountered during design process of thermal vision camera especially related to infrared data processing and transmission. Article explains main requirements for interface to transfer Infra-Red or Video digital data and describes the solution which we elaborated based on Low Voltage Differential Signaling (LVDS) physical layer and signaling scheme. Elaborated link for image transmission is built using FPGA integrated circuit with built-in high speed serial transceivers achieving up to 2500Gbps throughput. Image transmission is realized using proprietary packet protocol. Transmission protocol engine was described in VHDL language and tested in FPGA hardware. The link is able to transmit 1280x1024@60Hz 24bit video data using one signal pair. Link was tested to transmit thermal-vision camera picture to remote monitor. Construction of dedicated video link allows to reduce power consumption compared to solutions with ASIC based encoders and decoders realizing video links like DVI or packed based Display Port, with simultaneous reduction of wires needed to establish link to one pair. Article describes functions of modules integrated in FPGA design realizing several functions like: synchronization to video source, video stream packeting, interfacing transceiver module and dynamic clock generation for video standard conversion.

Social Orienting and Attention Is Influenced by the Presence of Competing Nonsocial Information in Adolescents with Autism

PubMed Central

Unruh, Kathryn E.; Sasson, Noah J.; Shafer, Robin L.; Whitten, Allison; Miller, Stephanie J.; Turner-Brown, Lauren; Bodfish, James W.

2016-01-01

Background: Our experiences with the world play a critical role in neural and behavioral development. Children with autism spectrum disorder (ASD) spend a disproportionate amount of time seeking out, attending to, and engaging with aspects of their environment that are largely nonsocial in nature. In this study we adapted an established method for eliciting and quantifying aspects of visual choice behavior related to preference to test the hypothesis that preference for nonsocial sources of stimulation diminishes orientation and attention to social sources of stimulation in children with ASD. Method: Preferential viewing tasks can serve as objective measures of preference, with a greater proportion of viewing time to one item indicative of increased preference. The current task used gaze-tracking technology to examine patterns of visual orientation and attention to stimulus pairs that varied in social (faces) and nonsocial content (high autism interest or low autism interest). Participants included both adolescents diagnosed with ASD and typically developing; groups were matched on IQ and gender. Results: Repeated measures ANOVA revealed that individuals with ASD had a significantly greater latency to first fixate on social images when this image was paired with a high autism interest image, compared to a low autism interest image pairing. Participants with ASD showed greater total look time to objects, while typically developing participants preferred to look at faces. Groups also differed in number and average duration of fixations to social and object images. In the ASD group only, a measure of nonsocial interest was associated with reduced preference for social images when paired with high autism interest images. Conclusions: In ASD, the presence of nonsocial sources of stimulation can significantly increase the latency of look time to social sources of information. These results suggest that atypicalities in social motivation in ASD may be context-dependent, with a greater degree of plasticity than is assumed by existing social motivation accounts of ASD. PMID:28066169

Understanding the kinetic mechanism of RNA single base pair formation

PubMed Central

Xu, Xiaojun; Yu, Tao; Chen, Shi-Jie

2016-01-01

RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model. PMID:26699466

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

PubMed

Kisand, Veljo; Lettieri, Teresa

2013-04-01

De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (<450 bps), which are presumed to aid in the analysis of uncharacterized genomes. The array of tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize unknown bacteria with modest effort.

Imino proton exchange and base-pair kinetics in the AMP-RNA aptamer complex.

PubMed

Nonin, S; Jiang, F; Patel, D J

1997-05-02

We report on the dynamics of base-pair opening in the ATP-binding asymmetric internal loop and flanking base-pairs of the AMP-RNA aptamer complex by monitoring the exchange characteristics of the extremely well resolved imino protons in the NMR spectrum of the complex. The kinetics of imino proton exchange as a function of basic pH or added ammonia catalyst are used to measure the apparent base-pair dissociation constants and lifetimes of Watson-Crick and mismatched base-pairs, as well as the solvent accessibility of the unpaired imino protons in the complex. The exchange characteristics of the imino protons identify the existence of four additional hydrogen bonds stabilizing the conformation of the asymmetric ATP-binding internal loop that were not detected by NOEs and coupling constants alone, but are readily accommodated in the previously reported solution structure of the AMP-RNA aptamer complex published from our laboratory. The hydrogen exchange kinetics of the non-Watson-Crick pairs in the asymmetric internal loop of the AMP-RNA aptamer complex have been characterized and yield apparent dissociation constants (alphaKd) that range from 10(-2) to 10(-7). Surprisingly, three of these alphaKd values are amongst the lowest measured for all base-pairs in the AMP-RNA aptamer complex. Comparative studies of hydrogen exchange of the imino protons in the free RNA aptamer and the AMP-RNA aptamer complex establish that complexation stabilizes not only the bases within the ATP-binding asymmetric internal loop, but also the flanking stem base-pairs (two pairs on either side) of the binding site. We also outline some preliminary results related to the exchange properties of a sugar 2'-hydroxyl proton of a guanosine residue involved in a novel hydrogen bond that has been shown to contribute to the immobilization of the bound AMP by the RNA aptamer, and whose resonance is narrow and downfield shifted in the spectrum.

The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure.

PubMed

Leontis, N B; Westhof, E

1998-09-01

A significant fraction of the bases in a folded, structured RNA molecule participate in noncanonical base pairing interactions, often in the context of internal loops or multi-helix junction loops. The appearance of each new high-resolution RNA structure provides welcome data to guide efforts to understand and predict RNA 3D structure, especially when the RNA in question is a functionally conserved molecule. The recent publication of the crystal structure of the "Loop E" region of bacterial 5S ribosomal RNA is such an event [Correll CC, Freeborn B, Moore PB, Steitz TA, 1997, Cell 91:705-712]. In addition to providing more examples of already established noncanonical base pairs, such as purine-purine sheared pairings, trans-Hoogsteen UA, and GU wobble pairs, the structure provides the first high-resolution views of two new purine-purine pairings and a new GU pairing. The goal of the present analysis is to expand the capabilities of both chemical probing and phylogenetic analysis to predict with greater accuracy the structures of RNA molecules. First, in light of existing chemical probing data, we investigate what lessons could be learned regarding the interpretation of this widely used method of RNA structure probing. Then we analyze the 3D structure with reference to molecular phylogeny data (assuming conservation of function) to discover what alternative base pairings are geometrically compatible with the structure. The comparisons between previous modeling efforts and crystal structures show that the intricate involvements of ions and water molecules in the maintenance of non-Watson-Crick pairs render the process of correctly identifying the interacting sites in such pairs treacherous, except in cases of trans-Hoogsteen A/U or sheared A/G pairs for the adenine N1 site. The phylogenetic analysis identifies A/A, A/C, A/U and C/A, C/C, and C/U pairings isosteric with sheared A/G, as well as A/A and A/C pairings isosteric with both G/U and G/G bifurcated pairings. Thus, each non-Watson-Crick pair could be characterized by a phylogenetic signature of variations between isosteric-like pairings. In addition to the conservative changes, which form a dictionary of pairings isosterically compatible with those observed in the crystal structure, concerted changes involving several base pairs also occur. The latter covariations may indicate transitions between related but distinctive motifs within the loop E of 5S ribosomal RNA.

The electrostatic characteristics of G·U wobble base pairs

PubMed Central

Xu, Darui; Landon, Theresa; Greenbaum, Nancy L.; Fenley, Marcia O.

2007-01-01

G·U wobble base pairs are the most common and highly conserved non-Watson–Crick base pairs in RNA. Previous surface maps imply uniformly negative electrostatic potential at the major groove of G·U wobble base pairs embedded in RNA helices, suitable for entrapment of cationic ligands. In this work, we have used a Poisson–Boltzmann approach to gain a more detailed and accurate characterization of the electrostatic profile. We found that the major groove edge of an isolated G·U wobble displays distinctly enhanced negativity compared with standard GC or AU base pairs; however, in the context of different helical motifs, the electrostatic pattern varies. G·U wobbles with distinct widening have similar major groove electrostatic potentials to their canonical counterparts, whereas those with minimal widening exhibit significantly enhanced electronegativity, ranging from 0.8 to 2.5 kT/e, depending upon structural features. We propose that the negativity at the major groove of G·U wobble base pairs is determined by the combined effect of the base atoms and the sugar-phosphate backbone, which is impacted by stacking pattern and groove width as a result of base sequence. These findings are significant in that they provide predictive power with respect to which G·U sites in RNA are most likely to bind cationic ligands. PMID:17526525

Analysis of b quark pair production signal from neutral 2HDM Higgs bosons at future linear colliders

NASA Astrophysics Data System (ADS)

Hashemi, Majid; MahdaviKhorrami, Mostafa

2018-06-01

In this paper, the b quark pair production events are analyzed as a source of neutral Higgs bosons of the two Higgs doublet model type I at linear colliders. The production mechanism is e+e- → Z^{(*)} → HA → b{\\bar{b}}b{\\bar{b}} assuming a fully hadronic final state. The analysis aim is to identify both CP-even and CP-odd Higgs bosons in different benchmark points accommodating moderate boson masses. Due to pair production of Higgs bosons, the analysis is most suitable for a linear collider operating at √{s} = 1 TeV. Results show that in selected benchmark points, signal peaks are observable in the b-jet pair invariant mass distributions at integrated luminosity of 500 fb^{-1}.

Energy correlations of photon pairs generated by a silicon microring resonator probed by Stimulated Four Wave Mixing.

PubMed

Grassani, Davide; Simbula, Angelica; Pirotta, Stefano; Galli, Matteo; Menotti, Matteo; Harris, Nicholas C; Baehr-Jones, Tom; Hochberg, Michael; Galland, Christophe; Liscidini, Marco; Bajoni, Daniele

2016-04-01

Compact silicon integrated devices, such as micro-ring resonators, have recently been demonstrated as efficient sources of quantum correlated photon pairs. The mass production of integrated devices demands the implementation of fast and reliable techniques to monitor the device performances. In the case of time-energy correlations, this is particularly challenging, as it requires high spectral resolution that is not currently achievable in coincidence measurements. Here we reconstruct the joint spectral density of photons pairs generated by spontaneous four-wave mixing in a silicon ring resonator by studying the corresponding stimulated process, namely stimulated four wave mixing. We show that this approach, featuring high spectral resolution and short measurement times, allows one to discriminate between nearly-uncorrelated and highly-correlated photon pairs.

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

Qian, Mr. Suxin; Gluesenkamp, Kyle R; Hwang, Dr. Yunho

Adsorption chillers are capable of utilizing inexpensive or free low grade thermal energy such as waste heat and concentrated solar thermal energy. Recently developed low regeneration temperature working pairs allow adsorption chillers to be driven by even lower temperature sources such as engine coolant and flat plate solar collectors. In this work, synthetic zeolite/water was implemented into a 3kW adsorption chiller test facility driven by hot water at 70 C. The zeolite was coated onto two fin-and-tube heat exchangers, with heat recovery employed between the two. Cyclic steady state parametric studies were experimentally conducted to evaluate the chiller's performance, resultingmore » in a cooling coefficient of performance (COP) ranging from 0.1 to 0.6 at different operating conditions. Its performance was compared with published values for other low regeneration temperature working pairs. The physical limitations of the synthetic zeolite revealed by parametric study results were then discussed. A novel operating control strategy was proposed based on the unique characteristics of synthetic zeolite. In addition, a physics-based COP prediction model was derived to predict the performance of the chiller under equilibrium loading, and was validated by the experiment results. This analytical expression can be used to estimate the cyclic steady state performance for future studies.« less

Visualization of RNA structure models within the Integrative Genomics Viewer.

PubMed

Busan, Steven; Weeks, Kevin M

2017-07-01

Analyses of the interrelationships between RNA structure and function are increasingly important components of genomic studies. The SHAPE-MaP strategy enables accurate RNA structure probing and realistic structure modeling of kilobase-length noncoding RNAs and mRNAs. Existing tools for visualizing RNA structure models are not suitable for efficient analysis of long, structurally heterogeneous RNAs. In addition, structure models are often advantageously interpreted in the context of other experimental data and gene annotation information, for which few tools currently exist. We have developed a module within the widely used and well supported open-source Integrative Genomics Viewer (IGV) that allows visualization of SHAPE and other chemical probing data, including raw reactivities, data-driven structural entropies, and data-constrained base-pair secondary structure models, in context with linear genomic data tracks. We illustrate the usefulness of visualizing RNA structure in the IGV by exploring structure models for a large viral RNA genome, comparing bacterial mRNA structure in cells with its structure under cell- and protein-free conditions, and comparing a noncoding RNA structure modeled using SHAPE data with a base-pairing model inferred through sequence covariation analysis. © 2017 Busan and Weeks; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Neural control of behavioural choice in juvenile crayfish.

PubMed

Liden, William H; Phillips, Mary L; Herberholz, Jens

2010-11-22

Natural selection leads to behavioural choices that increase the animal's fitness. The neuronal mechanisms underlying behavioural choice are still elusive and empirical evidence connecting neural circuit activation to adaptive behavioural output is sparse. We exposed foraging juvenile crayfish to approaching shadows of different velocities and found that slow-moving shadows predominantly activated a pair of giant interneurons, which mediate tail-flips that thrust the animals backwards and away from the approaching threat. Tail-flips also moved the animals farther away from an expected food source, and crayfish defaulted to freezing behaviour when faced with fast-approaching shadows. Under these conditions, tail-flipping, an ineffective and costly escape strategy was suppressed in favour of freezing, a more beneficial choice. The decision to freeze also dominated in the presence of a more desirable resource; however, the increased incentive was less effective in suppressing tail-flipping when paired with slow-moving visual stimuli that reliably evoked tail-flips in most animals. Together this suggests that crayfish make value-based decisions by weighing the costs and benefits of different behavioural options, and they select adaptive behavioural output based on the activation patterns of identifiable neural circuits.

BoD services in layer 1 VPN with dynamic virtual concatenation group

NASA Astrophysics Data System (ADS)

Du, Shu; Peng, Yunfeng; Long, Keping

2008-11-01

Bandwidth-on-Demand (BoD) services are characteristic of dynamic bandwidth provisioning based on customers' resource requirement, which will be a must for future networks. BoD services become possible with the development of make-before-break, Virtual Concatenation (VCAT) and Link Capacity Adjustment Scheme (LCAS). In this paper, we introduce BoD services into L1VPN, thus the resource assigned to a L1VPN can be gracefully adjusted at various bandwidth granularities based on customers' requirement. And we propose a dynamic bandwidth adjustment scheme, which is compromise between make-before-break and VCAT&LCAS and mainly based on the latter. The scheme minimizes the number of distinct paths to support a connection between a source-destination pair, and uses make-beforebreak technology for re-optimization.

Reactivity of cytosine and thymine in single-base-pair mismatches with hydroxylamine and osmium tetroxide and its application to the study of mutations.

PubMed Central

Cotton, R G; Rodrigues, N R; Campbell, R D

1988-01-01

The chemical reactivity of thymine (T), when mismatched with the bases cytosine, guanine, and thymine, and of cytosine (C), when mismatched with thymine, adenine, and cytosine, has been examined. Heteroduplex DNAs containing such mismatched base pairs were first incubated with osmium tetroxide (for T and C mismatches) or hydroxylamine (for C mismatches) and then incubated with piperidine to cleave the DNA at the modified mismatched base. This cleavage was studied with an internally labeled strand containing the mismatched T or C, such that DNA cleavage and thus reactivity could be detected by gel electrophoresis. Cleavage at a total of 13 T and 21 C mismatches isolated (by at least three properly paired bases on both sides) single-base-pair mismatches was identified. All T or C mismatches studied were cleaved. By using end-labeled DNA probes containing T or C single-base-pair mismatches and conditions for limited cleavage, we were able to show that cleavage was at the base predicted by sequence analysis and that mismatches in a length of DNA could be readily detected by such an approach. This procedure may enable detection of all single-base-pair mismatches by use of sense and antisense probes and thus may be used to identify the mutated base and its position in a heteroduplex. Images PMID:3260032

Electrostatics Explains the Position-Dependent Effect of G⋅U Wobble Base Pairs on the Affinity of RNA Kissing Complexes.

PubMed

Abi-Ghanem, Josephine; Rabin, Clémence; Porrini, Massimiliano; Dausse, Eric; Toulmé, Jean-Jacques; Gabelica, Valérie

2017-10-06

In the RNA realm, non-Watson-Crick base pairs are abundant and can affect both the RNA 3D structure and its function. Here, we investigated the formation of RNA kissing complexes in which the loop-loop interaction is modulated by non-Watson-Crick pairs. Mass spectrometry, surface plasmon resonance, and UV-melting experiments show that the G⋅U wobble base pair favors kissing complex formation only when placed at specific positions. We tried to rationalize this effect by molecular modeling, including molecular mechanics Poisson-Boltzmann surface area (MMPBSA) thermodynamics calculations and PBSA calculations of the electrostatic potential surfaces. Modeling reveals that the G⋅U stabilization is due to a specific electrostatic environment defined by the base pairs of the entire loop-loop region. The loop is not symmetric, and therefore the identity and position of each base pair matters. Predicting and visualizing the electrostatic environment created by a given sequence can help to design specific kissing complexes with high affinity, for potential therapeutic, nanotechnology or analytical applications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines

PubMed Central

2010-01-01

Background Protein-protein interaction (PPI) plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via domains instead of the whole molecules, predicting domain-domain interaction (DDI) is an important step toward PPI prediction. Computational methods developed so far have utilized information from various sources at different levels, from primary sequences, to molecular structures, to evolutionary profiles. Results In this paper, we propose a computational method to predict DDI using support vector machines (SVMs), based on domains represented as interaction profile hidden Markov models (ipHMM) where interacting residues in domains are explicitly modeled according to the three dimensional structural information available at the Protein Data Bank (PDB). Features about the domains are extracted first as the Fisher scores derived from the ipHMM and then selected using singular value decomposition (SVD). Domain pairs are represented by concatenating their selected feature vectors, and classified by a support vector machine trained on these feature vectors. The method is tested by leave-one-out cross validation experiments with a set of interacting protein pairs adopted from the 3DID database. The prediction accuracy has shown significant improvement as compared to InterPreTS (Interaction Prediction through Tertiary Structure), an existing method for PPI prediction that also uses the sequences and complexes of known 3D structure. Conclusions We show that domain-domain interaction prediction can be significantly enhanced by exploiting information inherent in the domain profiles via feature selection based on Fisher scores, singular value decomposition and supervised learning based on support vector machines. Datasets and source code are freely available on the web at http://liao.cis.udel.edu/pub/svdsvm. Implemented in Matlab and supported on Linux and MS Windows. PMID:21034480

Pinpointing the North Korea Nuclear tests with body waves scattered by surface topography

NASA Astrophysics Data System (ADS)

Wang, N.; Shen, Y.; Bao, X.; Flinders, A. F.

2017-12-01

On September 3, 2017, North Korea conducted its sixth and by far the largest nuclear test at the Punggye-ri test site. In this work, we apply a novel full-wave location method that combines a non-linear grid-search algorithm with the 3D strain Green's tensor database to locate this event. We use the first arrivals (Pn waves) and their immediate codas, which are likely dominated by waves scattered by the surface topography near the source, to pinpoint the source location. We assess the solution in the search volume using a least-squares misfit between the observed and synthetic waveforms, which are obtained using the collocated-grid finite difference method on curvilinear grids. We calculate the one standard deviation level of the 'best' solution as a posterior error estimation. Our results show that the waveform based location method allows us to obtain accurate solutions with a small number of stations. The solutions are absolute locations as opposed to relative locations based on relative travel times, because topography-scattered waves depend on the geometric relations between the source and the unique topography near the source. Moreover, we use both differential waveforms and traveltimes to locate pairs of the North Korea tests in years 2016 and 2017 to further reduce the effects of inaccuracies in the reference velocity model (CRUST 1.0). Finally, we compare our solutions with those of other studies based on satellite images and relative traveltimes.

Multi-source apportionment of polycyclic aromatic hydrocarbons using simultaneous linear equations

NASA Astrophysics Data System (ADS)

Marinaite, Irina; Semenov, Mikhail

2014-05-01

A new approach to identify multiple sources of polycyclic aromatic hydrocarbons (PAHs) and to evaluate the source contributions to atmospheric deposition of particulate PAHs is proposed. The approach is based on differences in concentrations of sums of PAHs with the same molecular weight among the sources. The data on PAHs accumulation in snow as well as the source profiles were used for calculations. Contributions of aluminum production plant, oil-fired central heating boilers, and residential wood and coal combustion were calculated using the linear mixing models. The concentrations of PAH pairs such as Benzo[b]fluorantene + Benzo[k]fluorantene and Benzo[g,h,i]perylene + Indeno[1,2,3-c,d]pyrene normalized to Benzo[a]antracene + Chrysene were used as tracers in mixing equations. The results obtained using ratios of sums of PAHs were compared with those obtained using molecular diagnostic ratios such as Benzo[a]antracene/Chrysene and Benzo[g,h,i]perylene/Indeno[1,2,3-c,d]pyrene. It was shown that the results obtained using diagnostic ratios as tracers are less reliable than results obtained using ratios of sums of PAHs. Funding was provided by Siberian Branch of Russian Academy of Sciences grant No. 8 (2012-2014).

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

PubMed Central

Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R.; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/. PMID:23082188

Method of incident low-energy gamma-ray direction reconstruction in the GAMMA-400 gamma-ray space telescope

NASA Astrophysics Data System (ADS)

Kheymits, M. D.; Leonov, A. A.; Zverev, V. G.; Galper, A. M.; Arkhangelskaya, I. V.; Arkhangelskiy, A. I.; Suchkov, S. I.; Topchiev, N. P.; Yurkin, Yu T.; Bakaldin, A. V.; Dalkarov, O. D.

2016-02-01

The GAMMA-400 gamma-ray space-based telescope has as its main goals to measure cosmic γ-ray fluxes and the electron-positron cosmic-ray component produced, theoretically, in dark-matter-particles decay or annihilation processes, to search for discrete γ-ray sources and study them in detail, to examine the energy spectra of diffuse γ-rays — both galactic and extragalactic — and to study gamma-ray bursts (GRBs) and γ-rays from the active Sun. Scientific goals of GAMMA-400 telescope require fine angular resolution. The telescope is of a pair-production type. In the converter-tracker, the incident gamma-ray photon converts into electron-positron pair in the tungsten layer and then the tracks are detected by silicon- strip position-sensitive detectors. Multiple scattering processes become a significant obstacle in the incident-gamma direction reconstruction for energies below several gigaelectronvolts. The method of utilising this process to improve the resolution is proposed in the presented work.

Superconductivity in metal coated graphene

NASA Astrophysics Data System (ADS)

Uchoa, Bruno; Castro Neto, Antonio

2007-03-01

Graphene, a single atomic layer of graphite, is a two dimensional (2D) zero gap insulator with a high electronic mobility between nearest neighbor carbon sites. The unique electronic properties of graphene, from the semi-metallic behavior to the observation of an anomalous quantum Hall effect and a zero field quantized minimum of conductivity derive from the relativistic nature of its quasiparticles. By doping graphene, it behaves in several aspects as a conventional Fermi liquid, where electrons may form Cooper pairs by coupling with a bosonic mode. In this talk, we develop a mean-field phenomenology of superconductivity in a honeycomb lattice. We predict the possibility of two distinct phases, a singlet s-wave phase and a novel p+ip wave phase in the singlet channel. At half filling, the p+ip phase is gapless and superconductivity is a hidden order. We propose a few possible sources of Cooper pairing instability in graphene coated with alkaline and transition metals, and similar low dimensional graphene based devices.

MOCAT: a metagenomics assembly and gene prediction toolkit.

PubMed

Kultima, Jens Roat; Sunagawa, Shinichi; Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/.

Passive measurement-device-independent quantum key distribution with orbital angular momentum and pulse position modulation

NASA Astrophysics Data System (ADS)

Wang, Lian; Zhou, Yuan-yuan; Zhou, Xue-jun; Chen, Xiao

2018-03-01

Based on the orbital angular momentum and pulse position modulation, we present a novel passive measurement-device-independent quantum key distribution (MDI-QKD) scheme with the two-mode source. Combining with the tight bounds of the yield and error rate of single-photon pairs given in our paper, we conduct performance analysis on the scheme with heralded single-photon source. The numerical simulations show that the performance of our scheme is significantly superior to the traditional MDI-QKD in the error rate, key generation rate and secure transmission distance, since the application of orbital angular momentum and pulse position modulation can exclude the basis-dependent flaw and increase the information content for each single photon. Moreover, the performance is improved with the rise of the frame length. Therefore, our scheme, without intensity modulation, avoids the source side channels and enhances the key generation rate. It has greatly utility value in the MDI-QKD setups.

MHz rate and efficient synchronous heralding of single photons at telecom wavelengths.

PubMed

Pomarico, Enrico; Sanguinetti, Bruno; Guerreiro, Thiago; Thew, Rob; Zbinden, Hugo

2012-10-08

We report on the realization of a synchronous source of heralded single photons at telecom wavelengths with MHz heralding rates and high heralding efficiency. This source is based on the generation of photon pairs at 810 and 1550 nm via Spontaneous Parametric Down Conversion (SPDC) in a 1 cm periodically poled lithium niobate (PPLN) crystal pumped by a 532 nm pulsed laser. As high rates are fundamental for multi-photon experiments, we show that single telecom photons can be announced at 4.4 MHz rate with 45% heralding efficiency. When we focus only on the optimization of the coupling of the heralded photon, the heralding efficiency can be increased up to 80%. Furthermore, we experimentally observe that group velocity mismatch inside long crystals pumped in a pulsed mode affects the spectrum of the emitted photons and their fibre coupling efficiency. The length of the crystal in this source has been chosen as a trade off between high brightness and high coupling efficiency.

An integral equation formulation for the diffraction from convex plates and polyhedra.

PubMed

Asheim, Andreas; Svensson, U Peter

2013-06-01

A formulation of the problem of scattering from obstacles with edges is presented. The formulation is based on decomposing the field into geometrical acoustics, first-order, and multiple-order edge diffraction components. An existing secondary-source model for edge diffraction from finite edges is extended to handle multiple diffraction of all orders. It is shown that the multiple-order diffraction component can be found via the solution to an integral equation formulated on pairs of edge points. This gives what can be called an edge source signal. In a subsequent step, this edge source signal is propagated to yield a multiple-order diffracted field, taking all diffraction orders into account. Numerical experiments demonstrate accurate response for frequencies down to 0 for thin plates and a cube. No problems with irregular frequencies, as happen with the Kirchhoff-Helmholtz integral equation, are observed for this formulation. For the axisymmetric scattering from a circular disc, a highly effective symmetric formulation results, and results agree with reference solutions across the entire frequency range.

The Impact of a Peer-Learning Agent Based on Pair Programming in a Programming Course

ERIC Educational Resources Information Center

Han, Keun-Woo; Lee, EunKyoung; Lee, YoungJun

2010-01-01

This paper analyzes the educational effects of a peer-learning agent based on pair programming in programming courses. A peer-learning agent system was developed to facilitate the learning of a programming language through the use of pair programming strategies. This system is based on the role of a peer-learning agent from pedagogical and…

Distribution of Base Pair Alternations in a Periodic DNA Chain: Application of Pólya Counting to a Physical System

NASA Astrophysics Data System (ADS)

Hillebrand, Malcolm; Paterson-Jones, Guy; Kalosakas, George; Skokos, Charalampos

2018-03-01

In modeling DNA chains, the number of alternations between Adenine-Thymine (AT) and Guanine-Cytosine (GC) base pairs can be considered as a measure of the heterogeneity of the chain, which in turn could affect its dynamics. A probability distribution function of the number of these alternations is derived for circular or periodic DNA. Since there are several symmetries to account for in the periodic chain, necklace counting methods are used. In particular, Polya's Enumeration Theorem is extended for the case of a group action that preserves partitioned necklaces. This, along with the treatment of generating functions as formal power series, allows for the direct calculation of the number of possible necklaces with a given number of AT base pairs, GC base pairs and alternations. The theoretically obtained probability distribution functions of the number of alternations are accurately reproduced by Monte Carlo simulations and fitted by Gaussians. The effect of the number of base pairs on the characteristics of these distributions is also discussed, as well as the effect of the ratios of the numbers of AT and GC base pairs.

Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine.

PubMed

Szulik, Marta W; Pallan, Pradeep S; Nocek, Boguslaw; Voehler, Markus; Banerjee, Surajit; Brooks, Sonja; Joachimiak, Andrzej; Egli, Martin; Eichman, Brandt F; Stone, Michael P

2015-02-10

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson-Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T(8)X(9)G(10)-3' sequence of the DDD, were compared. The presence of 5caC at the X(9) base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A(5):T(8), whereas 5caC did not. At the oxidized base pair G(4):X(9), 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C(3):G(10). No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G(4):X(9); each favored Watson-Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N(4) exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.

Differential stabilities and sequence-dependent base pair opening dynamics of Watson–Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine

DOE PAGES

Szulik, Marta W.; Pallan, Pradeep S.; Nocek, Boguslaw; ...

2015-01-29

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson–Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T 8X 9G 10-3' sequence of the DDD, were compared. The presence of 5caC at the X9 base increased the stability of the DDD, whereas 5hmC or 5fC didmore » not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A 5:T 8, whereas 5caC did not. At the oxidized base pair G 4:X 9, 5fC exhibited an increase in the imino proton exchange rate and the calculated k op. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C 3:G 10. No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G 4:X 9; each favored Watson–Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N 4 exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. Furthermore, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.« less

Differential Stabilities and Sequence-Dependent Base Pair Opening Dynamics of Watson–Crick Base Pairs with 5-Hydroxymethylcytosine, 5-Formylcytosine, or 5-Carboxylcytosine

PubMed Central

2016-01-01

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson–Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5′-CG-3′ sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5′-T8X9G10-3′ sequence of the DDD, were compared. The presence of 5caC at the X9 base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A5:T8, whereas 5caC did not. At the oxidized base pair G4:X9, 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C3:G10. No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G4:X9; each favored Watson–Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N4 exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes. PMID:25632825

Frontal Cortex Activation Causes Rapid Plasticity of Auditory Cortical Processing

PubMed Central

Winkowski, Daniel E.; Bandyopadhyay, Sharba; Shamma, Shihab A.

2013-01-01

Neurons in the primary auditory cortex (A1) can show rapid changes in receptive fields when animals are engaged in sound detection and discrimination tasks. The source of a signal to A1 that triggers these changes is suspected to be in frontal cortical areas. How or whether activity in frontal areas can influence activity and sensory processing in A1 and the detailed changes occurring in A1 on the level of single neurons and in neuronal populations remain uncertain. Using electrophysiological techniques in mice, we found that pairing orbitofrontal cortex (OFC) stimulation with sound stimuli caused rapid changes in the sound-driven activity within A1 that are largely mediated by noncholinergic mechanisms. By integrating in vivo two-photon Ca2+ imaging of A1 with OFC stimulation, we found that pairing OFC activity with sounds caused dynamic and selective changes in sensory responses of neural populations in A1. Further, analysis of changes in signal and noise correlation after OFC pairing revealed improvement in neural population-based discrimination performance within A1. This improvement was frequency specific and dependent on correlation changes. These OFC-induced influences on auditory responses resemble behavior-induced influences on auditory responses and demonstrate that OFC activity could underlie the coordination of rapid, dynamic changes in A1 to dynamic sensory environments. PMID:24227723