WorldWideScience

Sample records for base pair step

  1. A Simple Picosecond Pulse Generator Based on a Pair of Step Recovery Diodes

    CERN Document Server

    Zou, Lianfeng; Caloz, Christophe

    2016-01-01

    A picosecond pulse generator based on a pair of step recovery diodes (SRD), leveraging the transient response of the SRD PN junction and controlling the pulse width by a resistor, is proposed. We first explain the operation principle of the device, decomposing the pulse generation into different phases, and then demonstrate an experimental prototype with two different resistance, and hence pulse width, values.

  2. Density-fitted open-shell symmetry-adapted perturbation theory and application to π-stacking in benzene dimer cation and ionized DNA base pair steps

    Science.gov (United States)

    Gonthier, Jérôme F.; Sherrill, C. David

    2016-10-01

    Symmetry-Adapted Perturbation Theory (SAPT) is one of the most popular approaches to energy component analysis of non-covalent interactions between closed-shell systems, yielding both accurate interaction energies and meaningful interaction energy components. In recent years, the full open-shell equations for SAPT up to second-order in the intermolecular interaction and zeroth-order in the intramolecular correlation (SAPT0) were published [P. S. Zuchowski et al., J. Chem. Phys. 129, 084101 (2008); M. Hapka et al., ibid. 137, 164104 (2012)]. Here, we utilize density-fitted electron repulsion integrals to produce an efficient computational implementation. This approach is used to examine the effect of ionization on π-π interactions. For the benzene dimer radical cation, comparison against reference values indicates a good performance for open-shell SAPT0, except in cases with substantial charge transfer. For π stacking between hydrogen-bonded pairs of nucleobases, dispersion interactions still dominate binding, in spite of the creation of a positive charge.

  3. Report on Pairing-based Cryptography.

    Science.gov (United States)

    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.

  4. Electrical Conductivity through a Single Atomic Step Measured with the Proximity-Induced Superconducting Pair Correlation

    Science.gov (United States)

    Kim, Howon; Lin, Shi-Zeng; Graf, Matthias J.; Miyata, Yoshinori; Nagai, Yuki; Kato, Takeo; Hasegawa, Yukio

    2016-09-01

    Local disordered nanostructures in an atomically thick metallic layer on a semiconducting substrate play significant and decisive roles in transport properties of two-dimensional (2D) conductive systems. We measured the electrical conductivity through a step of monoatomic height in a truly microscopic manner by using as a signal the superconducting pair correlation induced by the proximity effect. The transport property across a step of a one-monolayer Pb surface metallic phase, formed on a Si(111) substrate, was evaluated by inducing the pair correlation around the local defect and measuring its response, i.e., the reduced density of states at the Fermi energy using scanning tunneling microscopy. We found that the step resistance has a significant contribution to the total resistance on a nominally flat surface. Our study also revealed that steps in the 2D metallic layer terminate the propagation of the pair correlation. Superconductivity is enhanced between the first surface step and the superconductor-normal-metal interface by reflectionless tunneling when the step is located within a coherence length.

  5. Alternative DNA base pairing through metal coordination.

    Science.gov (United States)

    Clever, Guido H; Shionoya, Mitsuhiko

    2012-01-01

    Base-pairing in the naturally occurring DNA and RNA oligonucleotide duplexes is based on π-stacking, hydrogen bonding, and shape complementarity between the nucleobases adenine, thymine, guanine, and cytosine as well as on the hydrophobic-hydrophilic balance in aqueous media. This complex system of multiple supramolecular interactions is the product of a long-term evolutionary process and thus highly optimized to serve its biological functions such as information storage and processing. After the successful implementation of automated DNA synthesis, chemists have begun to introduce artificial modifications inside the core of the DNA double helix in order to study various aspects of base pairing, generate new base pairs orthogonal to the natural ones, and equip the biopolymer with entirely new functions. The idea to replace the hydrogen bonding interactions with metal coordination between ligand-like nucleosides and suitable transition metal ions culminated in the development of a plethora of artificial base-pairing systems termed "metal base-pairs" which were shown to strongly enhance the DNA duplex stability. Furthermore, they show great potential for the use of DNA as a molecular wire in nanoscale electronic architectures. Although single electrons have proven to be transmitted by natural DNA over a distance of several base pairs, the high ohmic resistance of unmodified oligonucleotides was identified as a serious obstacle. By exchanging some or all of the Watson-Crick base pairs in DNA with metal complexes, this problem may be solved. In the future, these research efforts are supposed to lead to DNA-like materials with superior conductivity for nano-electronic applications. Other fields of potential application such as DNA-based supramolecular architecture and catalysis may be strongly influenced by these developments as well. This text is meant to illustrate the basic concepts of metal-base pairing and give an outline over recent developments in this field.

  6. Implementation of Cryptosystems Based on Tate Pairing

    Institute of Scientific and Technical Information of China (English)

    Lei Hu; Jun-Wu Dong; Ding-Yi Pei

    2005-01-01

    Tate pairings over elliptic curves are important in cryptography since they can be used to construct efficient identity-based cryptosystems, and their implementation dominantly determines the efficiencies of the cryptosystems. In this paper, the implementation of a cryptosystem is provided based on the Tate pairing over a supersingular elliptic curve of MOV degree 3. The implementation is primarily designed to re-use low-level codes developed in implementation of usual elliptic curve cryptosystems. The paper studies how to construct the underlying ground field and its extension to accelerate the finite field arithmetic, and presents a technique to speedup the time-consuming powering in the Tate pairing algorithm.

  7. DNA pairing is an important step in the process of targeted nucleotide exchange.

    Science.gov (United States)

    Drury, Miya D; Kmiec, Eric B

    2003-02-01

    Modified single-stranded DNA oligonucleotides can direct the repair of genetic mutations in yeast, plant and mammalian cells. The mechanism by which these molecules exert their effect is being elucidated, but the first phase is likely to involve the homologous alignment of the single strand with its complementary sequence in the target gene. In this study, we establish the importance of such DNA pairing in facilitating the gene repair event. Oligonucleotide-directed repair occurs at a low frequency in an Escherichia coli strain (DH10B) lacking the RECA DNA pairing function. Repair activity can be rescued by using purified RecA protein to catalyze the assimilation of oligonucleotide vectors into a plasmid containing a mutant kanamycin resistance gene in vitro. Electroporation of the preformed complex into DH10B cells results in high levels of gene repair activity, evidenced by the appearance of kanamycin-resistant colonies. Gene repair is dependent on the formation of a double-displacement loop (double-D-loop), a recombination intermediate containing two single-stranded oligonucleotides hybridized to opposite strands of the plasmid at the site of the point mutation. The heightened level of stability of the double-D-loop enables it to serve as an active template for the DNA repair events. The data establish DNA pairing and the formation of the double-D-loop as important first steps in the process of gene repair.

  8. One step paired electrochemical synthesis of iron and iron oxide nanoparticles

    Directory of Open Access Journals (Sweden)

    Ordoukhanian Juliet

    2016-09-01

    Full Text Available In this study, a new one step paired electrochemical method is developed for simultaneous synthesis of iron and iron oxide nanoparticles. iron and iron oxide are prepared as cathodic and anodic products from iron (ii sulfate aqueous solution in a membrane divided electrolytic cell by the pulsed current electrosynthesis. Because of organic solvent-free and electrochemical nature of the synthesis, the process could be considered as green and environmentally friendly. The reduction of energy consumption and low cost are the other significant advantages of this new method that would have a great application potential in the chemical industry. The nanostructure of prepared samples was characterized by Fourier transform infrared spectroscopy (FT-IR, X-ray diffraction (XRD, scanning electron microscopy (SEM and transmission electron microscopy (TEM. The magnetic properties were studied by vibrating sample magnetometer (VsM.

  9. Control of a Backward-Facing Step flow through vortex pairing and phase locking

    CERN Document Server

    Duriez, Thomas; Wesfreid, Jose Eduardo; Artana, Guillermo

    2014-01-01

    Many experimental and numerical studies report a large reduction of the recirculation bubble in Backward-Facing Step flows or airfoils in stall situation when excited at the natural shedding frequency $f_0$. Through a simple experiment using Dielectric Barrier Discharge actuator, we find a different result. For a given Reynolds number, the frequency of the perturbation is varied for a fixed duty-cycle dc = 27%. Through phase-averaging of Particle Image Velocimetry measurements, we show that the actuation creates a forced vortex which interacts with the natural shedding with a different phase velocity than the unforced one. The largest reduction of the recirculation bubble (-35%) is obtained in a very narrow frequency range around $0.73 f_0$ where early vortex pairing occurs between forced and unforced vortices. Phase averaging shows that in this case, the actuation clearly forces the vortex pairing in the shear layer. On the contrary, when the forcing frequency is higher, the shear layer behaves like an ampli...

  10. NMR analysis of base-pair opening kinetics in DNA

    Science.gov (United States)

    Szulik, Marta W.; Voehler, Markus; Stone, Michael P.

    2014-01-01

    Base pairing in nucleic acids plays a crucial role in their structure and function. Differences in the base pair opening and closing kinetics of individual double stranded DNA sequences or between chemically modified base pairs provide insight into the recognition of these base pairs by DNA processing enzymes. This unit describes how to quantify the kinetics for localized base pairs by observing changes in the imino proton signals by nuclear magnetic resonance spectroscopy. The determination of all relevant parameters using state of the art techniques and NMR instrumentation, including cryoprobes, is discussed. PMID:25501592

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

    CERN Document Server

    Savanier, Marc

    2016-01-01

    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 (JSI), which describes the frequency correlations of the photon pair. In particular, heralded single-photon generation requires uncorrelated photons, rather than the highly anti-correlated photons conventionally obtained under continuous-wave (CW) pumping. Recent attempts to achieve such a factorizable JSI have used short optical pulses from mode-locked lasers, which are much more expensive and bigger table-top or rack-sized instruments compared to the Si microchip pair generator, dominate the cost and inhibit the miniaturization of the source. Here, we generate photon pairs from a Si microring resonator by using an electronic step-recovery diode to drive an electro-optic modulator which carves the pump light from a CW optical diode ...

  12. An Identity Based Aggregate Signature from Pairings

    Directory of Open Access Journals (Sweden)

    Yike Yu

    2011-04-01

    Full Text Available An aggregate signature is a useful digital signature that supports aggregation: Given n signatures on n distinct messages from n distinct users, aggregate signature scheme is possible to aggregate all these signature into a single short signature. This single signature, along with the n original messages will convince any verifier that the n users did indeed sign the n original messages respectively (i.e., for i=1,...,n user i signed message  mi. In this paper, we propose an identity based aggregate signature scheme which requires constant pairing operations in the verification and the size of aggregate signature is independent of the number of signers. We prove that the proposed signature scheme is secure against existential forgery under adaptively chosen message and identity attack in the random oracle model assuming the intractability of the computational Diffie-Hellman problem.

  13. Natural versus artificial creation of base pairs in DNA: origin of nucleobases from the perspectives of unnatural base pair studies.

    Science.gov (United States)

    Hirao, Ichiro; Kimoto, Michiko; Yamashige, Rie

    2012-12-18

    Since life began on Earth, the four types of bases (A, G, C, and T(U)) that form two sets of base pairs have remained unchanged as the components of nucleic acids that replicate and transfer genetic information. Throughout evolution, except for the U to T modification, the four base structures have not changed. This constancy within the genetic code raises the question of how these complicated nucleotides were generated from the molecules in a primordial soup on the early Earth. At some prebiotic stage, the complementarity of base pairs might have accelerated the generation and accumulation of nucleotides or oligonucleotides. We have no clues whether one pair of nucleobases initially appeared on the early Earth during this process or a set of two base pairs appeared simultaneously. Recently, researchers have developed new artificial pairs of nucleobases (unnatural base pairs) that function alongside the natural base pairs. Some unnatural base pairs in duplex DNA can be efficiently and faithfully amplified in a polymerase chain reaction (PCR) using thermostable DNA polymerases. The addition of unnatural base pair systems could expand the genetic alphabet of DNA, thus providing a new mechanism for the generation novel biopolymers by the site-specific incorporation of functional components into nucleic acids and proteins. Furthermore, the process of unnatural base pair development might provide clues to the origin of the natural base pairs in a primordial soup on the early Earth. In this Account, we describe the development of three representative types of unnatural base pairs that function as a third pair of nucleobases in PCR and reconsider the origin of the natural nucleic acids. As researchers developing unnatural base pairs, they use repeated "proof of concept" experiments. As researchers design new base pairs, they improve the structures that function in PCR and eliminate those that do not. We expect that this process is similar to the one functioning in the

  14. Efficient Tate pairing computation using double-base chains

    Institute of Scientific and Technical Information of China (English)

    ZHAO ChangAn; ZHANG FangGuo; HUANG JiWu

    2008-01-01

    Pairing-based cryptosystems have developed very fast in the last few years. The effi-ciencies of these cryptosystems depend on the computation of the bilinear pairings. In this paper, a new efficient algorithm based on double-base chains for computing the Tate pairing is proposed for odd characteristic p > 3. The inherent sparseness of double-base number system reduces the computational cost for computing the Tate pairing evidently. The new algorithm is 9% faster than the previous fastest method for the embedding degree k = 6.

  15. STEP based Finish Machining CAPP system

    OpenAIRE

    A Arivazhagan; Mehta, NK; Jain, PK

    2012-01-01

    This research paper presents various methodologies developed in a STEP based Computer Aided Process Planning (CAPP) system named "Finish Machining – CAPP" (FM-CAPP). It is developed to generate automatic process plans for finish machining prismatic parts. It is designed in a modular fashion consisting of three main modules, namely (i) Feature Recognition module (FRM) (ii) Machining Planning Module (MPM) and (iii) Setup Planning Module (SPM). The FRM Module analyses the geometrical and topolog...

  16. Second generation silver(I-mediated imidazole base pairs

    Directory of Open Access Journals (Sweden)

    Susanne Hensel

    2014-09-01

    Full Text Available The imidazole–Ag(I–imidazole base pair is one of the best-investigated artificial metal-mediated base pairs. We show here that its stability can be further improved by formally replacing the imidazole moiety by a 2-methylimidazole or 4-methylimidazole moiety. A comparison of the thermal stability of several double helices shows that the addition of one equivalent of Ag(I leads to a 50% larger increase in the melting temperature when a DNA duplex with methylated imidazole nucleosides is applied. This significant effect can likely be attributed to a better steric shielding of the metal ion within the metal-mediated base pair.

  17. Statistical mechanics of base stacking and pairing in DNA melting

    OpenAIRE

    Ivanov, Vassili; Zeng, Yan; Zocchi, Giovanni

    2004-01-01

    We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary structure in the whole experimentally accessible temperature range. Base pairing is described through a zipper model, base stacking through an Ising model. We present experimental data on the unstacking transition, obtained exploiting the observation that at m...

  18. Structure of 2,4-Diaminopyrimidine - Theobromine Alternate Base Pairs

    Science.gov (United States)

    Gengeliczki, Zsolt; Callahan, Michael P.; Kabelac, Martin; Rijs, Anouk M.; deVries, Mattanjah S.

    2011-01-01

    We report the structure of clusters of 2,4-diaminopyrimidine with 3,7-dimethylxanthine (theobromine) in the gas phase determined by IR-UV double resonance spectroscopy in both the near-IR and mid-IR regions in combination with ab initio computations. These clusters represent potential alternate nucleobase pairs, geometrically equivalent to guanine-cytosine. We have found the four lowest energy structures, which include the Watson-Crick base pairing motif. This Watson-Crick structure has not been observed by resonant two-photon ionization (R2PI) in the gas phase for the canonical DNA base pairs.

  19. Product Information Platform Based on STEP

    Institute of Scientific and Technical Information of China (English)

    WANG Taiyong; ZHANG Zhiwei

    2009-01-01

    The intemational standard ISO 10303.called STEP.has been used to deal with problems in the ex change of product models and the associated data between difierent computer-aided systems.A platform based on STEP for managing product information is presented.This platform includes three components:a product geometry information model,a product feature model and a product visualization model.An information extracting pattern,in which information is extracted from low level elements to high level ones,is adopted in establishing the product geometry information model.Relative elements lists are created based on the extracted product information.With the traversing of these lists,feature extraction methods are proposed,which take advantage of boundary information in product model and avoid the determination of concavity and convexity of curves.Information correlating to features iS stored in a structure named as feature block and the product visualization model iS founded from it.The feature block is used in the platform for information communication and synchronous update among the three components.

  20. Effect of base pairing on the electrochemical oxidation of guanine.

    Science.gov (United States)

    Costentin, Cyrille; Hajj, Viviane; Robert, Marc; Savéant, Jean-Michel; Tard, Cédric

    2010-07-28

    The effect of base pairing by cytosine on the electrochemical oxidation of guanine is examined by means of cyclic voltammetry on carefully purified reactants in a solvent, CHCl(3), which strongly favors the formation of an H-bonded pair. The thermodynamics and kinetics of the oxidation reaction are not strongly influenced by the formation of the pair. They are actually similar to those of the reaction in which 2,6-lutidine, an encumbered base that cannot form a pair with guanine, replaces cytosine. The reaction does not entail a concerted proton-electron mechanism, as attested by the absence of H/D isotope effect. It rather involves the rate-determining formation of the cation radical, followed by its deprotonation and dimerization of the resulting neutral radical in competition with its further oxidation.

  1. Statistical mechanics of base stacking and pairing in DNA melting.

    Science.gov (United States)

    Ivanov, Vassili; Zeng, Yan; Zocchi, Giovanni

    2004-11-01

    We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary structure in the whole experimentally accessible temperature range. Base pairing is described through a zipper model, base stacking through an Ising model. We present experimental data on the unstacking transition, obtained exploiting the observation that at moderately low pH this transition is moved down to experimentally accessible temperatures. These measurements confirm that the Ising model approach is indeed a good description of base stacking. On the other hand, comparison with the experiments points to the limitations of the simple zipper model description of base pairing.

  2. Ultrafast dynamics in DNA base pairs following ultraviolet excitation.

    Science.gov (United States)

    Orr-Ewing, Andrew

    2015-03-01

    Photo-protective mechanisms in DNA are essential to maintain the integrity of the genetic code by preventing damage from absorption of solar ultraviolet (UV) radiation. We have used time-resolved infra-red (TRIR) spectroscopy to observe the dynamics of Watson-Crick nucleobase pairs following absorption of femtosecond UV laser pulses. The base pairs are prepared as nucleosides in solution, and photo-induced dynamics are probed in the carbonyl and N-H bond stretching regions using broadband IR pulses with picosecond time resolution. Results will be presented for the guanine-cytosine (G-C) base pair, contrasting the rapid recovery of ground-state products (the photo-protection pathway) with formation of other photoproducts which might represent photo-damage mechanisms. This work is a collaboration with the group of Prof F. Temps (Christian-Albrechts-Universitat zu Kiel). This research is supported by ERC Advanced Grant 290966 CAPRI.

  3. Using an Isomorphic Problem Pair to Learn Introductory Physics: Transferring from a Two-step Problem to a Three-step Problem

    CERN Document Server

    Lin, Shih-Yin

    2016-01-01

    In this study, we examine introductory physics students' ability to perform analogical reasoning between two isomorphic problems which employ the same underlying physics principles but have different surface features. Three hundred and eighty two students from a calculus-based and an algebra-based introductory physics course were asked to learn from a solved problem provided and take advantage of what they learned from it to solve another isomorphic problem (which we call the quiz problem). The solved problem provided has two sub-problems while the quiz problem has three sub-problems, which is known to be challenging for introductory students from previous research. In addition to the solved problem, students also received extra scaffolding supports that were intended to help them discern and exploit the underlying similarities of the isomorphic solved and quiz problems. The results suggest that students had great difficulty in transferring what they learned from a 2-step problem to a 3-step problem. Although...

  4. Theoretical analysis of noncanonical base pairing interactions in RNA molecules

    Indian Academy of Sciences (India)

    Dhananjay Bhattacharyya; Siv Chand Koripella; Abhijit Mitra; Vijay Babu Rajendran; Bhabdyuti Sinha

    2007-08-01

    Noncanonical base pairs in RNA have strong structural and functional implications but are currently not considered for secondary structure predictions. We present results of comparative ab initio studies of stabilities and interaction energies for the three standard and 24 selected unusual RNA base pairs reported in the literature. Hydrogen added models of isolated base pairs, with heavy atoms frozen in their ‘away from equilibrium’ geometries, built from coordinates extracted from NDB, were geometry optimized using HF/6-31G** basis set, both before and after unfreezing the heavy atoms. Interaction energies, including BSSE and deformation energy corrections, were calculated, compared with respective single point MP2 energies, and correlated with occurrence frequencies and with types and geometries of hydrogen bonding interactions. Systems having two or more N-H…O/N hydrogen bonds had reasonable interaction energies which correlated well with respective occurrence frequencies and highlighted the possibility of some of them playing important roles in improved secondary structure prediction methods. Several of the remaining base pairs with one N-H…O/N and/or one C-H…O/N interactions respectively, had poor interaction energies and negligible occurrences. High geometry variations on optimization of some of these were suggestive of their conformational switch like characteristics.

  5. Lewis pair polymerization by classical and frustrated Lewis pairs: Acid, base and monomer scope and polymerization mechanism

    KAUST Repository

    Zhang, Yuetao

    2012-01-01

    Classical and frustrated Lewis pairs (LPs) of the strong Lewis acid (LA) Al(C 6F 5) 3 with several Lewis base (LB) classes have been found to exhibit exceptional activity in the Lewis pair polymerization (LPP) of conjugated polar alkenes such as methyl methacrylate (MMA) as well as renewable α-methylene-γ-butyrolactone (MBL) and γ-methyl- α-methylene-γ-butyrolactone (γ-MMBL), leading to high molecular weight polymers, often with narrow molecular weight distributions. This study has investigated a large number of LPs, consisting of 11 LAs as well as 10 achiral and 4 chiral LBs, for LPP of 12 monomers of several different types. Although some more common LAs can also be utilized for LPP, Al(C 6F 5) 3-based LPs are far more active and effective than other LA-based LPs. On the other hand, several classes of LBs, when paired with Al(C 6F 5) 3, can render highly active and effective LPP of MMA and γ-MMBL; such LBs include phosphines (e.g., P tBu 3), chiral chelating diphosphines, N-heterocyclic carbenes (NHCs), and phosphazene superbases (e.g., P 4- tBu). The P 4- tBu/Al(C 6F 5) 3 pair exhibits the highest activity of the LP series, with a remarkably high turn-over frequency of 9.6 × 10 4 h -1 (0.125 mol% catalyst, 100% MMA conversion in 30 s, M n = 2.12 × 10 5 g mol -1, PDI = 1.34). The polymers produced by LPs at RT are typically atactic (P γMMBL with ∼47% mr) or syndio-rich (PMMA with ∼70-75% rr), but highly syndiotactic PMMA with rr ∼91% can be produced by chiral or achiral LPs at -78 °C. Mechanistic studies have identified and structurally characterized zwitterionic phosphonium and imidazolium enolaluminates as the active species of the current LPP system, which are formed by the reaction of the monomer·Al(C 6F 5) 3 adduct with P tBu 3 and NHC bases, respectively. Kinetic studies have revealed that the MMA polymerization by the tBu 3P/ Al(C 6F 5) 3 pair is zero-order in monomer concentration after an initial induction period, and the polymerization

  6. Semi-regular biorthogonal pairs and generalized Riesz bases

    Science.gov (United States)

    Inoue, H.

    2016-11-01

    In this paper we introduce general theories of semi-regular biorthogonal pairs, generalized Riesz bases and its physical applications. Here we deal with biorthogonal sequences {ϕn} and {ψn} in a Hilbert space H , with domains D ( ϕ ) = { x ∈ H ; ∑ k = 0 ∞ |" separators=" ( x | ϕ k ) | 2 |" separators=" ( x | ψ k ) | 2 paper [H. Inoue, J. Math. Phys. 57, 083511 (2016)], we have shown that if ({ϕn}, {ψn}) is a regular biorthogonal pair then both {ϕn} and {ψn} are generalized Riesz bases defined in the work of Inoue and Takakura [J. Math. Phys. 57, 083505 (2016)]. Here we shall show that the same result holds true if the pair is only semi-regular by using operators Tϕ,e, Te,ϕ, Tψ,e, and Te,ψ defined by an orthonormal basis e in H and a biorthogonal pair ({ϕn}, {ψn}). Furthermore, we shall apply this result to pseudo-bosons in the sense of the papers of Bagarello [J. Math. Phys. 51, 023531 (2010); J. Phys. A 44, 015205 (2011); Phys. Rev. A 88, 032120 (2013); and J. Math. Phys. 54, 063512 (2013)].

  7. The effect of base pair mismatch on DNA strand displacement

    CERN Document Server

    Broadwater, Bo

    2016-01-01

    DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single base pair mismatch. The apparent displacement rate varied significantly when the mismatch was introduced in the invading DNA strand. The rate generally decreased as the mismatch in the invader was encountered earlier in displacement. Our data indicate that a single base pair mismatch in the invader stalls branch migration, and displacement occurs via direct dissociation of the destabilized incumbent strand from the substrate strand. We combined both branch migration and direct dissociation into a model, which we term, the concurrent displacement model, and used the first passage t...

  8. Coherent pair production in deformed crystals with a complex base

    CERN Document Server

    Mkrtchyan, A R; Saharian, A A

    2006-01-01

    We investigate the coherent electron-positron pair creation by high-energy photons in a periodically deformed single crystal with a complex base. The formula for the corresponding differential cross-section is derived for an arbitrary deformation field. The conditions are specified under which the influence of the deformation is considerable. The case is considered in detail when the photon enters into the crystal at small angles with respect to a crystallographic axis. The results of the numerical calculations are presented for $\\mathrm{SiO}_{2}$ single crystal and Moliere parametrization of the screened atomic potentials in the case of the deformation field generated by the acoustic wave of $S$ type. In dependence of the parameters, the presence of deformation can either enhance or reduce the pair creation cross-section. This can be used to control the parameters of the positron sources for storage rings and colliders.

  9. Physics of base-pairing dynamics in DNA

    Science.gov (United States)

    Manghi, Manoel; Destainville, Nicolas

    2016-05-01

    As a key molecule of life, Deoxyribo-Nucleic Acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have brought quantitative insights into DNA base-pairing dynamics that we review in this Report, putting emphasis on theoretical developments. We discuss the dynamics at the base-pair scale and its pivotal coupling with the polymer one, with a polymerization index running from a few nucleotides to tens of kilo-bases. This includes opening and closure of short hairpins and oligomers as well as zipping and unwinding of long macromolecules. We review how different physical mechanisms are either used by Nature or utilized in biotechnological processes to separate the two intertwined DNA strands, by insisting on quantitative results. They go from thermally-assisted denaturation bubble nucleation to force- or torque-driven mechanisms. We show that the helical character of the molecule, possibly supercoiled, can play a key role in many denaturation and renaturation processes. We categorize the mechanisms according to the relative timescales associated with base-pairing and chain orientational degrees of freedom such as bending and torsional elastic ones. In some specific situations, these chain orientational degrees of freedom can be integrated out, and the quasi-static approximation is valid. The complex dynamics then reduces to the diffusion in a low-dimensional free-energy landscape. In contrast, some important cases of experimental interest necessarily appeal to far-from-equilibrium statistical mechanics and hydrodynamics.

  10. A Random Number Generator Based on Quantum Entangled Photon Pairs

    Institute of Scientific and Technical Information of China (English)

    MA Hai-Qiang; WANG Su-Mei; ZHANG Da; CHANG Jun-Tao; JI Ling-Ling; HOU Yan-Xue; WU Ling-An

    2004-01-01

    A new scheme for a random number generator based on quantum entangled photon pairs is demonstrated.Signal photons produced by optical parametric down-conversion are detected at two single-photon detectors after transmission or reflection at a 50/50% beamsplitter, to form a truly random binary sequence. Their arrival is signalled by their twin idler photons, so that a cw laser source may be used instead of attenuated laser pulses.Coincidence measurement is employed to obtain the bit sequences, which are shown to fully satisfy the standard tests for randomness.

  11. A STEPPING STONE TOWARDS KNOWLEDGE BASED MAINTENANCE

    Directory of Open Access Journals (Sweden)

    G. Waeyenbergh

    2012-01-01

    Full Text Available Maintenance decision making becomes more and more a management concern. Some decades ago, maintenance was still often considered as an unavoidable side effect of production. The perception of maintenance has evolved considerably. One of the current issues is the maintenance concept, being the mix of maintenance interventions and the general framework for determining this mix. In this paper we describe a modular framework, called Knowledge Based Maintenance, for developing a customised maintenance concept. After describing the general framework and its decision support use, some case experiences are given. This experience covers some elements of the proposed framework.

  12. Single-molecule measurements of synthesis by DNA polymerase with base-pair resolution.

    Science.gov (United States)

    Christian, Thomas D; Romano, Louis J; Rueda, David

    2009-12-15

    The catalytic mechanism of DNA polymerases involves multiple steps that precede and follow the transfer of a nucleotide to the 3'-hydroxyl of the growing DNA chain. Here we report a single-molecule approach to monitor the movement of E. coli DNA polymerase I (Klenow fragment) on a DNA template during DNA synthesis with single base-pair resolution. As each nucleotide is incorporated, the single-molecule Förster resonance energy transfer intensity drops in discrete steps to values consistent with single-nucleotide incorporations. Purines and pyrimidines are incorporated with comparable rates. A mismatched primer/template junction exhibits dynamics consistent with the primer moving into the exonuclease domain, which was used to determine the fraction of primer-termini bound to the exonuclease and polymerase sites. Most interestingly, we observe a structural change after the incorporation of a correctly paired nucleotide, consistent with transient movement of the polymerase past the preinsertion site or a conformational change in the polymerase. This may represent a previously unobserved step in the mechanism of DNA synthesis that could be part of the proofreading process.

  13. Using Pair Programming to Teach CAD Based Engineering Graphics

    Science.gov (United States)

    Leland, Robert P.

    2010-01-01

    Pair programming was introduced into a course in engineering graphics that emphasizes solid modeling using SolidWorks. In pair programming, two students work at a single computer, and periodically trade off roles as driver (hands on the keyboard and mouse) and navigator (discuss strategy and design issues). Pair programming was used in a design…

  14. Single base pair mutation analysis by PNA directed PCR clamping

    DEFF Research Database (Denmark)

    Ørum, H.; Nielsen, P.E.; Egholm, M.;

    1993-01-01

    A novel method that allows direct analysis of single base mutation by the polymerase chain reaction (PCR) is described. The method utilizes the finding that PNAs (peptide nucleic acids) recognize and bind to their complementary nucleic acid sequences with higher thermal stability and specificity...... than the corresponding deoxyribooligonucleotides and that they cannot function as primers for DNA polymerases. We show that a PNA/DNA complex can effectively block the formation of a PCR product when the PNA is targeted against one of the PCR primer sites. Furthermore, we demonstrate that this blockage...... allows selective amplification/suppression of target sequences that differ by only one base pair. Finally we show that PNAs can be designed in such a way that blockage can be accomplished when the PNA target sequence is located between the PCR primers....

  15. Comparative Analysis for NN-Based Adaptive Back-stepping Controller and Back-stepping Controller

    OpenAIRE

    Margarita Gjonaj; BetimÇiço; ArnisaMyrtellari

    2016-01-01

    This work primarily addresses the design and implementation of a neural network based controller for the trajectory tracking of a differential drive mobile robot. The proposed control algorithm is an NN-based adaptive controller which tunes the gains of the back-stepping controller online according to the robot reference trajectory and its initial posture. In this method, a neural network is needed to learn the characteristics of the plant dynamics and make use of it to determine the future i...

  16. [Web-based education: learning surgical procedures step-by-step with 3D visualization].

    Science.gov (United States)

    van der Velde, Susanne; Maljers, Jaap; Wiggers, Theo

    2014-01-01

    There is a need for more uniform, structured education focused on surgical procedures. We offer a standardized, step-by-step, web-based procedural training method with which surgeons can train more interns efficiently. The basis of this learning method is formed by 3D films in which surgical procedures are performed in clearly defined steps and the anatomic structures behind the surgical operating planes are further dissected. This basis is supported by online modules in which, aside from the operation, preparation and postoperative care are also addressed. Registrars can test their knowledge with exams. Trainers can see what the registrars studied, how they scored and how they progressed with their clinical skills. With the online portfolio we offer building blocks for certification and accreditation. With this clearly structured research method of constant quality, registrars are less dependent on the local trainer. In addition, through better preparation, the operation capacity can be used more efficiently for the training.

  17. Sorting Pairs of Points Based on Their Distances

    Directory of Open Access Journals (Sweden)

    Mohammad Farshi

    2016-02-01

    Full Text Available Sorting data is one of the main problems in computer science which studied vastly and used in several places. In several geometric problems, like problems on point sets or lines in the plane or Euclidean space with higher dimensions, the problem of sorting pairs of points based on the distance (between them is used. Using general sorting algorithms, sorting n 2 distances between n points can be done in O(n2 log n time. Ofcourse, sorting (n2 independent numbers does not have a faster solution, but since we have dependency between numbers in this case, finding a faster algorithm or showing that the problem in this case has O(n2 log n time complexity is interesting. In this paper, we try to answer this question.

  18. Unique magnetic signatures of mismatched base pairs in DNA

    Science.gov (United States)

    Apalkov, Vadim; Berashevich, Julia; Chakraborty, Tapash

    2010-02-01

    Magnetic properties of DNA containing mispairs, such as different conformations of the GṡA mispair, or a GṡT mispair inserted into the DNA chain, have been theoretically investigated. The essential ingredients for these studies, the charge transfer integrals, were evaluated from the DNA sequences containing the mispair and optimized in the solvent. We find that the magnetic susceptibilities of the host DNA chain containing a large number of Watson-Crick base pairs are significantly altered in the presence of the mispairs, and the effects depend on the choice of mispairs. In particular, insertion of even a single GṡA mispair changes the nature of magnetization (sign of the susceptibility) of the host DNA. We propose that measurement of the magnetic properties of DNA might provide a direct route to detection and identification of those mispairs.

  19. An efficient and near linear scaling pair natural orbital based local coupled cluster method

    Science.gov (United States)

    Riplinger, Christoph; Neese, Frank

    2013-01-01

    In previous publications, it was shown that an efficient local coupled cluster method with single- and double excitations can be based on the concept of pair natural orbitals (PNOs) [F. Neese, A. Hansen, and D. G. Liakos, J. Chem. Phys. 131, 064103 (2009), 10.1063/1.3173827]. The resulting local pair natural orbital-coupled-cluster single double (LPNO-CCSD) method has since been proven to be highly reliable and efficient. For large molecules, the number of amplitudes to be determined is reduced by a factor of 105-106 relative to a canonical CCSD calculation on the same system with the same basis set. In the original method, the PNOs were expanded in the set of canonical virtual orbitals and single excitations were not truncated. This led to a number of fifth order scaling steps that eventually rendered the method computationally expensive for large molecules (e.g., >100 atoms). In the present work, these limitations are overcome by a complete redesign of the LPNO-CCSD method. The new method is based on the combination of the concepts of PNOs and projected atomic orbitals (PAOs). Thus, each PNO is expanded in a set of PAOs that in turn belong to a given electron pair specific domain. In this way, it is possible to fully exploit locality while maintaining the extremely high compactness of the original LPNO-CCSD wavefunction. No terms are dropped from the CCSD equations and domains are chosen conservatively. The correlation energy loss due to the domains remains below 8800 basis functions and >450 atoms. In all larger test calculations done so far, the LPNO-CCSD step took less time than the preceding Hartree-Fock calculation, provided no approximations have been introduced in the latter. Thus, based on the present development reliable CCSD calculations on large molecules with unprecedented efficiency and accuracy are realized.

  20. Paired structures and other opposite-based models

    DEFF Research Database (Denmark)

    Rodríguez, J. Tinguaro; Franco, Camilo; Gómez, Daniel;

    2015-01-01

    In this paper we present a new class of fuzzy sets, paired fuzzy sets, that tries to overcome any conflict between families of fuzzy sets that share a main characteristic: that they are generated from two basic opposite fuzzy sets. Hence, the first issue is to formalize the notion of opposition, ...... as a particular paired structure when the classical fuzzy negation is considered; on the other hand, the relationship of this model with bipolarity is reconsidered from our paired view....

  1. Marker-based filtering of bilingual phrase pairs for SMT

    OpenAIRE

    Sánchez-Martínez, Felipe; Way, Andy

    2009-01-01

    State-of-the-art statistical machine translation systems make use of a large translation table obtained after scoring a set of bilingual phrase pairs automatically extracted from a parallel corpus. The number of bilingual phrase pairs extracted from a pair of aligned sentences grows exponentially as the length of the sentences increases; therefore, the number of entries in the phrase table used to carry out the translation may become unmanageable, especially when online, ‘on demand’ translati...

  2. Paired structures and other opposite-based models

    DEFF Research Database (Denmark)

    Rodríguez, J. Tinguaro; Franco, Camilo; Gómez, Daniel

    2015-01-01

    to a more complex valuation structure that still keeps the essence of being paired. In this way several neutral fuzzy sets can appear, in particular indeterminacy, ambivalence and conflict. Two consequences are then presented: on one hand, we will show how Atanassov´s Intuitionistic Fuzzy Sets can be viewed...... as a particular paired structure when the classical fuzzy negation is considered; on the other hand, the relationship of this model with bipolarity is reconsidered from our paired view....

  3. DNA duplex stability of the thio-iso-guanine•methyl-iso-Cytosine base pair.

    Science.gov (United States)

    Lee, Dongkye; Switzer, Christopher

    2015-01-01

    We report the synthesis, incorporation into oligonucleotides, and base-pairing properties of the 2-thio-variant of iso-guanine. Iso-guanine is the purine component of a nonstandard base pair with 5-methyl-iso-cytosine. The 2-thio-iso-guanine • 5-methyl-iso-cytosine base pair is found to have similar stability to an adenine • thymine pair.

  4. Analytic solutions for unconfined groundwater flow over a stepped base

    Science.gov (United States)

    Fitts, Charles R.; Strack, Otto D. L.

    1996-03-01

    Two new exact solutions are presented for uniform unconfined groundwater flow over a stepped base; one for a step down in the direction of flow, the other for a step up in the direction of flow. These are two-dimensional solutions of Laplace's equation in the vertical plane, and are derived using the hodograph method and conformal mappings on Riemann surfaces. The exact solutions are compared with approximate one-dimensional solutions which neglect the resistance to vertical flow. For small horizontal hydraulic gradients typical of regional groundwater flow, little error is introduced by neglecting the vertical resistance to flow. This conclusion may be extended to two-dimensional analytical models in the horizontal plane, which neglect the vertical resistance to flow and treat the aquifer base as a series of flat steps.

  5. Variable Step Size Maximum Correntropy Criteria Based Adaptive Filtering Algorithm

    Directory of Open Access Journals (Sweden)

    S. Radhika

    2016-04-01

    Full Text Available Maximum correntropy criterion (MCC based adaptive filters are found to be robust against impulsive interference. This paper proposes a novel MCC based adaptive filter with variable step size in order to obtain improved performance in terms of both convergence rate and steady state error with robustness against impulsive interference. The optimal variable step size is obtained by minimizing the Mean Square Deviation (MSD error from one iteration to the other. Simulation results in the context of a highly impulsive system identification scenario show that the proposed algorithm has faster convergence and lesser steady state error than the conventional MCC based adaptive filters.

  6. Base pairing in RNA structures: A computational analysis of structural aspects and interaction energies

    Indian Academy of Sciences (India)

    Purshotam Sharma; Abhijit Mitra; Sitansh Sharma; Harjinder Singh

    2007-09-01

    The base pairing patterns in RNA structures are more versatile and completely different as compared to DNA. We present here results of ab-initio studies of structures and interaction energies of eight selected RNA base pairs reported in literature. Interaction energies, including BSSE correction, of hydrogen added crystal geometries of base pairs have been calculated at the HF/6-31G∗∗ level. The structures and interaction energies of the base pairs in the crystal geometry are compared with those obtained after optimization of the base pairs. We find that the base pairs become more planar on full optimization. No change in the hydrogen bonding pattern is seen. It is expected that the inclusion of appropriate considerations of many of these aspects of RNA base pairing would significantly improve the accuracy of RNA secondary structure prediction.

  7. A new unnatural base pair system between fluorophore and quencher base analogues for nucleic acid-based imaging technology.

    Science.gov (United States)

    Kimoto, Michiko; Mitsui, Tsuneo; Yamashige, Rie; Sato, Akira; Yokoyama, Shigeyuki; Hirao, Ichiro

    2010-11-03

    In the development of orthogonal extra base pairs for expanding the genetic alphabet, we created novel, unnatural base pairs between fluorophore and quencher nucleobase analogues. We found that the nucleobase analogue, 2-nitropyrrole (denoted by Pn), and its 4-substitutions, such as 2-nitro-4-propynylpyrrole (Px) and 4-[3-(6-aminohexanamido)-1-propynyl]-2-nitropyrrole (NH(2)-hx-Px), act as fluorescence quenchers. The Pn and Px bases specifically pair with their pairing partner, 7-(2,2'-bithien-5-yl)imidazo[4,5-b]pyridine (Dss), which is strongly fluorescent. Thus, these unnatural Dss-Pn and Dss-Px base pairs function as reporter-quencher base pairs, and are complementarily incorporated into DNA by polymerase reactions as a third base pair in combination with the natural A-T and G-C pairs. Due to the static contact quenching, the Pn and Px quencher bases significantly decreased the fluorescence intensity of Dss by the unnatural base pairings in DNA duplexes. In addition, the Dss-Px pair exhibited high efficiency and selectivity in PCR amplification. Thus, this new unnatural base pair system would be suitable for detection methods of target nucleic acid sequences, and here we demonstrated the applications of the Dss-Pn and Dss-Px pairs as molecular beacons and in real-time PCR. The genetic alphabet expansion system with the replicable, unnatural fluorophore-quencher base pair will be a useful tool for sensing and diagnostic applications, as well as an imaging tool for basic research.

  8. Calculation of the Stabilization Energies of Oxidatively Damaged Guanine Base Pairs with Guanine

    Directory of Open Access Journals (Sweden)

    Hiroshi Miyazawa

    2012-06-01

    Full Text Available DNA is constantly exposed to endogenous and exogenous oxidative stresses. Damaged DNA can cause mutations, which may increase the risk of developing cancer and other diseases. G:C-C:G transversions are caused by various oxidative stresses. 2,2,4-Triamino-5(2H-oxazolone (Oz, guanidinohydantoin (Gh/iminoallantoin (Ia and spiro-imino-dihydantoin (Sp are known products of oxidative guanine damage. These damaged bases can base pair with guanine and cause G:C-C:G transversions. In this study, the stabilization energies of these bases paired with guanine were calculated in vacuo and in water. The calculated stabilization energies of the Ia:G base pairs were similar to that of the native C:G base pair, and both bases pairs have three hydrogen bonds. By contrast, the calculated stabilization energies of Gh:G, which form two hydrogen bonds, were lower than the Ia:G base pairs, suggesting that the stabilization energy depends on the number of hydrogen bonds. In addition, the Sp:G base pairs were less stable than the Ia:G base pairs. Furthermore, calculations showed that the Oz:G base pairs were less stable than the Ia:G, Gh:G and Sp:G base pairs, even though experimental results showed that incorporation of guanine opposite Oz is more efficient than that opposite Gh/Ia and Sp.

  9. RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs

    Science.gov (United States)

    Bhattacharyya, Dhananjay; Halder, Sukanya; Basu, Sankar; Mukherjee, Debasish; Kumar, Prasun; Bansal, Manju

    2017-02-01

    Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson-Crick or non-Watson-Crick base pairs. The original structure and the corresponding regenerated structure of double helices were found to be very close, as indicated by the small RMSD values between positions of the corresponding atoms. Structures of several usual and unusual double helices have been regenerated and compared with their original structures in terms of base pair RMSD, torsion angles and electrostatic potentials and very high agreements have been noted. RNAHelix can also be used to generate a structure with a sequence completely different from an experimentally determined one or to introduce single to multiple mutation, but with the same set of parameters and hence can also be an important tool in homology modeling and study of mutation induced structural changes.

  10. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

    Indian Academy of Sciences (India)

    Surjit B Dixit; Mihaly Mezei; David L Beveridge

    2012-07-01

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute–solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interactmore strongly with watermolecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning’s counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 Å from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general

  11. Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Yuan-Yan; Bao, Lei; Zhang, Xi; Tan, Zhi-Jie, E-mail: zjtan@whu.edu.cn [Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072 (China)

    2015-03-28

    Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher flexibility than those of kilo bps, while there is still the debate on such high flexibility. In the present work, we have studied the flexibility of short DNAs with finite-length of 5–50 bps by the all-atomistic molecular dynamics simulations and Monte Carlo simulations with the worm-like chain model. Our microscopic analyses reveal that short DNAs have apparently high flexibility which is attributed to the significantly strong bending and stretching flexibilities of ∼6 bps at each helix end. Correspondingly, the apparent persistence length l{sub p} of short DNAs increases gradually from ∼29 nm to ∼45 nm as DNA length increases from 10 to 50 bps, in accordance with the available experimental data. Our further analyses show that the short DNAs with excluding ∼6 bps at each helix end have the similar flexibility with those of kilo bps and can be described by the worm-like chain model with l{sub p} ∼ 50 nm.

  12. Flexibility of short DNA helices with finite-length effect: from base pairs to tens of base pairs

    CERN Document Server

    Wu, Yuan-Yan; Zhang, Xi; Tan, Zhi-Jie

    2015-01-01

    Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher flexibility than those of kilo bps, while there is still the debate on such high flexibility. In the present work, we have studied the flexibility of short DNAs with finite-length of 5 to 50 bps by the all-atomistic molecular dynamics simulations and Monte Carlo simulations with the worm-like chain model. Our microscopic analyses reveal that short DNAs have apparently high flexibility which is attributed to the significantly strong bending and stretching flexibilities of ~6 bps at each helix end. Correspondingly, the apparent persistence length lp of short DNAs increases gradually from ~29nm to ~45nm as DNA length increases from 10 to 50 bps, in accordance with the available experimental data. Our further analyses show that the short DNAs with excluding ~6 bps at each helix end have...

  13. Self-Similarity Based Corresponding-Point Extraction from Weakly Textured Stereo Pairs

    Directory of Open Access Journals (Sweden)

    Min Mao

    2014-01-01

    Full Text Available For the areas of low textured in image pairs, there is nearly no point that can be detected by traditional methods. The information in these areas will not be extracted by classical interest-point detectors. In this paper, a novel weakly textured point detection method is presented. The points with weakly textured characteristic are detected by the symmetry concept. The proposed approach considers the gray variability of the weakly textured local regions. The detection mechanism can be separated into three steps: region-similarity computation, candidate point searching, and refinement of weakly textured point set. The mechanism of radius scale selection and texture strength conception are used in the second step and the third step, respectively. The matching algorithm based on sparse representation (SRM is used for matching the detected points in different images. The results obtained on image sets with different objects show high robustness of the method to background and intraclass variations as well as to different photometric and geometric transformations; the points detected by this method are also the complement of points detected by classical detectors from the literature. And we also verify the efficacy of SRM by comparing with classical algorithms under the occlusion and corruption situations for matching the weakly textured points. Experiments demonstrate the effectiveness of the proposed weakly textured point detection algorithm.

  14. Plasmon switching effect based on graphene nanoribbon pair arrays

    Science.gov (United States)

    Liu, Dan; Wu, Lingxi; Liu, Qiong; Zhou, Renlong; Xie, Suxia; Chen, Jiangjiamin; Wu, Mengxiong; Zeng, Lisan

    2016-10-01

    We theoretically demonstrate the existence of plasmon switching effect in graphene nanostructure. By using finite-difference time-domain (FDTD) method, the plasmon resonance modes are studied in graphene nanoribbon pair arrays with the change of Fermi level, graphene width, and carrier mobility. It is found that the Fermi level and graphene width play an important role in changing the distribution of electric energy on different graphene nanoribbons, resulting in a significant plasmon switching effect. Moreover, we study the characteristic of resonance mode of one graphene ribbon by using glass rod with different shape. The effect of kerr material sandwiched between graphene nanoribbon pair is also considered.

  15. Uniform step-by-step observer for aerobic bioreactor based on super-twisting algorithm.

    Science.gov (United States)

    Martínez-Fonseca, N; Chairez, I; Poznyak, A

    2014-12-01

    This paper describes a fixed-time convergent step-by-step high order sliding mode observer for a certain type of aerobic bioreactor system. The observer was developed using a hierarchical structure based on a modified super-twisting algorithm. The modification included nonlinear gains of the output error that were used to prove uniform convergence of the estimation error. An energetic function similar to a Lyapunov one was used for proving the convergence between the observer and the bioreactor variables. A nonsmooth analysis was proposed to prove the fixed-time convergence of the observer states to the bioreactor variables. The observer was tested to solve the state estimation problem of an aerobic bioreactor described by the time evolution of biomass, substrate and dissolved oxygen. This last variable was used as the output information because it is feasible to measure it online by regular sensors. Numerical simulations showed the superior behavior of this observer compared to the one having linear output error injection terms (high-gain type) and one having an output injection obtaining first-order sliding mode structure. A set of numerical simulations was developed to demonstrate how the proposed observer served to estimate real information obtained from a real aerobic process with substrate inhibition.

  16. Comparable Stability of Hoogsteen and Watson–Crick Base Pairs in Ionic Liquid Choline Dihydrogen Phosphate

    OpenAIRE

    Hisae Tateishi-Karimata; Miki Nakano; Naoki Sugimoto

    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 stabi...

  17. Genomic analysis of plant chromosomes based on meiotic pairing

    Directory of Open Access Journals (Sweden)

    Lisete Chamma Davide

    2007-12-01

    Full Text Available This review presents the principles and applications of classical genomic analysis, with emphasis on plant breeding. The main mathematical models used to estimate the preferential chromosome pairing in diploid or polyploid, interspecific or intergenera hybrids are presented and discussed, with special reference to the applications and studies for the definition of genome relationships among species of the Poaceae family.

  18. [Under what conditions does G.C Watson-Crick DNA base pair acquire all four configurations characteristic for A.T Watson-Crick DNA base pair?].

    Science.gov (United States)

    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.

  19. Data-Based Predictive Control with Multirate Prediction Step

    Science.gov (United States)

    Barlow, Jonathan S.

    2010-01-01

    Data-based predictive control is an emerging control method that stems from Model Predictive Control (MPC). MPC computes current control action based on a prediction of the system output a number of time steps into the future and is generally derived from a known model of the system. Data-based predictive control has the advantage of deriving predictive models and controller gains from input-output data. Thus, a controller can be designed from the outputs of complex simulation code or a physical system where no explicit model exists. If the output data happens to be corrupted by periodic disturbances, the designed controller will also have the built-in ability to reject these disturbances without the need to know them. When data-based predictive control is implemented online, it becomes a version of adaptive control. One challenge of MPC is computational requirements increasing with prediction horizon length. This paper develops a closed-loop dynamic output feedback controller that minimizes a multi-step-ahead receding-horizon cost function with multirate prediction step. One result is a reduced influence of prediction horizon and the number of system outputs on the computational requirements of the controller. Another result is an emphasis on portions of the prediction window that are sampled more frequently. A third result is the ability to include more outputs in the feedback path than in the cost function.

  20. Contiguous metal-mediated base pairs comprising two Ag(I) ions.

    Science.gov (United States)

    Megger, Dominik A; Guerra, Célia Fonseca; Hoffmann, Jan; Brutschy, Bernhard; Bickelhaupt, F Matthias; Müller, Jens

    2011-05-27

    The incorporation of transition-metal ions into nucleic acids by using metal-mediated base pairs has proved to be a promising strategy for the site-specific functionalization of these biomolecules. We report herein the formation of Ag(+)-mediated Hoogsteen-type base pairs comprising 1,3-dideaza-2'-deoxyadenosine and thymidine. By defunctionalizing the Watson-Crick edge of adenine, the formation of regular base pairs is prohibited. The additional substitution of the N3 nitrogen atom of adenine by a methine moiety increases the basicity of the exocyclic amino group. Hence, 1,3-dideazaadenine and thymine are able to incorporate two Ag(+) ions into their Hoogsteen-type base pair (as compared with one Ag(+) ion in base pairs with 1-deazaadenine and thymine). We show by using a combination of experimental techniques (UV and circular dichroism (CD) spectroscopies, dynamic light scattering, and mass spectrometry) that this type of base pair is compatible with different sequence contexts and can be used contiguously in DNA double helices. The most stable duplexes were observed when using a sequence containing alternating purine and pyrimidine nucleosides. Dispersion-corrected density functional theory calculations have been performed to provide insight into the structure, formation and stabilization of the twofold metalated base pair. They revealed that the metal ions within a base pair are separated by an Ag···Ag distance of about 2.88 Å. The Ag-Ag interaction contributes some 16 kcal mol(-1) to the overall stability of the doubly metal-mediated base pair, with the dominant contribution to the Ag-Ag bonding resulting from a donor-acceptor interaction between silver 4d-type and 4s orbitals. These Hoogsteen-type base pairs enable a higher functionalization of nucleic acids with metal ions than previously reported metal-mediated base pairs, thereby increasing the potential of DNA-based nanotechnology.

  1. Molecular Design of Ionization-Induced Proton Switching Element Based on Fluorinated DNA Base Pair.

    Science.gov (United States)

    Tachikawa, Hiroto; Kawabata, Hiroshi

    2016-03-10

    To design theoretically the high-performance proton switching element based on DNA base pair, the effects of fluorine substitution on the rate of proton transfer (PT) in the DNA model base pair have been investigated by means of direct ab initio molecular dynamics (AIMD) method. The 2-aminopyridine dimer, (AP)2, was used as the model of the DNA base pair. One of the hydrogen atoms of the AP molecule in the dimer was substituted by a fluorine (F) atom, and the structures of the dimer, expressed by F-(AP)2, were fully optimized at the MP2/6-311++G(d,p) level. The direct AIMD calculations showed that the proton is transferred within the base pair after the vertical ionization. The rates of PT in F-(AP)2(+) were calculated and compared with that of (AP)2(+) without an F atom. It was found that PT rate is accelerated by the F-substitution. Also, the direction of PT between F-AP and AP molecules can be clearly controlled by the position of F-substitution (AP)2 in the dimer.

  2. A pipelined Reed-Solomon decoder based on a modified step-by-step algorithm

    Institute of Scientific and Technical Information of China (English)

    Xing-ru PENG; Wei ZHANG; Yan-yan LIU

    2016-01-01

    We propose a pipelined Reed-Solomon (RS) decoder for an ultra-wideband system using a modified step-by-step algorithm. To reduce the complexity, the modified step-by-step algorithm merges two cases of the original algorithm. The pipelined structure allows the decoder to work at high rates with minimum delay. Consequently, for RS(23,17) codes, the proposed architecture requires 42.5%and 24.4%less area compared with a modified Euclidean architecture and a pipelined degree-computationless modified Euclidean architecture, respectively. The area of the proposed decoder is 11.3% less than that of the previous step-by-step decoder with a lower critical path delay.

  3. Alternative radical pairs for cryptochrome-based magnetoreception

    Science.gov (United States)

    Lee, Alpha A.; Lau, Jason C. S.; Hogben, Hannah J.; Biskup, Till; Kattnig, Daniel R.; Hore, P. J.

    2014-01-01

    There is growing evidence that the remarkable ability of animals, in particular birds, to sense the direction of the Earth's magnetic field relies on magnetically sensitive photochemical reactions of the protein cryptochrome. It is generally assumed that the magnetic field acts on the radical pair [FAD•− TrpH•+] formed by the transfer of an electron from a group of three tryptophan residues to the photo-excited flavin adenine dinucleotide cofactor within the protein. Here, we examine the suitability of an [FAD•− Z•] radical pair as a compass magnetoreceptor, where Z• is a radical in which the electron spin has no hyperfine interactions with magnetic nuclei, such as hydrogen and nitrogen. Quantum spin dynamics simulations of the reactivity of [FAD•− Z•] show that it is two orders of magnitude more sensitive to the direction of the geomagnetic field than is [FAD•− TrpH•+] under the same conditions (50 µT magnetic field, 1 µs radical lifetime). The favourable magnetic properties of [FAD•− Z•] arise from the asymmetric distribution of hyperfine interactions among the two radicals and the near-optimal magnetic properties of the flavin radical. We close by discussing the identity of Z• and possible routes for its formation as part of a spin-correlated radical pair with an FAD radical in cryptochrome. PMID:24671932

  4. Functional renormalization-group study of the pairing symmetry and pairing mechanism of the FeAs-based high-temperature superconductor.

    Science.gov (United States)

    Wang, Fa; Zhai, Hui; Ran, Ying; Vishwanath, Ashvin; Lee, Dung-Hai

    2009-01-30

    We apply the fermion functional renormalization-group method to determine the pairing symmetry and pairing mechanism of the FeAs-Based materials. Within a five band model with pure repulsive interactions, we find an electronic-driven superconducting pairing instability. For the doping and interaction parameters we have examined, extended s wave, whose order parameter takes on opposite sign on the electron and hole pockets, is always the most favorable pairing symmetry. The pairing mechanism is the inter-Fermi-surface Josephson scattering generated by the antiferromagnetic correlation.

  5. A novel pseudo-complementary PNA G-C base pair

    DEFF Research Database (Denmark)

    Olsen, Anne G.; Dahl, Otto; Petersen, Asger Bjørn;

    2011-01-01

    Pseudo-complementary oligonucleotide analogues and mimics provide novel opportunities for targeting duplex structures in RNA and DNA. Previously, a pseudo-complementary A-T base pair has been introduced. Towards sequence unrestricted targeting, a pseudo-complementary G-C base pair consisting...

  6. Key technology of ship product data exchange based on STEP

    Science.gov (United States)

    Shi, Dong-Yan; Yang, Jing-Tong; Qiu, Chang-Hua; Xue, Kai

    2005-06-01

    In this paper, in order to implement the share and exchange of the ship product data, a new kind of global function model is established. By researching on the development and trend of the application of ship STEP (standard for the exchange of product model data) standards, the AIM (application interpreted model) of AP216 is developed and improved as an example, aiming at the characteristics and practical engineering of ship industry in our country. The data exchange interfaces are formed based on STEP in the CAD/CAM for the ship by all function modules and shared databases under the global function model. The share and exchange of all information and data are solved in the design, manufacture and all life-cycle of ship products among different computer application systems. The research work makes foundation for the ship industry informatization.

  7. Key technology of ship product data exchange based on STEP

    Institute of Scientific and Technical Information of China (English)

    SHI Dong-yan; YANG Jing-tong; QIU Chang-hua; XUE Kai

    2005-01-01

    In this paper, in order to implement the share and exchange of the ship product data, a new kind of global function model is established. By researching on the development and trend of the application of ship STEP (standard for the exchange of product model data) standards, the AIM (application interpreted model) of AP216 is developed and improved as an example, aiming at the characteristics and practical engineering of ship industry in our country. The data exchange interfaces are formed based on STEP in the CAD/CAM for the ship by all function modules and shared databases under the global function model. The share and exchange of all information and data are solved in the design, manufacture and all life-cycle of ship products among different computer application systems. The research work makes foundation for the ship industry informatization.

  8. Fingerprint Identification Using SIFT-Based Minutia Descriptors and Improved All Descriptor-Pair Matching

    Directory of Open Access Journals (Sweden)

    Jiuqiang Han

    2013-03-01

    Full Text Available The performance of conventional minutiae-based fingerprint authentication algorithms degrades significantly when dealing with low quality fingerprints with lots of cuts or scratches. A similar degradation of the minutiae-based algorithms is observed when small overlapping areas appear because of the quite narrow width of the sensors. Based on the detection of minutiae, Scale Invariant Feature Transformation (SIFT descriptors are employed to fulfill verification tasks in the above difficult scenarios. However, the original SIFT algorithm is not suitable for fingerprint because of: (1 the similar patterns of parallel ridges; and (2 high computational resource consumption. To enhance the efficiency and effectiveness of the algorithm for fingerprint verification, we propose a SIFT-based Minutia Descriptor (SMD to improve the SIFT algorithm through image processing, descriptor extraction and matcher. A two-step fast matcher, named improved All Descriptor-Pair Matching (iADM, is also proposed to implement the 1:N verifications in real-time. Fingerprint Identification using SMD and iADM (FISiA achieved a significant improvement with respect to accuracy in representative databases compared with the conventional minutiae-based method. The speed of FISiA also can meet real-time requirements.

  9. Fingerprint identification using SIFT-based minutia descriptors and improved all descriptor-pair matching.

    Science.gov (United States)

    Zhou, Ru; Zhong, Dexing; Han, Jiuqiang

    2013-03-06

    The performance of conventional minutiae-based fingerprint authentication algorithms degrades significantly when dealing with low quality fingerprints with lots of cuts or scratches. A similar degradation of the minutiae-based algorithms is observed when small overlapping areas appear because of the quite narrow width of the sensors. Based on the detection of minutiae, Scale Invariant Feature Transformation (SIFT) descriptors are employed to fulfill verification tasks in the above difficult scenarios. However, the original SIFT algorithm is not suitable for fingerprint because of: (1) the similar patterns of parallel ridges; and (2) high computational resource consumption. To enhance the efficiency and effectiveness of the algorithm for fingerprint verification, we propose a SIFT-based Minutia Descriptor (SMD) to improve the SIFT algorithm through image processing, descriptor extraction and matcher. A two-step fast matcher, named improved All Descriptor-Pair Matching (iADM), is also proposed to implement the 1:N verifications in real-time. Fingerprint Identification using SMD and iADM (FISiA) achieved a significant improvement with respect to accuracy in representative databases compared with the conventional minutiae-based method. The speed of FISiA also can meet real-time requirements.

  10. A Project Risk Ranking Approach Based on Set Pair Analysis

    Institute of Scientific and Technical Information of China (English)

    Gao Feng; Chen Yingwu

    2006-01-01

    Set Pair Analysis (SPA) is a new methodology to describe and process system uncertainty. It is different from stochastic or fuzzy methods in reasoning and operation, and it has been applied in many areas recently. In this paper, the application of SPA in risk ranking is presented, which includes review of risk ranking, introduction of Connecting Degree (CD) that is a key role in SPA., Arithmetic and Tendency Grade (TG) of CDs, and a risk ranking approach proposed. Finally a case analysis is presented to illustrate the reasonability of this approach. It is found that this approach is very convenient to operate, while the ranking result is more comprehensible.

  11. Roles of the Amino Group of Purine Bases in the Thermodynamic Stability of DNA Base Pairing

    Directory of Open Access Journals (Sweden)

    Shu-ichi Nakano

    2014-08-01

    Full Text Available The energetic aspects of hydrogen-bonded base-pair interactions are important for the design of functional nucleotide analogs and for practical applications of oligonucleotides. The present study investigated the contribution of the 2-amino group of DNA purine bases to the thermodynamic stability of oligonucleotide duplexes under different salt and solvent conditions, using 2'-deoxyriboinosine (I and 2'-deoxyribo-2,6-diaminopurine (D as non-canonical nucleotides. The stability of DNA duplexes was changed by substitution of a single base pair in the following order: G•C > D•T ≈ I•C > A•T > G•T > I•T. The apparent stabilization energy due to the presence of the 2-amino group of G and D varied depending on the salt concentration, and decreased in the water-ethanol mixed solvent. The effects of salt concentration on the thermodynamics of DNA duplexes were found to be partially sequence-dependent, and the 2-amino group of the purine bases might have an influence on the binding of ions to DNA through the formation of a stable base-paired structure. Our results also showed that physiological salt conditions were energetically favorable for complementary base recognition, and conversely, low salt concentration media and ethanol-containing solvents were effective for low stringency oligonucleotide hybridization, in the context of conditions employed in this study.

  12. Covering All the Bases in Genetics: Simple Shorthands and Diagrams for Teaching Base Pairing to Biology Undergraduates

    Directory of Open Access Journals (Sweden)

    Sergei Kuchin

    2011-03-01

    Full Text Available Explaining base pairing is an important element in teaching undergraduate genetics. I propose a teaching approach that aims to close the gap between the mantra “A pairs with T, and G pairs with C” and the “intimidating” chemical diagrams. The approach offers a set of simple “shorthands” for the key bases that can be used to quickly deduce all canonical and wobble pairs that the students need to know. The approach can be further developed to analyze mutagenic mismatch pairing.

  13. Feature Based Stereo Matching Using Two-Step Expansion

    Directory of Open Access Journals (Sweden)

    Liqiang Wang

    2014-01-01

    Full Text Available This paper proposes a novel method for stereo matching which is based on image features to produce a dense disparity map through two different expansion phases. It can find denser point correspondences than those of the existing seed-growing algorithms, and it has a good performance in short and wide baseline situations. This method supposes that all pixel coordinates in each image segment corresponding to a 3D surface separately satisfy projective geometry of 1D in horizontal axis. Firstly, a state-of-the-art method of feature matching is used to obtain sparse support points and an image segmentation-based prior is employed to assist the first region outspread. Secondly, the first-step expansion is to find more feature correspondences in the uniform region via initial support points, which is based on the invariant cross ratio in 1D projective transformation. In order to find enough point correspondences, we use a regular seed-growing algorithm as the second-step expansion and produce a quasi-dense disparity map. Finally, two different methods are used to obtain dense disparity map from quasi-dense pixel correspondences. Experimental results show the effectiveness of our method.

  14. Pairing state with a time-reversal symmetry breaking in FeAs-based superconductors.

    Science.gov (United States)

    Lee, Wei-Cheng; Zhang, Shou-Cheng; Wu, Congjun

    2009-05-29

    We investigate the competition between the extended s+/--wave and dx2-y2-wave pairing order parameters in the iron-based superconductors. Because of the frustrating pairing interactions among the electron and the hole Fermi pockets, a time-reversal symmetry breaking s+id pairing state could be favored. We analyze this pairing state within the Ginzburg-Landau theory and explore the experimental consequences. In such a state, spatial inhomogeneity induces a supercurrent near a nonmagnetic impurity and the corners of a square sample. The resonance mode between the s+/-- and dx2-y2-wave order parameters can be detected through the B1g Raman spectroscopy.

  15. THE CONSTRUCTIONS OF ALMOST BINARY SEQUENCE PAIRS WITH THREE-LEVEL CORRELATION BASED ON CYCLOTOMY

    Institute of Scientific and Technical Information of China (English)

    Peng Xiuping; Xu Chengqian

    2012-01-01

    In this paper,a new class of almost binary sequence pair with a single zero element is presented.The almost binary sequence pairs with three-level correlation are constructed based on cyclotomic numbers of order 2,4,and 6.Most of them have good correlation and balance property,whose maximum nontrivial correlation magnitudes are 2 and the difference between the numbers of occurrence of +1's and -1's are 0 or 1.In addition,the corresponding binary sequence pairs are investigated as well and we can also get some kinds of binary sequence pairs with optimum balance and good correlation.

  16. [Fourier Transform Spectrometer Based on Rotating Parallel-Mirror-Pair].

    Science.gov (United States)

    Zhao, Bao-wei; Xiangli, Bin; Cai, Qi-sheng; Lü, Qun-bo; Zhou, Jin-song

    2015-11-01

    In the temporally-modulated Fourier transform spectroscopy, the translational moving mirror is difficult to drive accurately, causing tilt and shear problems. While, a rotational moving mirror can solve these problems. A rotary Fourier transform spectrometer is recommanded in this paper. Its principle is analyzed and the optical path difference is deduced. Also, the constrains for engineering realization are presented. This spectrometer consists of one beamsplitter, two fixed mirrors, one rotating parallel mirror pair, a collimating lens, a collecting lens, and one detector. From it's principle, this spectrometer show a simple structure, and it is assembled and adjustmented easily because the two split light are interfered with each other after reflected through the same plane mirror; By calculating the expression of it's optical path difference, the spectrometer is easy to realize large optical path difference, meaning high spectral resolution; Through analyzing it's engineering design constraints and computer simulation, it is known that the spectrometer should get the high resolution sample by high-speed spinning motor, so it is easy to achieve precise motion control, good stability, fast measurement speed.

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

    DEFF Research Database (Denmark)

    Kumar, P.; Sharma, P. K.; Madsen, Charlotte S.

    2013-01-01

    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.......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....

  18. Reversibly locked thionucleobase pairs in DNA to study base flipping enzymes

    Directory of Open Access Journals (Sweden)

    Christine Beuck

    2014-10-01

    Full Text Available Covalently interstrand cross-linked DNA is an interesting tool to study DNA binding proteins that locally open up the DNA duplex by flipping single bases out of the DNA helix or melting whole stretches of base pairs to perform their function. The ideal DNA cross-link to study protein–DNA interactions should be specific and easy to synthesize, be stable during protein binding experiments, have a short covalent linker to avoid steric hindrance of protein binding, and should be available as a mimic for both A/T and G/C base pairs to cover all possible binding specificities. Several covalent interstrand cross-links have been described in the literature, but most of them fall short of at least one of the above criteria. We developed an efficient method to site-specifically and reversibly cross-link thionucleoside base pairs in synthetic duplex oligodeoxynucleotides by bisalkylation with 1,2-diiodoethane resulting in an ethylene-bridged base pair. Both linked A/T and G/C base pair analogs can conveniently be prepared which allows studying any base pair-opening enzyme regardless of its sequence specificity. The cross-link is stable in the absence of reducing agents but the linker can be quickly and tracelessly removed by the addition of thiol reagents like dithiothreitol. This property makes the cross-linking reaction fully reversible and allows for a switching of the linked base pair from locked to unlocked during biochemical experiments. Using the DNA methyltransferase from Thermus aquaticus (M.TaqI as example, we demonstrate that the presented cross-linked DNA with an ethylene-linked A/T base pair analog at the target position is a useful tool to determine the base-flipping equilibrium constant of a base-flipping enzyme which lies mostly on the extrahelical side for M.TaqI.

  19. Self-organised criticality in base-pair breathing in DNA with a defect

    CERN Document Server

    Duduiala, Ciprian-Ionut; Laughton, Charles A

    2011-01-01

    We analyse base-pair breathing in a DNA sequence of 12 base-pairs with a defective base at its centre. We use both all-atom molecular dynamics (MD) simulations and a system of stochastic differential equations (SDE). In both cases, Fourier analysis of the trajectories reveals self-organised critical behaviour in the breathing of base-pairs. The Fourier Transforms (FT) of the interbase distances show power-law behaviour with gradients close to -1. The scale-invariant behaviour we have found provides evidence for the view that base-pair breathing corresponds to the nucleation stage of large-scale DNA opening (or 'melting') and that this process is a (second-order) phase transition. Although the random forces in our SDE system were introduced as white noise, FTs of the displacements exhibit pink noise, as do the displacements in the AMBER/MD simulations.

  20. A new improved ID-based proxy ring signature scheme from bilinear pairings

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Ring signature and proxy signature are of vital importance to secure electronic commerce. Recently,the bilinear pairing such as Weil pairing or Tate pairing on elliptic curves and hyperelliptic curves is playing an important role in security solutions. Several ID-based signature schemes have been put forward, many of which are based on bilinear pairings. In key management and moderate security demand scenarios, ID-based public key cryptosystem is more preferable than other public key infrastructure based systems. In this paper, an improved ID-based proxy ring signature scheme from bilinear pairings is proposed which combines the advantages of proxy signature and of ring signatures. Our scheme can guarantee the profits of the proxy signer via preventing the original signer form generating the proxy ring signature. Furthermore, bilinear pairings are introduced to minimize the computation overhead and to improve the related performance of our scheme. In contrast with Zhang's scheme, our scheme is a computational efficiency improvement for signature verification because the computational cost of bilinear pairings required is reduced from O(n) to O( 1 ). In addition, the proxy ring signature presented in this paper can perfectly satisfy all the security requirements of proxy ring signature, i.e.signer-ambiguity, non-forgeability, verification, non-deniability and distinguishability.

  1. Metal-semiconductor pair nanoparticles by a physical route based on bipolar mixing.

    Science.gov (United States)

    Kala, Shubhra; Theissmann, Ralf; Rouenhoff, Marcel; Kruis, Frank Einar

    2016-03-29

    In this report a methodology is described and demonstrated for preparing Au-Ge pair nanoparticles with known compositions by extending and modifying the basic steps normally used to synthesize nanoparticles in carrier gas. For the formation of pair nanoparticles by bipolar mixing, two oppositely charged aerosols of nanoparticles having the desired size are produced with the help of two differential mobility analyzers. Then both are allowed to pass through a tube, which provides sufficient residence time to result in nanoparticle pair formation due to Brownian collisions influenced by Coulomb forces. The effect of residence time on the formation of nanoparticle pairs as well as the influence of diffusion and discharging is described. Subsequently, necessary modifications to the experimental setup are demonstrated systematically. The kinetics of nanoparticles pair formation in a carrier gas is also calculated and compared with measurements made with the help of an online aerosol size analysis technique. This synthesis of nanoparticle pairs can be seen as a possible route towards Janus-type nanoparticles.

  2. Vinylimidazole-Based Asymmetric Ion Pair Comonomers: Synthesis, Polymerization Studies and Formation of Ionically Crosslinked PMMA

    NARCIS (Netherlands)

    Jana, S.; Vasantha, V.A.; Stubbs, L.P.; Parthiban, A.; Vancso, G.J.

    2013-01-01

    Vinylimidazole-based asymmetric ion pair comonomers (IPCs) which are free from nonpolymerizable counter ions have been synthesized, characterized and polymerized by free radical polymerization (FRP), atom transfer radical polymerization (ATRP), and reversible addition-fragmentation chain transfer (R

  3. New Gradient-Based Variable Step Size LMS Algorithms

    Directory of Open Access Journals (Sweden)

    Yanling Hao

    2008-03-01

    Full Text Available Two new gradient-based variable step size least-mean-square (VSSLMS algorithms are proposed on the basis of a concise assessment of the weaknesses of previous VSSLMS algorithms in high-measurement noise environments. The first algorithm is designed for applications where the measurement noise signal is statistically stationary and the second for statistically nonstationary noise. Steady-state performance analyses are provided for both algorithms and verified by simulations. The proposed algorithms are also confirmed by simulations to obtain both a fast convergence rate and a small steady-state excess mean square error (EMSE, and to outperform existing VSSLMS algorithms. To facilitate practical application, parameter choice guidelines are provided for the new algorithms.

  4. Heuristic Based Adaptive Step Size CLMS Algorithms for Smart Antennas

    Directory of Open Access Journals (Sweden)

    Y Rama Krishna

    2013-05-01

    Full Text Available A smart antenna system combines multiple antenna elements with a signal processing capability to optimize its radiation and/or reception pattern automatically in response to the signal environment through complex weight selection. The weight selection process to get suitable Array factor with low Half Power Beam Width (HPBW and Side Lobe Level (SLL is a complex method. The aim of this task is to design a new approach for smart antennas to minimize the noise and interference effects from external sources with least number of iterations. This paper presents Heuristics based adaptive step size Complex Least Mean Square (CLMS model for Smart Antennas to speedup convergence. In this process Benveniste and Mathews algorithms are used as heuristics with CLMS and the improvement of performance of Smart Antenna System in terms of convergence rate and array factor are discussed and compared with the performance of CLMS and Augmented CLMS (ACLMS algorithms.

  5. Doppler Broadening Analysis of Steel Specimens Using Accelerator Based In Situ Pair Production

    Science.gov (United States)

    Makarashvili, V.; Wells, D. P.; Roy, A. K.

    2009-03-01

    Positron Annihilation Spectroscopy (PAS) techniques can be utilized as a sensitive probe of defects in materials. Studying these microscopic defects is very important for a number of industries in order to predict material failure or structural integrity. We have been developing gamma-induced pair-production techniques to produce positrons in thick samples (˜4-40 g/cm2, or ˜0.5-5 cm in steel). These techniques are called 'Accelerator-based Gamma-induced Positron Annihilation Spectroscopy' (AG-PAS). We have begun testing the capabilities of this technique for imaging of defect densities in thick structural materials. As a first step, a linear accelerator (LINAC) was employed to produce photon beams by stopping 15 MeV electrons in a 1 mm thick tungsten converter. The accelerator is capable of operating with 30-60 ns pulse width, up to 200 mA peak current at 1 kHz repetition rate. The highly collimated bremsstrahlung beam impinged upon our steel tensile specimens, after traveling through a 1.2 m thick concrete wall. Annihilation radiation was detected by a well-shielded and collimated high-purity germanium detector (HPGe). Conventional Doppler broadening spectrometry (DBS) was performed to determine S, W and T parameters for our samples.

  6. Fluorescent Protein Based FRET Pairs with Improved Dynamic Range for Fluorescence Lifetime Measurements.

    Directory of Open Access Journals (Sweden)

    Bobin George Abraham

    Full Text Available Fluorescence Resonance Energy Transfer (FRET using fluorescent protein variants is widely used to study biochemical processes in living cells. FRET detection by fluorescence lifetime measurements is the most direct and robust method to measure FRET. The traditional cyan-yellow fluorescent protein based FRET pairs are getting replaced by green-red fluorescent protein variants. The green-red pair enables excitation at a longer wavelength which reduces cellular autofluorescence and phototoxicity while monitoring FRET. Despite the advances in FRET based sensors, the low FRET efficiency and dynamic range still complicates their use in cell biology and high throughput screening. In this paper, we utilized the higher lifetime of NowGFP and screened red fluorescent protein variants to develop FRET pairs with high dynamic range and FRET efficiency. The FRET variations were analyzed by proteolytic activity and detected by steady-state and time-resolved measurements. Based on the results, NowGFP-tdTomato and NowGFP-mRuby2 have shown high potentials as FRET pairs with large fluorescence lifetime dynamic range. The in vitro measurements revealed that the NowGFP-tdTomato has the highest Förster radius for any fluorescent protein based FRET pairs yet used in biological studies. The developed FRET pairs will be useful for designing FRET based sensors and studies employing Fluorescence Lifetime Imaging Microscopy (FLIM.

  7. Flow-based market coupling. Stepping stone towards nodal pricing?

    Energy Technology Data Exchange (ETDEWEB)

    Van der Welle, A.J. [ECN Policy Studies, Petten (Netherlands)

    2012-07-15

    For achieving one internal energy market for electricity by 2014, market coupling is deployed to integrate national markets into regional markets and ultimately one European electricity market. The extent to which markets can be coupled depends on the available transmission capacities between countries. Since interconnections are congested from time to time, congestion management methods are deployed to divide the scarce available transmission capacities over market participants. For further optimization of the use of available transmission capacities while maintaining current security of supply levels, flow-based market coupling (FBMC) will be implemented in the CWE region by 2013. Although this is an important step forward, important hurdles for efficient congestion management remain. Hence, flow based market coupling is compared to nodal pricing, which is often considered as the most optimal solution from theoretical perspective. In the context of decarbonised power systems it is concluded that advantages of nodal pricing are likely to exceed its disadvantages, warranting further development of FBMC in the direction of nodal pricing.

  8. Comparison of Three Cre-LoxP Based Paired-End Library Construction Methods

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Ze; Nath, Nandita; Tritt, Andrew; Liang, Shoudan; Han, James; Pennacchio, Len; Chen, Feng

    2013-03-26

    Paired-end library sequencing has been proven useful in scaffold construction during de novo whole genome shotgun assembly. The ability of generating mate pairs with > 8 Kb insert sizes is especially important for genomes containing long repeats. To make mate paired libraries for next generation sequencing, DNA fragments need to be circularized to bring the ends together. There are several methods that can be used for DNA circulation, namely ligation, hybridization and Cre-LoxP recombination. With higher circularization efficiency with large insert DNA fragments, Cre-LoxP recombination method generally has been used for constructing >8 kb insert size paired-end libraries. Second fragmentation step is also crucial for maintaining high library complexity and uniform genome coverage. Here we will describe the following three fragmentation methods: restriction enzyme digestion, random shearing and nick translation. We will present the comparison results for these three methods. Our data showed that all three methods are able to generate paired-end libraries with greater than 20 kb insert. Advantages and disadvantages of these three methods will be discussed as well.

  9. Entanglement and Sources of Magnetic Anisotropy in Radical Pair-Based Avian Magnetoreceptors

    Science.gov (United States)

    Hogben, Hannah J.; Biskup, Till; Hore, P. J.

    2012-11-01

    One of the principal models of magnetic sensing in migratory birds rests on the quantum spin dynamics of transient radical pairs created photochemically in ocular cryptochrome proteins. We consider here the role of electron spin entanglement and coherence in determining the sensitivity of a radical pair-based geomagnetic compass and the origins of the directional response. It emerges that the anisotropy of radical pairs formed from spin-polarized molecular triplets could form the basis of a more sensitive compass sensor than one founded on the conventional hyperfine-anisotropy model. This property offers new and more flexible opportunities for the design of biologically inspired magnetic compass sensors.

  10. Entanglement and Sources of Magnetic Anisotropy in Radical Pair-Based Avian Magnetoreceptors

    CERN Document Server

    Hogben, Hannah J; Hore, P J

    2012-01-01

    One of the principal models of magnetic sensing in migratory birds rests on the quantum spin-dynamics of transient radical pairs created photochemically in ocular cryptochrome proteins. We consider here the role of electron spin entanglement and coherence in determining the sensitivity of a radical pair-based geomagnetic compass and the origins of the directional response. It emerges that the anisotropy of radical pairs formed from spin-polarized molecular triplets could form the basis of a more sensitive compass sensor than one founded on the conventional hyper?ne-anisotropy model. This property offers new and more flexible opportunities for the design of biologically inspired magnetic compass sensors.

  11. Static Dependency Pair Method based on Strong Computability for Higher-Order Rewrite Systems

    CERN Document Server

    Kusakari, Keiichirou; Sakai, Masahiko; Blanqui, Frédéric

    2011-01-01

    Higher-order rewrite systems (HRSs) and simply-typed term rewriting systems (STRSs) are computational models of functional programs. We recently proposed an extremely powerful method, the static dependency pair method, which is based on the notion of strong computability, in order to prove termination in STRSs. In this paper, we extend the method to HRSs. Since HRSs include \\lambda-abstraction but STRSs do not, we restructure the static dependency pair method to allow \\lambda-abstraction, and show that the static dependency pair method also works well on HRSs without new restrictions.

  12. Rule Based Ensembles Using Pair Wise Neural Network Classifiers

    Directory of Open Access Journals (Sweden)

    Moslem Mohammadi Jenghara

    2015-03-01

    Full Text Available In value estimation, the inexperienced people's estimation average is good approximation to true value, provided that the answer of these individual are independent. Classifier ensemble is the implementation of mentioned principle in classification tasks that are investigated in two aspects. In the first aspect, feature space is divided into several local regions and each region is assigned with a highly competent classifier and in the second, the base classifiers are applied in parallel and equally experienced in some ways to achieve a group consensus. In this paper combination of two methods are used. An important consideration in classifier combination is that much better results can be achieved if diverse classifiers, rather than similar classifiers, are combined. To achieve diversity in classifiers output, the symmetric pairwise weighted feature space is used and the outputs of trained classifiers over the weighted feature space are combined to inference final result. In this paper MLP classifiers are used as the base classifiers. The Experimental results show that the applied method is promising.

  13. An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies

    KAUST Repository

    Chawla, Mohit

    2015-06-27

    Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. ‘modified base pairs’. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson–Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in.

  14. Development of a one-step PCR assay with nine primer pairs for the detection of five diarrheagenic Escherichia coli types.

    Science.gov (United States)

    Oh, Kyung-Hwan; Kim, Soo-Bok; Park, Mi-Sun; Cho, Seung-Hak

    2014-06-28

    Certain Escherichia coli (E. coli) strains have the ability to cause diarrheal disease. Five types of diarrheagenic E. coli have been identified, including EHEC, ETEC, EPEC, EAEC, and EIEC. To detect these five diarrheagenic types rapidly, we developed a one-step multiplex PCR (MPPCR) assay using nine primer pairs to amplify nine virulence genes specific to the different virotypes, with each group being represented (i.e., stx1 and stx2 for EHEC, lt, sth, and stp for ETEC, eaeA and bfpA for EPEC, aggR for EAEC, and ipaH for EIEC). The PCR primers were constructed using MultAlin. The sensitivity and specificity of the constructed multiplex PCR primers were measured using DNA isolated from diarrheagenic E. coli strains representing each group. The limits of detection were as follows: 5 × 10(1) CFU/ml for EHEC, 5 × 10(3) CFU/ml for ETEC expressing lt and sth, 5 × 10(4) CFU/ml for ETEC expressing stp, 5 × 102 CFU/ml for EPEC, 5 × 10(4) CFU/ml for EAEC, and 5 × 10(2) CFU/ml for EIEC. To confirm the specificity, C. jejuni, C. perfringens, S. Typhimurium, V. parahaemolyticus, L. monocytogenes, Y. enterocolitica, B. cereus, and S. aureus were used as negative controls, and no amplification was obtained for these. Moreover, this kit was validated using 100 fecal samples from patients with diarrhea and 150 diarrheagenic E. coli strains isolated in Korea. In conclusion, the multiplex PCR assay developed in this study is very useful for the rapid and specific detection of five diarrheagenic E. coli types. This single-step assay will be useful as a rapid and economical method, as it reduces the cost and time required for the identification of diarrheagenic E. coli.

  15. STEPPING - Smartphone-Based Portable Pedestrian Indoor Navigation

    Science.gov (United States)

    Lukianto, C.; Sternberg, H.

    2011-12-01

    Many current smartphones are fitted with GPS receivers, which, in combination with a map application form a pedestrian navigation system for outdoor purposes. However, once an area with insufficient satellite signal coverage is entered, these navigation systems cease to function. For indoor positioning, there are already several solutions available which are usually based on measured distances to reference points. These solutions can achieve resolutions as low as the sub-millimetre range depending on the complexity of the set-up. STEPPING project, developed at HCU Hamburg Germany aims at designing an indoor navigation system consisting of a small inertial navigation system and a new, robust sensor fusion algorithm running on a current smartphone. As this system is theoretically able to integrate any available positioning method, it is independent of a particular method and can thus be realized on a smartphone without affecting user mobility. Potential applications include --but are not limited to: Large trade fairs, airports, parking decks and shopping malls, as well as ambient assisted living scenarios.

  16. A Step-by-Step Design Methodology for a Base Case Vanadium Redox-Flow Battery

    Science.gov (United States)

    Moore, Mark; Counce, Robert M.; Watson, Jack S.; Zawodzinski, Thomas A.; Kamath, Haresh

    2012-01-01

    The purpose of this work is to develop an evolutionary procedure to be used by Chemical Engineering students for the base-case design of a Vanadium Redox-Flow Battery. The design methodology is based on the work of Douglas (1985) and provides a profitability analysis at each decision level so that more profitable alternatives and directions can be…

  17. Comparable stability of Hoogsteen and Watson-Crick base pairs in ionic liquid choline dihydrogen phosphate.

    Science.gov (United States)

    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.

  18. Selection of a Portfolio of Pairs Based on Cointegration: A Statistical Arbitrage Strategy

    Directory of Open Access Journals (Sweden)

    João Frois Caldeira

    2013-03-01

    Full Text Available Statistical arbitrage strategies, such as pairs trading and its generalizations, rely on the construction of mean- reverting spreads with a certain degree of predictability. This paper applies cointegration tests to identify stocks to be used in pairs trading strategies. In addition to estimating long-term equilibrium and to model the resulting residuals, we select stock pairs to compose a pairs trading portfolio based on an indicator of profitability evaluated in-sample. The profitability of the strategy is assessed with data from the São Paulo stock exchange ranging from January 2005 to October 2012. Empirical analysis shows that the proposed strategy exhibit excess returns of 16.38% per year, Sharpe Ratio of 1.34 and low correlation with the market.

  19. Discrete Frequency Entangled Photon Pair Generation Based on Silicon Micro-ring Cavities

    Science.gov (United States)

    Suo, Jing; Zhang, Wei; Dong, Shuai; Huang, Yidong; Peng, Jiangde

    2016-10-01

    In this paper, we propose and demonstrate a scheme to generate discrete frequency entangled photon pairs based on a silicon micro-ring resonator. The resonator is placed in a Sagnac fiber loop. Stimulated by two pump lights at two different resonance wavelengths of the resonator, photon pairs at another two resonance wavelengths are generated along two opposite directions in the fiber loop, by the nondegenerate spontaneous four wave mixing in the resonator. Their states are superposed and interfered at the output ports of the fiber loop to generate frequency entangled photon pairs. On the other hand, since the pump lights come from two continuous wave lasers, energy-time entanglement is an intrinsic property of the generated photon pairs. The entanglements on frequency and energy-time are demonstrated experimentally by the experiments of spatial quantum beating and Franson-type interference, respectively, showing that the silicon micro-ring resonators are ideal candidates to realize complex photonic quantum state generation.

  20. Scalable wavelet-based active network detection of stepping stones

    Science.gov (United States)

    Gilbert, Joseph I.; Robinson, David J.; Butts, Jonathan W.; Lacey, Timothy H.

    2012-06-01

    Network intrusions leverage vulnerable hosts as stepping stones to penetrate deeper into a network and mask malicious actions from detection. Identifying stepping stones presents a significant challenge because network sessions appear as legitimate traffic. This research focuses on a novel active watermark technique using discrete wavelet transformations to mark and detect interactive network sessions. This technique is scalable, resilient to network noise, and difficult for attackers to discern that it is in use. Previously captured timestamps from the CAIDA 2009 dataset are sent using live stepping stones in the Amazon Elastic Compute Cloud service. The client system sends watermarked and unmarked packets from California to Virginia using stepping stones in Tokyo, Ireland and Oregon. Five trials are conducted in which the system sends simultaneous watermarked samples and unmarked samples to each target. The live experiment results demonstrate approximately 5% False Positive and 5% False Negative detection rates. Additionally, watermark extraction rates of approximately 92% are identified for a single stepping stone. The live experiment results demonstrate the effectiveness of discerning watermark traffic as applied to identifying stepping stones.

  1. Practical Biostatistics A Friendly Step-by-Step Approach for Evidence-based Medicine

    CERN Document Server

    Suchmacher, Mendel

    2012-01-01

    Evidence-based medicine aims to apply the best available evidence gained from the scientific method to medical decision making. It is a practice that uses statistical analysis of scientific methods and outcomes to drive further experimentation and diagnosis. The profusion of evidence-based medicine in medical practice and clinical research has produced a need for life scientists and clinical researchers to assimilate biostatistics into their work to meet efficacy and practical standards. Practical Biostatistics provides researchers, medical professionals, and students with a friendly, practica

  2. Does base-pairing strength play a role in microRNA repression?

    OpenAIRE

    2012-01-01

    In this paper, the authors explore the possibility that the base-pairing strength of miRNA–mRNA target plays a role in microRNA-mediated gene regulation. The authors found a significant correlation between the physiological temperature of the organism and the average G/C content of its miRNAs. This study suggests that an organism adapts its miRNA–target free energy according to its physiological temperature, thus highlighting the importance of base-pairing strength in miRNA activity.

  3. Inference Based on Simple Step Statistics for the Location Model.

    Science.gov (United States)

    1981-07-01

    function. Let TN,k(9) - Zak(’)Vi(e). Then TNk is called the k-step statistic. Noether (1973) studied the 1-step statistic with particular emphasis on...opposed to the sign statistic. These latter two comparisons were first discussed by Noether (1973) in a somewhat different setting. Notice that the...obtained by Noether (1973). If k - 3, we seek the (C + 1)’st and (2N - bI - b2 - C)’th ordered Walsh averages in D The algorithm of Section 3 modified to

  4. English Writing Strategy —Based on Three Steps

    Institute of Scientific and Technical Information of China (English)

    翁朝袅

    2012-01-01

    Many junior high school students have trouble in writing English composition,and this paper is primarily divided into three steps of pre-writing,while-writing and post-writing to answer the question:How to write a composition.

  5. Resumption-based big-step and small-step interpreters for While with interactive I/O

    CERN Document Server

    Nakata, Keiko

    2011-01-01

    In this tutorial, we program big-step and small-step total interpreters for the While language extended with input and output primitives. While is a simple imperative language consisting of skip, assignment, sequence, conditional and loop. We first develop trace-based interpreters for While. Traces are potentially infinite nonempty sequences of states. The interpreters assign traces to While programs: for us, traces are denotations of While programs. The trace is finite if the program is terminating and infinite if the program is non-terminating. However, we cannot decide (i.e., write a program to determine), for any given program, whether its trace is finite or infinite, which amounts to deciding the halting problem. We then extend While with interactive input/output primitives. Accordingly, we extend the interpreters by generalizing traces to resumptions. The tutorial is based on our previous work with T. Uustalu on reasoning about interactive programs in the setting of constructive type theory.

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

    Science.gov (United States)

    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.

  7. Single-molecule derivation of salt dependent base-pair free energies in DNA

    CERN Document Server

    Huguet, J M; Forns, N; Smith, S B; Bustamante, C; Ritort, F; 10.1073/pnas.1001454107

    2010-01-01

    Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which depend on several assumptions. Here we report measurements of the DNA base-pair free energies based on a simplified system, the mechanical unzipping of single DNA molecules. By combining experimental data with a physical model and an optimization algorithm for analysis, we measure the 10 unique nearest-neighbor base-pair free energies with 0.1 kcal mol-1 precision over two orders of magnitude of monovalent salt concentration. We find an improved set of standard energy values compared with Unified Oligonucleotide energies and a unique set of 10 base-pair-specific salt-correction values. The latter are found to be strongest for AA/TT and weakest for CC/GG. Our new energy values and salt corrections improve predictions of DNA unzipping forces and are fully compatible with melt...

  8. Construction of Hilbert Transform Pairs of Wavelet Bases and Gabor-like Transforms

    CERN Document Server

    Chaudhury, Kunal Narayan

    2009-01-01

    We propose a novel method for constructing Hilbert transform (HT) pairs of wavelet bases based on a fundamental approximation-theoretic characterization of scaling functions--the B-spline factorization theorem. In particular, starting from well-localized scaling functions, we construct HT pairs of biorthogonal wavelet bases of L^2(R) by relating the corresponding wavelet filters via a discrete form of the continuous HT filter. As a concrete application of this methodology, we identify HT pairs of spline wavelets of a specific flavor, which are then combined to realize a family of complex wavelets that resemble the optimally-localized Gabor function for sufficiently large orders. Analytic wavelets, derived from the complexification of HT wavelet pairs, exhibit a one-sided spectrum. Based on the tensor-product of such analytic wavelets, and, in effect, by appropriately combining four separable biorthogonal wavelet bases of L^2(R^2), we then discuss a methodology for constructing 2D directional-selective complex...

  9. Biological phosphorylation of an Unnatural Base Pair (UBP) using a Drosophila melanogaster deoxynucleoside kinase (DmdNK) mutant

    Science.gov (United States)

    Daugherty, Ashley B.; Yang, Zunyi; Shaw, Ryan; Dong, Mengxing; Lutz, Stefan; Benner, Steven A.

    2017-01-01

    One research goal for unnatural base pair (UBP) is to replicate, transcribe and translate them in vivo. Accordingly, the corresponding unnatural nucleoside triphosphates must be available at sufficient concentrations within the cell. To achieve this goal, the unnatural nucleoside analogues must be phosphorylated to the corresponding nucleoside triphosphates by a cascade of three kinases. The first step is the monophosphorylation of unnatural deoxynucleoside catalyzed by deoxynucleoside kinases (dNK), which is generally considered the rate limiting step because of the high specificity of dNKs. Here, we applied a Drosophila melanogaster deoxyribonucleoside kinase (DmdNK) to the phosphorylation of an UBP (a pyrimidine analogue (6-amino-5-nitro-3-(1’-b-d-2’-deoxyribofuranosyl)-2(1H)-pyridone, Z) and its complementary purine analogue (2-amino-8-(1’-b-d-2’-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one, P). The results showed that DmdNK could efficiently phosphorylate only the dP nucleoside. To improve the catalytic efficiency, a DmdNK-Q81E mutant was created based on rational design and structural analyses. This mutant could efficiently phosphorylate both dZ and dP nucleoside. Structural modeling indicated that the increased efficiency of dZ phosphorylation by the DmdNK-Q81E mutant might be related to the three additional hydrogen bonds formed between E81 and the dZ base. Overall, this study provides a groundwork for the biological phosphorylation and synthesis of unnatural base pair in vivo. PMID:28323896

  10. Control in the Rate-Determining Step Provides a Promising Strategy To Develop New Catalysts for CO2 Hydrogenation: A Local Pair Natural Orbital Coupled Cluster Theory Study.

    Science.gov (United States)

    Mondal, Bhaskar; Neese, Frank; Ye, Shengfa

    2015-08-03

    The development of efficient catalysts with base metals for CO2 hydrogenation has always been a major thrust of interest. A series of experimental and theoretical work has revealed that the catalytic cycle typically involves two key steps, namely, base-promoted heterolytic H2 splitting and hydride transfer to CO2, either of which can be the rate-determining step (RDS) of the entire reaction. To explore the determining factor for the nature of RDS, we present herein a comparative mechanistic investigation on CO2 hydrogenation mediated by [M(H)(η(2)-H2)(PP3(Ph))](n+) (M = Fe(II), Ru(II), and Co(III); PP3(Ph) = tris(2-(diphenylphosphino)phenyl)phosphine) type complexes. In order to construct reliable free energy profiles, we used highly correlated wave function based ab initio methods of the coupled cluster type alongside the standard density functional theory. Our calculations demonstrate that the hydricity of the metal-hydride intermediate generated by H2 splitting dictates the nature of the RDS for the Fe(II) and Co(III) systems, while the RDS for the Ru(II) catalyst appears to be ambiguous. CO2 hydrogenation catalyzed by the Fe(II) complex that possesses moderate hydricity traverses an H2-splitting RDS, whereas the RDS for the high-hydricity Co(III) species is found to be the hydride transfer. Thus, our findings suggest that hydricity can be used as a practical guide in future catalyst design. Enhancing the electron-accepting ability of low-hydricity catalysts is likely to improve their catalytic performance, while increasing the electron-donating ability of high-hydricity complexes may speed up CO2 conversion. Moreover, we also established the active roles of base NEt3 in directing the heterolytic H2 splitting and assisting product release through the formation of an acid-base complex.

  11. Measurement and theory of hydrogen bonding contribution to isosteric DNA base pairs.

    Science.gov (United States)

    Khakshoor, Omid; Wheeler, Steven E; Houk, K N; Kool, Eric T

    2012-02-15

    We address the recent debate surrounding the ability of 2,4-difluorotoluene (F), a low-polarity mimic of thymine (T), to form a hydrogen-bonded complex with adenine in DNA. The hydrogen bonding ability of F has been characterized as small to zero in various experimental studies, and moderate to small in computational studies. However, recent X-ray crystallographic studies of difluorotoluene in DNA/RNA have indicated, based on interatomic distances, possible hydrogen bonding interactions between F and natural bases in nucleic acid duplexes and in a DNA polymerase active site. Since F is widely used to measure electrostatic contributions to pairing and replication, it is important to quantify the impact of this isostere on DNA stability. Here, we studied the pairing stability and selectivity of this compound and a closely related variant, dichlorotoluene deoxyriboside (L), in DNA, using both experimental and computational approaches. We measured the thermodynamics of duplex formation in three sequence contexts and with all possible pairing partners by thermal melting studies using the van't Hoff approach, and for selected cases by isothermal titration calorimetry (ITC). Experimental results showed that internal F-A pairing in DNA is destabilizing by 3.8 kcal/mol (van't Hoff, 37 °C) as compared with T-A pairing. At the end of a duplex, base-base interactions are considerably smaller; however, the net F-A interaction remains repulsive while T-A pairing is attractive. As for selectivity, F is found to be slightly selective for adenine over C, G, T by 0.5 kcal mol, as compared with thymine's selectivity of 2.4 kcal/mol. Interestingly, dichlorotoluene in DNA is slightly less destabilizing and slightly more selective than F, despite the lack of strongly electronegative fluorine atoms. Experimental data were complemented by computational results, evaluated at the M06-2X/6-31+G(d) and MP2/cc-pVTZ levels of theory. These computations suggest that the pairing energy of F to A

  12. Concealed d-wave pairs in the s± condensate of iron-based superconductors.

    Science.gov (United States)

    Ong, Tzen; Coleman, Piers; Schmalian, Jörg

    2016-05-17

    A central question in iron-based superconductivity is the mechanism by which the paired electrons minimize their strong mutual Coulomb repulsion. In most unconventional superconductors, Coulomb repulsion is minimized through the formation of higher angular momentum Cooper pairs, with Fermi surface nodes in the pair wavefunction. The apparent absence of such nodes in the iron-based superconductors has led to a belief they form an s-wave ([Formula: see text]) singlet state, which changes sign between the electron and hole pockets. However, the multiorbital nature of these systems opens an alternative possibility. Here, we propose a new class of [Formula: see text] state containing a condensate of d-wave Cooper pairs, concealed by their entanglement with the iron orbitals. By combining the d-wave ([Formula: see text]) motion of the pairs with the internal angular momenta [Formula: see text] of the iron orbitals to make a singlet ([Formula: see text]), an [Formula: see text] superconductor with a nontrivial topology is formed. This scenario allows us to understand the development of octet nodes in potassium-doped Ba1-x KXFe2As2 as a reconfiguration of the orbital and internal angular momentum into a high spin ([Formula: see text]) state; the reverse transition under pressure into a fully gapped state can then be interpreted as a return to the low-spin singlet. The formation of orbitally entangled pairs is predicted to give rise to a shift in the orbital content at the Fermi surface, which can be tested via laser-based angle-resolved photoemission spectroscopy.

  13. Compatibility of pedigree-based and marker-based relationships for single-step genomic prediction

    DEFF Research Database (Denmark)

    Christensen, Ole Fredslund

    2012-01-01

    Single-step methods for genomic prediction have recently become popular because they are conceptually simple and in practice such a method can completely replace a pedigree-based method for routine genetic evaluation. An issue with single-step methods is compatibility between the marker-based rel...... for the phenotypes conditional on the observed markers, whereas the second term is the likelihood for t he observed markers. The performance of the proposed method is studied on simulated data examples....... that it may be important that a single-step method is based on a model conditional on the observed markers. When data are from routine evaluation systems, selection affects the allele frequencies, and therefore both observed markers and observed phenotypes contain information about allele frequencies...... in the base population. Here, two ideas are explored. The first idea is to instead adjust the pedigree-based relationship matrix to be compatible to the marker-based relationship matrix, whereas the second idea is to include the likelihood for the observed markers. A single-step method is used where...

  14. Step-size selection for split-step based nonlinear compensation with coherent detection in 112-Gb/s 16-QAM transmission

    Institute of Scientific and Technical Information of China (English)

    Chien-Yu Lin; Rameez Asif; Michael Holtmannspoetter; Bernhard Schmauss

    2012-01-01

    Non-uniform step-size distribution is implemented for split-step based nonlinear compensation in single-channel 112-Gb/s 16 quadrature amplitude modulation (QAM) transmission. Numerical simulations of the system including a 20x80 km uncompensated link are performed using logarithmic step size distribution to compensate signal distortions. 50% of reduction in number of steps with respect to using constant step sizes is observed. The performance is further improved by optimizing nonlinear calculating position (NLCP) in case of using constant step sizes while NLCP optimization becomes unnecessary when using logarithmic step sizes, which reduces the computational effort due to uniformly distributed nonlinear phase for all successive steps.%Non-uniform step-size distribution is implemented for split-step based nonlinear compensation in singlechannel 112-Gb/s 16 quadrature amplitude modulation (QAM) transmission.Numerical simulations of the system including a 20×80 km uncompensated link are performed using logarithmic step size distribution to compensate signal distortions.50% of reduction in number of steps with respect to using constant step sizes is observed.The performance is further improved by optimizing nonlinear calculating position (NLCP) in case of using constant step sizes while NLCP optimization becomes unnecessary when using logarithmic step sizes,which reduces the computational effort due to uniformly distributed nonlinear phase for all successive steps.

  15. Scalable Wavelet-Based Active Network Stepping Stone Detection

    Science.gov (United States)

    2012-03-22

    Joseph I. Gilbert, B.S. Eng. Physics Major, USA Approved: Lt Col David J. Robinson, PhD (Chairman) Date Major Jonathan W. Butts, PhD (Committee Member...UNIVERSITY OF ILLINOIS, 1998. [5] Donoho, David L., Ana Georgina Flesia, Umesh Shankar, Vern Paxson, Jason Coit, and Stuart Staniford. “Multiscale stepping...Schnackenberg, Harley Holliday, and Travis Reid. “Autonomic Response to Distributed Denial of Service Attacks”. Proceedings of the 4th International Symposium

  16. Genome filtering using methylation-sensitive restriction enzymes with six-base pair recognition sites

    Science.gov (United States)

    The large fraction of repetitive DNA in many plant genomes has complicated all aspects of DNA sequencing and assembly, and thus techniques that enrich for genes and low-copy sequences have been employed to isolate gene space. Methyl sensitive restriction enzymes with six base pair recognition sites...

  17. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays

    NARCIS (Netherlands)

    Urakawa, H.; Fantroussi, El S.; Smidt, H.; Smoot, J.C.; Tribou, E.H.; Kelly, J.J.; Noble, P.A.; Stahl, D.A.

    2003-01-01

    The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of

  18. Facile syntheses of dissymmetric ferrocene-functionalized Lewis acids and acid-base pairs.

    Science.gov (United States)

    Morgan, Ian R; Di Paolo, Angela; Vidovic, Dragoslav; Fallis, Ian A; Aldridge, Simon

    2009-12-21

    A facile synthetic approach is reported for the synthesis of dissymmetric 1,2-ferrocenediyl Lewis acids and mixed acid-base pairs including the first example of a 1-phosphino-2-borylferrocene; the use of non-racemic electrophiles allows for the isolation of single diastereomer products.

  19. New ab initio based pair potential for accurate simulation of phase transitions in ZnO

    NARCIS (Netherlands)

    Wang, Shuaiwei; Fan, Zhaochuan; Koster, Rik S.; Fang, Changming; Van Huis, Marijn A.; Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W.; Vlugt, Thijs J H

    2014-01-01

    A set of interatomic pair potentials is developed for ZnO based on the partially charged rigid ion model (PCRIM). The derivation of the potentials combines lattice inversion, empirical fitting, and ab initio energy surface fitting. We show that, despite the low number of parameters in this model (8)

  20. Pair correlation functions of FeAs-based superconductors: Quantum Monte Carlo study

    Science.gov (United States)

    Kashurnikov, V. A.; Krasavin, A. V.

    2015-01-01

    The new generalized quantum continuous time world line Monte Carlo algorithm was developed to calculate pair correlation functions for two-dimensional FeAs-clusters modeling of iron-based superconductors within the framework of the two-orbital model. The analysis of pair correlations depending on the cluster size, temperature, interaction, and the type of symmetry of the order parameter is carried out. The data obtained for clusters with sizes up to 1 0x1 0 FeAs-cells favor the possibility of an effective charge carrier's attraction that is corresponding the A1g-symmetry, at some parameters of interaction.

  1. Identity-based authenticated key exchange protocols from the Tate pairing

    Science.gov (United States)

    Shen, Jun; Jin, Hong; Yang, Zhiyong; Cui, Xiang

    2011-12-01

    Key agreement protocols are designed to establish a session keys between two or multiple entities oven an insecure network and the session key is used to assure confidentiality thought encryption. With the advantages of identity-based (ID-based) cryptography, there have been many ID-based key agreement protocols proposed. However, most of them are based on Weil pairing, which is more cost of computation compared with Tate paring. In this paper, we propose a newly ID-based key agreement protocol from the Tate pairing. Compared with previous protocols, the new protocol minimizes the cost of computation with no extra message exchange time. In addition, the proposed protocol provides known key security, no key control, no key-compromise impersonation and perfect forward secrecy.

  2. Pair correlations in iron-based superconductors: Quantum Monte Carlo study

    Energy Technology Data Exchange (ETDEWEB)

    Kashurnikov, V.A.; Krasavin, A.V., E-mail: avkrasavin@gmail.com

    2014-08-01

    The new generalized quantum continuous time world line Monte Carlo algorithm was developed to calculate pair correlation functions for two-dimensional FeAs-clusters modeling of iron-based superconductors using a two-orbital model. The data obtained for clusters with sizes up to 10×10 FeAs-cells favor the possibility of an effective charge carrier's attraction that is corresponding the A{sub 1g}-symmetry, at some parameters of interaction. The analysis of pair correlations depending on the cluster size, temperature, interaction, and the type of symmetry of the order parameter is carried out. - Highlights: • New generalized quantum continuous time world line Monte Carlo algorithm is developed. • Pair correlation functions for two-dimensional FeAs-clusters are calculated. • Parameters of two-orbital model corresponding to attraction of carriers are defined.

  3. Far-end Crosstalk Modeling Based on Capacitive and Inductive Unbalances Between Pairs in a Cable

    Directory of Open Access Journals (Sweden)

    Pavel Lafata

    2011-01-01

    Full Text Available This article deals with new ways of far-end crosstalk (FEXT modeling in multi-pair and multi-quad metallic cables. Current standard modeling methods provide only rough estimations of FEXT characteristics based on average values of crosstalk for the whole cable. However, for practical implementation of vector discrete multi-tone modulation (VDMT is necessary to predict and simulate FEXT characteristics with sufficient accuracy and simulate FEXT transfer functions individually for each combination of symmetrical pairs in a cable. This article contains a theoretical analysis and description of the problem and suggests a new method for modeling of FEXT crosstalk using capacitive and inductive unbalances between pairs in a cable. This proposed model offers more accurate and realistic results of crosstalk. Theoretical simulations and results are also compared with the measured characteristics for specific metallic cable.

  4. Design and development of three-dimensional DNA crystals utilizing CGAA parallel base paired motifs

    Science.gov (United States)

    Muser, Stephanie Elizabeth

    Three-dimensional (3D) DNA crystals hold great potential for various applications such as the development of molecular scaffolds for use in protein structure determination by x-ray crystallography. The programmability and predictability of DNA make it a powerful tool for self-assembly but it is hindered by the linearity of the duplex structure. Predictable noncanonical base pairs and motifs have the potential to connect linear double-helical DNA segments into complex 3D structures. The sequence d(GCGAAAGCT) has been observed to form 3D crystals containing both noncanonical parallel pairs and canonical Watson-Crick pairs. This provided a template structure that we used in expanding the design and development of 3D DNA crystals along with exploring the use of predictable noncanonical motifs. The structures we determined contained all but one or two of the designed secondary structure interactions, depending on pH.

  5. The Sentiment Trend Analysis of Twitter Based on Set Pair Contact Degree

    Directory of Open Access Journals (Sweden)

    Chunying Zhang

    2013-01-01

    Full Text Available Sentiment trend of twitter users have a great influence on their friends and the crowd listened. This paper directs at the user sentiment state of twitter, the unique medium, and applies set pair analysis method for trend analysis. First, we begin with set pair contact degree, then based on set pair affective computing model to make comparison with the size relationship of same degree, difference degree, opposition degree of the emotion, to build the user sentiment trend analysis model; Secondly, we analyze the influence for the user's own sentiment trend when the value changed of difference coefficient ; thirdly, after analyze to obtain one user's sentiment orientation threshold as prerequisite for user behavior prediction. Finally, setting an example to calculate the sentiment trend of one twitter, then to get the conclusion is that the analysis of user emotion from a three-dimensional angle is more realistic than the single angle.

  6. Ionic force field optimization based on single-ion and ion-pair solvation properties: going beyond standard mixing rules.

    Science.gov (United States)

    Fyta, Maria; Netz, Roland R

    2012-03-28

    Using molecular dynamics (MD) simulations in conjunction with the SPC/E water model, we optimize ionic force-field parameters for seven different halide and alkali ions, considering a total of eight ion-pairs. Our strategy is based on simultaneous optimizing single-ion and ion-pair properties, i.e., we first fix ion-water parameters based on single-ion solvation free energies, and in a second step determine the cation-anion interaction parameters (traditionally given by mixing or combination rules) based on the Kirkwood-Buff theory without modification of the ion-water interaction parameters. In doing so, we have introduced scaling factors for the cation-anion Lennard-Jones (LJ) interaction that quantify deviations from the standard mixing rules. For the rather size-symmetric salt solutions involving bromide and chloride ions, the standard mixing rules work fine. On the other hand, for the iodide and fluoride solutions, corresponding to the largest and smallest anion considered in this work, a rescaling of the mixing rules was necessary. For iodide, the experimental activities suggest more tightly bound ion pairing than given by the standard mixing rules, which is achieved in simulations by reducing the scaling factor of the cation-anion LJ energy. For fluoride, the situation is different and the simulations show too large attraction between fluoride and cations when compared with experimental data. For NaF, the situation can be rectified by increasing the cation-anion LJ energy. For KF, it proves necessary to increase the effective cation-anion Lennard-Jones diameter. The optimization strategy outlined in this work can be easily adapted to different kinds of ions.

  7. Theory of phase segregation in DNA assemblies containing two different base-pair sequence types

    Science.gov (United States)

    (O’ Lee, Dominic J.; Wynveen, Aaron; Kornyshev, Alexei A.

    2017-01-01

    Spontaneous pairing of homologous DNA sequences—a challenging subject in molecular biophysics, often referred to as ‘homology recognition’—has been observed in vitro for several DNA systems. One of these experiments involved liquid crystalline quasi-columnar phases formed by a mixture of two kinds of double stranded DNA oligomer. Both oligomer types were of the same length and identical stoichiometric base-pair composition, but the base-pairs followed a different order. Phase segregation of the two DNA types was observed in the experiments, with the formation of boundaries between domains rich in molecules of one type (order) of base pair sequence. We formulate here a modified ‘X–Y model’ for phase segregation in such assemblies, obtain approximate solutions of the model, compare analytical results to Monte Carlo simulations, and rationalise past experimental observations. This study, furthermore, reveals the factors that affect the degree of segregation. Such information could be used in planning new versions of similar segregation experiments, needed for deepening our understanding of forces that might be involved, e.g., in gene–gene recognition.

  8. Acid-Base Pairs in Lewis Acidic Zeolites Promote Direct Aldol Reactions by Soft Enolization.

    Science.gov (United States)

    Lewis, Jennifer D; Van de Vyver, Stijn; Román-Leshkov, Yuriy

    2015-08-17

    Hf-, Sn-, and Zr-Beta zeolites catalyze the cross-aldol condensation of aromatic aldehydes with acetone under mild reaction conditions with near quantitative yields. NMR studies with isotopically labeled molecules confirm that acid-base pairs in the Si-O-M framework ensemble promote soft enolization through α-proton abstraction. The Lewis acidic zeolites maintain activity in the presence of water and, unlike traditional base catalysts, in acidic solutions.

  9. Model-based risk analysis of coupled process steps.

    Science.gov (United States)

    Westerberg, Karin; Broberg-Hansen, Ernst; Sejergaard, Lars; Nilsson, Bernt

    2013-09-01

    A section of a biopharmaceutical manufacturing process involving the enzymatic coupling of a polymer to a therapeutic protein was characterized with regards to the process parameter sensitivity and design space. To minimize the formation of unwanted by-products in the enzymatic reaction, the substrate was added in small amounts and unreacted protein was separated using size-exclusion chromatography (SEC) and recycled to the reactor. The quality of the final recovered product was thus a result of the conditions in both the reactor and the SEC, and a design space had to be established for both processes together. This was achieved by developing mechanistic models of the reaction and SEC steps, establishing the causal links between process conditions and product quality. Model analysis was used to complement the qualitative risk assessment, and design space and critical process parameters were identified. The simulation results gave an experimental plan focusing on the "worst-case regions" in terms of product quality and yield. In this way, the experiments could be used to verify both the suggested process and the model results. This work demonstrates the necessary steps of model-assisted process analysis, from model development through experimental verification.

  10. Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides.

    Science.gov (United States)

    Hudson, Graham A; Bloomingdale, Richard J; Znosko, Brent M

    2013-11-01

    Pseudouridine (Ψ) is the most common noncanonical nucleotide present in naturally occurring RNA and serves a variety of roles in the cell, typically appearing where structural stability is crucial to function. Ψ residues are isomerized from native uridine residues by a class of highly conserved enzymes known as pseudouridine synthases. In order to quantify the thermodynamic impact of pseudouridylation on U-A base pairs, 24 oligoribonucleotides, 16 internal and eight terminal Ψ-A oligoribonucleotides, were thermodynamically characterized via optical melting experiments. The thermodynamic parameters derived from two-state fits were used to generate linearly independent parameters for use in secondary structure prediction algorithms using the nearest-neighbor model. On average, internally pseudouridylated duplexes were 1.7 kcal/mol more stable than their U-A counterparts, and terminally pseudouridylated duplexes were 1.0 kcal/mol more stable than their U-A equivalents. Due to the fact that Ψ-A pairs maintain the same Watson-Crick hydrogen bonding capabilities as the parent U-A pair in A-form RNA, the difference in stability due to pseudouridylation was attributed to two possible sources: the novel hydrogen bonding capabilities of the newly relocated imino group as well as the novel stacking interactions afforded by the electronic configuration of the Ψ residue. The newly derived nearest-neighbor parameters for Ψ-A base pairs may be used in conjunction with other nearest-neighbor parameters for accurately predicting the most likely secondary structure of A-form RNA containing Ψ-A base pairs.

  11. Nucleic Acid Base Analog FRET-Pair Facilitating Detailed Structural Measurements in Nucleic Acid Containing Systems

    DEFF Research Database (Denmark)

    Börjesson, Karl; Preus, Søren; El-Sagheer, Afaf;

    2009-01-01

    toward detailed studies of the inherent dynamics of nucleic acid structures. Moreover, the placement of FRET-pair chromophores inside the base stack will be a great advantage in studies where other (biomacro)molecules interact with the nucleic acid. Lastly, our study gives possibly the first truly solid...... distances covering up to more than one turn of the DNA duplex. Importantly, we show that the rigid stacking of the two base analogs, and consequently excellent control of their exact positions and orientations, results in a high control of the orientation factor and hence very distinct FRET changes...... as the number of bases separating tCO and tC(nitro) is varied. A set of DNA strands containing the FRET-pair at wisely chosen locations will, thus, make it possible to accurately distinguish distance- from orientation-changes using FRET. In combination with the good nucleobase analog properties, this points...

  12. Fluorescence detection in capillary arrays based on galvanometer step scanning.

    Science.gov (United States)

    Xue, G; Yeung, E S

    2001-10-01

    A computer-controlled galvanometer scanner is adapted for scanning a focused laser beam across a 96-capillary array for laser-induced fluorescence detection. The signal at a single photomultiplier tube is temporally sorted to distinguish among the capillaries. The limit of detection for fluoresceins is 3 x 10(-11) M (S/N = 3) for 5 mW of total laser power scanned at 4 Hz. The observed cross-talk among capillaries is 0.2%. Advantages include the efficient utilization of light due to the high duty-cycle of step scan, good detection performance due to the reduction of stray light, ruggedness due to the small mass of the galvanometer mirror, low cost due to the simplicity of components, and flexibility due to the independent paths for excitation and emission.

  13. Finite element based optimization study on hydroformed stepped tube

    Science.gov (United States)

    Harisankar, K. R.; Omar, A.; Narasimhan, K.

    2016-08-01

    Tube hydroforming process is an advanced manufacturing process in which tube is placed in between the dies and deformed with the help of hydraulic pressure. A sound tube hydroformed part depends upon die conditions, material properties and process conditions. In this work, a finite element study, along with response surface methodology (RSM) for designing the simulation, has been used to construct models with loading path, friction, anisotropic index, strain hardening exponent and tube thickness. The responses studied are the die corner radius filling and strain non-uniformity index (SNI) chosen in each step of the tube with maximum 30% thinning as stopping criteria. The factors effect and their interactions on each response were determined and analysed.

  14. A light scattering study of the evolution of pairing in Fe-based superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Hackl, Rudi; Kretzschmar, Florian; Muschler, Bernhard; Boehm, Thomas [Walther-Meissner-Institut, DE-85748 Garching (Germany); Wen, Hai-Hu [Nanjing University, Nanjing 210093 (China); Tsurkan, Vladimir [University of Augsburg, DE-86159 Augsburg (Germany); Academy of Sciences of Moldova, MD-2028 Chisinau (Moldova, Republic of); Deisenhofer, Joachim; Loidl, Alois [University of Augsburg, DE-86159 Augsburg (Germany)

    2013-07-01

    The iron-based superconductors are a laboratory for exploring the relevance of electron-electron interactions beyond electron-phonon coupling, being at work in conventional superconductors, since the Fermi surfaces can be varied systematically by atomic substitution. This enables one to systematically study magnetism and superconductivity as a function of the Fermi surface topology. Inelastic light scattering affords a window into the electronic properties of the ordered states. In particular, the evolution of the superconducting pairing upon doping can be probed since light scattering allows access to the anisotropy of the energy gap and, in some cases, of the pairing potential. Ba{sub 1-x}K{sub x}Fe{sub 2}As{sub 2} is one of those cases since the competition between s- and d-wave pairing leads to the appearance of exciton-like modes below the gap edges of the various bands. Along with the results from other materials having different Fermi surface cross-sections the data in Ba{sub 1-x}K{sub x}Fe{sub 2}As{sub 2} support the spin fluctuation scenario driven by interband coupling. The experiments show that there exist alternative routes for the analysis of the pairing interaction in superconductors with unconventional coupling and anisotropic gaps.

  15. DSP-Based Stepping Motor Drivers for the LHC Collimators

    CERN Document Server

    Masi, A; Losito, R; Martino, M

    2008-01-01

    The control electronics of the LHC collimators stepping motors will be located in radiation safe zones up to 800 meters far from the motors. With such cable lengths the standard chopping drivers do not work properly because of the voltage losses on the cable and even more because of the high cable capacitance. The capacitance in fact produces a ringing phenomenon on the driver feedback current that limits the control chopping frequency to the point of being incompatible with the tight EM emissions requirements of the LHC tunnel. In some cases the feedback loop may even become unstable and the driver would fail. The problem was solved by accurately modeling the overall motor-cable system taking into account non-linearities due to hysteresis and eddy currents and by designing an adaptive digital controller, self-tuning to the real cable length. The controller will aim at increasing the chopping frequency to reduce the spectral density of the emissions and at damping the oscillations of the feedback current to a...

  16. Spontaneous formation and base pairing of plausible prebiotic nucleotides in water.

    Science.gov (United States)

    Cafferty, Brian J; Fialho, David M; Khanam, Jaheda; Krishnamurthy, Ramanarayanan; Hud, Nicholas V

    2016-04-25

    The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life.

  17. Hydrogen bonding: a channel for protons to transfer through acid-base pairs.

    Science.gov (United States)

    Wu, Liang; Huang, Chuanhui; Woo, Jung-Je; Wu, Dan; Yun, Sung-Hyun; Seo, Seok-Jun; Xu, Tongwen; Moon, Seung-Hyeon

    2009-09-10

    Different from H(3)O(+) transport as in the vehicle mechanism, protons find another channel to transfer through the poorly hydrophilic interlayers in a hydrated multiphase membrane. This membrane was prepared from poly(phthalazinone ether sulfone kentone) (SPPESK) and H(+)-form perfluorosulfonic resin (FSP), and poorly hydrophilic electrostatically interacted acid-base pairs constitute the interlayer between two hydrophilic phases (FSP and SPPESK). By hydrogen bonds forming and breaking between acid-base pairs and water molecules, protons transport directly through these poorly hydrophilic zones. The multiphase membrane, due to this unique transfer mechanism, exhibits better electrochemical performances during fuel cell tests than those of pure FSP and Nafion-112 membranes: 0.09-0.12 S cm(-1) of proton conductivity at 25 degrees C and 990 mW cm(-2) of the maximum power density at a current density of 2600 mA cm(-2) and a cell voltage of 0.38 V.

  18. Investigation on traceability of 3D Scanning Electron Microscopy based on the Stereo Pair Technique

    DEFF Research Database (Denmark)

    Bariani, Paolo

    The scanning electron microscope (SEM) has a big potential as a metrology instrument for micro and nanotechnology due to its unique combination of three imaging properties: • Lateral ultimate resolution down to 2nm • Large range of possible magnification levels ranging from a few hundred times...... that addresses the performance of 3D topography calculation based on surface topography imaging using secondary electrons and the Stereo Pair Technique....

  19. Optimized distance-dependent atom-pair-based potential DOOP for protein structure prediction.

    Science.gov (United States)

    Chae, Myong-Ho; Krull, Florian; Knapp, Ernst-Walter

    2015-05-01

    The DOcking decoy-based Optimized Potential (DOOP) energy function for protein structure prediction is based on empirical distance-dependent atom-pair interactions. To optimize the atom-pair interactions, native protein structures are decomposed into polypeptide chain segments that correspond to structural motives involving complete secondary structure elements. They constitute near native ligand-receptor systems (or just pairs). Thus, a total of 8609 ligand-receptor systems were prepared from 954 selected proteins. For each of these hypothetical ligand-receptor systems, 1000 evenly sampled docking decoys with 0-10 Å interface root-mean-square-deviation (iRMSD) were generated with a method used before for protein-protein docking. A neural network-based optimization method was applied to derive the optimized energy parameters using these decoys so that the energy function mimics the funnel-like energy landscape for the interaction between these hypothetical ligand-receptor systems. Thus, our method hierarchically models the overall funnel-like energy landscape of native protein structures. The resulting energy function was tested on several commonly used decoy sets for native protein structure recognition and compared with other statistical potentials. In combination with a torsion potential term which describes the local conformational preference, the atom-pair-based potential outperforms other reported statistical energy functions in correct ranking of native protein structures for a variety of decoy sets. This is especially the case for the most challenging ROSETTA decoy set, although it does not take into account side chain orientation-dependence explicitly. The DOOP energy function for protein structure prediction, the underlying database of protein structures with hypothetical ligand-receptor systems and their decoys are freely available at http://agknapp.chemie.fu-berlin.de/doop/.

  20. A chemical approach to mapping nucleosomes at base pair resolution in yeast.

    Science.gov (United States)

    Brogaard, Kristin R; Xi, Liqun; Wang, Ji-Ping; Widom, Jonathan

    2012-01-01

    Most eukaryotic DNA exists in DNA-protein complexes known as nucleosomes. The exact locations of nucleosomes along the genome play a critical role in chromosome functions and gene regulation. However, the current methods for nucleosome mapping do not provide the necessary accuracy to identify the precise nucleosome locations. Here we describe a new experimental approach that directly maps nucleosome center locations in vivo genome-wide at single base pair resolution.

  1. Pairing-Free ID-Based Key-Insulated Signature Scheme

    Institute of Scientific and Technical Information of China (English)

    Guo-Bin Zhu; Hu Xiong; Zhi-Guang Qin

    2015-01-01

    Abstract⎯Without the assumption that the private keys are kept secure perfectly, cryptographic primitives cannot be deployed in the insecure environments where the key leakage is inevitable. In order to reduce the damage caused by the key exposure in the identity-based (ID-based) signature scenarios efficiently, we propose an ID-based key-insulated signature scheme in this paper, which eliminates the expensive bilinear pairing operations. Compared with the previous work, our scheme minimizes the computation cost without any extra cost. Under the discrete logarithm (DL) assumption, a security proof of our scheme in the random oracle model has also been given.

  2. Chemical Reasoning Based on an Invariance Property: Bond and Lone Pair Pictures in Quantum Structural Formulas

    Directory of Open Access Journals (Sweden)

    Joseph Alia

    2010-07-01

    Full Text Available Chemists use one set of orbitals when comparing to a structural formula, hybridized AOs or NBOs for example, and another for reasoning in terms of frontier orbitals, MOs usually. Chemical arguments can frequently be made in terms of energy and/or electron density without the consideration of orbitals at all. All orbital representations, orthogonal or not, within a given function space are related by linear transformation. Chemical arguments based on orbitals are really energy or electron density arguments; orbitals are linked to these observables through the use of operators. The Valency Interaction Formula, VIF, offers a system of chemical reasoning based on the invariance of observables from one orbital representation to another. VIF pictures have been defined as one-electron density and Hamiltonian operators. These pictures are classified in a chemically meaningful way by use of linear transformations applied to them in the form of two pictorial rules and the invariance of the number of doubly, singly, and unoccupied orbitals or bonding, nonbonding, and antibonding orbitals under these transformations. The compatibility of the VIF method with the bond pair – lone pair language of Lewis is demonstrated. Different electron lone pair representations are related by the pictorial rules and have stability understood in terms of Walsh’s rules. Symmetries of conjugated ring systems are related to their electronic state by simple mathematical formulas. Description of lone pairs in conjugated systems is based on the strength and sign of orbital interactions around the ring. Simple models for bonding in copper clusters are tested, and the bonding of O2 to Fe(II in hemoglobin is described. Arguments made are supported by HF, B3LYP, and MP2 computations.

  3. Orbital-Parity Selective Superconducting Pairing Structures of Fe-based Superconductors under Glide Symmetry

    Science.gov (United States)

    Lin, Chiahui; Chou, Chung-Pin; Yin, Wei-Guo; Ku, Wei

    2014-03-01

    We show that the superconductivity in Fe-based superconductors consists of zero and finite momentum (π , π , 0) Cooper pairs with the same and different parities of the Fe 3 d orbitals respectively. The former develops the distinct gap structures for each orbital parity, and the latter is characteristic of spin singlet, spacial oddness and time reversal symmetry breaking. This originates from the unit cell containing two Fe atoms and two anions of staggered positioning with respect to the Fe square lattice. The in-plane translation is turned into glide translation, which dictates orbital-parity selective quasiparticles. Such novel pairing structures explain the unusual gap angular modulation on the hole pockets in recent ARPES and STS experiments. Work supported by DOE DE-AC02-98CH10886 and Chinese Academy of Engineering Physics and Ministry of Science and Technology.

  4. Renormalization group analysis of competing orders and the pairing symmetry in Fe-based superconductors

    Science.gov (United States)

    Chubukov, A. V.

    2009-05-01

    We analyze antiferromagnetism and superconductivity in novel Fe-based superconductors within the weak-coupling, itinerant model of electron and hole pockets near (0, 0) and ( π, π) in the folded Brillouin zone. We discuss the interaction Hamiltonian, the nesting, the RG flow of the couplings at energies above and below the Fermi energy, and the interplay between SDW magnetism, superconductivity and charge orbital order. We argue that SDW antiferromagnetism wins at zero doping but looses to superconductivity upon doping. We show that the most likely symmetry of the superconducting gap is A1 g in the folded zone. This gap has no nodes on the Fermi surface but changes sign between hole and electron pockets. We also argue that at weak coupling, this pairing predominantly comes not from spin fluctuation exchange but from a direct pair hopping between hole and electron pockets.

  5. CPK-based grid authentication: a step forward

    Institute of Scientific and Technical Information of China (English)

    WANG Hai-yan; WANG Ru-chuan

    2007-01-01

    Effective grid authentication plays a critical role in grid security, which has been recognized as a key issue in the designing and extension of grid technologies. At present, public key infrastructure (PKI) has been widely applied for grid authentication, and this article proposes a novel grid authentication mechanism, which is based on combined public key (CPK) employing elliptic curve cryptography (ECC). The designing structure of the new grid authentication mechanism and its implementation procedure are described in details.Property analysis of the new mechanism is also made in comparison with that of the globus security infrastructure (GSI) authentication, which leads to the conclusion that CPK-based grid authentication, may be applied as an optimized approach towards efficient and effective grid authentication.

  6. A self-adaptive step Cuckoo search algorithm based on dimension by dimension improvement

    Directory of Open Access Journals (Sweden)

    Lu REN

    2015-10-01

    Full Text Available The choice of step length plays an important role in convergence speed and precision of Cuckoo search algorithm. In the paper, a self-adaptive step Cuckoo search algorithm based on dimensional improvement is provided. First, since the step in the original self-adaptive step Cuckoo search algorithm is not updated when the current position of the nest is in the optimal position, simple modification of the step is made for the update. Second, evaluation strategy based on dimension by dimension update is introduced to the modified self-adaptive step Cuckoo search algorithm. The experimental results show that the algorithm can balance the contradiction between the global convergence ability and the precision of optimization. Moreover, the proposed algorithm has better convergence speed.

  7. Prediction of plant promoters based on hexamers and random triplet pair analysis

    Directory of Open Access Journals (Sweden)

    Noman Nasimul

    2011-06-01

    Full Text Available Abstract Background With an increasing number of plant genome sequences, it has become important to develop a robust computational method for detecting plant promoters. Although a wide variety of programs are currently available, prediction accuracy of these still requires further improvement. The limitations of these methods can be addressed by selecting appropriate features for distinguishing promoters and non-promoters. Methods In this study, we proposed two feature selection approaches based on hexamer sequences: the Frequency Distribution Analyzed Feature Selection Algorithm (FDAFSA and the Random Triplet Pair Feature Selecting Genetic Algorithm (RTPFSGA. In FDAFSA, adjacent triplet-pairs (hexamer sequences were selected based on the difference in the frequency of hexamers between promoters and non-promoters. In RTPFSGA, random triplet-pairs (RTPs were selected by exploiting a genetic algorithm that distinguishes frequencies of non-adjacent triplet pairs between promoters and non-promoters. Then, a support vector machine (SVM, a nonlinear machine-learning algorithm, was used to classify promoters and non-promoters by combining these two feature selection approaches. We referred to this novel algorithm as PromoBot. Results Promoter sequences were collected from the PlantProm database. Non-promoter sequences were collected from plant mRNA, rRNA, and tRNA of PlantGDB and plant miRNA of miRBase. Then, in order to validate the proposed algorithm, we applied a 5-fold cross validation test. Training data sets were used to select features based on FDAFSA and RTPFSGA, and these features were used to train the SVM. We achieved 89% sensitivity and 86% specificity. Conclusions We compared our PromoBot algorithm to five other algorithms. It was found that the sensitivity and specificity of PromoBot performed well (or even better with the algorithms tested. These results show that the two proposed feature selection methods based on hexamer frequencies

  8. Higher order structural effects stabilizing the reverse watson-crick guanine-cytosine base pair in functional RNAs

    KAUST Repository

    Chawla, Mohit

    2013-10-10

    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. 2013 The Author(s).

  9. Community-based Participatory Research: Necessary Next Steps

    Directory of Open Access Journals (Sweden)

    Zubaida Faridi, MBBS, MPH

    2007-07-01

    Full Text Available Community-based participatory research (CBPR is gaining increasing credence among public health researchers and practitioners. However, there is no standardization in assessing the quality of research methods, the effectiveness of the interventions, and the reporting requirements in the literature. The absence of standardization precludes meaningful comparisons of CBPR studies. Several authors have proposed a broad set of competencies required for CBPR research for both individuals and organizations, but the discussion remains fragmented. The Prevention Research Centers (PRC Program recently began a qualitative assessment of its national efforts, including an evaluation of how PRCs implement CBPR studies. Topics of interest include types of community partnerships; community capacity for research, evaluation, and training; and factors that help and hinder partner relationships. The assessment will likely contribute to the development of a standard set of competencies and resources required for effective CBPR.

  10. Developing evidence-based librarianship: practical steps for implementation.

    Science.gov (United States)

    Crumley, Ellen; Koufogiannakis, Denise

    2002-06-01

    Evidence-based librarianship (EBL) is a relatively new concept for librarians. This paper lays out a practical framework for the implementation of EBL. A new way of thinking about research in librarianship is introduced using the well-built question process and the assignment of librarian research questions to one of six domains specific to librarianship. As a profession, librarianship tends to reflect more qualitative, social sciences/humanities in its research methods and study types which tend to be less rigorous and more prone to bias. Randomised controlled trials (RCT) do not have to be placed at the top of an evidence 'hierarchy' for librarianship. Instead, a more encompassing model reflecting librarianship as a whole and the kind of research likely to be done by librarians is proposed. 'Evidence' from a number of disciplines including health sciences, business and education can be utilized by librarians and applied to their practice. However, access to and availability of librarianship literature needs to be further studied. While using other disciplines (e.g. EBHC) as a model for EBL has been explored in the literature, the authors develop models unique to librarianship. While research has always been a minor focus in the profession, moving research into practice is becoming more important and librarians need to consider the issues surrounding research in order to move EBL forward.

  11. Python-based geometry preparation and simulation visualization toolkits for STEPS.

    Science.gov (United States)

    Chen, Weiliang; De Schutter, Erik

    2014-01-01

    STEPS is a stochastic reaction-diffusion simulation engine that implements a spatial extension of Gillespie's Stochastic Simulation Algorithm (SSA) in complex tetrahedral geometries. An extensive Python-based interface is provided to STEPS so that it can interact with the large number of scientific packages in Python. However, a gap existed between the interfaces of these packages and the STEPS user interface, where supporting toolkits could reduce the amount of scripting required for research projects. This paper introduces two new supporting toolkits that support geometry preparation and visualization for STEPS simulations.

  12. Python-Based Geometry Preparation and Simulation Visualization Toolkits for STEPS

    Directory of Open Access Journals (Sweden)

    Weiliang eChen

    2014-04-01

    Full Text Available STEPS is a stochastic reaction-diffusion simulation engine that implements a spatial extension of Gillespie’s Stochastic Simulation Algorithm (SSA in complex tetrahedral geometries. An extensive Python-based interface is provided to STEPS so that it can interact with the large number of scientific packages in Python. However, a gap existed between the interfaces of these packages and the STEPS user interface, where supporting toolkits could reduce the amount of scripting required for research projects. This paper introduces two new supporting toolkits that support geometry preparation and visualization for STEPS simulations.

  13. One-step discrimination scheme on N-particle Greenberger-Horne-Zeilinger bases

    Institute of Scientific and Technical Information of China (English)

    Wang Xin-Wen; Liu Xiang; Fang Mao-Fa

    2007-01-01

    We present an experimentally feasible one-step discrimination scheme on Bell bases with trapped ions, and then generalize it to the case of N-ion Greenberger-Horne-Zeilinger (GHZ) bases. In the scheme, all the orthogonal and complete N-ion GHZ internal states can be exactly discriminated only by one step, and thus it takes very short time. Moreover, the scheme is insensitive to thermal motion and dose not require the individual addressing of the ions. The Bell-state and GHZ-state one-step discrimination scheme can be widely used in quantum information processing based on ion-trap set-up.

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

    Science.gov (United States)

    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

  15. Efficient and Provable Secure Pairing-Free Security-Mediated Identity-Based Identification Schemes

    Directory of Open Access Journals (Sweden)

    Ji-Jian Chin

    2014-01-01

    Full Text Available Security-mediated cryptography was first introduced by Boneh et al. in 2001. The main motivation behind security-mediated cryptography was the capability to allow instant revocation of a user’s secret key by necessitating the cooperation of a security mediator in any given transaction. Subsequently in 2003, Boneh et al. showed how to convert a RSA-based security-mediated encryption scheme from a traditional public key setting to an identity-based one, where certificates would no longer be required. Following these two pioneering papers, other cryptographic primitives that utilize a security-mediated approach began to surface. However, the security-mediated identity-based identification scheme (SM-IBI was not introduced until Chin et al. in 2013 with a scheme built on bilinear pairings. In this paper, we improve on the efficiency results for SM-IBI schemes by proposing two schemes that are pairing-free and are based on well-studied complexity assumptions: the RSA and discrete logarithm assumptions.

  16. Ion Pair in Extreme Aqueous Environments, Molecular-Based and Electric Conductance Approaches

    Energy Technology Data Exchange (ETDEWEB)

    Chialvo, Ariel A [ORNL; Gruszkiewicz, Miroslaw {Mirek} S [ORNL; Simonson, J Michael {Mike} [ORNL; Palmer, Donald [ORNL; Cole, David R [ORNL

    2009-01-01

    We determine by molecular-based simulation the density profiles of the Na+!Cl! ion-pair association constant in steam environments along three supercritical isotherms to interrogate the behavior of ion speciation in dilute aqueous solutions at extreme conditions. Moreover, we describe a new ultra-sensitive flow-through electric conductance apparatus designed to bridge the gap between the currently lowest steam-density conditions at which we are experimentally able to attain electric conductance measurements and the theoretically-reachable zero-density limit. Finally, we highlight important modeling challenges encountered near the zero-density limit and discuss ways to overcome them.

  17. Chemistry of stannylene-based Lewis pairs: dynamic tin coordination switching between donor and acceptor character.

    Science.gov (United States)

    Krebs, Kilian M; Freitag, Sarah; Schubert, Hartmut; Gerke, Birgit; Pöttgen, Rainer; Wesemann, Lars

    2015-03-16

    The coordination chemistry of cyclic stannylene-based intramolecular Lewis pairs is presented. The P→Sn adducts were treated with [Ni(COD)2] and [Pd(PCy3)2] (COD = 1,5-cyclooctadiene, PCy3 = tricyclohexylphosphine). In the isolated coordination compounds the stannylene moiety acts either as an acceptor or a donor ligand. Examples of a dynamic switch between these two coordination modes of the P-Sn ligand are illustrated and the structures in the solid state together with heteronuclear NMR spectroscopic findings are discussed. In the case of a Ni(0) complex, (119)Sn Mössbauer spectroscopy of the uncoordinated and coordinated phosphastannirane ligand is presented.

  18. DFT Description of Intermolecular Forces between 9-Aminoacridines and DNA Base Pairs

    Directory of Open Access Journals (Sweden)

    Sandra Cotes Oyaga

    2013-01-01

    Full Text Available The B3LYP method with 6-31G* basis set was used to predict the geometries of five 9-aminoacridines (9-AA 1(a–e, DNA base pairs, and respective complexes. Polarizabilities, charge distribution, frontier molecular orbital (FMO, and dipole moments were used to analyze the nature of interactions that allow reasonable drug diffusion levels. The results showed that charge delocalization, high polarizabilities, and high dipole moments play an important role in intermolecular interactions with DNA. The interactions of 9-AA 1(a–e with GC are the strongest. 9-AA 1(d displayed the strongest interaction and 9-AA 1(b the weakest.

  19. A map of nucleosome positions in yeast at base-pair resolution.

    Science.gov (United States)

    Brogaard, Kristin; Xi, Liqun; Wang, Ji-Ping; Widom, Jonathan

    2012-06-28

    The exact positions of nucleosomes along genomic DNA can influence many aspects of chromosome function. However, existing methods for mapping nucleosomes do not provide the necessary single-base-pair accuracy to determine these positions. Here we develop and apply a new approach for direct mapping of nucleosome centres on the basis of chemical modification of engineered histones. The resulting map locates nucleosome positions genome-wide in unprecedented detail and accuracy. It shows new aspects of the in vivo nucleosome organization that are linked to transcription factor binding, RNA polymerase pausing and the higher-order structure of the chromatin fibre.

  20. Powered Tate Pairing Computation

    Science.gov (United States)

    Kang, Bo Gyeong; Park, Je Hong

    In this letter, we provide a simple proof of bilinearity for the eta pairing. Based on it, we show an efficient method to compute the powered Tate pairing as well. Although efficiency of our method is equivalent to that of the Tate pairing on the eta pairing approach, but ours is more general in principle.

  1. Pairings on hyperelliptic curves

    CERN Document Server

    Balakrishnan, Jennifer; Chisholm, Sarah; Eisentraeger, Kirsten; Stange, Katherine; Teske, Edlyn

    2009-01-01

    We assemble and reorganize the recent work in the area of hyperelliptic pairings: We survey the research on constructing hyperelliptic curves suitable for pairing-based cryptography. We also showcase the hyperelliptic pairings proposed to date, and develop a unifying framework. We discuss the techniques used to optimize the pairing computation on hyperelliptic curves, and present many directions for further research.

  2. Enersy basis of recognition of base pair for platinum-based antitumour drug ZD0473 and cisplatin

    Institute of Scientific and Technical Information of China (English)

    HAO Lan; LI XiChen; TAN HongWei; CHEN GuangJu; JIA MuXin

    2008-01-01

    Platinum-based antitumour drug ZD0473 was designed to reduce the cisplatin resistance to the tumor cells. In this paper, the mixed method of molecular mechanics and quantum chemistry, HF/lan12dz//MM/uff and B3LYP/lan12dz//6-31G*, are used to investigate the differences between four types of GG, 3'AG5', 3'GA5', and AA complexes, which are formed from four discrete DNA fragments recognized by ZD0473 and cisplatin. The results show that the binding interaction of both ZD0473 and cisplatin drugs with the GG base pair is much stronger than with other base pairs, namely the recognition capability of such drugs to the GG base pair is more considerable. Moreover, the interaction of four complexes of ZD0473 with DNA fragments is stronger than that of cisplatin with corresponding DNA fragments, which indicates the stronger binding capability of ZD0473 with DNA fragments and high antitumour activity of ZD0473. The main reason for easier forming of 3'GA5' complex than the 3'AG5' one is that the drug molecule prefers to bind with a single G base to form a monoligand compound firstly; then the con-figuration transformation from such monoligand compound to the bi-ligand one is limited.

  3. Energy basis of recognition of base pair for platinum-based antitumour drug ZD0473 and cisplatin

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Platinum-based antitumour drug ZD0473 was designed to reduce the cisplatin resistance to the tumor cells. In this paper, the mixed method of molecular mechanics and quantum chemistry, HF/lanl2dz// MM/uff and B3LYP/lanl2dz//6-31G*, are used to investigate the differences between four types of GG, 3′AG5′, 3′GA5′, and AA complexes, which are formed from four discrete DNA fragments recognized by ZD0473 and cisplatin. The results show that the binding interaction of both ZD0473 and cisplatin drugs with the GG base pair is much stronger than with other base pairs, namely the recognition capability of such drugs to the GG base pair is more considerable. Moreover, the interaction of four complexes of ZD0473 with DNA fragments is stronger than that of cisplatin with corresponding DNA fragments, which indicates the stronger binding capability of ZD0473 with DNA fragments and high antitumour activity of ZD0473. The main reason for easier forming of 3′GA5′ complex than the 3′AG5′ one is that the drug molecule prefers to bind with a single G base to form a monoligand compound firstly; then the con- figuration transformation from such monoligand compound to the bi-ligand one is limited.

  4. Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs

    Directory of Open Access Journals (Sweden)

    Ye Zhi-Qiang

    2011-08-01

    Full Text Available Abstract Background Differential coexpression analysis (DCEA is increasingly used for investigating the global transcriptional mechanisms underlying phenotypic changes. Current DCEA methods mostly adopt a gene connectivity-based strategy to estimate differential coexpression, which is characterized by comparing the numbers of gene neighbors in different coexpression networks. Although it simplifies the calculation, this strategy mixes up the identities of different coexpression neighbors of a gene, and fails to differentiate significant differential coexpression changes from those trivial ones. Especially, the correlation-reversal is easily missed although it probably indicates remarkable biological significance. Results We developed two link-based quantitative methods, DCp and DCe, to identify differentially coexpressed genes and gene pairs (links. Bearing the uniqueness of exploiting the quantitative coexpression change of each gene pair in the coexpression networks, both methods proved to be superior to currently popular methods in simulation studies. Re-mining of a publicly available type 2 diabetes (T2D expression dataset from the perspective of differential coexpression analysis led to additional discoveries than those from differential expression analysis. Conclusions This work pointed out the critical weakness of current popular DCEA methods, and proposed two link-based DCEA algorithms that will make contribution to the development of DCEA and help extend it to a broader spectrum.

  5. Integrated CAD/CAM/CNC system based on STEP-NC and intelligent manufacturing

    Science.gov (United States)

    Du, Juan; Tian, Xitian; Zhang, Zhenming; Xu, Jianxin; Zhu, Mingquan

    2005-12-01

    In order to realize bi-direction exchange of information and knowledge sharing between CAD/CAM systems and CNC machines, a method of information integration was proposed based on process data model and STEP-NC neutral file. A frame of integrated CAD/CAM/CNC systems was established, and the key integration techniques including process data modeling based on XML form and automatic feature recognition were studied. Since the STEP-NC based CNC (STEP- CNC) system can undertake various intelligent functions that cannot be performed by the conventional CNC based on ISO 6983, the intelligent manufacturing functions of STEP- CNC system was also discussed. The presented methodology combining with the modern net and communication technologies provides an effective means for developing intelligent, integrated manufacturing systems for the 21 century.

  6. Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs

    DEFF Research Database (Denmark)

    van Beest, M; Dooijes, D; van De Wetering, M;

    2000-01-01

    of promoter elements controlled by the yeast genes ste11 and Rox1 has indicated strict conservation of a larger DNA motif. By site selection, we identify a highly specific 12-base pair motif for Ste11, AGAACAAAGAAA. Similarly, we show that Tcf1, MatMc, and Sox4 bind unique, highly specific DNA motifs of 12......, 12, and 10 base pairs, respectively. Footprinting with a deletion mutant of Ste11 reveals a novel interaction between the 3' base pairs of the extended DNA motif and amino acids C-terminal to the HMG domain. The sequence-specific interaction of Ste11 with these 3' base pairs contributes significantly......Sequence-specific high mobility group (HMG) box factors bind and bend DNA via interactions in the minor groove. Three-dimensional NMR analyses have provided the structural basis for this interaction. The cognate HMG domain DNA motif is generally believed to span 6-8 bases. However, alignment...

  7. Close Color Pair Signature ensemble Adaptive Threshold based Steganalsis for LSB Embedding in Digital Images

    Directory of Open Access Journals (Sweden)

    S. Geetha

    2008-12-01

    Full Text Available We present a novel technique for effective steganalysis of high-color-depth digital images that have been subjected to embedding by LSB steganographic algorithms. The detection theory is based on the idea that under repeated embedding, the disruption of the signal characteristics is the highest for the first embedding and decreases subsequently. That is the marginal distortions due to repeated embeddings decrease monotonically. This decreasing distortion property exploited with Close Color Pair signature is used to construct the classifier that can distinguish between stego and cover images. For evaluation, a database composed of 1200 plain and stego images (at 10% and 20% payload and each one artificially adulterated with 20% additional data was established. Based on this database, extensive experiments were conducted to prove the feasibility of our proposed system. Our main results are (i a 90%+ positive-detection rate; (ii Close Color Pair ratio is not modified significantly when additional bit streams are embedded into a test image that is already tampered with a message.; (iii an image quality metric Czenakowski Measure, that is substantially sensitive to LSB embedding is utilized to derive the effective image adaptive threshold; (iv capable of detecting stego images with an embedding of even 10% payload while the earlier methods can achieve the same detection rate only with 20% payload.

  8. A model for avian magnetoreception by coupling magnetite-based mechanism with radical-pair-based mechanism

    CERN Document Server

    Lu, Yan

    2012-01-01

    Many species of animals have been testified to use the geomagnetic field for their navigation, but the biophysical mechanism of magnetoreception has remained enigmatic. This paper presents a biophysical model consisting of magnetite-based mechanism and radical-pair-based mechanism for the avian magnetoreception. The amplitude of resultant magnetic field outside the magnetic particles correspond to the geomagnetic field direction and effect the yield of singlet/triplet state products in the radical pair reactions, therefore the yield of singlet/triplet state products can connect with the geomagnetic field information for orientational detection by the proposed model. The resultant magnetic fields corresponds to two materials with different magnetic properties were analysed under different directions of the geomagnetic field. The results shown that the ferromagnetic particles in organisms could provide more significant change of singlet state products than that of superparamagnetic particles, and the period of ...

  9. Simulation Based on Negative ion pair Techniques of Electric propulsion In Satellite Mission Using Chlorine Gas

    Science.gov (United States)

    Bakkiyaraj, R.

    R.Bakkiyaraj,Assistant professor,Government college of Engineering ,Bargur,Tamilnadu. *C.Sathiyavel, PG Student and Department of Aeronautical Engineering/Branch of Avionics, PSN college of Engineering and Technology,Tirunelveli,India. Abstract: Ion propulsion rocket system is expected to become popular with the development of ion-ion pair techniques because of their stimulated of low propellant, Design of repulsive between negative ions with low electric power and high efficiency. A Negative ion pair of ion propulsion rocket system is proposed in this work .Negative Ion Based Rocket system consists of three parts 1.ionization chamber 2. Repulsion force and ion accelerator 3. Exhaust of Nozzle. The Negative ions from electro negatively gas are produced by attachment of the gas ,such as chlorine with electron emitted from a Electron gun ionization chamber. The formulate of large stable negative ion is achievable in chlorine gas with respect to electron affinity (∆E). When a neutral chlorine atom in the gaseous form picks up an electron to form a cl- ion, it releases energy of 349 kJ/mol or 3.6 eV/atom. It is said to have an electron affinity of -349 kJ/mol ,the negative sign indicating that energy is released during this process .The distance between negative ions pair is important for the evaluation of the rocket thrust and is also determined by the exhaust velocity of the propellant. The mass flow rate of ions is related to the ion beam current. Accelerate the Negative ions to a high velocity in the thrust vector direction with a significantly intense grids and the exhaust of negative ions through Nozzle. The simulation of the ion propulsion system has been carried out by MATLAB. By comparing the simulation results with the theoretical and previous results, we have found that the proposed method is achieved of thrust value with low electric power for simulating the ion propulsion rocket system

  10. Evaluating changes in matrix based, recovery-adjusted concentrations in paired data for pesticides in groundwater

    Science.gov (United States)

    Zimmerman, Tammy M.; Breen, Kevin J.

    2012-01-01

    Pesticide concentration data for waters from selected carbonate-rock aquifers in agricultural areas of Pennsylvania were collected in 1993–2009 for occurrence and distribution assessments. A set of 30 wells was visited once in 1993–1995 and again in 2008–2009 to assess concentration changes. The data include censored matched pairs (nondetections of a compound in one or both samples of a pair). A potentially improved approach for assessing concentration changes is presented where (i) concentrations are adjusted with models of matrix-spike recovery and (ii) area-wide temporal change is tested by use of the paired Prentice-Wilcoxon (PPW) statistical test. The PPW results for atrazine, simazine, metolachlor, prometon, and an atrazine degradate, deethylatrazine (DEA), are compared using recovery-adjusted and unadjusted concentrations. Results for adjusted compared with unadjusted concentrations in 2008–2009 compared with 1993–1995 were similar for atrazine and simazine (significant decrease; 95% confidence level) and metolachlor (no change) but differed for DEA (adjusted, decrease; unadjusted, increase) and prometon (adjusted, decrease; unadjusted, no change). The PPW results were different on recovery-adjusted compared with unadjusted concentrations. Not accounting for variability in recovery can mask a true change, misidentify a change when no true change exists, or assign a direction opposite of the true change in concentration that resulted from matrix influences on extraction and laboratory method performance. However, matrix-based models of recovery derived from a laboratory performance dataset from multiple studies for national assessment, as used herein, rather than time- and study-specific recoveries may introduce uncertainty in recovery adjustments for individual samples that should be considered in assessing change.

  11. Cloud Base Height Measurements at Manila Observatory: Initial Results from Constructed Paired Sky Imaging Cameras

    Science.gov (United States)

    Lagrosas, N.; Tan, F.; Antioquia, C. T.

    2014-12-01

    Fabricated all sky imagers are efficient and cost effective instruments for cloud detection and classification. Continuous operation of this instrument can result in the determination of cloud occurrence and cloud base heights for the paired system. In this study, a fabricated paired sky imaging system - consisting two commercial digital cameras (Canon Powershot A2300) enclosed in weatherproof containers - is developed in Manila Observatory for the purpose of determining cloud base heights at the Manila Observatory area. One of the cameras is placed on the rooftop of Manila Observatory and the other is placed on the rooftop of the university dormitory, 489m from the first camera. The cameras are programmed to simultaneously gather pictures every 5 min. Continuous operation of these cameras were implemented since the end of May of 2014 but data collection started end of October 2013. The data were processed following the algorithm proposed by Kassianov et al (2005). The processing involves the calculation of the merit function that determines the area of overlap of the two pictures. When two pictures are overlapped, the minimum of the merit function corresponds to the pixel column positions where the pictures have the best overlap. In this study, pictures of overcast sky prove to be difficult to process for cloud base height and were excluded from processing. The figure below shows the initial results of the hourly average of cloud base heights from data collected from November 2013 to July 2014. Measured cloud base heights ranged from 250m to 1.5km. These are the heights of cumulus and nimbus clouds that are dominant in this part of the world. Cloud base heights are low in the early hours of the day indicating low convection process during these times. However, the increase in the convection process in the atmosphere can be deduced from higher cloud base heights in the afternoon. The decrease of cloud base heights after 15:00 follows the trend of decreasing solar

  12. The selective tRNA aminoacylation mechanism based on a single G•U pair.

    Science.gov (United States)

    Naganuma, Masahiro; Sekine, Shun-ichi; Chong, Yeeting Esther; Guo, Min; Yang, Xiang-Lei; Gamper, Howard; Hou, Ya-Ming; Schimmel, Paul; Yokoyama, Shigeyuki

    2014-06-26

    Ligation of tRNAs with their cognate amino acids, by aminoacyl-tRNA synthetases, establishes the genetic code. Throughout evolution, tRNA(Ala) selection by alanyl-tRNA synthetase (AlaRS) has depended predominantly on a single wobble base pair in the acceptor stem, G3•U70, mainly on the kcat level. Here we report the crystal structures of an archaeal AlaRS in complex with tRNA(Ala) with G3•U70 and its A3•U70 variant. AlaRS interacts with both the minor- and the major-groove sides of G3•U70, widening the major groove. The geometry difference between G3•U70 and A3•U70 is transmitted along the acceptor stem to the 3'-CCA region. Thus, the 3'-CCA region of tRNA(Ala) with G3•U70 is oriented to the reactive route that reaches the active site, whereas that of the A3•U70 variant is folded back into the non-reactive route. This novel mechanism enables the single wobble pair to dominantly determine the specificity of tRNA selection, by an approximate 100-fold difference in kcat.

  13. Peptide tag/probe pairs based on the coordination chemistry for protein labeling.

    Science.gov (United States)

    Uchinomiya, Shohei; Ojida, Akio; Hamachi, Itaru

    2014-02-17

    Protein-labeling methods serve as essential tools for analyzing functions of proteins of interest under complicated biological conditions such as in live cells. These labeling methods are useful not only to fluorescently visualize proteins of interest in biological systems but also to conduct protein and cell analyses by harnessing the unique functions of molecular probes. Among the various labeling methods available, an appropriate binding pair consisting of a short peptide and a de novo designed small molecular probe has attracted attention because of its wide utility and versatility. Interestingly, most peptide tag/probe pairs exploit metal-ligand coordination interactions as the main binding force responsible for their association. Herein, we provide an overview of the recent progress of these coordination-chemistry-based protein-labeling methods and their applications for fluorescence imaging and functional analysis of cellular proteins, while highlighting our originally developed labeling methods. These successful examples clearly exemplify the utility and versatility of metal coordination chemistry in protein functional analysis.

  14. Homosexual Pairing within a Swarm-Based Mating System: The Case of the Chironomid Midge

    Directory of Open Access Journals (Sweden)

    Athol J. McLachlan

    2011-01-01

    Full Text Available Homosexuality has been dubbed the Darwinian paradox, because it raises the question of how behaviour that would seem to reduce the chance of successful mating can be maintained by natural selection. This question rests on the assumption that same sex mating is the result of active choice of partner, hardwired into the mating behaviour, but there is an alternative explanation for such behaviour. I refer to the possibility that same-sex mating is the result, not of adaptive behaviour at all, but rather of errors due to imprecise sensory machinery. Such an explanation finds support within the mating system of insects with swarm-based mating systems. To explore this case, I turn to the common chironomid midge. I show that homosexual pairing here, exclusively involving male/male pairs, is common. I attempt to show that this observation, together with data on insect predators of swarming midges, can be used to penetrate the mysteries of this fascinating but elusive mating system.

  15. Exploiting bounded signal flow for graph orientation based on cause-effect pairs

    Directory of Open Access Journals (Sweden)

    Niedermeier Rolf

    2011-08-01

    Full Text Available Abstract Background We consider the following problem: Given an undirected network and a set of sender-receiver pairs, direct all edges such that the maximum number of "signal flows" defined by the pairs can be routed respecting edge directions. This problem has applications in understanding protein interaction based cell regulation mechanisms. Since this problem is NP-hard, research so far concentrated on polynomial-time approximation algorithms and tractable special cases. Results We take the viewpoint of parameterized algorithmics and examine several parameters related to the maximum signal flow over vertices or edges. We provide several fixed-parameter tractability results, and in one case a sharp complexity dichotomy between a linear-time solvable case and a slightly more general NP-hard case. We examine the value of these parameters for several real-world network instances. Conclusions Several biologically relevant special cases of the NP-hard problem can be solved to optimality. In this way, parameterized analysis yields both deeper insight into the computational complexity and practical solving strategies.

  16. Determination of electron pairing symmetry of iron-based superconductor FeSe%Determination of electron pairing symmetry of iron-based superconductor FeSe

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    The research team led by Prof. Qi-Kun Xue at Department of Physics, Tsinghua University, and Prof. Xucun Ma at Institute of Physics, Chinese Academy of Sciences, has made a major breakthrough in study of the electron pairing symmetry of FeSe superconductor.

  17. Identification of Mine-Shaped Objects based on an Efficient Phase Stepped-Frequency Radar Approach

    DEFF Research Database (Denmark)

    Sørensen, Helge Bjarup Dissing; Jakobsen, Kaj Bjarne; Nymann, Ole

    1997-01-01

    a radar probe is moved automatically to measure in each grid point a set of reflection coefficients from which phase and amplitude information are extracted. Based on a simple processing of the phase information, quarternary image and template cross-correlation a successful detection of metal- and non...... clearance. Our approach consists of three stages, the phase stepped-frequency radar method, generation of a quarternary image and template crosscorrelation. The phase stepped-frequency radar method belongs to the class of stepped-frequency radar methods. In a two-dimensional mesh-grid above the ground...

  18. Chemical shifts assignments of the archaeal MC1 protein and a strongly bent 15 base pairs DNA duplex in complex.

    Science.gov (United States)

    Loth, Karine; Landon, Céline; Paquet, Françoise

    2015-04-01

    MC1 is the most abundant architectural protein present in Methanosarcina thermophila CHTI55 in laboratory growth conditions and is structurally unrelated to other DNA-binding proteins. MC1 functions are to shape and to protect DNA against thermal denaturation by binding to it. Therefore, MC1 has a strong affinity for any double-stranded DNA. However, it recognizes and preferentially binds to bent DNA, such as four-way junctions and negatively supercoiled DNA minicircles. Combining NMR data, electron microscopy data, biochemistry, molecular modelisation and docking approaches, we proposed recently a new type of DNA/protein complex, in which the monomeric protein MC1 binds on the concave side of a strongly bent 15 base pairs DNA. We present here the NMR chemical shifts assignments of each partner in the complex, (1)H (15)N MC1 protein and (1)H (13)C (15)N bent duplex DNA, as first step towards the first experimental 3D structure of this new type of DNA/protein complex.

  19. Isolation breeds naivety: island living robs Australian varanid lizards of toad-toxin immunity via four-base-pair mutation.

    Science.gov (United States)

    Ujvari, Beata; Mun, Hee-chang; Conigrave, Arthur D; Bray, Alessandra; Osterkamp, Jens; Halling, Petter; Madsen, Thomas

    2013-01-01

    Since their introduction to the toad-free Australian continent cane toads (Bufo marinus) have caused a dramatic increase in naïve varanid mortality when these large lizards attempt to feed on this toxic amphibian. In contrast Asian-African varanids, which have coevolved with toads, are resistant to toad toxin. Toad toxins, such as Bufalin target the H1-H2 domain of the α(1) subunit of the sodium-potassium-ATPase enzyme. Sequencing of this domain revealed identical nucleotide sequences in four Asian as well as in three African varanids, and identical sequences in all 11 Australian varanids. However, compared to the Asian-African varanids, the Australian varanids showed four-base-pair substitutions, resulting in the alteration in three of the 12 amino acids representing the H1-H2 domain. The phenotypic effect of the substitutions was investigated in human embryonic kidney (HEK) 293 cells stably transfected with the Australian and the Asian-African H1-H2 domains. The transfections resulted in an approximate 3000-fold reduction in resistance to Bufalin in the Australian HEK293 cells compared to the Asian-African HEK293 cells, demonstrating the critical role of this minor mutation in providing Bufalin resistance. Our study hence presents a clear link between genotype and phenotype, a critical step in understanding the evolution of phenotypic diversity.

  20. Investigation to biodiesel production by the two-step homogeneous base-catalyzed transesterification.

    Science.gov (United States)

    Ye, Jianchu; Tu, Song; Sha, Yong

    2010-10-01

    For the two-step transesterification biodiesel production made from the sunflower oil, based on the kinetics model of the homogeneous base-catalyzed transesterification and the liquid-liquid phase equilibrium of the transesterification product, the total methanol/oil mole ratio, the total reaction time, and the split ratios of methanol and reaction time between the two reactors in the stage of the two-step reaction are determined quantitatively. In consideration of the transesterification intermediate product, both the traditional distillation separation process and the improved separation process of the two-step reaction product are investigated in detail by means of the rigorous process simulation. In comparison with the traditional distillation process, the improved separation process of the two-step reaction product has distinct advantage in the energy duty and equipment requirement due to replacement of the costly methanol-biodiesel distillation column.

  1. Calculating Distortions of Short DNA Duplexes with Base Pairing Between an Oxidatively Damaged Guanine and a Guanine

    Directory of Open Access Journals (Sweden)

    Masayo Suzuki

    2014-07-01

    Full Text Available DNA is constantly being oxidized, and oxidized DNA is prone to mutation; moreover, guanine is highly sensitive to several oxidative stressors. Several oxidatively damaged forms of guanine—including 2,2,4-triamino-5(2H-oxazolone (Oz, iminoallantoin (Ia, and spiroiminodihydantoin (Sp—can be paired with guanine, and cause G:C-C:G transversions. Previous findings indicate that guanine is incorporated more efficiently opposite Oz than opposite Ia or Sp, and that these differences in efficiency cannot be explained by differences in the stabilities of G:Oz, G:Ia, and G:Sp base pairs calculated ab initio. Here, to explain previous experimental result, we used a 3-base-pair model DNA duplex to calculate the difference in the stability and the distortion of DNA containing a G:Oz, G:Ia, or G:Sp base pair. We found that the stability of the structure containing 5ꞌ and 3ꞌ base pairs adjacent to G:Oz was more stable than that containing the respective base pairs adjacent to G:Ia or G:Sp. Moreover, the distortion of the structure in the DNA model duplex that contained a G:Oz was smaller than that containing a G:Ia or G:Sp. Therefore, our discussion can explain the previous results involving translesion synthesis past an oxidatively damaged guanine.

  2. PID controller auto-tuning based on process step response and damping optimum criterion.

    Science.gov (United States)

    Pavković, Danijel; Polak, Siniša; Zorc, Davor

    2014-01-01

    This paper presents a novel method of PID controller tuning suitable for higher-order aperiodic processes and aimed at step response-based auto-tuning applications. The PID controller tuning is based on the identification of so-called n-th order lag (PTn) process model and application of damping optimum criterion, thus facilitating straightforward algebraic rules for the adjustment of both the closed-loop response speed and damping. The PTn model identification is based on the process step response, wherein the PTn model parameters are evaluated in a novel manner from the process step response equivalent dead-time and lag time constant. The effectiveness of the proposed PTn model parameter estimation procedure and the related damping optimum-based PID controller auto-tuning have been verified by means of extensive computer simulations.

  3. POINT PATTERN MATCHING ALGORITHM BASED ON POINT PAIR TOPOLOGICAL CHARACTERISTICS AND SPECTRAL MATCHING

    Institute of Scientific and Technical Information of China (English)

    Lu Chunyan; Zou Huanxin; Zhao Jian; Zhou Shilin

    2012-01-01

    Most of the Point Pattern Matching (PPM) algorithm performs poorly when the noise of the point's position and outliers exist.This paper presents a novel and robust PPM algorithm which combined Point Pair Topological Characteristics (PPTC) and Spectral Matching (SM) together to solve the afore mentioned issues.In which PPTC,a new shape descriptor,is firstly proposed.A new comparability measurement based on PPTC is defined as the matching probability.Finally,the correct matching results are achieved by the spectral matching method.The synthetic data experiments show its robustness by comparing with the other state-of-art algorithms and the real world data experiments show its effectiveness.

  4. Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs

    CERN Document Server

    Fang, Wei; Rossi, Mariana; Feng, Yexin; Li, Xin-Zheng; Michaelides, Angelos

    2016-01-01

    Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general.

  5. A bilinear pairing based anonymous authentication scheme in wireless body area networks for mHealth.

    Science.gov (United States)

    Jiang, Qi; Lian, Xinxin; Yang, Chao; Ma, Jianfeng; Tian, Youliang; Yang, Yuanyuan

    2016-11-01

    Wireless body area networks (WBANs) have become one of the key components of mobile health (mHealth) which provides 24/7 health monitoring service and greatly improves the quality and efficiency of healthcare. However, users' concern about the security and privacy of their health information has become one of the major obstacles that impede the wide adoption of WBANs. Anonymous and unlinkable authentication is critical to protect the security and privacy of sensitive physiological information in transit from the client to the application provider. We first show that the anonymous authentication scheme of Wang and Zhang based on bilinear pairing is prone to client impersonation attack. Then, we propose an enhanced anonymous authentication scheme to remedy the flaw in Wang and Zhang's scheme. We give the security analysis to demonstrate that the enhanced scheme achieves the desired security features and withstands various known attacks.

  6. Theoretical Analysis of Lattice Parameter Effect on Order-Disorder Transformation Based on Pair Potential

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Based on pair potential, the Bragg Williams (B-W) model is modified to take into account the effect of the lattice parameter on theoretical order-disorder transformation analysis. The main purpose of this work is to understand the basic aspects of this effect and related reasonable model on order-disorder transformation. In the present approach, the configuration free energy is chosen as function of the lattice parameter and the long-range order. This energy is calculated through Taylor's expansion, starting from the disordered state. It was found that the configuration free energy has been strongly modified when the lattice parameter is taken into account. It was also found only one type of order-disorder transformation exists in AB alloy and three kinds of order-disorder transformations for non-equiatomic alloy system such as A3B alloy. This result is in agreement with experiments.

  7. Pair normalized channel feature and statistics-based learning for high-performance pedestrian detection

    Science.gov (United States)

    Zeng, Bobo; Wang, Guijin; Ruan, Zhiwei; Lin, Xinggang; Meng, Long

    2012-07-01

    High-performance pedestrian detection with good accuracy and fast speed is an important yet challenging task in computer vision. We design a novel feature named pair normalized channel feature (PNCF), which simultaneously combines and normalizes two channel features in image channels, achieving a highly discriminative power and computational efficiency. PNCF applies to both gradient channels and color channels so that shape and appearance information are described and integrated in the same feature. To efficiently explore the formidably large PNCF feature space, we propose a statistics-based feature learning method to select a small number of potentially discriminative candidate features, which are fed into the boosting algorithm. In addition, channel compression and a hybrid pyramid are employed to speed up the multiscale detection. Experiments illustrate the effectiveness of PNCF and its learning method. Our proposed detector outperforms the state-of-the-art on several benchmark datasets in both detection accuracy and efficiency.

  8. Comment Fail-Stop Blind Signature Scheme Design Based on Pairings

    Institute of Scientific and Technical Information of China (English)

    HU Xiaoming; HUANG Shangteng

    2006-01-01

    Fail-stop signature schemes provide security for a signer against forgeries of an enemy with unlimited computational power by enabling the signer to provide a proof of forgery when a forgery happens. Chang et al proposed a robust fail-stop blind signature scheme based on bilinear pairings. However, in this paper, it will be found that there are several mistakes in Chang et al' fail-stop blind signature scheme. Moreover, it will be pointed out that this scheme doesn' meet the property of a fail-stop signature: unconditionally secure for a signer. In Chang et al' scheme, a forger can forge a valid signature that can' be proved by a signer using the "proof of forgery". The scheme also doesn' possess the unlinkability property of a blind signature.

  9. Use of Manganese(II)-Schiff Base Complexes for Carrying Polar Organometallics and Inorganic Ion Pairs.

    Science.gov (United States)

    Gallo, Emma; Solari, Euro; Floriani, Carlo; Chiesi-Villa, Angiola; Rizzoli, Corrado

    1997-05-07

    This report concerns the carrier properties of [Mn(acacen)]-derived compounds toward polar organometallics, inorganic ion pairs, and salts. Such properties are the consequence of Mn(II) behaving as a Lewis acid and the O&arcraise;O bite of the bidentate Schiff base ligand toward alkali cations. The starting compounds, which occur in a dimeric form, [Mn(acac-L-en)](2) [L' = CH(2)CH(2) (1); L" = C(6)H(10) (2); L"' = R,R-C(6)H(10) (3)] have been synthesized either via a metathesis reaction from MnCl(2) or using [Mn(3)Mes(6)]. The reaction of 1-3 with lithium organometallics allowed the isolation of [Mn(acac-L-en)(R)Li(DME)] [R = Me, L = L' (4); R = Ph, L = L' (5); R = Mes, L = L' (6); R = Me, L = L" (7); R = Me, L = L"' (8)] as metalated forms, where the alkyl or aryl group is sigma-bonded to Mn(II), while the lithium cation is anchored to the Schiff base ligand. The metalated forms 4-8 react with PhCHO to give the corresponding lithium alkoxide, which remains bound in its ion-pair form to the [Mn(acacen)] skeleton in [Mn(2)(acac-L'-en)(2)Li(2)(OCH(Ph)Me)(2)](n)() (9). The use of 8, which has a chiral bridge across two nitrogen atoms, did not lead to a significant asymmetric induction in the reaction with PhCHO, because of the long separation between the lithium cation and the stereogenic center. The metalated form 4 was able to transfer the methyl group to the nitrile function to give the corresponding lithium-imide which then remains bonded to [Mn(acacen)] as the ion pair in a dimeric structure, as revealed for [Mn(2)(acac-L'-en)(2)Li(2)(DME){N=C(Ph)Me}(2)](n)() (10). Their reaction with 1 appears to depend on the steric bulkiness of the alkyl group in NaOR, resulting in either monomeric adducts, i.e. in [Mn(acac-L'-en)(2,6-Bu(t)(2)C(6)H(3)O)Na(DME)(2)] (11.2DME), or polymeric structures, like in [Mn(acac-L'-en)Na(DME)(&mgr;-OEt)](n)() (13). All the dimeric units reported in this paper show a slight antiferromagnetic coupling between the two Mn(II) assisted by

  10. Hydrogen-bonded proton transfer in the protonated guanine-cytosine (GC+H)+ base pair.

    Science.gov (United States)

    Lin, Yuexia; Wang, Hongyan; Gao, Simin; Schaefer, Henry F

    2011-10-13

    The single proton transfer at the different sites of the Watson-Crick (WC) guanine-cytosine (GC) DNA base pair are studied here using density functional methods. The conventional protonated structures, transition state (TS) and proton-transferred product (PT) structures of every relevant species are optimized. Each transition state and proton-transferred product structure has been compared with the corresponding conventional protonated structure to demonstrate the process of proton transfer and the change of geometrical structures. The relative energies of the protonated tautomers and the proton-transfer energy profiles in gas and solvent are analyzed. The proton-transferred product structure G(+H(+))-H(+)C(N3)(-H(+))(PT) has the lowest relative energy for which only two hydrogen bonds exist. Almost all 14 isomers of the protonated GC base pair involve hydrogen-bonded proton transfer following the three pathways, with the exception of structure G-H(+)C(O2). When the positive charge is primarily "located" on the guanine moiety (H(+)G-C, G-H(+)C(C4), and G-H(+)C(C6)), the H(1) proton transfers from the N(1) site of guanine to the N(3) site of cytosine. The structures G-H(+)C(C5) and G-H(+)C(C4) involve H(4a) proton transfer from the N(4) of cytosine to the O(6) site of guanine. H(2a) proton transfer from the N(2) site of guanine to the O(2) site of cytosine is found only for the structure G-H(+)C(C4). The structures to which a proton is added on the six-centered sites adjoining the hydrogen bonds are more prone to proton transfer in the gas phase, whereas a proton added on the minor groove and the sites adjoining the hydrogen bonds is favorable to the proton transfer in energy in the aqueous phase.

  11. Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.

    Directory of Open Access Journals (Sweden)

    Miguel M Fonseca

    Full Text Available BACKGROUND: Vertebrate mitochondrial genomes typically have one transfer RNA (tRNA for each synonymous codon family. This limited anticodon repertoire implies that each tRNA anticodon needs to wobble (establish a non-Watson-Crick base pairing between two nucleotides in RNA molecules to recognize one or more synonymous codons. Different hypotheses have been proposed to explain the factors that determine the nucleotide composition of wobble sites in vertebrate mitochondrial tRNA anticodons. Until now, the two major postulates--the "codon-anticodon adaptation hypothesis" and the "wobble versatility hypothesis"--have not been formally tested in vertebrate mitochondria because both make the same predictions regarding the composition of anticodon wobble sites. The same is true for the more recent "wobble cost hypothesis". PRINCIPAL FINDINGS: In this study we have analyzed the occurrence of synonymous codons and tRNA anticodon wobble sites in 1553 complete vertebrate mitochondrial genomes, focusing on three fish species with mtDNA codon usage bias reversal (L-strand is GT-rich. These mitogenomes constitute an excellent opportunity to study the evolution of the wobble nucleotide composition of tRNA anticodons because due to the reversal the predictions for the anticodon wobble sites differ between the existing hypotheses. We observed that none of the wobble sites of tRNA anticodons in these unusual mitochondrial genomes coevolved to match the new overall codon usage bias, suggesting that nucleotides at the wobble sites of tRNA anticodons in vertebrate mitochondrial genomes are determined by wobble versatility. CONCLUSIONS/SIGNIFICANCE: Our results suggest that, at wobble sites of tRNA anticodons in vertebrate mitogenomes, selection favors the most versatile nucleotide in terms of wobble base-pairing stability and that wobble site composition is not influenced by codon usage. These results are in agreement with the "wobble versatility hypothesis".

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

    Science.gov (United States)

    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.

  13. Student Responses to a Context- and Inquiry-Based Three-Step Teaching Model

    Science.gov (United States)

    Walan, Susanne; Rundgren, Shu-Nu Chang

    2015-01-01

    Research has indicated that both context- and inquiry-based approaches could increase student interest in learning sciences. This case study aims to present a context- and inquiry-based combined teaching approach, using a three-step teaching model developed by the PROFILES project, and investigates Swedish students' responses to the activity. A…

  14. Current Hormonal Contraceptive Use Predicts Female Extra-Pair and Dyadic Sexual Behavior: Evidence Based on Czech National Survey Data

    Directory of Open Access Journals (Sweden)

    Kateřina Klapilová

    2014-01-01

    Full Text Available Data from 1155 Czech women (493 using oral contraception, 662 non-users, obtained from the Czech National Survey of Sexual Behavior, were used to investigate evolutionary-based hypotheses concerning the predictive value of current oral contraceptive (OC use on extra-pair and dyadic (in-pair sexual behavior of coupled women. Specifically, the aim was to determine whether current OC use was associated with lower extra-pair and higher in-pair sexual interest and behavior, because OC use suppresses cyclical shifts in mating psychology that occur in normally cycling women. Zero-inflated Poisson (ZIP regression and negative binomial models were used to test associations between OC use and these sexual measures, controlling for other relevant predictors (e.g., age, parity, in-pair sexual satisfaction, relationship length. The overall incidence of having had an extra-pair partner or one-night stand in the previous year was not related to current OC use (the majority of the sample had not. However, among the women who had engaged in extra-pair sexual behavior, OC users had fewer one-night stands than non-users, and tended to have fewer partners, than non-users. OC users also had more frequent dyadic intercourse than non-users, potentially indicating higher commitment to their current relationship. These results suggest that suppression of fertility through OC use may alter important aspects of female sexual behavior, with potential implications for relationship functioning and stability.

  15. Cell pairing using a dielectrophoresis-based device with interdigitated array electrodes.

    Science.gov (United States)

    Şen, Mustafa; Ino, Kosuke; Ramón-Azcón, Javier; Shiku, Hitoshi; Matsue, Tomokazu

    2013-09-21

    We present a chip device with an array of 900 gourd-shaped microwells designed to pair single cells of different types. The device consists of interdigitated array (IDA) electrodes and uses positive dielectrophoresis to trap cells within the microwells. Each side of a microwell is on a different comb of the IDA, so that cells of different types are trapped on opposite sides of the microwells, leading to close cell pairing. Using this device, a large number of cell pairs can be formed easily and rapidly, making it a highly attractive tool for controllable cell pairing in a range of biological applications.

  16. Workplace based assessment: a step to promote competency based postgraduate training.

    Science.gov (United States)

    Singh, Tejinder; Modi, Jyoti Nath

    2013-06-08

    There has been an increasing emphasis on defining outcomes of medical education in terms of performance of trainees. This is a step beyond the description of outcomes in terms of competence that encompasses mostly potential abilities rather than the actual performance. The contextual adaptations and behavior judgments of the trainees are best assessed by a program of in-training assessment. Workplace based assessment (WPBA) is one of the modalities, which assesses the trainee in authentic settings. Though Postgraduate (PG) medical training in India is said to be competency-based, most institutions do not have any formative or in-training assessment program for the same. The two cardinal elements of WPBA are direct observation and conducted in work place in addition to provision of feedback to the trainee. The WPBA conforms to the highest (Level 4: Does) of Millers pyramid and also has the potential to assess at all four levels. Some of the tools used for WPBA are: Logbooks, Clinical Encounter Cards (CEC), mini-Clinical Evaluation Exercise (mini-CEX), Case based discussions, Direct Observation of Procedural Skills (DOPS), Multisource feedback (peers, co-workers, seniors, patients) etc. These can be documented in the form of a portfolio that provides a longitudinal view of experiences and progress of the trainee. The WPBA scores high on validity and educational impact by virtue of being based on direct observation in real situation and contextual feedback. The feasibility and acceptability is enhanced by making appropriate choices of tools, advance planning, building of mutual trust, and training of assessors. Given the established benefits of WPBA in shaping clinical learning, there is an imminent need for including this mode of assessment in our clinical training programs especially PG training.

  17. Novel H+-Ion Sensor Based on a Gated Lateral BJT Pair

    Directory of Open Access Journals (Sweden)

    Heng Yuan

    2015-12-01

    Full Text Available An H+-ion sensor based on a gated lateral bipolar junction transistor (BJT pair that can operate without the classical reference electrode is proposed. The device is a special type of ion-sensitive field-effect transistor (ISFET. Classical ISFETs have the advantage of miniaturization, but  they are difficult to fabricate by a single fabrication process because of the bulky and brittle reference electrode materials. Moreover, the reference electrodes need to be separated from the sensor device in some cases. The proposed device is composed of two gated lateral BJT components, one of which had a silicide layer while the other was without the layer. The two components were operated under the metal-oxide semiconductor field-effect transistor (MOSFET-BJT hybrid mode, which can be controlled by emitter voltage and base current. Buffer solutions with different pH values were used as the sensing targets to verify the characteristics of the proposed device. Owing to their different sensitivities, both components could simultaneously detect the H+-ion concentration and function as a reference to each other. Per the experimental results, the sensitivity of the proposed device was found to be approximately 0.175 μA/pH. This experiment demonstrates enormous potential to lower the cost of the ISFET-based sensor technology.

  18. An innovative monolithic column preparation for the isolation of 25 kilo base pairs DNA.

    Science.gov (United States)

    Ongkudon, Clarence M; Pan, Sharadwata; Danquah, Michael K

    2013-11-29

    The use of large DNAs in preparing multivalent vaccines that will eventually give protective immunity against multiple pathogenic microbes is becoming a major debate nowadays. One of the important issues in ensuring the successful implementation of the new vaccine technology is the development of a chromatographic technique that can handle larger DNAs. This paper reports the development of a novel conical monolithic column format with pore and surface characteristics engineered for the isolation of 25 kbp DNA in a single step fashion. An effective method of eliminating wall channelling, a defect of most conventional monolithic chromatography systems which has caused significant loss of product, was applied to maximise DNA recovery. This method was based on a systematic reduction of wall channel size based on a predetermined correlation between column’s back pressure and wall channel size of a particular monolith pore size.

  19. Pairing symmetries of several iron-based superconductor families and some similarities with cuprates and heavy-fermions

    Directory of Open Access Journals (Sweden)

    Das Tanmoy

    2012-03-01

    Full Text Available We show that, by using the unit-cell transformation between 1 Fe per unit cell to 2 Fe per unit cell, one can qualitatively understand the pairing symmetry of several families of iron-based superconductors. In iron-pnictides and iron-chalcogenides, the nodeless s±-pairing and the resulting magnetic resonance mode transform nicely between the two unit cells, while retaining all physical properties unchanged. However, when the electron-pocket disappears from the Fermi surface with complete doping in KFe2As2, we find that the unit-cell invariant requirement prohibits the occurrence of s±-pairing symmetry (caused by inter-hole-pocket nesting. However, the intra-pocket nesting is compatible here, which leads to a nodal d-wave pairing. The corresponding Fermi surface topology and the pairing symmetry are similar to Ce-based heavy-fermion superconductors. Furthermore, when the Fermi surface hosts only electron-pockets in KyFe2-xSe2, the inter-electron-pocket nesting induces a nodeless and isotropic d-wave pairing. This situation is analogous to the electron-doped cuprates, where the strong antiferromagnetic order creates similar disconnected electron-pocket Fermi surface, and hence nodeless d-wave pairing appears. The unit-cell transformation in KyFe2-xSe2 exhibits that the d-wave pairing breaks the translational symmetry of the 2 Fe unit cell, and thus cannot be realized unless a vacancy ordering forms to compensate for it. These results are consistent with the coexistence picture of a competing order and nodeless d-wave superconductivity in both cuprates and KyFe1.6Se2.

  20. A Bayesian Target Predictor Method based on Molecular Pairing Energies estimation.

    Science.gov (United States)

    Oliver, Antoni; Canals, Vincent; Rosselló, Josep L

    2017-03-06

    Virtual screening (VS) is applied in the early drug discovery phases for the quick inspection of huge molecular databases to identify those compounds that most likely bind to a given drug target. In this context, there is the necessity of the use of compact molecular models for database screening and precise target prediction in reasonable times. In this work we present a new compact energy-based model that is tested for its application to Virtual Screening and target prediction. The model can be used to quickly identify active compounds in huge databases based on the estimation of the molecule's pairing energies. The greatest molecular polar regions along with its geometrical distribution are considered by using a short set of smart energy vectors. The model is tested using similarity searches within the Directory of Useful Decoys (DUD) database. The results obtained are considerably better than previously published models. As a Target prediction methodology we propose the use of a Bayesian Classifier that uses a combination of different active compounds to build an energy-dependent probability distribution function for each target.

  1. Cryptanalysis on Identity-based Authenticated Key Agreement Protocols from Pairings

    Directory of Open Access Journals (Sweden)

    Mengbo Hou

    2010-07-01

    Full Text Available Two-party authenticated key agreement protocol is used to authenticate entities and establish session keys in an open network in order to provide secure communications between two parties. Several security attributes are highly desired for such protocols, such as perfect forward secrecy (the corruption of long-term keys of all the entities should not compromise any session key, PKG forward secrecy (the corruption of the PKG's master key in the ID-based system should not compromise the established session keys, and known session-key specific temporary information secrecy (The exposure of private temporary information should not compromise the secrecy of generated session keys. In 2005, Choie et al. proposed three identity-based authenticated key agreement protocols from pairings. Our analysis shows that they all didn't provide protection against known session-key specific temporary information attack and some of them are vulnerable against man-in-the-middle attack, such as the key replicating attack. We analyze some of the attacks under the BR93 security model.

  2. New Extensions of Pairing-based Signatures into Universal (Multi) Designated Verifier Signatures

    CERN Document Server

    Vergnaud, Damien

    2008-01-01

    The concept of universal designated verifier signatures was introduced by Steinfeld, Bull, Wang and Pieprzyk at Asiacrypt 2003. These signatures can be used as standard publicly verifiable digital signatures but have an additional functionality which allows any holder of a signature to designate the signature to any desired verifier. This designated verifier can check that the message was indeed signed, but is unable to convince anyone else of this fact. We propose new efficient constructions for pairing-based short signatures. Our first scheme is based on Boneh-Boyen signatures and its security can be analyzed in the standard security model. We prove its resistance to forgery assuming the hardness of the so-called strong Diffie-Hellman problem, under the knowledge-of-exponent assumption. The second scheme is compatible with the Boneh-Lynn-Shacham signatures and is proven unforgeable, in the random oracle model, under the assumption that the computational bilinear Diffie-Hellman problem is untractable. Both s...

  3. A Bayesian Target Predictor Method based on Molecular Pairing Energies estimation

    Science.gov (United States)

    Oliver, Antoni; Canals, Vincent; Rosselló, Josep L.

    2017-03-01

    Virtual screening (VS) is applied in the early drug discovery phases for the quick inspection of huge molecular databases to identify those compounds that most likely bind to a given drug target. In this context, there is the necessity of the use of compact molecular models for database screening and precise target prediction in reasonable times. In this work we present a new compact energy-based model that is tested for its application to Virtual Screening and target prediction. The model can be used to quickly identify active compounds in huge databases based on the estimation of the molecule’s pairing energies. The greatest molecular polar regions along with its geometrical distribution are considered by using a short set of smart energy vectors. The model is tested using similarity searches within the Directory of Useful Decoys (DUD) database. The results obtained are considerably better than previously published models. As a Target prediction methodology we propose the use of a Bayesian Classifier that uses a combination of different active compounds to build an energy-dependent probability distribution function for each target.

  4. Fast intensity-modulated arc therapy based on 2-step beam segmentation

    Energy Technology Data Exchange (ETDEWEB)

    Bratengeier, Klaus; Gainey, Mark; Sauer, Otto A.; Richter, Anne; Flentje, Michael [Department of Radiation Oncology, University of Wuerzburg, Josef-Schneider-Str. 11, 97080 Wuerzburg (Germany)

    2011-01-15

    Purpose: Single or few arc intensity-modulated arc therapy (IMAT) is intended to be a time saving irradiation method, potentially replacing classical intensity-modulated radiotherapy (IMRT). The aim of this work was to evaluate the quality of different IMAT methods with the potential of fast delivery, which also has the possibility of adapting to the daily shape of the target volume. Methods: A planning study was performed. Novel double and triple IMAT techniques based on the geometrical analysis of the target organ at risk geometry (2-step IMAT) were evaluated. They were compared to step and shoot IMRT reference plans generated using direct machine parameter optimization (DMPO). Volumetric arc (VMAT) plans from commercial preclinical software (SMARTARC) were used as an additional benchmark to classify the quality of the novel techniques. Four cases with concave planning target volumes (PTV) with one dominating organ at risk (OAR), viz., the PTV/OAR combination of the ESTRO Quasimodo phantom, breast/lung, spine metastasis/spinal cord, and prostate/rectum, were used for the study. The composite objective value (COV) and other parameters representing the plan quality were studied. Results: The novel 2-step IMAT techniques with geometry based segment definition were as good as or better than DMPO and were superior to the SMARTARC VMAT techniques. For the spine metastasis, the quality measured by the COV differed only by 3%, whereas the COV of the 2-step IMAT for the other three cases decreased by a factor of 1.4-2.4 with respect to the reference plans. Conclusions: Rotational techniques based on geometrical analysis of the optimization problem (2-step IMAT) provide similar or better plan quality than DMPO or the research version of SMARTARC VMAT variants. The results justify pursuing the goal of fast IMAT adaptation based on 2-step IMAT techniques.

  5. Testing for direct genetic effects using a screening step in family-based association studies

    Directory of Open Access Journals (Sweden)

    Sharon M Lutz

    2013-11-01

    Full Text Available In genome wide association studies (GWAS, families based studies tend to have less power to detect genetic associations than population based studies, such as case-control studies. This can be an issue when testing if genes in a family based GWAS have a direct effect on the phenotype of interest or if the genes act indirectly through a secondary phenotype. When multiple SNPs are tested for a direct effect in the family based study, a screening step can be used to minimize the burden of multiple comparisons in the causal analysis. We propose a 2-stage screening step that can be incorporated into the family based association test (FBAT approach similar to the conditional mean model approach in the VanSteen-algorithm [1]. Simulations demonstrate that the type 1 error is preserved and this method is advantageous when multiple markers are tested. This method is illustrated by an application to the Framingham Heart Study.

  6. A Review of Recent Experiments on Step-to-Step “Hand-off” of the DNA Intermediates in Mammalian Base Excision Repair Pathways1

    OpenAIRE

    Prasad, R.; Beard, W A; Batra, V. K.; Liu, Y.; Shock, D. D.; Wilson, S H

    2011-01-01

    The current “working model” for mammalian base excision repair involves two sub-pathways termed single-nucleotide base excision repair and long patch base excision repair that are distinguished by their repair patch sizes and the enzymes/co-factors involved. These base excision repair sub-pathways are designed to sequester the various DNA intermediates, passing them along from one step to the next without allowing these toxic molecules to trigger cell cycle arrest, necrotic cell death, or apo...

  7. Mismatch base pairing of the mutagen 8-oxoguanine and its derivatives with adenine: A theoretical search for possible antimutagenic agents

    Science.gov (United States)

    Singh, A. K.; Mishra, P. C.

    Molecular geometries of 8-oxoguanine (8OG), those of its substituted derivatives with the substitutions CH2, CF2, CO, CNH, O, and S in place of the N7H7 group, adenine (A), and the base pairs of 8OG and its substituted derivatives with adenine were optimized using the RHF/6-31+G* and B3LYP/6-31+G* methods in gas phase. All the molecules and their hydrogen-bonded complexes were solvated in aqueous media employing the polarized continuum model (PCM) of the self-consistent reaction field (SCRF) theory using the RHF/6-31+G* and B3LYP/6-31+G* methods. The optimized geometrical parameters of the 8OG-A base pair at the RHF/6-31+G* and B3LYP/6-31+G* levels of theory agree satisfactorily with those of an oligonucleotide containing the base pair found from X-ray crystallography. The pattern of hydrogen bonding in the CF2- and O-substituted 8OG-A base pair is of Watson-Crick type and that in the unsubstituted and CH2-, CNH-, and S-substituted base pairs is of Hoogsteen type. In the CO-substituted base pair, the hydrogen bonding pattern is of neither Watson-Crick nor Hoogsteen type. The CF2-substitution appears to introduce steric hindrance for stacking of DNA bases. On the basis of these results, it appears that among all the substituted 8OG molecules considered here, the O-substituted derivative may be useful as an antimutagenic drug. It is, however, subject to experimental verification. Content:text/plain; charset="UTF-8"

  8. STEP: spatiotemporal enhancement pattern for MR-based breast tumor diagnosis.

    Science.gov (United States)

    Zheng, Yuanjie; Englander, Sarah; Baloch, Sajjad; Zacharaki, Evangelia I; Fan, Yong; Schnall, Mitchell D; Shen, Dinggang

    2009-07-01

    The authors propose a spatiotemporal enhancement pattern (STEP) for comprehensive characterization of breast tumors in contrast-enhanced MR images. By viewing serial contrast-enhanced MR images as a single spatiotemporal image, they formulate the STEP as a combination of (1) dynamic enhancement and architectural features of a tumor, and (2) the spatial variations of pixelwise temporal enhancements. Although the latter has been widely used by radiologists for diagnostic purposes, it has rarely been employed for computer-aided diagnosis. This article presents two major contributions. First, the STEP features are introduced to capture temporal enhancement and its spatial variations. This is essentially carried out through the Fourier transformation and pharmacokinetic modeling of various temporal enhancement features, followed by the calculation of moment invariants and Gabor texture features. Second, for effectively extracting the STEP features from tumors, we develop a graph-cut based segmentation algorithm that aims at refining coarse manual segmentations of tumors. The STEP features are assessed through their diagnostic performance for differentiating between benign and malignant tumors using a linear classifier (along with a simple ranking-based feature selection) in a leave-one-out cross-validation setting. The experimental results for the proposed features exhibit superior performance, when compared to the existing approaches, with the area under the ROC curve approaching 0.97.

  9. Avian magnetoreception model realized by coupling a magnetite-based mechanism with a radical-pair-based mechanism

    Institute of Scientific and Technical Information of China (English)

    Lü Yan; Song Tao

    2013-01-01

    Many animal species have been proven to use the geomagnetic field for their navigation,but the biophysical mechanism of magnetoreception has remained enigmatic.In this paper,we present a special biophysical model that consists of magnetite-based and radical-pair-based mechanisms for avian magnetoreception.The amplitude of the resultant magnetic field around the magnetic particles corresponds to the geomagnetic field direction and affects the yield of singlet/triplet state products in the radical-pair reactions.Therefore,in the proposed model,the singlet/triplet state product yields are related to the geomagnetic field information for orientational detection.The resultant magnetic fields corresponding to two materials with different magnetic properties are analyzed under different geomagnetic field directions.The results show that ferromagnetic particles in organisms can provide more significant changes in singlet state products than superparamagnetic particles,and the period of variation for the singlet state products with an included angle in the geomagnetic field is approximately 180° when the magnetic particles are ferromagnetic materials,consistent with the experimental results obtained from the avian magnetic compass.Further,the calculated results of the singlet state products in a reception plane show that the proposed model can explain the avian magnetoreception mechanism with an inclination compass.

  10. Students' Errors in Solving the Permutation and Combination Problems Based on Problem Solving Steps of Polya

    Science.gov (United States)

    Sukoriyanto; Nusantara, Toto; Subanji; Chandra, Tjang Daniel

    2016-01-01

    This article was written based on the results of a study evaluating students' errors in problem solving of permutation and combination in terms of problem solving steps according to Polya. Twenty-five students were asked to do four problems related to permutation and combination. The research results showed that the students still did a mistake in…

  11. Initial steps towards an evidence-based classification system for golfers with a physical impairment

    NARCIS (Netherlands)

    Stoter, Inge K; Hettinga, Florentina J; Altmann, Viola; Eisma, Wim; Arendzen, Hans; Bennett, Tony; van der Woude, Lucas H; Dekker, Rienk

    2015-01-01

    PURPOSE: The present narrative review aims to make a first step towards an evidence-based classification system in handigolf following the International Paralympic Committee (IPC). It intends to create a conceptual framework of classification for handigolf and an agenda for future research. METHOD:

  12. Initial steps towards an evidence-based classification system for golfers with a physical impairment

    NARCIS (Netherlands)

    Stoter, Inge K.; Hettinga, Florentina J.; Altmann, Viola; Eisma, Wim; Arendzen, Hans; Bennett, Tony; van der Woude, Lucas H.; Dekker, Rienk

    2017-01-01

    Purpose: The present narrative review aims to make a first step towards an evidence-based classification system in handigolf following the International Paralympic Committee (IPC). It intends to create a conceptual framework of classification for handigolf and an agenda for future research. Method:

  13. Monte Carlo simulations of biaxial structure in thin hybrid nematic film based upon spatially anisotropic pair potential

    Institute of Scientific and Technical Information of China (English)

    Zhang Zhi-Dong; Chang Chun-Rui; Ma Dong-Lai

    2009-01-01

    Hybrid nematic films have been studied by Monte Carlo simulations using a lattice spin model,in which the pair potential is spatially anisotropic and dependent on elastic constants of liquid crystals.We confirm in the thin hybrid nematic film the existence of a biaxially nonbent structure and the structarc transition from the biaxial to the bent-director structure,which is similar to the result obtained using the Lebwohl-Lasher model.However,the step-like director's profile,characteristic for the biaxial structure,is spatially asymmetric in the film because the pair potential leads to K1≠K3.We estimate the upper cell thickness to be 69 spin layers,in which the biaxial structure can be found.

  14. Nucleon-pair states of even-even Sn isotopes based on realistic effective interactions

    Science.gov (United States)

    Cheng, Y. Y.; Qi, C.; Zhao, Y. M.; Arima, A.

    2016-08-01

    In this paper we study yrast states of 128,126,124Sn and 104,106,108Sn by using the monopole-optimized realistic interactions in terms of both the shell model (SM) and the nucleon-pair approximation (NPA). For yrast states of 128,126Sn and 104,106Sn, we calculate the overlaps between the wave functions obtained in the full SM space and those obtained in the truncated NPA space, and find that most of these overlaps are very close to 1. Very interestingly, for most of these states with positive parity and even spin or with negative parity and odd spin, the SM wave function is found to be well represented by one nucleon-pair basis state, viz., a simple picture of "nucleon-pair states" (nucleon-pair configuration without mixings) emerges. In 128,126Sn, the positive-parity (or negative-parity) yrast states with spin J >10 (or J >7 ) are found to be well described by breaking one or two S pairs in the 101+ (or 71-) state, i.e., the yrast state of seniority-two, spin-maximum, and positive-parity (or negative-parity), into non-S pair(s). Similar regularity is also pointed out for 104,106Sn. The evolution of E 2 transition rates between low-lying states in 128,126,124Sn is discussed in terms of the seniority scheme.

  15. Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory

    Energy Technology Data Exchange (ETDEWEB)

    Riplinger, Christoph; Pinski, Peter; Becker, Ute; Neese, Frank, E-mail: frank.neese@cec.mpg.de, E-mail: evaleev@vt.edu [Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr (Germany); Valeev, Edward F., E-mail: frank.neese@cec.mpg.de, E-mail: evaleev@vt.edu [Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061 (United States)

    2016-01-14

    Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate

  16. Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory

    Science.gov (United States)

    Riplinger, Christoph; Pinski, Peter; Becker, Ute; Valeev, Edward F.; Neese, Frank

    2016-01-01

    Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate previous

  17. Base pairing enhances fluorescence and favors cyclobutane dimer formation induced upon absorption of UVA radiation by DNA.

    Science.gov (United States)

    Banyasz, Akos; Vayá, Ignacio; Changenet-Barret, Pascale; Gustavsson, Thomas; Douki, Thierry; Markovitsi, Dimitra

    2011-04-13

    The photochemical properties of the DNA duplex (dA)(20)·(dT)(20) are compared with those of the parent single strands. It is shown that base pairing increases the probability of absorbing UVA photons, probably due to the formation of charge-transfer states. UVA excitation induces fluorescence peaking at ∼420 nm and decaying on the nanosecond time scale. The fluorescence quantum yield, the fluorescence lifetime, and the quantum yield for cyclobutane dimer formation increase upon base pairing. Such behavior contrasts with that of the UVC-induced processes.

  18. DNA base pair resolution measurements using resonance energy transfer efficiency in lanthanide doped nanoparticles.

    Directory of Open Access Journals (Sweden)

    Aleksandra Delplanque

    Full Text Available Lanthanide-doped nanoparticles are of considerable interest for biodetection and bioimaging techniques thanks to their unique chemical and optical properties. As a sensitive luminescence material, they can be used as (bio probes in Förster Resonance Energy Transfer (FRET where trivalent lanthanide ions (La3+ act as energy donors. In this paper we present an efficient method to transfer ultrasmall (ca. 8 nm NaYF4 nanoparticles dispersed in organic solvent to an aqueous solution via oxidation of the oleic acid ligand. Nanoparticles were then functionalized with single strand DNA oligomers (ssDNA by inducing covalent bonds between surface carboxylic groups and a 5' amine modified-ssDNA. Hybridization with the 5' fluorophore (Cy5 modified complementary ssDNA strand demonstrated the specificity of binding and allowed the fine control over the distance between Eu3+ ions doped nanoparticle and the fluorophore by varying the number of the dsDNA base pairs. First, our results confirmed nonradiative resonance energy transfer and demonstrate the dependence of its efficiency on the distance between the donor (Eu3+ and the acceptor (Cy5 with sensitivity at a nanometre scale.

  19. All-pairs Shortest Path Algorithm based on MPI+CUDA Distributed Parallel Programming Model

    Directory of Open Access Journals (Sweden)

    Qingshuang Wu

    2013-12-01

    Full Text Available In view of the problem that computing shortest paths in a graph is a complex and time-consuming process, and the traditional algorithm that rely on the CPU as computing unit solely can't meet the demand of real-time processing, in this paper, we present an all-pairs shortest paths algorithm using MPI+CUDA hybrid programming model, which can take use of the overwhelming computing power of the GPU cluster to speed up the processing. This proposed algorithm can combine the advantages of MPI and CUDA programming model, and can realize two-level parallel computing. In the cluster-level, we take use of the MPI programming model to achieve a coarse-grained parallel computing between the computational nodes of the GPU cluster. In the node-level, we take use of the CUDA programming model to achieve a GPU-accelerated fine grit parallel computing in each computational node internal. The experimental results show that the MPI+CUDA-based parallel algorithm can take full advantage of the powerful computing capability of the GPU cluster, and can achieve about hundreds of time speedup; The whole algorithm has good computing performance, reliability and scalability, and it is able to meet the demand of real-time processing of massive spatial shortest path analysis

  20. Heterochromatin base pair composition and diversification in holocentric chromosomes of kissing bugs (Hemiptera, Reduviidae)

    Science.gov (United States)

    Bardella, Vanessa Bellini; Pita, Sebastián; Vanzela, André Luis Laforga; Galvão, Cleber; Panzera, Francisco

    2016-01-01

    The subfamily Triatominae (Hemiptera, Reduviidae) includes 150 species of blood-sucking insects, vectors of Chagas disease or American trypanosomiasis. Karyotypic information reveals a striking stability in the number of autosomes. However, this group shows substantial variability in genome size, the amount and distribution of C-heterochromatin, and the chromosome positions of 45S rDNA clusters. Here, we analysed the karyotypes of 41 species from six different genera with C-fluorescence banding in order to evaluate the base-pair richness of heterochromatic regions. Our results show a high heterogeneity in the fluorescent staining of the heterochromatin in both autosomes and sex chromosomes, never reported before within an insect subfamily with holocentric chromosomes. This technique allows a clear discrimination of the heterochromatic regions classified as similar by C-banding, constituting a new chromosome marker with taxonomic and evolutionary significance. The diverse fluorescent patterns are likely due to the amplification of different repeated sequences, reflecting an unusual dynamic rearrangement in the genomes of this subfamily. Further, we discuss the evolution of these repeated sequences in both autosomes and sex chromosomes in species of Triatominae. PMID:27759763

  1. Biomolecule Analogues 2-Hydroxypyridine and 2-Pyridone Base Pairing on Ice Nanoparticles.

    Science.gov (United States)

    Rubovič, Peter; Pysanenko, Andriy; Lengyel, Jozef; Nachtigallová, Dana; Fárník, Michal

    2016-07-14

    Ice nanoparticles (H2O)N, N ≈ 450 generated in a molecular beam experiment pick up individual gas phase molecules of 2-hydroxypyridine and 2-pyridone (HP) evaporated in a pickup cell at temperatures between 298 and 343 K. The mass spectra of the doped nanoparticles show evidence for generation of clusters of adsorbed molecules (HP)n up to n = 8. The clusters are ionized either by 70 eV electrons or by two photons at 315 nm (3.94 eV). The two ionization methods yield different spectra, and their comparison provides an insight into the neutral cluster composition, ionization and intracluster ion-molecule reactions, and cluster fragmentation. Quite a few molecules were reported not to coagulate on ice nanoparticles previously. The (HP)n cluster generation on ice nanoparticles represents the first evidence for coagulating of molecules and cluster formation on free ice nanoparticles. For comparison, we investigate the coagulation of HP molecules picked up on large clusters ArN, N ≈ 205, and also (HP)n clusters generated in supersonic expansions with Ar buffer gas. This comparison points to a propensity for the (HP)2 dimer generation on ice nanoparticles. This shows the feasibility of base pairing for model of biological molecules on free ice nanoparticles. This result is important for hypotheses of the biomolecule synthesis on ice grains in the space. We support our findings by theoretical calculations that show, among others, the HP dimer structures on water clusters.

  2. Proton tunneling in the A∙T Watson-Crick DNA base pair: myth or reality?

    Science.gov (United States)

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

    2015-01-01

    The results and conclusions reached by Godbeer et al. in their recent work, that proton tunneling in the A∙T(WC) Watson-Crick (WC) DNA base pair occurs according to the Löwdin's (L) model, but with a small (~10(-9)) probability were critically analyzed. Here, it was shown that this finding overestimates the possibility of the proton tunneling at the A∙T(WC)↔A*∙T*(L) tautomerization, because this process cannot be implemented as a chemical reaction. Furthermore, it was outlined those biologically important nucleobase mispairs (A∙A*↔A*∙A, G∙G*↔G*∙G, T∙T*↔T*∙T, C∙C*↔C*∙C, H∙H*↔H*∙H (H - hypoxanthine)) - the players in the field of the spontaneous point mutagenesis - where the tunneling of protons is expected and for which the application of the model proposed by Godbeer et al. can be productive.

  3. An operationally flexible fuel cell based on quaternary ammonium-biphosphate ion pairs

    Science.gov (United States)

    Lee, Kwan-Soo; Spendelow, Jacob S.; Choe, Yoong-Kee; Fujimoto, Cy; Kim, Yu Seung

    2016-09-01

    Fuel cells are promising devices for clean power generation in a variety of economically and environmentally significant applications. Low-temperature proton exchange membrane (PEM) fuel cells utilizing Nafion require a high level of hydration, which limits the operating temperature to less than 100 ∘C. In contrast, high-temperature PEM fuel cells utilizing phosphoric acid-doped polybenzimidazole can operate effectively up to 180 ∘C however, these devices degrade when exposed to water below 140 ∘C. Here we present a different class of PEM fuel cells based on quaternary ammonium-biphosphate ion pairs that can operate under conditions unattainable with existing fuel cell technologies. These fuel cells exhibit stable performance at 80-160 ∘C with a conductivity decay rate more than three orders of magnitude lower than that of a commercial high-temperature PEM fuel cell. By increasing the operational flexibility, this class of fuel cell can simplify the requirements for heat and water management, and potentially reduce the costs associated with the existing fully functional fuel cell systems.

  4. Video Image Block-matching Motion Estimation Algorithm Based on Two-step Search

    Institute of Scientific and Technical Information of China (English)

    Wei-qi JIN; Yan CHEN; Ling-xue WANG; Bin LIU; Chong-liang LIU; Ya-zhong SHEN; Gui-qing ZHANG

    2010-01-01

    Aiming at the shortcoming that certain existing blocking-matching algorithms, such as full search, three-step search, and diamond search algorithms, usually can not keep a good balance between high accuracy and low computational complexity, a block-matching motion estimation algorithm based on two-step search is proposed in this paper. According to the fact that the gray values of adjacent pixels will not vary fast, the algorithm employs an interlaced search pattern in the search window to estimate the motion vector of the object-block. Simulation and actual experiments demonstrate that the proposed algorithm greatly outperforms the well-known three-step search and diamond search algorithms, no matter the motion vector is large or small. Compared with the full search algorithm, the proposed one achieves similar performance but requires much less computation, therefore, the algorithm is well qualified for real-time video image processing.

  5. Multi-agent System for Process Planning in Step-nc Based Manufacturing

    Directory of Open Access Journals (Sweden)

    Juan Du

    2012-09-01

    Full Text Available In order to realize STEP-NC-oriented computer numerical control machining and achieve optimal performance in manufacturing, a multi-agent system for process planning in STEP-NC based manufacturing was designed. By analyzing the characteristic of STEP-NC data model, a manufacturing feature-oriented process planning method was proposed in this study and the distributed artificial intelligence methods, namely collaborative multi-agent was employed to accomplish process planning of part. The proposed multi-agent system consists of three types of autonomous agents, which are global manager agents, planning agents and manufacturing resource agents, respectively. Process planning can be automatically completed by multiple agents’ cooperation. Each agent is capable of communicating to each other through improved Knowledge Query and Manipulation Language (KQML. At last, one test part was designed and simulated to demonstrate the capabilities of this research in the study.

  6. A Bloch decomposition based split-step pseudo spectral method for quantum dynamics with periodic potentials

    CERN Document Server

    Huang, Zhongyi; Markowich, Peter; Sparber, Christof

    2012-01-01

    We present a new numerical method for accurate computations of solutions to (linear) one dimensional Schr\\"odinger equations with periodic potentials. This is a prominent model in solid state physics where we also allow for perturbations by non-periodic potentials describing external electric fields. Our approach is based on the classical Bloch decomposition method which allows to diagonalize the periodic part of the Hamiltonian operator. Hence, the dominant effects from dispersion and periodic lattice potential are computed together, while the non-periodic potential acts only as a perturbation. Because the split-step communicator error between the periodic and non-periodic parts is relatively small, the step size can be chosen substantially larger than for the traditional splitting of the dispersion and potential operators. Indeed it is shown by the given examples, that our method is unconditionally stable and more efficient than the traditional split-step pseudo spectral schemes. To this end a particular fo...

  7. Universal quantum gates for Single Cooper Pair Box based quantum computing

    Science.gov (United States)

    Echternach, P.; Williams, C. P.; Dultz, S. C.; Braunstein, S.; Dowling, J. P.

    2000-01-01

    We describe a method for achieving arbitrary 1-qubit gates and controlled-NOT gates within the context of the Single Cooper Pair Box (SCB) approach to quantum computing. Such gates are sufficient to support universal quantum computation.

  8. Predicting Bond Dissociation Energies of Transition-Metal Compounds by Multiconfiguration Pair-Density Functional Theory and Second-Order Perturbation Theory Based on Correlated Participating Orbitals and Separated Pairs.

    Science.gov (United States)

    Bao, Junwei Lucas; Odoh, Samuel O; Gagliardi, Laura; Truhlar, Donald G

    2017-02-14

    We study the performance of multiconfiguration pair-density functional theory (MC-PDFT) and multireference perturbation theory for the computation of the bond dissociation energies in 12 transition-metal-containing diatomic molecules and three small transition-metal-containing polyatomic molecules and in two transition-metal dimers. The first step is a multiconfiguration self-consistent-field calculation, for which two choices must be made: (i) the active space and (ii) its partition into subspaces, if the generalized active space formulation is used. In the present work, the active space is chosen systematically by using three correlated-participating-orbitals (CPO) schemes, and the partition is chosen by using the separated-pair (SP) approximation. Our calculations show that MC-PDFT generally has similar accuracy to CASPT2, and the active-space dependence of MC-PDFT is not very great for transition-metal-ligand bond dissociation energies. We also find that the SP approximation works very well, and in particular SP with the fully translated BLYP functional SP-ftBLYP is more accurate than CASPT2. SP greatly reduces the number of configuration state functions relative to CASSCF. For the cases of FeO and NiO with extended-CPO active space, for which complete active space calculations are unaffordable, SP calculations are not only affordable but also of satisfactory accuracy. All of the MC-PDFT results are significantly better than the corresponding results with broken-symmetry spin-unrestricted Kohn-Sham density functional theory. Finally we test a perturbation theory method based on the SP reference and find that it performs slightly worse than CASPT2 calculations, and for most cases of the nominal-CPO active space, the approximate SP perturbation theory calculations are less accurate than the much less expensive SP-PDFT calculations.

  9. Design System of the Two-step Gear Reducer on Case-based Reasoning

    Institute of Scientific and Technical Information of China (English)

    JI Aimin; HUANG Quansheng; HUANG Quansheng; XU Huanmin; CHEN Zhengming

    2009-01-01

    The design of the two-step gear reducer is a tedious and time-consuming process. For the purpose of improving the efficiency and intelligence of design process, case-based reasoning(CBR) technology was applied to the design of the two-step gear reducer. Firstly, the current design method for the two-step gear reducer was analyzed and the principle of CBR was described. Secondly, according to the characteristics of the reducer, three key technologies of CBR were studied and the corresponding methods were provided, which are as follows:(a) an object-oriented knowledge representation method, (b) a retrieval method combining the nearest neighbor with the induction indexing, and (c) a case adaptation algorithm combining the revision based on rule with artificial revision. Also, for the purpose of improving the credibility of case retrieval, a new method for determining the weights of characteristics and a similarity formula were presented, which is a combinatorial weighting method with the analytic hierarchy process(AHP) and roughness set theory. Lastly, according to the above analytic results, a design system of the two-step gear reducer on CBR was developed by VC++, UG and Access 2003.A new method for the design of the two-step gear reducer is provided in this study. If the foregoing developed system is applied to design the two-step gear reducer, design efficiency is improved, which enables the designer to release from the tedious design process of the gear reducer so as to put more efforts on innovative design. The study result fully reflects the feasibility and validity of CBR technology in the process of the design of the mechanical parts.

  10. Uncertainty evaluation for three-dimensional scanning electron microscope reconstructions based on the stereo-pair technique

    DEFF Research Database (Denmark)

    Carli, Lorenzo; Genta, G; Cantatore, Angela;

    2011-01-01

    3D-SEM is a method, based on the stereophotogrammetry technique, which obtains three-dimensional topographic reconstructions starting typically from two SEM images, called the stereo-pair. In this work, a theoretical uncertainty evaluation of the stereo-pair technique, according to GUM (Guide...... to the Expression of Uncertainty in Measurement), was carried out, considering 3D-SEM reconstructions of a wire gauge with a reference diameter of 250 µm. Starting from the more commonly used tilting strategy, one based on the item rotation inside the SEM chamber was also adopted. The latter enables multiple......-view reconstructions of the cylindrical item under consideration. Uncertainty evaluation was performed starting from a modified version of the Piazzesi equation, enabling the calculation of the z-coordinate from a given stereo-pair. The metrological characteristics of each input variable have been taken into account...

  11. Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs

    Energy Technology Data Exchange (ETDEWEB)

    Patra, Amritraj [Vanderbilt Univ., Nashville, TN (United States); Harp, Joel [Vanderbilt Univ., Nashville, TN (United States); Pallan, Pradeep S. [Vanderbilt Univ., Nashville, TN (United States); Zhao, Linlin [Vanderbilt Univ., Nashville, TN (United States); Abramov, Mikhail [Rega Inst. for Medical Research (Belgium); Herdewijn, Piet [Rega Inst. for Medical Research (Belgium); Univ. of Evry-Val-d' Essonne (France); Egli, Martin [Vanderbilt Univ., Nashville, TN (United States)

    2012-12-28

    The thymine analog 5-chlorouridine, first reported in the 1950s as anti-tumor agent, is known as an effective mutagen, clastogen and toxicant as well as an effective inducer of sister-chromatid exchange. Recently, the first microorganism with a chemically different genome was reported; the selected Escherichia coli strain relies on the four building blocks 5-chloro-2'-deoxyuridine (ClU), A, C and G instead of the standard T, A, C, G alphabet [Marlière,P., Patrouix,J., Döring,V., Herdewijn,P., Tricot,S., Cruveiller,S., Bouzon,M. and Mutzel,R. (2011) Chemical evolution of a bacterium’s genome. Angew. Chem. Int. Ed., 50, 7109–7114]. The residual fraction of T in the DNA of adapted bacteria was <2% and the switch from T to ClU was accompanied by a massive number of mutations, including >1500 A to G or G to A transitions in a culture. The former is most likely due to wobble base pairing between ClU and G, which may be more common for ClU than T. To identify potential changes in the geometries of base pairs and duplexes as a result of replacement of T by ClU, we determined four crystal structures of a B-form DNA dodecamer duplex containing ClU:A or ClU:G base pairs. The structures reveal nearly identical geometries of these pairs compared with T:A or T:G, respectively, and no consequences for stability and cleavage by an endonuclease (EcoRI). The lack of significant changes in the geometry of ClU:A and ClU:G base pairs relative to the corresponding native pairs is consistent with the sustained unlimited self-reproduction of E. coli strains with virtually complete T→ClU genome substitution.

  12. LiLEDDA: A Six-Step Forum-Based Netnographic Research Method for Nursing Science

    Directory of Open Access Journals (Sweden)

    MARTIN SALZMANN-ERIKSON

    2012-01-01

    Full Text Available Internet research methods in nursing science are less developed than in other sciences. We choose to present an approach to conducting nursing research on an internet-based forum. This paper presents LiLEDDA, a six-step forum-based netnographic research method for nursing science. The steps consist of: 1. Literature review and identification of the research question(s; 2. Locating the field(s online; 3. Ethical considerations; 4. Data gathering; 5. Data analysis and interpretation; and 6. Abstractions and trustworthiness. Traditional research approaches are limiting when studying non-normative and non-mainstream life-worlds and their cultures. We argue that it is timely to develop more up-to-date research methods and study designs applicable to nursing science that reflect social developments and human living conditions that tend to be increasingly online-based.

  13. [Structural and energetic properties of the four configurations of the A.T and G.C DNA base pairs].

    Science.gov (United States)

    Brovarets', O O

    2013-01-01

    Using the methods of non-empirical quantum chemistry 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 Hoogsteen, reverse Hoogsteen, Watson-Crick and reverse Watson-Crick configurations of the A.T and G.C DNA base pairs are isoelectronic and isomorphic structures with similar dynamic properties. Based on these results, non-ionisation mechanism of the Hoogsteen <"breathing" of the G*.C* DNA base pair, namely transformation of the tautomerised (Lowdin's) G-C base pair with Watson-Crick geometry into the Hoogsteen electroneutral G*.C* H base pair stabilized by the three O6H...N4, N3H...N7 and C8H...02 H-bonds, was postulated. It is suggested that such scenario activates only in those cases, when DNA is not located in aqueous solution, but works together with proteins and cytosine protonation at the N3 atom is precluded.

  14. Stepping Control Method of Linear Displacement Mechanism Driven by TRUM Based on PSoC

    Institute of Scientific and Technical Information of China (English)

    Wang Junping; Liu Weidong; Zhu Hua; Li Yijun; Li Jianjun

    2015-01-01

    A method based on programmable system-on-chip (PSoC) is proposed to realize high resolution stepping motion control of liner displacement mechanism driven by traveling wave rotary ultrasonic motors (TRUM ) .Intel-ligent controller of stepping ultrasonic motor consists of PSoC microprocessor .Continuous square wave signal is sent out by the pulse width modulator (PWM) module inside PSoC ,and converted into sinusoidal signal which is essential to the motor′s normal working by power amplifier circuit .Subsequently ,signal impulse transmission is realized by the counter control break ,and the stepping motion of linear displacement mechanism based on TRUM is achieved .Running status of the ultrasonic motor is controlled by an upper computer .Control command is sent to PSoC through serial communication circuit of RS-232 .Relative program and control interface are written in Lab-View .Finally the mechanism is tested by XL-80 laser interferometer .Test results show that the mechanism can provide a stable motion and a fixed step pitch with the displacement resolution of 6 nm .

  15. High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like C-Silver(I)-C Metallo-Base Pairs.

    Science.gov (United States)

    Kondo, Jiro; Tada, Yoshinari; Dairaku, Takenori; Saneyoshi, Hisao; Okamoto, Itaru; Tanaka, Yoshiyuki; Ono, Akira

    2015-11-02

    Metallo-base pairs have been extensively studied for applications in nucleic acid-based nanodevices and genetic code expansion. Metallo-base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo-base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T-Hg(II)-T base pairs. Herein, we have determined a high-resolution crystal structure of the second natural metallo-base pair between pyrimidine bases C-Ag(I)-C formed in an RNA duplex. One Ag(I) occupies the center between two cytosines and forms a C-Ag(I)-C base pair through N3-Ag(I)-N3 linear coordination. The C-Ag(I)-C base pair formation does not disturb the standard A-form conformation of RNA. Since the C-Ag(I)-C base pair is structurally similar to the canonical Watson-Crick base pairs, it can be a useful building block for structure-based design and fabrication of nucleic acid-based nanodevices.

  16. Lethal osteogenesis imperfecta congenita and a 300 base pair gene deletion for an α1(I)-like collagen.

    NARCIS (Netherlands)

    F.M. Pope; K.S.E. Cheah (Kathryn); A.C. Nicholls; A.B. Price; F.G. Grosveld (Frank)

    1984-01-01

    textabstractBroad boned lethal osteogenesis imperfecta is a severely crippling disease of unknown cause. By means of recombinant DNA technology a 300 base pair deletion in an alpha 1(I)-like collagen gene was detected in six patients and four complete parent-child groups including patients with this

  17. Transitions between Short-Term and Long-Term Memory in Learning Meaningful Unrelated Paired Associates Using Computer Based Drills.

    Science.gov (United States)

    Goldenberg, Tzvika Y.; Turnure, James E.

    1989-01-01

    Discussion of short-term and long-term memory in learning paired associates focuses on two microcomputer-based instructional design experiments with eleventh and twelfth graders that were modeled after traditional drill and practice routines. Research questions are presented, treatment conditions are explained, and additional research is…

  18. Computer simulation of acetonitrile and methanol with ab initio-based pair potentials

    Science.gov (United States)

    Hloucha, M.; Sum, A. K.; Sandler, S. I.

    2000-10-01

    This study address the adequacy of ab initio pair interaction energy potentials for the prediction of macroscopic properties. Recently, Bukowski et al. [J. Phys. Chem. A 103, 7322 (1999)] performed a comprehensive study of the potential energy surfaces for several pairs of molecules using symmetry-adapted perturbation theory. These ab initio energies were then fit to an appropriate site-site potential form. In an attempt to bridge the gap between ab initio interaction energy information and macroscopic properties prediction, we performed Gibbs ensemble Monte Carlo (GEMC) simulations using their developed pair potentials for acetonitrile and methanol. The simulations results show that the phase behavior of acetonitrile is well described by just the pair interaction potential. For methanol, on the other hand, pair interactions are insufficient to properly predict its vapor-liquid phase behavior, and its saturated liquid density. We also explored simplified forms for representing the ab initio interaction energies by refitting a selected range of the data to a site-site Lennard-Jones and to a modified Buckingham (exponential-6) potentials plus Coulombic interactions. These were also used in GEMC simulations in order to evaluate the quality and computational efficiency of these different potential forms. It was found that the phase behavior prediction for acetonitrile and methanol are highly dependent on the details of the interaction potentials developed.

  19. Mitochondrial DNA 4977-base pair common deletion in blood leukocytes and melanoma risk.

    Science.gov (United States)

    Shen, Jie; Wan, Jie; Huff, Chad; Fang, Shenying; Lee, Jeffrey E; Zhao, Hua

    2016-05-01

    The 4977-base pair common deletion DmtDNA4977 is the most frequently observed mitochondrial DNA mutation in human tissues. Because mitochondrial DNA mutations are mainly caused by reactive oxygen species (ROS), and given that oxidative stress plays an important role in melanoma carcinogenesis, the investigation of DmtDNA4977 may be particularly relevant to the development of melanoma. In this study, we compared DmtDNA4977 levels in blood leukocytes from 206 melanoma patients and 219 healthy controls. Overall, melanoma cases had significantly higher levels of DmtDNA4977 than healthy controls (median: 0.60 vs 0.20, P = 0.008). The difference was evident among individuals who were older than 47 yrs, women, and had pigmentation risk factors (e.g., blond or red hair, blue eye, fair skin, light, or none tanning ability after prolonged sun exposure, and freckling in the sun as a child). The difference was also evident among those who had at least one lifetime sunburn with blistering and had no reported use of a sunlamp. Interestingly, among controls, DmtDNA4977 levels differed by phenotypic index and reported use of a sunlamp. In the risk assessment, increased levels of DmtDNA4977 were associated with a 1.23-fold increased risk of melanoma (odds ratio (OR): 1.23, 95% confidence interval (90% CI): 1.01, 1.50). A significant dose-response relationship was observed in quartile analysis (P = 0.001). In summary, our study suggests that high levels of DmtDNA4977 in blood leukocytes are associated with increased risk of melanoma and that association is affected by both pigmentation and personal history of sun exposure.

  20. Mass renormalization and unconventional pairing in multi-band Fe-based superconductors- a phenomenological approach

    Energy Technology Data Exchange (ETDEWEB)

    Drechsler, S.L.; Efremov, D.; Grinenko, V. [IFW-Dresden (Germany); Johnston, S. [Inst. of Quantum Matter, University of British Coulumbia, Vancouver (Canada); Rosner, H. [MPI-cPfS, Dresden, (Germany); Kikoin, K. [Tel Aviv University (Israel)

    2015-07-01

    Combining DFT calculations of the density of states and plasma frequencies with experimental thermodynamic, optical, ARPES, and dHvA data taken from the literature, we estimate both the high-energy (Coulomb, Hund's rule coupling) and the low-energy (el-boson coupling) electronic mass renormalization [H(L)EMR] for typical Fe-pnictides with T{sub c}<40 K, focusing on (K,Rb,Cs)Fe{sub 2}As{sub 2}, (Ca,Na)122, (Ba,K)122, LiFeAs, and LaFeO{sub 1-x}F{sub x}As with and without As-vacancies. Using Eliashberg theory we show that these systems can NOT be described by a very strong el-boson coupling constant λ ≥ ∝ 2, being in conflict with the HEMR as seen by DMFT, ARPES and optics. Instead, an intermediate s{sub ±} coupling regime is realized, mainly based on interband spin fluctuations from one predominant pair of bands. For (Ca,Na)122, there is also a non-negligible intraband el-phonon/orbital fluctuation intraband contribution. The coexistence of magnetic As-vacancies and high-T{sub c}=28 K for LaFeO{sub 1-x}F{sub x}As{sub 1-δ} excludes an orbital fluctuation dominated s{sub ++} scenario at least for that system. In contrast, the line nodal BaFe{sub 2}(As,P){sub 2} near the quantum critical point is found as a superstrongly coupled system. The role of a pseudo-gap is briefly discussed for some of these systems.

  1. SVM with Quadratic Polynomial Kernel Function Based Nonlinear Model One-step-ahead Predictive Control

    Institute of Scientific and Technical Information of China (English)

    钟伟民; 何国龙; 皮道映; 孙优贤

    2005-01-01

    A support vector machine (SVM) with quadratic polynomial kernel function based nonlinear model one-step-ahead predictive controller is presented. The SVM based predictive model is established with black-box identification method. By solving a cubic equation in the feature space, an explicit predictive control law is obtained through the predictive control mechanism. The effect of controller is demonstrated on a recognized benchmark problem and on the control of continuous-stirred tank reactor (CSTR). Simulation results show that SVM with quadratic polynomial kernel function based predictive controller can be well applied to nonlinear systems, with good performance in following reference trajectory as well as in disturbance-rejection.

  2. Compatibility of pedigree-based and marker-based relationship matrices for single-step genetic evaluation

    DEFF Research Database (Denmark)

    Christensen, Ole Fredslund

    2012-01-01

    Single-step methods for genomic prediction have recently become popular because they are conceptually simple and in practice such a method can completely replace a pedigree-based method for routine genetic evaluation. An issue with single-step methods is compatibility between the marker-based rel...... for the phenotypes conditional on the observed markers, whereas the second term is the likelihood for t he observed markers. The performance of the proposed method is studied on simulated data examples....... that it may be important that a single-step method is based on a model conditional on the observed markers. When data are from routine evaluation systems, selection affects the allele frequencies, and therefore both observed markers and observed phenotypes contain information about allele frequencies...... in the base population. Here, two ideas are explored. The first idea is to instead adjust the pedigree-based relationship matrix to be compatible to the marker-based relationship matrix, whereas the second idea is to include the likelihood for the observed markers. A single-step method is used where...

  3. Carcinogenesis of asbestos switched on by inducing cross-linkage between DNA complementary pair bases

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Since the beginning of the 1980s, Dai Qianhuan predicted based upon his di-region theory that the carcinogenesis switched on by the so-called physical carcinogenic factors including radiation, asbestos and foreign matter implantation, is just initiated through the cross-linking between DNA complementary pair bases induced by them. In this note, it was evidenced with the DNA filter elution method that the oxygenase activated by asbestos induces the cross-linking between DNA inter-strands and DNA-protein with dosage correlation, in which over 80% of DNA inter-strand cross-link ratio account for the total cross-link ratio. Obviously, both of the cross-linkages are just induced by hydroxyl free radical, HO@, because the ferrous ion increased the cross-link ratios up to several times through Fenton reaction and vitamin C inhibited the cross-link ratios with factors of 8-9 by destroying the hydroxyl radical. Non-carcinogen but with lower free radical formation energy, pyrene, by culturing with asbestos gave 3-4 times cross-link ratios than the original ratios induced by asbestos only. Estradiol, an endogenous carcinogen, as a bio-electrophilic species but with higher free radical formation energy by culturing with asbestos, gave only 1.2 time cross-link ratios than expected ones. Ferrous ion which can increase HO@ concentration through Fenton reaction, increased the ratios to 2-2.5 times in the former case but only 1.2 time in the latter case. Vitamin C, a free radical scavenger, gave a powerful inhibition to the cross-linking with a factor of 8-11 in the former case but a weak inhibition with a factor of 1.2 only in the latter case. So, it is evidenced further that the cross-linkages induced by asbestos are originated from hydroxyl radical. Reasonable structures of the cross-linking products induced by asbestos or hydroxyl radical have been depicted based upon AM1 MO theory. These structures have been verified further by a reasonable explanation of the mutational

  4. A Method of MPPT Control Based on Power Variable Step-size in Photovoltaic Converter System

    Directory of Open Access Journals (Sweden)

    Xu Hui-xiang

    2016-01-01

    Full Text Available Since the disadvantage of traditional MPPT algorithms of variable step-size, proposed power tracking based on variable step-size with the advantage method of the constant-voltage and the perturb-observe (P&O[1-3]. The control strategy modify the problem of voltage fluctuation caused by perturb-observe method, at the same time, introducing the advantage of constant-voltage method and simplify the circuit topology. With the theoretical derivation, control the output power of photovoltaic modules to change the duty cycle of main switch. Achieve the maximum power stabilization output, reduce the volatility of energy loss effectively, and improve the inversion efficiency[3,4]. Given the result of experimental test based theoretical derivation and the curve of MPPT when the prototype work.

  5. NURBS Interpolation Technology in CNC System Based on STEP-NC%基于STEP-NC的CNC系统中NURBS插补技术研究

    Institute of Scientific and Technical Information of China (English)

    杜娟; 田锡天; 张振明; 朱名铨; 李建克

    2007-01-01

    STEP-NC is a new interface standard for data exchanging and sharing between CAD/CAM and CNC, and the CNC based on STEP-NC will be the next generation of CNC controller, which not only holds linear and circular interpolation but also possesses the capability of spline interpolation. A universal NURBS ( non-uniform rational B-spline) based interpolator was designed and the interpolation technique based on constant arc increment and interpolation algorithm were inverstigated arc increment. The validity and reliability of algorithm was tested by an instance simulation and machining.%STEP-NC是一个用来实现CAD/CAM与CNC系统间数据交换的接口标准,基于STEP-NC的CNC系统是未来数控技术发展方向之一,该系统不但具有直线和圆弧插补功能,而且还具有样条曲线插补功能.为此设计了一个统一的基于NURBS样条曲线插补的通用插补器,并开发了一种基于等弧长的插补技术和插补算法.最后通过仿真和实例加工验证了该算法的有效性和可靠性.

  6. Cooper pairing in the insulating valence band in iron-based superconductors

    Science.gov (United States)

    Hu, Lun-Hui; Chen, Wei-Qiang; Zhang, Fu-Chun

    2015-04-01

    Conventional Cooper pairing arises from attractive interaction of electrons in the metallic bands. A recent experiment on Co-doped LiFeAs shows superconductivity in the insulating valence band, which is evolved from a metallic hole band upon doping. Here we examine this phenomenon by studying superconductivity in a three-orbital Hamiltonian relevant to the doped LiFeAs. We show explicitly that Cooper pairing of the insulating hole band requires a finite pairing interaction strength. For strong coupling, the superconductivity in the hole band is robust against the sink of the hole band below the Fermi level. Our theory predicts a substantial upward shift of the chemical potential in the superconducting transition for Co-doped LiFeAs.

  7. Profilometry with Grating Projection Based on One-step Phase Shift

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    An optical technique for 3-D shape measurement is presented. This technique, based on a deformed projected grating pattern which carries 3-D information of the measured object, can automatically and accurately obtain the phase map of a measured object by using one-step phase shift algorithm.In comparison with traditional phase-shift technique, the technique is much faster, with the equivalent accuracy. Only one frame image is sufficient for measuring. Experimental result of typical object is presented.

  8. A phase retrieval method of interferograms add-subtracting based on two-step phase shifting.

    Science.gov (United States)

    Xu, Yuanyuan; Wang, Yawei; Ji, Ying; Jin, Weifeng; Bu, Min; Shang, Xuefu

    2014-01-01

    A phase retrieval method is introduced in quantitative phase imaging (QPI) based on two-step phase-shifting technique. By acquiring two measured interferograms and calculating the addition and subtraction between them, the quantitative phase information can be directly retrieved. This method is illustrated by both theory and simulation experiments of a ball. The results of the simulation and the experiment of the red blood cell show a good agreement, demonstrating its application for studying cells.

  9. Multi-Step Deep Reactive Ion Etching Fabrication Process for Silicon-Based Terahertz Components

    Science.gov (United States)

    Jung-Kubiak, Cecile (Inventor); Reck, Theodore (Inventor); Chattopadhyay, Goutam (Inventor); Perez, Jose Vicente Siles (Inventor); Lin, Robert H. (Inventor); Mehdi, Imran (Inventor); Lee, Choonsup (Inventor); Cooper, Ken B. (Inventor); Peralta, Alejandro (Inventor)

    2016-01-01

    A multi-step silicon etching process has been developed to fabricate silicon-based terahertz (THz) waveguide components. This technique provides precise dimensional control across multiple etch depths with batch processing capabilities. Nonlinear and passive components such as mixers and multipliers waveguides, hybrids, OMTs and twists have been fabricated and integrated into a small silicon package. This fabrication technique enables a wafer-stacking architecture to provide ultra-compact multi-pixel receiver front-ends in the THz range.

  10. Compatibility of pedigree-based and marker-based relationship matrices for single-step genetic evaluation

    Directory of Open Access Journals (Sweden)

    Christensen Ole F

    2012-12-01

    Full Text Available Abstract Background Single-step methods provide a coherent and conceptually simple approach to incorporate genomic information into genetic evaluations. An issue with single-step methods is compatibility between the marker-based relationship matrix for genotyped animals and the pedigree-based relationship matrix. Therefore, it is necessary to adjust the marker-based relationship matrix to the pedigree-based relationship matrix. Moreover, with data from routine evaluations, this adjustment should in principle be based on both observed marker genotypes and observed phenotypes, but until now this has been overlooked. In this paper, I propose a new method to address this issue by 1 adjusting the pedigree-based relationship matrix to be compatible with the marker-based relationship matrix instead of the reverse and 2 extending the single-step genetic evaluation using a joint likelihood of observed phenotypes and observed marker genotypes. The performance of this method is then evaluated using two simulated datasets. Results The method derived here is a single-step method in which the marker-based relationship matrix is constructed assuming all allele frequencies equal to 0.5 and the pedigree-based relationship matrix is constructed using the unusual assumption that animals in the base population are related and inbred with a relationship coefficient γ and an inbreeding coefficient γ / 2. Taken together, this γ parameter and a parameter that scales the marker-based relationship matrix can handle the issue of compatibility between marker-based and pedigree-based relationship matrices. The full log-likelihood function used for parameter inference contains two terms. The first term is the REML-log-likelihood for the phenotypes conditional on the observed marker genotypes, whereas the second term is the log-likelihood for the observed marker genotypes. Analyses of the two simulated datasets with this new method showed that 1 the parameters involved

  11. A 3-Step Algorithm Using Region-Based Active Contours for Video Objects Detection

    Directory of Open Access Journals (Sweden)

    Stéphanie Jehan-Besson

    2002-06-01

    Full Text Available We propose a 3-step algorithm for the automatic detection of moving objects in video sequences using region-based active contours. First, we introduce a very full general framework for region-based active contours with a new Eulerian method to compute the evolution equation of the active contour from a criterion including both region-based and boundary-based terms. This framework can be easily adapted to various applications, thanks to the introduction of functions named descriptors of the different regions. With this new Eulerian method based on shape optimization principles, we can easily take into account the case of descriptors depending upon features globally attached to the regions. Second, we propose a 3-step algorithm for detection of moving objects, with a static or a mobile camera, using region-based active contours. The basic idea is to hierarchically associate temporal and spatial information. The active contour evolves with successively three sets of descriptors: a temporal one, and then two spatial ones. The third spatial descriptor takes advantage of the segmentation of the image in intensity homogeneous regions. User interaction is reduced to the choice of a few parameters at the beginning of the process. Some experimental results are supplied.

  12. Ferrocene-based Lewis acids and Lewis pairs: Synthesis and structural characterization

    Indian Academy of Sciences (India)

    Pagidi Sudhakar; Pakkirisamy Thilagar

    2013-01-01

    Optically active Lewis acids and Lewis pairs were synthesized and characterized by multinuclear NMR, UV/Vis spectroscopy and elemental analysis. Optical rotation measurements were carried out and the absolute configuration of the new chiral molecules confirmed by single crystal X-ray diffraction.

  13. Classification between normal and tumor tissues based on the pair-wise gene expression ratio

    Directory of Open Access Journals (Sweden)

    Wong YC

    2004-10-01

    Full Text Available Abstract Background Precise classification of cancer types is critically important for early cancer diagnosis and treatment. Numerous efforts have been made to use gene expression profiles to improve precision of tumor classification. However, reliable cancer-related signals are generally lacking. Method Using recent datasets on colon and prostate cancer, a data transformation procedure from single gene expression to pair-wise gene expression ratio is proposed. Making use of the internal consistency of each expression profiling dataset this transformation improves the signal to noise ratio of the dataset and uncovers new relevant cancer-related signals (features. The efficiency in using the transformed dataset to perform normal/tumor classification was investigated using feature partitioning with informative features (gene annotation as discriminating axes (single gene expression or pair-wise gene expression ratio. Classification results were compared to the original datasets for up to 10-feature model classifiers. Results 82 and 262 genes that have high correlation to tissue phenotype were selected from the colon and prostate datasets respectively. Remarkably, data transformation of the highly noisy expression data successfully led to lower the coefficient of variation (CV for the within-class samples as well as improved the correlation with tissue phenotypes. The transformed dataset exhibited lower CV when compared to that of single gene expression. In the colon cancer set, the minimum CV decreased from 45.3% to 16.5%. In prostate cancer, comparable CV was achieved with and without transformation. This improvement in CV, coupled with the improved correlation between the pair-wise gene expression ratio and tissue phenotypes, yielded higher classification efficiency, especially with the colon dataset – from 87.1% to 93.5%. Over 90% of the top ten discriminating axes in both datasets showed significant improvement after data transformation. The

  14. Interrupt-Based Step-Counting to Extend Battery Life in an Activity Monitor

    Directory of Open Access Journals (Sweden)

    Seung Young Kim

    2016-01-01

    Full Text Available Most activity monitors use an accelerometer and gyroscope sensors to characterize the wearer’s physical activity. The monitor measures the motion by polling an accelerometer or gyroscope sensor or both every 20–30 ms and frequent polling affects the battery life of a wearable device. One of the key features of a commercial daily-activity monitoring device is longer battery life so that the user can keep track of his or her activity for a week or so without recharging the battery of the monitoring device. Many low-power approaches for a step-counting system use either a polling-based algorithm or an interrupt-based algorithm. In this paper, we propose a novel approach that uses the tap interrupt of an accelerometer to count steps while consuming low power. We compared the accuracy of step counting and measured system-level power consumption to a periodic sensor-reading algorithm. Our tap interrupt approach shows a battery lifetime that is 175% longer than that of a 30 ms polling method without gyroscope. The battery lifetime can be extended up to 863% with a gyroscope by putting both the processor and the gyroscope into sleep state during the majority of operation time.

  15. Two-Step Time of Arrival Estimation for Pulse-Based Ultra-Wideband Systems

    Directory of Open Access Journals (Sweden)

    H. Vincent Poor

    2008-05-01

    Full Text Available In cooperative localization systems, wireless nodes need to exchange accurate position-related information such as time-of-arrival (TOA and angle-of-arrival (AOA, in order to obtain accurate location information. One alternative for providing accurate position-related information is to use ultra-wideband (UWB signals. The high time resolution of UWB signals presents a potential for very accurate positioning based on TOA estimation. However, it is challenging to realize very accurate positioning systems in practical scenarios, due to both complexity/cost constraints and adverse channel conditions such as multipath propagation. In this paper, a two-step TOA estimation algorithm is proposed for UWB systems in order to provide accurate TOA estimation under practical constraints. In order to speed up the estimation process, the first step estimates a coarse TOA of the received signal based on received signal energy. Then, in the second step, the arrival time of the first signal path is estimated by considering a hypothesis testing approach. The proposed scheme uses low-rate correlation outputs and is able to perform accurate TOA estimation in reasonable time intervals. The simulation results are presented to analyze the performance of the estimator.

  16. Ask the right question: a critical step for practicing evidence-based laboratory medicine.

    Science.gov (United States)

    Price, Christopher P; Christenson, Robert H

    2013-07-01

    The purpose of laboratory medicine is to facilitate better decision making in clinical practice and healthcare delivery. Decision making implies an unresolved issue, problem or unmet need. The most important criterion for any investigation to be of value in clinical practice is that it addresses an unmet need. The different ways in which laboratory investigations are utilized in patient care can be represented in the form of questions. It is important that these questions are articulated to highlight the variables that will impact on the effectiveness of the investigation in the scenario being considered. These variables include the characteristics of the patient (or population) and clinical setting, the nature of the decision and action taken on receipt of the test result and the expected outcome. Asking a question is the first step of the evidence-based laboratory medicine (EBLM) cycle, the other steps being acquiring the evidence, critically appraising the evidence, applying the evidence and auditing use of the evidence. Getting the question right determines the quality of the whole process, thus, defines the quality in practice of laboratory medicine. Whilst the main focus of the EBLM cycle is to provide a strong evidence base for use in clinical practice, it is clear that the five steps are equally applicable in commissioning, delivery and audit (performance management) of services. Asking the right question is crucial to improving the quality of evidence, and practice, in laboratory medicine, and should be used in routine laboratory medicine practice and management throughout healthcare.

  17. Region-based multi-step optic disk and cup segmentation from color fundus image

    Science.gov (United States)

    Xiao, Di; Lock, Jane; Manresa, Javier Moreno; Vignarajan, Janardhan; Tay-Kearney, Mei-Ling; Kanagasingam, Yogesan

    2013-02-01

    Retinal optic cup-disk-ratio (CDR) is a one of important indicators of glaucomatous neuropathy. In this paper, we propose a novel multi-step 4-quadrant thresholding method for optic disk segmentation and a multi-step temporal-nasal segmenting method for optic cup segmentation based on blood vessel inpainted HSL lightness images and green images. The performance of the proposed methods was evaluated on a group of color fundus images and compared with the manual outlining results from two experts. Dice scores of detected disk and cup regions between the auto and manual results were computed and compared. Vertical CDRs were also compared among the three results. The preliminary experiment has demonstrated the robustness of the method for automatic optic disk and cup segmentation and its potential value for clinical application.

  18. Microstructural evolution of TiAl base alloy during three-stepped thermo-mechanical treatment

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A TiAl base alloy ingot with a height-to-diameter ratio of 2.2 was broken down by multiple step canned forging. The microstructures after every deformation and subsequent recrystallization were observed by optical microscopy. Results show that at the first step the reduction should be carefully controlled in case of double-bulge and crack of the ingot. After the first annealing, recrystallization occurred at the deformed grain boundaries and inside the grain. The recrystallized microstructure is favorable for further deformation. After the second deformation and annealing, coarsening of the lamellae occurred and the microstructure became equiaxed. By the final deformation and subsequent recrystallization, the coarse lamellar colony can be refined to about 20 μm, and homogeneous microstructure was obtained from the ingot with a large initial height-to-diameter ratio.

  19. Investigating the Effectiveness of Teaching Methods Based on a Four-Step Constructivist Strategy

    Science.gov (United States)

    Çalik, Muammer; Ayas, Alipaşa; Coll, Richard K.

    2010-02-01

    This paper reports on an investigation of the effectiveness an intervention using several different methods for teaching solution chemistry. The teaching strategy comprised a four-step approach derived from a constructivist view of learning. A sample consisting of 44 students (18 boys and 26 girls) was selected purposively from two different Grade 9 classes in the city of Trabzon, Turkey. Data collection employed a purpose-designed `solution chemistry concept test', consisting of 17 items, with the quantitative data from the survey supported by qualitative interview data. The findings suggest that using different methods embedded within the four-step constructivist-based teaching strategy enables students to refute some alternative conceptions, but does not completely eliminate student alternative conceptions for solution chemistry.

  20. Two-step Classification Algorithm Based on Decision-Theoretic Rough Set Theory

    Directory of Open Access Journals (Sweden)

    Jun Wang

    2013-07-01

    Full Text Available This paper introduces rough set theory and decision-theoretic rough set theory. Then based on the latter, a two-step classification algorithm is proposed. Compared with primitive DTRST algorithms, our method decreases the range of negative domain and employs a two-steps strategy in classification. New samples and unknown samples can be estimated whether it belongs to the negative domain when they are found. Then, fewer wrong samples will be classified in negative domain. Therefore, error rate and loss of classification is lowered. Compared with traditional information filtering methods, such as Naive Bayes algorithm and primitive DTRST algorithm, the proposed method can gain high accuracy and low loss.  

  1. DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution.

    Directory of Open Access Journals (Sweden)

    Yingying Zhang

    2009-03-01

    Full Text Available Differential DNA methylation is an essential epigenetic signal for gene regulation, development, and disease processes. We mapped DNA methylation patterns of 190 gene promoter regions on chromosome 21 using bisulfite conversion and subclone sequencing in five human cell types. A total of 28,626 subclones were sequenced at high accuracy using (long-read Sanger sequencing resulting in the measurement of the DNA methylation state of 580427 CpG sites. Our results show that average DNA methylation levels are distributed bimodally with enrichment of highly methylated and unmethylated sequences, both for amplicons and individual subclones, which represent single alleles from individual cells. Within CpG-rich sequences, DNA methylation was found to be anti-correlated with CpG dinucleotide density and GC content, and methylated CpGs are more likely to be flanked by AT-rich sequences. We observed over-representation of CpG sites in distances of 9, 18, and 27 bps in highly methylated amplicons. However, DNA sequence alone is not sufficient to predict an amplicon's DNA methylation status, since 43% of all amplicons are differentially methylated between the cell types studied here. DNA methylation in promoter regions is strongly correlated with the absence of gene expression and low levels of activating epigenetic marks like H3K4 methylation and H3K9 and K14 acetylation. Utilizing the single base pair and single allele resolution of our data, we found that i amplicons from different parts of a CpG island frequently differ in their DNA methylation level, ii methylation levels of individual cells in one tissue are very similar, and iii methylation patterns follow a relaxed site-specific distribution. Furthermore, iv we identified three cases of allele-specific DNA methylation on chromosome 21. Our data shed new light on the nature of methylation patterns in human cells, the sequence dependence of DNA methylation, and its function as epigenetic signal in gene

  2. Investigations on therapeutic glucocerebrosidases through paired detection with fluorescent activity-based probes

    Science.gov (United States)

    Kallemeijn, Wouter W.; Scheij, Saskia; Hoogendoorn, Sascha; Witte, Martin D.; Herrera Moro Chao, Daniela; van Roomen, Cindy P. A. A.; Ottenhoff, Roelof; Overkleeft, Herman S.; Boot, Rolf G.; Aerts, Johannes M. F. G.

    2017-01-01

    Deficiency of glucocerebrosidase (GBA) causes Gaucher disease (GD). In the common non-neuronopathic GD type I variant, glucosylceramide accumulates primarily in the lysosomes of visceral macrophages. Supplementing storage cells with lacking enzyme is accomplished via chronic intravenous administration of recombinant GBA containing mannose-terminated N-linked glycans, mediating the selective uptake by macrophages expressing mannose-binding lectin(s). Two recombinant GBA preparations with distinct N-linked glycans are registered in Europe for treatment of type I GD: imiglucerase (Genzyme), contains predominantly Man(3) glycans, and velaglucerase (Shire PLC) Man(9) glycans. Activity-based probes (ABPs) enable fluorescent labeling of recombinant GBA preparations through their covalent attachment to the catalytic nucleophile E340 of GBA. We comparatively studied binding and uptake of ABP-labeled imiglucerase and velaglucerase in isolated dendritic cells, cultured human macrophages and living mice, through simultaneous detection of different GBAs by paired measurements. Uptake of ABP-labeled rGBAs by dendritic cells was comparable, as well as the bio-distribution following equimolar intravenous administration to mice. ABP-labeled rGBAs were recovered largely in liver, white-blood cells, bone marrow and spleen. Lungs, brain and skin, affected tissues in severe GD types II and III, were only poorly supplemented. Small, but significant differences were noted in binding and uptake of rGBAs in cultured human macrophages, in the absence and presence of mannan. Mannan-competed binding and uptake were largest for velaglucerase, when determined with single enzymes or as equimolar mixtures of both enzymes. Vice versa, imiglucerase showed more prominent binding and uptake not competed by mannan. Uptake of recombinant GBAs by cultured macrophages seems to involve multiple receptors, including several mannose-binding lectins. Differences among cells from different donors (n = 12

  3. Free energy landscape and transition pathways from Watson-Crick to Hoogsteen base pairing in free duplex DNA.

    Science.gov (United States)

    Yang, Changwon; Kim, Eunae; Pak, Youngshang

    2015-09-18

    Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson-Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine-thymine (A-T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events.

  4. 4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening

    Directory of Open Access Journals (Sweden)

    Jahn Andreas

    2011-07-01

    Full Text Available Abstract Background The performance of 3D-based virtual screening similarity functions is affected by the applied conformations of compounds. Therefore, the results of 3D approaches are often less robust than 2D approaches. The application of 3D methods on multiple conformer data sets normally reduces this weakness, but entails a significant computational overhead. Therefore, we developed a special conformational space encoding by means of Gaussian mixture models and a similarity function that operates on these models. The application of a model-based encoding allows an efficient comparison of the conformational space of compounds. Results Comparisons of our 4D flexible atom-pair approach with over 15 state-of-the-art 2D- and 3D-based virtual screening similarity functions on the 40 data sets of the Directory of Useful Decoys show a robust performance of our approach. Even 3D-based approaches that operate on multiple conformers yield inferior results. The 4D flexible atom-pair method achieves an averaged AUC value of 0.78 on the filtered Directory of Useful Decoys data sets. The best 2D- and 3D-based approaches of this study yield an AUC value of 0.74 and 0.72, respectively. As a result, the 4D flexible atom-pair approach achieves an average rank of 1.25 with respect to 15 other state-of-the-art similarity functions and four different evaluation metrics. Conclusions Our 4D method yields a robust performance on 40 pharmaceutically relevant targets. The conformational space encoding enables an efficient comparison of the conformational space. Therefore, the weakness of the 3D-based approaches on single conformations is circumvented. With over 100,000 similarity calculations on a single desktop CPU, the utilization of the 4D flexible atom-pair in real-world applications is feasible.

  5. Steps towards a SAR-based wind atlas in the Baltic Sea

    DEFF Research Database (Denmark)

    Hasager, Charlotte Bay; Badger, Merete; Pena Diaz, Alfredo;

    In the EU-Norsewind project (2008-2012) one task was to assess the wind climate in the Baltic Sea using Synthetic Aperture Radar (SAR) observations. The presentation outlines the methodology and key results. The Baltic Sea has been mapped relatively frequently by Envisat ASAR since 2002 and during...... deviation of 1.88 m/s (20.11°), and linear correlation coefficient R2 of 0.783 (0.95°). The second step was estimation of the mean wind speed, the Weibull scale and shape parameters, and energy density based on over 1000 SAR-based wind maps for the Baltic Sea. The results were compared to the FINO-2...... these years several offshore meteorological masts have been in operation. The first step was to assess the accuracy of SAR-based wind mapping in this region. We compared SAR-based wind maps retrieved from ANSWRS the APL/NOAA SAR Wind Retrieval System. The NOGAPS wind direction data were interpolated in space...

  6. Adaptive Step Size Control of LMS-based Interference Cancellationfor ICS Repeater in Wibro Environment

    Institute of Scientific and Technical Information of China (English)

    Jeong-gon KIM; Won-geon BAE; Won-seok CHOI

    2010-01-01

    The use of repeater for the support of high rate data transmission and the extension of cell coverage is imperative for the Wibrc system,which based on the IEEE 8M.16e standardization.Generally,if the separation between transmitting and receiving antennas isnot sufficient,the oscillation of repeater and the interference due to the feedback signals from original transmitted signal may be ocerur.Hence,the Interference Cancellation System(ICS)should be implemented as the important part of the repeater system far the mobile cellular systems in order to eliminate unwanted signals from the corruptW signals in the receiver.In this paper,we propose an adaptive technique for the Least Mean Square(LMS)-based interference cancellation methods by changing the step size according to the variation of channel environment in order to improve the performance degradation which oceuurs by using the fixed step size approach.Simrlatim results show that the proposed sclxme attains a little lower Berafor Rate(BER)performance and much faster convergence speed compared to the conventional LMS-based interference cancellation techniques.The proposed scheme can be applied to other Orthogonal Frequency Division Multiple(OFDM)-based cellular systems and also be expected to achieve a similar performance improvement to W17-advanced system,which is called as the next generation mobile communication standards.

  7. A Practical Parallel Algorithm for All-Pair Shortest Path Based on Pipelining

    Institute of Scientific and Technical Information of China (English)

    Hua Wang; Ling Tian; Chun-Hua Jiang

    2008-01-01

    On the basis of Floyd algorithm with theextended path matrix, a parallel algorithm whichresolves all-pair shortest path (APSP) problem oncluster environment is analyzed and designed.Meanwhile, the parallel APSP pipelining algorithmmakes full use of overlapping technique betweencomputation and communication. Compared withbroadcast operation, the parallel algorithm reducescommunication cost. This algorithm has beenimplemented on MPI on PC-cluster. The theoreticalanalysis and experimental results show that the parallelalgorithm is an efficient and scalable algorithm.

  8. Self-Diffusion Coefficients in Liquid Ag Using the Embedded Atom Model Based Effective Pair Potentials

    OpenAIRE

    DALGIÇ, Seyfettin; ÇOLAKOĞULLARI, Mutlu

    2006-01-01

    We present the dynamical properties of liquid Ag at different temperatures, using the Mishin and Doyoma-Kagure version of the Embedded Atom Model (EAM) potentials. They have been evaluated within the framework of the mode-coupling theory, using a self-consistent scheme that uses as input data only the static structure functions and the interatomic pair potentials of the liquid Ag. We have computed single-particle and collective time dependent properties of liquid Ag, and thereby calc...

  9. Watson-Crick Base Pairing, Electronic and Photophysical Properties of Triazole Modified Adenine Analogues: A Computational Study

    KAUST Repository

    Das, Shubhajit

    2015-09-17

    We employ first-principles Density Functional Theory (DFT) and time-dependent DFT (TDDFT) to elucidate structural, electronic and optical properties of a few recently reported triazole adenine nucleobase analogues. The results are compared against the findings obtained for both natural adenine nucleobase and available experimental data. The optical absorption of these adenine analogues are calculated both in gas-phase and in solvent (methanol) using Polarized Continuum Model (PCM). We find that all the analogues show a red-shifted absorption profile as compared to adenine. Our simulated emission spectra in solvent compare fairly well with experimentally observed results. We investigate base paring ability of these adenine analogues with thymine. The calculations on the intrinsic stability of these base pairs ascertain that all the adenine analogues form the hydrogen bonded Watson-Crick base pair with similar H-bonding energy as obtained for natural adenine-thymine base pair. In our study, we provide a microscopic origin of the low-energy absorption and emission peaks, observed experimentally.

  10. A single Watson-Crick G x C base pair in water: aqueous hydrogen bonds in hydrophobic cavities.

    Science.gov (United States)

    Sawada, Tomohisa; Fujita, Makoto

    2010-05-26

    Hydrogen bond (H-bond) formation in water has been a challenging task because water molecules are constant competitors. In biological systems, however, stable H-bonds are formed by shielding the H-bonding sites from the competing water molecules within hydrophobic pockets. Inspired by the nature's elaborated way, we found that even mononucleotides (G and C) can form the minimal G x C Watson-Crick pair in water by simply providing a synthetic cavity that efficiently shields the Watson-Crick H-bonding sites. The minimal Watson-Crick structure in water was elucidated by NMR study and firmly characterized by crystallographic analysis. The crystal structure also displays that, within the cavity, coencapsulated anions and solvents efficiently mediate the minimal G x C Watson-Crick pair formation. Furthermore, the competition experiments with the other nucleobases clearly revealed the evident selectivity for the G x C base pairing in water. These results show the fact that a H-bonded nucleobase pair was effectively induced and stabilized in the local environment of an artificial hydrophobic cavity.

  11. Si-based tunable flattop photodetector with a stepped Fabry-Perot cavity.

    Science.gov (United States)

    Wang, Wei; Huang, Yongqing; Duan, Xiaofeng; Tian, Jia; Guo, Jingwei; Ren, Xiaomin

    2012-04-01

    This paper presents the design and analysis of a Si-based tunable flattop photodetector realized by the introduction of a stepped Fabry-Perot cavity, which can be thermally tuned via applying tuning power on its tuning electrode. By using a transfer matrix method, the spectral response of the photodetector is simulated in detail, indicating a flattop line shape can be achieved with an optimum step height. A trade-off residing in this device between the free spectrum range and the ease of fabrication of step height is also revealed and analyzed. In the final design of the photodetector, 1 dB linewidth of 0.5 nm, 3 dB linewidth of 0.8 nm, 6 dB linewidth of 1.2 nm, peak quantum efficiency of 40%, tuning efficiency of 91 mW/nm are theoretically obtained. We discuss the epitaxial growth and fabrication of the photodetector in the end, exhibiting the mature technique available for this device.

  12. A new image reconstruction method for 3-D PET based upon pairs of near-missing lines of response

    Energy Technology Data Exchange (ETDEWEB)

    Kawatsu, Shoji [Department of Radiology, Kyoritu General Hospital, 4-33 Go-bancho, Atsuta-ku, Nagoya-shi, Aichi 456-8611 (Japan) and Department of Brain Science and Molecular Imaging, National Institute for Longevity Sciences, National Center for Geriatrics and Gerontology, 36-3, Gengo Moriaka-cho, Obu-shi, Aichi 474-8522 (Japan)]. E-mail: b6rgw@fantasy.plala.or.jp; Ushiroya, Noboru [Department of General Education, Wakayama National College of Technology, 77 Noshima, Nada-cho, Gobo-shi, Wakayama 644-0023 (Japan)

    2007-02-01

    We formerly introduced a new image reconstruction method for three-dimensional positron emission tomography, which is based upon pairs of near-missing lines of response. This method uses an elementary geometric property of lines of response, namely that two lines of response which originate from radioactive isotopes located within a sufficiently small voxel, will lie within a few millimeters of each other. The effectiveness of this method was verified by performing a simulation using GATE software and a digital Hoffman phantom.

  13. A Study on the Storage Reliability of LSINS Based on Step-stress Accelerated Life Test

    Directory of Open Access Journals (Sweden)

    Teng Fei

    2015-01-01

    Full Text Available Based on the step-stress accelerated life test and the laser strap-down inertial navigation system, this paper studies the accelerated life model and the test method, provides the likelihood function, the likelihood equation and the two-order derivative when the stress level is k, evaluates the effectiveness of the method with the simulation test model established by MATLAB, applies the research findings in the storage reliability study of the XX laser strap-down inertial navigation system, and puts forward an effective evaluation method of the storage life of the inertial navigation system.

  14. Step-coordination Algorithm of Traffic Control Based on Multi-agent System

    Institute of Scientific and Technical Information of China (English)

    Hai-Tao Zhang; Fang Yu; Wen Li

    2009-01-01

    Aiming at the deficiency of conventional traffic control method, this paper proposes a new method based on multi-agent technology for traffic control. Different from many existing methods, this paper distinguishes traffic control on the basis of the agent technology from conventional traffic control method. The composition and structure of a multi-agent system (MAS) is first discussed. Then, the step-coordination strategies of intersection-agent, segment-agent, and area-agent are put forward. The advantages of the algorithm are demonstrated by a simulation study.

  15. Agent Based Manufacturing Capability Assessment in the Extended Enterprise Using Step AP224 and XML

    Science.gov (United States)

    Ratchev, Svetan; Medani, Omar

    Data exchange in the extended enterprise is one of the most critical tasks in supporting collaborative decision-making. Companies often rely on geographically distributed suppliers for efficient product design and manufacture. Early design assessment can substantially reduce the cost of product development and production. This research proposes a new STEP AP224 EXPRESS based data model to facilitate the exchange of part and process data between distributed key agents in the early design process. The approach is illustrated using a prototype XML/CORBA environment to support the information exchange between collaborating design and manufacturing agents.

  16. First steps towards the realization of a double layer perceptron based on organic memristive devices

    Directory of Open Access Journals (Sweden)

    A. V. Emelyanov

    2016-11-01

    Full Text Available Memristors are widely considered as promising elements for the efficient implementation of synaptic weights in artificial neural networks (ANNs since they are resistors that keep memory of their previous conductive state. Whereas demonstrations of simple neural networks (e.g., a single-layer perceptron based on memristors already exist, the implementation of more complicated networks is more challenging and has yet to be reported. In this study, we demonstrate linearly nonseparable combinational logic classification (XOR logic task using a network implemented with CMOS-based neurons and organic memrisitive devices that constitutes the first step toward the realization of a double layer perceptron. We also show numerically the ability of such network to solve a principally analogue task which cannot be realized by digital devices. The obtained results prove the possibility to create a multilayer ANN based on memristive devices that paves the way for designing a more complex network such as the double layer perceptron.

  17. First steps towards the realization of a double layer perceptron based on organic memristive devices

    Science.gov (United States)

    Emelyanov, A. V.; Lapkin, D. A.; Demin, V. A.; Erokhin, V. V.; Battistoni, S.; Baldi, G.; Dimonte, A.; Korovin, A. N.; Iannotta, S.; Kashkarov, P. K.; Kovalchuk, M. V.

    2016-11-01

    Memristors are widely considered as promising elements for the efficient implementation of synaptic weights in artificial neural networks (ANNs) since they are resistors that keep memory of their previous conductive state. Whereas demonstrations of simple neural networks (e.g., a single-layer perceptron) based on memristors already exist, the implementation of more complicated networks is more challenging and has yet to be reported. In this study, we demonstrate linearly nonseparable combinational logic classification (XOR logic task) using a network implemented with CMOS-based neurons and organic memrisitive devices that constitutes the first step toward the realization of a double layer perceptron. We also show numerically the ability of such network to solve a principally analogue task which cannot be realized by digital devices. The obtained results prove the possibility to create a multilayer ANN based on memristive devices that paves the way for designing a more complex network such as the double layer perceptron.

  18. [Quantum-chemical investigation of tautomerization ways of Watson-Crick DNA base pair guanine-cytosine].

    Science.gov (United States)

    Brovarets', O O; Hovorun, D M

    2010-01-01

    A novel physico-chemical mechanism of the Watson-Crick DNA base pair Gua.Cyt tautomerization Gua.Cyt*Gua.CytGua*.Cyt (mutagenic tautomers of bases are marked by asterisks) have been revealed and realized in a pathway of single proton transfer through two mutual isoenergetic transition states with Gibbs free energy of activation 30.4 and 30.6 kcal/mol and they are ion pairs stabilized by three (N2H...N3, N1H...N4- and O6+H...N4-) and five (N2H...O2, N1H...O2, N1H...N3, O6+H...N4- and 06+H...N4-) H-bonds accordingly. Stable base pairs Gua-Cyt* and Gua*.Cyt which dissociate comparably easy into monomers have acceptable relative Gibbs energies--12.9 and 14.3 kcal/mol--for the explanation of the nature of the spontaneous transitions of DNA replication. Results are obtained at the MP2/6-311++G(2df,pd)//B3LYP/6-31 1++G(d,p) level of theory in vacuum approach.

  19. O⁶-carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine.

    Science.gov (United States)

    Zhang, Fang; Tsunoda, Masaru; Kikuchi, Yuji; Wilkinson, Oliver; Millington, Christopher L; Margison, Geoffrey P; Williams, David M; Takénaka, Akio

    2014-06-01

    N-Nitrosation of glycine and its derivatives generates potent alkylating agents that can lead to the formation of O(6)-carboxymethylguanine (O(6)-CMG) in DNA. O(6)-CMG has been identified in DNA derived from human colon tissue and its occurrence has been linked to diets high in red and processed meats, implying an association with the induction of colorectal cancer. By analogy to O(6)-methylguanine, O(6)-CMG is expected to be mutagenic, inducing G-to-A mutations that may be the molecular basis of increased cancer risk. Previously, the crystal structure of the DNA dodecamer d(CGCG[O(6)-CMG]ATTCGCG) has been reported, in which O(6)-CMG forms a Watson-Crick-type pair with thymine similar to the canonical A:T pair. In order to further investigate the versatility of O(6)-CMG in base-pair formation, the structure of the DNA dodecamer d(CGC[O(6)-CMG]AATTTGCG) containing O(6)-CMG at a different position has been determined by X-ray crystallography using four crystal forms obtained under conditions containing different solvent ions (Sr(2+), Ba(2+), Mg(2+), K(+) or Na(+)) with and without Hoechst 33258. The most striking finding is that the pairing modes of O(6)-CMG with T are quite different from those previously reported. In the present dodecamer, the T bases are displaced (wobbled) into the major groove to form a hydrogen bond between the thymine N(3) N-H and the carboxyl group of O(6)-CMG. In addition, a water molecule is bridged through two hydrogen bonds between the thymine O(2) atom and the 2-amino group of O(6)-CMG to stabilize the pairing. These interaction modes commonly occur in the four crystal forms, regardless of the differences in crystallization conditions. The previous and the present results show that O(6)-CMG can form a base pair with T in two alternative modes: the Watson-Crick type and a high-wobble type, the nature of which may depend on the DNA-sequence context.

  20. Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation.

    Science.gov (United States)

    Sampoli Benítez, Benedetta A; Arora, Karunesh; Balistreri, Lisa; Schlick, Tamar

    2008-12-31

    DNA polymerase X (pol X) from the African swine fever virus is a 174-amino-acid repair polymerase that likely participates in a viral base excision repair mechanism, characterized by low fidelity. Surprisingly, pol X's insertion rate of the G*G mispair is comparable to that of the four Watson-Crick base pairs. This behavior is in contrast with another X-family polymerase, DNA polymerase beta (pol beta), which inserts G*G mismatches poorly, and has higher DNA repair fidelity. Using molecular dynamics simulations, we previously provided support for an induced-fit mechanism for pol X in the presence of the correct incoming nucleotide. Here, we perform molecular dynamics simulations of pol X/DNA complexes with different incoming incorrect nucleotides in various orientations [C*C, A*G, and G*G (anti) and A*G and G*G (syn)] and compare the results to available kinetic data and prior modeling. Intriguingly, the simulations reveal that the G*G mispair with the incoming nucleotide in the syn configuration undergoes large-scale conformational changes similar to that observed in the presence of correct base pair (G*C). The base pairing in the G*G mispair is achieved via Hoogsteen hydrogen bonding with an overall geometry that is well poised for catalysis. Simulations for other mismatched base pairs show that an intermediate closed state is achieved for the A*G and G*G mispair with the incoming dGTP in anti conformation, while the protein remains near the open conformation for the C*C and the A*G syn mismatches. In addition, catalytic site geometry and base pairing at the nascent template-incoming nucleotide interaction reveal distortions and misalignments that range from moderate for A*G anti to worst for the C*C complex. These results agree well with kinetic data for pol X and provide a structural/dynamic basis to explain, at atomic level, the fidelity of this polymerase compared with other members of the X family. In particular, the more open and pliant active site of pol X

  1. Development of a membrane adsorber based capture step for the purification of yellow fever virus.

    Science.gov (United States)

    Pato, Tânia P; Souza, Marta Cristina O; Silva, Andréa N M R; Pereira, Renata C; Silva, Marlon V; Caride, Elena; Gaspar, Luciane P; Freire, Marcos S; Castilho, Leda R

    2014-05-19

    Yellow fever (YF) is an endemic disease in some tropical areas of South America and Africa that presents lethality rate between 20 and 50%. There is no specific treatment and to control this disease a highly effective live-attenuated egg based vaccine is widely used for travelers and residents of areas where YF is endemic. However, recent reports of rare, sometimes fatal, adverse events post-vaccination have raised concerns. In order to increase safety records, alternative strategies should be considered, such as developing a new inactivated vaccine using a cell culture based technology, capable of meeting the demands in cases of epidemic. With this goal, the production of YF virus in Vero cells grown on microcarriers and its subsequent purification by chromatographic techniques was studied. In this work we investigate the capture step of the purification process of the YF virus. At first, virus stability was studied over a wide pH range, showing best results for the alkaline region. Considering this result and the pI of the envelope protein previously determined in silico, a strong anion exchanger was considered most suitable. Due to the easy scalability, simplicity to handle, absence of diffusional limitations and suitability for virus handling of membrane adsorbers, a Q membrane was evaluated. The amount of antigen adsorbed onto the membrane was investigated within the pH range for virus stability, and the best pH for virus adsorption was considered to be 8.5. Finally, studies on gradient and step elution allowed to determine the most adequate salt concentration for washing (0.15M) and virus elution (0.30 M). Under these operating conditions, it was shown that this capture step is quite efficient, showing high product recovery (93.2±30.3%) and efficient DNA clearance (0.9±0.3 ng/dose).

  2. Cold Fermions with Pairing Interactions: New Results Based on Fluiddynamical Descriptions

    Science.gov (United States)

    Capuzzi, P.; Hernández, E. S.; Szybisz, L.

    2012-03-01

    We present a rigorous derivation of the moment hierarchy of the density and pair density matrices of a two species fermion superfluid in coordinate representation. We discuss the tools to truncate at any desired level and present the derivation of the Extended Superfluid Thomas-Fermi (ESTF) fluiddynamical scheme. In order to establish the equation of state in equilibrium to be incorporated in the truncation, we extend the method of Papenbrock and Bertsch. We examine the dynamics of fluctuations in homogeneous fermion matter and show that it is consistent with the ordinary Random-Phase-approximation. We discuss some numerical results for equilibrium profiles and collective fluctuations of trapped cold gases.

  3. A Practical Parallel Algorithm for All-Pair Shortest Path Based on Pipelining

    Institute of Scientific and Technical Information of China (English)

    Hua Wang; Ling Tian; Chun-Hua Jiang

    2008-01-01

    On the basis of Floyd algorithm with the extended path matrix, a parallel algorithm which resolves all-pair shortest path (APSP) problem on cluster environment is analyzed and designed. Meanwhile, the parallel APSP pipelining algorithm makes full use of overlapping technique between computation and communication. Compared with broadcast operation, the parallel algorithm reduces communication cost. This algorithm has been implemented on MPI on PC-cluster. The theoretical analysis and experimental results show that the parallel algorithm is an efficient and scalable algorithm.

  4. An FPGA-Based Multiple-Axis Velocity Controller and Stepping Motors Drives Design

    Directory of Open Access Journals (Sweden)

    Lai Chiu-Keng

    2016-01-01

    Full Text Available A Field Programmable Gate Array based system is a great hardware platform to support the implementation of hardware controllers such as PID controller and fuzzy controller. It is also programmed as hardware accelerator to speed up the mathematic calculation and greatly enhance the performance as applied to motor drive and motion control. Furthermore, the open structure of FPGA-based system is suitable for those designs with the ability of parallel processing or soft code processor embedded. In this paper, we apply the FPGA to a multi-axis velocity controller design. The developed system integrated three functions inside the FPGA chip, which are respectively the stepping motor drive, the multi-axis motion controller and the motion planning. Furthermore, an embedded controller with a soft code processor compatible to 8051 micro-control unit (MCU is built to handle the data transfer between the FPGA board and host PC. The MCU is also used to initialize the motion control and run the interpolator. The designed system is practically applied to a XYZ motion platform which is driven by stepping motors to verify its performance.

  5. Path integral molecular dynamics method based on a pair density matrix approximation: An algorithm for distinguishable and identical particle systems

    Science.gov (United States)

    Miura, Shinichi; Okazaki, Susumu

    2001-09-01

    In this paper, the path integral molecular dynamics (PIMD) method has been extended to employ an efficient approximation of the path action referred to as the pair density matrix approximation. Configurations of the isomorphic classical systems were dynamically sampled by introducing fictitious momenta as in the PIMD based on the standard primitive approximation. The indistinguishability of the particles was handled by a pseudopotential of particle permutation that is an extension of our previous one [J. Chem. Phys. 112, 10 116 (2000)]. As a test of our methodology for Boltzmann statistics, calculations have been performed for liquid helium-4 at 4 K. We found that the PIMD with the pair density matrix approximation dramatically reduced the computational cost to obtain the structural as well as dynamical (using the centroid molecular dynamics approximation) properties at the same level of accuracy as that with the primitive approximation. With respect to the identical particles, we performed the calculation of a bosonic triatomic cluster. Unlike the primitive approximation, the pseudopotential scheme based on the pair density matrix approximation described well the bosonic correlation among the interacting atoms. Convergence with a small number of discretization of the path achieved by this approximation enables us to construct a method of avoiding the problem of the vanishing pseudopotential encountered in the calculations by the primitive approximation.

  6. Infrared spectrum of the Ag(+)-(pyridine)2 ionic complex: probing interactions in artificial metal-mediated base pairing.

    Science.gov (United States)

    Chakraborty, Shamik; Dopfer, Otto

    2011-07-11

    The isolated pyridine-Ag(+)-pyridine unit (Py-Ag(+)-Py) is employed as a model system to characterize the recently observed Ag(+)-mediated base pairing in DNA oligonucleotides at the molecular level. The structure and infrared (IR) spectrum of the Ag(+)-Py(2) cationic complex are investigated in the gas phase by IR multiple-photon dissociation (IRMPD) spectroscopy and quantum chemical calculations to determine the preferred metal-ion binding site and other salient properties of the potential-energy surface. The IRMPD spectrum has been obtained in the 840-1720 cm(-1) fingerprint region by coupling the IR free electron laser at the Centre Laser Infrarouge d'Orsay (CLIO) with a Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with an electrospray ionization source. The spectroscopic results are interpreted with quantum chemical calculations conducted at the B3LYP/aug-cc-pVDZ level. The analysis of the IRMPD spectrum is consistent with a σ complex, in which the Ag(+) ion binds to the nitrogen lone pairs of the two Py ligands in a linear configuration. The binding motif of Py-Ag(+)-Py in the gas phase is the same as that observed in Ag(+)-mediated base pairing in solution. Ag(+) bonding to the π-electron system of the aromatic ring is predicted to be a substantially less-favorable binding motif.

  7. Weighted profile likelihood-based confidence interval for the difference between two proportions with paired binomial data.

    Science.gov (United States)

    Pradhan, Vivek; Saha, Krishna K; Banerjee, Tathagata; Evans, John C

    2014-07-30

    Inference on the difference between two binomial proportions in the paired binomial setting is often an important problem in many biomedical investigations. Tang et al. (2010, Statistics in Medicine) discussed six methods to construct confidence intervals (henceforth, we abbreviate it as CI) for the difference between two proportions in paired binomial setting using method of variance estimates recovery. In this article, we propose weighted profile likelihood-based CIs for the difference between proportions of a paired binomial distribution. However, instead of the usual likelihood, we use weighted likelihood that is essentially making adjustments to the cell frequencies of a 2 × 2 table in the spirit of Agresti and Min (2005, Statistics in Medicine). We then conduct numerical studies to compare the performances of the proposed CIs with that of Tang et al. and Agresti and Min in terms of coverage probabilities and expected lengths. Our numerical study clearly indicates that the weighted profile likelihood-based intervals and Jeffreys interval (cf. Tang et al.) are superior in terms of achieving the nominal level, and in terms of expected lengths, they are competitive. Finally, we illustrate the use of the proposed CIs with real-life examples.

  8. A Search for Spectral Galaxy Pairs of Overlapping Galaxies based on Fuzzy Recognition

    CERN Document Server

    Yang, Haifeng; Chen, Xiaoyan; Zhang, Jifu; Hou, Wen; Cai, Jianghui; Wei, Peng; Ren, Juanjuan; Liu, Xiaojie; Zhao, Yongheng

    2014-01-01

    The Spectral Galaxy Pairs (SGPs) are de?ned as the composite galaxy spectra which contain two independent redshift systems. These spectra are useful for studying dust properties of the foreground galaxies. In this paper, a total of 165 spectra of SGPs are mined out from Sloan Digital Sky Survey (SDSS) Data Release 9 (DR9) using the concept of membership degree from the fuzzy set theory particularly de?ned to be suitable for fuzzily identifying emission lines. The spectra and images of this sample are classi?ed according to the membership degree and their image features, respectively. Many of these 2nd redshift systems are too small or too dim to select from the SDSS images alone, making the sample a potentially unique source of information on dust e?ects in low-luminosity or low-surface-brightness galaxies that are underrepresented in morphological pair samples. The dust extinction of the objects with high membership degree is also estimated by Balmer decrement. Additionally, analyses for a series of spectros...

  9. A simplified concentration series to produce a pair of 2D asynchronous spectra based on the DAOSD approach

    Science.gov (United States)

    Kang, Xiaoyan; He, Anqi; Guo, Ran; Zhai, Yanjun; Xu, Yizhuang; Noda, Isao; Wu, Jinguang

    2016-11-01

    We propose a substantially simplified approach to construct a pair of 2D asynchronous spectra based on the DAOSD approach proposed in our previous papers. By using a new concentration series, only three 1D spectra are used to generate a pair of 2D correlation spectra together with two reference spectra. By using this method, the previous problem of labor intensive traditional DAOSD approach has been successfully addressed. We apply the new approach to characterize intermolecular interaction between acetonitrile and butanone dissolved in carbon tetrachloride. The existence of intermolecular interaction between the two solutes can be confirmed by the presence of a cross peak in the resultant 2D IR spectra. In addition, the absence of cross peak around (2254, 2292) in Ψbutanone provides another experimental evidence to reveal the intrinsic relationship between the Ctbnd N stretching band and an overtone band (δCH3+νC-C).

  10. Microstructural and electrical properties of cordierite-based ceramics obtained after two-step sintering technique

    Directory of Open Access Journals (Sweden)

    Obradović Nina

    2016-01-01

    Full Text Available Cordierite-based ceramic materials are attracting much interest for their various applications in industry, for manufacturing multilayer circuit boards, catalytic converters, filters, thermal insulation, kiln furniture, components of portable electronic devices, etc. In order to reduce production costs and modify cordierite-based materials, mechanical activation can be used. In this study, microstructural and electrical properties of mechanically activated MgO-Al2O3-SiO2 system have been analyzed. The mixtures of MgO-Al2O3-SiO2 powders were mechanically activated in a planetary ball mill for the time periods from 0 to 160 min. Morphological investigations have been performed on the obtained powders. The effects of activation and two-step sintering process on microstructure were investigated by scanning electron microscopy (SEM. Electrical measurements showed variations of the dielectric constant (εr and loss tangent (tan δ as a function of time of mechanical treatment.

  11. First Steps Toward Incorporating Image Based Diagnostics Into Particle Accelerator Control Systems Using Convolutional Neural Networks

    Energy Technology Data Exchange (ETDEWEB)

    Edelen, A. L.; Biedron, S. G.; Milton, S. V.; Edelen, J. P.

    2016-12-16

    At present, a variety of image-based diagnostics are used in particle accelerator systems. Often times, these are viewed by a human operator who then makes appropriate adjustments to the machine. Given recent advances in using convolutional neural networks (CNNs) for image processing, it should be possible to use image diagnostics directly in control routines (NN-based or otherwise). This is especially appealing for non-intercepting diagnostics that could run continuously during beam operation. Here, we show results of a first step toward implementing such a controller: our trained CNN can predict multiple simulated downstream beam parameters at the Fermilab Accelerator Science and Technology (FAST) facility's low energy beamline using simulated virtual cathode laser images, gun phases, and solenoid strengths.

  12. Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

    Institute of Scientific and Technical Information of China (English)

    Muralidhar L Hegde; Tapas K Hazra; Sankar Mitra

    2008-01-01

    Base excision repair (BER) is an evolutionarily conserved process for maintaining genomic integrity by eliminating several dozen damaged (oxidized or alkylated) or inappropriate bases that are generated endogenously or induced by genotoxicants, predominantly, reactive oxygen species (ROS). BER involves 4-5 steps starting with base excision by a DNA glycosylase, followed by a common pathway usually involving an AP-endonuclease (APE) to generate 3' OH terminus at the damage site, followed by repair synthesis with a DNA polymerase and nick sealing by a DNA ligase. This pathway is also responsible for repairing DNA single-strand breaks with blocked termini directly generated by ROS. Nearly all glycosylases, far fewer than their substrate lesions particularly for oxidized bases, have broad and overlapping substrate range, and could serve as back-up enzymes in vivo. In contrast, mammalian cells encode only one APE, APEl, unlike two APEs in lower organisms. In spite of overall similarity, BER with distinct subpathways in the mammals is more complex than in E.coli. The glycosylases form complexes with downstream proteins to carry out efficient repair via distinct subpathways one of which, responsible for repair of strand breaks with 3' phosphate ter-mini generated by the NEIL family glycosylases or by ROS, requires the phosphatase activity of polynucleotide kinase instead of APEl. Different complexes may utilize distinct DNA polymerases and ligases. Mammalian glycosylases have nonconserved extensions at one of the termini, dispensable for enzymatic activity but needed for interaction with other BER and non-BER proteins for complex formation and organelle targeting. The mammalian enzymes are sometimes covalently modified which may affect activity and complex formation. The focus of this review is on the early steps in mammalian BER for oxidized damage.

  13. DFT study on the attacking mechanisms of H and OH radicals to G-C and A-T base pairs in water

    Energy Technology Data Exchange (ETDEWEB)

    Okutsu, N.; Shimamura, K.; Shimizu, E.; Kurita, N., E-mail: kurita@cs.tut.ac.jp [Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Aichi, 441-8580 (Japan); Shulga, S. [Institute for Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv (Ukraine); Danilov, V. I. [Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv (Ukraine)

    2016-02-01

    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-C 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.

  14. XP结对编程探究%Research of Pair Programming Based on Extreme Programming

    Institute of Scientific and Technical Information of China (English)

    李云超

    2009-01-01

    结对编程(Pair Programming)是限编程(Extreme Programming,简称XP)的十二个实践之一.它指的是两个软件开发人员共用一台计算机.其中一个人负责具体细节工作,而另一个人关注整体,但这两个人的角色可以随时互换.这是一种轻量、高效、低风险、柔性、可预测、科学而充满乐趣的软件开发方式.结对编程可改进设计质量、减少程序缺陷、降低人员风险、提高技术技能和团队合作精神.

  15. Alpha–beta monitoring system based on pair of simultaneous Multi-Wire Proportional Counters

    Energy Technology Data Exchange (ETDEWEB)

    Wengrowicz, U.; Amidan, D. [Department of Nuclear Engineering, Ben Gurion University of the Negev, Beer-Sheva 84105 (Israel); NRC-Negev, P.O. Box 9001, Beer-Sheva 84190 (Israel); Orion, I. [Department of Nuclear Engineering, Ben Gurion University of the Negev, Beer-Sheva 84105 (Israel)

    2016-08-11

    A new approach for a simultaneous alpha–beta Multi-wire Proportional Counter (MWPC) is presented. The popular approach for alpha–beta monitoring systems consists of a large area MWPC using noble gas flow such as Argon Methane. This method of measurement is effective but requires large-scale and expensive maintenance due to the needs of gas flow control and periodic replacements. In this work, a pair of simultaneous MWPCs for alpha–beta measuring is presented. The developed detector consists of a sealed gas MWPC sensor for beta particles, behind a free air alpha sensor. This approach allows effective simultaneous detection and discrimination of both alpha and beta radiation without the maintenance cost noble gas flow required for unsealed detectors.

  16. Alpha-beta monitoring system based on pair of simultaneous Multi-Wire Proportional Counters

    Science.gov (United States)

    Wengrowicz, U.; Amidan, D.; Orion, I.

    2016-08-01

    A new approach for a simultaneous alpha-beta Multi-wire Proportional Counter (MWPC) is presented. The popular approach for alpha-beta monitoring systems consists of a large area MWPC using noble gas flow such as Argon Methane. This method of measurement is effective but requires large-scale and expensive maintenance due to the needs of gas flow control and periodic replacements. In this work, a pair of simultaneous MWPCs for alpha-beta measuring is presented. The developed detector consists of a sealed gas MWPC sensor for beta particles, behind a free air alpha sensor. This approach allows effective simultaneous detection and discrimination of both alpha and beta radiation without the maintenance cost noble gas flow required for unsealed detectors.

  17. The ALHAMBRA survey: An empirical estimation of the cosmic variance for merger fraction studies based on close pairs

    Science.gov (United States)

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

    2014-04-01

    Aims: Our goal is to estimate empirically the cosmic variance that affects merger fraction studies based on close pairs for the first time. Methods: We compute the merger fraction from photometric redshift close pairs with 10 h-1 kpc ≤ rp ≤ 50 h-1 kpc and Δv ≤ 500 km s-1 and measure it in the 48 sub-fields of the ALHAMBRA survey. We study the distribution of the measured merger fractions that follow a log-normal function and estimate the cosmic variance σv as the intrinsic dispersion of the observed distribution. We develop a maximum likelihood estimator to measure a reliable σv and avoid the dispersion due to the observational errors (including the Poisson shot noise term). Results: The cosmic variance σv of the merger fraction depends mainly on (i) the number density of the populations under study for both the principal (n1) and the companion (n2) galaxy in the close pair and (ii) the probed cosmic volume Vc. We do not find a significant dependence on either the search radius used to define close companions, the redshift, or the physical selection (luminosity or stellar mass) of the samples. Conclusions: We have estimated the cosmic variance that affects the measurement of the merger fraction by close pairs from observations. We provide a parametrisation of the cosmic variance with n1, n2, and Vc, σv ∝ n1-0.54Vc-0.48 (n_2/n_1)-0.37 . Thanks to this prescription, future merger fraction studies based on close pairs could properly account for the cosmic variance on their results. 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 (IAA-CSIC).Appendix is available in electronic form at http://www.aanda.org

  18. One-Step Targeted Minimum Loss-based Estimation Based on Universal Least Favorable One-Dimensional Submodels.

    Science.gov (United States)

    van der Laan, Mark; Gruber, Susan

    2016-05-01

    Consider a study in which one observes n independent and identically distributed random variables whose probability distribution is known to be an element of a particular statistical model, and one is concerned with estimation of a particular real valued pathwise differentiable target parameter of this data probability distribution. The targeted maximum likelihood estimator (TMLE) is an asymptotically efficient substitution estimator obtained by constructing a so called least favorable parametric submodel through an initial estimator with score, at zero fluctuation of the initial estimator, that spans the efficient influence curve, and iteratively maximizing the corresponding parametric likelihood till no more updates occur, at which point the updated initial estimator solves the so called efficient influence curve equation. In this article we construct a one-dimensional universal least favorable submodel for which the TMLE only takes one step, and thereby requires minimal extra data fitting to achieve its goal of solving the efficient influence curve equation. We generalize these to universal least favorable submodels through the relevant part of the data distribution as required for targeted minimum loss-based estimation. Finally, remarkably, given a multidimensional target parameter, we develop a universal canonical one-dimensional submodel such that the one-step TMLE, only maximizing the log-likelihood over a univariate parameter, solves the multivariate efficient influence curve equation. This allows us to construct a one-step TMLE based on a one-dimensional parametric submodel through the initial estimator, that solves any multivariate desired set of estimating equations.

  19. First Steps Towards AN Integrated Citygml-Based 3d Model of Vienna

    Science.gov (United States)

    Agugiaro, G.

    2016-06-01

    This paper presents and discusses the results regarding the initial steps (selection, analysis, preparation and eventual integration of a number of datasets) for the creation of an integrated, semantic, three-dimensional, and CityGML-based virtual model of the city of Vienna. CityGML is an international standard conceived specifically as information and data model for semantic city models at urban and territorial scale. It is being adopted by more and more cities all over the world. The work described in this paper is embedded within the European Marie-Curie ITN project "Ci-nergy, Smart cities with sustainable energy systems", which aims, among the rest, at developing urban decision making and operational optimisation software tools to minimise non-renewable energy use in cities. Given the scope and scale of the project, it is therefore vital to set up a common, unique and spatio-semantically coherent urban model to be used as information hub for all applications being developed. This paper reports about the experiences done so far, it describes the test area and the available data sources, it shows and exemplifies the data integration issues, the strategies developed to solve them in order to obtain the integrated 3D city model. The first results as well as some comments about their quality and limitations are presented, together with the discussion regarding the next steps and some planned improvements.

  20. Beam steering and deflecting device using step-based micro-blazed grating

    Science.gov (United States)

    Yang, Junbo; Su, Xianyu; Xu, Ping; Gu, Zheng

    2008-08-01

    The rapidly evolving demands of optical communications and optical switching systems have created a new market for high capacity all-optical beam steering and deflecting techniques. One technology potentially capable of realizing such systems uses the multistep micro-blazed grating optical beam deflectors based on binary and multiple-phase modulation methods. The micro-optical element has been fabricated by introducing very large scale integration (VLSI), stepping photolithography and reactive ion etching (RIE), which can realize beam steering, deflecting, splitting, and switching in free space, and its diffraction properties are determined by the blazed-grating parameters, such as the number of steps, grating depth, grating period, as well as blazed profile. The theoretical analysis and primarily experimental result show that this phase-type element has the advantages of high diffractive efficiency, low cross talk, small feature size, and high reliability due to nonmechanical beam steering without any moving parts. Hence it is ideally suited to applications in optical communication and optical interconnection network.

  1. A critical base pair in k-turns that confers folding characteristics and correlates with biological function

    Science.gov (United States)

    McPhee, Scott A.; Huang, Lin; Lilley, David M. J.

    2014-10-01

    Kink turns (k-turns) are widespread elements in RNA that mediate tertiary contacts by kinking the helical axis. We have found that the ability of k-turns to undergo ion-induced folding is conferred by a single base pair that follows the conserved A·G pairs, that is, the 3b·3n position. A Watson-Crick pair leads to an inability to fold in metal ions alone, while 3n=G or 3b=C (but not both) permits folding. Crystallographic study reveals two hydrated metal ions coordinated to O6 of G3n and G2n of Kt-7. Removal of either atom impairs Mg2+-induced folding in solution. While SAM-I riboswitches have 3b·3n sequences that would predispose them to ion-induced folding, U4 snRNA are strongly biased to an inability to such folding. Thus riboswitch sequences allow folding to occur independently of protein binding, while U4 should remain unfolded until bound by protein. The empirical rules deduced for k-turn folding have strong predictive value.

  2. The ALHAMBRA survey: an empirical estimation of the cosmic variance for merger fraction studies based on close pairs

    CERN Document Server

    López-Sanjuan, C; Hernández-Monteagudo, C; Varela, J; Molino, A; Arnalte-Mur, P; Ascaso, B; Castander, F J; Fernández-Soto, A; Huertas-Company, M; Márquez, I; Martínez, V J; Masegosa, J; Moles, M; Pović, M; Aguerri, J A L; Alfaro, E; Benítez, N; Broadhurst, T; Cabrera-Caño, J; Cepa, J; Cerviño, M; Cristóbal-Hornillos, D; Del Olmo, A; Delgado, R M González; Husillos, C; Infante, L; Perea, J; Prada, F; Quintana, J M

    2014-01-01

    Our goal is to estimate empirically, for the first time, the cosmic variance that affects merger fraction studies based on close pairs. We compute the merger fraction from photometric redshift close pairs with 10h^-1 kpc <= rp <= 50h^-1 kpc and Dv <= 500 km/s, and measure it in the 48 sub-fields of the ALHAMBRA survey. We study the distribution of the measured merger fractions, that follow a log-normal function, and estimate the cosmic variance sigma_v as the intrinsic dispersion of the observed distribution. We develop a maximum likelihood estimator to measure a reliable sigma_v and avoid the dispersion due to the observational errors (including the Poisson shot noise term). The cosmic variance of the merger fraction depends mainly on (i) the number density of the populations under study, both for the principal (n_1) and the companion (n_2) galaxy in the close pair, and (ii) the probed cosmic volume V_c. We find a significant dependence on neither the search radius used to define close companions, t...

  3. Return and Risk of Pairs Trading Using a Simulation-Based Bayesian Procedure for Predicting Stable Ratios of Stock Prices

    Directory of Open Access Journals (Sweden)

    David Ardia

    2016-03-01

    Full Text Available We investigate the direct connection between the uncertainty related to estimated stable ratios of stock prices and risk and return of two pairs trading strategies: a conditional statistical arbitrage method and an implicit arbitrage one. A simulation-based Bayesian procedure is introduced for predicting stable stock price ratios, defined in a cointegration model. Using this class of models and the proposed inferential technique, we are able to connect estimation and model uncertainty with risk and return of stock trading. In terms of methodology, we show the effect that using an encompassing prior, which is shown to be equivalent to a Jeffreys’ prior, has under an orthogonal normalization for the selection of pairs of cointegrated stock prices and further, its effect for the estimation and prediction of the spread between cointegrated stock prices. We distinguish between models with a normal and Student t distribution since the latter typically provides a better description of daily changes of prices on financial markets. As an empirical application, stocks are used that are ingredients of the Dow Jones Composite Average index. The results show that normalization has little effect on the selection of pairs of cointegrated stocks on the basis of Bayes factors. However, the results stress the importance of the orthogonal normalization for the estimation and prediction of the spread—the deviation from the equilibrium relationship—which leads to better results in terms of profit per capital engagement and risk than using a standard linear normalization.

  4. A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties.

    Science.gov (United States)

    Tiller, Thomas; Schuster, Ingrid; Deppe, Dorothée; Siegers, Katja; Strohner, Ralf; Herrmann, Tanja; Berenguer, Marion; Poujol, Dominique; Stehle, Jennifer; Stark, Yvonne; Heßling, Martin; Daubert, Daniela; Felderer, Karin; Kaden, Stefan; Kölln, Johanna; Enzelberger, Markus; Urlinger, Stefanie

    2013-01-01

    This report describes the design, generation and testing of Ylanthia, a fully synthetic human Fab antibody library with 1.3E+11 clones. Ylanthia comprises 36 fixed immunoglobulin (Ig) variable heavy (VH)/variable light (VL) chain pairs, which cover a broad range of canonical complementarity-determining region (CDR) structures. The variable Ig heavy and Ig light (VH/VL) chain pairs were selected for biophysical characteristics favorable to manufacturing and development. The selection process included multiple parameters, e.g., assessment of protein expression yield, thermal stability and aggregation propensity in fragment antigen binding (Fab) and IgG1 formats, and relative Fab display rate on phage. The framework regions are fixed and the diversified CDRs were designed based on a systematic analysis of a large set of rearranged human antibody sequences. Care was taken to minimize the occurrence of potential posttranslational modification sites within the CDRs. Phage selection was performed against various antigens and unique antibodies with excellent biophysical properties were isolated. Our results confirm that quality can be built into an antibody library by prudent selection of unmodified, fully human VH/VL pairs as scaffolds.

  5. Stereo pairs in Astrophysics

    Science.gov (United States)

    Vogt, Frédéric; Wagner, Alexander Y.

    2012-01-01

    Stereoscopic visualization is seldom used in Astrophysical publications and presentations compared to other scientific fields, e.g., Biochemistry, where it has been recognized as a valuable tool for decades. We put forth the view that stereo pairs can be a useful tool for the Astrophysics community in communicating a truer representation of astrophysical data. Here, we review the main theoretical aspects of stereoscopy, and present a tutorial to easily create stereo pairs using Python. We then describe how stereo pairs provide a way to incorporate 3D data in 2D publications of standard journals. We illustrate the use of stereo pairs with one conceptual and two Astrophysical science examples: an integral field spectroscopy study of a supernova remnant, and numerical simulations of a relativistic AGN jet. We also use these examples to make the case that stereo pairs are not merely an ostentatious way to present data, but an enhancement in the communication of scientific results in publications because they provide the reader with a realistic view of multi-dimensional data, be it of observational or theoretical nature. In recognition of the ongoing 3D expansion in the commercial sector, we advocate an increased use of stereo pairs in Astrophysics publications and presentations as a first step towards new interactive and multi-dimensional publication methods.

  6. A Three Step B2B Sales Model Based on Satisfaction Judgments

    DEFF Research Database (Denmark)

    Grünbaum, Niels Nolsøe

    2015-01-01

    . The insights produces can be applied for selling companies to craft close collaborative customer relationships in a systematic a d efficient way. The process of building customer relationships will be guided through actions that yields higher satisfaction judgments leading to loyal customers and finally......This paper aims to provide a coherent, detailed and integrative understanding of the mental processes (i.e. dimensions) that industrial buyers apply when forming satisfaction judgments in adjacent to new task buying situations. A qualitative inductive research strategy is utilized in this study...... companies’ perspective. The buying center members applied satisfaction dimension when forming satisfaction judgments. Moreover, the focus and importance of the identified satisfaction dimensions fluctuated pending on the phase of the buying process. Based on the findings a three step sales model is proposed...

  7. A Three Step B2B Sales Model Based on Satisfaction Judgments

    DEFF Research Database (Denmark)

    Grünbaum, Niels Nolsøe

    2015-01-01

    . The insights produces can be applied for selling companies to craft close collaborative customer relationships in a systematic ad efficient way. The process of building customer relationships will be guided through actions that yields higher satisfaction judgments leading to loyal customers and finally......This paper aims to provide a coherent, detailed and integrative understanding of the mental processes (i.e. dimensions) that industrial buyers apply when forming satisfaction judgments in adjacent to new task buying situations. A qualitative inductive research strategy is utilized in this study...... companies‘ perspective. The buying center members applied satisfaction dimension when forming satisfaction judgments. Moreover, the focus and importance of the identified satisfaction dimensions fluctuated pending on the phase of the buying process. Based on the findings a three step sales model is proposed...

  8. CSSF MIMO RADAR: Low-Complexity Compressive Sensing Based MIMO Radar That Uses Step Frequency

    CERN Document Server

    Yu, Yao; Poor, H Vincent

    2011-01-01

    A new approach is proposed, namely CSSF MIMO radar, which applies the technique of step frequency (SF) to compressive sensing (CS) based multi-input multi-output (MIMO) radar. The proposed approach enables high resolution range, angle and Doppler estimation, while transmitting narrowband pulses. The problem of joint angle-Doppler-range estimation is first formulated to fit the CS framework, i.e., as an L1 optimization problem. Direct solution of this problem entails high complexity as it employs a basis matrix whose construction requires discretization of the angle-Doppler-range space. Since high resolution requires fine space discretization, the complexity of joint range, angle and Doppler estimation can be prohibitively high. For the case of slowly moving targets, a technique is proposed that achieves significant complexity reduction by successively estimating angle-range and Doppler in a decoupled fashion and by employing initial estimates obtained via matched filtering to further reduce the space that nee...

  9. Minimising complications in abdominoplasty: An approach based on the root cause analysis and focused preventive steps.

    Science.gov (United States)

    Rangaswamy, Mohan

    2013-05-01

    Significant complications still occur after abdominoplasty, the rate varies widely in different series. This variation suggests that there is a lot of scope for improvement. This paper reviews the various complications and also the technical improvements reported in the last 20 years. The root cause of each complication is analysed and preventive steps are suggested based on the literature and the author's own personal series with very low complication rates. Proper case selection, risk stratified prophylaxis of thromboembolism, initial synchronous liposuction, flap elevation at the Scarpa fascia level, discontinuous incremental flap dissection, vascular preservation and obliteration of the sub-flap space by multiple sutures emerge as the strongest preventive factors. It is proposed that most of the complications of abdominoplasty are preventable and that it is possible to greatly enhance the aesthetic and safety profile of this surgery.

  10. Minimising complications in abdominoplasty: An approach based on the root cause analysis and focused preventive steps

    Directory of Open Access Journals (Sweden)

    Mohan Rangaswamy

    2013-01-01

    Full Text Available Significant complications still occur after abdominoplasty, the rate varies widely in different series. This variation suggests that there is a lot of scope for improvement. This paper reviews the various complications and also the technical improvements reported in the last 20 years. The root cause of each complication is analysed and preventive steps are suggested based on the literature and the author′s own personal series with very low complication rates. Proper case selection, risk stratified prophylaxis of thromboembolism, initial synchronous liposuction, flap elevation at the Scarpa fascia level, discontinuous incremental flap dissection, vascular preservation and obliteration of the sub-flap space by multiple sutures emerge as the strongest preventive factors. It is proposed that most of the complications of abdominoplasty are preventable and that it is possible to greatly enhance the aesthetic and safety profile of this surgery.

  11. Phosphorus recovery by one or two-step technology with use of acids and bases

    Energy Technology Data Exchange (ETDEWEB)

    Stark, Kristina; Hultman, Bengt

    2003-07-01

    The method of using sludge fractionation is considered to be a sustainable solution where the sludge is seen as the raw material from which products are recovered. This paper will present solutions of advanced technology system for a large wastewater treatment plant. Use of enhanced biological phosphorus removal and fractionation of the sludge in two stages is advantageous both with respect to low necessary chemical and energy demands and recovery efficiency. Phosphorous recovery may be based on one- or two-step technology. Experimental studies have shown that it is possible to recover phosphorus from sludge by the combination of supercritical water oxidation process and alkaline leaching. When the concentration of sodium hydroxide is around 1 M, approximate 50 % of total phosphorus is recovered in room temperature. Meanwhile, over 98 % of the soluble phosphorus is recovered from the liquid phase by adding calcium chloride (CaCl{sub 2}). (author)

  12. A Back-stepping Based Trajectory Tracking Controller for a Non-chained Nonholonomic Spherical Robot

    Institute of Scientific and Technical Information of China (English)

    Zhan Qiang; Liu Zengbo; Cai Yao

    2008-01-01

    Spherical robot has good static and dynamic stability, which provides it with strong viability in hostile environment, but the lack of effective control methods has hindered its application and development. This article deals with the dynamic trajectory tracking problem of the spherical robot BHQ-2 designed for unmanned environment exploration. The dynamic model of the spherical robot is established with a simplified Boltzmann-Hamel equation, based on which a trajectory tracking controller is designed by using the back-stepping method. The convergence of the controller is proved with the Lyapunov stability theory. Numerical simulations show that with the controller the robot can globally and asymptotically track desired trajectories, both linear and circular.

  13. Reversible phospholipid nanogels for deoxyribonucleic acid fragment size determinations up to 1500 base pairs and integrated sample stacking.

    Science.gov (United States)

    Durney, Brandon C; Bachert, Beth A; Sloane, Hillary S; Lukomski, Slawomir; Landers, James P; Holland, Lisa A

    2015-06-23

    Phospholipid additives are a cost-effective medium to separate deoxyribonucleic acid (DNA) fragments and possess a thermally-responsive viscosity. This provides a mechanism to easily create and replace a highly viscous nanogel in a narrow bore capillary with only a 10°C change in temperature. Preparations composed of dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) self-assemble, forming structures such as nanodisks and wormlike micelles. Factors that influence the morphology of a particular DMPC-DHPC preparation include the concentration of lipid in solution, the temperature, and the ratio of DMPC and DHPC. It has previously been established that an aqueous solution containing 10% phospholipid with a ratio of [DMPC]/[DHPC]=2.5 separates DNA fragments with nearly single base resolution for DNA fragments up to 500 base pairs in length, but beyond this size the resolution decreases dramatically. A new DMPC-DHPC medium is developed to effectively separate and size DNA fragments up to 1500 base pairs by decreasing the total lipid concentration to 2.5%. A 2.5% phospholipid nanogel generates a resolution of 1% of the DNA fragment size up to 1500 base pairs. This increase in the upper size limit is accomplished using commercially available phospholipids at an even lower material cost than is achieved with the 10% preparation. The separation additive is used to evaluate size markers ranging between 200 and 1500 base pairs in order to distinguish invasive strains of Streptococcus pyogenes and Aspergillus species by harnessing differences in gene sequences of collagen-like proteins in these organisms. For the first time, a reversible stacking gel is integrated in a capillary sieving separation by utilizing the thermally-responsive viscosity of these self-assembled phospholipid preparations. A discontinuous matrix is created that is composed of a cartridge of highly viscous phospholipid assimilated into a separation matrix

  14. Physicochemical Properties of Jatropha Oil-Based Polyol Produced by a Two Steps Method

    Directory of Open Access Journals (Sweden)

    Sariah Saalah

    2017-03-01

    Full Text Available A low cost, abundant, and renewable vegetable oil source has been gaining increasing attention due to its potential to be chemically modified to polyol and thence to become an alternative replacement for the petroleum-based polyol in polyurethane production. In this study, jatropha oil-based polyol (JOL was synthesised from non-edible jatropha oil by a two steps process, namely epoxidation and oxirane ring opening. In the first step, the effect of the reaction temperature, the molar ratio of the oil double bond to formic acid, and the reaction time on the oxirane oxygen content (OOC of the epoxidised jatropha oil (EJO were investigated. It was found that 4.3% OOC could be achieved with a molar ratio of 1:0.6, a reaction temperature of 60 °C, and 4 h of reaction. Consequently, a series of polyols with hydroxyl numbers in the range of 138–217 mgKOH/g were produced by oxirane ring opening of EJOs, and the physicochemical and rheological properties were studied. Both the EJOs and the JOLs are liquid and have a number average molecular weight (Mn in the range of 834 to 1457 g/mol and 1349 to 2129 g/mol, respectively. The JOLs exhibited Newtonian behaviour, with a low viscosity of 430–970 mPas. Finally, the JOL with a hydroxyl number of 161 mgKOH/g was further used to synthesise aqueous polyurethane dispersion, and the urethane formation was successfully monitored by Fourier Transform Infrared (FTIR.

  15. On the role of the cis Hoogsteen:sugar-edge family of base pairs in platforms and triplets-quantum chemical insights into RNA structural biology.

    Science.gov (United States)

    Sharma, Purshotam; Sponer, Judit E; Sponer, Jirí; Sharma, Sitansh; Bhattacharyya, Dhananjay; Mitra, Abhijit

    2010-03-11

    Base pairs belonging to the cis Hoogsteen:sugar-edge (H:S) family play important structural roles in folded RNA molecules. Several of these are present in internal loops, where they are involved in interactions leading to planar dinucleotide platforms which stabilize higher order structures such as base triplets and quartets. We report results of analysis of 30 representative examples spanning 16 possible base pair combinations, with several of them showing multimodality of base pairing geometry. The geometries of 23 of these base pairs were modeled directly from coordinates extracted from RNA crystal structures. The other seven were predicted structures which were modeled on the basis of observed isosteric analogues. After appropriate satisfaction of residual valencies, these structures were relaxed using the B3LYP/6-31G(d,p) method and interaction energies were derived at the RIMP2/aug-cc-pVDZ level of theory. The geometries for each of the studied base pairs have been characterized in terms of the number and nature of H-bonds, rmsd values observed on optimization, base pair geometrical parameters, and sugar pucker analysis. In addition to its evaluation, the nature of intermolecular interaction in these complexes was also analyzed using Morokuma decomposition. The gas phase interaction energies range between -5.2 and -20.6 kcal/mol and, in contrast to the H:S trans base pairs, show enhanced relative importance of the electron correlation component, indicative of the greater role of dispersion energy in stabilization of these base pairs. The rich variety of hydrogen bonding pattern, involving the flexible sugar edge, appears to hold the key to several features of structural motifs, such as planarity and propensity to participate in triplets, observed in this family of base pairs. This work explores these aspects by integrating database analysis, and detailed base pairing geometry analysis at the atomistic level, with ab initio computation of interaction energies

  16. 基于XSLT的通用STEP-NC后置处理器开发%Development of universal STEP-NC post processor based on XSLT

    Institute of Scientific and Technical Information of China (English)

    肖文磊; 郇极

    2012-01-01

    To make STandard for the Exchange of Product model data-Numerical Control(STEP-NC)was compatible with traditional NC systems,the special STEP-NC post-processor was necessary for each traditional NC system.Thus,a general post-processor was created to reduce the development workloads and difficulties in constructing the special STEP-NC post-processor.By using STEP-NC code in eXtensible Markup Language(XML)mode as the post-processor input and the eXtensible Stylesheet Language Transformations(XSLT)based transformation mechanism,the post processing oriented to unification of different NC machining equipments was realized.According to transfer principle and requirement of XSLT,the data converters for EXPRESS-X and P21-P28 were individually developed.A general post-processor was constructed which took P28 file as data input and XSLT style sheet as machine equipment interface format.A cutting robot and a 3-Axis NC machining were taken as application examples,which accepted robot language and G-code respectively as the cutter location data.The results testified and verified the functionality and feasibility of the proposed post-processor.%为了使STEP-NC兼容传统的数控系统,需要在传统数控系统上构建专用的STEP-NC后置处理器。为此,建立了一个通用的后置处理器,以降低构建专用STEP后置处理器的开发工作量和开发难度。采用可扩展标记语言模式下的STEP-NC代码作为输入和基于可扩展样式表语言转换的转换机制,实现面向不同数控加工设备统一化的后置处理过程。根据可扩展样式表语言转换原理和要求,分别开发了EXPRESS-X和P21-P28的文件格式转换器。构建了以P28格式作为输入和以XSLT样式表语言定义机床设备接口格式的通用后置处理器。以一台切削加工机器人和一台三轴数控铣床为应用实例,分别以机器人语言和G代码作为后置处理结果,对后置处理器的功能性和可行性进行了验证。

  17. Bilinear Pairing Implementation Based on Three Type Algebraic Curves%基于三类代数曲线上的双线性对实现

    Institute of Scientific and Technical Information of China (English)

    年晓宇; 游林

    2016-01-01

    In pairings,the most common is the Tate pairing,Eta pairing and Ate pairing are the variations of the Tate pairing. For the elliptic curve y 2 + y = x 3 + x + b where b ∈ F 2 , the implementation algorithms of Tate pairing and Eta pairing in four cases are given by discussing respectively.Meanwhile,the implementation algorithms of Tate pairing and Ate pairing based on the hyperelliptic curve y 2 + y =x 5 +ax +b where a,b ∈ F 2 and the implementation algorithms of Ate pairing based on the hyperelliptic curve y 2 =x p -ax -b where a ,b ∈F p are proposed.It provides a reference for the research and application of the pairing-based cryptosystem.%双线性对中,最常见的是 Tate 对,Eta 对和 Ate 对是 Tate 对的变种。针对椭圆曲线 y 2+y =x 3+x+b,其中 b∈F 2,通过分类讨论,给出了4种情况下的 Tate 对和 Eta 对实现算法。同时,还提出了基于超椭圆曲线 y 2+y =x 5+ax+b(其中 a,b∈F 2)上的 Tate 对和 Ate 对实现算法,以及基于超椭圆曲线 y 2=x p -ax-b(其中 a,b∈F p )上的 Ate 对实现算法。为基于双线性对密码体制的研究和应用提供了一定的参考。

  18. Cryptanalysis and Improvement on "Robust EPR-Pairs-Based Quantum Secure Communication with Authentication Resisting Collective Noise"

    Science.gov (United States)

    Yue, Qiu-Ling; Yu, Chao-Hua; Liu, Bin; Wang, Qing-Le

    2016-10-01

    Recently, Chang et al. [Sci Chin-Phys Mech Astron. 57(10), 1907-1912, 2014] proposed two robust quantum secure communication protocols with authentication based on Einstein-Podolsky-Rosen (EPR) pairs, which can resist collective noise. In this paper, we analyze the security of their protocols, and show that there is a kind of security flaw in their protocols. By a kind of impersonation attack, the eavesdropper can obtain half of the message on average. Furthermore, an improved method of their protocols is proposed to close the security loophole.

  19. A 2×2 SOI mach-zehnder thermo-optical switch based on strongly guided paired multimode interference couplers

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A silicon-on-insulator 2×2 Mach-Zehnder thermo-optical switch is developed based on strongly guided paired multimode interference couplers. The multimode-interference couplers were etched deeply for improving coupler characteristics such as self-imaging quality, uniformity and fabrication tolerance. The proposed switch achieves good performances, including a low insertion loss of -11 .OdB, a fiber-waveguide coupling loss of -4.3dB and a fast response speed measured to be 3.5 and 8.8 μs for raise and fall switching time, respectively.

  20. Characteristic analysis of a novel F-P interferometer based on a pair of FBGs with built-in LPFGs

    Institute of Scientific and Technical Information of China (English)

    WANG Chun-bao; ZHANG Wei-gang; RUAN Juan; SHANG Jia-bin; YAN Ai-dong

    2012-01-01

    The transmission characteristics of a Fabry-Pérot (F-P) interferometer based on a fiber Bragg grating (FBG) pair with a built-in long-period fiber grating (LPFG) are theoretically analyzed,and the shift of transmission interference fringe as a function of environmental refractive index is acquired.The influence of the lengths of F-P cavity,LPFG and FBG on the transmission characteristics of the proposed interferometer has been numerically investigated,and the simulation results indicate that the sensitivity of refractive index reaches 2.27 × 10-6 for an optical spectrum analyzer (OSA) with a resolution of 1 pm.

  1. Polarization entangled photon-pair source based on quantum nonlinear photonics and interferometry

    Science.gov (United States)

    Kaiser, F.; Ngah, L. A.; Issautier, A.; Delord, T.; Aktas, D.; D'Auria, V.; De Micheli, M. P.; Kastberg, A.; Labonté, L.; Alibart, O.; Martin, A.; Tanzilli, S.

    2014-09-01

    We present a versatile, high-brightness, guided-wave source of polarization entangled photons, emitted at a telecom wavelength. Photon-pairs are generated using an integrated type-0 nonlinear waveguide, and subsequently prepared in a polarization entangled state via a stabilized fiber interferometer. We show that the single photon emission wavelength can be tuned over more than 50 nm, whereas the single photon spectral bandwidth can be chosen at will over more than five orders of magnitude (from 25 MHz to 4 THz). Moreover, by performing entanglement analysis, we demonstrate a high degree of control of the quantum state via the violation of the Bell inequalities by more than 40 standard deviations. This makes this scheme suitable for a wide range of quantum optics experiments, ranging from fundamental research to quantum information applications. We report on details of the setup, as well as on the characterization of all included components, previously outlined in Kaiser et al. (Laser Phys. Lett. 10 (2013) 045202).

  2. SEMIAUTOMATIC BUILDING EXTRACTION FROM STEREOIMAGE PAIR BASED ON LINES GROUPING AND LEAST SQUARES MATCHING

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The paper presents a general paradigm of semiautomatic building extrac tion from aerial stereo image pair.In the semiautomatic extraction system,the building model is defined by selected roof type through human-machine interface and input the approximation of area where the extracted building exists.Then un der the knowledge of the roof type,low-level and mid-level processing including edge detection,straight line segments extraction and line segments grouping ar e used to establish the initial geometrical model of the roof-top.However,the initial geometrical model is not so accurate in geometry.To attain accurate res ults,a general least squares adjustment integrating the linear templates matchin g model with geometrical constraints in object-space is applied to refine the ini tial geometrical model.The adjustment model integrating the straight edge pat tern and 3D constraints together is a well-studied optimal and ant i-noise method.After gaining proper initial values,this adjustment model can f lexibly process extraction of kinds of roof types by changing or assembling the geometrical constraints in object-space.

  3. Au pair trajectories

    DEFF Research Database (Denmark)

    Dalgas, Karina Märcher

    2015-01-01

    and dreams for the future become intertwined with their financial possibilities, limitations and responsibilities. The following three articles employ the notion of relatedness to explore the transnational and local social networks, including family relations, of which the au pairs are part. Arguing...... that Filipina au pairs see their stay abroad as an avenue of personal development and social recognition, I examine how the au pairs re-position themselves within their families at home through migration, and how they navigate between the often conflicting expectations of participation in the sociality...... important remittances back home. Their time in Denmark is also often part of long-term migration trajectories involving future stays in Scandinavia and southern Europe. Based on ten months of fieldwork among current and former au pairs in Denmark and ten weeks of fieldwork among prospective au pairs and au...

  4. Analysis of difference spectra of protonated DNA: determination of degree of protonation of nitrogen bases and the fractions of disordered nucleotide pairs.

    Science.gov (United States)

    Smol'janinova, T I; Zhidkov, V A; Sokolov, G V

    1982-01-01

    The titration curves of nitrogen bases and fractions of disordered nucleotide pairs are obtained during DNA protonation. It is shown that purine bases are the first sites of the DNA double helix protonation. The cytosine protonation is due to proton-induced conformational transition within GC pairs with the sequence proton transfer from (N-7) of guanine to (N-3) of cytosine. Within DNA with unwound regions the bases are protonated in the following order: cytosine, adenine, guanine. It is shown that GC pairs are the primary centres in which the unwinding of protonated DNAs occurs. PMID:7079177

  5. One-step electrochemical deposition of Schiff base cobalt complex as effective water oxidation catalyst

    Science.gov (United States)

    Huang, Binbin; Wang, Yan; Zhan, Shuzhong; Ye, Jianshan

    2017-02-01

    Schiff base metal complexes have been applied in many fields, especially, a potential homogeneous catalyst for water splitting. However, the high overpotential, time consumed synthesis process and complicated working condition largely limit their application. In the present work, a one-step approach to fabricate Schiff base cobalt complex modified electrode is developed. Microrod clusters (MRC) and rough spherical particles (RSP) can be obtained on the ITO electrode through different electrochemical deposition condition. Both of the MRC and RSP present favorable activity for oxygen evolution reaction (OER) compared to the commercial Co3O4, taking an overpotential of 650 mV and 450 mV to drive appreciable catalytic current respectively. The highly active and stable RSP shows a Tafel plot of 84 mV dec-1 and negligible decrease of the current density for 12 h bulk electrolysis. The synthesis strategy of effective and stable catalyst in this work provide a simple method to fabricate heterogeneous OER catalyst with Schiff base metal complex.

  6. PNA(T).DNA(AT) triplexes with Hoogsteen base pairing are more favorable

    Institute of Scientific and Technical Information of China (English)

    XIE Jun; LIU Ciquan; QU Lianghu

    2003-01-01

    Peptide nucleic acids (PNAs) are nucleic acid analogs with the deoxyribose phosphate backbone replaced by pseudo-peptide polymers to which the nucleobases are linked. The achiral, uncharged and rather flexible properties of the peptide backbone permit peptide nucleic acids more potential than oligonucleotides in application to antisence and antigenic reagents. The process of PNA binding to DNA duplex and forming triplex is the first step of PNA interacting with PNA. But there are no PNA.2DNA triplex crystal data up to date and little has been reported on the structure features and the force of the PNA.2DNA triplex. In this work,PNA(T).DNA(AT) triplexes are successfully built and the structures and forces to stabilize the triplex after optimizations and molecule dynamics are systematically examined,which are expected to aid in the application of PNAs as anticense and antigene agents.

  7. Comprehensive evaluation of medium and long range correlated density functionals in TD-DFT investigation of DNA bases and base pairs: gas phase and water solution study

    Science.gov (United States)

    Shukla, Manoj K.; Leszczynski, Jerzy

    2010-11-01

    A comprehensive analysis of the performance of the TD-DFT method using different density functionals including recently developed medium and long-range correlation corrected density functionals have been carried out for lower-lying electronic singlet valence transitions of nucleic acid bases and the Watson-Crick base pairs in the gas phase and in the water solution. The standard 6-311++G(d,p) basis set was used. Ground state geometries of bases and base pairs were optimized at the M05-2X/6-311++G(d,p) level. The nature of potential energy surfaces (PES) was ascertained through the harmonic vibrational frequency analysis; all geometries were found to be minima at the respective PES. Electronic singlet vertical transition energies were also computed at the CC2/def2-TZVP level in the gas phase. The effect of state-specific water solvation on TD-DFT computed transition energies was considered using the PCM model. For the isolated bases the performance of the B3LYP functional was generally found to be superior among all functionals, but it measurably fails for charge-transfer states in the base pairs. The CC2/def2-TZVP computed transition energies were also revealed to be inferior compared with B3LYP results for the isolated bases. The performance of the ωB97XD, CAM-B3LYP and BMK functionals were found to be similar and comparable with the CC2 results for the isolated bases. However, for the Watson-Crick adenine-thymine and guanine-cytosine base pairs the performance of the ωB97XD functional was found to be the best among all the studied functionals in the present work in predicting the locally excited transitions as well as charge transfer states.

  8. Experimental demonstration of wavelength domain rogue-free ONU based on wavelength-pairing for TDM/WDM optical access networks.

    Science.gov (United States)

    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.

  9. Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase

    Energy Technology Data Exchange (ETDEWEB)

    Reha-Krantz, Linda J.; Hariharan, Chithra; Subuddhi, Usharani; Xia, Shuangluo; Zhao, Chao; Beckman, Jeff; Christian, Thomas; Konigsberg, William (Yale); (Alberta)

    2011-11-21

    The adenine base analogue 2-aminopurine (2AP) is a potent base substitution mutagen in prokaryotes because of its enhanceed ability to form a mutagenic base pair with an incoming dCTP. Despite more than 50 years of research, the structure of the 2AP-C base pair remains unclear. We report the structure of the 2AP-dCTP base pair formed within the polymerase active site of the RB69 Y567A-DNA polymerase. A modified wobble 2AP-C base pair was detected with one H-bond between N1 of 2AP and a proton from the C4 amino group of cytosine and an apparent bifurcated H-bond between a proton on the 2-amino group of 2-aminopurine and the ring N3 and O2 atoms of cytosine. Interestingly, a primer-terminal region rich in AT base pairs, compared to GC base pairs, facilitated dCTP binding opposite template 2AP. We propose that the increased flexibility of the nucleotide binding pocket formed in the Y567A-DNA polymerase and increased 'breathing' at the primer-terminal junction of A+T-rich DNA facilitate dCTP binding opposite template 2AP. Thus, interactions between DNA polymerase residues with a dynamic primer-terminal junction play a role in determining base selectivity within the polymerase active site of RB69 DNA polymerase.

  10. An efficient reconstruction method for bioluminescence tomography based on two-step iterative shrinkage approach

    Science.gov (United States)

    Guo, Wei; Jia, Kebin; Tian, Jie; Han, Dong; Liu, Xueyan; Wu, Ping; Feng, Jinchao; Yang, Xin

    2012-03-01

    Among many molecular imaging modalities, Bioluminescence tomography (BLT) is an important optical molecular imaging modality. Due to its unique advantages in specificity, sensitivity, cost-effectiveness and low background noise, BLT is widely studied for live small animal imaging. Since only the photon distribution over the surface is measurable and the photo propagation with biological tissue is highly diffusive, BLT is often an ill-posed problem and may bear multiple solutions and aberrant reconstruction in the presence of measurement noise and optical parameter mismatches. For many BLT practical applications, such as early detection of tumors, the volumes of the light sources are very small compared with the whole body. Therefore, the L1-norm sparsity regularization has been used to take advantage of the sparsity prior knowledge and alleviate the ill-posedness of the problem. Iterative shrinkage (IST) algorithm is an important research achievement in a field of compressed sensing and widely applied in sparse signal reconstruction. However, the convergence rate of IST algorithm depends heavily on the linear operator. When the problem is ill-posed, it becomes very slow. In this paper, we present a sparsity regularization reconstruction method for BLT based on the two-step iterated shrinkage approach. By employing Two-step strategy of iterative reweighted shrinkage (IRS) to improve IST, the proposed method shows faster convergence rate and better adaptability for BLT. The simulation experiments with mouse atlas were conducted to evaluate the performance of proposed method. By contrast, the proposed method can obtain the stable and comparable reconstruction solution with less number of iterations.

  11. Milestones and Millennials: A Perfect Pairing-Competency-Based Medical Education and the Learning Preferences of Generation Y.

    Science.gov (United States)

    Desy, Janeve R; Reed, Darcy A; Wolanskyj, Alexandra P

    2017-02-01

    Millennials are quickly becoming the most prevalent generation of medical learners. These individuals have a unique outlook on education and have different preferences and expectations than their predecessors. As evidenced by its implementation by the Accreditation Council for Graduate Medical Education in the United States and the Royal College of Physicians and Surgeons in Canada, competency based medical education is rapidly gaining international acceptance. Characteristics of competency based medical education can be perfectly paired with Millennial educational needs in several dimensions including educational expectations, the educational process, attention to emotional quotient and professionalism, assessment, feedback, and intended outcomes. We propose that with its attention to transparency, personalized learning, and frequent formative assessment, competency based medical education is an ideal fit for the Millennial generation as it realigns education and assessment with the needs of these 21st century learners.

  12. Research on a Nonlinear Robust Adaptive Control Method of the Elbow Joint of a Seven-Function Hydraulic Manipulator Based on Double-Screw-Pair Transmission

    Directory of Open Access Journals (Sweden)

    Gaosheng Luo

    2014-01-01

    Full Text Available A robust adaptive control method with full-state feedback is proposed based on the fact that the elbow joint of a seven-function hydraulic manipulator with double-screw-pair transmission features the following control characteristics: a strongly nonlinear hydraulic system, parameter uncertainties susceptible to temperature and pressure changes of the external environment, and unknown outer disturbances. Combined with the design method of the back-stepping controller, the asymptotic stability of the control system in the presence of disturbances from uncertain systematic parameters and unknown external disturbances was demonstrated using Lyapunov stability theory. Based on the elbow joint of the seven-function master-slave hydraulic manipulator for the 4500 m Deep-Sea Working System as the research subject, a comparative study was conducted using the control method presented in this paper for unknown external disturbances. Simulations and experiments of different unknown outer disturbances showed that (1 the proposed controller could robustly track the desired reference trajectory with satisfactory dynamic performance and steady accuracy and that (2 the modified parameter adaptive laws could also guarantee that the estimated parameters are bounded.

  13. WRIST FORCE SENSOR'S DYNAMIC PERFORMANCE CALIBRATION BASED ON NEGATIVE STEP RESPONSE

    Institute of Scientific and Technical Information of China (English)

    ZHENG Hongmei

    2008-01-01

    Negative step response experimental method is used in wrist force sensor's dynamic performance calibration. The exciting manner of negative step response method is the same as wrist force sensor's load in working. This experimental method needn't special experiment equipments. Experiment's dynamic repeatability is good. So wrist force sensor's dynamic performance is suitable to be calibrated by negative step response method. A new correlation wavelet transfer method is studied. By wavelet transfer method, the signal is decomposed into two dimensional spaces of time-frequency. So the problem of negative step exciting energy concentrating in the low frequency band is solved. Correlation wavelet transfer doesn't require that wavelet primary function be orthogonal and needn't wavelet reconstruction. So analyzing efficiency is high. An experimental bench is designed and manufactured to load the wrist force sensor orthogonal excitation force/moment. A piezoelectric force sensor is used to setup soft trigger and calculate the value of negative step excitation. A wrist force sensor is calibrated. The pulse response function is calculated after negative step excitation and step response have been transformed to positive step excitation and step response. The pulse response function is transferred to frequency response function. The wrist force sensor's dynamic characteristics are identified by the frequency response function.

  14. Early Steps in the DNA Base Excision Repair Pathway of a Fission Yeast Schizosaccharomyces pombe

    Directory of Open Access Journals (Sweden)

    Kyoichiro Kanamitsu

    2010-01-01

    Full Text Available DNA base excision repair (BER accounts for maintaining genomic integrity by removing damaged bases that are generated endogenously or induced by genotoxic agents. In this paper, we describe the roles of enzymes functioning in the early steps of BER in fission yeast. Although BER is an evolutionarily conserved process, some unique features of the yeast repair pathway were revealed by genetic and biochemical approaches. AP sites generated by monofunctional DNA glycosylases are incised mainly by AP lyase activity of Nth1p, a sole bifunctional glycosylase in yeast, to leave a blocked 3′ end. The major AP endonuclease Apn2p functions predominantly in removing the 3′ block. Finally, a DNA polymerase fills the gap, and a DNA ligase seals the nick (Nth1p-dependent or short patch BER. Apn1p backs up Apn2p. In long patch BER, Rad2p endonuclease removes flap DNA containing a lesion after DNA synthesis. A UV-specific endonuclease Uve1p engages in an alternative pathway by nicking DNA on the 5′ side of oxidative damage. Nucleotide excision repair and homologous recombination are involved in repair of BER intermediates including the AP site and single-strand break with the 3′ block. Other enzymes working in 3′ end processing are also discussed.

  15. Light-emitting self-assembled peptide nucleic acids exhibit both stacking interactions and Watson-Crick base pairing

    Science.gov (United States)

    Berger, Or; Adler-Abramovich, Lihi; Levy-Sakin, Michal; Grunwald, Assaf; Liebes-Peer, Yael; Bachar, Mor; Buzhansky, Ludmila; Mossou, Estelle; Forsyth, V. Trevor; Schwartz, Tal; Ebenstein, Yuval; Frolow, Felix; Shimon, Linda J. W.; Patolsky, Fernando; Gazit, Ehud

    2015-05-01

    The two main branches of bionanotechnology involve the self-assembly of either peptides or DNA. Peptide scaffolds offer chemical versatility, architectural flexibility and structural complexity, but they lack the precise base pairing and molecular recognition available with nucleic acid assemblies. Here, inspired by the ability of aromatic dipeptides to form ordered nanostructures with unique physical properties, we explore the assembly of peptide nucleic acids (PNAs), which are short DNA mimics that have an amide backbone. All 16 combinations of the very short di-PNA building blocks were synthesized and assayed for their ability to self-associate. Only three guanine-containing di-PNAs—CG, GC and GG—could form ordered assemblies, as observed by electron microscopy, and these di-PNAs efficiently assembled into discrete architectures within a few minutes. The X-ray crystal structure of the GC di-PNA showed the occurrence of both stacking interactions and Watson-Crick base pairing. The assemblies were also found to exhibit optical properties including voltage-dependent electroluminescence and wide-range excitation-dependent fluorescence in the visible region.

  16. Advanced formulation of base pair changes in the stem regions of ribosomal RNAs; its application to mitochondrial rRNAs for resolving the phylogeny of animals.

    Science.gov (United States)

    Otsuka, Jinya; Sugaya, Nobuyoshi

    2003-06-21

    The ribosomal RNAs (rRNAs) of animal mitochondria, especially those of arthropod mitochondria, have a higher content of G:U and U:G base pairs in their stem regions than the nuclear rRNAs. Thus, the theoretical formulation of base pair changes is extended to incorporate the faster base pair changes A:UG:UG:C and U:AU:GC:G into the previous formulation of the slower base pair changes between A:U, G:C, C:G and U:A. The relative base pair change probability containing the faster and slower base pair changes is theoretically derived to estimate the divergence time of rRNAs under the influence of selection for these base pairs. Using the cartilaginous fish-teleost fish divergence and the crustacean-insect divergence as calibration points, the present method successfully predicts the divergence times of the main branches of animals: Deuterostomia and Protostomia diverged 9.2 x 10(8) years ago, the divergence of Echinodermata, Hemichordata and Cephalochordata succeedingly occurred during the period from 8 x 10(8) to 6 x 10(8) years ago, while Arthropoda, Annelida and Mollusca diverged almost concomitantly about 7 x 10(8) years ago. The dating for the divergence of Platyhelminthes and Cnidaria is traced back to 1.2 x 10(9) years ago. This result is consistent with the fossil records in the Stirling Range Formation of southwestern Australia, the Ediacara and Avalon faunas and the Cambrian Burgess Shale. Thus, the present method may be useful for estimating the divergence times of animals ranging from 10(8) to 10(9) years ago, resolving the difficult problems, e.g. deviation from rate constancy and large sampling variances, in the usual methods of treating apparent change rates between individual bases and/or base pairs.

  17. Evaluating changes in matrix-based, recovery-adjusted concentrations in paired data for pesticides in groundwater.

    Science.gov (United States)

    Zimmerman, Tammy M; Breen, Kevin J

    2012-01-01

    Pesticide concentration data for waters from selected carbonate-rock aquifers in agricultural areas of Pennsylvania were collected in 1993-2009 for occurrence and distribution assessments. A set of 30 wells was visited once in 1993-1995 and again in 2008-2009 to assess concentration changes. The data include censored matched pairs (nondetections of a compound in one or both samples of a pair). A potentially improved approach for assessing concentration changes is presented where (i) concentrations are adjusted with models of matrix-spike recovery and (ii) area-wide temporal change is tested by use of the paired Prentice-Wilcoxon (PPW) statistical test. The PPW results for atrazine, simazine, metolachlor, prometon, and an atrazine degradate, deethylatrazine (DEA), are compared using recovery-adjusted and unadjusted concentrations. Results for adjusted compared with unadjusted concentrations in 2008-2009 compared with 1993-1995 were similar for atrazine and simazine (significant decrease; 95% confidence level) and metolachlor (no change) but differed for DEA (adjusted, decrease; unadjusted, increase) and prometon (adjusted, decrease; unadjusted, no change). The PPW results were different on recovery-adjusted compared with unadjusted concentrations. Not accounting for variability in recovery can mask a true change, misidentify a change when no true change exists, or assign a direction opposite of the true change in concentration that resulted from matrix influences on extraction and laboratory method performance. However, matrix-based models of recovery derived from a laboratory performance dataset from multiple studies for national assessment, as used herein, rather than time- and study-specific recoveries may introduce uncertainty in recovery adjustments for individual samples that should be considered in assessing change.

  18. Chain propagation and termination mechanisms for polymerization of conjugated polar alkenes by [Al]-based frustrated Lewis pairs

    KAUST Repository

    He, Jianghua

    2014-11-25

    A combined experimental and theoretical study on mechanistic aspects of polymerization of conjugated polar alkenes by frustrated Lewis pairs (FLPs) based on N-heterocyclic carbene (NHC) and Al(C6F5)3 pairs is reported. This study consists of three key parts: structural characterization of active propagating intermediates, propagation kinetics, and chain-termination pathways. Zwitterionic intermediates that simulate the active propagating species in such polymerization have been generated or isolated from the FLP activation of monomers such as 2-vinylpyridine and 2-isopropenyl-2-oxazoline-one of which, IMes+-CH2C(Me)=(C3H2NO)Al(C6F5)3 - (2), has been structurally characterized. Kinetics performed on the polymerization of 2-vinylpyridine by ItBu/Al(C6F5)3 revealed that the polymerization follows a zero-order dependence on monomer concentration and a first-order dependence on initiator (ItBu) and activator [Al(C6F5)3] concentrations, indicating a bimolecular, activated monomer propagation mechanism. The Lewis pair polymerization of conjugate polar alkenes such as methacrylates is accompanied by competing chain-termination side reactions; between the two possible chain-termination pathways, the one that proceeds via intramolecular backbiting cyclization involving nucleophilic attack of the activated ester group of the growing polymer chain by the O-ester enolate active chain end to generate a six-membered lactone (δ-valerolactone)-terminated polymer chain is kinetically favored, but thermodynamically disfavored, over the pathway leading to the -ketoester-terminated chain, as revealed by computational studies.

  19. A new laser-based system for obstacle detection including step, hole and slope for Personal Mobility Vehicles

    OpenAIRE

    POLLARD, Evangeline; Fawzi NASHASHIBI

    2013-01-01

    International audience; Personal Mobility Vehicles (PMV) is is an important part of the Intelligent Transportation System (ITS) domain. These new transport systems have been designed for urban traffic areas, pedestrian streets, green zones and private parks. In these areas, steps and curbs make the movement of disable or mobility reduced people with PMV, and with standard chair wheels difficult. In this paper, we present a step and curb detection system based on laser sensors. This system is ...

  20. Step and curb detection for autonomous vehicles with an algebraic derivative-based approach applied on laser rangefinder data

    OpenAIRE

    POLLARD, Evangeline; Pérez Rastelli, Joshué; Fawzi NASHASHIBI

    2013-01-01

    International audience; Personal Mobility Vehicles (PMV) is is an important part of the Intelligent Transportation System (ITS) domain. These new transport systems have been designed for urban traffic areas, pedestrian streets, green zones and private parks. In these areas, steps and curbs make the movement of disable or mobility reduced people with PMV, and with standard chair wheels difficult. In this paper, we present a step and curb detection system based on laser sensors. This system is ...

  1. The Distribution of Technetium in U/Pu Partition Step of Advanced Purex Process Based on Organic Reagents

    Institute of Scientific and Technical Information of China (English)

    WANG; Hui; WEI; Yan; LIU; Fang; JIA; Yong-fen; LIU; Zhan-yuan

    2012-01-01

    <正>Advanced Purex process based on organic reagents (APOR) is an advanced Purex process, where monomethylhydrazine (MMH)-dimethylhydroxylamine (DMHAN) are adopted as salt-free plutonium- reductant in the partition step. During this step, technetium mainly goes into aqueous plutonium stream, and the aim of our work is to explain this phenomena. Reaction kinetic experiments and process experiments with mixer-settler were carried out for this purpose.

  2. Nonmagnetic impurity resonances as a signature of sign-reversal pairing in FeAs-based superconductors.

    Science.gov (United States)

    Zhang, Degang

    2009-10-30

    The energy band structure of FeAs-based superconductors is fitted by a tight-binding model with two Fe ions per unit cell and two degenerate orbitals per Fe ion. Based on this, superconductivity with extended s-wave pairing symmetry of the form cosk(x)+cosk(y) is examined. The local density of states near an impurity is also investigated by using the T-matrix approach. For the nonmagnetic scattering potential, we found that there exist two major resonances inside the gap. The height of the resonance peaks depends on the strength of the impurity potential. These in-gap resonances are originated in the Andreev's bound states due to the quasiparticle scattering between the hole Fermi surfaces around Gamma point with positive order parameter and the electron Fermi surfaces around M point with negative order parameter.

  3. Atomistic understanding of the C·T mismatched DNA base pair tautomerization via the DPT: QM and QTAIM computational approaches.

    Science.gov (United States)

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

    2013-11-15

    It was established that the cytosine·thymine (C·T) mismatched DNA base pair with cis-oriented N1H glycosidic bonds has propeller-like structure (|N3C4C4N3| = 38.4°), which is stabilized by three specific intermolecular interactions-two antiparallel N4H…O4 (5.19 kcal mol(-1)) and N3H…N3 (6.33 kcal mol(-1)) H-bonds and a van der Waals (vdW) contact O2…O2 (0.32 kcal mol(-1)). The C·T base mispair is thermodynamically stable structure (ΔG(int) = -1.54 kcal mol(-1) ) and even slightly more stable than the A·T Watson-Crick DNA base pair (ΔG(int) = -1.43 kcal mol(-1)) at the room temperature. It was shown that the C·T ↔ C*·T* tautomerization via the double proton transfer (DPT) is assisted by the O2…O2 vdW contact along the entire range of the intrinsic reaction coordinate (IRC). The positive value of the Grunenberg's compliance constants (31.186, 30.265, and 22.166 Å/mdyn for the C·T, C*·T*, and TS(C·T ↔ C*·T*), respectively) proves that the O2…O2 vdW contact is a stabilizing interaction. Based on the sweeps of the H-bond energies, it was found that the N4H…O4/O4H…N4, and N3H…N3 H-bonds in the C·T and C*·T* base pairs are anticooperative and weaken each other, whereas the middle N3H…N3 H-bond and the O2…O2 vdW contact are cooperative and mutually reinforce each other. It was found that the tautomerization of the C·T base mispair through the DPT is concerted and asynchronous reaction that proceeds via the TS(C·T ↔ C*·T*) stabilized by the loosened N4-H-O4 covalent bridge, N3H…N3 H-bond (9.67 kcal mol(-1) ) and O2…O2 vdW contact (0.41 kcal mol(-1) ). The nine key points, describing the evolution of the C·T ↔ C*·T* tautomerization via the DPT, were detected and completely investigated along the IRC. The C*·T* mispair was revealed to be the dynamically unstable structure with a lifetime 2.13·× 10(-13) s. In this case, as for the A·T Watson-Crick DNA base pair, activates the mechanism of the quantum protection of the C

  4. Application of Acupoints in Pairs

    Institute of Scientific and Technical Information of China (English)

    季扬

    2004-01-01

    @@ Application of acupoints in pairs is a kind of point association in which only a pair of compatible points is used. Based on the principle of compatibility, the author of this article often uses the "pair-point needling" to treat some common diseases, and have obtained very good therapeutic results. Some examples are introduced below.

  5. Adaptive statistic tracking control based on two-step neural networks with time delays.

    Science.gov (United States)

    Yi, Yang; Guo, Lei; Wang, Hong

    2009-03-01

    This paper presents a new type of control framework for dynamical stochastic systems, called statistic tracking control (STC). The system considered is general and non-Gaussian and the tracking objective is the statistical information of a given target probability density function (pdf), rather than a deterministic signal. The control aims at making the statistical information of the output pdfs to follow those of a target pdf. For such a control framework, a variable structure adaptive tracking control strategy is first established using two-step neural network models. Following the B-spline neural network approximation to the integrated performance function, the concerned problem is transferred into the tracking of given weights. The dynamic neural network (DNN) is employed to identify the unknown nonlinear dynamics between the control input and the weights related to the integrated function. To achieve the required control objective, an adaptive controller based on the proposed DNN is developed so as to track a reference trajectory. Stability analysis for both the identification and tracking errors is developed via the use of Lyapunov stability criterion. Simulations are given to demonstrate the efficiency of the proposed approach.

  6. A two-step process for controlling the surface smoothness of polyelectrolyte-based microcapsules.

    Science.gov (United States)

    Lacík, I; Anilkumar, A V; Wang, T G

    2001-01-01

    Biocompatibility is one of the crucial requirements to be fulfilled when designing devices for immunoisolation of transplanted cells. The quality of the capsule surface (smoothness/roughness) influences the nature of cell overgrowth on it by immunocytes, which eventually may lead to the transplant failure. A microcapsule has been developed based on the polyelectrolyte complexation of the polyanions sodium alginate and cellulose sulphate with the polycation poly(methylene-co-guanidine), which was successfully tested in rodent animal models. Recently, the principles for controlling the surface smoothness of these capsules has been identified. This paper reports on a two-step process used for production of stable capsules with improved surface properties. The methodology involves separating the process of drop shape recovery and precursor capsule formation from the process of membrane formation by applying a two-reactor design. The multi-loop reactors are connected in series, and the process separation is given by the different composition of cation solutions flowing in each reactor. This process enables one to prepare the microcapsule immunoisolation device, which can differ in the extent of surface roughness and, thus, is suitable for studying the effect of surface morphology of the immunoisolation device on cell overgrowth. The effect of this process on the capsule permeability has also been evaluated.

  7. Lightning path simulation based on the stepped leader: Electrical conductivity effects

    Science.gov (United States)

    Mendes, Odim; Domingues, Margarete Oliveira

    2005-09-01

    A numerical simulation for the stepped leader path in the earth atmosphere has been developed to study the influence of the tropospheric electric conductivity on the lightning behaviour. This model is based on the assumption that the leader path follows the gradient of the electric potential. In the model, the charge configuration (amount of charge and location), the variation of the atmospheric conductivity, the charge deposited along the leader channel and the charge at the leader tip are considered. A perfectly conducting ground surface and a curl-free electric field assumption are considered too. The result of the simulation is that the inclusion of an atmospheric conductivity of exponentially increasing value with height alters the percentage of positive cloud-to-ground flashes compared to that percentage obtained assuming a constant conductivity profile. A higher amount of positive flashes occur for high altitude (low latitude) clouds even in the case of little horizontal displacement between the positive and the negative dipole charges in the cloud, that is, with no significant wind shear in the horizontal wind. The simulation has shown that positive lightning, the most dangerous kind, can occur in clear air at great distances from the thundercloud, with safety risk implications.

  8. Primary step for endoscopic sinonasal tract and anterior skull base robotics

    Directory of Open Access Journals (Sweden)

    Crampette Louis

    2011-12-01

    Full Text Available Introduction: Surgeons have evolved a lot their surgical procedures in sinus surgery and are now able to resect malignant tumors. These progresses are now leading new difficulties like impairing vision (bleeding and LCR flow and necessity of multiple simultaneous tasks. With the aim of designing a new endoscope-holder, primary step was to characterize the surgeon gesture, the kinematics, and the type of man-machine interface acceptable by the surgeon. Methods: We worked on thirteen sinonasal tracts of cadaver heads. Surgical procedures were: opening all the sinuses, the carotid, the sella turcica, the lamina papyracea and the anterior skull base. We used conventional instruments which were instrumented with a force-torque sensor and a navigation system. Then we have experimentally evaluated robots with three different kinematics and two types of man-machine interfaces. Results: We collected enough position and force data as well as kinematics constraints and interface requirements to specify a robot for endoscopic sinus surgery.

  9. Repairing the sickle cell mutation. I. Specific covalent binding of a photoreactive third strand to the mutated base pair.

    Science.gov (United States)

    Broitman, S; Amosova, O; Dolinnaya, N G; Fresco, J R

    1999-07-30

    A DNA third strand with a 3'-psoralen substituent was designed to form a triplex with the sequence downstream of the T.A mutant base pair of the human sickle cell beta-globin gene. Triplex-mediated psoralen modification of the mutant T residue was sought as an approach to gene repair. The 24-nucleotide purine-rich target sequence switches from one strand to the other and has four pyrimidine interruptions. Therefore, a third strand sequence favorable to two triplex motifs was used, one parallel and the other antiparallel to it. To cope with the pyrimidine interruptions, which weaken third strand binding, 5-methylcytosine and 5-propynyluracil were used in the third strand. Further, a six residue "hook" complementary to an overhang of a linear duplex target was added to the 5'-end of the third strand via a T(4) linker. In binding to the overhang by Watson-Crick pairing, the hook facilitates triplex formation. This third strand also binds specifically to the target within a supercoiled plasmid. The psoralen moiety at the 3'-end of the third strand forms photoadducts to the targeted T with high efficiency. Such monoadducts are known to preferentially trigger reversion of the mutation by DNA repair enzymes.

  10. Demonstration of polarization sensitivity of emulsion-based pair conversion telescope for cosmic gamma-ray polarimetry

    CERN Document Server

    Ozaki, Keita; Aoki, Shigeki; Kamada, Keiki; Kaneyama, Taichi; Nakagawa, Ryo; Rokujo, Hiroki

    2016-01-01

    Linear polarization of high-energy gamma-rays (10 MeV-100 GeV) can be detected by measuring the azimuthal angle of electron-positron pairs and observing the modulation of the azimuthal distribution. To demonstrate the gamma-ray polarization sensitivity of emulsion, we conducted a test using a polarized gamma-ray beam at SPring-8/LEPS. Emulsion tracks were reconstructed using scanning data, and gamma-ray events were selected automatically. Using an optical microscope, out of the 2381 gamma-ray conversions that were observed, 1372 remained after event selection, on the azimuthal angle distribution of which we measured the modulation. From the distribution of the azimuthal angles of the selected events, a modulation factor of 0.21 + 0.11 - 0.09 was measured, from which the detection of a non-zero modulation was established with a significance of 3.06 $\\sigma$. This attractive polarimeter will be applied to the GRAINE project, a balloon-borne experiment that observes cosmic gamma-rays with an emulsion-based pair ...

  11. Detection of Wuchereria bancrofti DNA in paired serum and urine samples using polymerase chain reaction-based systems

    Directory of Open Access Journals (Sweden)

    Camila Ximenes

    2014-12-01

    Full Text Available The Global Program for the Elimination of Lymphatic Filariasis (GPELF aims to eliminate this disease by the year 2020. However, the development of more specific and sensitive tests is important for the success of the GPELF. The present study aimed to standardise polymerase chain reaction (PCR-based systems for the diagnosis of filariasis in serum and urine. Twenty paired biological urine and serum samples from individuals already known to be positive for Wuchereria bancrofti were collected during the day. Conventional PCR and semi-nested PCR assays were optimised. The detection limit of the technique for purified W. bancrofti DNA extracted from adult worms was 10 fg for the internal systems (WbF/Wb2 and 0.1 fg by using semi-nested PCR. The specificity of the primers was confirmed experimentally by amplification of 1 ng of purified genomic DNA from other species of parasites. Evaluation of the paired urine and serum samples by the semi-nested PCR technique indicated only two of the 20 tested individuals were positive, whereas the simple internal PCR system (WbF/Wb2, which has highly promising performance, revealed that all the patients were positive using both samples. This study successfully demonstrated the possibility of using the PCR technique on urine for the diagnosis of W. bancrofti infection.

  12. A likelihood-based approach for assessment of extra-pair paternity and conspecific brood parasitism in natural populations

    Science.gov (United States)

    Lemons, Patrick R.; Marshall, T.C.; McCloskey, Sarah E.; Sethi, S.A.; Schmutz, Joel A.; Sedinger, James S.

    2015-01-01

    Genotypes are frequently used to assess alternative reproductive strategies such as extra-pair paternity and conspecific brood parasitism in wild populations. However, such analyses are vulnerable to genotyping error or molecular artifacts that can bias results. For example, when using multilocus microsatellite data, a mismatch at a single locus, suggesting the offspring was not directly related to its putative parents, can occur quite commonly even when the offspring is truly related. Some recent studies have advocated an ad-hoc rule that offspring must differ at more than one locus in order to conclude that they are not directly related. While this reduces the frequency with which true offspring are identified as not directly related young, it also introduces bias in the opposite direction, wherein not directly related young are categorized as true offspring. More importantly, it ignores the additional information on allele frequencies which would reduce overall bias. In this study, we present a novel technique for assessing extra-pair paternity and conspecific brood parasitism using a likelihood-based approach in a new version of program cervus. We test the suitability of the technique by applying it to a simulated data set and then present an example to demonstrate its influence on the estimation of alternative reproductive strategies.

  13. Identification of genes that promote or antagonize somatic homolog pairing using a high-throughput FISH-based screen.

    Directory of Open Access Journals (Sweden)

    Eric F Joyce

    Full Text Available The pairing of homologous chromosomes is a fundamental feature of the meiotic cell. In addition, a number of species exhibit homolog pairing in nonmeiotic, somatic cells as well, with evidence for its impact on both gene regulation and double-strand break (DSB repair. An extreme example of somatic pairing can be observed in Drosophila melanogaster, where homologous chromosomes remain aligned throughout most of development. However, our understanding of the mechanism of somatic homolog pairing remains unclear, as only a few genes have been implicated in this process. In this study, we introduce a novel high-throughput fluorescent in situ hybridization (FISH technology that enabled us to conduct a genome-wide RNAi screen for factors involved in the robust somatic pairing observed in Drosophila. We identified both candidate "pairing promoting genes" and candidate "anti-pairing genes," providing evidence that pairing is a dynamic process that can be both enhanced and antagonized. Many of the genes found to be important for promoting pairing are highly enriched for functions associated with mitotic cell division, suggesting a genetic framework for a long-standing link between chromosome dynamics during mitosis and nuclear organization during interphase. In contrast, several of the candidate anti-pairing genes have known interphase functions associated with S-phase progression, DNA replication, and chromatin compaction, including several components of the condensin II complex. In combination with a variety of secondary assays, these results provide insights into the mechanism and dynamics of somatic pairing.

  14. On the stability of two-step predictive controller based on state observer

    Institute of Scientific and Technical Information of China (English)

    Cao Muliang; Wu Zhiming; Ding Baocang; Wang Chuanxu

    2006-01-01

    For input saturated Hammerstein systems, the two-step predictive control strategy is adopted. The first step calculates the desired intermediate variable applying unconstrained linear model and predictive control. The second step obtains the real-time control action by solving algebraic equation and desaturation. The case of measurable state is considered where the observer gain matrix is solved by Sylvester equation. The sufficient closed-loop stability condition is given and the designing and tuning algorithm for the domain of attraction is proposed. The theoretical results are validated by an example.

  15. Next Step for STEP

    Energy Technology Data Exchange (ETDEWEB)

    Wood, Claire [CTSI; Bremner, Brenda [CTSI

    2013-08-09

    The Siletz Tribal Energy Program (STEP), housed in the Tribe’s Planning Department, will hire a data entry coordinator to collect, enter, analyze and store all the current and future energy efficiency and renewable energy data pertaining to administrative structures the tribe owns and operates and for homes in which tribal members live. The proposed data entry coordinator will conduct an energy options analysis in collaboration with the rest of the Siletz Tribal Energy Program and Planning Department staff. An energy options analysis will result in a thorough understanding of tribal energy resources and consumption, if energy efficiency and conservation measures being implemented are having the desired effect, analysis of tribal energy loads (current and future energy consumption), and evaluation of local and commercial energy supply options. A literature search will also be conducted. In order to educate additional tribal members about renewable energy, we will send four tribal members to be trained to install and maintain solar panels, solar hot water heaters, wind turbines and/or micro-hydro.

  16. Discovering Pair-Wise Genetic Interactions: An Information Theory-Based Approach

    Science.gov (United States)

    Ignac, Tomasz M.; Skupin, Alexander; Sakhanenko, Nikita A.; Galas, David J.

    2014-01-01

    Phenotypic variation, including that which underlies health and disease in humans, results in part from multiple interactions among both genetic variation and environmental factors. While diseases or phenotypes caused by single gene variants can be identified by established association methods and family-based approaches, complex phenotypic traits resulting from multi-gene interactions remain very difficult to characterize. Here we describe a new method based on information theory, and demonstrate how it improves on previous approaches to identifying genetic interactions, including both synthetic and modifier kinds of interactions. We apply our measure, called interaction distance, to previously analyzed data sets of yeast sporulation efficiency, lipid related mouse data and several human disease models to characterize the method. We show how the interaction distance can reveal novel gene interaction candidates in experimental and simulated data sets, and outperforms other measures in several circumstances. The method also allows us to optimize case/control sample composition for clinical studies. PMID:24670935

  17. Distance-dependent proton transfer along water wires connecting acid-base pairs

    NARCIS (Netherlands)

    Cox, M.J.; Timmer, R.L.A.; Bakker, H.J.; Park, S.; Agmon, N.

    2009-01-01

    We report time-resolved mid-IR kinetics for the ultrafast acid−base reaction between photoexcited 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS), and acetate at three concentrations (0.5, 1.0, and 2.0 M) and three temperatures (5, 30, and 65 °C) in liquid D2O. The observed proton-trans

  18. Timing of Colonization of Caries-Producing Bacteria: An Approach Based on Studying Monozygotic Twin Pairs

    OpenAIRE

    Bockmann, Michelle R.; Harris, Abbe V.; Bennett, Corinna N.; Ruba Odeh; Hughes, Toby E.; Townsend, Grant C

    2011-01-01

    Findings are presented from a prospective cohort study of timing of primary tooth emergence and timing of oral colonization of Streptococcus mutans (S. mutans) in Australian twins. The paper focuses on differences in colonization timing in genetically identical monozygotic (MZ) twins. Timing of tooth emergence was based on parental report. Colonization timing of S. mutans were established by plating samples of plaque and saliva on selective media at 3 monthly intervals and assessing colony mo...

  19. Stepped Fault Line Selection Method Based on Spectral Kurtosis and Relative Energy Entropy of Small Current to Ground System

    Directory of Open Access Journals (Sweden)

    Xiaowei Wang

    2014-01-01

    Full Text Available This paper proposes a stepped selection method based on spectral kurtosis relative energy entropy. Firstly, the length and type of window function are set; then when fault occurs, enter step 1: the polarity of first half-wave extremes is analyzed; if the ratios of extremes between neighboring lines are positive, the bus bar is the fault line, else, the SK relative energy entropies are calculated, and then enter step 2: if the obtained entropy multiple is bigger than the threshold or equal to the threshold, the overhead line of max entropy corresponding is the fault line, if not, enter step 3: the line of max entropy corresponding is the fault line. At last, the applicability of the proposed algorithm is presented, and the comparison results are discussed.

  20. Operator care and eco-concerned development of a fast, facile and economical assay for basic nitrogenous drugs based on simplified ion-pair mini-scale extraction using safer solvent combined with drop-based spectrophotometry.

    Science.gov (United States)

    Plianwong, Samarwadee; Sripattanaporn, Areerut; Waewsa-nga, Kwanrutai; Buacheen, Parin; Opanasopit, Praneet; Ngawhirunpat, Tanasait; Rojanarata, Theerasak

    2012-08-30

    A fast, facile, and economical assay for basic nitrogenous drugs has been developed based on the mini-scale extraction of the drug-dye ion pair complex combined with the use of safe-for-analyst and eco-friendlier organic extractant and drop-based micro-spectrophotometry. Instead of using large volume devices, the extraction was simply carried out in typical 1.5 mL microcentrifuge tubes along with the use of micropipettes for accurate transfer of liquids, vortex mixer for efficient partitioning of solutes and benchtop centrifuge for rapid phase separation. In the last step, back-extraction was performed by using the microvolume of acidic solution in order to concentrate the colored species into a confined aqueous microdrop and to keep the analyst away from unwanted contact and inhalation of organic solvents during the quantitation step which was achieved by using cuvetteless UV-vis micro-spectrophotometry without any prior dilutions. Using chlorpheniramine maleate as a representative analyte and n-butyl acetate as a less toxic and non-ozone depleting extractant, the miniaturized method was less laborious and much faster. It was accurate, precise and insensitive to the interferences from common excipients. Notably, it gave the assay results of drug in tablets and oral solution comparable to the large-scale pharmacopeial method while the consumption of organic solvents and the release of wastes were lowered by 200-400 folds.

  1. Nematic fluctuations, fermiology and the pairing potential in iron-based superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Kretzschmar, Florian

    2015-08-18

    The thesis comprises a systematic study on the doping, temperature and momentum dependent electron dynamics in iron-based superconductors using inelastic light scattering. The observation of Bardasis-Schrieffer modes in the excitation spectrum of superconducting Ba{sub 0.6}K{sub 0.4}Fe{sub 2}As{sub 2} is reported and the energy and symmetry dependence of the modes are analyzed. The analysis yields the identification of a strong subdominant component of the interaction potential V(k,k{sup '}). Strong nematic fluctuations are investigated in Ba(Fe{sub 1-x}Co{sub x}){sub 2}As{sub 2}. The nature of the fluctuations and the origin of nematicity in Ba(Fe{sub 1-x}Co{sub x}){sub 2}As{sub 2} are identified.

  2. Cyanine-based probe\\tag-peptide pair fluorescence protein imaging and fluorescence protein imaging methods

    Science.gov (United States)

    Mayer-Cumblidge, M. Uljana; Cao, Haishi

    2013-01-15

    A molecular probe comprises two arsenic atoms and at least one cyanine based moiety. A method of producing a molecular probe includes providing a molecule having a first formula, treating the molecule with HgOAc, and subsequently transmetallizing with AsCl.sub.3. The As is liganded to ethanedithiol to produce a probe having a second formula. A method of labeling a peptide includes providing a peptide comprising a tag sequence and contacting the peptide with a biarsenical molecular probe. A complex is formed comprising the tag sequence and the molecular probe. A method of studying a peptide includes providing a mixture containing a peptide comprising a peptide tag sequence, adding a biarsenical probe to the mixture, and monitoring the fluorescence of the mixture.

  3. ATMS Step By Step.

    Science.gov (United States)

    National Library of Australia, Canberra.

    This manual is designed to provide an introduction and basic guide to the use of IBM's Advanced Text Management System (ATMS), the text processing system to be used for the creation of Australian data bases within AUSINET. Instructions are provided for using the system to enter, store, retrieve, and modify data, which may then be displayed at the…

  4. Andreev reflection and bound states in topological insulator based planar and step Josephson junctions

    Science.gov (United States)

    Choudhari, Tarun; Deo, Nivedita

    2017-01-01

    A superconductor-topological insulator-superconductor (S/TI/S) junction having normal region at angle θ is studied theoretically to investigate the junction angle dependency of the Andreev reflection and the formation of the Andreev bound states in the step and planar S/TI/S structures. It is found that the Andreev reflection becomes θ dependent only in the presence of the potential barrier at the TI/S interface. In particular, the step and planar TI/S junction have totally different conductive behavior with bias voltage and potential barrier in the regime of retro and specular Andreev reflection. Interestingly, we find that the elliptical cross section of Dirac cone, an important feature of topological insulator with step surface defect, affects the Fabry-Perot resonance of the Andreev reflection induced Andreev bound states (which become Majorana zero energy states at low chemical potential) in the step S/TI/S structure. Unlike the usual planar S/TI/S structures, we find these ellipticity affected Andreev bound states lead to non-monotonic Josephson super-current in the step S/TI/S structure whose non-monotonicity can be controlled with the use of the potential barrier, which may find applications in nanoelectronics.

  5. A model for gamma-ray binaries, based on the effect of pair production feedback in shocked pulsar winds

    CERN Document Server

    Derishev, E

    2016-01-01

    We analyze the model of gamma-ray binaries, consisting of a massive star and a pulsar with ultrarelativistic wind. We consider radiation from energetic particles, accelerated at the pulsar wind termination shock, and feedback of this radiation on the wind through production of secondary electron-positron pairs. We show that the pair feedback limits the Lorentz factor of the pulsar wind and creates a population of very energetic pairs, whose radiation may be responsible for the observed gamma-ray signal.

  6. Implementation of Real-Time Machining Process Control Based on Fuzzy Logic in a New STEP-NC Compatible System

    Directory of Open Access Journals (Sweden)

    Po Hu

    2016-01-01

    Full Text Available Implementing real-time machining process control at shop floor has great significance on raising the efficiency and quality of product manufacturing. A framework and implementation methods of real-time machining process control based on STEP-NC are presented in this paper. Data model compatible with ISO 14649 standard is built to transfer high-level real-time machining process control information between CAPP systems and CNC systems, in which EXPRESS language is used to define new STEP-NC entities. Methods for implementing real-time machining process control at shop floor are studied and realized on an open STEP-NC controller, which is developed using object-oriented, multithread, and shared memory technologies conjunctively. Cutting force at specific direction of machining feature in side mill is chosen to be controlled object, and a fuzzy control algorithm with self-adjusting factor is designed and embedded in the software CNC kernel of STEP-NC controller. Experiments are carried out to verify the proposed framework, STEP-NC data model, and implementation methods for real-time machining process control. The results of experiments prove that real-time machining process control tasks can be interpreted and executed correctly by the STEP-NC controller at shop floor, in which actual cutting force is kept around ideal value, whether axial cutting depth changes suddenly or continuously.

  7. Numerical research of dynamic characteristics in tower solar cavity receiver based on step-change radiation flux

    Science.gov (United States)

    Chen, Zhengwei; Wang, Yueshe; Hao, Yun; Wang, Qizhi

    2013-07-01

    The solar cavity receiver is an important light-energy to thermal-energy convector in the tower solar thermal power plant system. The heat flux in the inner surface of the cavity will show the characteristics of non-continuous step change especially in non-normal and transient weather conditions, which may result in a continuous dynamic variation of the characteristic parameters. Therefore, the research of dynamic characteristics of the receiver plays a very important role in the operation and the control safely in solar cavity receiver system. In this paper, based on the non-continuous step change of radiation flux, a non-linear dynamic model is put forward to obtain the effects of the non-continuous step change radiation flux and step change feed water flow on the receiver performance by sequential modular approach. The subject investigated in our study is a 1MW solar power station constructed in Yanqing County, Beijing. This study has obtained the dynamic responses of the characteristic parameters in the cavity receiver, such as drum pressure, drum water level, main steam flow and main steam enthalpy under step change radiation flux. And the influence law of step-change feed water flow to the dynamic characteristics in the receiver also has been analyzed. The results have a reference value for the safe operation and the control in solar cavity receiver system.

  8. Simulation and Prototype Design of Variable Step Angle Techniques Based Asteroid Deflection for Future Planetary Mission

    Science.gov (United States)

    Sathiyavel, C.

    2016-07-01

    Asteroids are minor planets, especially those of the inner Solar System. The most desirable asteroids for cross the geo-synchronous orbit are the carbonaceous C-type asteroids that are deemed by the astronomy community to have a planetary protection categorization of unrestricted Earth return. The mass of near earth Asteroids (assuming spherical asteroid) as a function of its diameter varies from 2 m to 10m, the corresponding densities from 1.9/cm3 to 3.8 g/cm3. For example, a 6.5-m diameter asteroid with a density of 2.8 g/cm3 has a mass of order 4,00,000 kg. If this Asteroid falls on earth then the earth will be destroyed at when the equally of inclination angle both of earth and Asteroid. My proposed work is how we can avert this great danger for near feature the above mass of Asteroid. The present work is Simulation and Prototype Design of a Variable Step Angle Techniques Based Asteroid Deflection for future planetary Mission. Proposed method is comparing with previous method that will be very useful to achieving hit the ion velocity to asteroid surface in several direction at static position of Asteroid deviate mission[ADM].The deviate angle α1 to α2 with help of Variable step angle techniques, it is containing Stepper Motor with attach of Ion propulsion module system.VASAT module is locating the top edge on the three axis stabilized Method in ADM.The three axis stabilized method is including the devices are like Gyroscope sensor ,Arduino Microcontroller system and ion propulsion techniques. Arduino Microcontroller system determines the orientation from gyroscope sensor. Then it uses ion Propulsion techniques modules to control the required motion like pitch, yaw and roll attitude of the ADM. The exhaust thrust value is 1500 mN and velocity is 10,000 m/s [from simulation results but experimental output results is small because low quality of Components is used in research lab] .The propulsion techniques also used as a static position of ADM Mission [both

  9. Vortex scattering by step topography

    Science.gov (United States)

    Hinds, A. K.; Johnson, E. R.; McDonald, N. R.

    The scattering at a rectilinear step change in depth of a shallow-water vortex pair consisting of two patches of equal but opposite-signed vorticity is studied. Using the constants of motion, an explicit relationship is derived relating the angle of incidence to the refracted angle after crossing. A pair colliding with a step from deep water crosses the escarpment and subsequently propagates in shallow water refracted towards the normal to the escarpment. A pair colliding with a step from shallow water either crosses and propagates in deep water refracted away from the normal or, does not cross the step and is instead totally internally reflected by the escarpment. For large depth changes, numerical computations show that the coherence of the vortex pair is lost on encountering the escarpment.

  10. Estimating Digital Inter-Symbol Interference Channel Blindly Based on the One-Step Branch Transition Rules in Trellises

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A novel discrete-time digital inter-symbol interference (ISI) channel blind estimation sub-optimal algorithm is proposed. This algorithm reduces the complexity of the optimal maximum likelihood sequence estimation(MLSE) considerably based on the one-step branch transition rules in trellises, and is suitable for the estimation of the channels with small lengths of ISI.

  11. Step-based translation of physical activity guidelines in the Lower Mississippi Delta

    Science.gov (United States)

    To determine how many steps/day equate to current moderate-to-vigorous physical activity (MVPA) guidelines in a population from the Lower Mississippi Delta (LMD) of the United States, 58 overweight adults wore an Actigraph accelerometer (GT3X) for up to two weeks. Minutes/day in MVPA was a good pred...

  12. Multi-step Attack Modelling and Simulation (MsAMS) Framework based on Mobile Ambients

    NARCIS (Netherlands)

    Nunes Leal Franqueira, V.; Lopes, R H C; Eck, van P.A.T.

    2008-01-01

    Attackers take advantage of any security breach to penetrate an organisation perimeter and exploit hosts as stepping stones to reach valuable assets, deeper in the network. The exploitation of hosts is possible not only when vulnerabilities in commercial off-the-shelf (COTS) software components ar

  13. Taking Steps Together: A Family- and Community-Based Obesity Intervention for Urban, Multiethnic Children

    Science.gov (United States)

    Anderson, John D.; Newby, Rachel; Kehm, Rebecca; Barland, Patricia; Hearst, Mary O.

    2015-01-01

    Objectives: Successful childhood obesity intervention models that build sustainable behavioral change are needed, particularly in low-income, ethnic minority communities disparately affected by this problem. Method: Families were referred to Taking Steps Together (TST) by their primary care provider if at least one child had a body mass index…

  14. Differentiation between solid-ankle cushioned heel and energy storage and return prosthetic foot based on step-to-step transition cost.

    Science.gov (United States)

    Wezenberg, Daphne; Cutti, Andrea G; Bruno, Antonino; Houdijk, Han

    2014-01-01

    Decreased push-off power by the prosthetic foot and inadequate roll-over shape of the foot have been shown to increase the energy dissipated during the step-to-step transition in human walking. The aim of this study was to determine whether energy storage and return (ESAR) feet are able to reduce the mechanical energy dissipated during the step-to-step transition. Fifteen males with a unilateral lower-limb amputation walked with their prescribed ESAR foot (Vari-Flex, Ossur; Reykjavik, Iceland) and with a solid-ankle cushioned heel foot (SACH) (1D10, Ottobock; Duderstadt, Germany), while ground reaction forces and kinematics were recorded. The positive mechanical work on the center of mass performed by the trailing prosthetic limb was larger (33%, p = 0.01) and the negative work performed by the leading intact limb was lower (13%, p = 0.04) when walking with the ESAR foot compared with the SACH foot. The reduced step-to-step transition cost coincided with a higher mechanical push-off power generated by the ESAR foot and an extended forward progression of the center of pressure under the prosthetic ESAR foot. Results can explain the proposed improvement in walking economy with this kind of energy storing and return prosthetic foot.

  15. An Analysis of Step, Jt, and Pdf Format Translation Between Constraint-based Cad Systems with a Benchmark Model

    OpenAIRE

    McKenzie-Veal, Dillon

    2012-01-01

    This research was conducted to provide greater depth into the ability of STEP AP 203 Edition 2, JT, and 3D PDF to translate and preserve information while using a benchmark model. The benchmark model was designed based on four industry models and created natively in the five industry leading 3D CAD programs. The native CAD program models were translated using STEP, JT, and 3D PDF. Several criteria were analyzed along the paths of translation from one disparate CAD program to another. Along wi...

  16. A Versatile Strategy to Synthesize Perfluoropolyether-Based Thermoplastic Fluoropolymers by Alkyne-Azide Step-Growth Polymerization.

    Science.gov (United States)

    Lopez, Gérald; Ameduri, Bruno; Habas, Jean-Pierre

    2016-04-01

    Perfluoropolyether (PFPE)-based thermoplastic fluoropolymers are synthesized by A2 + B2 step-growth polymerization between PFPE-diyne and fluorinated diazides. This versatile method allows synthesizing PFPE-based materials with tunable physicochemical properties depending on the exact nature of the fluorinated segment of the diazide precursor. Semicrystalline or amorphous materials endowed with high thermostability (≈300 °C under air) and low glass transition temperature (≈-100 °C) are obtained, as confirmed by differential scanning calorimetry, thermogravimetry, and rheometry. Step-growth polymerizations can be copper-catalyzed but also thermally activated in some cases, thus avoiding the presence of copper residues in the final materials. This strategy opens up new opportunities to easily access PFPE-based materials on an industrial scale. Furthermore, a plethora of developments can be envisioned (e.g., by adding a third trifunctional component to the formulations for the synthesis of PFPE-based elastomers).

  17. Ambiguous base pairing of the purine analogue 1-(2-deoxy-beta-D-ribofuranosyl)-imidazole-4-carboxamide during PCR.

    Science.gov (United States)

    Sala, M; Pezo, V; Pochet, S; Wain-Hobson, S

    1996-09-01

    In principle the hydrogen bonding capacities of 1-(2-deoxy-beta-D-ribofuranosyl)-imidazole-4-carboxamide (dY), and its N-propyl derivative (dYPr), allow them to pair to all four deoxynucleosides. Their triphosphate derivatives (dYTP and dYPrTP) are preferentially incorporated as dATP analogues in a PCR reaction. However, once incorporated into a DNA template their ambiguous hydrogen bonding potential gave rise to misincorporation at frequencies of approximately 3 x 10(-2) per base per amplification. Most of the substitutions were transitions resulting from rotation about the carboxamide bond when part of the template. Between 11-15% of transversions were noted implying rotation of purine or imidazole moieties about the glycosidic bond. As part of a DNA template, dYPr behaved in the same way as dY, despite its propyl moiety. These deoxyimidazole derivatives are among the most radical departures from the canonical bases used so far as substrates in PCR and could be used to generate mutant gene libraries.

  18. Design of A 5-Bit Fully Parallel Analog to Digital Converter Using Common Gate Differrential Mos Pair-Based Comparator

    Science.gov (United States)

    Aytar, Oktay

    2015-09-01

    This paper presents a novel comparator structure based on the common gate differential MOS pair. The proposed comparator has been applied to fully parallel analog to digital converter (A/D converter). Furthermore, this article presents 5 bit fully parallel A/D Converter design using the cadence IC5141 design platform and NCSU(North Carolina State University) design kit with 0.18 μm CMOS technology library. The proposed fully parallel A/D converter consist of resistor array block, comparator block, 1-n decoder block and programmable logic array. The 1-n decoder block includes latch block and thermometer code circuit that is implemented using transmission gate based multiplexer circuit. Thus, sampling frequency and analog bandwidth are increased. The INL and DNL of the proposed fully parallel A/D converter are (0/ + 0.63) LSB and (-0.26/ + 0.31) LSB at a sampling frequency of 5 GS/s with an input signal of 50 MHz, respectively. The proposed fully parallel A/D Converter consumes 340 mW from 1.8 V supply.

  19. Deconstructing Chronic Low Back Pain in the Older Adult – Step by Step Evidence and Expert-Based Recommendations for Evaluation and Treatment: Part III: Fibromyalgia Syndrome

    Science.gov (United States)

    Fatemi, Gita; Fang, Meika A.; Breuer, Paula; Cherniak, Paul E.; Gentili, Angela; Hanlon, Joseph T.; Karp, Jordan F.; Morone, Natalia E.; Rodriguez, Eric; Rossi, Michelle I.; Schmader, Kenneth; Weiner, Debra K.

    2016-01-01

    Objective To present the third in a series of articles designed to deconstruct chronic low back pain (CLBP) in older adults. The series presents CLBP as a syndrome, a final common pathway for the expression of multiple contributors rather than a disease localized exclusively to the lumbosacral spine. Each article addresses one of twelve important contributors to pain and disability in older adults with CLBP. This article focuses on fibromyalgia syndrome (FMS). Methods A modified Delphi approach was used to create the evaluation and treatment algorithm, the table discussing the rationale behind each of the algorithm components, and the stepped-care drug recommendations. The team involved in the creation of these materials consisted of a principal investigator, a 5-member content expert panel, and a 9-member primary care panel. The evaluation and treatment recommendations were based on availability of medications and other resources within the Veterans Health Administration (VHA) facilities. However, non-VHA panelists were also involved in the development of these materials, which can be applied to both VA and civilian settings. The illustrative clinical case was taken from the clinical practice of the principal investigator. Results Following expert consultations and a review of the literature, we developed an evaluation and treatment algorithm with supporting materials to aid in the care of older adults with CLBP who have concomitant FMS. A case is presented that demonstrates the complexity of pain evaluation and management in older patients with CLBP and concomitant FMS Conclusions Recognition of FMS as a common contributor to CLBP in older adults and initiating treatment targeting both FMS and CLBP will lead to improved outcomes in pain and disability. PMID:26272644

  20. Life Cost Based FMEA Manual: A Step by Step Guide to Carrying Out a Cost-based Failure Modes and Effects Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Rhee, Seung; Spencer, Cherrill; /Stanford U. /SLAC

    2009-01-23

    definition of detection difficulty (D) is how well the organization controls the development process. Another definition relates to the detectability of a particular failure in the product when it is in the hands of the customer. The former asks 'What is the chance of catching the problem before we give it to the customer'? The latter asks 'What is the chance of the customer catching the problem before the problem results in a catastrophic failure?' (Palady, 1995) These differing definitions confuse the FMEA users when one tries to determine detection difficulty. Are we trying to measure how easy it is to detect where a failure has occurred or when it has occurred? Or are we trying to measure how easy or difficult it is to prevent failures? Ordinal scale variables are used to rank-order industries such as, hotels, restaurants, and movies (Note that a 4 star hotel is not necessarily twice as good as a 2 star hotel). Ordinal values preserve rank in a group of items, but the distance between the values cannot be measured since a distance function does not exist. Thus, the product or sum of ordinal variables loses its rank since each parameter has different scales. The RPN is a product of 3 independent ordinal variables, it can indicate that some failure types are 'worse' than others, but give no quantitative indication of their relative effects. To resolve the ambiguity of measuring detection difficulty and the irrational logic of multiplying 3 ordinal indices, a new methodology was created to overcome these shortcomings, Life Cost-Based FMEA. Life Cost-Based FMEA measures failure/risk in terms of monetary cost. Cost is a universal parameter that can be easily related to severity by engineers and others. Thus, failure cost can be estimated using the following simplest form: Expected Failure Cost = {sup n}{Sigma}{sub i=1}p{sub i}c{sub i}, p: Probability of a particular failure occurring; c: Monetary cost associated with that particular failure; and

  1. Investigation on the ion pair amphiphiles and their in vitro release of amantadine drug based on PLGA–PEG–PLGA gel

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaoxia, E-mail: yxx-678@163.com; Ji, Xiaoqing; Shi, Chunhuan; Liu, Jing [Shandong University, School of Pharmaceutical Science and Center for Pharmaceutical Research & Drug Delivery Systems (China); Wang, Haiyang [Institute of Materia Medica Shandong Academy of Medical Sciences, Shandong Taitian Newdrug Discovery Co.Ltd (China); Luan, Yuxia, E-mail: yuxialuan@sdu.edu.cn [Shandong University, School of Pharmaceutical Science and Center for Pharmaceutical Research & Drug Delivery Systems (China)

    2014-12-15

    The amantadine drug and oleic acid surfactant are used to form amantadine-based ion pair amphiphiles based on proton transfer reaction between the drug and the surfactant molecules. The ion pair amphiphiles are characterized by {sup 1}H-nuclear magnetic resonance, Fourier transform infrared spectroscopy, and X-ray diffraction. Self-assembly properties of amantadine-based ion pair amphiphiles are studied by surface tension determination, transmission electron microscopy, zeta potential, and dynamic light scattering. The aggregation behavior studies indicate that the as-prepared ion pair amphiphiles can self-assemble into vesicles with the size of 200–300 nm in aqueous solution. The drug release results show that the amantadine release rate could be well controlled by incorporating the amantadine-based ion pair vesicles in poly (lactic-co-glycolic acid)-poly (ethylene glycol)-poly (lactic-co-glycolic acid) (PLGA–PEG–PLGA) copolymer hydrogel. The drug release from the AT–OA vesicle-loaded PLGA–PEG–PLGA hydrogel is significantly inhibited in comparison with the AT-loaded PLGA–PEG–PLGA hydrogel. The present work thus demonstrates that the vesicle-loaded hydrogel is a good candidate for the drug delivery system with long-term controlled drug release behavior.

  2. Design of laser pulses for selective vibrational excitation of the N6-H bond of adenine and adenine-thymine base pair using optimal control theory.

    Science.gov (United States)

    Sharma, Sitansh; Sharma, Purshotam; Singh, Harjinder; Balint-Kurti, Gabriel G

    2009-06-01

    Time dependent quantum dynamics and optimal control theory are used for selective vibrational excitation of the N6-H (amino N-H) bond in free adenine and in the adenine-thymine (A-T) base pair. For the N6-H bond in free adenine we have used a one dimensional model while for the hydrogen bond, N6-H(A)...O4(T), present in the A-T base pair, a two mathematical dimensional model is employed. The conjugate gradient method is used for the optimization of the field dependent cost functional. Optimal laser fields are obtained for selective population transfer in both the model systems, which give virtually 100% excitation probability to preselected vibrational levels. The effect of the optimized laser field on the other hydrogen bond, N1(A)...H-N3(T), present in A-T base pair is also investigated.

  3. Surface chemical modification of TEOS based silica aerogels synthesized by two step (acid-base) sol-gel process

    Energy Technology Data Exchange (ETDEWEB)

    Bhagat, Sharad D. [Air Glass Laboratory, Department of Physics, Shivaji University, Kolhapur 416 004, Maharashtra (India); Rao, A. Venkateswara [Air Glass Laboratory, Department of Physics, Shivaji University, Kolhapur 416 004, Maharashtra (India)]. E-mail: avrao_phy@unishivaji.ac.in

    2006-04-15

    The present paper describes the comparative studies on the hydrophobic and physical properties of the tetraethoxysilane (TEOS) based silica aerogels prepared by two step sol-gel process followed by supercritical drying. Silica alcogels were prepared by keeping the molar ratio of TEOS:methanol (MeOH):H{sub 2}O (acidic):H{sub 2}O (basic) constant at 1:33:3.5:3.5 with oxalic acid and ammonium hydroxide concentrations fixed at 0.001 and 1 M, respectively. In all, nine different co-precursors (CP) of the type R {sub n}SiX{sub 4-n}, have been used. The aerogels have been characterized by density, porosity, percentage of volume shrinkage, optical transmission, contact angle and thermal conductivity measurements. The surface chemical modification of silica aerogels was confirmed by the presence of C-H and Si-C peaks at 2900, 1450 and 840 cm{sup -1}, respectively, from the Fourier transform-infrared spectroscopy (FT-IR). The microstructure of the aerogels was studied using transmission electron microscopy (TEM) and scanning electron microscopy (SEM) techniques. In addition to these studies, the stability of the hydrophobic aerogels against an organic impurity (methanol, in the present studies) in water has also been studied.

  4. Surface chemical modification of TEOS based silica aerogels synthesized by two step (acid base) sol gel process

    Science.gov (United States)

    Bhagat, Sharad D.; Rao, A. Venkateswara

    2006-04-01

    The present paper describes the comparative studies on the hydrophobic and physical properties of the tetraethoxysilane (TEOS) based silica aerogels prepared by two step sol-gel process followed by supercritical drying. Silica alcogels were prepared by keeping the molar ratio of TEOS:methanol (MeOH):H 2O (acidic):H 2O (basic) constant at 1:33:3.5:3.5 with oxalic acid and ammonium hydroxide concentrations fixed at 0.001 and 1 M, respectively. In all, nine different co-precursors (CP) of the type R nSiX 4 - n, have been used. The aerogels have been characterized by density, porosity, percentage of volume shrinkage, optical transmission, contact angle and thermal conductivity measurements. The surface chemical modification of silica aerogels was confirmed by the presence of C sbnd H and Si sbnd C peaks at 2900, 1450 and 840 cm -1, respectively, from the Fourier transform-infrared spectroscopy (FT-IR). The microstructure of the aerogels was studied using transmission electron microscopy (TEM) and scanning electron microscopy (SEM) techniques. In addition to these studies, the stability of the hydrophobic aerogels against an organic impurity (methanol, in the present studies) in water has also been studied.

  5. Multi-step-prediction of chaotic time series based on co-evolutionary recurrent neural network

    Institute of Scientific and Technical Information of China (English)

    Ma Qian-Li; Zheng Qi-Lun; Peng Hong; Zhong Tan-Wei; Qin Jiang-Wei

    2008-01-01

    This paper proposes a co-evolutionary recurrent neural network (CERNN) for the multi-step-prediction of chaotic time series,it estimates the proper parameters of phase space reconstruction and optimizes the structure of recurrent neural networks by co-evolutionary strategy.The searching space was separated into two subspaces and the individuals are trained in a parallel computational procedure.It can dynamically combine the embedding method with the capability of recurrent neural network to incorporate past experience due to internal recurrence.The effectiveness of CERNN is evaluated by using three benchmark chaotic time series data sets:the Lorenz series,Mackey-Glass series and real-world sun spot series.The simulation results show that CERNN improves the performances of multi-step-prediction of chaotic time series.

  6. Double loop control strategy with different time steps based on human characteristics.

    Science.gov (United States)

    Gu, Gwang Min; Lee, Jinoh; Kim, Jung

    2012-01-01

    This paper proposes a cooperative control strategy in consideration of the force sensitivity of human. The strategy consists of two loops: one is the intention estimation loop whose sampling time can be variable in order to investigate the effect of the sampling time; the other is the position control loop with fixed time step. A high sampling rate is not necessary for the intention estimation loop due to the bandwidth of the mechanoreceptors in humans. In addition, the force sensor implemented in the robot is sensitive to the noise induced from the sensor itself and tremor of the human. Multiple experiments were performed with the experimental protocol using various time steps of the intention estimation loop to find the suitable sampling times in physical human robot interaction. The task involves pull-and-push movement with a two-degree-of-freedom robot, and the norm of the interaction force was obtained for each experiment as the measure of the cooperative control performance.

  7. Control of a Uniform Step Asymmetrical 9-Level Inverter Based on Artificial Neural Network Strategy

    Directory of Open Access Journals (Sweden)

    Rachid Taleb

    2009-12-01

    Full Text Available A neural implementation of a harmonic elimination strategy for the control auniform step asymmetrical 9-level inverter is proposed and described in this paper. AMulti-Layer Perceptrons (MLP neural network is used to approximate the mappingbetween the modulation rate and the required switching angles. After learning, the neuralnetwork generates the appropriate switching angles for the inverter. This leads to a lowcomputational-cost neural controller which is therefore well suited for real-timeapplications. This neural approach is compared to the well-known Multi-Carrier Pulse-Width Modulation (MCPWM. Simulation results demonstrate the technical advantages ofthe neural implementation of the harmonic elimination strategy over the conventionalmethod for the control of an uniform step asymmetrical 9-level inverter. The approach isused to supply an asynchronous machine and results show that the neural method ensures ahighest quality torque by efficiently canceling the harmonics generated by the inverter.

  8. FIRST STEPS TOWARDS AN INTEGRATED CITYGML-BASED 3D MODEL OF VIENNA

    Directory of Open Access Journals (Sweden)

    G. Agugiaro

    2016-06-01

    This paper reports about the experiences done so far, it describes the test area and the available data sources, it shows and exemplifies the data integration issues, the strategies developed to solve them in order to obtain the integrated 3D city model. The first results as well as some comments about their quality and limitations are presented, together with the discussion regarding the next steps and some planned improvements.

  9. SmartFit: A Step Count Based Mobile Application for Engagement in Physical Activities

    Directory of Open Access Journals (Sweden)

    Atifa Sarwar

    2015-08-01

    Full Text Available Research has found that relatively few people en-gage in regular exercise or other physical activities. Despite the availability of numerous mobile applications and specialized devices for self-tracking, people mostly lack the motivation for performing physical activities. In this article we present SmartFit, a mobile application that uses step count for promoting the physical activities in adults. This article points out that while considering walk, activity duration is not sufficient for deter-mining users activeness state. Step count is another factor that should be taken into account. For this we propose an approach for converting the steps into duration for which activity has been performed. This duration is then used in Smartfit for categorizing user into different activeness levels. Gamification techniques have been incorporated in SmartFit as they are found to serve the purpose of motivating and encouraging the user. Gamification is used for awarding/deducting points to user in order to keep them engaged for longer period. Furthermore feedback is also provided to users depending upon their goal and achieved progress. The objective is to facilitate and motivate the user and then keep them engaged in carrying out the recommended level of physical activities.

  10. A Large Scale Daylighting System Based on a Stepped Thickness Waveguide

    Directory of Open Access Journals (Sweden)

    Ngoc Hai Vu

    2016-01-01

    Full Text Available This paper presents a study on the use of optical fiber and a solar concentrator for a building daylighting system. Daylighting is essential for improving indoor environments and reducing electric lighting power consumption in office buildings. Traditionally, optical fiber daylighting systems were implemented only on a small scale. More complicated technologies are required for more amounts of daylight over further distance via a smaller light guider. The proposed solar lighting system with optical fiber is composed of an array of linear Fresnel lenses and a stepped thickness waveguide. The linear Fresnel lenses collect light into the stepped thickness waveguide. The stepped-thickness waveguide is an optical component which redirects focused sunlight from the vertical direction to the horizontal direction, and it guides light to the attached optical fiber. Simulation models were developed using commercial optical simulation tools (LightTools™. The optical efficiency and angular tolerance of the system are analyzed. The overall system cost is also estimated. Some considerations on the economic expansion of the system in terms of efficiency and estimated annual average energy saving are discussed. The results show that the presented optical fiber daylighting system is a strong candidate for low-price and highly efficient solution for solar energy application to building energy savings.

  11. Coupled Inductor Based High Step-Up DC-DC Converter for Multi Input PV System

    Directory of Open Access Journals (Sweden)

    G. Shiny Vikram

    2014-09-01

    Full Text Available With the shortage of the energy and ever increasing of the oil price, research on the renewable and green energy sources, especially the solar arrays and the fuel cells, becomes more and more important. How to achieve high step-up and high efficiency DC/DC converters is the major consideration in the renewable power applications due to the low voltage of PV arrays and fuel cells. In this paper a coupled inductor dc-dc converter for photovoltaic system is proposed. The circuit configuration of the proposed converter is very simple. Thus, the proposed converter has higher step-up and step-down voltage gains than the conventional bidirectional dc–dc boost/buck converter. Under same electric specifications for the proposed converter and the conventional bidirectional boost/buck converter, the average value of the switch current in the proposed converter is less than the conventional bidirectional boost/buck converter. The operating principles have been applied to multi input photovoltaic system and outputs have been observed.

  12. Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition.

    Directory of Open Access Journals (Sweden)

    Edze R Westra

    Full Text Available Discriminating self and non-self is a universal requirement of immune systems. Adaptive immune systems in prokaryotes are centered around repetitive loci called CRISPRs (clustered regularly interspaced short palindromic repeat, into which invader DNA fragments are incorporated. CRISPR transcripts are processed into small RNAs that guide CRISPR-associated (Cas proteins to invading nucleic acids by complementary base pairing. However, to avoid autoimmunity it is essential that these RNA-guides exclusively target invading DNA and not complementary DNA sequences (i.e., self-sequences located in the host's own CRISPR locus. Previous work on the Type III-A CRISPR system from Staphylococcus epidermidis has demonstrated that a portion of the CRISPR RNA-guide sequence is involved in self versus non-self discrimination. This self-avoidance mechanism relies on sensing base pairing between the RNA-guide and sequences flanking the target DNA. To determine if the RNA-guide participates in self versus non-self discrimination in the Type I-E system from Escherichia coli we altered base pairing potential between the RNA-guide and the flanks of DNA targets. Here we demonstrate that Type I-E systems discriminate self from non-self through a base pairing-independent mechanism that strictly relies on the recognition of four unchangeable PAM sequences. In addition, this work reveals that the first base pair between the guide RNA and the PAM nucleotide immediately flanking the target sequence can be disrupted without affecting the interference phenotype. Remarkably, this indicates that base pairing at this position is not involved in foreign DNA recognition. Results in this paper reveal that the Type I-E mechanism of avoiding self sequences and preventing autoimmunity is fundamentally different from that employed by Type III-A systems. We propose the exclusive targeting of PAM-flanked sequences to be termed a target versus non-target discrimination mechanism.

  13. Paired fuzzy sets

    DEFF Research Database (Denmark)

    Rodríguez, J. Tinguaro; Franco de los Ríos, Camilo; Gómez, Daniel

    2015-01-01

    In this paper we want to stress the relevance of paired fuzzy sets, as already proposed in previous works of the authors, as a family of fuzzy sets that offers a unifying view for different models based upon the opposition of two fuzzy sets, simply allowing the existence of different types...

  14. Pairing Learners in Pair Work Activity

    Science.gov (United States)

    Storch, Neomy; Aldosari, Ali

    2013-01-01

    Although pair work is advocated by major theories of second language (L2) learning and research findings suggest that pair work facilitates L2 learning, what is unclear is how to best pair students in L2 classes of mixed L2 proficiency. This study investigated the nature of pair work in an English as a Foreign Language (EFL) class in a college in…

  15. 基于双线性对的WSN密钥协商和认证协议%WSN Key Negotiation and Authentication Protocol Based on Bilinear Pairings

    Institute of Scientific and Technical Information of China (English)

    赵跃华; 黄淑美

    2012-01-01

    无线传感器网络(WSN)节点在电源、计算能力和内存容量等方面存在局限性,且面临的安全威胁更复杂.为此,提出一种适用于类LEACH路由的WSN密钥协商和认证协议.通过引入当前轮数,实现节点间的双向身份认证,以抵御选择性转发、Sybil和Hello泛洪等常见攻击.利用ID和双线性对原理生成节点间的动态会话密钥,从而减少节点间的交互步骤,降低能耗.SVO逻辑推理和性能分析结果表明,该协议同时满足安全性要求和WSN的特殊应用要求.%Due to the limitations of power, computation capability and storage resources, as well as the more complex security threats the current network faces, a pairings-based key negotiation and authentication protocol for class LEACH routing in Wireless Sensor Netwoik(WSN) is proposed, which achieves bidirectional authentication between nodes by introducing the current round of routing to defend familiar attacks such as selective forwarding, Sybil attack, and Hello flood attack in WSN. And dynamic session keys between nodes are generated by using ID and bilinear principle, which reduces the interaction steps between nodes and energy costs. SVO logic reasoning and performance analysis show that the protocol can guarantee the security of WSN, and it meet the special application requirements of WSN.

  16. Base pairing interaction between 5'- and 3'-UTRs controls icaR mRNA translation in Staphylococcus aureus.

    Directory of Open Access Journals (Sweden)

    Igor Ruiz de los Mozos

    Full Text Available The presence of regulatory sequences in the 3' untranslated region (3'-UTR of eukaryotic mRNAs controlling RNA stability and translation efficiency is widely recognized. In contrast, the relevance of 3'-UTRs in bacterial mRNA functionality has been disregarded. Here, we report evidences showing that around one-third of the mapped mRNAs of the major human pathogen Staphylococcus aureus carry 3'-UTRs longer than 100-nt and thus, potential regulatory functions. We selected the long 3'-UTR of icaR, which codes for the repressor of the main exopolysaccharidic compound of the S. aureus biofilm matrix, to evaluate the role that 3'-UTRs may play in controlling mRNA expression. We showed that base pairing between the 3'-UTR and the Shine-Dalgarno (SD region of icaR mRNA interferes with the translation initiation complex and generates a double-stranded substrate for RNase III. Deletion or substitution of the motif (UCCCCUG within icaR 3'-UTR was sufficient to abolish this interaction and resulted in the accumulation of IcaR repressor and inhibition of biofilm development. Our findings provide a singular example of a new potential post-transcriptional regulatory mechanism to modulate bacterial gene expression through the interaction of a 3'-UTR with the 5'-UTR of the same mRNA.

  17. Perturbative triples correction for local pair natural orbital based explicitly correlated CCSD(F12*) using Laplace transformation techniques

    Science.gov (United States)

    Schmitz, Gunnar; Hättig, Christof

    2016-12-01

    We present an implementation of pair natural orbital coupled cluster singles and doubles with perturbative triples, PNO-CCSD(T), which avoids the quasi-canonical triples approximation (T0) where couplings due to off-diagonal Fock matrix elements are neglected. A numerical Laplace transformation of the canonical expression for the perturbative (T) triples correction is used to avoid an I/O and storage bottleneck for the triples amplitudes. Results for a test set of reaction energies show that only very few Laplace grid points are needed to obtain converged energy differences and that PNO-CCSD(T) is a more robust approximation than PNO-CCSD(T0) with a reduced mean absolute deviation from canonical CCSD(T) results. We combine the PNO-based (T) triples correction with the explicitly correlated PNO-CCSD(F12*) method and investigate the use of specialized F12-PNOs in the conventional triples correction. We find that no significant additional errors are introduced and that PNO-CCSD(F12*)(T) can be applied in a black box manner.

  18. Implementation of FFT by using MATLAB: SIMULINK on Xilinx Virtex-4 FPGAs: Performance of a Paired Transform Based FFT

    Directory of Open Access Journals (Sweden)

    Ranganadh Narayanam

    2013-06-01

    Full Text Available Discrete Fourier Transform is principal mathematical method for the frequency analysis and is having wide applications in Engineering and Sciences. Because the DFT is so ubiquitous, fast methods for computing DFT have been studied extensively, and continuous to be an active research. The way of splitting the DFT gives out various fast algorithms. In this paper, we present the implementation of two fast algorithms for the DFT for evaluating their performance. One of them is the popular radix-2 Cooley-Tukey fast Fourier transform algorithm (FFT [1] and the other one is the Grigoryan FFT based on the splitting by the paired transform [2]. We evaluate the performance of these algorithms by implementing them on the Xilinx Virtex-4 FPGAs [3], by developing our own FFT processor architectures. Finally we show that the Grigoryan FFT is working faster than Cooley-Tukey FFT, consequently it is useful for higher sampling rates. Operating at higher sampling rates is a challenge in DSP applications.

  19. Representation of multi-target activity landscapes through target pair-based compound encoding in self-organizing maps.

    Science.gov (United States)

    Iyer, Preeti; Bajorath, Jürgen

    2011-11-01

    Activity landscape representations provide access to structure-activity relationships information in compound data sets. In general, activity landscape models integrate molecular similarity relationships with biological activity data. Typically, activity against a single target is monitored. However, for steadily increasing numbers of compounds, activity against multiple targets is reported, resulting in an opportunity, and often a need, to explore multi-target structure-activity relationships. It would be attractive to utilize activity landscape representations to aid in this process, but the design of activity landscapes for multiple targets is a complicated task. Only recently has a first multi-target landscape model been introduced, consisting of an annotated compound network focused on the systematic detection of activity cliffs. Herein, we report a conceptually different multi-target activity landscape design that is based on a 2D projection of chemical reference space using self-organizing maps and encodes compounds as arrays of pair-wise target activity relationships. In this context, we introduce the concept of discontinuity in multi-target activity space. The well-ordered activity landscape model highlights centers of discontinuity in activity space and is straightforward to interpret. It has been applied to analyze compound data sets with three, four, and five target annotations and identify multi-target structure-activity relationships determinants in analog series.

  20. Base pairing interaction between 5'- and 3'-UTRs controls icaR mRNA translation in Staphylococcus aureus.

    Science.gov (United States)

    Ruiz de los Mozos, Igor; Vergara-Irigaray, Marta; Segura, Victor; Villanueva, Maite; Bitarte, Nerea; Saramago, Margarida; Domingues, Susana; Arraiano, Cecilia M; Fechter, Pierre; Romby, Pascale; Valle, Jaione; Solano, Cristina; Lasa, Iñigo; Toledo-Arana, Alejandro

    2013-01-01

    The presence of regulatory sequences in the 3' untranslated region (3'-UTR) of eukaryotic mRNAs controlling RNA stability and translation efficiency is widely recognized. In contrast, the relevance of 3'-UTRs in bacterial mRNA functionality has been disregarded. Here, we report evidences showing that around one-third of the mapped mRNAs of the major human pathogen Staphylococcus aureus carry 3'-UTRs longer than 100-nt and thus, potential regulatory functions. We selected the long 3'-UTR of icaR, which codes for the repressor of the main exopolysaccharidic compound of the S. aureus biofilm matrix, to evaluate the role that 3'-UTRs may play in controlling mRNA expression. We showed that base pairing between the 3'-UTR and the Shine-Dalgarno (SD) region of icaR mRNA interferes with the translation initiation complex and generates a double-stranded substrate for RNase III. Deletion or substitution of the motif (UCCCCUG) within icaR 3'-UTR was sufficient to abolish this interaction and resulted in the accumulation of IcaR repressor and inhibition of biofilm development. Our findings provide a singular example of a new potential post-transcriptional regulatory mechanism to modulate bacterial gene expression through the interaction of a 3'-UTR with the 5'-UTR of the same mRNA.

  1. Can copper(II) mediate Hoogsteen base-pairing in a left-handed DNA duplex? A pulse EPR study.

    Science.gov (United States)

    Santangelo, Maria Grazia; Antoni, Philipp M; Spingler, Bernhard; Jeschke, Gunnar

    2010-02-22

    Pulse EPR spectroscopy is used to investigate possible structural features of the copper(II) ion coordinated to poly(dG-dC).poly(dG-dC) in a frozen aqueous solution, and the structural changes of the polynucleotide induced by the presence of the metal ion. Two different copper species were identified and their geometry explained by a molecular model. According to this model, one species is exclusively coordinated to a single guanine with the N7 nitrogen atom forming a coordinative bond with the copper. In the other species, a guanine and a cytosine form a ternary complex together with the copper ion. A copper crosslink between the N7 of guanine and N3 of cytosine is proposed as the most probable coordination site. Moreover, no evidence was found for an interaction of either copper species with a phosphate group or equatorial water molecules. In addition, circular dichroism (CD) spectroscopy showed that the DNA of the Cu(II)-poly(dG-dC).poly(dG-dC) adducts resembles the left-handed Z-form. These results suggest that metal-mediated Hoogsteen base pairing, as previously proposed for a right-handed DNA duplex, can also occur in a double-stranded left-handed DNA.

  2. The Design of Drive Circuit with High-power Output for Two-phase Hybrid Stepping Motor Based on BY-5064

    Institute of Scientific and Technical Information of China (English)

    MA Xiao-jiao; LI Cheng-gui; CAI Zheng; ZHAO Li-guo

    2011-01-01

    A kind of drive circuit which high-power output for stepping motor, based two-phase hybrid stepping motor are designed, achieved. is low power consumption, high-performance and on BY-5064, and a kind of dedicated circuit for drive control for stepping motor with high-power is

  3. 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.

    Science.gov (United States)

    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

  4. 网络化制造中基于STEP-NC的编程方法%Based on the STEP-NC programming method on networked manufacture

    Institute of Scientific and Technical Information of China (English)

    王军; 孙军; 聂新刚; 王宛山

    2005-01-01

    STEP-NC是由欧美提出的新的数控接口标准,目的是取代旧的数控标准ISO6983.本文首先分析了STEP-NC的二种应用标准即ISO14649(ARM)和STEP AP238(AIM),并且分析了Part 21和Part28的应用领域及其Part21文件格式和其中的信息产生方法.介绍了ST-Developer环境下ROSEC++类库编程接口及其应用程序的早、迟联编方式,并且以此为基础设计了整个程序的编程流程,重点介绍了工艺规划设计.最后给出了在C++编程环境下利用ROSE库函数写入形成STEP AP238文件的方法

  5. A mesh deformation technique based on two-step solution of the elasticity equations

    Science.gov (United States)

    Huang, Guo; Huang, Haiming; Guo, Jin

    2016-12-01

    In the computation of fluid mechanics problems with moving boundaries, including fluid-structure interaction, fluid mesh deformation is a common problem to be solved. An automatic mesh deformation technique for large deformations of the fluid mesh is presented on the basis of a pseudo-solid method in which the fluid mesh motion is governed by the equations of elasticity. A two-dimensional mathematical model of a linear elastic body is built by using the finite element method. The numerical result shows that the proposed method has a better performance in moving the fluid mesh without producing distorted elements than that of the classic one-step methods.

  6. A mesh deformation technique based on two-step solution of the elasticity equations

    Science.gov (United States)

    Huang, Guo; Huang, Haiming; Guo, Jin

    2017-04-01

    In the computation of fluid mechanics problems with moving boundaries, including fluid-structure interaction, fluid mesh deformation is a common problem to be solved. An automatic mesh deformation technique for large deformations of the fluid mesh is presented on the basis of a pseudo-solid method in which the fluid mesh motion is governed by the equations of elasticity. A two-dimensional mathematical model of a linear elastic body is built by using the finite element method. The numerical result shows that the proposed method has a better performance in moving the fluid mesh without producing distorted elements than that of the classic one-step methods.

  7. LifeSteps: An Evidence-based Health Promotion Program for Underserved Populations – A Community Service Learning Approach

    Directory of Open Access Journals (Sweden)

    Melanie Austin-McCain

    2015-04-01

    Full Text Available Chronic diseases are the most common, costly, and preventable of all health problems in the United States. Chronic diseases represent the leading causes of death and are experienced at higher rates by minority populations (CDC, 2012. Innovative community-based health promotion programs are recommended that meet the diverse needs of underserved populations (Yeary, et al., 2011. LifeSteps is being developed as an evidence-based health promotion program focusing on health and wellness, a domain area defined within the Occupational Therapy Practice Framework (OTPF, 2008. LifeSteps will utilize a client-centered approach to coach individuals in making health behavior changes. Fieldwork and service-learning components are incorporated integrating clinical practice, academic study, and collaboration with community providers. Program evaluation measures based on the Transtheoretical Model (TTM have been identified to address all phases of program planning. The LifeSteps health promotion program aligns with local, national, and international objectives and addresses the need for programs that meet the diverse needs of underserved populations. Occupational therapists are in a unique position for implementing community-based interventions that promote health and contribute to a healthier society.

  8. Ion pairs of indobenzimidazolo cyanines: a structural study based on conductivity, absorption, fluorescence and 1H-NMR

    Science.gov (United States)

    Tatikolov, Aleksandr S.; Ishchenko, Aleksandr A.; Ghelli, Stefano; Ponterini, Glauco

    1998-11-01

    Asymmetric benzimidazolo carbo, di- and tricarbocyanines form ion pairs of the solvent-separated and contact types with different counterions in tetrahydrofuran, toluene and toluene-nitrile mixtures. The dissociation constants of the ion pairs in tetrahydrofuran, evaluated from conductivity data, do not depend on the length of the polymethine chain and show only a small decrease with decreasing counterion size. The absorption and fluorescence excitation spectra of the contact ion pairs exhibit a pronounced hypsochromic shift with respect to the solvated ions and the solvent-separated ion pairs. 1H-NMR experiments have provided information about the electronic structures of the ions of both the asymmetric dyes and the corresponding symmetric carbocyanines. They have also revealed different preferred anion locations in the contact ion pairs of the symmetric indocarbocyanine on one hand, and of the benzimidazolo carbocyanine and the asymmetric dyes on the other. This structural difference is suggested to be a cause of the observed opposite effects of ion pairing on the isomerization kinetics of the two groups of dyes.

  9. Efficient Certificateless Signcryption Scheme from Weil Pairing

    Directory of Open Access Journals (Sweden)

    Gang Yu

    2011-08-01

    Full Text Available Certificateless signcryption has both the advantage of certificateless public key cryptography, which overcome the escrow problem inherited from identity based cryptography without the use of certificates as in traditional public key cryptography, and signcryption which can fulfill both the functions of signature and encryption in a logical signal step. In this paper, we explicit the security model for certificateless signcryption and propose an efficient certificateless signcryption scheme from Weil pairings. The new scheme not only can be proved to be secure in our model but also can simultaneously provide public verifiability and forward security. Furthermore, compared with existing schemes, the new scheme is more efficient.

  10. Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field.

    Science.gov (United States)

    Liu, Cui; Wang, Yang; Zhao, Dongxia; Gong, Lidong; Yang, Zhongzhi

    2014-02-01

    The integrity of the genetic information is constantly threatened by oxidizing agents. Oxidized guanines have all been linked to different types of cancers. Theoretical approaches supplement the assorted experimental techniques, and bring new sight and opportunities to investigate the underlying microscopic mechanics. Unfortunately, there is no specific force field to DNA system including oxidized guanines. Taking high level ab initio calculations as benchmark, we developed the ABEEMσπ fluctuating charge force field, which uses multiple fluctuating charges per atom. And it was applied to study the energies, structures and mutations of base pairs containing oxidized guanines. The geometries were obtained in reference to other studies or using B3LYP/6-31+G* level optimization, which is more rational and timesaving among 24 quantum mechanical methods selected and tested by this work. The energies were determined at MP2/aug-cc-pVDZ level with BSSE corrections. Results show that the constructed potential function can accurately simulate the change of H-bond and the buckled angle formed by two base planes induced by oxidized guanine, and it provides reliable information of hydrogen bonding, stacking interaction and the mutation processes. The performance of ABEEMσπ polarizable force field in predicting the bond lengths, bond angles, dipole moments etc. is generally better than those of the common force fields. And the accuracy of ABEEMσπ PFF is close to that of the MP2 method. This shows that ABEEMσπ model is a reliable choice for further research of dynamics behavior of DNA fragment including oxidized guanine.

  11. ACL2 Meets the GPU: Formalizing a CUDA-based Parallelizable All-Pairs Shortest Path Algorithm in ACL2

    Directory of Open Access Journals (Sweden)

    David S. Hardin

    2013-04-01

    Full Text Available As Graphics Processing Units (GPUs have gained in capability and GPU development environments have matured, developers are increasingly turning to the GPU to off-load the main host CPU of numerically-intensive, parallelizable computations. Modern GPUs feature hundreds of cores, and offer programming niceties such as double-precision floating point, and even limited recursion. This shift from CPU to GPU, however, raises the question: how do we know that these new GPU-based algorithms are correct? In order to explore this new verification frontier, we formalized a parallelizable all-pairs shortest path (APSP algorithm for weighted graphs, originally coded in NVIDIA's CUDA language, in ACL2. The ACL2 specification is written using a single-threaded object (stobj and tail recursion, as the stobj/tail recursion combination yields the most straightforward translation from imperative programming languages, as well as efficient, scalable executable specifications within ACL2 itself. The ACL2 version of the APSP algorithm can process millions of vertices and edges with little to no garbage generation, and executes at one-sixth the speed of a host-based version of APSP coded in C – a very respectable result for a theorem prover. In addition to formalizing the APSP algorithm (which uses Dijkstra's shortest path algorithm at its core, we have also provided capability that the original APSP code lacked, namely shortest path recovery. Path recovery is accomplished using a secondary ACL2 stobj implementing a LIFO stack, which is proven correct. To conclude the experiment, we ported the ACL2 version of the APSP kernels back to C, resulting in a less than 5% slowdown, and also performed a partial back-port to CUDA, which, surprisingly, yielded a slight performance increase.

  12. Adaptive multi-step Full Waveform Inversion based on Waveform Mode Decomposition

    Science.gov (United States)

    Hu, Yong; Han, Liguo; Xu, Zhuo; Zhang, Fengjiao; Zeng, Jingwen

    2017-04-01

    Full Waveform Inversion (FWI) can be used to build high resolution velocity models, but there are still many challenges in seismic field data processing. The most difficult problem is about how to recover long-wavelength components of subsurface velocity models when seismic data is lacking of low frequency information and without long-offsets. To solve this problem, we propose to use Waveform Mode Decomposition (WMD) method to reconstruct low frequency information for FWI to obtain a smooth model, so that the initial model dependence of FWI can be reduced. In this paper, we use adjoint-state method to calculate the gradient for Waveform Mode Decomposition Full Waveform Inversion (WMDFWI). Through the illustrative numerical examples, we proved that the low frequency which is reconstructed by WMD method is very reliable. WMDFWI in combination with the adaptive multi-step inversion strategy can obtain more faithful and accurate final inversion results. Numerical examples show that even if the initial velocity model is far from the true model and lacking of low frequency information, we still can obtain good inversion results with WMD method. From numerical examples of anti-noise test, we see that the adaptive multi-step inversion strategy for WMDFWI has strong ability to resist Gaussian noise. WMD method is promising to be able to implement for the land seismic FWI, because it can reconstruct the low frequency information, lower the dominant frequency in the adjoint source, and has a strong ability to resist noise.

  13. Process for separating carbon dioxide from flue gas using sweep-based membrane separation and absorption steps

    Science.gov (United States)

    Wijmans, Johannes G.; Baker, Richard W.; Merkel, Timothy C.

    2012-08-21

    A gas separation process for treating flue gases from combustion processes, and combustion processes including such gas separation. The invention involves routing a first portion of the flue gas stream to be treated to an absorption-based carbon dioxide capture step, while simultaneously flowing a second portion of the flue gas across the feed side of a membrane, flowing a sweep gas stream, usually air, across the permeate side, then passing the permeate/sweep gas to the combustor.

  14. Use of a problem-based learning exercise to teach the lean 8-step problem-solving method.

    Science.gov (United States)

    Tovar, Elizabeth G; Warshawsky, Nora

    2015-01-01

    Doctor of nursing practice (DNP) graduates must be prepared to lead quality improvement (QI) initiatives in health care settings; however, effective and feasible teaching strategies pose a challenge for many DNP program faculties. This article describes a successful and practical problem-based learning exercise for students to work through the QI process using the Lean 8-step problem-solving method. Suggestions for faculty and recommendations for future activities are discussed.

  15. 基于STEP-NC的工艺规划优化方法研究%Optimal Methods of Process Plans Based on STEP-NC

    Institute of Scientific and Technical Information of China (English)

    李亮; 孙军; 王军; 李仁堂; 王淑红

    2006-01-01

    在重点分析零件特征典型加工方案及加工方案组合优化原则的基础上,基于STEP-NC应用遗传算法建立了零件加工方案组合优化的数学模型.并将该方法应用到具体零件的工艺排序决策过程中,通过编码、杂交、复制、变异等得到满足零件要求的最优或接近最优的工艺路线.验证了遗传算法在STEP-NC工艺路线排序中的有效性.

  16. A Machining Feature- based CAD/CAPP System for STEP- NC%面向STEP-NC的特征CAD/CAPP系统

    Institute of Scientific and Technical Information of China (English)

    张莉彦; 王奎升; 梁若琼

    2007-01-01

    将特征建模技术与STEP及STEP-NC标准相结合,为实现CAD/CAPP/CAM及CNC的集成,探索了一条有效的途径.建立基于STEP AP224的特征模型,它包含工艺设计所需要的产品管理、材料、精度等信息.另外,将特征与加工方法链相对应,并建立相应的数据库,同时讨论了工步排序的若干规则.在Pro/ENGINEER软件平台上,实现了CAD/CAPP/CAM高层次的集成.以三轴数控加工的棱柱体零件为例,阐述了工步的产生以及排序,最终生成符合STEP-NC标准的加工文件.

  17. Polymerase recognition of 2-thio-iso-guanine·5-methyl-4-pyrimidinone (iGs·P)--A new DD/AA base pair.

    Science.gov (United States)

    Lee, Dong-Kye; Switzer, Christopher

    2016-02-15

    Polymerase specificity is reported for a previously unknown base pair with a non-standard DD/AA hydrogen bonding pattern: 2-thio-iso-guanine·5-methyl-4-pyrimidinone. Our findings suggest that atomic substitution may provide a solution for low fidelity previously associated with enzymatic copying of iso-guanine.

  18. Seven-step problem-based learning in an interaction design course

    DEFF Research Database (Denmark)

    Schultz, Nette; Christensen, Hans Peter

    2004-01-01

    The objective in this paper is the implementation of the highly structured seven-step PBL procedure as part of the learning process in a human-computer interaction design course at the Technical University of Denmark, taking into account the common learning processes in PBL and the interaction...... individual reports after each case in the PBL-process in order to explore the students’ inter- and intra-personal team skills development in the learning process. Different qualitative and quantitative evaluation methods have been used to obtain a thorough evaluation of PBL used as a learning method among...... others in a single course. The evaluation results showed that the students definitely took a deep approach to learning, and indicated clearly that the students had obtained competences not only within the traditional HCI curriculum but also in terms of team-work skills....

  19. Multi-step Redox Systems with NIR-Fluorescence Based on 4H-Imidazoles

    Directory of Open Access Journals (Sweden)

    Martin Matschke

    2007-04-01

    Full Text Available A new class of 4H-imidazoles was synthesized starting from fused-ring aromatic dinitriles. Strong bathochromic shifts of the longest wavelength absorptions were observed in the corresponding UV/vis spectra due to a conversion of the merocyanine chromophores into cyanines/(azaoxonoles upon protonation/deprotonation of the 4H-imidazoles. Novel boratetraazapentalenes were synthesized via a cyclization reaction with boron trifluoride. These mesoionic species bearing a cyanine chromophore not only show NIR-fluorescence, they also participate as part of a quasi-reversible multi-step redox system. Large calculated semiquinone formation constants KSEM (3x1010 to 5x1011 indicate a high thermodynamic stability of the corresponding radical anions (SEM.

  20. Industrial Process Identification and Control Design Step-test and Relay-experiment-based Methods

    CERN Document Server

    Liu, Tao

    2012-01-01

      Industrial Process Identification and Control Design is devoted to advanced identification and control methods for the operation of continuous-time processes both with and without time delay, in industrial and chemical engineering practice.   The simple and practical step- or relay-feedback test is employed when applying the proposed identification techniques, which are classified in terms of common industrial process type: open-loop stable; integrating; and unstable, respectively. Correspondingly, control system design and tuning models that follow are presented for single-input-single-output processes.   Furthermore, new two-degree-of-freedom control strategies and cascade control system design methods are explored with reference to independently-improving, set-point tracking and load disturbance rejection. Decoupling, multi-loop, and decentralized control techniques for the operation of multiple-input-multiple-output processes are also detailed. Perfect tracking of a desire output trajectory is realiz...

  1. Creeping Ray Tracing Algorithm for Arbitrary NURBS Surfaces Based on Adaptive Variable Step Euler Method

    Directory of Open Access Journals (Sweden)

    Song Fu

    2015-01-01

    Full Text Available Although the uniform theory of diffraction (UTD could be theoretically applied to arbitrarilyshaped convex objects modeled by nonuniform rational B-splines (NURBS, one of the great challenges in calculation of the UTD surface diffracted fields is the difficulty in determining the geodesic paths along which the creeping waves propagate on arbitrarilyshaped NURBS surfaces. In differential geometry, geodesic paths satisfy geodesic differential equation (GDE. Hence, in this paper, a general and efficient adaptive variable step Euler method is introduced for solving the GDE on arbitrarilyshaped NURBS surfaces. In contrast with conventional Euler method, the proposed method employs a shape factor (SF ξ to efficiently enhance the accuracy of tracing and extends the application of UTD for practical engineering. The validity and usefulness of the algorithm can be verified by the numerical results.

  2. Practical Design Guidelines of qZSI Based Step-Up DC/DC Converter

    Science.gov (United States)

    Zakis, Janis; Vinnikov, Dmitri; Roasto, Indrek; Jalakas, Tanel

    2010-01-01

    This paper presents some design guidelines for a new voltage fed step-up DC/DC isolated converter. The most significant advantage of proposed converter is voltage buck-boost operation on single stage. The most promising application for proposed converter is in the field of distributed power generation e.g. fuel cells or photovoltaic. The most sensitive issues - such as power losses caused by high currents in the input side of converter and high transient overvoltages across the inverter bridge caused by stray inductances were discussed and solved. The proposals and recommendations to overcome these issues are given in the paper. The Selection and design guidelines of converter elements are proposed and explained. The prototype of proposed converter was built and experimentally tested. Some results are presented and evaluated.

  3. Self-deflection of bright soliton in a separate bright-dark screening soliton pair based on higher-order space charge field

    Institute of Scientific and Technical Information of China (English)

    Zhonghua Hao(郝中华); Jinsong Liu(刘劲松)

    2003-01-01

    Based on the interaction of the separate soliton pair, the self-deflection of the bright screening soliton in a bright-dark pair is studied by taking the higher order space charge field into account. Both numerical and analytical methods are adopted to obtain the result that the higher order of space charge field can enhance the deflection process of the bright soliton and varying the peak intensity of the dark soliton can influence the self-deflection strongly. The expression of the deflection distance with the dark soliton's peak intensity is derived, and some corresponding properties of the self-deflection process are figured out.

  4. Correlation Analysis and Modeling of Multiple Wind Power Based on Pair Copula%基于 Pair Copula 的多维风电功率相关性分析及建模

    Institute of Scientific and Technical Information of China (English)

    吴巍; 汪可友; 李国杰; 王志林

    2015-01-01

    Large-scale integration of wind farms leads to the complex dependence among wind power outputs.It is important to model the stochastic and dependent wind generation accurately to analyze the impact of wind generation on power system operation.Current methods,such as the Copula theory,are accurate enough for describing two dependent random variables. However,they are inadequate for modeling more random variables as accurately.Thus,a high-dimensional probabilistic model is proposed for dependent wind power outputs based on the canonical-vine Pair Copula theory.The corresponding sampling method is also introduced.Pair Copula can describe different patterns of dependence between pairs of wind power outputs. Hence high-dimensional wind power outputs with complex dependence can be modeled accurately.Moreover,The Pair Copula model can be easily constructed and has wide applicability as well as flexibility.The modeling and analysis of wind generation in a number of wind farms in Australia are implemented to prove the effectiveness of the proposed model. Finally, the probabilistic load flow of an IEEE 1 18-bus system is solved.Simulation results show that the operation characteristics of power systems incorporating wind farms can be analyzed more accurately if dependent wind power outputs are rationally described.%大规模风电场的接入使风电相关性更加复杂,合理描述多风电场出力的随机性和相关性特性,对准确分析风电对电力系统运行的影响具有重要意义。现有的 Copula 等方法能较准确描述二元相关性,但对于更高维模型的相关性描述则不够准确。基于此,提出了基于 C 藤 Pair Copula 的风电功率高维相关性模型,以及相应的采样方法。Pair Copula 能够描述风电功率两两之间不同的相关性结构,从而能较好描述复杂的多维相关性,且建模步骤简单,使用灵活,适用范围广。对澳大利亚多个风电场出力样本进行分析和

  5. Pairing the Volcano

    CERN Document Server

    Ionica, Sorina

    2011-01-01

    Isogeny volcanoes are graphs whose vertices are elliptic curves and whose edges are $\\ell$-isogenies. Algorithms allowing to travel on these graphs were developed by Kohel in his thesis (1996) and later on, by Fouquet and Morain (2001). However, up to now, no method was known, to predict, before taking a step on the volcano, the direction of this step. Hence, in Kohel's and Fouquet-Morain algorithms, many steps are taken before choosing the right direction. In particular, ascending or horizontal isogenies are usually found using a trial-and-error approach. In this paper, we propose an alternative method that efficiently finds all points $P$ of order $\\ell$ such that the subgroup generated by $P$ is the kernel of an horizontal or an ascending isogeny. In many cases, our method is faster than previous methods. This is an extended version of a paper published in the proceedings of ANTS 2010. In addition, we treat the case of 2-isogeny volcanoes and we derive from the group structure of the curve and the pairing ...

  6. 2012 IUPAP C10 Young Scientist Prize on the Structure and Dynamics of Condensed Matter Lecture: Spin Fluctuations and Pairing in Fe-based Superconductors

    Science.gov (United States)

    Christianson, A. D.

    2012-02-01

    The origin of superconductivity in the Fe-based superconductors, like that in other unconventional superconductors, remains shrouded in mystery. How the pairing bosons emerge either due to or in spite of the strong magnetic interactions found in the Fe-based superconductors is one of the most thoroughly investigated questions in the field. A prominent example of the interplay of superconductivity and magnetism is the dramatic shift of spectral weight from the low energy spin excitations to an energy which is related to the superconducting gap resulting in a peak in the spin excitation spectrum localized in both momentum and energy which occurs at the onset of superconductivity. The appearance of the new peak in the spin excitation spectrum below the superconducting transition temperature is referred to as s spin resonance and is most commonly interpreted as indicating a sign change of the superconducting order parameter on different portions of the Fermi surface and thus is consistent with an extended s-wave or s± pairing symmetry in many Fe-based superconductors. We will review the observations and implications of the spin resonance across the Fe-based superconductors. In particular we will examine the relationship between the resonance energy and the superconducting transition temperature as a function of chemical doping and pressure. While the spin resonance provides important information about pairing symmetry, there does not appear to be sufficient spectral to explain the pairing strength. Thus the remainder of the spin excitation spectrum must be examined to determine if spin fluctuations are ultimately responsible for pairing in the Fe-based materials. Consequently, we will discuss in detail the way in which the spin excitations evolve from the nonsuperconducting compounds to their superconducting relatives as a function of chemical doping.

  7. Robustness of s-wave pairing symmetry in iron-based superconductors and its implications for fundamentals of magnetically driven high-temperature superconductivity

    Science.gov (United States)

    Hu, Jiangping; Yuan, Jing

    2016-10-01

    Based on the assumption that the superconducting state belongs to a single irreducible representation of lattice symmetry, we propose that the pairing symmetry in all measured iron-based superconductors is generally consistent with the A 1 g s-wave. Robust s-wave pairing throughout the different families of iron-based superconductors at different doping regions signals two fundamental principles behind high- T c superconducting mechanisms: (i) the correspondence principle: the short-range magnetic-exchange interactions and the Fermi surfaces act collaboratively to achieve high- T c superconductivity and determine pairing symmetries; (ii) the magnetic-selection pairing rule: superconductivity is only induced by the magnetic-exchange couplings from the super-exchange mechanism through cation-anion-cation chemical bonding. These principles explain why unconventional high- T c superconductivity appears to be such a rare but robust phenomena, with its strict requirements regarding the electronic environment. The results will help us to identify new electronic structures that can support high- T c superconductivity.

  8. Systematic exploration of a class of hydrophobic unnatural base pairs yields multiple new candidates for the expansion of the genetic alphabet.

    Science.gov (United States)

    Dhami, Kirandeep; Malyshev, Denis A; Ordoukhanian, Phillip; Kubelka, Tomáš; Hocek, Michal; Romesberg, Floyd E

    2014-01-01

    We have developed a family of unnatural base pairs (UBPs), which rely on hydrophobic and packing interactions for pairing and which are well replicated and transcribed. While the pair formed between d5SICS and dNaM (d5SICS-dNaM) has received the most attention, and has been used to expand the genetic alphabet of a living organism, recent efforts have identified dTPT3-dNaM, which is replicated with even higher fidelity. These efforts also resulted in more UBPs than could be independently analyzed, and thus we now report a PCR-based screen to identify the most promising. While we found that dTPT3-dNaM is generally the most promising UBP, we identified several others that are replicated nearly as well and significantly better than d5SICS-dNaM, and are thus viable candidates for the expansion of the genetic alphabet of a living organism. Moreover, the results suggest that continued optimization should be possible, and that the putatively essential hydrogen-bond acceptor at the position ortho to the glycosidic linkage may not be required. These results clearly demonstrate the generality of hydrophobic forces for the control of base pairing within DNA, provide a wealth of new structure-activity relationship data and importantly identify multiple new candidates for in vivo evaluation and further optimization.

  9. Pair-bonded humans conform to sexual stereotypes in web-based advertisements for extra-marital partners.

    Science.gov (United States)

    Kelley, Trish C; Hare, James F

    2010-10-20

    Partners advertisements provide advertisers with access to a large pool of prospective mates, and have proven useful in documenting sex differences in human mating preferences. We coded data from an Internet site (AshleyMadison.com) catering to advertisers engaged in existing pair-bonded relationships. While we predicted that pair-bonding may liberate advertisers from conforming to sexual stereotypes of male promiscuity and female choosiness, our results are uniformly consistent with those stereotypes. Our findings thus provide further evidence that human mating behavior is highly constrained by fundamental biological differences between males and females.

  10. High Output Voltage Based Multiphase Step-Up DC-DC Converter Topology with Voltage Doubler Rectifiers

    Directory of Open Access Journals (Sweden)

    Liao Xiaozhong

    2013-02-01

    Full Text Available High Output Voltage Based Multiphase Step-Up DC-DC Converter topology with voltage doubler rectifiers is presented in this paper. High output voltage is obtained due to the series combination of voltage doubler rectifiers on the secondary side of high frequency transformers. This topology is useful in the application where the output voltage is greater than the input. The two loop control strategy has been developed in order to analyze the stable and effective working of the converter topology. Therefore the working mode analysis of the converter topology has been described in detail. The multiphase step-up DC-DC converter topology is first simulated on MATLAB and then a prototype has been designed in order to verify the simulation and experimental results. Finally the simulation and experimental results are found to be satisfactory.

  11. One step gold (bio)functionalisation based on CS{sub 2}-amine reaction

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Ines [Centro de Quimica e Bioquimica, Faculdade de Ciencias da Universidade de Lisboa, Ed. C8, Campo Grande, 1749-016 Lisboa (Portugal); Cascalheira, Antonio C. [Lumisense, Lda, Campus Faculdade de Ciencias da Universidade de Lisboa, Ed. ICAT, Campo Grande, 1749-016 Lisboa (Portugal); Viana, Ana S., E-mail: anaviana@fc.ul.p [Centro de Quimica e Bioquimica, Faculdade de Ciencias da Universidade de Lisboa, Ed. C8, Campo Grande, 1749-016 Lisboa (Portugal)

    2010-12-01

    Dithiocarbamates have been regarded as alternative anchor groups to thiols on gold surfaces, and claimed to be formed in situ through the reaction between secondary amines and carbon disulphide. In this paper, we further exploit this methodology for a convenient one step biomolecule immobilisation onto gold surfaces. First, the reactivity between CS{sub 2} and electroactive compounds containing amines, primary (dopamine), secondary (epinephrine), and an amino acid (tryptophan) has been investigated by electrochemical methods. Cyclic voltammetric characterisation of the modified electrodes confirmed the immobilisation of all the target compounds, allowing the estimation of their surface concentration. The best result was obtained with epinephrine, a secondary amine, for which a typical quasi-reversible behaviour of surface confined electroactive species could be clearly depicted. Electrochemical reductive desorption studies enabled to infer on the extent of the reaction and on the relative stability of the generated monolayers. Bio-functionalisation studies have been accomplished through the reaction of CS{sub 2} with glucose oxidase in aqueous medium, and the catalytic activity of the immobilised enzyme was evaluated towards glucose, by electrochemical methods in the presence of a redox mediator. Scanning tunnelling microscopy (STM) and Atomic force microscopy (AFM) were used respectively, to characterize the gold electrodes and Glucose Oxidase coverage and distribution on the modified surfaces.

  12. Structure-Based Mechanism for Early PLP-Mediated Steps of Rabbit Cytosolic Serine Hydroxymethyltransferase Reaction

    Directory of Open Access Journals (Sweden)

    Martino L. Di Salvo

    2013-01-01

    Full Text Available Serine hydroxymethyltransferase catalyzes the reversible interconversion of L-serine and glycine with transfer of one-carbon groups to and from tetrahydrofolate. Active site residue Thr254 is known to be involved in the transaldimination reaction, a crucial step in the catalytic mechanism of all pyridoxal 5′-phosphate- (PLP- dependent enzymes, which determines binding of substrates and release of products. In order to better understand the role of Thr254, we have expressed, characterized, and determined the crystal structures of rabbit cytosolic serine hydroxymethyltransferase T254A and T254C mutant forms, in the absence and presence of substrates. These mutants accumulate a kinetically stable gem-diamine intermediate, and their crystal structures show differences in the active site with respect to wild type. The kinetic and crystallographic data acquired with mutant enzymes permit us to infer that conversion of gem-diamine to external aldimine is significantly slowed because intermediates are trapped into an anomalous position by a misorientation of the PLP ring, and a new energy barrier hampers the transaldimination reaction. This barrier likely arises from the loss of the stabilizing hydrogen bond between the hydroxymethyl group of Thr254 and the ε-amino group of active site Lys257, which stabilizes the external aldimine intermediate in wild type SHMTs.

  13. Population-Based Precision Cancer Screening: A Symposium on Evidence, Epidemiology, and Next Steps.

    Science.gov (United States)

    Marcus, Pamela M; Pashayan, Nora; Church, Timothy R; Doria-Rose, V Paul; Gould, Michael K; Hubbard, Rebecca A; Marrone, Michael; Miglioretti, Diana L; Pharoah, Paul D; Pinsky, Paul F; Rendle, Katherine A; Robbins, Hilary A; Roberts, Megan C; Rolland, Betsy; Schiffman, Mark; Tiro, Jasmin A; Zauber, Ann G; Winn, Deborah M; Khoury, Muin J

    2016-11-01

    Precision medicine, an emerging approach for disease treatment that takes into account individual variability in genes, environment, and lifestyle, is under consideration for preventive interventions, including cancer screening. On September 29, 2015, the National Cancer Institute sponsored a symposium entitled "Precision Cancer Screening in the General Population: Evidence, Epidemiology, and Next Steps". The goal was two-fold: to share current information on the evidence, practices, and challenges surrounding precision screening for breast, cervical, colorectal, lung, and prostate cancers, and to allow for in-depth discussion among experts in relevant fields regarding how epidemiology and other population sciences can be used to generate evidence to inform precision screening strategies. Attendees concluded that the strength of evidence for efficacy and effectiveness of precision strategies varies by cancer site, that no one research strategy or methodology would be able or appropriate to address the many knowledge gaps in precision screening, and that issues surrounding implementation must be researched as well. Additional discussion needs to occur to identify the high priority research areas in precision cancer screening for pertinent organs and to gather the necessary evidence to determine whether further implementation of precision cancer screening strategies in the general population would be feasible and beneficial. Cancer Epidemiol Biomarkers Prev; 25(11); 1449-55. ©2016 AACR.

  14. Managing chronic pathologies with a stepped mHealth-based approach in clinical psychology and medicine

    Directory of Open Access Journals (Sweden)

    Gianluca eCastelnuovo

    2015-04-01

    Full Text Available Chronic diseases and conditions typically require long-term monitoring and treatment protocols both in traditional settings and in out-patient frameworks. The economic burden of chronic conditions is a key challenge and new and mobile technologies could offer good solutions. mHealth could be considered an evolution of ehealth and could be defined as the practice of medicine and public health supported by mobile communication devices. mHealth approach could overcome limitations linked with the traditional, restricted and highly expensive in-patient treatment of many chronic pathologies. Possible applications include stepped mHealth approach, where patients can be monitored and treated in their everyday contexts. Unfortunately, many barriers for the spread of mHealth are still present. Due the significant impact of psychosocial factors on disease evolution, psychotherapies have to be included into the chronic disease protocols. Existing psychological theories of health behavior change have to be adapted to the new technological contexts and requirements. In conclusion, clinical psychology and medicine have to face the chronic care management challenge in both traditional and mHealth settings.

  15. Direct and two-step activity-based profiling of proteases and glycosidases

    NARCIS (Netherlands)

    Willems, Lianne Irene

    2014-01-01

    Activity-based protein profiling provides a powerful approach for the monitoring of active enzyme populations in complex biological samples by making use of activity-based probes (ABPs), chemical probes that are designed to bind specifically to the active site of an enzyme (family). The research des

  16. 铁基超导体材料和物理研究%Iron-Based Superconducting Materials and Pairing Mechanism

    Institute of Scientific and Technical Information of China (English)

    闻海虎

    2015-01-01

    .In addition,we will give an introduction about the present understanding of the pairing mechanism.Finally we will try to give a perspective on the potential applications of the iron-based superconductors.

  17. Steps in Moving Evidence-Based Health Informatics from Theory to Practice.

    OpenAIRE

    M. Rigby; Magrabi, F; Scott, P.; Doupi, P.; Hypponen, H; Ammenwerth, E.

    2016-01-01

    OBJECTIVES: To demonstrate and promote the importance of applying a scientific process to health IT design and implementation, and of basing this on research principles and techniques. METHODS: A review by international experts linked to the IMIA Working Group on Technology Assessment and Quality Development. RESULTS: Four approaches are presented, linking to the creation of national professional expectations, adherence to research-based standards, quality assurance approaches to ensure safet...

  18. The physico-chemical "anatomy" of the tautomerization through the DPT of the biologically important pairs of hypoxanthine with DNA bases: QM and QTAIM perspectives.

    Science.gov (United States)

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

    2013-10-01

    The biologically important tautomerization of the Hyp·Cyt, Hyp·Thy and Hyp·Hyp base pairs to the Hyp·Cyt, Hyp·Thy and Hyp·Hyp base pairs, respectively, by the double proton transfer (DPT) was comprehensively studied in vacuo and in the continuum with a low dielectric constant (ε = 4) corresponding to hydrophobic interfaces of protein-nucleic acid interactions by combining theoretical investigations at the B3LYP/6-311++G(d,p) level of QM theory with QTAIM topological analysis. Based on the sweeps of the energetic, electron-topological, geometric and polar parameters, which describe the course of the tautomerization along the intrinsic reaction coordinate (IRC), it was proved that the tautomerization through the DPT is concerted and asynchronous process for the Hyp·Cyt and Hyp·Thy base pairs, while concerted and synchronous for the Hyp·Hyp homodimer. The continuum with ε = 4 does not affect qualitatively the course of the tautomerization reaction for all studied complexes. The nine key points along the IRC of the Hyp·Cyt↔Hyp·Cyt and Hyp·Thy↔Hyp·Thy tautomerizations and the six key points of the Hyp·Hyp↔Hyp·Hyp tautomerization have been identified and fully characterized. These key points could be considered as electron-topological "fingerprints" of concerted asynchronous (for Hyp·Cyt and Hyp·Thy) or synchronous (for Hyp·Hyp) tautomerization process via the DPT. It was found, that in the Hyp·Cyt, Hyp·Thy, Hyp·Hyp and Hyp·Hyp base pairs all H-bonds are significantly cooperative and mutually reinforce each other, while the C2H…O2 H-bond in the Hyp·Cyt base pair and the O6H…O4 H-bond in the Hyp·Thy base pair behave anti-cooperatively, i.e., they become weakened, while two others become strengthened.

  19. A proposed adaptive step size perturbation and observation maximum power point tracking algorithm based on photovoltaic system modeling

    Science.gov (United States)

    Huang, Yu

    Solar energy becomes one of the major alternative renewable energy options for its huge abundance and accessibility. Due to the intermittent nature, the high demand of Maximum Power Point Tracking (MPPT) techniques exists when a Photovoltaic (PV) system is used to extract energy from the sunlight. This thesis proposed an advanced Perturbation and Observation (P&O) algorithm aiming for relatively practical circumstances. Firstly, a practical PV system model is studied with determining the series and shunt resistances which are neglected in some research. Moreover, in this proposed algorithm, the duty ratio of a boost DC-DC converter is the object of the perturbation deploying input impedance conversion to achieve working voltage adjustment. Based on the control strategy, the adaptive duty ratio step size P&O algorithm is proposed with major modifications made for sharp insolation change as well as low insolation scenarios. Matlab/Simulink simulation for PV model, boost converter control strategy and various MPPT process is conducted step by step. The proposed adaptive P&O algorithm is validated by the simulation results and detail analysis of sharp insolation changes, low insolation condition and continuous insolation variation.

  20. Designing for interaction: Six steps to designing computer-supported group-based learning

    OpenAIRE

    2004-01-01

    At present, the design of computer-supported group-based learning (CS)GBL) is often based on subjective decisions regarding tasks, pedagogy and technology, or concepts such as ‘cooperative learning’ and ‘collaborative learning’. Critical review reveals these concepts as insufficiently substantial to serve as a basis for (CS)GBL design. Furthermore, the relationship between outcome and group interaction is rarely specified a priori. Thus, there is a need for a more systematic approach to desig...

  1. Single-step scanner-based digital image correlation (SB-DIC) method for large deformation mapping in rubber

    Science.gov (United States)

    Goh, C. P.; Ismail, H.; Yen, K. S.; Ratnam, M. M.

    2017-01-01

    The incremental digital image correlation (DIC) method has been applied in the past to determine strain in large deformation materials like rubber. This method is, however, prone to cumulative errors since the total displacement is determined by combining the displacements in numerous stages of the deformation. In this work, a method of mapping large strains in rubber using DIC in a single-step without the need for a series of deformation images is proposed. The reference subsets were deformed using deformation factors obtained from the fitted mean stress-axial stretch ratio curve obtained experimentally and the theoretical Poisson function. The deformed reference subsets were then correlated with the deformed image after loading. The recently developed scanner-based digital image correlation (SB-DIC) method was applied on dumbbell rubber specimens to obtain the in-plane displacement fields up to 350% axial strain. Comparison of the mean axial strains determined from the single-step SB-DIC method with those from the incremental SB-DIC method showed an average difference of 4.7%. Two rectangular rubber specimens containing circular and square holes were deformed and analysed using the proposed method. The resultant strain maps from the single-step SB-DIC method were compared with the results of finite element modeling (FEM). The comparison shows that the proposed single-step SB-DIC method can be used to map the strain distribution accurately in large deformation materials like rubber at much shorter time compared to the incremental DIC method.

  2. Atomic Steps with tuning-fork-based noncontact atomic force microscopy

    NARCIS (Netherlands)

    Rensen, W.H.J.; Hulst, van N.F.; Ruiter, A.G.T.; West, P.E.

    1999-01-01

    Tuning forks as tip-sample distance detectors are a promising and versatile alternative to conventional cantilevers with optical beam deflection in noncontact atomic force microscopy (AFM). Both theory and experiments are presented to make a comparison between conventional and tuning-fork-based AFM.

  3. A One-Step-Ahead Smoothing-Based Joint Ensemble Kalman Filter for State-Parameter Estimation of Hydrological Models

    KAUST Repository

    El Gharamti, Mohamad

    2015-11-26

    The ensemble Kalman filter (EnKF) recursively integrates field data into simulation models to obtain a better characterization of the model’s state and parameters. These are generally estimated following a state-parameters joint augmentation strategy. In this study, we introduce a new smoothing-based joint EnKF scheme, in which we introduce a one-step-ahead smoothing of the state before updating the parameters. Numerical experiments are performed with a two-dimensional synthetic subsurface contaminant transport model. The improved performance of the proposed joint EnKF scheme compared to the standard joint EnKF compensates for the modest increase in the computational cost.

  4. Web based health surveys: Using a Two Step Heckman model to examine their potential for population health analysis.

    Science.gov (United States)

    Morrissey, Karyn; Kinderman, Peter; Pontin, Eleanor; Tai, Sara; Schwannauer, Mathias

    2016-08-01

    In June 2011 the BBC Lab UK carried out a web-based survey on the causes of mental distress. The 'Stress Test' was launched on 'All in the Mind' a BBC Radio 4 programme and the test's URL was publicised on radio and TV broadcasts, and made available via BBC web pages and social media. Given the large amount of data created, over 32,800 participants, with corresponding diagnosis, demographic and socioeconomic characteristics; the dataset are potentially an important source of data for population based research on depression and anxiety. However, as respondents self-selected to participate in the online survey, the survey may comprise a non-random sample. It may be only individuals that listen to BBC Radio 4 and/or use their website that participated in the survey. In this instance using the Stress Test data for wider population based research may create sample selection bias. Focusing on the depression component of the Stress Test, this paper presents an easy-to-use method, the Two Step Probit Selection Model, to detect and statistically correct selection bias in the Stress Test. Using a Two Step Probit Selection Model; this paper did not find a statistically significant selection on unobserved factors for participants of the Stress Test. That is, survey participants who accessed and completed an online survey are not systematically different from non-participants on the variables of substantive interest.

  5. Zeolite-Based Organic Synthesis (ZeoBOS) of Acortatarin A: First Total Synthesis Based on Native and Metal-Doped Zeolite-Catalyzed Steps.

    Science.gov (United States)

    Wimmer, Eric; Borghèse, Sophie; Blanc, Aurélien; Bénéteau, Valérie; Pale, Patrick

    2017-01-31

    Similarly to polymer-supported assisted synthesis (PSAS), organic synthesis could be envisaged being performed by using zeolites, native or metal-doped, as heterogeneous catalysts. To illustrate this unprecedented Zeolite-Based Organic Synthesis (ZeoBOS), the total synthesis of acortatarin A was achieved through a novel strategy and using five out of eleven synthetic steps catalyzed by H- or metal-doped zeolites as catalysts. Notably, the formation of an yne-pyrrole intermediate with a copper-doped zeolite and the spiroketalization of an alkyne diol with a silver-doped zeolite have been developed as key steps of the synthesis.

  6. Present and next steps of the JAERI superconducting rf linac based FEL program

    Energy Technology Data Exchange (ETDEWEB)

    Minehara, E.J.; Yamauchi, T.; Sugimoto, M. [FEL Laboratory at Tokai, Advanced Photon Research Center, Kansai Research Establishment, Japan Atomic Energy Research Institute, Tokai, Ibaraki (JP)] (and others)

    2000-03-01

    The JAERI superconducting rf linac based FEL has successfully been lased to produce a 0.3 kW FEL light and 100 kW or larger electron beam output in quasi continuous wave operation in 1999. The 1 kW class output as our present program goal will be achieved to improve the optical out coupling method in the FEL optical resonator, the electron gun, and the electron beam optics in the JAERI FEL driver. As our next 5 year program goal is the 100 kW class FEL light and a few tens MW class electron beam output in average, quasi continuous wave operation of the light and electron beam will be planned in the JAERI superconducting rf linac based FEL facility. Conceptual design options needed for such a very high power operation and shorter wavelength light sources will be discussed to improve and to upgrade the exciting facility. (author)

  7. First Steps towards Evidence-Based Preventive Home Visits: Experiences Gathered in a Swedish Municipality

    Directory of Open Access Journals (Sweden)

    Charlotte Löfqvist

    2012-01-01

    Full Text Available The purpose of preventive home visits is to promote overall health and wellbeing in old age. The aim of this paper was to describe the process of the development of evidence-based preventive home visits, targeting independent community-living older persons. The evidence base was generated from published studies and practical experiences. The results demonstrate that preventive home visits should be directed to persons 80 years old and older and involve various professional competences. The visits should be personalized, lead to concrete interventions, and be followed up. The health areas assessed should derive from a broad perspective and include social, psychological, and medical aspects. Core components in the protocol developed in this study captured physical, medical, psychosocial, and environmental aspects. Results of a pilot study showed that the protocol validly identified health risks among older people with different levels of ADL dependence.

  8. Nano-Sim: A Step Wise Equivalent Conductance based Statistical Simulator for Nanotechnology Circuit Design

    CERN Document Server

    Sukhwani, Bharat; Wang, Janet M; 10.1109/DATE.2005.221

    2011-01-01

    New nanotechnology based devices are replacing CMOS devices to overcome CMOS technology's scaling limitations. However, many such devices exhibit non-monotonic I-V characteristics and uncertain properties which lead to the negative differential resistance (NDR) problem and the chaotic performance. This paper proposes a new circuit simulation approach that can effectively simulate nanotechnology devices with uncertain input sources and negative differential resistance (NDR) problem. The experimental results show a 20-30 times speedup comparing with existing simulators.

  9. Solar radiation concentrators paired with multijunction photoelectric converters in ground-based solar power plants (part I)

    Science.gov (United States)

    Ionova, E. A.; Ulanov, M. V.; Davidyuk, N. Yu.; Sadchikov, N. A.

    2016-12-01

    We have developed a method for determining parameters of radiation concentrator in solar power plants. To estimate the efficiency of concentrators in the form of Fresnel lenses in setups with three-junction photoelectric converters, the concept of the efficiency of the concentrator-photoelectric converter pair has been introduced. We have proposed a method for calculating the refracting profile of concentrators taking into account the dispersion relation for the refractive index and its variations with temperature for the material of the refracting profile of the concentrator (Wacker RT604 silicone compound). The results of calculation make it possible to achieve the maximal efficiency of the concentrator-photoelectric converter pair in the presence of chromatic aberrations in the optical system of solar radiation concentration.

  10. Steps toward subject-specific classification in ECG-based detection of sleep apnea.

    Science.gov (United States)

    Maier, Christoph; Wenz, Heinrich; Dickhaus, Hartmut

    2011-11-01

    This study deals with ECG-based recognition of sleep apnea in epochs of 1 min duration using spectral- and correlation-based features extracted from the modulation of QRS amplitude, respiratory myogram interference and RR intervals. On a database comprising 140 simultaneous recordings of polysomnograms (PSGs) and 8-lead Holter-ECGs, it is shown that a single-parameter ROC threshold classification can achieve high detection rates up to 81.0% sensitivity and 85.6% specificity. Still, individual accuracy may be low, and the improvement employing feature combination by means of second order polynomial classifiers is only marginal. We speculate that individual differences, like co-morbidities, and even intra-individual confounding factors, like nocturnal changes in body position (BP), are major reasons for the difficulties to significantly raise the detection rate using multivariate techniques, which is evident in virtually all papers on that subject. Using the BP information in the PSG, we show a potential benefit for individualized single-feature classifiers by comparing the maximally achievable individual and global accuracy when either one optimal global threshold for the total dataset, individual threshold values for each subject or individual thresholds for each BP are applied. We developed an ECG-based BP segmentation algorithm and finally suggest a potential strategy to derive individually optimized subject-specific threshold values.

  11. Design-Based Research in Science Education: One Step Towards Methodology

    Directory of Open Access Journals (Sweden)

    Kalle Juuti

    2012-10-01

    Full Text Available Recently, there has been critiques towards science education research, as the potential of this research has not been actualised in science teaching and learning praxis. The paper describes an analysis of a design-based research approach (DBR that has been suggested as a solution for the discontinuation between science education research and praxis. We propose that a pragmatic frame helps to clarify well the design-based research endeavour. We abstracted three aspects from the analysis that constitute design-based research: (a a design process is essentially iterative starting from the recognition of the change of the environment of praxis, (b it generates a widely usable artefact, (c and it provides educational knowledge for more intelligible praxis. In the knowledge acquisition process, the pragmatic viewpoint emphasises the role of a teacher’s reflected actions as well as the researches’ involvement in the authentic teaching and learning settings.

  12. Historical Matching Strategies in Kidney Paired Donation: The 7-Year Evolution of a Web-Based Virtual Matching System.

    Science.gov (United States)

    Fumo, D E; Kapoor, V; Reece, L J; Stepkowski, S M; Kopke, J E; Rees, S E; Smith, C; Roth, A E; Leichtman, A B; Rees, M A

    2015-10-01

    Failure to convert computer-identified possible kidney paired donation (KPD) exchanges into transplants has prohibited KPD from reaching its full potential. This study analyzes the progress of exchanges in moving from "offers" to completed transplants. Offers were divided into individual segments called 1-way transplants in order to calculate success rates. From 2007 to 2014, the Alliance for Paired Donation performed 243 transplants, 31 in collaboration with other KPD registries and 194 independently. Sixty-one of 194 independent transplants (31.4%) occurred via cycles, while the remaining 133 (68.6%) resulted from nonsimultaneous extended altruistic donor (NEAD) chains. Thirteen of 35 (37.1%) NEAD chains with at least three NEAD segments accounted for 68% of chain transplants (8.6 tx/chain). The "offer" and 1-way success rates were 21.9 and 15.5%, respectively. Three reasons for failure were found that could be prospectively prevented by changes in protocol or software: positive laboratory crossmatch (28%), transplant center declined donor (17%) and pair transplanted outside APD (14%). Performing a root cause analysis on failures in moving from offer to transplant has allowed the APD to improve protocols and software. These changes have improved the success rate and the number of transplants performed per year.

  13. Homogeneous DNA Detection Based on Fluorescence Quenching by Nanoparticles in Single-step Format :Target-Induced Configuration Transform

    Institute of Scientific and Technical Information of China (English)

    ZHANG,Songbai; WU,Zaisheng; XIE,Ming; SHEN,Guoli; YU,Ruqin

    2009-01-01

    A new strategy for homogeneous detection of DNA hybridization in single-step format was developed based on fluorescence quenching by gold nanoparticles.The gold nanoparticle is functionalized with 5'-thiolated 48-base oligonucleotide(probe sequence),whose 3'-terminus is labeled with fluorescein(FAM),a negatively charged fluo-rescencc dye.The oligonucleotide adopts all extended configuration due to the electrostatic repulsion between nega-tively charged gold nanoparticle and the FAM-attached probe sequence.After addition of the complementary target sequence,specific DNA hybridization induces a conformation change of the probe from an extended stmcture to an arch.1ike configuration,which brings the fluorophore and the gold nanoparticle in close proximity.The fluorescence is efficiently quenched by gold nanoparticles.The fluorescence quenching efficiency is related to the target concen.tration,which allows the quantitative detection for target sequence in a sample.A linear detection range from 1.6 to 209.4 nmoI/L Was obtained under the optimized experimental conditions with a detection limit of 0.1 nmol,L.In the assay system,the gold nanoparticles act as both nanoscaffolds and nanoquenchers.Furthermore,the proposed strategy.in which only two DNA sequences arc involved,is not only different from the traditional molecular bea-cons or reverse molecular beacons but also different from the commonly used sandwich hybridization methods.In addition,the DNA hybridization detection was achieved in homogenous solution in a single-step format,which al-lows real.time detection and quantification with other advantages such as easy operation and elimination of washing steps.

  14. Step-by-Step Design of an FPGA-Based Digital Compensator for DC/DC Converters Oriented to an Introductory Course

    Science.gov (United States)

    Zumel, P.; Fernandez, C.; Sanz, M.; Lazaro, A.; Barrado, A.

    2011-01-01

    In this paper, a short introductory course to introduce field-programmable gate array (FPGA)-based digital control of dc/dc switching power converters is presented. Digital control based on specific hardware has been at the leading edge of low-medium power dc/dc switching converters in recent years. Besides industry's interest in this topic, from…

  15. Solution NMR determination of hydrogen bonding and base pairing between the glyQS T box riboswitch Specifier domain and the anticodon loop of tRNA(Gly).

    Science.gov (United States)

    Chang, Andrew T; Nikonowicz, Edward P

    2013-11-01

    In Gram-positive bacteria the tRNA-dependent T box riboswitch regulates the expression of many amino acid biosynthetic and aminoacyl-tRNA synthetase genes through a transcription attenuation mechanism. The Specifier domain of the T box riboswitch contains the Specifier sequence that is complementary to the tRNA anticodon and is flanked by a highly conserved purine nucleotide that could result in a fourth base pair involving the invariant U33 of tRNA. We show that the interaction between the T box Specifier domain and tRNA consists of three Watson-Crick base pairs and that U33 confers stability to the complex through intramolecular hydrogen bonding. Enhanced packing within the Specifier domain loop E motif may stabilize the complex and contribute to cognate tRNA selection.

  16. Ion pair-based liquid-phase microextraction combined with cuvetteless UV-vis micro-spectrophotometry as a miniaturized assay for monitoring ammonia in waters.

    Science.gov (United States)

    Senra-Ferreiro, Sonia; Pena-Pereira, Francisco; Costas-Mora, Isabel; Romero, Vanesa; Lavilla, Isela; Bendicho, Carlos

    2011-09-15

    A miniaturized method based on liquid-phase microextraction (LPME) in combination with microvolume UV-vis spectrophotometry for monitoring ammonia in waters is proposed. The methodology is based on the extraction of the ion pair formed between the blue indophenol obtained according to the Berthelot reaction and a quaternary ammonium salt into a microvolume of organic solvent. Experimental parameters affecting the LPME performance such as type and concentration of the quaternary ammonium ion salt required to form the ion pair, type and volume of extractant solvent, effect of disperser solvent, ionic strength and extraction time, were optimized. A detection limit of 5.0 μg L(-1) ammonia and an enrichment factor of 30 can be attained after a microextraction time of 4 min. The repeatability, expressed as relative standard deviation, was 7.6% (n=7). The proposed method can be successfully applied to the determination of trace amounts of ammonia in several environmental water samples.

  17. A Step Forward To Component-based Software Cost Estimation in Object-oriented Environment

    CERN Document Server

    Ahmed, Nadeem; Qureshi, M Rizwan Jameel

    2012-01-01

    Software cost estimation (SCE) of a project is pivotal to the acceptance or rejection of the development of software project. Various SCE techniques have been in practice with their own strengths and limitations. The latest of these is object-oriented one. Currently object-oriented approach for SCE is based on Line of Code (LOC), function points, functions and classes etc. Relatively less attention has been paid to the SCE in component-based software engineering (CBSE). So there is a pressing need to search parameters/variables that have a vital role for the SCE using CBSE which is taken up in this paper. This paper further looks at level of significance of all the parameters/variables thus searched. The time is being used as an independent variable because time is a parameter which is almost, all previous in one. Therefore this approach may be in a way an alternate of all previous approaches. Infact the underlying research ultimately may lead towards SCE of complex systems, using CBSE, in a scientific, syste...

  18. Abundance and composition of indigenous bacterial communities in a multi-step biofiltration-based drinking water treatment plant.

    Science.gov (United States)

    Lautenschlager, Karin; Hwang, Chiachi; Ling, Fangqiong; Liu, Wen-Tso; Boon, Nico; Köster, Oliver; Egli, Thomas; Hammes, Frederik

    2014-10-01

    Indigenous bacterial communities are essential for biofiltration processes in drinking water treatment systems. In this study, we examined the microbial community composition and abundance of three different biofilter types (rapid sand, granular activated carbon, and slow sand filters) and their respective effluents in a full-scale, multi-step treatment plant (Zürich, CH). Detailed analysis of organic carbon degradation underpinned biodegradation as the primary function of the biofilter biomass. The biomass was present in concentrations ranging between 2-5 × 10(15) cells/m(3) in all filters but was phylogenetically, enzymatically and metabolically diverse. Based on 16S rRNA gene-based 454 pyrosequencing analysis for microbial community composition, similar microbial taxa (predominantly Proteobacteria, Planctomycetes, Acidobacteria, Bacteriodetes, Nitrospira and Chloroflexi) were present in all biofilters and in their respective effluents, but the ratio of microbial taxa was different in each filter type. This change was also reflected in the cluster analysis, which revealed a change of 50-60% in microbial community composition between the different filter types. This study documents the direct influence of the filter biomass on the microbial community composition of the final drinking water, particularly when the water is distributed without post-disinfection. The results provide new insights on the complexity of indigenous bacteria colonizing drinking water systems, especially in different biofilters of a multi-step treatment plant.

  19. Laser ablation-based one-step generation and bio-functionalization of gold nanoparticles conjugated with aptamers

    Directory of Open Access Journals (Sweden)

    Walter Johanna G

    2010-08-01

    Full Text Available Abstract Background Bio-conjugated nanoparticles are important analytical tools with emerging biological and medical applications. In this context, in situ conjugation of nanoparticles with biomolecules via laser ablation in an aqueous media is a highly promising one-step method for the production of functional nanoparticles resulting in highly efficient conjugation. Increased yields are required, particularly considering the conjugation of cost-intensive biomolecules like RNA aptamers. Results Using a DNA aptamer directed against streptavidin, in situ conjugation results in nanoparticles with diameters of approximately 9 nm exhibiting a high aptamer surface density (98 aptamers per nanoparticle and a maximal conjugation efficiency of 40.3%. We have demonstrated the functionality of the aptamer-conjugated nanoparticles using three independent analytical methods, including an agglomeration-based colorimetric assay, and solid-phase assays proving high aptamer activity. To demonstrate the general applicability of the in situ conjugation of gold nanoparticles with aptamers, we have transferred the method to an RNA aptamer directed against prostate-specific membrane antigen (PSMA. Successful detection of PSMA in human prostate cancer tissue was achieved utilizing tissue microarrays. Conclusions In comparison to the conventional generation of bio-conjugated gold nanoparticles using chemical synthesis and subsequent bio-functionalization, the laser-ablation-based in situ conjugation is a rapid, one-step production method. Due to high conjugation efficiency and productivity, in situ conjugation can be easily used for high throughput generation of gold nanoparticles conjugated with valuable biomolecules like aptamers.

  20. Microfluidics-based single-step preparation of injection-ready polymeric nanosystems for medical imaging and drug delivery

    Science.gov (United States)

    Liu, Kegang; Zhu, Zhen; Wang, Xueya; Gonçalves, Daniel; Zhang, Bei; Hierlemann, Andreas; Hunziker, Patrick

    2015-10-01

    Translation of therapeutic polymeric nanosystems to patients and industry requires simplified, reproducible and scalable methods for assembly and loading. A single-step in-line process based on nanocoprecipitation of oxazoline-siloxane block copolymers in flow-focusing poly(dimethylsiloxane) microfluidics was designed to manufacture injection-ready nanosystems. Nanosystem characteristics could be controlled by copolymer concentration, block length and chemistry, microchannel geometry, flow rate, aqueous/organic flow rate ratio and payload concentration. The well-tolerated nanosystems exhibited differential cell binding and payload delivery and could confer sensitivity to photodynamic therapy to HeLa cancer cells. Such injection-ready nanosystems carrying drugs, diagnostic or functional materials may facilitate translation to clinical application.Translation of therapeutic polymeric nanosystems to patients and industry requires simplified, reproducible and scalable methods for assembly and loading. A single-step in-line process based on nanocoprecipitation of oxazoline-siloxane block copolymers in flow-focusing poly(dimethylsiloxane) microfluidics was designed to manufacture injection-ready nanosystems. Nanosystem characteristics could be controlled by copolymer concentration, block length and chemistry, microchannel geometry, flow rate, aqueous/organic flow rate ratio and payload concentration. The well-tolerated nanosystems exhibited differential cell binding and payload delivery and could confer sensitivity to photodynamic therapy to HeLa cancer cells. Such injection-ready nanosystems carrying drugs, diagnostic or functional materials may facilitate translation to clinical application. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03543k

  1. One step shift towards flexible supercapacitors based on carbon nanotubes - A review

    Energy Technology Data Exchange (ETDEWEB)

    Yar, A., E-mail: asfandyarhargan@gmail.com, E-mail: johndennis@petronas.com.my, E-mail: noranimuti-mohamed@petronas.com.my, E-mail: asad-032@yahoo.com, E-mail: imrancssp@gmail.com; Dennis, J. O., E-mail: asfandyarhargan@gmail.com, E-mail: johndennis@petronas.com.my, E-mail: noranimuti-mohamed@petronas.com.my, E-mail: asad-032@yahoo.com, E-mail: imrancssp@gmail.com; Mohamed, N. M., E-mail: asfandyarhargan@gmail.com, E-mail: johndennis@petronas.com.my, E-mail: noranimuti-mohamed@petronas.com.my, E-mail: asad-032@yahoo.com, E-mail: imrancssp@gmail.com; Mumtaz, A., E-mail: asfandyarhargan@gmail.com, E-mail: johndennis@petronas.com.my, E-mail: noranimuti-mohamed@petronas.com.my, E-mail: asad-032@yahoo.com, E-mail: imrancssp@gmail.com; Irshad, M. I., E-mail: asfandyarhargan@gmail.com, E-mail: johndennis@petronas.com.my, E-mail: noranimuti-mohamed@petronas.com.my, E-mail: asad-032@yahoo.com, E-mail: imrancssp@gmail.com [Department of Fundamental and Applied Sciences, Universiti Teknologi PETRONAS (Malaysia); Ahmad, F., E-mail: ahmad-1234farooq@yahoo.com [Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS (Malaysia)

    2014-10-24

    Supercapacitors have emerged as prominent energy storage devices that offer high energy density compared to conventional capacitors and high power density which is not found in batteries. Carbon nanotubes (CNTs) because of their high surface area and tremendous electrical properties are used as electrode material for supercapacitors. In this review we focused on the factors like surface area, role of the electrolyte and techniques adopted to improve performance of CNTs based supercapacitors. The supercapacitors are widely tested in liquid electrolytes which are normally hazardous in nature, toxic, flammable and their leakage has safety concerns. This review also focuses on research which is replacing these unsafe electrolytes by solid electrolytes with the combination of low cost CNTs deposited flexible supports for supercapacitors.

  2. Double side multicrystalline silicon passivation by one step stain etching-based porous silicon

    Energy Technology Data Exchange (ETDEWEB)

    Mohamed, Seifeddine Belhadj; Ben Rabha, Mohamed; Bessais, Brahim [Laboratoire de Photovoltaique, Centre de Recherches et des Technologies de l' Energie, Technopole de Borj-Cedria, BP 95, 2050 Hammam-Lif (Tunisia)

    2012-10-15

    In this paper, we investigate the effect of stain etching-based porous silicon on the double side multicrystalline silicon. Special attention is given to the use of the stain etched PS as an antireflection coating as well as for surface passivating capabilities. Stain etching of double side multicrystalline silicon leads to the formation of PS nanostructures, that dramatically decrease the surface reflectivity from 30% to about 7% and increase the effective lifetime from 1 {mu}s to 10 {mu}s at a minority carrier density ({Delta}n) of 10{sup 15} cm{sup -3}. These results let us correlate the rise of the lifetime values to the photoluminescence intensity to the hydrogen and oxide passivation as shown by FTIR analysis. This low-cost PS formation process can be applied in the photovoltaic cell technology as a standard procedure (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  3. Ecological and Economic System Health Assessment Based on Fuzzy Set Pair Analysis: A Case Study of Northwest Region, China%Ecological and Economic System Health Assessment Based on Fuzzy Set Pair Analysis: A Case Study of Northwest Region, China

    Institute of Scientific and Technical Information of China (English)

    Chen Junfei; Zhou Xiaolan; Wang Huimin

    2012-01-01

    Due to the increasingly serious environmental pollution and destruction, especially humans' unreasonable activities, the ecological and economic system (EES) issues of Northwest region in China have attracted more and more attention of the researchers. Aiming at evaluating its ecological and economic system health, a multi-objective evaluation framework called Pressure- State-Response (PSR) was established to. describe the ecological and economic health situations. Meanwhile, an integrative set pair model combining set pair analysis (SPA) and fuzzy analytic hierarchy process (FAHP) was proposed to assess the ecological and economic system. Then the EES status of five northwest provinces (Shanxi, Gansu, Qinghai, Ningxia and Xinjiang) of Northwest region in China was evaluated during 1985 to 2009. The EES development trends of five provinces are obtained. In general, the health values of five provinces showed a rising trend. The health values of five provinces grew rapidly during 1985 to 2000. After 2000, the health values of five provinces still followed the present growth trend, but the growth is relatively smooth. The results show that the method proposed is effective for assessing the health of ecological and economic system.

  4. Design of step-by-step motor control system based on PLC%基于PLC的步进电机控制系统设计

    Institute of Scientific and Technical Information of China (English)

    毛昀; 杨峰

    2014-01-01

    基于设计步进电机控制系统的目的,主要设计以PLC为核心控制器的步进电机控制系统。在对常见的三相反应式步进电动机工作原理详细阐述的基础上,对步进电机的控制原理进行分析说明。以西门子S7-200系列PLC对步进电机的控制为例,通过对S7-200系列PLC的高速输出点直接对步进电机进行运动控制的方案设计,设计相应的外部接线图、程序,并对具体的控制参数进行说明。%For the purpose of design stepper motor control system, this paper mainly design PLC as the core controller of stepper motor control system. The analysis and explanation about the stepper motor control system depends on the three-phase reaction step common motor working principle of the detailed elaboration on the stepper motor control principle. Taking the Siemens S7-200 series PLC to control the stepper motor as an example. Through high speed output points of S7-200 series PLC directly to the mo-tion of the stepper motor control program design, design appropriate external wiring diagrams, procedures and make a specific description about the control parameters.

  5. The Healthy Steps Study: A randomized controlled trial of a pedometer-based Green Prescription for older adults. Trial protocol

    Directory of Open Access Journals (Sweden)

    Schluter Philip J

    2009-11-01

    Full Text Available Abstract Background Graded health benefits of physical activity have been demonstrated for the reduction of coronary heart disease, some cancers, and type-2 diabetes, and for injury reduction and improvements in mental health. Older adults are particularly at risk of physical inactivity, and would greatly benefit from successful targeted physical activity interventions. Methods/Design The Healthy Steps study is a 12-month randomized controlled trial comparing the efficacy of a pedometer-based Green Prescription with the conventional time-based Green Prescription in increasing and maintaining physical activity levels in low-active adults over 65 years of age. The Green Prescription interventions involve a primary care physical activity prescription with 3 follow-up telephone counselling sessions delivered by trained physical activity counsellors over 3 months. Those in the pedometer group received a pedometer and counselling based around increasing steps that can be monitored on the pedometer, while those in the standard Green Prescription group received counselling using time-based goals. Baseline, 3 month (end of intervention, and 12 month measures were assessed in face-to-face home visits with outcomes measures being physical activity (Auckland Heart Study Physical Activity Questionnaire, quality of life (SF-36 and EQ-5D, depressive symptoms (Geriatric Depression Scale, blood pressure, weight status, functional status (gait speed, chair stands, and tandem balance test and falls and adverse events (self-report. Utilisation of health services was assessed for the economic evaluation carried out alongside this trial. As well, a process evaluation of the interventions and an examination of barriers and motives for physical activity in the sample were conducted. The perceptions of primary care physicians in relation to delivering physical activity counselling were also assessed. Discussion The findings from the Healthy Steps trial are due in late

  6. Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Y.; Zhang, X.; Dantas Machado, A. C.; Ding, Y.; Chen, Z.; Qin, P. Z.; Rohs, R.; Chen, L.

    2013-07-08

    The p53 core domain binds to response elements (REs) that contain two continuous half-sites as a cooperative tetramer, but how p53 recognizes discontinuous REs is not well understood. Here we describe the crystal structure of the p53 core domain bound to a naturally occurring RE located at the promoter of the Bcl-2-associated X protein (BAX) gene, which contains a one base-pair insertion between the two half-sites. Surprisingly, p53 forms a tetramer on the BAX-RE that is nearly identical to what has been reported on other REs with a 0-bp spacer. Each p53 dimer of the tetramer binds in register to a half-site and maintains the same protein–DNA interactions as previously observed, and the two dimers retain all the protein–protein contacts without undergoing rotation or translation. To accommodate the additional base pair, the DNA is deformed and partially disordered around the spacer region, resulting in an apparent unwinding and compression, such that the interactions between the dimers are maintained. Furthermore, DNA deformation within the p53-bound BAX-RE is confirmed in solution by site-directed spin labeling measurements. Our results provide a structural insight into the mechanism by which p53 binds to discontinuous sites with one base-pair spacer.

  7. Refinements of Double-Base Chains Algorithm for Computing Tate Pairing%双基数链算法计算Tate对的一种改进

    Institute of Scientific and Technical Information of China (English)

    翁江; 豆允旗; 马传贵

    2012-01-01

    Pairings have been widely used in the study of identity-based cryptosystems (BC) .Miller algorithm is the key of computing pairings.We propose an efficient Miller algorithm computing Tate pairing based on the double-base chain.Through the application of norm function and conjugate technique, our refinements reduce the total number of lines and vertical lines in the rational function,and replace the inverse by its conjugate in Miller algorithm.Results show that the efficiency of our algorithm can be improved by more than 10% compared with the previous method.%双线性对在基于身份的密码体制中有着广泛的应用.Miller算法是计算双线性对的核心算法,本文在双基数链计算Tate对的基础上给出了一种高效的Miller算法.通过范函数和共轭技巧的应用,减少了Miller算法中有理函数直线和垂线的数量并用共轭代替了求逆运算.结果表明新算法与已有算法相比效率提高了10%以上.

  8. Non-Watson Crick base pairs might stabilize RNA structural motifs in ribozymes – A comparative study of group-I intron structures

    Indian Academy of Sciences (India)

    K Chandrasekhar; R Malathi

    2003-09-01

    In recent decades studies on RNA structure and function have gained significance due to discoveries on diversified functions of RNA. A common element for RNA secondary structure formed by series of non-Watson/Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural motifs in ribozymes, playing a crucial role in their enzymatic activity. To understand the functional significance of these non-canonical base pairs in catalytic RNA, we analysed the sequences of group-I introns from nuclear genes. The results suggest that they might form the building blocks of folded RNA motifs which are crucial to the catalytic activity of the ribozyme. The conservation of these, as observed from divergent organisms, argues for the presence of non-canonical base pairs as an important requisite for the structure and enzymatic property of ribozymes by enabling them to carry out functions such as replication, polymerase activity etc. in primordial conditions in the absence of proteins.

  9. A Trajectory Correction based on Multi-Step Lining-up for the CLIC Main Linac

    CERN Document Server

    D'Amico, T E

    1999-01-01

    In the CLIC main linac it is very important to minimise the trajectory excursion and consequently the emittance dilution in order to obtain the required luminosity. Several algorithms have been proposed and lately the ballistic method has proved to be very effective. The trajectory method described in this Note retains the main advantages of the latter while adding some interesting features. It is based on the separation of the unknown variables like the quadrupole misalignments, the offset and slope of the injection straight line and the misalignments of the beam position monitors (BPM). This is achieved by referring the trajectory relatively to the injection line and not to the average pre-alignment line and by using two trajectories each corresponding to slightly different quadrupole strengths. A reference straight line is then derived onto which the beam is bent by a kick obtained by moving the first quadrupole. The other quadrupoles are then aligned on that line. The quality of the correction depends mai...

  10. Baby steps: The expanding financial base of local government in Ireland

    Directory of Open Access Journals (Sweden)

    Considine John

    2015-08-01

    Full Text Available There are two essential elements to this paper. In the first instance, we explore the specific details of revenue and expenditure trends for local authorities over the last decade. The analysis is framed against a longer-term political context of forty years which focuses especially on the weakness of local government in Ireland. Despite an official narrative of financial overdependence on central government, the comparative examination of budgetary records of local authorities reveals considerable diversity in both the revenue and expenditure patterns of authorities across the state. While some authorities are heavily reliant on central government funding, others have a much stronger base of local funding, and indeed the financial crisis since 2008 may have increased these differences. The second dimension to the research is an exploration of the impact of the great recession from 2008 on local government finance in Ireland. Using a framework of new institutionalism, we identify the crisis as another critical moment for local government. We consider the political, economic and administrative variables which have brought local government to a financial crossroads, and we explore the potential for long-lasting financial change in local government, as well as speculating on the nature and outcome of that change.

  11. Direct Interconversion of BINOL and H8-BINOL-Based Chiral Brønsted Acids Using Single-Step Red/Ox Manipulations.

    Science.gov (United States)

    Tay, Jia-Hui; Arguelles, Alonso J; Nagorny, Pavel

    2015-08-07

    A direct single-step hydrogenation of BINOL-based chiral phosphoric acids, N-triflyl phosphoramides, and disulfonimides to the corresponding H8-BINOL Brønsted acids in excellent yields and chemoselectivities is described. In addition, the conditions for the single-step oxidation of H8-BINOL-based Brønsted acids into the corresponding BINOL-based acids have been identified and employed to accomplish these interconversions in 41-81% yield.

  12. Base-pair opening dynamics of the microRNA precursor pri-miR156a affect temperature-responsive flowering in Arabidopsis.

    Science.gov (United States)

    Kim, Hee-Eun; Kim, Wanhui; Lee, Ae-Ree; Jin, Suhyun; Jun, A Rim; Kim, Nak-Kyoon; Lee, Joon-Hwa; Ahn, Ji Hoon

    2017-03-18

    Internal and environmental cues, including ambient temperature changes, regulate the timing of flowering in plants. Arabidopsis miR156 represses flowering and plays an important role in the regulation of temperature-responsive flowering. However, the molecular basis of miR156 processing at lower temperatures remains largely unknown. Here, we performed nuclear magnetic resonance studies to investigate the base-pair opening dynamics of model RNAs at 16 °C and investigated the in vivo effects of the mutant RNAs on temperature-responsive flowering. The A9C and A10CG mutations in the B5 bulge of the lower stem of pri-miR156a stabilized the C15∙G98 and U16∙A97 base-pairs at the cleavage site of pri-miR156a at 16 °C. Consistent with this, production of mature miR156 was severely affected in plants overexpressing the A9C and A10CG constructs and these plants exhibited almost no delay in flowering at 16 °C. The A10G and A9AC mutations did not strongly affect C15∙G98 and U16∙A97 base-pairs at 16 °C, and plants overexpressing A10G and A9AC mutants of miR156 produced more mature miR156 than plants overexpressing the A9C and A10CG mutants and showed a strong delay in flowering at 16 °C. Interestingly, the A9AC mutation had distinct effects on the opening dynamics of the C15∙G98 and U16∙A97 base-pairs between 16 °C and 23 °C, and plants expressing the A9AC mutant miR156 showed only a moderate delay in flowering at 16 °C. Based on these results, we propose that fine-tuning of the base-pair stability at the cleavage site is essential for efficient processing of pri-miR156a at a low temperature and for reduced flowering sensitivity to ambient temperature changes.

  13. First Steps Toward K-12 Teacher Professional Development Using Internet-based Telescopes

    Science.gov (United States)

    Berryhill, K. J.; Gershun, D.; Slater, T. F.; Armstrong, J. D.

    2012-12-01

    How can science teachers become more familiar with emerging technology, excite their students and give students a taste of astronomy research? Astronomy teachers do not always have research experience, so it is difficult for them to convey to students how researchers use telescopes. The nature of astronomical observation (e.g., remote sites, expensive equipment, and odd hours) has been a barrier to providing teachers with insight into the process. Robotic telescopes (operated automatically with queued observing schedules) and remotely controlled telescopes (controlled by the user via the Internet) allow scientists to conduct observing sessions on research-grade telescopes half a world away. The same technology can now be harnessed by STEM educators to engage students and reinforce what is being taught in the classroom, as seen in some early research in elementary schools (McKinnon and Mainwaring 2000 and McKinnon and Geissinger 2002), and middle/high schools (Sadler et al. 2001, 2007 and Gehret et al. 2005). However, teachers need to be trained to use these resources. Responding to this need, graduate students and faculty at the University of Wyoming and CAPER Center for Astronomy & Physics Education Research are developing teacher professional development programs using Internet-based telescopes. We conducted an online course in the science education graduate program at the University of Wyoming. This course was designed to sample different types of Internet-based telescopes to evaluate them as resources for teacher professional development. The 10 participants were surveyed at the end of the course to assess their experiences with each activity. In addition, pre-test/post-test data were collected focusing specifically on one of the telescopes (Gershun, Berryhill and Slater 2012). Throughout the course, the participants learned to use a variety of robotic and remote telescopes including SLOOH Space Camera (www.slooh.com), Sky Titan Observatory (www

  14. Interdependent chemical-electrochemical steps in retrometabolism-based drug and safer chemical design.

    Science.gov (United States)

    Tókés, B; Suciu, G; Nagy, G

    2002-02-01

    An extension of the retrometabolic based drug (chemical) design concept, specifically the soft drug approach, to the family of nitrone compounds is presented. Nitrones oppose oxidative challenges by virtue of their ability to very rapidly trap free radical species that are more stable and biochemically less harmful than the original molecular fragments. Moreover, the spin adducts may undergo further transformations including reaction with a second radical and decomposition (hydrolysis) to hydroxylamines and carbonyl compounds. Nitrones and their spin adducts may generate nitric oxide in vivo, which, like nitrones themselves, exerts a number of diverse activities in phylogenetically distant species as well as opposing effects in related biological systems. It was described as a major messenger in the cardiovascular, immune, and nervous systems, in which it plays regulatory, signaling, cytoprotective, and cytotoxic effects. Nitrones play an important role in the synthesis of drugs belonging to chemically and pharmacologically very different classes. A combined chemical-electrochemical synthesis of nitrones has been elaborated. These compounds may be obtained from aldehydes or ketones and N-substituted hydroxylamines. These reactions were performed directly, in situ in the electrochemical cell, where phenylhydroxylamine obtained by electroreduction of nitrobenzene derivatives reacts with the carbonyl compound introduced in the cell. The kinetic and thermodynamic parameters of the processes were determined by analyzing the adequate polarographic curves. Differences between purely chemical and mixed chemical-electrochemical methods are discussed. Analysis of the experimental data permits optimization of the investigated process from a preparative point of view. Effects of structural factors were systematically evaluated. The proposed method may be useful for combinatorial chemistry as well.

  15. Physical activity of female children and adolescents based on step counts: meeting the recommendation and relation to BMI

    Directory of Open Access Journals (Sweden)

    Kantanista Adam

    2015-06-01

    Full Text Available Study aim: the aim of this study was to assess the step counts of children and adolescents with different BMIs and to present the results in relation to the step count recommendation.

  16. Atomic-Level Organization of Vicinal Acid-Base Pairs through the Chemisorption of Aniline and Derivatives onto Mesoporous SBA15

    KAUST Repository

    Basset, Jean-Marie

    2016-06-09

    The design of novel heterogeneous catalysts with multiple adjacent functionalities is of high interest for heterogeneous catalysis. Herein, we report a method to obtain a majority bifunctional acid-base pairs on SBA15. Aniline reacts with SBA15 by opening siloxane bridges leading to N-phenylsilanamine-silanol pairs. In contrast with ammonia treated surfaces, the material is stable under air/moisture. Advanced solid state MAS NMR: 2D ¹H-¹H double-quantum, ¹H-¹³C HETCOR experiments and dynamic nuclear polarization enhanced ²⁹Si and ¹⁵N spectra demonstrate both the close proximity between the two moieties and the formation of a covalent Si-N surface bond and confirm the design of vicinal acid-base pairs. This approach was successfully applied to the design of a series of aniline derivatives bifunctional SBA15. A correlation of the substituents effects on the aromatic ring (Hammet parameters) on the kinetics of the model reaction of Knoevenagel is observed.

  17. A Co-expression System Based on Phage and Phagemid to Select Cognate Antibody-antigen Pairs in vivo

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A modified selectively-infective phage (SIP) is developed to facilitate the selection of interacting antibody-antigen pairs from a large single-chain antibody (scFv) library in vivo. The system is constructed with a modified helper phage M13KO7 and phagemid pCANTAB 5 E. The antigen fused to the C-terminal of N1-N2 domain and the scFv to the N-terminal of CT domain of the gIIIp of filamentous phage are encoded on the phage and phagemid vectors respectively. The phages produced by co-transformants restore infectivity via interaction between antigen and antibody fusions in the cell periplasm. In a model system, the scFv fragment of the anti-hemagglutinin 17/9 antibody and its corresponding antigen are detected in the presence of a 105 fold excess of a non-interacting control pairs, which demonstrates this system to be very sensitive and facile to screen a large single-chain antibody library.

  18. Design, analysis and experimental performance of a stepping type piezoelectric linear actuator based on compliant foot driving

    Science.gov (United States)

    Wang, Shupeng; Rong, Weibin; Wang, Lefeng; Sun, Lining

    2016-11-01

    A stepping type piezoelectric linear actuator based on compliant foot driving is proposed in this paper. With the help of four piezo-stacks and four compliant feet, the designed actuator can produce large range linear motions in both positive and negative directions with high accuracy. The mechanical structure and the operating principle are discussed. Mohr integration method is used to analyze the deformation of the key component compliant foot. To investigate the working performance, a prototype is fabricated and a series of experiments are carried out. The experimental results indicate that the displacement outputs under various driving voltages and various driving frequencies show good linear relationships with the time. The driving resolution and the maximum output force are 10.98 nm and 43 N, respectively. The displacements deviation between the forward and backward motions within 30 steps is 6.82 μm and the amplitude of the parasitic motions is about 0.638 μm. The experimental results also confirm that the designed actuator can achieve various speeds by changing the driving voltage and driving frequency.

  19. Investigation on the traceability of three dimensional scanning electron microscope measurements based on the stereo-pair technique

    DEFF Research Database (Denmark)

    Bariani, Paolo; De Chiffre, Leonardo; Hansen, Hans Nørgaard;

    2005-01-01

    involving: (i) magnification calibration using a steel scale with 50 ìm pitch at low magnifications, and a 2D calibration grating with 2.120 ìm pitch at high magnifications; (ii) tilt angle calibration by laser interferometry; (iii) vertical elevation calibration using gauge-block steps; (iv) calibration...... angle and the magnification calibration. An equation describing the theoretically determined uncertainty of the vertical elevation was produced. An experimental investigation was carried out involving: (i) magnification calibration using a steel scale with 50 ìm pitch at low magnifications, and a 2D...... calibration grating with 2.120 ìm pitch at high magnifications; (ii) tilt angle calibration by laser interferometry; (iii) vertical elevation calibration using gauge-block steps; (iv) calibration in the vertical plane using two ISO 5436 type C roughness standards. Results from magnification calibration...

  20. Preparation of Thermo-Responsive Poly(ionic liquids-Based Nanogels via One-Step Cross-Linking Copolymerization

    Directory of Open Access Journals (Sweden)

    Jing Zhang

    2015-09-01

    Full Text Available In this study, thermo-responsive polymeric nanogels were facilely prepared via one-step cross-linking copolymerization of ethylene glycol dimethacrylate/divinylbenzene and ionic liquid (IL-based monomers, 1,n-dialkyl-3,3′-bis-1-vinyl imidazolium bromides ([CnVIm]Br; n = 6, 8, 12 in selective solvents. The results revealed that stable and blue opalescent biimidazolium (BIm-based nanogel solutions could be obtained without any precipitation when the copolymerizations were conducted in methanol. Most importantly, these novel nanogels were thermo-response, and could reversibly transform to precipitation in methanol with temperature changes. Turbidity analysis and dynamic light scatting (DLS measurement illustrated that PIL-based nanogel solutions presented the phase transform with upper critical solution temperature (UCST in the range of 5–25 °C. The nanogels were characterized using Fourier transform infrared (FTIR, thermogravimetric analyses (TGA, and scanning electron microscopy (SEM. In addition, BIm-based nanogels could also be used as highly active catalysts in the cycloaddition reaction of CO2 and epoxides. As a result, our attributes build a robust platform suitable for the preparation of polymeric nanomaterials, as well as CO2 conversion.

  1. Microfluidics-based single-step preparation of injection-ready polymeric nanosystems for medical imaging and drug delivery.

    Science.gov (United States)

    Liu, Kegang; Zhu, Zhen; Wang, Xueya; Gonçalves, Daniel; Zhang, Bei; Hierlemann, Andreas; Hunziker, Patrick

    2015-10-28

    Translation of therapeutic polymeric nanosystems to patients and industry requires simplified, reproducible and scalable methods for assembly and loading. A single-step in-line process based on nanocoprecipitation of oxazoline-siloxane block copolymers in flow-focusing poly(dimethylsiloxane) microfluidics was designed to manufacture injection-ready nanosystems. Nanosystem characteristics could be controlled by copolymer concentration, block length and chemistry, microchannel geometry, flow rate, aqueous/organic flow rate ratio and payload concentration. The well-tolerated nanosystems exhibited differential cell binding and payload delivery and could confer sensitivity to photodynamic therapy to HeLa cancer cells. Such injection-ready nanosystems carrying drugs, diagnostic or functional materials may facilitate translation to clinical application.

  2. One-step fabrication of 3D silver paste electrodes into microfluidic devices for enhanced droplet-based cell sorting

    Directory of Open Access Journals (Sweden)

    Lang Rao

    2015-05-01

    Full Text Available 3D microelectrodes are one-step fabricated into a microfluidic droplet separator by filling conductive silver paste into PDMS microchambers. The advantages of 3D silver paste electrodes in promoting droplet sorting accuracy are systematically demonstrated by theoretical calculation, numerical simulation and experimental validation. The employment of 3D electrodes also helps to decrease the droplet sorting voltage, guaranteeing that cells encapsulated in droplets undergo chip-based sorting processes are at better metabolic status for further potential cellular assays. At last, target droplet containing single cell are selectively sorted out from others by an appropriate electric pulse. This method provides a simple and inexpensive alternative to fabricate 3D electrodes, and it is expected our 3D electrode-integrated microfluidic droplet separator platform can be widely used in single cell operation and analysis.

  3. Synthesis and integration of Fe-soc-MOF cubes into colloidosomes via a single-step emulsion-based approach

    KAUST Repository

    Pang, Maolin

    2013-07-17

    Bottom-up fabrication of complex 3D hollow superstructures from nonspherical building blocks (BBs) poses a significant challenge for scientists in materials chemistry and physics. Spherical colloidal silica or polystyrene particles are therefore often integrated as BBs for the preparation of an emerging class of materials, namely colloidosomes (using colloidal particles for Pickering stabilization and fusing them to form a permeable shell). Herein, we describe for the first time a one-step emulsion-based technique that permits the assembly of metal-organic framework (MOF) faceted polyhedral BBs (i.e., cubes instead of spheres) into 3D hollow superstructures (or "colloidosomes" ). The shell of each resultant hollow MOF colloidosome is constructed from a monolayer of cubic BBs, whose dimensions can be precisely controlled by varying the amount of emulsifier used in the synthesis. © 2013 American Chemical Society.

  4. A fully automatic three-step liver segmentation method on LDA-based probability maps for multiple contrast MR images.

    Science.gov (United States)

    Gloger, Oliver; Kühn, Jens; Stanski, Adam; Völzke, Henry; Puls, Ralf

    2010-07-01

    Automatic 3D liver segmentation in magnetic resonance (MR) data sets has proven to be a very challenging task in the domain of medical image analysis. There exist numerous approaches for automatic 3D liver segmentation on computer tomography data sets that have influenced the segmentation of MR images. In contrast to previous approaches to liver segmentation in MR data sets, we use all available MR channel information of different weightings and formulate liver tissue and position probabilities in a probabilistic framework. We apply multiclass linear discriminant analysis as a fast and efficient dimensionality reduction technique and generate probability maps then used for segmentation. We develop a fully automatic three-step 3D segmentation approach based upon a modified region growing approach and a further threshold technique. Finally, we incorporate characteristic prior knowledge to improve the segmentation results. This novel 3D segmentation approach is modularized and can be applied for normal and fat accumulated liver tissue properties.

  5. A pair of novel Cd(II) enantiomers based on lactate derivatives: Synthesis, crystal structures and properties

    Science.gov (United States)

    Xu, Zhong-Xuan; Ao, Ke-Hou; Zhang, Jian

    2016-09-01

    A pair of novel 3D homochiral metal-organic frameworks (HMOFs), namely [Cd2.5((R)-CIA)6(1,4-DIB)(H2O)2]·((CH3)2NH2)·H2O (1-D), [Cd2.5((S)-CIA)6(1,4-DIB)(H2O)2]·((CH3)2NH2)·H2O (1-L), have been synthesized using lactic acid derivative ligands ((R)-H3CIA and (S)-H3CIA) and 1,4-DIB. Crystallographic analyses indicate that the complexes 1-D and 1-L are packed by cage substructures. Some physical characteristics, such as solid-state circular dichroism (CD), thermal stabilities and photoluminescent properties are also investigated. Our results highlight the effective method to apply lactic acid derivative ligands to form interesting HMOFs.

  6. Novel cationic surfactant ion pair based solid phase microextraction fiber for nano-level analysis of BTEX.

    Science.gov (United States)

    Hosseinzadeh, Reza; Tahmasebi, Raheleh; Farhadi, Khalil; Moosavi-Movahedi, Ali Akbar; Jouyban, Abolghasem; Badraghi, Jalil

    2011-05-01

    Ion pair of cationic surfactant (cetytrimethylammonium bromide) and tungestosilicic acid incorporated in PVC matrix, was used for coating a piece of copper wire as a new high sensitive SPME fiber in extraction and determination of BTEX compounds from the headspace of water samples prior to GC/FID analysis. Under optimum extraction conditions, limits of detection for benzene, toluene, ethylbenzene, p-xylene, m-xylene and o-xylene were found to be 1.18, 5.61, 0.87, 0.29, 0.22 and 0.33 ng L(-1) respectively. Low detection limits, wide linear dynamic ranges, good reproducibility (RSD% 1.48-4.27), high fiber capacity and high mechanical durability are some of the most important advantages of the new fiber.

  7. S-1-Based versus capecitabine-based preoperative chemoradiotherapy in the treatment of locally advanced rectal cancer: a matched-pair analysis.

    Directory of Open Access Journals (Sweden)

    Meng Su

    Full Text Available OBJECTIVE: The aim of this paper was to compare the efficacy and safety of S-1-based and capecitabine-based preoperative chemoradiotherapy regimens in patients with locally advanced rectal cancer through a retrospective matched-pair analysis. MATERIALS AND METHODS: Between Jan 2010 and Mar 2014, 24 patients with locally advanced rectal cancer who received preoperative radiotherapy concurrently with S-1 were individually matched with 24 contemporary patients with locally advanced rectal cancer who received preoperative radiotherapy concurrently with capecitabine according to clinical stage (as determined by pelvic magnetic resonance imaging and computed tomography and age (within five years. All these patients performed mesorectal excision 4-8 weeks after the completion of chemoradiotherapy. RESULTS: The tumor volume reduction rates were 55.9±15.1% in the S-1 group and 53.8±16.0% in the capecitabine group (p = 0.619. The overall downstaging, including both T downstaging and N downstaging, occurred in 83.3% of the S-1 group and 70.8% of the capecitabine group (p = 0.508. The significant tumor regression, including regression grade I and II, occurred in 33.3% of S-1 patients and 25.0% of capecitabine patients (p = 0.754. In the two groups, Grade 4 adverse events were not observed and Grade 3 consisted of only two cases of diarrhea, and no patient suffered hematologic adverse event of Grade 2 or higher. However, the incidence of diarrhea (62.5% vs 33.3%, p = 0.014 and hand-foot syndrome (29.2% vs 0%, p = 0.016 were higher in capecitabine group. Other adverse events did not differ significantly between two groups. CONCLUSIONS: The two preoperative chemoradiotherapy regimens were effective and safe for patients of locally advanced rectal cancer, but regimen with S-1 exhibited a lower incidence of adverse events.

  8. Key Roles of Lewis Acid-base Pairs on ZnxZryOz in Direct Ethanol/Acetone to Isobutene Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Junming; Baylon, Rebecca A.; Liu, Changjun; Mei, Donghai; Martin, Kevin J.; Venkitasubramanian, Padmesh; Wang, Yong

    2016-01-20

    The effects of surface acidity on the cascade ethanol-to-isobutene conversion were studied using ZnxZryOz catalysts. The ethanol-to-isobutene reaction was found to be limited by the secondary reaction of the key intermediate, acetone, namely the acetone-to-isobutene reaction. Although the catalysts with coexisting Brønsted acidity could catalyze the rate-limiting acetone-to-isobutene reaction, the presence of Brønsted acidity is also detrimental. First, secondary isobutene isomerization is favored, producing a mixture of butene isomers. Second, undesired polymerization and coke formation prevail, leading to rapid catalyst deactivation. Most importantly, both steady-state and kinetic reaction studies as well as FTIR analysis of adsorbed acetone-d6 and D2O unambiguously showed that a highly active and selective nature of balanced Lewis acid-base pairs was masked by the coexisting Brønsted acidity in the aldolization and self-deoxygenation of acetone to isobutene. As a result, ZnxZryOz catalysts with only Lewis acid-base pairs were discovered, on which nearly a theoretical selectivity to isobutene (~88.9%) was successfully achieved, which has never been reported before. Moreover, the absence of Brønsted acidity in such ZnxZryOz catalysts also eliminates the side isobutene isomerization and undesired polymerization/coke reactions, resulting in the production of high purity isobutene with significantly improved catalyst stability (< 2% activity loss after 200 h time-on-stream). This work not only demonstrates a balanced Lewis acid-base pair for the highly active and selective cascade ethanol-to-isobutene reaction, but also sheds light on the rational design of selective and robust acid-base catalyst for C-C coupling via aldolization reaction.

  9. One Step Quick Detection of Cancer Cell Surface Marker by Integrated NiFe-based Magnetic Biosensing Cell Cultural Chip

    Institute of Scientific and Technical Information of China (English)

    Chenchen Bao; Lei Chen; Tao Wang; Chong Lei; Furong Tian; Daxiang Cui; Yong Zhou

    2013-01-01

    RGD peptides has been used to detect cell surface integrin and direct clinical effective therapeutic drug selection. Herein we report that a quick one step detection of cell surface marker that was realized by a specially designed NiFe-based magnetic biosensing cell chip combined with functionalized magnetic nanoparti-cles. Magnetic nanoparticles with 20-30 nm in diameter were prepared by coprecipitation and modified with RGD-4C, and the resultant RGD-functionalized magnetic nanoparticles were used for targeting cancer cells cul-tured on the NiFe-based magnetic biosensing chip and distinguish the amount of cell surface receptor-integrin. Cell lines such as Calu3, Hela, A549, CaFbr, HEK293 and HUVEC exhibiting different integrin expression were chosen as test samples. Calu3, Hela, HEK293 and HUVEC cells were successfully identified. This approach has advantages in the qualitative screening test. Compared with traditional method, it is fast, sensitive, low cost, easy-operative, and needs very little human intervention. The novel method has great potential in applications such as fast clinical cell surface marker detection, and diagnosis of early cancer, and can be easily extended to other biomedical applications based on molecular recognition.

  10. A 2-D process-based model for suspended sediment dynamics: A first step towards ecological modeling

    Science.gov (United States)

    Achete, F. M.; van der Wegen, M.; Roelvink, D.; Jaffe, B.

    2015-01-01

    In estuaries suspended sediment concentration (SSC) is one of the most important contributors to turbidity, which influences habitat conditions and ecological functions of the system. Sediment dynamics differs depending on sediment supply and hydrodynamic forcing conditions that vary over space and over time. A robust sediment transport model is a first step in developing a chain of models enabling simulations of contaminants, phytoplankton and habitat conditions. This works aims to determine turbidity levels in the complex-geometry delta of the San Francisco estuary using a process-based approach (Delft3D Flexible Mesh software). Our approach includes a detailed calibration against measured SSC levels, a sensitivity analysis on model parameters and the determination of a yearly sediment budget as well as an assessment of model results in terms of turbidity levels for a single year, water year (WY) 2011. Model results show that our process-based approach is a valuable tool in assessing sediment dynamics and their related ecological parameters over a range of spatial and temporal scales. The model may act as the base model for a chain of ecological models assessing the impact of climate change and management scenarios. Here we present a modeling approach that, with limited data, produces reliable predictions and can be useful for estuaries without a large amount of processes data.

  11. A 2-D process-based model for suspended sediment dynamics: a first step towards ecological modeling

    Directory of Open Access Journals (Sweden)

    F. M. Achete

    2015-02-01

    Full Text Available In estuaries most of the sediment load is carried in suspension. Sediment dynamics differ depending on sediment supply and hydrodynamic forcing conditions that vary over space and over time. Suspended sediment concentration (SSC is one of the most important contributors to turbidity, which influences habitat conditions and ecological functions of the system. A robust sediment model is the first step towards a chain of model including contaminants and phytoplankton dynamics and habitat modeling. This works aims to determine turbidity levels in the complex-geometry Delta of San Francisco Estuary using a process-based approach (D-Flow Flexible Mesh software. Our approach includes a detailed calibration against measured SSC levels, a sensitivity analysis on model parameters, the determination of a yearly sediment budget as well as an assessment of model results in terms of turbidity levels for a single year (Water Year 2011. Model results shows that our process-based approach is a valuable tool in assessing sediment dynamics and their related ecological parameters over a range of spatial and temporal scales. The current model may act as the base model for a chain of ecological models and climate scenario forecasting.

  12. Casimir light: photon pairs.

    OpenAIRE

    1993-01-01

    Expressions are developed for weak single pair emission probability and strong emission average number of pairs. The water transparency cutoff is closely realized, showing that the fundamental time scale is even shorter.

  13. Magnetic properties and pairing tendencies of the iron-based superconducting ladder BaFe2S3 : Combined ab initio and density matrix renormalization group study

    Science.gov (United States)

    Patel, Niravkumar D.; Nocera, Alberto; Alvarez, Gonzalo; Arita, Ryotaro; Moreo, Adriana; Dagotto, Elbio

    2016-08-01

    The recent discovery of superconductivity under high pressure in the two-leg ladder compound BaFe2S3 [H. Takahashi et al., Nat. Mater. 14, 1008 (2015), 10.1038/nmat4351] opens a broad avenue of research, because it represents the first report of pairing tendencies in a quasi-one-dimensional iron-based high-critical-temperature superconductor. Similarly, as in the case of the cuprates, ladders and chains can be far more accurately studied using many-body techniques and model Hamiltonians than their layered counterparts, particularly if several orbitals are active. In this publication, we derive a two-orbital Hubbard model from first principles that describes individual ladders of BaFe2S3 . The model is studied with the density matrix renormalization group. These first reported results are exciting for two reasons: (i) at half-filling, ferromagnetic order emerges as the dominant magnetic pattern along the rungs of the ladder, and antiferromagnetic order along the legs, in excellent agreement with neutron experiments; and (ii) with hole doping, pairs form in the strong coupling regime, as found by studying the binding energy of two holes doped on the half-filled system. In addition, orbital selective Mott phase characteristics develop with doping, with only one Wannier orbital receiving the hole carriers while the other remains half-filled. These results suggest that the analysis of models for iron-based two-leg ladders could clarify the origin of pairing tendencies and other exotic properties of iron-based high-critical-temperature superconductors in general.

  14. Effect of LNA- and OMeN-modified oligonucleotide probes on the stability and discrimination of mismatched base pairs of duplexes

    Indian Academy of Sciences (India)

    Ying Yan; Jing Yan; Xianyu Piao; Tianbiao Zhang; Yifu Guan

    2012-06-01

    Locked nucleic acid (LNA) and 2′--methyl nucleotide (OMeN) are the most extensively studied nucleotide analogues. Although both LNA and OMeN are characterized by the C3′-endo sugar pucker conformation, which is dominant in A-form DNA and RNA nucleotides, they demonstrate different binding behaviours. Previous studies have focused attention on their properties of duplex stabilities, hybridization kinetics and resistance against nuclease digestion; however, their ability to discriminate mismatched hybridizations has been explored much less. In this study, LNA- and OMeN-modified oligonucleotide probes have been prepared and their effects on the DNA duplex stability have been examined: LNA modifications can enhance the duplex stability, whereas OMeN modifications reduce the duplex stability. Next, we studied how the LNA:DNA and OMeN:DNA mismatches reduced the duplex stability. Melting temperature measurement showed that different LNA:DNA or OMeN:DNA mismatches indeed influence the duplex stability differently. LNA purines can discriminate LNA:DNA mismatches more effectively than LNA pyrimidines as well as DNA nucleotides. Furthermore, we designed five LNA- and five OMeN-modified oligonucleotide probes to simulate realistic situations where target–probe duplexes contain a complementary LNA:DNA or OMeN:DNA base pairs and a DNA:DNA mismatch simultaneously. The measured collective effect showed that the duplex stability was enhanced by the complementary LNA:DNA base pair but decreased by the DNA:DNA mismatch in a position-dependent manner regardless of the chemical identity and position of the complementary LNA:DNA base pair. On the other hand, the OMeN-modified probes also showed that the duplex stability was reduced by both the OMeN modification and the OMeN:DNA mismatch in a position-dependent manner.

  15. Electron-hole pair mechanism for the magnetic field effect in organic light emitting diodes based on poly(paraphenylene vinylene)

    Science.gov (United States)

    Bagnich, S. A.; Niedermeier, U.; Melzer, C.; Sarfert, W.; von Seggern, H.

    2009-12-01

    We investigated the magnetic field effect (MFE) on current and electroluminescence in organic light emitting diodes based on poly(paraphenylene vinylene). The MFE was strictly positive in the full range of device operation and showed nonmonotonic dependencies on applied voltage and temperature. Furthermore, the MFE on current obtained in bipolar devices was significantly larger than in hole-dominated devices. We discuss our results in the framework of an electron-hole pair model and show that the model can explain all functional dependencies observed in our devices.

  16. A 33fJ/Step SAR Capacitance-to-Digital Converter Using a Chain of Inverter-Based Amplifiers

    KAUST Repository

    Omran, Hesham

    2016-11-16

    A 12 - bit energy-efficient capacitive sensor interface circuit that fully relies on capacitance-domain successive approximation (SAR) technique is presented. Analysis shows that for SAR capacitance-to-digital converter (CDC) comparator offset voltage will result in parasitic-dependent conversion errors, which necessitates using an offset cancellation technique. Based on the presented analysis, a SAR CDC that uses a chain of cascode inverter-based amplifiers with near-threshold biasing is proposed to provide robust, energy-efficient, and fast operation. A hybrid coarse-fine capacitive digital-to-analog converter (CapDAC) achieves 11.7 - bit effective resolution, and provides 83% area saving compared to a conventional binary weighted implementation. The prototype fabricated in a 0.18μm CMOS technology is experimentally verified using MEMS capacitive pressure sensor. Experimental results show an energy efficiency figure-of-merit (FoM) of 33 f J/Step which outperforms the state-of-the-art. The CDC output is insensitive to analog references; thus, a very low temperature sensitivity of 2.3 ppm/°C is achieved without the need for calibration.

  17. Three-dimensional paper-based slip device for one-step point-of-care testing

    Science.gov (United States)

    Han, Kwi Nam; Choi, Jong-Soon; Kwon, Joseph

    2016-05-01

    In this study, we developed a new type of paper-based analytical device (PAD), the three-dimensional (3D) slip-PAD, to detect infectious human norovirus for global healthcare. The 3D configuration of the papers combined with a slip design provides unique features and versatility that overcome the limitations of fluidic manipulation and sensitivity in point-of-care (POC) tests. The assay can be carried out in a single step based on a moveable slip design, making it suitable for unskilled users. The 3D fluidic network developed by layered construction of wax-patterned papers provides different fluidic paths for the sequential delivery of multiple fluids without the need for peripheral equipment. The release and mixing of enhancement reagents on the device improved the sensitivity and detection limit. The assay results could be visualized by naked eye within 10 min, with subsequent amplification of the signal over time (human norovirus. These results demonstrate that the 3D slip-PAD is a sensitive diagnostic assay for detecting human norovirus infection that is particularly suitable for POC testing in regions where resources are scarce.

  18. Correlates of pedometer use: Results from a community-based physical activity intervention trial (10,000 Steps Rockhampton

    Directory of Open Access Journals (Sweden)

    Schofield Grant

    2007-07-01

    Full Text Available Abstract Background Pedometers have become common place in physical activity promotion, yet little information exists on who is using them. The multi-strategy, community-based 10,000 Steps Rockhampton physical activity intervention trial provided an opportunity to examine correlates of pedometer use at the population level. Methods Pedometer use was promoted across all intervention strategies including: local media, pedometer loan schemes through general practice, other health professionals and libraries, direct mail posted to dog owners, walking trail signage, and workplace competitions. Data on pedometer use were collected during the 2-year follow-up telephone interviews from random population samples in Rockhampton, Australia, and a matched comparison community (Mackay. Logistic regression analyses were used to determine the independent influence of interpersonal characteristics and program exposure variables on pedometer use. Results Data from 2478 participants indicated that 18.1% of Rockhampton and 5.6% of Mackay participants used a pedometer in the previous 18-months. Rockhampton pedometer users (n = 222 were more likely to be female (OR = 1.59, 95% CI: 1.11, 2.23, aged 45 or older (OR = 1.69, 95% CI: 1.16, 2.46 and to have higher levels of education (university degree OR = 4.23, 95% CI: 1.86, 9.6. Respondents with a BMI > 30 were more likely to report using a pedometer (OR = 1.68, 95% CI: 1.11, 2.54 than those in the healthy weight range. Compared with those in full-time paid work, respondents in 'home duties' were significantly less likely to report pedometer use (OR = 0.18, 95% CI: 0.06, 0.53. Exposure to individual program components, in particular seeing 10,000 Steps street signage and walking trails or visiting the website, was also significantly associated with greater pedometer use. Conclusion Pedometer use varies between population subgroups, and alternate strategies need to be investigated to engage men, people with lower levels

  19. A stabilized pairing functional

    CERN Document Server

    Erler, J; Reinhard, P --G

    2008-01-01

    We propose a modified pairing functional for nuclear structure calculations which avoids the abrupt phase transition between pairing and non-pairing states. The intended application is the description of nuclear collective motion where the smoothing of the transition is compulsory to remove singularities. The stabilized pairing functional allows a thoroughly variational formulation, unlike the Lipkin-Nogami (LN) scheme which is often used for the purpose of smoothing. First applications to nuclear ground states and collective excitations prove the reliability and efficiency of the proposed stabilized pairing.

  20. Can an excess electron localize on a purine moiety in the adenine-thymine Watson-Crick base pair? A computational study

    Science.gov (United States)

    Mazurkiewicz, Kamil; Harańczyk, Maciej; Gutowski, Maciej; Rak, Janusz

    The electron affinity and the propensity to electron-induced proton transfer (PT) of hydrogen-bonded complexes between the Watson-Crick adenine-thymine pair (AT) and simple organic acid (HX), attached to adenine in the Hoogsteen-type configuration, were studied at the B3LYP/6-31+G** level. Although the carboxyl group is deprotonated at physiological pH, its neutral form, COOH, resembles the peptide bond or the amide fragment in the side chain of asparagine (Asn) or glutamine (Gln). Thus, these complexes mimic the interaction between the DNA environment (e.g., proteins) and nucleobase pairs incorporated in the biopolymer. Electron attachment is thermodynamically feasible and adiabatic electron affinities range from 0.41 to 1.28 eV, while the vertical detachment energies of the resulting anions span the range of 0.39-2.88 eV. Low-energy activation barriers separate the anionic minima: aHX(AT) from the more stable single-PT anionic geometry, aHX(AT)-SPT, and aHX(AT)-SPT from the double-PT anionic geometry, aHX(AT)-DPT. Interaction between the adenine of the Watson-Crick AT base pair with an acidic proton donor probably counterbalances the larger EA of isolated thymine, as SOMO is almost evenly delocalized over both types of nucleic bases in the aHX(AT) anions. Moreover, as a result of PT the excess electron localizes entirely on adenine. Thus, in DNA interacting with its physiological environment, damage induced by low-energy electrons could begin, contrary to the current view, with the formation of purine anions, which are not formed in isolated DNA because of the greater stability of anionic pyrimidines.0