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Sample records for ahlers phys rev

  1. Erratum: Binary neutron stars with arbitrary spins in numerical relativity [Phys. Rev. D 92, 124012 (2015)

    NASA Astrophysics Data System (ADS)

    Tacik, Nick; Foucart, Francois; Pfeiffer, Harald P.; Haas, Roland; Ossokine, Serguei; Kaplan, Jeff; Muhlberger, Curran; Duez, Matt D.; Kidder, Lawrence E.; Scheel, Mark A.; Szilágyi, Béla

    2016-08-01

    The code used in [Phys. Rev. D 92, 124012 (2015)] erroneously computed the enthalpy at the center of the neutron stars. Upon correcting this error, density oscillations in evolutions of rotating neutron stars are significantly reduced (from ˜20 % to ˜0.5 % ). Furthermore, it is possible to construct neutron stars with faster rotation rates.

  2. Erratum: Studying the precision of ray tracing techniques with Szekeres models [Phys. Rev. D 92, 023532 (2015)

    NASA Astrophysics Data System (ADS)

    Koksbang, S. M.; Hannestad, S.

    2015-09-01

    This erratum serves to give corrections of two errors made in Koksbang and Hannestad [Phys. Rev. D, 92, 023532 (2015)]. One error consists of having used the expression for the Doppler convergence for a flat background to study the convergence on curved backgrounds. The other error which was made, is a typo in the numerical code used to study the convergence in onion models with curved backgrounds. After correcting this typo, the results of Sec. VI A in Koksbang and Hannestad [Phys. Rev. D, 92, 023532 (2015)] were recomputed. Contrary to the original results, the new results show that the ray-tracing scheme studied in Koksbang and Hannestad [Phys. Rev. D, 92, 023532 (2015)] can reproduce the exact results in LTB onion models very well. The corrections and new results are described more elaborately below.

  3. Reply to 'Comment on 'All quantum observables in a hidden-variable model must commute simultaneously'' [Phys. Rev. A 73, 066101 (2006)

    SciTech Connect

    Malley, J. D.; Fine, A.

    2006-06-15

    Nagata [Phys. Rev. A 73, 066101 (2006)] questions whether a general no-go theorem of Malley [Phys. Rev. A 69, 022118 (2004)] applies to local hidden variables and outlines a 'counterexample.' In fact this is not a counterexample at all, but in seeing why it fails we clarify the significance of Malley's result and its relation to other no-go theorems.

  4. Comment on “Diffusion of n-type dopants in germanium” [Appl. Phys. Rev. 1, 011301 (2014)

    SciTech Connect

    Cowern, N. E. B. Simdyankin, S.; Goss, J. P.; Napolitani, E.; De Salvador, D.; Bruno, E.; Mirabella, S.; Ahn, C.; Bennett, N. S.

    2015-09-15

    The authors of the above paper call into question recent evidence on the properties of self-interstitials, I, in Ge [Cowern et al., Phys. Rev. Lett. 110, 155501 (2013)]. We show that this judgment stems from invalid model assumptions during analysis of data on B marker-layer diffusion during proton irradiation, and that a corrected analysis fully supports the reported evidence. As previously stated, I-mediated self-diffusion in Ge exhibits two distinct regimes of temperature, T: high-T, dominated by amorphous-like mono-interstitial clusters—i-morphs—with self-diffusion entropy ≈30 k, and low-T, where transport is dominated by simple self-interstitials. In a transitional range centered on 475 °C both mechanisms contribute. The experimental I migration energy of 1.84 ± 0.26 eV reported by the Münster group based on measurements of self-diffusion during irradiation at 550 °C < T < 680 °C further establishes our proposed i-morph mechanism.

  5. Comment on 'Turbulent equipartition theory of toroidal momentum pinch' [Phys. Plasmas 15, 055902 (2008)

    SciTech Connect

    Peeters, A. G.; Angioni, C.; Strintzi, D.

    2009-03-15

    The comment addresses questions raised on the derivation of the momentum pinch velocity due to the Coriolis drift effect [A. G. Peeters et al., Phys. Rev. Lett. 98, 265003 (2007)]. These concern the definition of the gradient, and the scaling with the density gradient length. It will be shown that the turbulent equipartition mechanism is included within the derivation using the Coriolis drift, with the density gradient scaling being the consequence of drift terms not considered in [T. S. Hahm et al., Phys. Plasmas 15, 055902 (2008)]. Finally the accuracy of the analytic models is assessed through a comparison with the full gyrokinetic solution.

  6. Summary of PhysPAG Activities

    NASA Astrophysics Data System (ADS)

    Ritz, Steven M.

    2013-01-01

    The Physics of the Cosmos (PCOS) Program Analysis Group (PhysPAG) provides an important interface between the scientific community and NASA in matters related to PCOS objectives, and also provides opportunities for community discussions. An Executive Committee facilitates the work of several subgroups, including an Inflation Probe Science Analysis Group (IPSAG), an X-ray group (XRSAG) , a gamma-ray,group (GRSAG), a gravitational wave group (GWSAG), and a cosmic-ray group (CRSAG). In addition to identifying opportunities and issues, these groups also help articulate technology needs. Membership in all the SAGs is completely open, with information and newsletter signups available on the PhysPAG pages at the PCOS program website. The PhysPAG reports to the Astrophysics Subcommittee of the NASA Advisory Council. A summary of PhysPAG activities will be given, along with time for questions and discussion.

  7. Summary of PhysPAG Activity

    NASA Astrophysics Data System (ADS)

    Nousek, John A.

    2014-01-01

    The Physics of the Cosmos Program Analysis Group (PhysPAG) is responsible for solicitiing and coordinating community input for the development and execution of NASA's Physics of the Cosmos (PCOS) program. In this session I will report on the activity of the PhysPAG, and solicit community involvement in the process of defining PCOS objectives, planning SMD architecture, and prioritizing PCOS activities. I will also report on the activities of the PhysPAG Executive Committee, which include the chairs of the Science Analysis Groups/ Science Interest Groups which fall under the PhysPAG sphere of interest. Time at the end of the presentation willl be reserved for questions and discussion from the community.

  8. Comment on ``On the role of dissipation on the Casimir-Polder potential between molecules in dielectric media'' [J. Chem. Phys. 133, 164501 (2010)

    NASA Astrophysics Data System (ADS)

    Dalvit, D. A. R.; Milonni, P. W.

    2011-07-01

    J. J. Rodriguez and A. Salam [J. Chem. Phys. 133, 164501 (2010)], 10.1063/1.3495954 find discrepancies between their calculation and a previously published one [S. Spagnolo, D. A. R. Dalvit, and P. W. Milonni, Phys. Rev. A 75, 052117 (2007)], 10.1103/PhysRevA.75.052117 for the van der Waals interaction of two guest molecules in a host dielectric medium. We trace these discrepancies to what we regard as fundamental errors in the calculation by Rodriguez and Salam.

  9. Publisher's Note: Bogoliubov excitations of disordered Bose-Einstein condensates [Phys. Rev. A 83, 063629 (2011)

    SciTech Connect

    Gaul, Christopher; Mueller, Cord A.

    2011-08-15

    This paper was published online on 23 June 2011 without some of the author's corrections incorporated into the published article. Most of these corrections relate to text citations of Refs. [19] and [20]. The paper has been corrected as of 3 August 2011. The text is incorrect in the printed version of the journal.

  10. Corrected Article: Wormholes in Einstein-Born-Infeld theory [Phys. Rev. D 80, 104033 (2009)

    SciTech Connect

    Richarte, Martin G.; Simeone, Claudio

    2010-05-15

    Spherically symmetric thin-shell wormholes are studied within the framework of Einstein-Born-Infeld theory. We analyze the exotic matter content, and find that for certain values of the Born-Infeld parameter the amount of exotic matter on the shell can be reduced in relation with the Maxwell case. We also examine the mechanical stability of the wormhole configurations under radial perturbations preserving the spherical symmetry.

  11. Erratum: Quantum superconducting criticality in graphene and topological insulators [Phys. Rev. B 87, 041401(R) (2013)

    NASA Astrophysics Data System (ADS)

    Roy, Bitan; Juričić, Vladimir; Herbut, Igor F.

    2016-09-01

    We correct our previous conclusion regarding the fate of a charged quantum critical point across the superconducting transition for two dimensional massless Dirac fermion. Within the leading order $\\epsilon$ expansion, we now find that the requisite number of four-component Dirac fermion flavors ($N_f$) for the continuous phase transition through a charged critical point is $N_f>18.2699$. For $N_f\\geq1/2$, the critical number of bosonic flavors for this transition is significantly reduced as compared to the value determined in the absence of the Dirac fermions in the theory.

  12. Summary of PhysPAG Activities

    NASA Astrophysics Data System (ADS)

    Ritz, Steven M.

    2012-01-01

    The Physics of the Cosmos (PCOS) Program Analysis Group (PhysPAG) provides an important interface between the scientific community and NASA in matters related to PCOS objectives. An Executive Committee facilitates the work of several subgroups, including a Technology Science Analysis Group and an Inflation Probe Science Analysis Group. Work is also starting in areas of X-ray, gamma-ray, and gravitational wave astrophysics. The PAG reports to the Astrophysics Subcommittee of the NASA Advisory Council. A summary of PhysPAG activities will be given, along with time for questions and discussion.

  13. Comment on ''Scalings for radiation from plasma bubbles''[Phys. Plasmas 17, 056708 (2010)

    SciTech Connect

    Corde, S.; Stordeur, A.; Malka, V.

    2011-03-15

    Thomas has recently derived scaling laws for x-ray radiation from electrons accelerated in plasma bubbles, as well as a threshold for the self-injection of background electrons into the bubble [A. G. R. Thomas, Phys. Plasmas 17, 056708 (2010)]. To obtain this threshold, the equations of motion for a test electron are studied within the frame of the bubble model, where the bubble is described by prescribed electromagnetic fields and has a perfectly spherical shape. The author affirms that any elliptical trajectory of the form x{sup '2}/{gamma}{sub p}{sup 2}+y{sup '2}=R{sup 2} is solution of the equations of motion (in the bubble frame), within the approximation p{sub y}{sup '2}/p{sub x}{sup '2}<<1. In addition, he highlights that his result is different from the work of Kostyukov et al. [Phys. Rev. Lett. 103, 175003 (2009)], and explains the error committed by Kostyukov-Nerush-Pukhov-Seredov (KNPS). In this comment, we show that numerically integrated trajectories, based on the same equations than the analytical work of Thomas, lead to a completely different result for the self-injection threshold, the result published by KNPS [Phys. Rev. Lett. 103, 175003 (2009)]. We explain why the analytical analysis of Thomas fails and we provide a discussion based on numerical simulations which show exactly where the difference arises. We also show that the arguments of Thomas concerning the error of KNPS do not hold, and that their analysis is mathematically correct. Finally, we emphasize that if the KNPS threshold is found not to be verified in PIC (Particle In Cell) simulations or experiments, it is due to a deficiency of the model itself, and not to an error in the mathematical derivation.

  14. Comment on ``Unified explanation of the anomalous dynamic properties of highly asymmetric polymer blends'' [J. Chem. Phys. 138, 054903 (2013)

    NASA Astrophysics Data System (ADS)

    Colmenero, J.

    2013-05-01

    In a recent paper by Ngai and Capaccioli ["Unified explanation of the anomalous dynamic properties of highly asymmetric polymer blends," J. Chem. Phys. 138, 054903 (2013), 10.1063/1.4789585] the authors claimed that the so-called coupling model (CM) provides a unified explanation of all dynamical anomalies that have been reported for dynamically asymmetric blends over last ten years. Approximately half of the paper is devoted to chain-dynamic properties involving un-entangled polymers. According to the authors, the application of the CM to these results is based on the existence of a crossover at a time tc ≈ 1-2 ns of the magnitudes describing chain-dynamics. Ngai and Capaccioli claimed that the existence of such a crossover is supported by the neutron scattering and MD-simulation results, corresponding to the blend poly(methyl methacrylate)/poly(ethylene oxide), by Niedzwiedz et al. [Phys. Rev. Lett. 98, 168301 (2007), 10.1103/PhysRevLett.98.168301] and Brodeck et al. [Macromolecules 43, 3036 (2010), 10.1021/ma902820a], respectively. Being one of the authors of these two papers, I will demonstrate here that there is no evidence supporting such a crossover in the data reported in these papers.

  15. Comment on 'Power loss in open cavity diodes and a modified Child-Langmuir law' [Phys. Plasmas 12, 093102 (2005)

    SciTech Connect

    Swanekamp, S. B.; Ottinger, P. F.

    2007-09-15

    In this Comment, it is shown that no modification of the Child-Langmuir law [Phys. Rev.32, 492 (1911); Phys. Rev. 2, 450 (1913)] is necessary to treat the space-charge-limited flow from a diode with an open boundary as reported in Phys. Plasmas 12, 093102 (2005). The open boundary condition in their simulations can be represented by a voltage source and a resistor whose value is the vacuum-wave impedance of the opening. The diode can be represented as a variable resistor whose value depends on the voltage drop across the diode (as measured by the line integral of E across the diode gap). This is a simple voltage-divider circuit whose analysis shows that the real diode voltage drops as the vacuum-wave impedance increases. Furthermore, it is shown that in equilibrium, the voltage drop between the anode and cathode is independent of the path chosen for the line integral of the electric field so that E=-{nabla}{phi} is valid. In this case, the equations of electrostatics are applicable. This clearly demonstrates that the electric field is electrostatic and static fields DO NOT RADIATE. It is shown that the diode voltage drops as the vacuum wave impedance increases and the current drops according to the Child-Langmuir law. Therefore, the observed drop in circuit current can be explained by a real drop in voltage across the diode and not an effective drop as claimed by the authors.

  16. The new PhysTEC program at Boston University

    NASA Astrophysics Data System (ADS)

    Jenkins, Juliet; Duffy, Andrew

    2011-11-01

    The Boston University Physics Department was recently awarded a three-year grant from the Physics Teacher Education Coalition (PhysTEC). PhysTEC's main aims are to improve the education of future physics teachers, and to increase the number of qualified physics teachers in the school system. Although there have been over 20 PhysTEC-funded sites across the country, BU is the first PhysTEC site in New England. Our goals with this poster are to raise awareness about PhysTEC, and to talk about what we are doing and what we plan to do at BU with our PhysTEC funding. A key part of the PhysTEC program is the teacher-in-residence (TIR), an experienced physics teacher who comes to campus for a year to promote physics teaching as a profession and to lend their experience to education-related efforts. Our first TIR is Juliet Jenkins. The poster will discuss Ms. Jenkins' role in the Department of Physics and in the School of Education as we move forward with new efforts to promote teaching, including a Learning Assistant program, a pilot studio section of one of our introductory physics courses, and a new education course that allows undergraduate students to observe teachers in the classroom.

  17. Publisher's Note: Kelvin-Helmholtz versus Hall magnetoshear instability in astrophysical flows [Phys. Rev. E 89, 053105 (2014)

    NASA Astrophysics Data System (ADS)

    Gómez, Daniel O.; Bejarano, Cecilia; Mininni, Pablo D.

    2014-06-01

    We study the stability of shear flows in a fully ionized plasma. Kelvin-Helmholtz is a well known, macroscopic and ideal shear-driven instability. In sufficiently low density plasmas, also the microscopic Hall magneto-shear instability can take place. We performed three-dimensional simulations of the Hall-MHD equations where these two instabilities are present, and carried out a comparative study. We find that when the shear flow is so intense that its vorticity surpasses the ion-cyclotron frequency of the plasma, the Hall magneto-shear instability is not only non-negligible, but it actually displays growth rates larger than those of the Kelvin-Helmholtz instability.

  18. Erratum: Optical and transport properties in three-dimensional Dirac and Weyl semimetals [Phys. Rev. B 93, 085426 (2016)

    NASA Astrophysics Data System (ADS)

    Tabert, C. J.; Carbotte, J. P.; Nicol, E. J.

    2016-07-01

    Within a Kubo formalism, we study dc transport and ac optical properties of 3D Dirac and Weyl semimetals. Emphasis is placed on the approach to charge neutrality and on the differences between Dirac and Weyl materials. At charge neutrality, the zero-temperature limit of the dc conductivity is not universal and also depends on the residual scattering model employed. However, the Lorenz number L retains its usual value L_0. With increasing temperature, the Wiedemann-Franz law is violated. At high temperatures, L exhibits a new plateau at a value dependent on the details of the scattering rate. Such details can also appear in the optical conductivity, both in the Drude response and interband background. In the clean limit, the interband background is linear in photon energy and always extrapolates to the origin. This background can be shifted to the right through the introduction of a massless gap. In this case, the extrapolation can cut the axis at a finite photon energy as is observed in some experiments. It is also of interest to differentiate between the two types of Weyl semimetals: those with broken time-reversal symmetry and those with broken spatial-inversion symmetry. We show that, while the former will follow the same behaviour as the 3D Dirac semimetals, for the zero magnetic field properties discussed here, the latter type will show a double step in the optical conductivity at finite doping and a single absorption edge at charge neutrality. The Drude conductivity is always finite in this case, even at charge neutrality.

  19. Erratum: Axion Dark Matter Coupling to Resonant Photons via Magnetic Field [Phys. Rev. Lett. 116, 161804 (2016)

    NASA Astrophysics Data System (ADS)

    McAllister, Ben T.; Parker, Stephen R.; Tobar, Michael E.

    2016-10-01

    A recent comment highlights a discussion at the PATRAS Workshop on Axions, WIMPs and WISPs relating to a recent publication. We respond to this comment, and detail a calculation error in the original letter.

  20. Stable complex formation between HIV Rev and the nucleosome assembly protein, NAP1, affects Rev function

    SciTech Connect

    Cochrane, Alan; Murley, Laura Lea; Gao Mian; Wong, Raymond; Clayton, Kiera; Brufatto, Nicole; Canadien, Veronica; Mamelak, Daniel; Chen, Tricia; Richards, Dawn; Zeghouf, Mahel; Greenblatt, Jack; Burks, Christian; Frappier, Lori

    2009-05-25

    The Rev protein of HIV-1 is essential for HIV-1 proliferation due to its role in exporting viral RNA from the nucleus. We used a modified version of tandem affinity purification (TAP) tagging to identify proteins interacting with HIV-1 Rev in human cells and discovered a prominent interaction between Rev and nucleosome assembly protein 1 (Nap1). This interaction was also observed by specific retention of Nap1 from human cell lysates on a Rev affinity column. Nap1 was found to bind Rev through the Rev arginine-rich domain and altered the oligomerization state of Rev in vitro. Overexpression of Nap1 stimulated the ability of Rev to export RNA, reduced the nucleolar localization of Rev, and affected Rev nuclear import rates. The results suggest that Nap-1 may influence Rev function by increasing the availability of Rev.

  1. The PhysTEC Teacher Education Program at FIU

    NASA Astrophysics Data System (ADS)

    Kramer, Laird

    2010-10-01

    The FIU PhysTEC Project is an integral component of the Physics Department's educational transformation that has led to more than a ten-fold increase in majors. The transformation seeks to increase the quality and quantity of physics majors and future physics teachers, including those from historically underrepresented groups. Elements of the efforts include transformed introductory physics courses, establishment of a physics research and learning community, engagement of stakeholders spanning high school through the university administration, and advocacy by a physics education research group. The PhysTEC Project supports future physics teachers through a Learning Assistant program coupled to newly revised secondary education programs. The Learning Assistant program is an experiential program that recruits new students into teaching careers while providing a mechanism for transforming courses - undergraduates experience the rewards and intellectual challenges of teaching through providing interactive engagement learning experiences for their peers in introductory physics courses. Students that continue in the program enroll in a multidisciplinary teacher preparation program and may receive significant financial support. FIU is a minority-serving urban public research institution in Miami, Florida serving over 39,000 students, of which 64% are Hispanic, 13% are Black, and 56% are women. Programmatic strategies and impacts of the program will be provided.

  2. Comments on ``The Euclidean gravitational action as black hole entropy, singularities, and space-time voids'' [J. Math. Phys. 49, 042501 (2008)

    NASA Astrophysics Data System (ADS)

    Mitra, Abhas

    2009-04-01

    We point out that the space-time void inferred by Castro [J. Math. Phys. 49, 042501 (2008)] results from his choice of a discontinuous radial gauge. Further since the integration constant α0=2M0 (G =c=1) occurring in the vacuum Hilbert/Schwarzschild solution of a neutral "point mass" is zero [Arnowitt et al., in Gravitation: An Introduction to Current Research, edited by L. Witten (Wiley, New York, 1962), Chap. 7, p. 227; also Phys. Rev. Lett. 4, 375 (1960). A. Mitra, Adv. Space Res. 38, 2917 (2006); Proceedings of the XIth Marcel-Grossmann Conference on General Relativity (World Scientific, Singapore, 2008), Vol. 3, p. 1968], Castro's gauge reduces to the well behaved and physical Hilbert gauge. Physically this means that true Hilbert/Schwarzschild black holes have unique gravitational mass M =0. Accordingly, the unphysical space-time void inferred by Castro is actually nonexistent.

  3. Optimized chemical probes for REV-ERBα.

    PubMed

    Trump, Ryan P; Bresciani, Stefano; Cooper, Anthony W J; Tellam, James P; Wojno, Justyna; Blaikley, John; Orband-Miller, Lisa A; Kashatus, Jennifer A; Boudjelal, Mohamed; Dawson, Helen C; Loudon, Andrew; Ray, David; Grant, Daniel; Farrow, Stuart N; Willson, Timothy M; Tomkinson, Nicholas C O

    2013-06-13

    REV-ERBα has emerged as an important target for regulation of circadian rhythm and its associated physiology. Herein, we report on the optimization of a series of REV-ERBα agonists based on GSK4112 (1) for potency, selectivity, and bioavailability. (1) Potent REV-ERBα agonists 4, 10, 16, and 23 are detailed for their ability to suppress BMAL and IL-6 expression from human cells while also demonstrating excellent selectivity over LXRα. Amine 4 demonstrated in vivo bioavailability after either iv or oral dosing.

  4. The Structure of HIV-1 Rev Filaments Suggests a Bilateral Model for Rev-RRE Assembly.

    PubMed

    DiMattia, Michael A; Watts, Norman R; Cheng, Naiqian; Huang, Rick; Heymann, J Bernard; Grimes, Jonathan M; Wingfield, Paul T; Stuart, David I; Steven, Alasdair C

    2016-07-01

    HIV-1 Rev protein mediates the nuclear export of viral RNA genomes. To do so, Rev oligomerizes cooperatively onto an RNA motif, the Rev response element (RRE), forming a complex that engages with the host nuclear export machinery. To better understand Rev oligomerization, we determined four crystal structures of Rev N-terminal domain dimers, which show that they can pivot about their dyad axis, giving crossing angles of 90° to 140°. In parallel, we performed cryoelectron microscopy of helical Rev filaments. Filaments vary from 11 to 15 nm in width, reflecting variations in dimer crossing angle. These structures contain additional density, indicating that C-terminal domains become partially ordered in the context of filaments. This conformational variability may be exploited in the assembly of RRE/Rev complexes. Our data also revealed a third interface between Revs, which offers an explanation for how the arrangement of Rev subunits adapts to the "A"-shaped architecture of the RRE in export-active complexes. PMID:27265851

  5. PREFACE: Prospects in Neutrino Physics 2013 - NuPhys2013

    NASA Astrophysics Data System (ADS)

    2015-04-01

    The first "Prospects in Neutrino Physics 2013 - NuPhys2013" conference was held at the Institute of Physics, IoP, London, 19-20 December 2013 and was attended by about 130 delegates from institutions worldwide. Lunch and coffee breaks allowed discussions among delegates and speakers to take place in an informal setting. This conference is unique in discussing the worldwide strategy to address unresolved issues in neutrino physics, and shape the future directions of particle physics. We discussed the current status and focussed especially on the prospects of future experiments, their performance and physics reach. It is particularly timely due to the recent measurements in neutrino physics and planned worldwide experiments. The following topics were addressed: • Theory and Phenomenology Perspectives • Future Long and Short Baseline Neutrino Oscillation Experiments • Reactor neutrino and flux • Neutrinoless double beta decays • Solar, atmospheric, supernova neutrinos • Neutrino cosmology in which both the phenomenological and experimental aspects were equally addressed. World-leading experts in the different neutrino areas were invited to give review talks. To encourage and facilitate the participation of early-career researchers and PhD students, a poster session formed a key aspect of this meeting. The conference was organized by Francesca Di Lodovico and Silvia Pascoli. It was sponsored by the IoP through their Topic Research Meeting Grant, and also supported by Durham IPPP, ERC-207282, FP7 invisibles project, Queen Mary University of London.

  6. Thermodynamics of Rev-RNA interactions in HIV-1 Rev-RRE assembly.

    PubMed

    Jayaraman, Bhargavi; Mavor, David; Gross, John D; Frankel, Alan D

    2015-10-27

    The HIV-1 protein Rev facilitates the nuclear export of intron-containing viral mRNAs by recognizing a structured RNA site, the Rev-response-element (RRE), contained in an intron. Rev assembles as a homo-oligomer on the RRE using its α-helical arginine-rich-motif (ARM) for RNA recognition. One unique feature of this assembly is the repeated use of the ARM from individual Rev subunits to contact distinct parts of the RRE in different binding modes. How the individual interactions differ and how they contribute toward forming a functional complex is poorly understood. Here we examine the thermodynamics of Rev-ARM peptide binding to two sites, RRE stem IIB, the high-affinity site that nucleates Rev assembly, and stem IA, a potential intermediate site during assembly, using NMR spectroscopy and isothermal titration calorimetry (ITC). NMR data indicate that the Rev-IIB complex forms a stable interface, whereas the Rev-IA interface is highly dynamic. ITC studies show that both interactions are enthalpy-driven, with binding to IIB being 20-30 fold tighter than to IA. Salt-dependent decreases in affinity were similar at both sites and predominantly enthalpic in nature, reflecting the roles of electrostatic interactions with arginines. However, the two interactions display strikingly different partitioning between enthalpy and entropy components, correlating well with the NMR observations. Our results illustrate how the variation in binding modes to different RRE target sites may influence the stability or order of Rev-RRE assembly and disassembly, and consequently its function. PMID:26422686

  7. Thermodynamics of Rev-RNA interactions in HIV-1 Rev-RRE assembly.

    PubMed

    Jayaraman, Bhargavi; Mavor, David; Gross, John D; Frankel, Alan D

    2015-10-27

    The HIV-1 protein Rev facilitates the nuclear export of intron-containing viral mRNAs by recognizing a structured RNA site, the Rev-response-element (RRE), contained in an intron. Rev assembles as a homo-oligomer on the RRE using its α-helical arginine-rich-motif (ARM) for RNA recognition. One unique feature of this assembly is the repeated use of the ARM from individual Rev subunits to contact distinct parts of the RRE in different binding modes. How the individual interactions differ and how they contribute toward forming a functional complex is poorly understood. Here we examine the thermodynamics of Rev-ARM peptide binding to two sites, RRE stem IIB, the high-affinity site that nucleates Rev assembly, and stem IA, a potential intermediate site during assembly, using NMR spectroscopy and isothermal titration calorimetry (ITC). NMR data indicate that the Rev-IIB complex forms a stable interface, whereas the Rev-IA interface is highly dynamic. ITC studies show that both interactions are enthalpy-driven, with binding to IIB being 20-30 fold tighter than to IA. Salt-dependent decreases in affinity were similar at both sites and predominantly enthalpic in nature, reflecting the roles of electrostatic interactions with arginines. However, the two interactions display strikingly different partitioning between enthalpy and entropy components, correlating well with the NMR observations. Our results illustrate how the variation in binding modes to different RRE target sites may influence the stability or order of Rev-RRE assembly and disassembly, and consequently its function.

  8. The bovine immunodeficiency virus Rev protein: identification of a novel nuclear import pathway and nuclear export signal among retroviral Rev/Rev-like proteins.

    PubMed

    Gomez Corredor, Andrea; Archambault, Denis

    2012-05-01

    The Rev protein is essential for the replication of lentiviruses. Rev is a shuttling protein that transports unspliced and partially spliced lentiviral RNAs from the nucleus to the cytoplasm via the nucleopore. To transport these RNAs, the human immunodeficiency virus type 1 (HIV-1) Rev uses the karyopherin β family importin β and CRM1 proteins that interact with the Rev nuclear localization signal (NLS) and nuclear exportation signal (NES), respectively. Recently, we reported the presence of new types of bipartite NLS and nucleolar localization signal (NoLS) in the bovine immunodeficiency virus (BIV) Rev protein. Here we report the characterization of the nuclear import and export pathways of BIV Rev. By using an in vitro nuclear import assay, we showed that BIV Rev is transported into the nucleus by a cytosolic and energy-dependent importin α/β classical pathway. Results from glutathione S-transferase (GST) pulldown assays that showed the binding of BIV Rev with importins α3 and α5 were in agreement with those from the nuclear import assay. We also identified a leptomycin B-sensitive NES in BIV Rev, which indicates that the protein is exported via CRM1 like HIV-1 Rev. Mutagenesis experiments showed that the BIV Rev NES maps between amino acids 109 to 121 of the protein. Remarkably, the BIV Rev NES was found to be of the cyclic AMP (cAMP)-dependent protein kinase inhibitor (PKI) type instead of the HIV-1 Rev type. In summary, our data showed that the nuclear import mechanism of BIV Rev is novel among Rev proteins characterized so far in lentiviruses.

  9. Physics of the Cosmos Program Analysis Group (PhysPAG) Report

    NASA Astrophysics Data System (ADS)

    Nousek, John A.

    2015-01-01

    The Physics of the Cosmos Program Analysis Group (PhysPAG) serves as a forum for soliciting and coordinating input and analysis from the scientific community in support of the PCOS program objectives. I will outline the activities of the PhysPAG over the past year, since the last meeting during the AAS meeting in National Harbor, and mention the activities of the PhysPAG related Scientific Interest Groups.

  10. Preface: phys. stat. sol. (a) 202/12

    NASA Astrophysics Data System (ADS)

    Neumann, Wolfgang; Stutzmann, Martin; Hildebrandt, Stefan

    2005-09-01

    The present special issue contains a collection of Original Papers dedicated to Professor Johannes Heydenreich on the occasion of his 75th birthday.Johannes Heydenreich, born on 20 June 1930 in Plauen/Vogtland near Dresden, studied physics at the Pädagogische Hochschule Potsdam, where he obtained his first academic degree Dipl. Phys. in 1958. He received his doctoral degree at the Martin Luther University in Halle in 1961 and the Habilitation degree in 1969. Already during his studies in Potsdam, he showed an interest in electron microscopy due to the influence of his teacher and supervisor Prof. Picht, one of the pioneers in electron optics. His interests were strengthened when Johannes Heydenreich did the experimental work for his Diploma degree at the Institute for Experimental Physics of the University of Halle, where he met Prof. Heinz Bethge for the first time. This was the beginning of a fruitful and longstanding collaboration. In 1962 Johannes Heydenreich joined the team of the later Institute for Solid State Physics and Electron Microscopy of the Academy of Sciences of the GDR, in Halle, for which the basis was laid by Prof. Bethge in 1960.Heydenreich has been working as Assistant Director for many years and played a decisive role in introducing and organising the various techniques of electron microscopy in the institute.The research activities of Prof. Heydenreich covered a broad spectrum over the years. At the beginning of his career he made significant contributions in the field of electron mirror microscopy. After that, his main interests were focused on transmission electron microscopy, ranging from diffraction contrast analysis of crystal defects to high-resolution electron microscopy and image processing. His favourite field was studies of defect-induced phenomena in advanced materials. The so-called Bethge-Heydenreich, the book Electron Microscopy in Solid State Physics, published at first in a German edition in 1982 and later in a revised

  11. Erratum: Evidence of b-jet quenching in PbPb collisions at sNN=2.76TeV [Phys. Rev. Lett. 113 , 132301 (2014)

    DOE PAGES

    Chatrchyan, S.

    2015-07-10

    In our Letter, there was a component of the statistical uncertainty from the simulated PbPb Monte Carlo samples. This uncertainty was not propagated to all of the results. Figures 3 and 4 have been updated to reflect this source of uncertainty. In this case, the statistical uncertainties remain smaller than the systematic uncertainties in all cases such that the conclusions of the Letter are unaltered.

  12. Publisher's Note: Search for ultrahigh energy neutrinos in highly inclined events at the Pierre Auger Observatory [Phys. Rev. D 84, 122005 (2011)

    NASA Astrophysics Data System (ADS)

    Abreu, P.; Aglietta, M.; Ahlers, M.; Ahn, E. J.; Albuquerque, I. F. M.; Allard, D.; Allekotte, I.; Allen, J.; Allison, P.; Almela, A.; Alvarez Castillo, J.; Alvarez-Muñiz, J.; Ambrosio, M.; Aminaei, A.; Anchordoqui, L.; Andringa, S.; Anticic, T.; Aramo, C.; Arganda, E.; Arqueros, F.; Asorey, H.; Assis, P.; Aublin, J.; Ave, M.; Avenier, M.; Avila, G.; Bäcker, T.; Badescu, A. M.; Balzer, M.; Barber, K. B.; Barbosa, A. F.; Bardenet, R.; Barroso, S. L. C.; Baughman, B.; Bäuml, J.; Beatty, J. J.; Becker, B. R.; Becker, K. H.; Bellétoile, A.; Bellido, J. A.; Benzvi, S.; Berat, C.; Bertou, X.; Biermann, P. L.; Billoir, P.; Blanco, F.; Blanco, M.; Bleve, C.; Blümer, H.; Bohácová, M.; Boncioli, D.; Bonifazi, C.; Bonino, R.; Borodai, N.; Brack, J.; Brancus, I.; Brogueira, P.; Brown, W. C.; Bruijn, R.; Buchholz, P.; Bueno, A.; Burton, R. E.; Caballero-Mora, K. S.; Caccianiga, B.; Caramete, L.; Caruso, R.; Castellina, A.; Catalano, O.; Cataldi, G.; Cazon, L.; Cester, R.; Chauvin, J.; Cheng, S. H.; Chiavassa, A.; Chinellato, J. A.; Chirinos Diaz, J.; Chudoba, J.; Clay, R. W.; Coluccia, M. R.; Conceição, R.; Contreras, F.; Cook, H.; Cooper, M. J.; Coppens, J.; Cordier, A.; Coutu, S.; Covault, C. E.; Creusot, A.; Criss, A.; Cronin, J.; Curutiu, A.; Dagoret-Campagne, S.; Dallier, R.; Dasso, S.; Daumiller, K.; Dawson, B. R.; de Almeida, R. M.; de Domenico, M.; de Donato, C.; de Jong, S. J.; de La Vega, G.; de Mello, W. J. M., Jr.; de Mello Neto, J. R. T.; de Mitri, I.; de Souza, V.; de Vries, K. D.; Del Peral, L.; Del Río, M.; Deligny, O.; Dembinski, H.; Dhital, N.; di Giulio, C.; Díaz Castro, M. L.; Diep, P. N.; Diogo, F.; Dobrigkeit, C.; Docters, W.; D'Olivo, J. C.; Dong, P. N.; Dorofeev, A.; Dos Anjos, J. C.; Dova, M. T.; D'Urso, D.; Dutan, I.; Ebr, J.; Engel, R.; Erdmann, M.; Escobar, C. O.; Espadanal, J.; Etchegoyen, A.; Facal San Luis, P.; Fajardo Tapia, I.; Falcke, H.; Farrar, G.; Fauth, A. C.; Fazzini, N.; Ferguson, A. P.; Fick, B.; Filevich, A.; Filipcic, A.; Fliescher, S.; Fracchiolla, C. E.; Fraenkel, E. D.; Fratu, O.; Fröhlich, U.; Fuchs, B.; Gaior, R.; Gamarra, R. F.; Gambetta, S.; García, B.; Garcia Roca, S. T.; Garcia-Gamez, D.; Garcia-Pinto, D.; Gascon, A.; Gemmeke, H.; Ghia, P. L.; Giaccari, U.; Giller, M.; Glass, H.; Gold, M. S.; Golup, G.; Gomez Albarracin, F.; Gómez Berisso, M.; Gómez Vitale, P. F.; Gonçalves, P.; Gonzalez, D.; Gonzalez, J. G.; Gookin, B.; Gorgi, A.; Gouffon, P.; Grashorn, E.; Grebe, S.; Griffith, N.; Grigat, M.; Grillo, A. F.; Guardincerri, Y.; Guarino, F.; Guedes, G. P.; Guzman, A.; Hansen, P.; Harari, D.; Harmsma, S.; Harrison, T. A.; Harton, J. L.; Haungs, A.; Hebbeker, T.; Heck, D.; Herve, A. E.; Hojvat, C.; Hollon, N.; Holmes, V. C.; Homola, P.; Hörandel, J. R.; Horneffer, A.; Horvath, P.; Hrabovský, M.; Huber, D.; Huege, T.; Insolia, A.; Ionita, F.; Italiano, A.; Jarne, C.; Jiraskova, S.; Josebachuili, M.; Kadija, K.; Kampert, K. H.; Karhan, P.; Kasper, P.; Kégl, B.; Keilhauer, B.; Keivani, A.; Kelley, J. L.; Kemp, E.; Kieckhafer, R. M.; Klages, H. O.; Kleifges, M.; Kleinfeller, J.; Knapp, J.; Koang, D.-H.; Kotera, K.; Krohm, N.; Krömer, O.; Kruppke-Hansen, D.; Kuehn, F.; Kuempel, D.; Kulbartz, J. K.; Kunka, N.; La Rosa, G.; Lachaud, C.; Lauer, R.; Lautridou, P.; Le Coz, S.; Leão, M. S. A. B.; Lebrun, D.; Lebrun, P.; Leigui de Oliveira, M. A.; Letessier-Selvon, A.; Lhenry-Yvon, I.; Link, K.; López, R.; Lopez Agüera, A.; Louedec, K.; Lozano Bahilo, J.; Lu, L.; Lucero, A.; Ludwig, M.; Lyberis, H.; Macolino, C.; Maldera, S.; Mandat, D.; Mantsch, P.; Mariazzi, A. G.; Marin, J.; Marin, V.; Maris, I. C.; Marquez Falcon, H. R.; Marsella, G.; Martello, D.; Martin, L.; Martinez, H.; Martínez Bravo, O.; Mathes, H. J.; Matthews, J.; Matthews, J. A. J.; Matthiae, G.; Maurel, D.; Maurizio, D.; Mazur, P. O.; Medina-Tanco, G.; Melissas, M.; Melo, D.; Menichetti, E.; Menshikov, A.; Mertsch, P.; Meurer, C.; Micanovic, S.; Micheletti, M. I.; Miramonti, L.; Molina-Bueno, L.; Mollerach, S.; Monasor, M.; Monnier Ragaigne, D.; Montanet, F.; Morales, B.; Morello, C.; Moreno, E.; Moreno, J. C.; Mostafá, M.; Moura, C. A.; Muller, M. A.; Müller, G.; Münchmeyer, M.; Mussa, R.; Navarra, G.; Navarro, J. L.; Navas, S.; Necesal, P.; Nellen, L.; Nelles, A.; Neuser, J.; Newton, D.; Nhung, P. T.; Niechciol, M.; Niemietz, L.; Nierstenhoefer, N.; Nitz, D.; Nosek, D.; Nožka, L.; Nyklicek, M.; Oehlschläger, J.; Olinto, A.; Ortiz, M.; Pacheco, N.; Pakk Selmi-Dei, D.; Palatka, M.; Pallotta, J.; Palmieri, N.; Parente, G.; Parizot, E.; Parra, A.; Pastor, S.; Paul, T.; Pech, M.; Pekala, J.; Pelayo, R.; Pepe, I. M.; Perrone, L.; Pesce, R.; Petermann, E.; Petrera, S.; Petrinca, P.; Petrolini, A.; Petrov, Y.; Pfendner, C.; Piegaia, R.; Pierog, T.; Pieroni, P.; Pimenta, M.; Pirronello, V.; Platino, M.; Ponce, V. H.; Pontz, M.; Porcelli, A.; Privitera, P.; Prouza, M.; Quel, E. J.; Querchfeld, S.; Rautenberg, J.; Ravel, O.; Ravignani, D.; Revenu, B.; Ridky, J.; Riggi, S.; Risse, M.; Ristori, P.; Rivera, H.; Rizi, V.; Roberts, J.; Rodrigues de Carvalho, W.; Rodriguez, G.; Rodriguez Martino, J.; Rodriguez Rojo, J.; Rodriguez-Cabo, I.; Rodríguez-Frías, M. D.; Ros, G.; Rosado, J.; Rossler, T.; Roth, M.; Rouillé-D'Orfeuil, B.; Roulet, E.; Rovero, A. C.; Rühle, C.; Saftoiu, A.; Salamida, F.; Salazar, H.; Salesa Greus, F.; Salina, G.; Sánchez, F.; Santo, C. E.; Santos, E.; Santos, E. M.; Sarazin, F.; Sarkar, B.; Sarkar, S.; Sato, R.; Scharf, N.; Scherini, V.; Schieler, H.; Schiffer, P.; Schmidt, A.; Scholten, O.; Schoorlemmer, H.; Schovancova, J.; Schovánek, P.; Schröder, F.; Schulte, S.; Schuster, D.; Sciutto, S. J.; Scuderi, M.; Segreto, A.; Settimo, M.; Shadkam, A.; Shellard, R. C.; Sidelnik, I.; Sigl, G.; Silva Lopez, H. H.; Sima, O.; Smialkowski, A.; Šmída, R.; Snow, G. R.; Sommers, P.; Sorokin, J.; Spinka, H.; Squartini, R.; Srivastava, Y. N.; Stanic, S.; Stapleton, J.; Stasielak, J.; Stephan, M.; Stutz, A.; Suarez, F.; Suomijärvi, T.; Supanitsky, A. D.; Šuša, T.; Sutherland, M. S.; Swain, J.; Szadkowski, Z.; Szuba, M.; Tapia, A.; Tartare, M.; Tascau, O.; Tavera Ruiz, C. G.; Tcaciuc, R.; Tegolo, D.; Thao, N. T.; Thomas, D.; Tiffenberg, J.; Timmermans, C.; Tkaczyk, W.; Todero Peixoto, C. J.; Toma, G.; Tomé, B.; Tonachini, A.; Travnicek, P.; Tridapalli, D. B.; Tristram, G.; Trovato, E.; Tueros, M.; Ulrich, R.; Unger, M.; Urban, M.; Valdés Galicia, J. F.; Valiño, I.; Valore, L.; van den Berg, A. M.; Varela, E.; Vargas Cárdenas, B.; Vázquez, J. R.; Vázquez, R. A.; Veberic, D.; Verzi, V.; Vicha, J.; Videla, M.; Villaseñor, L.; Wahlberg, H.; Wahrlich, P.; Wainberg, O.; Walz, D.; Watson, A. A.; Weber, M.; Weidenhaupt, K.; Weindl, A.; Werner, F.; Westerhoff, S.; Whelan, B. J.; Widom, A.; Wieczorek, G.; Wiencke, L.; Wilczynska, B.; Wilczynski, H.; Will, M.; Williams, C.; Winchen, T.; Wommer, M.; Wundheiler, B.; Yamamoto, T.; Yapici, T.; Younk, P.; Yuan, G.; Yushkov, A.; Zamorano, B.; Zas, E.; Zavrtanik, D.; Zavrtanik, M.; Zaw, I.; Zepeda, A.; Zhu, Y.; Zimbres Silva, M.; Ziolkowski, M.

    2012-01-01

    The Surface Detector of the Pierre Auger Observatory is sensitive to neutrinos of all flavours above 0.1 EeV. These interact through charged and neutral currents in the atmosphere giving rise to extensive air showers. When interacting deeply in the atmosphere at nearly horizontal incidence, neutrinos can be distinguished from regular hadronic cosmic rays by the broad time structure of their shower signals in the water-Cherenkov detectors. In this paper we present for the first time an analysis based on down-going neutrinos. We describe the search procedure, the possible sources of background, the method to compute the exposure and the associated systematic uncertainties. No candidate neutrinos have been found in data collected from 1 January 2004 to 31 May 2010. Assuming an E^-2 differential energy spectrum the limit on the single flavour neutrino is (E^2 * dN/dE) < 1.74x10^-7 GeV cm^-2 s^-1 sr^-1 at 90% C.L. in the energy range 1x10^17 eV < E < 1x10^20 eV.

  13. Corrected Article: Measure of the impact of future dark energy experiments based on discriminating power among quintessence models [Phys. Rev. D 78, 043528 (2008)

    NASA Astrophysics Data System (ADS)

    Barnard, Michael; Abrahamse, Augusta; Albrecht, Andreas; Bozek, Brandon; Yashar, Mark

    2009-12-01

    We evaluate the ability of future data sets to discriminate among different quintessence dark energy models. This approach gives an alternative (and complementary) measure for assessing the impact of future experiments, as compared with the large body of literature that compares experiments in abstract parameter spaces (such as the well-known w0-wa parameters) and more recent work that evaluates the constraining power of experiments on individual parameter spaces of specific quintessence models. We use the Dark Energy Task Force (DETF) models of future data sets and compare the discriminative power of experiments designated by the DETF as stages 2, 3, and 4 (denoting increasing capabilities). Our work reveals a minimal increase in discriminating power when comparing stage 3 to stage 2, but a very striking increase in discriminating power when going to stage 4 (including the possibility of completely eliminating some quintessence models). We also see evidence that even modest improvements over DETF stage 4 (which many believe are realistic) could result in even more dramatic discriminating power among quintessence dark energy models. We develop and demonstrate the technique of using the independently measured modes of the equation of state (derived from principle component analysis) as a common parameter space in which to compare the different quintessence models, and we argue that this technique is a powerful one. We use the pseudo-Nambu-Goldstone boson, exponential, Albrecht-Skordis, and inverse tracker (or inverse power law) quintessence models for this work. One of our main results is that the goal of discriminating among these models sets a concrete measure on the capabilities of future dark energy experiments. Experiments have to be somewhat better than DETF stage 4 simulated experiments to fully meet this goal.

  14. Publisher's Note: State-projective scheme for generating pair coherent states in traveling-wave optical fields [Phys. Rev. A 84, 023810 (2011)

    SciTech Connect

    Gerry, Christopher C.; Mimih, Jihane; Birrittella, Richard

    2011-08-15

    This paper was published online on 9 August 2011 with a duplication of Fig. 4 in place of Fig. 1. Figure 1 has been correctly replaced as of 22 August 2011. Figure 1 is correct in the printed version of the journal.

  15. Publisher's Note: Lightness of a Higgs boson and spontaneous C P -violation in the Lee model: An alternative scenario [Phys. Rev. D 94, 055008 (2016)

    NASA Astrophysics Data System (ADS)

    Mao, Ying-nan; Zhu, Shou-hua

    2016-09-01

    Based on the weakly-coupled two-Higgs-doublet model with spontaneous CP-violation (named Lee model) and the mechanism to generate the correlation between smallness of CP-violation and lightness of scalar mass, as we proposed earlier, we predicted a light CP-mixing scalar $\\eta$ in which pseudoscalar component is dominant. It is a natural scenario in which $m_{\\eta}\\sim\\mathcal{O}(10\\textrm{GeV})\\ll v$. Masses of all other scalars ($h$, $H$, $H^\\pm$) should be around the electro-weak scale $v$. Among them, the 125 GeV Higgs ($h$) couplings are standard-model like, and the charged Higgs ($H^\\pm$) mass should be around the heaviest neutral scalar ($H$) mass. We discussed all experimental constraints and showed that this scenario is still allowed by data. The strictest constraints come from the experiments of the flavor-changing processes and the EDM of lepton and neutron. We also discussed the future tests for this scenario. It is possible to discover the extra scalars or exclude this scenario at future colliders, especially at the LHC and $e^+e^-$ colliders with $\\mathcal{O}(\\textrm{ab}^{-1})$ luminosity. We also pointed out that the $Z$-mediated Higgs pair production via $e^+e^-\\rightarrow h_ih_j$ ($h_i, h_j$ stand for two of the $\\eta, h, H$) would be the key observable to confirm or exclude CP-violation in Higgs sector. The sensitivity to test this scenario is worth further studying in greater detail.

  16. Publisher's Note: Level structure 18Ne and its importance in the 14O(α,p)17F reaction rate [Phys. Rev. C 86, 025801(2012)

    DOE PAGES

    Almaraz-Calderon, S.; Tan, W. P.; Aprahamian, A.; Bucher, B.; Roberts, A.; Wiescher, M.; Brune, C. R.; Massey, T. N.; Ozkan, N.; Guray, R. T.; et al

    2012-08-10

    The level structure of 18Ne above the α-decay threshold has been studied using the 16O(3He,n) reaction. A coincidence measurement of neutrons and charged particles decaying from populated states in 18Ne has been made. Decay branching ratios were measured for six resonances and used to calculate the 14O(α,p)17F reaction rate which is a measure of one of two breakout paths from the Hot CNO cycle. As a result, the new experimental information combined with previous experimental and theoretical information, provides a more accurate calculation of the reaction rate.

  17. A nucleolar localizing Rev binding element inhibits HIV replication.

    PubMed

    Michienzi, Alessandro; De Angelis, Fernanda G; Bozzoni, Irene; Rossi, John J

    2006-01-01

    The Rev protein of the human immunodeficiency virus (HIV) facilitates the nuclear export of intron containing viral mRNAs allowing formation of infectious virions. Rev traffics through the nucleolus and shuttles between the nucleus and cytoplasm. Rev multimerization and interaction with the export protein CRM1 takes place in the nucleolus. To test the importance of Rev nucleolar trafficking in the HIV-1 replication cycle, we created a nucleolar localizing Rev Response Element (RRE) decoy and tested this for its anti-HIV activity. The RRE decoy provided marked inhibition of HIV-1 replication in both the CEM T-cell line and in primary CD34+ derived monocytes. These results demonstrate that titration of Rev in the nucleolus impairs HIV-1 replication and supports a functional role for Rev trafficking in this sub-cellular compartment.

  18. Human Rev1 polymerase disrupts G-quadruplex DNA

    PubMed Central

    Eddy, Sarah; Ketkar, Amit; Zafar, Maroof K.; Maddukuri, Leena; Choi, Jeong-Yun; Eoff, Robert L.

    2014-01-01

    The Y-family DNA polymerase Rev1 is required for successful replication of G-quadruplex DNA (G4 DNA) in higher eukaryotes. Here we show that human Rev1 (hRev1) disrupts G4 DNA structures and prevents refolding in vitro. Nucleotidyl transfer by hRev1 is not necessary for mechanical unfolding to occur. hRev1 binds G4 DNA substrates with Kd,DNA values that are 4–15-fold lower than those of non-G4 DNA substrates. The pre-steady-state rate constant of deoxycytidine monophosphate (dCMP) insertion opposite the first tetrad-guanine by hRev1 is ∼56% as fast as that observed for non-G4 DNA substrates. Thus, hRev1 can promote fork progression by either dislodging tetrad guanines to unfold the G4 DNA, which could assist in extension by other DNA polymerases, or hRev1 can prevent refolding of G4 DNA structures. The hRev1 mechanism of action against G-quadruplexes helps explain why replication progress is impeded at G4 DNA sites in Rev1-deficient cells and illustrates another unique feature of this enzyme with important implications for genome maintenance. PMID:24366879

  19. Suppression of atherosclerosis by synthetic REV-ERB agonist

    SciTech Connect

    Sitaula, Sadichha; Billon, Cyrielle; Kamenecka, Theodore M.; Solt, Laura A.; Burris, Thomas P.

    2015-05-08

    The nuclear receptors for heme, REV-ERBα and REV-ERBβ, play important roles in the regulation of metabolism and inflammation. Recently it was demonstrated that reduced REV-ERBα expression in hematopoetic cells in LDL receptor null mice led to increased atherosclerosis. We sought to determine if synthetic REV-ERB agonists that we have developed might have the ability to suppress atherosclerosis in this model. A previously characterized synthetic REV-ERB agonist, SR9009, was used to determine if activation of REV-ERB activity would affect atherosclerosis in LDL receptor deficient mice. Atherosclerotic plaque size was significantly reduced (p < 0.05) in mice administered SR9009 (100 mg/kg) for seven weeks compared to control mice (n = 10 per group). SR9009 treatment of bone marrow-derived mouse macrophages (BMDM) reduced the polarization of BMDMs to proinflammatory M1 macrophage while increasing the polarization of BMDMs to anti-inflammatory M2 macrophages. Our results suggest that pharmacological targeting of REV-ERBs may be a viable therapeutic option for treatment of atherosclerosis. - Highlights: • Synthetic REV-ERB agonist treatment reduced atherosclerosis in a mouse model. • Pharmacological activation of REV-ERB decreased M1 macrophage polarization. • Pharmacological activation of REV-ERB increased M2 macrophage polarization.

  20. Comment on "A study of vertical and in-plane electron mobility due to interface roughness scattering at low temperature in InAs-GaSb superlattices" [J. Appl. Phys. 114, 053712 (2013)

    NASA Astrophysics Data System (ADS)

    Szmulowicz, F.

    2014-04-01

    The purpose of this comment is to point out that the paper by Safa, Asgari, and Faraone [J. Appl. Phys. 114, 053712 (2013)] (SAF) on electronic transport in superlattices contains a number of errors in physics and execution. By dealing with a finite number of periods and forcing the wave function to be zero at the upper and lower boundaries of the superlattice stack, SAF have turned the system into a quantum well for which the momentum along the growth axis is not a good quantum number, so that the bands in the growth direction are flat and the corresponding carrier velocities and vertical mobilities are zero. A number of other errors allow the authors to get nonzero results and to reach conclusions that qualitatively mirror those of Szmulowicz, Haugan, Elhamri, and Brown [Phys. Rev. B 84, 155307 (2011)].

  1. Comment on “A study of vertical and in-plane electron mobility due to interface roughness scattering at low temperature in InAs-GaSb superlattices” [J. Appl. Phys. 114, 053712 (2013)

    SciTech Connect

    Szmulowicz, F.

    2014-04-14

    The purpose of this comment is to point out that the paper by Safa, Asgari, and Faraone [J. Appl. Phys. 114, 053712 (2013)] (SAF) on electronic transport in superlattices contains a number of errors in physics and execution. By dealing with a finite number of periods and forcing the wave function to be zero at the upper and lower boundaries of the superlattice stack, SAF have turned the system into a quantum well for which the momentum along the growth axis is not a good quantum number, so that the bands in the growth direction are flat and the corresponding carrier velocities and vertical mobilities are zero. A number of other errors allow the authors to get nonzero results and to reach conclusions that qualitatively mirror those of Szmulowicz, Haugan, Elhamri, and Brown [Phys. Rev. B 84, 155307 (2011)].

  2. Comment on ``Laser controlled magnetism in hydrogenated fullerene films'' [J. Appl. Phys. 109, 083941 (2011)

    NASA Astrophysics Data System (ADS)

    Talyzin, A.

    2013-01-01

    Hydrogenation of C60 films with formation of single hydrogen adduct reported by Makarova et al. [J. Appl. Phys. 109, 083941 (2011); Phys. Status Solidi B 246, 2778 (2009)] was supported only by several features found in Raman spectra of treated samples. However, no spectra were shown for untreated samples. Data shown in this comment prove that all Raman peaks assigned by Makarova et al. [J. Appl. Phys. 109, 083941 (2011); Phys. Status Solidi B 246, 2778 (2009)] to effects of hydrogenation can be found in spectra of pristine untreated commercial C60 powder. These peaks represent some second order vibrations of C60 as well as some possible solvent impurities. Therefore, all magnetic effects reported in this study should be assigned to unknown effects but not necessarily to hydrogenation.

  3. Comment on ``Curvy-steps approach to constraint-free extended-Lagrangian ab initio molecular dynamics, using atom-centered basis functions: Convergence toward Born-Oppenheimer trajectories'' [J. Chem. Phys. 121, 11542 (2004)

    NASA Astrophysics Data System (ADS)

    Iyengar, Srinivasan S.; Schlegel, H. Bernhard; Scuseria, Gustavo E.; Millam, John M.; Frisch, Michael J.

    2005-07-01

    The curvy-extended-Lagrangian molecular-dynamics (ELMD) approach [J. M. Herbert and M. Head-Gordon, J. Chem. Phys. 121, 11542 (2004)] is similar to atom-centered density-matrix propagation (ADMP) [H. B. Schlegel, J. M. Millam, S. S. Iyengar, G. A. Voth, A. D. Daniels, G. E. Scuseria, and M. J. Frisch, J. Chem. Phys. 114, 9758 (2001); S. S. Iyengar, H.B. Schlegel, J.M. Millam, G.A. Voth, G.E. Scuseria, and M.J. Frisch, ibid.115, 10291 (2001); H.B. Schlegel, S.S. Iyengar, X. Li, J.M. Millam, G.A. Voth, G.E. Scuseria, and M.J. Frisch, ibid. 117, 8694 (2002); S.S. Iyengar, H.B. Schlegel, G.A. Voth, J.M. Millam, G.E. Scuseria, and M.J. Frisch, Israel J. Chem. 42, 191 (2002)] and based on Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] extended-Lagrangian [H.C. Andersen, J. Chem. Phys. 72, 2384 (1980)] molecular dynamics. Similarities between curvy-ELMD and ADMP arise from using unconverged electronic single-particle density matrices within Gaussian basis functions as dynamical variables. Curvy-ELMD differs from ADMP in not requiring idempotency to be explicitly enforced. In this Comment, we address several misleading remarks in Refs. 1 [J.M. Herbert and M. Head-Gordon, J. Chem. Phys. 121, 11542 (2004)] and 8 [J.M. Herbert and M. Head-Gordon, J. Chem. Phys. (submitted)].

  4. RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev–Rev response element complex

    PubMed Central

    Jayaraman, Bhargavi; Crosby, David C; Homer, Christina; Ribeiro, Isabel; Mavor, David; Frankel, Alan D

    2014-01-01

    The HIV-1 protein Rev controls a critical step in viral replication by mediating the nuclear export of unspliced and singly-spliced viral mRNAs. Multiple Rev subunits assemble on the Rev Response Element (RRE), a structured region present in these RNAs, and direct their export through the Crm1 pathway. Rev-RRE assembly occurs via several Rev oligomerization and RNA-binding steps, but how these steps are coordinated to form an export–competent complex is unclear. Here, we report the first crystal structure of a Rev dimer-RRE complex, revealing a dramatic rearrangement of the Rev-dimer upon RRE binding through re-packing of its hydrophobic protein–protein interface. Rev-RNA recognition relies on sequence-specific contacts at the well-characterized IIB site and local RNA architecture at the second site. The structure supports a model in which the RRE utilizes the inherent plasticity of Rev subunit interfaces to guide the formation of a functional complex. DOI: http://dx.doi.org/10.7554/eLife.04120.001 PMID:25486594

  5. Analysis of the influence of subcellular localization of the HIV Rev protein on Rev-dependent gene expression by multi-fluorescence live-cell imaging

    SciTech Connect

    Wolff, Horst; Hadian, Kamyar; Ziegler, Manja; Weierich, Claudia; Kramer-Hammerle, Susanne; Kleinschmidt, Andrea; Erfle, Volker; Brack-Werner, Ruth . E-mail: brack@gsf.de

    2006-02-15

    The human immunodeficiency virus Rev protein is a post-transcriptional activator of HIV gene expression. Rev is a nucleocytoplasmic shuttle protein that displays characteristic nuclear/nucleolar subcellular localization in various cell lines. Cytoplasmic localization of Rev occurs under various conditions disrupting Rev function. The goal of this study was to investigate the relationship between localization of Rev and its functional activity in living cells. A triple-fluorescent imaging assay, called AQ-FIND, was established for automatic quantitative evaluation of nucleocytoplasmic distribution of fluorescently tagged proteins. This assay was used to screen 500 rev genes generated by error-prone PCR for Rev mutants with different localization phenotypes. Activities of the Rev mutants were determined with a second quantitative, dual-fluorescent reporter assay. In HeLa cells, the majority of nuclear Rev mutants had activities similar to wild-type Rev. The activities of Rev mutants with abnormal cytoplasmic localization ranged from moderately impaired to nonfunctional. There was no linear correlation between subcellular distribution and levels of Rev activity. In astrocytes, nuclear Rev mutants showed similar impaired activities as the cytoplasmic wild-type Rev. Our data suggest that steady-state subcellular localization is not a primary regulator of Rev activity but may change as a secondary consequence of altered Rev function. The methodologies described here have potential for studying the significance of subcellular localization for functions of other regulatory factors.

  6. Comment on ``Morphology-dependent stimulated Raman scattering imaging'' [J. Chem. Phys. 105, 7276 (1996)

    NASA Astrophysics Data System (ADS)

    Campillo, A. J.; Eversole, J. D.; Lin, H.-B.

    1998-11-01

    We comment on a recent paper by J.-X. Zhang, P. A. Moortgat, and P. M. Aker [J. Chem. Phys. 105, 7276 (1996)]. We disagree with their interpretation of droplet stimulated Raman scattering spectral data as well as claims that surface electrical charge greatly affects hydrogen bonding at micrometer depths into water droplets.

  7. Biallelic inactivation of REV7 is associated with Fanconi anemia.

    PubMed

    Bluteau, Dominique; Masliah-Planchon, Julien; Clairmont, Connor; Rousseau, Alix; Ceccaldi, Raphael; Dubois d'Enghien, Catherine; Bluteau, Olivier; Cuccuini, Wendy; Gachet, Stéphanie; Peffault de Latour, Régis; Leblanc, Thierry; Socié, Gérard; Baruchel, André; Stoppa-Lyonnet, Dominique; D'Andrea, Alan D; Soulier, Jean

    2016-09-01

    Fanconi anemia (FA) is a recessive genetic disease characterized by congenital abnormalities, chromosome instability, progressive bone marrow failure (BMF), and a strong predisposition to cancer. Twenty FA genes have been identified, and the FANC proteins they encode cooperate in a common pathway that regulates DNA crosslink repair and replication fork stability. We identified a child with severe BMF who harbored biallelic inactivating mutations of the translesion DNA synthesis (TLS) gene REV7 (also known as MAD2L2), which encodes the mutant REV7 protein REV7-V85E. Patient-derived cells demonstrated an extended FA phenotype, which included increased chromosome breaks and G2/M accumulation upon exposure to DNA crosslinking agents, γH2AX and 53BP1 foci accumulation, and enhanced p53/p21 activation relative to cells derived from healthy patients. Expression of WT REV7 restored normal cellular and functional phenotypes in the patient's cells, and CRISPR/Cas9 inactivation of REV7 in a non-FA human cell line produced an FA phenotype. Finally, silencing Rev7 in primary hematopoietic cells impaired progenitor function, suggesting that the DNA repair defect underlies the development of BMF in FA. Taken together, our genetic and functional analyses identified REV7 as a previously undescribed FA gene, which we term FANCV. PMID:27500492

  8. EPA`s CEM Certification Review (C{_}REV) System

    SciTech Connect

    Lieberman, E.R.; Warren-Hicks, W.

    1995-12-31

    Electric utility units covered under the Acid Rain Regulations are required by the Clean Air Act Amendments of 1990 to install and operate continuous emission monitoring systems (CEMS). To ensure efficient, objective, and consistent evaluation of the results of certification tests performed on the Continuous Emission Monitoring Systems (CEMS) required under the Acid Rain Program, EPA has developed the Certification Review System (C{_}REV), a sophisticated calculation tool for screening and analyzing the test data. This paper describes the components of C{_}REV and how they fit into the process of reaching a certification determination. The paper discusses the types of data entry errors that C{_}REV identifies and discusses ways that sources can prevent fatal errors that would otherwise require time-consuming correction and re-submission. The four test analysis operations performed by C{_}REV are presented and the resulting outputs are described.

  9. Improving Science Teacher Preparation through the APS PhysTEC and NSF Noyce Programs

    NASA Astrophysics Data System (ADS)

    Williams, Tasha; Tyler, Micheal; van Duzor, Andrea; Sabella, Mel

    2013-03-01

    Central to the recruitment of students into science teaching at a school like CSU, is a focus on the professional nature of teaching. The purpose of this focus is twofold: it serves to change student perceptions about teaching and it prepares students to become teachers who value continued professional development and value the science education research literature. The Noyce and PhysTEC programs at CSU place the professional nature of teaching front and center by involving students in education research projects, paid internships, attendance at conferences, and participation in a new Teacher Immersion Institute and a Science Education Journal Reading Class. This poster will focus on specific components of our teacher preparation program that were developed through these two programs. In addition we will describe how these new components provide students with diverse experiences in the teaching of science to students in the urban school district. Supported by the NSF Noyce Program (0833251) and the APS PhysTEC Program.

  10. Altered Sleep Homeostasis in Rev-erbα Knockout Mice

    PubMed Central

    Mang, Géraldine M.; La Spada, Francesco; Emmenegger, Yann; Chappuis, Sylvie; Ripperger, Jürgen A.; Albrecht, Urs; Franken, Paul

    2016-01-01

    Study Objectives: The nuclear receptor REV-ERBα is a potent, constitutive transcriptional repressor critical for the regulation of key circadian and metabolic genes. Recently, REV-ERBα's involvement in learning, neurogenesis, mood, and dopamine turnover was demonstrated suggesting a specific role in central nervous system functioning. We have previously shown that the brain expression of several core clock genes, including Rev-erbα, is modulated by sleep loss. We here test the consequences of a loss of REV-ERBα on the homeostatic regulation of sleep. Methods: EEG/EMG signals were recorded in Rev-erbα knockout (KO) mice and their wild type (WT) littermates during baseline, sleep deprivation, and recovery. Cortical gene expression measurements after sleep deprivation were contrasted to baseline. Results: Although baseline sleep/wake duration was remarkably similar, KO mice showed an advance of the sleep/wake distribution relative to the light-dark cycle. After sleep onset in baseline and after sleep deprivation, both EEG delta power (1–4 Hz) and sleep consolidation were reduced in KO mice indicating a slower increase of homeostatic sleep need during wakefulness. This slower increase might relate to the smaller increase in theta and gamma power observed in the waking EEG prior to sleep onset under both conditions. Indeed, the increased theta activity during wakefulness predicted delta power in subsequent NREM sleep. Lack of Rev-erbα increased Bmal1, Npas2, Clock, and Fabp7 expression, confirming the direct regulation of these genes by REV-ERBα also in the brain. Conclusions: Our results add further proof to the notion that clock genes are involved in sleep homeostasis. Because accumulating evidence directly links REV-ERBα to dopamine signaling the altered homeostatic regulation of sleep reported here are discussed in that context. Citation: Mang GM, La Spada F, Emmenegger Y, Chappuis S, Ripperger JA, Albrecht U, Franken P. Altered sleep homeostasis in Rev

  11. Using the PhysX engine for Physics-based Virtual Surgery with Force Feedback

    PubMed Central

    Maciel, Anderson; Halic, Tansel; Lu, Zhonghua; Nedel, Luciana P.; De, Suvranu

    2010-01-01

    Background The development of modern surgical simulators is highly challenging as they must support complex simulation environments. The demand for higher realism in such simulators has driven researchers to adopt physics-based models which are computationally very demanding. This poses a major problem since real time interactions must permit graphical updates of 30 Hz and a much higher rate of 1 kHz for force feedback (haptics). Recently several physics engines have been developed which offer multi-physics simulation capabilities including rigid and deformable bodies, cloth and fluids. While such physics engines provide unique opportunities for the development of surgical simulators, their higher latencies, compared to what is necessary for real time graphics and haptics, offer significant barriers to their use in interactive simulation environments. Methods In this work, we propose solutions to this problem and demonstrate how a multimodal surgical simulation environment may be developed based on NVIDIA’s PhysX physics library. Hence, models that are undergoing relatively low frequency updates in PhysX can exist in an environment that demands much higher frequency updates for haptics. We use a collision handling layer to interface between the physical response provided by PhysX and the haptic rendering device to provide both real time tissue response and force feedback. Results Our simulator integrates a bimanual haptic interface for force-feedback and per-pixel shaders for graphics realism in real time. To demonstrate the effectiveness of our approach, we present the simulation of the Laparoscopic Adjustable Gastric Banding (LAGB) procedure as a case study. Conclusions To develop complex and realistic surgical trainers with realistic organ geometries and tissue properties demands stable physics-based deformation methods which are not always compatible with the interaction level required for such trainers. We have shown that combining different modeling

  12. Comment on 'General nonlocality in quantum fields'[J. Math. Phys. 49, 033513 (2008)

    SciTech Connect

    Wang Haijun

    2010-05-15

    In a recent paper [H.-J. Wang, J. Math. Phys. 49, 033513 (2008)] a complex-geometry model was proposed to interpret the interaction of electromagnetism and the interaction between quarks while the nonlocal effects are involved. In that theoretical frame, from the metric matrix one can obtain a determinant-form condition to describe qualitatively the typical characteristics for the aforementioned interactions. In this comment we attempt to extend this kind of qualitative description to weak interaction by finding out an appropriate metric tensor for it.

  13. Comment on 'Undamped electrostatic plasma waves'[Phys. Plasmas 19, 092103 (2012)

    SciTech Connect

    Schamel, Hans

    2013-03-15

    The relevance of linear 'corner modes' for the description of coherent electrostatic structures, as proposed by Valentini et al.[Phys. Plasmas 19, 092103 (2012)], is questioned. Coherency in their on-dispersion simulation is instead found to be caused by particle trapping in agreement with Schamel's nonlinear wave model [Phys. Plasmas 19, 020501 (2012)]. The revealed small amplitude structures are hence of cnoidal electron hole type exhibiting vortices in phase space. They are ruled by trapping nonlinearity rather than by linearity or quasi-linear effects, as commonly assumed. Arguments are presented, which give preference to these cnoidal hole modes over Bernstein-Greene-Kruskal modes. To fully account for a realistic theoretical scenario, however, at least four ingredients are mandatory. Several corrections of the conventional body of thought about the proper kinetic wave description are proposed. They may prove useful for the general acceptance of this 'new' nonlinear wave concept concerning structure formation, updating several prevailing concepts such as the general validity of a linear wave Ansatz for small amplitudes, as assumed in their paper. It is conjectured that this nonlinear trapping model can be generalized to the vortex structures of similar type found in the more general setting of driven turbulence of magnetized plasmas. They appear as eddies in both, the phase and the position spaces, embedded intermittently on the Debye length scale.

  14. Comment on "Stationary self-focusing of Gaussian laser beam in relativistic thermal quantum plasma" [Phys. Plasmas 20, 072703 (2013)

    NASA Astrophysics Data System (ADS)

    Habibi, M.; Ghamari, F.

    2014-06-01

    Patil and Takale in their recent article [Phys. Plasmas 20, 072703 (2013)], by evaluating the quantum dielectric response in thermal quantum plasma, have modeled the relativistic self-focusing of Gaussian laser beam in a plasma. We have found that there are some important shortcomings and fundamental mistakes in Patil and Takale [Phys. Plasmas 20, 072703 (2013)] that we give a brief description about them and refer readers to important misconception about the use of the Fermi temperature in quantum plasmas, appearing in Patil and Takale [Phys. Plasmas 20, 072703 (2013)].

  15. Comment on "Effects of damping solitary wave in a viscosity bounded plasma" [Phys. Plasmas 21, 022118 (2014)

    NASA Astrophysics Data System (ADS)

    Ghosh, Uday Narayan; Chatterjee, Prasanta; Roychoudhury, Rajkumar

    2015-07-01

    Recently Gun Li et al. discussed "Effects of damping solitary wave in a viscosity bounded plasma" [Phys. Plasmas 21, 022118 (2014)]. The paper contains some serious errors which have been pointed out in this Comment.

  16. Comment on “Effects of damping solitary wave in a viscosity bounded plasma” [Phys. Plasmas 21, 022118 (2014)

    SciTech Connect

    Ghosh, Uday Narayan Chatterjee, Prasanta; Roychoudhury, Rajkumar

    2015-07-15

    Recently Gun Li et al. discussed “Effects of damping solitary wave in a viscosity bounded plasma” [Phys. Plasmas 21, 022118 (2014)]. The paper contains some serious errors which have been pointed out in this Comment.

  17. Response to ''Comment on 'Cosmic ray diffusion: Detailed investigation of a recent model''' [Phys. Plasmas 18, 114701 (2011)

    SciTech Connect

    Lerche, Ian; Tautz, R. C.

    2011-11-15

    Recently [Phys. Plasmas 18, 082305 (2011)], the otherwise successful unified non-linear transport (UNLT) theory was critically examined. In a comment [Phys. Plasmas 18, 114701 (2011)], it was argued that the deviation from the original UNLT theory is marginal. Here, it is emphasized that the main point was to investigate the basic mathematical properties of the UNLT formulation by showing model approaches rather than deriving complete solutions.

  18. Rev-RRE Functional Activity Differs Substantially Among Primary HIV-1 Isolates.

    PubMed

    Jackson, Patrick E; Tebit, Denis M; Rekosh, David; Hammarskjold, Marie-Louise

    2016-09-01

    The HIV-1 replication cycle requires the nucleocytoplasmic export of intron-containing viral RNAs, a process that is ordinarily restricted. HIV overcomes this by means of the viral Rev protein, which binds to an RNA secondary structure called the Rev response element (RRE) present in all unspliced or incompletely spliced viral RNA transcripts. The resulting mRNP complex is exported through interaction with cellular factors. The Rev-RRE binding interaction is increasingly understood to display remarkable structural plasticity, but little is known about how Rev-RRE sequence differences affect functional activity. To study this issue, we utilized a lentiviral vector assay in which vector titer is dependent on the activity of selected Rev-RRE pairs. We found that Rev-RRE functional activity varies significantly (up to 24-fold) between naturally occurring viral isolates. The activity differences of the Rev-RRE cognate pairs track closely with Rev, but not with RRE activity. This variation in Rev activity is not correlated with differences in Rev steady state protein levels. These data suggest that Rev sequence differences drive substantial variation in Rev-RRE functional activity between patients. Such variation may play a role in viral adaptation to different immune milieus within and between patients and may be significant in the establishment of latency. The identification of differences in Rev-RRE functional activity in naturally occurring isolates may also permit more efficient production of lentiviral vectors. PMID:27147495

  19. User Instructions for the Systems Assessment Capability, Rev. 1, Computer Codes Volume 3: Utility Codes

    SciTech Connect

    Eslinger, Paul W.; Aaberg, Rosanne L.; Lopresti, Charles A.; Miley, Terri B.; Nichols, William E.; Strenge, Dennis L.

    2004-09-14

    This document contains detailed user instructions for a suite of utility codes developed for Rev. 1 of the Systems Assessment Capability. The suite of computer codes for Rev. 1 of Systems Assessment Capability performs many functions.

  20. PREFACE: International Symposium "Nanoscience and Quantum Physics 2011" (nanoPHYS'11)

    NASA Astrophysics Data System (ADS)

    Saito, Susumu; Tanaka, Hidekazu; Nakamura, Takashi; Nakamura, Masaaki

    2011-07-01

    Quantum physics has developed modern views of nature for more than a century. In addition to this traditional role, quantum physics has acquired new significance in the 21st century as the field responsible for driving and supporting nanoscience research, which will have even greater importance in the future because nanoscience will be the academic foundation for new technologies. The Department of Physics, Tokyo Institute of Technology, are now conducting a "Nanoscience and Quantum Physics" project (Physics G-COE project) supported by the Global Center of Excellence Program of the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) in order to promote research and education in these important academic fields. The International Symposium on Nanoscience and Quantum Physics, held in Tokyo, Japan, 26-28 January 2011 (nanoPHYS'11) was organized by the Physics G-COE project of the Tokyo Institute of Technology to provide an international forum for the open exchange of topical information and for stimulating discussion on novel concepts and future prospects of nanoscience and quantum physics. There were a total of 118 papers including 34 invited papers. This nanoPHYS'11 is the fourth symposium of this kind organized by the Tokyo Institute of Technology. Topics focused on in the symposium included: Category 1: Novel nanostructure (Nanowires, Nanotubes, Spin-related structure, etc) Category 2: Novel transport and electronic properties (Graphene, Topological insulators, Coherent control, etc) Category 3: Electronic and optical properties of nanostructure Category 4: Fundamental physics and new concept in quantum physics Category 5: Quantum Physics - Quantum information Category 6: Quantum Physics - Nuclear and Hadron Physics Category 7: Quantum Physics - Astrophysics, etc All the papers submitted to this issue have been reviewed under a stringent refereeing process, according to the normal rules of this Journal. The editors are grateful to all the

  1. Analysis of the virulence-associated RevSR two-component signal transduction system of Clostridium perfringens.

    PubMed

    Cheung, Jackie K; Wisniewski, Jessica A; Adams, Vicki M; Quinsey, Noelene S; Rood, Julian I

    2016-09-01

    Clostridium perfringens is a Gram-positive, anaerobic, spore-forming bacterium that causes human gas gangrene (clostridial myonecrosis) and food poisoning. Early studies showed that virulence was regulated by the VirSR two-component signal transduction system. However, our identification of the RevR orphan response regulator indicated that more than one system was involved in controlling virulence. To further characterize this virulence-associated regulator, gel mobility shift experiments, coupled with DNase I footprinting, were used to identify the RevR DNA binding sequence. Bioinformatics analysis suggested that an orphan sensor histidine kinase, CPE1757 (renamed RevS), was the cognate sensor of RevR. Interaction between RevS and RevR was demonstrated by use of a bacterial two-hybrid system and validated by protein-protein interaction studies using biolayer interferometry. To assess the involvement of RevS in virulence regulation, the revS gene was inactivated by Targetron insertion. When isogenic wild-type, revS and complemented revS strains were tested in a mouse myonecrosis model, the revS mutant was found to be attenuated in virulence, which was similar to the attenuation observed previously with the revR mutant. However, transcriptional analysis of selected RevR-regulated genes in the revS mutant revealed a different pattern of expression to a revR mutant, suggesting that the RevSR system is more complex than originally thought. Taken together, the results have led to the identification and characterization of the two essential parts of a new regulatory network that is involved in the regulation of virulence in C. perfringens. PMID:27267179

  2. Analysis of the virulence-associated RevSR two-component signal transduction system of Clostridium perfringens.

    PubMed

    Cheung, Jackie K; Wisniewski, Jessica A; Adams, Vicki M; Quinsey, Noelene S; Rood, Julian I

    2016-09-01

    Clostridium perfringens is a Gram-positive, anaerobic, spore-forming bacterium that causes human gas gangrene (clostridial myonecrosis) and food poisoning. Early studies showed that virulence was regulated by the VirSR two-component signal transduction system. However, our identification of the RevR orphan response regulator indicated that more than one system was involved in controlling virulence. To further characterize this virulence-associated regulator, gel mobility shift experiments, coupled with DNase I footprinting, were used to identify the RevR DNA binding sequence. Bioinformatics analysis suggested that an orphan sensor histidine kinase, CPE1757 (renamed RevS), was the cognate sensor of RevR. Interaction between RevS and RevR was demonstrated by use of a bacterial two-hybrid system and validated by protein-protein interaction studies using biolayer interferometry. To assess the involvement of RevS in virulence regulation, the revS gene was inactivated by Targetron insertion. When isogenic wild-type, revS and complemented revS strains were tested in a mouse myonecrosis model, the revS mutant was found to be attenuated in virulence, which was similar to the attenuation observed previously with the revR mutant. However, transcriptional analysis of selected RevR-regulated genes in the revS mutant revealed a different pattern of expression to a revR mutant, suggesting that the RevSR system is more complex than originally thought. Taken together, the results have led to the identification and characterization of the two essential parts of a new regulatory network that is involved in the regulation of virulence in C. perfringens.

  3. Single-molecule studies reveal that DEAD box protein DDX1 promotes oligomerization of HIV-1 Rev on the Rev response element.

    PubMed

    Robertson-Anderson, Rae M; Wang, Jun; Edgcomb, Stephen P; Carmel, Andrew B; Williamson, James R; Millar, David P

    2011-07-29

    Oligomeric assembly of Rev on the Rev response element (RRE) is essential for the nuclear export of unspliced and singly spliced human immunodeficiency virus type 1 viral mRNA transcripts. Several host factors, including the human DEAD box protein DDX1, are also known to be required for efficient Rev function. In this study, spontaneous assembly and dissociation of individual Rev-RRE complexes in the presence or absence of DDX1 were observed in real time via single-molecule total internal reflection fluorescence microscopy. Binding of up to eight fluorescently labeled Rev monomers to a single RRE molecule was visualized, and the event frequencies and corresponding binding and dissociation rates for the different Rev-RRE stoichiometries were determined. The presence of DDX1 eliminated a second kinetic phase present during the initial Rev binding step, attributed to nonproductive nucleation events, resulting in increased occurrence of higher-order Rev-RRE stoichiometries. This effect was further enhanced upon the addition of a non-hydrolyzable ATP analog (adenylyl-imidophosphate), whereas ADP had no effect beyond that of DDX1 alone. Notably, the first three Rev monomer binding events were accelerated in the presence of DDX1 and adenylyl-imidophosphate, while the dissociation rates remained unchanged. Measurements performed across a range of DDX1 concentrations suggest that DDX1 targets Rev rather than the RRE to promote oligomeric assembly. Moreover, DDX1 is able to restore the oligomerization activity of a Rev mutant that is otherwise unable to assemble on the RRE beyond a monomeric complex. Taken together, these results suggest that DDX1 acts as a cellular cofactor by promoting oligomerization of Rev on the RRE. PMID:21763499

  4. The PhysTEC project: A perspective on what it takes to recruit and educate more physics teachers

    NASA Astrophysics Data System (ADS)

    Plisch, Monica

    2012-03-01

    The PhysTEC project has more than doubled the number of physics teachers educated at supported sites. These institutions were selected for their potential to implement change primarily in physics departments and build model teacher education programs. Key components of PhysTEC programs include active recruiting, early teaching experiences, pedagogical content knowledge, Learning Assistants, and induction and mentoring. Important structural elements include a program champion, a Teacher in Residence, assessment, collaboration, and institutional commitment. The PhysTEC project has supported about 20 institutions to date. In order to more fully address the national need for qualified physics teachers, the effort would need to be scaled up substantially. There is evidence of growing interest among physics departments in taking on this issue, and a national coalition committed to improving the education of future physics teachers has expanded to include more than 250 member institutions. The project is experimenting with targeted sites, funded at a lower level, to implement focused programs. In addition, PhysTEC is partnering with aligned efforts to magnify its impact. PhysTEC is a project led by APS with AAPT, and supported by the NSF and the APS Campaign for the 21st Century.

  5. PyDecay/GraphPhys: A Unified Language and Storage System for Particle Decay Process Descriptions

    SciTech Connect

    Dunietz, Jesse N.; /MIT /SLAC

    2011-06-22

    To ease the tasks of Monte Carlo (MC) simulation and event reconstruction (i.e. inferring particle-decay events from experimental data) for long-term BaBar data preservation and analysis, the following software components have been designed: a language ('GraphPhys') for specifying decay processes, common to both simulation and data analysis, allowing arbitrary parameters on particles, decays, and entire processes; an automated visualization tool to show graphically what decays have been specified; and a searchable database storage mechanism for decay specifications. Unlike HepML, a proposed XML standard for HEP metadata, the specification language is designed not for data interchange between computer systems, but rather for direct manipulation by human beings as well as computers. The components are interoperable: the information parsed from files in the specification language can easily be rendered as an image by the visualization package, and conversion between decay representations was implemented. Several proof-of-concept command-line tools were built based on this framework. Applications include building easier and more efficient interfaces to existing analysis tools for current projects (e.g. BaBar/BESII), providing a framework for analyses in future experimental settings (e.g. LHC/SuperB), and outreach programs that involve giving students access to BaBar data and analysis tools to give them a hands-on feel for scientific analysis.

  6. Comment on 'Microwave attenuation of hydrogen plasma in carbon nanotubes' [J. Appl. Phys. 104, 124315 (2008)

    SciTech Connect

    Moradi, Afshin

    2010-03-15

    In a recent article, Babaei and Solari [J. Appl. Phys. 104, 124315 (2008)] studied the effects of the electron temperature, and the external static magnetic field on the attenuation (ATT) of the microwave in the hydrogen plasma embedded inside the carbon nanotubes (CNTs), which were grown by iron-catalyzed high-pressure disproportionation (HiPco). They showed that the position of ATT peak shifts significantly toward high frequency with increasing thermal frequency and in the presence of an external magnetic field in the Faraday configuration, for {upsilon}{sub c}<20 GHz, the ATT coefficient increases with increasing cyclotron frequency, and for {upsilon}{sub c}>20 GHz, the ATT level variations extremely increase, where {upsilon}{sub c} is the cyclotron frequency. Here we derive the correct form of the microwave absorption coefficient of the magnetized hydrogen plasma embedded inside the CNTs and show that the absorption band moves from low to high frequencies when the magnetic field strength increases. Also, we show that the ATT of the microwave in the system is not sensitive to the thermal frequency.

  7. Comment on ``The application of the thermodynamic perturbation theory to study the hydrophobic hydration'' [J. Chem. Phys. 139, 024101 (2013)

    NASA Astrophysics Data System (ADS)

    Graziano, Giuseppe

    2013-09-01

    It is shown that the behaviour of the hydration thermodynamic functions obtained in the 3D Mercedes-Benz model of water by Mohoric et al. [J. Chem. Phys. 139, 024101 (2013)] is not qualitatively correct with respect to experimental data for a solute whose diameter is 1.5-fold larger than that of a water molecule. It is also pointed out that the failure is due to the fact that the used 3D Mercedes-Benz model of water [A. Bizjak, T. Urbic, V. Vlachy, and K. A. Dill, J. Chem. Phys. 131, 194504 (2009)] does not reproduce in a quantitatively correct manner the peculiar temperature dependence of water density.

  8. Circadian and glucocorticoid regulation of Rev-erbalpha expression in liver.

    PubMed

    Torra, I P; Tsibulsky, V; Delaunay, F; Saladin, R; Laudet, V; Fruchart, J C; Kosykh, V; Staels, B

    2000-10-01

    Rev-erbalpha [NR1D1], a member of the nuclear receptor superfamily, is an orphan receptor that constitutively represses gene transcription. Rev-erbalpha has been shown to play a role in myocyte differentiation and to be induced during adipogenesis. Furthermore, Rev-erbalpha is a regulator of lipoprotein metabolism. It was recently shown that Rev-erbalpha messenger RNA (mRNA) levels oscillate diurnally in rat liver. Here, we report that the circadian rhythm of Rev-erbalpha in liver is maintained in primary cultures of rat hepatocytes. Because glucocorticoids have been shown to regulate other transcription factors with circadian expression, it was furthermore examined whether hepatic Rev-erbalpha expression is also regulated by glucocorticoids. Treatment of rats with dexamethasone resulted in a decrease of Rev-erbalpha mRNA levels by 70% after 6 h. Furthermore, dexamethasone decreased Rev-erbalpha expression in rat primary hepatocytes in a dose-dependent fashion. This effect was mediated by the glucocorticoid receptor because simultaneous addition of the glucocorticoid antagonist RU486 prevented the decrease in Rev-erbalpha mRNA levels by dexamethasone. Protein synthesis inhibition with cycloheximide markedly induced Rev-erbalpha mRNA levels; however, this induction was reduced by dexamethasone supplementation in both rat and human primary hepatocytes. Treatment with actinomycin D blocked the repression of Rev-erbalpha expression by dexamethasone in rat hepatocytes, suggesting that glucocorticoids regulate Rev-erbalpha expression at the transcriptional level. Transient transfection experiments further indicated that Rev-erbalpha promoter activity is repressed by dexamethasone in the presence of cotransfected glucocorticoid receptor. Taken together, these data demonstrate that Rev-erbalpha expression is under the control of both the circadian clock and glucocorticoids in the liver.

  9. Erratum: Evolution of precipitate morphology during heat treatment and its implications for the superconductivity in KxFe1.6+ySe2 single crystals [Phys. Rev. B 86 , 144507 (2012)

    DOE PAGES

    Liu, Y.; Xing, Q.; Dennis, K. W.; McCallum, R. W.; Lograsso, T. A.

    2015-08-14

    In this article, we study the relationship between precipitate morphology and superconductivity in KxFe1.6+ySe2 single crystals grown by self-flux method. Scanning electron microscopy (SEM) measurements revealed that the superconducting phase forms a network in the samples quenched above iron vacancy order-disorder transition temperature Ts, whereas it aggregates into micrometer-sized rectangular bars and aligns as disconnected chains in the furnace-cooled samples.

  10. Erratum: Measurement of azimuthal asymmetries in inclusive production of hadron pairs in e⁺e⁻ annihilation at √s=10.58 GeV [Phys. Rev. D 78, 032011 (2008)

    DOE PAGES

    Seidl, R.; Grosse Perdekamp, M.; Ogawa, A.; Adachi, I.; Aihara, H.; Bahinipati, S.; Bakich, A. M.; Bartel, W.; Bitenc, U.; Bondar, A.; et al

    2012-08-09

    In the original article, it was found in Monte Carlo simulations that the reconstructed A₀ results are roughly consistent with the generated asymmetries, while the A₁₂ results systematically underestimate the generated asymmetries. This underestimation can be attributed to the difference between the reconstructed thrust axis and the original quark-antiquark axis. The corresponding correction factors are 1.6 ± 0.04 for the A₁₂ results and 1.11 ± 0.05 for the A₀ results. Because of a flaw in the original analysis program, these correction factors were not applied to the AUC-type asymmetries in Table V as well as in some figures. In addition,more » a small mistake in the error propagation in the charm correction resulted in slightly underestimated statistical uncertainties. These omissions affect all but the charm asymmetry results. The correct central values are therefore given in Tables IV and V of this Erratum. The systematic uncertainties of the original publication remain unchanged.« less

  11. Response to 'Comment on 'Nonlinear properties of small amplitude dust ion acoustic solitary waves'' [Phys. Plasmas 15, 104703 (2008)

    SciTech Connect

    Gupta, M. R.; Sarkar, S.; Khan, Manoranjan; Ghosh, Samiran

    2008-10-15

    The objections are not justified. It should have been noted that ion charge number z{sub i}=1 throughout the referred paper [Ghosh et al., Phys. Plasmas 7, 3594 (2000)]. There is no inconsistency in the formulation of the referred paper as explained in the text.

  12. Comment on "Replica-exchange-with-tunneling for fast exploration of protein landscapes" [J. Chem. Phys. 143, 224102 (2015)].

    PubMed

    Sakuraba, Shun

    2016-08-01

    In "Replica-exchange-with-tunneling for fast exploration of protein landscapes" [F. Yaşar et al., J. Chem. Phys. 143, 224102 (2015)], a novel sampling algorithm called "Replica Exchange with Tunneling" was proposed. However, due to its violation of the detailed balance, the algorithm fails to sample from the correct canonical ensemble.

  13. Comment on "Replica-exchange-with-tunneling for fast exploration of protein landscapes" [J. Chem. Phys. 143, 224102 (2015)

    NASA Astrophysics Data System (ADS)

    Sakuraba, Shun

    2016-08-01

    In "Replica-exchange-with-tunneling for fast exploration of protein landscapes" [F. Yaşar et al., J. Chem. Phys. 143, 224102 (2015)], a novel sampling algorithm called "Replica Exchange with Tunneling" was proposed. However, due to its violation of the detailed balance, the algorithm fails to sample from the correct canonical ensemble.

  14. Comment on: “Complete resolution of the quantum Zeno paradox for outside observers” [Phys. Lett. A 326 (2004) 32

    NASA Astrophysics Data System (ADS)

    Wallentowitz, S.; Toschek, P. E.

    2006-07-01

    In a Letter by Hotta and Morikawa [M. Hotta, M. Morikawa, Phys. Lett. A 326 (2004) 32 41] the complete resolution of the quantum Zeno paradox has been claimed, invoking non-existence of the effect. It is shown here that the pertinent proof is incorrect, and the claim unfounded. We identify the logical errors made using an illustrative counterexample.

  15. Erratum: “Hamiltonian magnetohydrodynamics: Lagrangian, Eulerian, and dynamically accessible stability—Theory” [Phys. Plasmas 20, 092104 (2013)

    SciTech Connect

    Andreussi, T.; Morrison, P. J.; Pegoraro, F.

    2015-03-15

    An algebraic mistake in the rendering of the Energy Casimir stability condition for a symmetric magnetohydrodynamics plasma configuration with flows made in the article Andreussi et al. “Hamiltonian magnetohydrodynamics: Lagrangian, Eulerian, and dynamically accessible stability—Theory,” Phys. Plasmas 20, 092104 (2013) is corrected.

  16. Comment on "Replica-exchange-with-tunneling for fast exploration of protein landscapes" [J. Chem. Phys. 143, 224102 (2015)].

    PubMed

    Sakuraba, Shun

    2016-08-01

    In "Replica-exchange-with-tunneling for fast exploration of protein landscapes" [F. Yaşar et al., J. Chem. Phys. 143, 224102 (2015)], a novel sampling algorithm called "Replica Exchange with Tunneling" was proposed. However, due to its violation of the detailed balance, the algorithm fails to sample from the correct canonical ensemble. PMID:27497579

  17. Comments on ''theory of dissipative density-gradient-driven turbulence in the tokamak edge'' (Phys. Fluids 28, 1419 (1985))

    SciTech Connect

    Krommes, J.A.

    1985-11-01

    The author critiques the model of tokamak edge turbulence by P.W. Terry and P.H. Diamond (Phys. Fluids 28, 1419, 1985). The critique includes a discussion of the physical basis, consistency and quantitative accuracy of the Terry-Diamond model. 19 refs. (WRF)

  18. Comment on ``A proposal for in vitro/GFR molecular erythema action spectrum'' [J. Appl. Phys. 104, 034701 (2008)

    NASA Astrophysics Data System (ADS)

    Björn, Lars Olof; de Gruijl, Frank R.; Diffey, Brian; Norval, Mary

    2009-06-01

    The recent article by de Souza, Lorenzini and Rizzatti [J. A. V. de Souza, F. Lorenzini, and M. R. Rizatti, J. Appl. Phys. 104, 034701 (2008)] in this journal needs corrections and clarifications on several points. The model used by them is not suitable for the study of erythema.

  19. Fluctuations below a stationary supercritical bifurcation to electroconvection in a nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Qiu, Xin-Liang; Ahlers, Guenter

    2003-03-01

    We report measurements of thermally driven fluctuations near the onset of electroconvection in a nematic liquid crystal (NLC). The cell (from E.H.C Co, Ltd Japan) had a nominal spacing of 25 μm and planar alignment. It was filled with the NLC Merck phase IV (N4). The NLC was doped with 0.1% by weight of tetra butylammonium bromide(TBAB) and the conductivity was near 9 × 10-7 (Ω m)-1 at 30^oC. The system was driven by an alternating voltage of frequency 25 Hz and amplitude V. The initial bifurcation to electroconvection was supercritical and yielded oblique stationary rolls. For small but negative ɛ ≡ V^2/V_c^2 - 1 the mean-square amplitude of the fluctuations was proportional to |ɛ|^-γ with γ larger than the value γ_LT = 1/2 given by linear theory (LT). This result differs from the one obtained earlier (M.A. Scherer ,G. Ahlers, F. Hörner, and I. Rehberg, Phys. Rev. Lett. 85), 3754 (2000); M.A. Scherer and G. Ahlers, Phys. Rev. E 65, 051101 (2002) for the NLC 5CB, which undergoes a supercritical Hopf bifurcation to oblique rolls and which yields γ ˜= 0.25 < γ_LT . We conclude that the two systems belong to different universality classes.

  20. Targeted cleavage of HIV RRE RNA by Rev-coupled transition metal chelates.

    PubMed

    Joyner, Jeff C; Cowan, J A

    2011-06-29

    A series of compounds that target reactive metal chelates to the HIV-1 Rev response element (RRE) mRNA have been synthesized. Dissociation constants and chemical reactivity toward HIV RRE RNA have been determined and evaluated in terms of reduction potential, coordination unsaturation, and overall charge associated with the metal-chelate-Rev complex. Ethylenediaminetetraacetic acid (EDTA), nitrilotriacetic acid (NTA), diethylenetriaminepentaacetic acid (DTPA), and 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) were linked to a lysine side chain of a Rev-derived peptide by either EDC/NHS or isothiocyanate coupling. The resulting chelate-Rev (EDTA-Rev, DTPA-Rev, NTA-Rev, and DOTA-Rev) conjugates were used to form coordination complexes with Fe(2+), Co(2+), Ni(2+), and Cu(2+) such that the arginine-rich Rev peptide could mediate localization of the metal chelates to the Rev peptide's high-affinity mRNA binding partner, RRE stem loop IIB. Metal complexes of the extended peptides GGH-Rev and KGHK-Rev, which also contain N-terminal peptidic chelators (ATCUN motifs), were studied for comparison. A fluorescence titration assay revealed high-affinity RRE RNA binding by all 22 metal-chelate-Rev species, with K(D) values ranging from ~0.2 to 16 nM, indicating little to no loss of RNA affinity due to the coupling of the metal chelates to the Rev peptide. Dissociation constants for binding at a previously unobserved low-affinity site are also reported. Rates of RNA modification by each metal-chelate-Rev species were determined and varied from ~0.28 to 4.9 nM/min but were optimal for Cu(2+)-NTA-Rev. Metal-chelate reduction potentials were determined and varied from -228 to +1111 mV vs NHE under similar solution conditions, allowing direct comparison of reactivity with redox thermodynamics. Optimal activity was observed when the reduction potential for the metal center was poised between those of the two principal co-reagents for metal-promoted formation of

  1. Human REV3 DNA Polymerase Zeta Localizes to Mitochondria and Protects the Mitochondrial Genome.

    PubMed

    Singh, Bhupendra; Li, Xiurong; Owens, Kjerstin M; Vanniarajan, Ayyasamy; Liang, Ping; Singh, Keshav K

    2015-01-01

    To date, mitochondrial DNA polymerase γ (POLG) is the only polymerase known to be present in mammalian mitochondria. A dogma in the mitochondria field is that there is no other polymerase present in the mitochondria of mammalian cells. Here we demonstrate localization of REV3 DNA polymerase in the mammalian mitochondria. We demonstrate localization of REV3 in the mitochondria of mammalian tissue as well as cell lines. REV3 associates with POLG and mitochondrial DNA and protects the mitochondrial genome from DNA damage. Inactivation of Rev3 leads to reduced mitochondrial membrane potential, reduced OXPHOS activity, and increased glucose consumption. Conversely, inhibition of the OXPHOS increases expression of Rev3. Rev3 expression is increased in human primary breast tumors and breast cancer cell lines. Inactivation of Rev3 decreases cell migration and invasion, and localization of Rev3 in mitochondria increases survival and the invasive potential of cancer cells. Taken together, we demonstrate that REV3 functions in mammalian mitochondria and that mitochondrial REV3 is associated with the tumorigenic potential of cells.

  2. The Nuclear Receptor Rev-erbα Controls Circadian Thermogenic Plasticity

    PubMed Central

    Gerhart-Hines, Zachary; Everett, Logan J.; Loro, Emanuele; Briggs, Erika R.; Bugge, Anne; Hou, Catherine; Ferrara, Christine; Seale, Patrick; Pryma, Daniel A.; Khurana, Tejvir S.; Lazar, Mitchell A.

    2013-01-01

    Circadian oscillation of body temperature is a basic, evolutionary-conserved feature of mammalian biology1. Additionally, homeostatic pathways allow organisms to protect their core temperatures in response to cold exposure2. However, the mechanism responsible for coordinating daily body temperature rhythm and adaptability to environmental challenges is unknown. Here we show that the nuclear receptor Rev-erbα, a powerful transcriptional repressor, links circadian and thermogenic networks through the regulation of brown adipose tissue (BAT) function. Mice exposed to cold fare dramatically better at 5 AM (Zeitgeber time 22) when Rev-erbα is barely expressed than at 5 PM (ZT10) when Rev-erbα is abundant. Deletion of Rev-erbα markedly improves cold tolerance at 5 PM, indicating that overcoming Rev-erbα-dependent repression is a fundamental feature of the thermogenic response to cold. Physiological induction of uncoupling protein 1 (UCP1) by cold temperatures is preceded by rapid down-regulation of Rev-erbα in BAT. Rev-erbα represses UCP1 in a brown adipose cell-autonomous manner and BAT UCP1 levels are high in Rev-erbα-null mice even at thermoneutrality. Genetic loss of Rev-erbα also abolishes normal rhythms of body temperature and BAT activity. Thus, Rev-erbα acts as a thermogenic focal point required for establishing and maintaining body temperature rhythm in a manner that is adaptable to environmental demands. PMID:24162845

  3. The nuclear receptor Rev-erbα controls circadian thermogenic plasticity.

    PubMed

    Gerhart-Hines, Zachary; Feng, Dan; Emmett, Matthew J; Everett, Logan J; Loro, Emanuele; Briggs, Erika R; Bugge, Anne; Hou, Catherine; Ferrara, Christine; Seale, Patrick; Pryma, Daniel A; Khurana, Tejvir S; Lazar, Mitchell A

    2013-11-21

    Circadian oscillation of body temperature is a basic, evolutionarily conserved feature of mammalian biology. In addition, homeostatic pathways allow organisms to protect their core temperatures in response to cold exposure. However, the mechanism responsible for coordinating daily body temperature rhythm and adaptability to environmental challenges is unknown. Here we show that the nuclear receptor Rev-erbα (also known as Nr1d1), a powerful transcriptional repressor, links circadian and thermogenic networks through the regulation of brown adipose tissue (BAT) function. Mice exposed to cold fare considerably better at 05:00 (Zeitgeber time 22) when Rev-erbα is barely expressed than at 17:00 (Zeitgeber time 10) when Rev-erbα is abundant. Deletion of Rev-erbα markedly improves cold tolerance at 17:00, indicating that overcoming Rev-erbα-dependent repression is a fundamental feature of the thermogenic response to cold. Physiological induction of uncoupling protein 1 (Ucp1) by cold temperatures is preceded by rapid downregulation of Rev-erbα in BAT. Rev-erbα represses Ucp1 in a brown-adipose-cell-autonomous manner and BAT Ucp1 levels are high in Rev-erbα-null mice, even at thermoneutrality. Genetic loss of Rev-erbα also abolishes normal rhythms of body temperature and BAT activity. Thus, Rev-erbα acts as a thermogenic focal point required for establishing and maintaining body temperature rhythm in a manner that is adaptable to environmental demands. PMID:24162845

  4. The human endogenous retrovirus K Rev response element coincides with a predicted RNA folding region.

    PubMed Central

    Yang, J; Bogerd, H; Le, S Y; Cullen, B R

    2000-01-01

    Human endogenous retrovirus K (HERV-K) is the name given to an approximately 30-million-year-old family of endogenous retroviruses present at >50 copies per haploid human genome. Previously, the HERV-K were shown to encode a nuclear RNA export factor, termed K-Rev, that is the functional equivalent of the H-Rev protein encoded by human immunodeficiency virus type 1. HERV-K was also shown to contain a cis-acting target element, the HERV-K Rev response element (K-RRE), that allowed the nuclear export of linked RNA transcripts in the presence of either K-Rev or H-Rev. Here, we demonstrate that the functionally defined K-RRE coincides with a statistically highly significant unusual RNA folding region and present a potential RNA secondary structure for the approximately 416-nt K-RRE. Both in vitro and in vivo assays of sequence specific RNA binding were used to map two primary binding sites for K-Rev, and one primary binding site for H-Rev, within the K-RRE. Of note, all three binding sites map to discrete predicted RNA stem-loop subdomains within the larger K-RRE structure. Although almost the entire 416-nt K-RRE was required for the activation of nuclear RNA export in cells expressing K-Rev, mutational inactivation of the binding sites for K-Rev resulted in the selective loss of the K-RRE response to K-Rev but not to H-Rev. Together, these data strongly suggest that the K-RRE, like the H-RRE, coincides with an extensive RNA secondary structure and identify specific sites within the K-RRE that can recruit either K-Rev or H-Rev to HERV-K RNA transcripts. PMID:11105755

  5. New Rev-export inhibitor from Alpinia galanga and structure-activity relationship.

    PubMed

    Tamura, Satoru; Shiomi, Atsushi; Kaneko, Masafumi; Ye, Ying; Yoshida, Minoru; Yoshikawa, Masayuki; Kimura, Tominori; Kobayashi, Motomasa; Murakami, Nobutoshi

    2009-05-01

    Bioassay-guided separation by use of the fission yeast expressing NES of Rev, an HIV-1 viral regulatory protein, disclosed 1'-acetoxychavicol acetate (ACA, 1) as a new inhibitor for nuclear export of Rev from the roots of Alpinia galanga. Both analysis for mechanism of action with biotinylated probe (2) and several synthesized analogs established crucial portions in 1 for Rev-export inhibitory activity.

  6. Comment on ``Equation of state of aluminum nitride and its shock response'' [J. Appl. Phys. 76, 4077 (1994)

    NASA Astrophysics Data System (ADS)

    Rosenberg, Z.; Brar, N. S.

    1995-11-01

    A recent article by Dandekar, Abbate, and Frankel [J. Appl. Phys. 76, 4077 (1994)] reviews existing data on high-pressure properties of aluminum nitride (AlN) in an effort to build an equation of state for this material. A rather large portion of that article is devoted to the shear strength of AlN and, in particular, to our data of 1991 with longitudinal and lateral stress gauges [Z. Rosenberg, N. S. Brar, and S. J. Bless, J. Appl. Phys. 70, 167 (1991)]. Since our highest data point has an error of 1 GPa, much of the discussion and conclusions of Dandekar and co-workers are not relevant once this error in data reduction is corrected. We also discuss the relevance of our shear strength data for various issues, such as the phase transformation of AlN at 20 GPa and the general shape of Hugoniot curves for brittle solids.

  7. Comment on “Maxwell's equations and electromagnetic Lagrangian density in fractional form” [J. Math. Phys. 53, 033505 (2012)

    SciTech Connect

    Rabei, Eqab M.; Al-Jamel, A.; Widyan, H.; Baleanu, D.

    2014-03-15

    In a recent paper, Jaradat et al. [J. Math. Phys. 53, 033505 (2012)] have presented the fractional form of the electromagnetic Lagrangian density within the Riemann-Liouville fractional derivative. They claimed that the Agrawal procedure [O. P. Agrawal, J. Math. Anal. Appl. 272, 368 (2002)] is used to obtain Maxwell's equations in the fractional form, and the Hamilton's equations of motion together with the conserved quantities obtained from fractional Noether's theorem are reported. In this comment, we draw the attention that there are some serious steps of the procedure used in their work are not applicable even though their final results are correct. Their work should have been done based on a formulation as reported by Baleanu and Muslih [Phys. Scr. 72, 119 (2005)].

  8. Corrigendum to “Robust limits on Lorentz violation from gamma-ray bursts” [Astropart. Phys. 25 (2006) 402

    NASA Astrophysics Data System (ADS)

    Ellis, John; Mavromatos, N. E.; Nanopoulos, D. V.; Sakharov, A. S.; Sarkisyan, E. K. G.

    2008-03-01

    We correct the fitting formula used [J.R. Ellis, N.E. Mavromatos, D.V. Nanopoulos, A.S. Sakharov, E.K.G. Sarkisyan, Astropart. Phys. 25 (2006) 402. Available from: arxiv:] to obtain a robust limit on a violation of Lorentz invariance that depends linearly on the photon energy. The correction leads to a slight increase of the limit on the scale of the violation, to M > 1.4 ×1016GeV .

  9. Comment on ''Electron acceleration by a chirped Gaussian laser pulse in vacuum'' [Phys. Plasmas 13, 123108 (2006)

    SciTech Connect

    Gupta, D. N.; Hur, M. S.; Suk, H.

    2007-04-15

    Sohbatzadeh et al. [Phys. Plasmas 13, 123108 (2006)] have presented a scheme of vacuum electron acceleration by using a chirped Gaussian laser pulse. They assume a linear polarization of the laser pulse in this scheme. We point out that this might be an important assumption in their work and it can seriously influence the electron energy gain during laser acceleration. In this Comment, the circular polarization of a chirped laser pulse is employed and our results show higher electron energy gains.

  10. Identification of trans-dominant HIV-1 rev protein mutants by direct transfer of bacterially produced proteins into human cells.

    PubMed Central

    Mermer, B; Felber, B K; Campbell, M; Pavlakis, G N

    1990-01-01

    A synthetic rev gene containing substitutions which introduced unique restriction sites but did not alter the deduced amino acid sequence was used as a vehicle to construct mutations in rev. Insertion or substitution mutations within a domain of Rev resulted in proteins able to inhibit the function of Rev protein in trans. Rev function was monitored in a cell line, HLfB, which contained a rev- mutant provirus. HLfB cells require the presence of rev for virus production, which was conveniently monitored by immunoblot detection of p24gag. Trans-dominant mutants were identified after expression in bacteria and delivery into HLfB cells by protoplast fusion. In addition, the trans-dominant phenotype was verified by expression of the mutant proteins in HLfB cells after cotransfection. These studies define a region between amino acid residues 81 and 88 of rev, in which different mutations result in proteins capable of inhibiting Rev function. Images PMID:2186373

  11. Rev-erb-α modulates skeletal muscle oxidative capacity by regulating mitochondrial biogenesis and autophagy

    PubMed Central

    Woldt, Estelle; Sebti, Yasmine; Solt, Laura A.; Duhem, Christian; Lancel, Steve; Eeckhoute, Jérôme; Hesselink, Matthijs K.C.; Paquet, Charlotte; Delhaye, Stéphane; Shin, Youseung; Kamenecka, Theodore M.; Schaart, Gert; Lefebvre, Philippe; Nevière, Rémi; Burris, Thomas P.; Schrauwen, Patrick; Staels, Bart; Duez, Hélène

    2013-01-01

    The nuclear receptor Rev-erb-α modulates hepatic lipid and glucose metabolism, adipogenesis and the inflammatory response in macrophages. We show here that Rev-erb-α is highly expressed in oxidative skeletal muscle and plays a role in mitochondrial biogenesis and oxidative function, in gain- and loss-of function studies. Rev-erb-α-deficiency in skeletal muscle leads to reduced mitochondrial content and oxidative function, resulting in compromised exercise capacity. This phenotype was recapitulated in isolated fibers and in muscle cells upon Rev-erbα knock-down, while Rev-erb-α over-expression increased the number of mitochondria with improved respiratory capacity. Rev-erb-α-deficiency resulted in deactivation of the Stk11–Ampk–Sirt1–Ppargc1-α signaling pathway, whereas autophagy was up-regulated, resulting in both impaired mitochondrial biogenesis and increased clearance. Muscle over-expression or pharmacological activation of Rev-erb-α increased respiration and exercise capacity. This study identifies Rev-erb-α as a pharmacological target which improves muscle oxidative function by modulating gene networks controlling mitochondrial number and function. PMID:23852339

  12. Pharmacological and Genetic Modulation of REV-ERB Activity and Expression Affects Orexigenic Gene Expression

    PubMed Central

    Amador, Ariadna; Wang, Yongjun; Banerjee, Subhashis; Kameneka, Theodore M.; Solt, Laura A.; Burris, Thomas P.

    2016-01-01

    The nuclear receptors REV-ERBα and REV-ERBβ are transcription factors that play pivotal roles in the regulation of the circadian rhythm and various metabolic processes. The circadian rhythm is an endogenous mechanism, which generates entrainable biological changes that follow a 24-hour period. It regulates a number of physiological processes, including sleep/wakeful cycles and feeding behaviors. We recently demonstrated that REV-ERB-specific small molecules affect sleep and anxiety. The orexinergic system also plays a significant role in mammalian physiology and behavior, including the regulation of sleep and food intake. Importantly, orexin genes are expressed in a circadian manner. Given these overlaps in function and circadian expression, we wanted to determine whether the REV-ERBs might regulate orexin. We found that acute in vivo modulation of REV-ERB activity, with the REV-ERB-specific synthetic ligand SR9009, affects the circadian expression of orexinergic genes in mice. Long term dosing with SR9009 also suppresses orexinergic gene expression in mice. Finally, REV-ERBβ-deficient mice present with increased orexinergic transcripts. These data suggest that the REV-ERBs may be involved in the repression of orexinergic gene expression. PMID:26963516

  13. Protective efficacy of a recombinant BAC clone of Marek's disease virus containing REV-LTR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Insertion of reticuloendotheliosis virus (REV) long-terminal repeat (LTR) into a bacterial artificial chromosome (BAC) clone of a very virulent strain of Marek’s disease (MD) virus (MDV), Md5 (Kim et al, 2011) rendered the resultant recombinant virus termed rMd5 REV-LTR BAC fully attenuated at passa...

  14. HIV-1 pre-mRNA commitment to Rev mediated export through PSF and Matrin 3

    SciTech Connect

    Kula, Anna; Gharu, Lavina; Marcello, Alessandro

    2013-01-20

    Human immunodeficiency virus gene expression and replication are regulated at several levels. Incompletely spliced viral RNAs and full-length genomic RNA contain the RRE element and are bound by the viral trans-acting protein Rev to be transported out of the nucleus. Previously we found that the nuclear matrix protein MATR3 was a cofactor of Rev-mediated RNA export. Here we show that the pleiotropic protein PSF binds viral RNA and is associated with MATR3. PSF is involved in the maintenance of a pool of RNA available for Rev activity. However, while Rev and PSF bind the viral pre-mRNA at the site of viral transcription, MATR3 interacts at a subsequent step. We propose that PSF and MATR3 define a novel pathway for RRE-containing HIV-1 RNAs that is hijacked by the viral Rev protein.

  15. RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

    PubMed Central

    Höhna, Sebastian; Landis, Michael J.

    2016-01-01

    Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com. [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.] PMID:27235697

  16. RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.

    PubMed

    Höhna, Sebastian; Landis, Michael J; Heath, Tracy A; Boussau, Bastien; Lartillot, Nicolas; Moore, Brian R; Huelsenbeck, John P; Ronquist, Fredrik

    2016-07-01

    Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.].

  17. The orphan receptor Rev-erbα gene is a target of the circadian clock pacemaker

    PubMed Central

    Triqueneaux, Gérard; Thenot, Sandrine; Kakizawa, Tomoko; Antoch, Marina P; Safi, Rachid; Takahashi, Joseph S; Delaunay, Franck; Laudet, Vincent

    2013-01-01

    Rev-erbα is a ubiquitously expressed orphan nuclear receptor which functions as a constitutive transcriptional repressor and is expressed in vertebrates according to a robust circadian rhythm. We report here that two Rev-erbα mRNA isoforms, namely Rev-erbα1 and Rev-erbα2, are generated through alternative promoter usage and that both show a circadian expression pattern in an in vitro system using serum-shocked fibroblasts. Both promoter regions P1 (Rev-erbα1) and P2 (Rev-erbα2) contain several E-box DNA sequences, which function as response elements for the core circadian-clock components: CLOCK and BMAL1. The CLOCK–BMAL1 heterodimer stimulates the activity of both P1 and P2 promoters in transient transfection assay by 3–6-fold. This activation was inhibited by the overexpression of CRY1, a component of the negative limb of the circadian transcriptional loop. Critical E-box elements were mapped within both promoters. This regulation is conserved in vertebrates since we found that the CLOCK–BMAL1 heterodimer also regulates the zebrafish Rev-erbα gene. In line with these data Rev-erbα circadian expression was strongly impaired in the livers of Clock mutant mice and in the pineal glands of zebrafish embryos treated with Clock and Bmal1 antisense oligonucleotides. Together these data demonstrate that CLOCK is a critical regulator of Rev-erbα circadian gene expression in evolutionarily distant vertebrates and suggest a role for Rev-erbα in the circadian clock output. PMID:15591021

  18. RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.

    PubMed

    Höhna, Sebastian; Landis, Michael J; Heath, Tracy A; Boussau, Bastien; Lartillot, Nicolas; Moore, Brian R; Huelsenbeck, John P; Ronquist, Fredrik

    2016-07-01

    Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.]. PMID:27235697

  19. Rev-erb beta regulates the Srebp-1c promoter and mRNA expression in skeletal muscle cells

    SciTech Connect

    Ramakrishnan, Sathiya N.; Lau, Patrick; Crowther, Lisa M.; Cleasby, Mark E.; Millard, Susan; Leong, Gary M.; Cooney, Gregory J.; Muscat, George E.O.

    2009-10-30

    The nuclear hormone receptor, Rev-erb beta operates as a transcriptional silencer. We previously demonstrated that exogenous expression of Rev-erb{beta}{Delta}E in skeletal muscle cells increased Srebp-1c mRNA expression. We validated these in vitro observations by injection of an expression vector driving Rev-erb{beta}{Delta}E expression into mouse tibialis muscle that resulted in increased Srebp-1c mRNA expression. Paradoxically, Rev-erb{beta} siRNA expression in skeletal muscle cells repressed Srebp-1c expression, and indicated that Rev-erb{beta} expression was necessary for Srebp-1c expression. ChIP analysis demonstrated that Rev-erb{beta} was recruited to the Srebp-1c promoter. Moreover, Rev-erb{beta} trans-activated the Srebp-1c promoter, in contrast, Rev-erb{beta} efficiently repressed the Rev-erb{alpha} promoter, a previously characterized target gene. Finally, treatment with the Rev-erb agonist (hemin) (i) increased the trans-activation of the Srebp-1c promoter by Rev-erb{beta}; and (ii) increased Rev-erb{beta} and Srebp-1c mRNA expression. These data suggest that Rev-erb{beta} has the potential to activate gene expression, and is a positive regulator of Srebp-1c, a regulator of lipogenesis.

  20. Comment on: “Electromagnetic wave propagation in single-wall carbon nanotubes” [Phys. Lett. A 333 (2004) 303

    NASA Astrophysics Data System (ADS)

    Khosravi, Heidar; Moradi, Afshin

    2007-05-01

    In a recent article [L. Wei, Y.-N. Wang, Phys. Lett. A 333 (2004) 303], Li Wei and You-Nian Wang studied the propagation of electromagnetic wave in single-wall carbon nanotubes and presented different expressions of the dispersions relations of TE and TM modes, respectively. Here we have derived the correct form of the dispersion relation for TM mode on low-frequency electromagnetic wave. It is shown numerically that asymptotic behaviours of the TM and TE modes are quite similar in single-wall carbon nanotubes.

  1. Comment on 'Experimental observation of carbon dioxide reduction in exhaust gas from hydrocarbon fuel burning' [Phys. Plasmas 16, 114502 (2009)

    SciTech Connect

    Byun, Youngchul; Shin, Dong Nam

    2010-01-15

    The following comments are intended to clarify whether it is possible to convert CO{sub 2} into C+O{sub 2} by supplying just one-twentieth of energy required thermodynamically, only under the condition that the negative high voltage of dc is applied to the gas stream perpendicularly, in a recent article by Uhm and Kim [H. S. Uhm and C. H. Kim, Phys. Plasmas 16, 114502 (2009)]. Of particular concern is the disobedience of the first and second laws of thermodynamics together with the indistinct measurement of experimental data.

  2. Comment on "Propagation of surface waves on a semi-bounded quantum magnetized collisional plasma" [Phys. Plasmas 20, 122106 (2013)

    NASA Astrophysics Data System (ADS)

    Moradi, Afshin

    2016-04-01

    In a recent article [Niknam et al., Phys. Plasmas 20, 122106 (2013)], Niknam et al. investigated the propagation of TM surface waves on a semi-bounded quantum magnetized collisional plasma in the Faraday configuration (in this case, the magnetic field is parallel to the both of the plasma surface and direction of propagation). Here, we present a fresh look at the problem and show that TM surface waves cannot propagate on surface of the present system. We find in the Faraday configuration the surface waves acquire both TM and TE components due to the cyclotron motion of electrons. Therefore, the main result of the work by Niknam et al. is incorrect.

  3. Comment on "Surface electromagnetic wave equations in a warm magnetized quantum plasma" [Phys. Plasmas 21, 072114 (2014)

    NASA Astrophysics Data System (ADS)

    Moradi, Afshin

    2016-07-01

    In a recent article [C. Li et al., Phys. Plasmas 21, 072114 (2014)], Li et al. studied the propagation of surface waves on a magnetized quantum plasma half-space in the Voigt configuration (in this case, the magnetic field is parallel to the surface but is perpendicular to the direction of propagation). Here, we present a fresh look at the problem and obtain a new form of dispersion relation of surface waves of the system. We find that our new dispersion relation does not agree with the result obtained by Li et al.

  4. Comment on “On the quantum theory of molecules” [J. Chem. Phys. 137, 22A544 (2012)

    SciTech Connect

    Sutcliffe, Brian T.; Woolley, R. Guy

    2014-01-21

    In our previous paper [B. T. Sutcliffe and R. G. Woolley, J. Chem. Phys. 137, 22A544 (2012)] we argued that the Born-Oppenheimer approximation could not be based on an exact transformation of the molecular Schrödinger equation. In this Comment we suggest that the fundamental reason for the approximate nature of the Born-Oppenheimer model is the lack of a complete set of functions for the electronic space, and the need to describe the continuous spectrum using spectral projection.

  5. Comment on ``Free energy simulations of single and double ion occupancy in gramicidin A'' [J. Chem. Phys. 126, 105103 (2007)

    NASA Astrophysics Data System (ADS)

    Roux, Benoît; Andersen, Olaf S.; Allen, Toby W.

    2008-06-01

    In a recent article published by Bastug and Kuyucak [J. Chem. Phys.126, 105103 (2007)] investigated the microscopic factors affecting double ion occupancy in the gramicidin channel. The analysis relied largely on the one-dimensional potential of mean force of ions along the axis of the channel (the so-called free energy profile of the ion along the channel axis), as well as on the calculation of the equilibrium association constant of the ions in the channel binding sites. It is the purpose of this communication to clarify this issue.

  6. PhysBinder: improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties

    PubMed Central

    Broos, Stefan; Soete, Arne; Hooghe, Bart; Moran, Raymond; van Roy, Frans; De Bleser, Pieter

    2013-01-01

    The most important mechanism in the regulation of transcription is the binding of a transcription factor (TF) to a DNA sequence called the TF binding site (TFBS). Most binding sites are short and degenerate, which makes predictions based on their primary sequence alone somewhat unreliable. We present a new web tool that implements a flexible and extensible algorithm for predicting TFBS. The algorithm makes use of both direct (the sequence) and several indirect readout features of protein–DNA complexes (biophysical properties such as bendability or the solvent-excluded surface of the DNA). This algorithm significantly outperforms state-of-the-art approaches for in silico identification of TFBS. Users can submit FASTA sequences for analysis in the PhysBinder integrative algorithm and choose from >60 different TF-binding models. The results of this analysis can be used to plan and steer wet-lab experiments. The PhysBinder web tool is freely available at http://bioit.dmbr.ugent.be/physbinder/index.php. PMID:23620286

  7. Tamavidin 2-REV: an engineered tamavidin with reversible biotin-binding capability.

    PubMed

    Takakura, Yoshimitsu; Sofuku, Kozue; Tsunashima, Masako

    2013-03-10

    A biotin-binding protein with reversible biotin-binding capability is of great technical value in the affinity purification of biotinylated biomolecules. Although several proteins, chemically or genetically modified from avidin or streptavidin, with reversible biotin-binding have been reported, they have been problematic in one way or another. Tamavidin 2 is a fungal protein similar to avidin and streptavidin in biotin-binding. Here, a mutein, tamavidin 2-REV, was engineered from tamavidin 2 by replacing the serine at position 36 (S36) with alanine. S36 is thought to form a hydrogen bond with biotin in tamavidin 2/biotin complexes and two hydrogen bonds with V38 within the protein. Tamavidin 2-REV bound to biotin-agarose and was eluted with excess free biotin at a neutral pH. In addition, the model substrate biotinylated bovine serum albumin was efficiently purified from a crude extract from Escherichia coli by means of single-step affinity chromatography with tamavidin 2-REV-immobilized resin. Tamavidin 2-REV thus demonstrated reversible biotin-binding capability. The Kd value of tamavidin 2-REV to biotin was 2.8-4.4×10(-7)M.Tamavidin 2-REV retained other convenient characteristics of tamavidin 2, such as high-level expression in E. coli, resistance to proteases, and a neutral isoelectric point, demonstrating that tamavidin 2-REV is a powerful tool for the purification of biotinylated biomolecules. PMID:23333918

  8. RNA helicase MOV10 functions as a co-factor of HIV-1 Rev to facilitate Rev/RRE-dependent nuclear export of viral mRNAs.

    PubMed

    Huang, Feng; Zhang, Junsong; Zhang, Yijun; Geng, Guannan; Liang, Juanran; Li, Yingniang; Chen, Jingliang; Liu, Chao; Zhang, Hui

    2015-12-01

    Human immunodeficiency virus type 1 (HIV-1) exploits multiple host factors during its replication. The REV/RRE-dependent nuclear export of unspliced/partially spliced viral transcripts needs the assistance of host proteins. Recent studies have shown that MOV10 overexpression inhibited HIV-1 replication at various steps. However, the endogenous MOV10 was required in certain step(s) of HIV-1 replication. In this report, we found that MOV10 potently enhances the nuclear export of viral mRNAs and subsequently increases the expression of Gag protein and other late products through affecting the Rev/RRE axis. The co-immunoprecipitation analysis indicated that MOV10 interacts with Rev in an RNA-independent manner. The DEAG-box of MOV10 was required for the enhancement of Rev/RRE-dependent nuclear export and the DEAG-box mutant showed a dominant-negative activity. Our data propose that HIV-1 utilizes the anti-viral factor MOV10 to function as a co-factor of Rev and demonstrate the complicated effects of MOV10 on HIV-1 life cycle.

  9. FANCD2 and REV1 cooperate in the protection of nascent DNA strands in response to replication stress

    PubMed Central

    Yang, Yeran; Liu, Zhenbo; Wang, Fengli; Temviriyanukul, Piya; Ma, Xiaolu; Tu, Yingfeng; Lv, Lingna; Lin, Yu-Fen; Huang, Min; Zhang, Ting; Pei, Huadong; Chen, Benjamin P.C.; Jansen, Jacob G.; de Wind, Niels; Fischhaber, Paula L.; Friedberg, Errol C.; Tang, Tie-Shan; Guo, Caixia

    2015-01-01

    REV1 is a eukaryotic member of the Y-family of DNA polymerases involved in translesion DNA synthesis and genome mutagenesis. Recently, REV1 is also found to function in homologous recombination. However, it remains unclear how REV1 is recruited to the sites where homologous recombination is processed. Here, we report that loss of mammalian REV1 results in a specific defect in replication-associated gene conversion. We found that REV1 is targeted to laser-induced DNA damage stripes in a manner dependent on its ubiquitin-binding motifs, on RAD18, and on monoubiquitinated FANCD2 (FANCD2-mUb) that associates with REV1. Expression of a FANCD2-Ub chimeric protein in RAD18-depleted cells enhances REV1 assembly at laser-damaged sites, suggesting that FANCD2-mUb functions downstream of RAD18 to recruit REV1 to DNA breaks. Consistent with this suggestion we found that REV1 and FANCD2 are epistatic with respect to sensitivity to the double-strand break-inducer camptothecin. REV1 enrichment at DNA damage stripes also partially depends on BRCA1 and BRCA2, components of the FANCD2/BRCA supercomplex. Intriguingly, analogous to FANCD2-mUb and BRCA1/BRCA2, REV1 plays an unexpected role in protecting nascent replication tracts from degradation by stabilizing RAD51 filaments. Collectively these data suggest that REV1 plays multiple roles at stalled replication forks in response to replication stress. PMID:26187992

  10. 75 FR 10524 - NUREG-0654/FEMA-REP-1, Rev. 1, Supplement 3, Guidance for Protective Action Recommendations for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-08

    ... COMMISSION NUREG-0654/FEMA-REP-1, Rev. 1, Supplement 3, Guidance for Protective Action Recommendations for... document entitled: ``NUREG-0654/FEMA-REP-1, Rev. 1, Supplement 3, Guidance for Protective Action...-4737, or by e-mail to pdr.resource@nrc.gov . NUREG-0654/FEMA-REP-1, Rev. 1, Supplement 3,...

  11. 75 FR 69741 - Proposed Collection; Comment Request for Rev. Proc. 2007-99 (RP-127367-07), 9100 Relief Under...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-15

    ... Internal Revenue Service Proposed Collection; Comment Request for Rev. Proc. 2007-99 (RP- 127367-07), 9100... comments concerning Rev. Proc. 2007-99 (RP-127367-07), 9100 Relief Under Sections 897 and 1445. DATES... Internet at Joel.P.Goldberger@irs.gov . SUPPLEMENTARY INFORMATION: Title: Rev. Proc. 2007-99...

  12. Comment on “Stationary self-focusing of Gaussian laser beam in relativistic thermal quantum plasma” [Phys. Plasmas 20, 072703 (2013)

    SciTech Connect

    Habibi, M.; Ghamari, F.

    2014-06-15

    Patil and Takale in their recent article [Phys. Plasmas 20, 072703 (2013)], by evaluating the quantum dielectric response in thermal quantum plasma, have modeled the relativistic self-focusing of Gaussian laser beam in a plasma. We have found that there are some important shortcomings and fundamental mistakes in Patil and Takale [Phys. Plasmas 20, 072703 (2013)] that we give a brief description about them and refer readers to important misconception about the use of the Fermi temperature in quantum plasmas, appearing in Patil and Takale [Phys. Plasmas 20, 072703 (2013)].

  13. REV7/MAD2L2: the multitasking maestro emerges as a barrier to recombination

    PubMed Central

    Sale, Julian E

    2015-01-01

    REV7/MAD2L2 plays important roles in translesion DNA synthesis and mitotic control. Two new papers extend its gamut by revealing its unexpected participation in pathway choice during DNA double-strand break repair. By inhibiting 5′ DNA end resection downstream of 53BP1 and RIF1, REV7/MAD2L2 promotes non-homologous end joining at the expense of homologous recombination. Importantly, loss of REV7/MAD2L2 renders PARP inhibitors ineffective in BRCA1-deficient tumours, suggesting another possible mechanism for the acquisition of resistance to this important new class of drug. PMID:25896508

  14. The human immunodeficiency virus type 1 Rev protein shuttles between the cytoplasm and nuclear compartments.

    PubMed Central

    Kalland, K H; Szilvay, A M; Brokstad, K A; Saetrevik, W; Haukenes, G

    1994-01-01

    A retroviral regulatory protein, Rev (regulator of virion protein expression), is made in cells infected by human immunodeficiency virus (HIV). Rev is essential for the completion of the retroviral life cycle and interacts with the host cell at some posttranscriptional step in order to express the incompletely spliced HIV mRNAs from which HIV structural proteins are translated. Neither the host cell components nor the mechanisms responsible for this important regulation have been defined. We now report that Rev is a nucleocytoplasmic shuttle protein which is continuously transported between the cytoplasm, the nucleoli, and nucleoplasmic speckles enriched in RNA splicing and processing factors. The results show that Rev has the potential to interfere specifically with the splicing of the HIV pre-mRNA in the nucleoplasm and, next, guide such mRNAs to the cytoplasm for translation. Images PMID:7935458

  15. Comment on “Deterministic six states protocol for quantum communication” [Phys. Lett. A 358 (2006) 85

    NASA Astrophysics Data System (ADS)

    El-Orany, Faisal A. A.

    2010-02-01

    In [J.S. Shaari, M. Lucamarini, M.R.B. Wahiddin, Phys. Lett. A 358 (2006) 85] the deterministic six states protocol (6DP) for quantum communication has been developed. This protocol is based on three mutually unbiased bases and four encoding operators. Information is transmitted between the users via two qubits from different bases. Three attacks have been studied; namely intercept-resend attack (IRA), double-CNOT attack (2CNOTA) and quantum man-in-the-middle attack. In this Letter, we show that the IRA and 2CNOTA are not properly addressed. For instance, we show that the probability of detecting Eve in the control mode of the IRA is 70% instead of 50% in the previous study. Moreover, in the 2CNOTA, Eve can only obtain 50% of the data not all of it as argued earlier.

  16. Comment on 'The diatomic dication CuZn{sup 2+} in the gas phase' [J. Chem. Phys. 135, 034306 (2011)

    SciTech Connect

    Fiser, Jiri; Diez, Reinaldo Pis; Franzreb, Klaus; Alonso, Julio A.

    2013-02-21

    In this Comment, the density functional theory (DFT) calculations carried out by Diez et al. [J. Chem. Phys. 135, 034306 (2011)] are revised within the framework of the coupled-cluster single double triple method. These more sophisticated calculations allow us to show that the {sup 2}{Sigma}{sup +} electronic ground state of CuZn{sup 2+}, characterized as the metastable ground state by DFT calculations, is a repulsive state instead. The {sup 2}{Delta} and {sup 2}{Pi} metastable states of CuZn{sup 2+}, on the other hand, should be responsible for the formation mechanism of the dication through the near-resonant electron transfer CuZn{sup +}+ Ar{sup +}{yields} CuZn{sup 2+}+ Ar reaction.

  17. Comment on "Fe2: As simple as a Herculean labour. Neutral (Fe2), cationic (Fe2(+)), and anionic (Fe2(-)) species" [J. Chem. Phys. 142, 244304 (2015)].

    PubMed

    Hoyer, Chad E; Li Manni, Giovanni; Truhlar, Donald G; Gagliardi, Laura

    2016-01-14

    A recent paper on Fe2 [A. Kalemos, J. Chem. Phys. 142, 244304 (2015)] critiqued our previous work on the system [Hoyer et al., J. Chem. Phys. 141, 204309 (2014)]. In this comment, we explain the nature of our previously reported potential energy curve for Fe2 and we discuss our computed properties for Fe2. Additionally, we fix a labeling error that was present in our previous work, although this error is unrelated to the main point of discussion.

  18. Comments on ''Rayleigh-Taylor instability of a continuously stratified magnetofluid under a general rotation field'' [Phys. Fluids A 1, 1600 (1989)

    NASA Astrophysics Data System (ADS)

    Chakraborty, B. B.; Tuteja, G. S.

    1991-08-01

    Rayleigh-Taylor instability of a continuously stratified magnetofluid under a general rotation field, earlier studied by Dávalos-Orozco and Aguilar-Rosas [Phys. Fluids A 1, 1600 (1989)] is reconsidered. Some corrections in their analysis are made and the discrepancies between their results in some special cases and those obtained by Chakraborty [Phys. Fluids 25, 743 (1982)] and Hide [J. Fluid Mech. 39, 283 (1969)] are removed.

  19. DDX1 is an RNA-dependent ATPase Involved in HIV-1 Rev Function and Virus Replication

    PubMed Central

    Edgcomb, Stephen P.; Carmel, Andrew B.; Naji, Souad; Ambrus-Aikelin, Geza; Reyes, Jason R.; Saphire, Andrew C.S.; Gerace, Larry; Williamson, James R.

    2011-01-01

    The HIV-1 Rev protein is essential for the virus because it promotes nuclear export of alternatively-processed mRNAs, and Rev is also linked to translation of viral mRNAs and genome encapsidation. Previously, the human DEAD-box helicase DDX1 was suggested to be involved in Rev functions, but this relationship is not well understood. Biochemical studies of DDX1 and its interactions with Rev and model RNA oligonucleotides were carried out to investigate the molecular basis for association of these components. A combination of gel-filtration chromatography and circular dichroism spectroscopy demonstrated that recombinant DDX1 expressed in E. coli is a well-behaved folded protein. Binding assays using fluorescently-labeled Rev and cell-based immunoprecipitation analysis confirmed a specific RNA-independent DDX1-Rev interaction. Additionally, DDX1 was shown to be an RNA-activated ATPase, wherein Rev-bound RNA was equally effective at stimulating ATPase activity as protein-free RNA. Gel mobility shift assays further demonstrated that DDX1 forms complexes with Rev-bound RNA. RNA silencing of DDX1 provided strong evidence that DDX1 is required for both Rev activity and HIV production from infected cells. Collectively, these studies demonstrate a clear link between DDX1 and HIV-1 Rev in cell based assays of HIV-1 production, and provide the first demonstration that recombinant DDX1 binds Rev and RNA, and has RNA dependent catalytic activity. PMID:22051512

  20. Pharmacological Targeting the REV-ERBs in Sleep/Wake Regulation.

    PubMed

    Amador, Ariadna; Huitron-Resendiz, Salvador; Roberts, Amanda J; Kamenecka, Theodore M; Solt, Laura A; Burris, Thomas P

    2016-01-01

    The circadian clock maintains appropriate timing for a wide range of behaviors and physiological processes. Circadian behaviors such as sleep and wakefulness are intrinsically dependent on the precise oscillation of the endogenous molecular machinery that regulates the circadian clock. The identical core clock machinery regulates myriad endocrine and metabolic functions providing a link between sleep and metabolic health. The REV-ERBs (REV-ERBα and REV-ERBβ) are nuclear receptors that are key regulators of the molecular clock and have been successfully targeted using small molecule ligands. Recent studies in mice suggest that REV-ERB-specific synthetic agonists modulate metabolic activity as well as alter sleep architecture, inducing wakefulness during the light period. Therefore, these small molecules represent unique tools to extensively study REV-ERB regulation of sleep and wakefulness. In these studies, our aim was to further investigate the therapeutic potential of targeting the REV-ERBs for regulation of sleep by characterizing efficacy, and optimal dosing time of the REV-ERB agonist SR9009 using electroencephalographic (EEG) recordings. Applying different experimental paradigms in mice, our studies establish that SR9009 does not lose efficacy when administered more than once a day, nor does tolerance develop when administered once a day over a three-day dosing regimen. Moreover, through use of a time response paradigm, we determined that although there is an optimal time for administration of SR9009 in terms of maximal efficacy, there is a 12-hour window in which SR9009 elicited a response. Our studies indicate that the REV-ERBs are potential therapeutic targets for treating sleep problems as those encountered as a consequence of shift work or jet lag. PMID:27603791

  1. Pharmacological Targeting the REV-ERBs in Sleep/Wake Regulation

    PubMed Central

    Amador, Ariadna; Huitron-Resendiz, Salvador; Roberts, Amanda J.; Kamenecka, Theodore M.; Solt, Laura A.; Burris, Thomas P.

    2016-01-01

    The circadian clock maintains appropriate timing for a wide range of behaviors and physiological processes. Circadian behaviors such as sleep and wakefulness are intrinsically dependent on the precise oscillation of the endogenous molecular machinery that regulates the circadian clock. The identical core clock machinery regulates myriad endocrine and metabolic functions providing a link between sleep and metabolic health. The REV-ERBs (REV-ERBα and REV-ERBβ) are nuclear receptors that are key regulators of the molecular clock and have been successfully targeted using small molecule ligands. Recent studies in mice suggest that REV-ERB-specific synthetic agonists modulate metabolic activity as well as alter sleep architecture, inducing wakefulness during the light period. Therefore, these small molecules represent unique tools to extensively study REV-ERB regulation of sleep and wakefulness. In these studies, our aim was to further investigate the therapeutic potential of targeting the REV-ERBs for regulation of sleep by characterizing efficacy, and optimal dosing time of the REV-ERB agonist SR9009 using electroencephalographic (EEG) recordings. Applying different experimental paradigms in mice, our studies establish that SR9009 does not lose efficacy when administered more than once a day, nor does tolerance develop when administered once a day over a three-day dosing regimen. Moreover, through use of a time response paradigm, we determined that although there is an optimal time for administration of SR9009 in terms of maximal efficacy, there is a 12-hour window in which SR9009 elicited a response. Our studies indicate that the REV-ERBs are potential therapeutic targets for treating sleep problems as those encountered as a consequence of shift work or jet lag. PMID:27603791

  2. Pharmacological Targeting the REV-ERBs in Sleep/Wake Regulation.

    PubMed

    Amador, Ariadna; Huitron-Resendiz, Salvador; Roberts, Amanda J; Kamenecka, Theodore M; Solt, Laura A; Burris, Thomas P

    2016-01-01

    The circadian clock maintains appropriate timing for a wide range of behaviors and physiological processes. Circadian behaviors such as sleep and wakefulness are intrinsically dependent on the precise oscillation of the endogenous molecular machinery that regulates the circadian clock. The identical core clock machinery regulates myriad endocrine and metabolic functions providing a link between sleep and metabolic health. The REV-ERBs (REV-ERBα and REV-ERBβ) are nuclear receptors that are key regulators of the molecular clock and have been successfully targeted using small molecule ligands. Recent studies in mice suggest that REV-ERB-specific synthetic agonists modulate metabolic activity as well as alter sleep architecture, inducing wakefulness during the light period. Therefore, these small molecules represent unique tools to extensively study REV-ERB regulation of sleep and wakefulness. In these studies, our aim was to further investigate the therapeutic potential of targeting the REV-ERBs for regulation of sleep by characterizing efficacy, and optimal dosing time of the REV-ERB agonist SR9009 using electroencephalographic (EEG) recordings. Applying different experimental paradigms in mice, our studies establish that SR9009 does not lose efficacy when administered more than once a day, nor does tolerance develop when administered once a day over a three-day dosing regimen. Moreover, through use of a time response paradigm, we determined that although there is an optimal time for administration of SR9009 in terms of maximal efficacy, there is a 12-hour window in which SR9009 elicited a response. Our studies indicate that the REV-ERBs are potential therapeutic targets for treating sleep problems as those encountered as a consequence of shift work or jet lag.

  3. Rev-erbα in the brain is essential for circadian food entrainment.

    PubMed

    Delezie, Julien; Dumont, Stéphanie; Sandu, Cristina; Reibel, Sophie; Pevet, Paul; Challet, Etienne

    2016-01-01

    Foraging is costly in terms of time and energy. An endogenous food-entrainable system allows anticipation of predictable changes of food resources in nature. Yet the molecular mechanism that controls food anticipation in mammals remains elusive. Here we report that deletion of the clock component Rev-erbα impairs food entrainment in mice. Rev-erbα global knockout (GKO) mice subjected to restricted feeding showed reduced elevations of locomotor activity and body temperature prior to mealtime, regardless of the lighting conditions. The failure to properly anticipate food arrival was accompanied by a lack of phase-adjustment to mealtime of the clock protein PERIOD2 in the cerebellum, and by diminished expression of phosphorylated ERK 1/2 (p-ERK) during mealtime in the mediobasal hypothalamus and cerebellum. Furthermore, brain-specific knockout (BKO) mice for Rev-erbα display a defective suprachiasmatic clock, as evidenced by blunted daily activity under a light-dark cycle, altered free-running rhythm in constant darkness and impaired clock gene expression. Notably, brain deletion of Rev-erbα totally prevented food-anticipatory behaviour and thermogenesis. In response to restricted feeding, brain deletion of Rev-erbα impaired changes in clock gene expression in the hippocampus and cerebellum, but not in the liver. Our findings indicate that Rev-erbα is required for neural network-based prediction of food availability. PMID:27380954

  4. Rev-erbα in the brain is essential for circadian food entrainment

    PubMed Central

    Delezie, Julien; Dumont, Stéphanie; Sandu, Cristina; Reibel, Sophie; Pevet, Paul; Challet, Etienne

    2016-01-01

    Foraging is costly in terms of time and energy. An endogenous food-entrainable system allows anticipation of predictable changes of food resources in nature. Yet the molecular mechanism that controls food anticipation in mammals remains elusive. Here we report that deletion of the clock component Rev-erbα impairs food entrainment in mice. Rev-erbα global knockout (GKO) mice subjected to restricted feeding showed reduced elevations of locomotor activity and body temperature prior to mealtime, regardless of the lighting conditions. The failure to properly anticipate food arrival was accompanied by a lack of phase-adjustment to mealtime of the clock protein PERIOD2 in the cerebellum, and by diminished expression of phosphorylated ERK 1/2 (p-ERK) during mealtime in the mediobasal hypothalamus and cerebellum. Furthermore, brain-specific knockout (BKO) mice for Rev-erbα display a defective suprachiasmatic clock, as evidenced by blunted daily activity under a light-dark cycle, altered free-running rhythm in constant darkness and impaired clock gene expression. Notably, brain deletion of Rev-erbα totally prevented food-anticipatory behaviour and thermogenesis. In response to restricted feeding, brain deletion of Rev-erbα impaired changes in clock gene expression in the hippocampus and cerebellum, but not in the liver. Our findings indicate that Rev-erbα is required for neural network-based prediction of food availability. PMID:27380954

  5. Discrete Functions of Nuclear Receptor Rev-erbα Couple Metabolism to the Clock

    PubMed Central

    Zhang, Yuxiang; Fang, Bin; Emmett, Matthew J.; Damle, Manashree; Sun, Zheng; Feng, Dan; Armour, Sean M.; Remsberg, Jarrett R.; Jager, Jennifer; Soccio, Raymond E.; Steger, David J.; Lazar, Mitchell A.

    2015-01-01

    SUMMARY Circadian and metabolic physiology are intricately intertwined, as illustrated by Rev-erbα, a transcription factor (TF) that functions both as a core repressive component of the cell autonomous clock and as a regulator of metabolic genes. Here we show that Rev-erbα modulates the clock and metabolism by different genomic mechanisms. Clock control requires Rev-erbα to bind directly to the genome at its cognate sites, where it competes with activating ROR TFs. By contrast, Rev-erbα regulates metabolic genes primarily by recruiting the HDAC3 corepressor to sites to which it is tethered by cell type-specific transcription factors. Thus, direct competition between Rev-erbα and ROR TFs provides a universal mechanism for self-sustained control of molecular clock across all tissues, whereas Rev-erbα utilizes lineage-determining factors to convey a tissue-specific epigenomic rhythm that regulates metabolism tailored to the specific need of that tissue. PMID:26044300

  6. Nuclear Factor 90, a cellular dsRNA binding protein inhibits the HIV Rev-export function

    PubMed Central

    Urcuqui-Inchima, Silvio; Castaño, Maria Eugenia; Hernandez-Verdun, Danièle; St-Laurent, Georges; Kumar, Ajit

    2006-01-01

    Background The HIV Rev protein is known to facilitate export of incompletely spliced and unspliced viral transcripts to the cytoplasm, a necessary step in virus life cycle. The Rev-mediated nucleo-cytoplasmic transport of nascent viral transcripts, dependents on interaction of Rev with the RRE RNA structural element present in the target RNAs. The C-terminal variant of dsRNA-binding nuclear protein 90 (NF90ctv) has been shown to markedly attenuate viral replication in stably transduced HIV-1 target cell line. Here we examined a mechanism of interference of viral life cycle involving Rev-NF90ctv interaction. Results Since Rev:RRE complex formations depend on protein:RNA and protein:protein interactions, we investigated whether the expression of NF90ctv might interfere with Rev-mediated export of RRE-containing transcripts. When HeLa cells expressed both NF90ctv and Rev protein, we observed that NF90ctv inhibited the Rev-mediated RNA transport. In particular, three regions of NF90ctv protein are involved in blocking Rev function. Moreover, interaction of NF90ctv with the RRE RNA resulted in the expression of a reporter protein coding sequences linked to the RRE structure. Moreover, Rev influenced the subcellular localization of NF90ctv, and this process is leptomycin B sensitive. Conclusion The dsRNA binding protein, NF90ctv competes with HIV Rev function at two levels, by competitive protein:protein interaction involving Rev binding to specific domains of NF90ctv, as well as by its binding to the RRE-RNA structure. Our results are consistent with a model of Rev-mediated HIV-1 RNA export that envisions Rev-multimerization, a process interrupted by NF90ctv. PMID:17125513

  7. The vital role of polymerase ζ and REV1 in mutagenic, but not correct, DNA synthesis across benzo[a]pyrene-dG and recruitment of polymerase ζ by REV1 to replication-stalled site.

    PubMed

    Hashimoto, Keiji; Cho, Youngjin; Yang, In-Young; Akagi, Jun-ichi; Ohashi, Eiji; Tateishi, Satoshi; de Wind, Niels; Hanaoka, Fumio; Ohmori, Haruo; Moriya, Masaaki

    2012-03-16

    The DNA synthesis across DNA lesions, termed translesion synthesis (TLS), is a complex process influenced by various factors. To investigate this process in mammalian cells, we examined TLS across a benzo[a]pyrene dihydrodiol epoxide-derived dG adduct (BPDE-dG) using a plasmid bearing a single BPDE-dG and genetically engineered mouse embryonic fibroblasts (MEFs). In wild-type MEFs, TLS was extremely miscoding (>90%) with G → T transversions being predominant. Knockout of the Rev1 gene decreased both the TLS efficiency and the miscoding frequency. Knockout of the Rev3L gene, coding for the catalytic subunit of pol ζ, caused even greater decreases in these two TLS parameters; almost all residual TLS were error-free. Thus, REV1 and pol ζ are critical to mutagenic, but not accurate, TLS across BPDE-dG. The introduction of human REV1 cDNA into Rev1(-/-) MEFs restored the mutagenic TLS, but a REV1 mutant lacking the C terminus did not. Yeast and mammalian three-hybrid assays revealed that the REV7 subunit of pol ζ mediated the interaction between REV3 and the REV1 C terminus. These results support the hypothesis that REV1 recruits pol ζ through the interaction with REV7. Our results also predict the existence of a minor REV1-independent pol ζ recruitment pathway. Finally, although mutagenic TLS across BPDE-dG largely depends on RAD18, experiments using Polk(-/-) Polh(-/-) Poli(-/-) triple-gene knockout MEFs unexpectedly revealed that another polymerase(s) could insert a nucleotide opposite BPDE-dG. This indicates that a non-Y family polymerase(s) can insert a nucleotide opposite BPDE-dG, but the subsequent extension from miscoding termini depends on REV1-polζ in a RAD18-dependent manner. PMID:22303021

  8. Comment on ``Interaction of two solitary waves in quantum electron-positron-ion plasma'' [Phys. Plasmas 18, 052301 (2011)

    NASA Astrophysics Data System (ADS)

    Akbari-Moghanjoughi, M.

    2011-08-01

    Recently, Xu et al. [Phys. Plasmas 18, 052301 (2011)] have studied the effects of various plasma parameters on interaction of two ion-acoustic solitary waves in an unmagnetized three-dimensional electron-positron-ion quantum plasma. They have used the extended reductive perturbation technique, the so-called, extended Poincare-Lighthill-Kuo technique, to deduce from the model governing the quantum hydrodynamics differential equations leading to the soliton dynamical properties, namely, Korteweg-de Vries evolution equations (one for each wave) and coupled differential equations describing the phase-shift in trajectories of solitons due to the two dimensional collision. The variation of the calculated collision phase-shifts are then numerically inspected in terms of numerous plasma fractional parameters. In this comment, we give some notes specific to the validity of the results of above-mentioned article and refer to important misconceptions about the use of the Fermi-temperature in quantum plasmas, appearing in this article and many other recently published ones.

  9. Structure of the Human Rev1-DNA-dNTP Ternary Complex

    SciTech Connect

    Swan, M.; Johnson, R; Prakash, L; Prakash, S; Aggarwal, A

    2009-01-01

    Y-family DNA polymerases have proven to be remarkably diverse in their functions and in strategies for replicating through DNA lesions. The structure of yeast Rev1 ternary complex has revealed the most radical replication strategy, where the polymerase itself dictates the identity of the incoming nucleotide, as well as the identity of the templating base. We show here that many of the key elements of this highly unusual strategy are conserved between yeast and human Rev1, including the eviction of template G from the DNA helix and the pairing of incoming deoxycytidine 5'-triphosphate with a surrogate arginine residue. We also show that the catalytic core of human Rev1 is uniquely augmented by two large inserts, I1 and I2, wherein I1 extends > 20 A away from the active site and may serve as a platform for protein-protein interactions specific for Rev1's role in translesion DNA synthesis in human cells, and I2 acts as a 'flap' on the hydrophobic pocket accommodating template G. We suggest that these novel structural features are important for providing human Rev1 greater latitude in promoting efficient and error-free translesion DNA synthesis through the diverse array of bulky and potentially carcinogenic N2-deoxyguanosine DNA adducts in human cells.

  10. A rev1-vpu polymorphism unique to HIV-1 subtype A and C strains impairs envelope glycoprotein expression from rev-vpu-env cassettes and reduces virion infectivity in pseudotyping assays

    SciTech Connect

    Kraus, Matthias H.; Parrish, Nicholas F.; Shaw, Katharina S.; Decker, Julie M.; Keele, Brandon F.; Salazar-Gonzalez, Jesus F.; Grayson, Truman; McPherson, David T.; Ping, Li-Hua; Anderson, Jeffrey A.; Swanstrom, Ronald; Williamson, Carolyn; Shaw, George M.; Hahn, Beatrice H.

    2010-02-20

    Functional studies of HIV-1 envelope glycoproteins (Envs) commonly include the generation of pseudoviruses, which are produced by co-transfection of rev-vpu-env cassettes with an env-deficient provirus. Here, we describe six Env constructs from transmitted/founder HIV-1 that were defective in the pseudotyping assay, although two produced infectious virions when expressed from their cognate proviruses. All of these constructs exhibited an unusual gene arrangement in which the first exon of rev (rev1) and vpu were in the same reading frame without an intervening stop codon. Disruption of the rev1-vpu fusion gene by frameshift mutation, stop codon, or abrogation of the rev initiation codon restored pseudovirion infectivity. Introduction of the fusion gene into wildtype Env cassettes severely compromised their function. The defect was not due to altered env and rev transcription or a dominant negative effect of the expressed fusion protein, but seemed to be caused by inefficient translation at the env initiation codon. Although the rev1-vpu polymorphism affects Env expression only in vitro, it can cause problems in studies requiring Env complementation, such as analyses of co-receptor usage and neutralization properties, since 3% of subtype A, 20% of subtype C and 5% of CRF01{sub A}/E viruses encode the fusion gene. A solution is to eliminate the rev initiation codon when amplifying rev-vpu-env cassettes since this increases Env expression irrespective of the presence of the polymorphism.

  11. The strength of the HIV-1 3' splice sites affects Rev function

    PubMed Central

    Kammler, Susanne; Otte, Marianne; Hauber, Ilona; Kjems, Jørgen; Hauber, Joachim; Schaal, Heiner

    2006-01-01

    Background The HIV-1 Rev protein is a key component in the early to late switch in HIV-1 splicing from early intronless (e.g. tat, rev) to late intron-containing Rev-dependent (e.g. gag, vif, env) transcripts. Previous results suggested that cis-acting sequences and inefficient 5' and 3' splice sites are a prerequisite for Rev function. However, we and other groups have shown that two of the HIV-1 5' splice sites, D1 and D4, are efficiently used in vitro and in vivo. Here, we focus on the efficiency of the HIV-1 3' splice sites taking into consideration to what extent their intrinsic efficiencies are modulated by their downstream cis-acting exonic sequences. Furthermore, we delineate their role in RNA stabilization and Rev function. Results In the presence of an efficient upstream 5' splice site the integrity of the 3' splice site is not essential for Rev function whereas an efficient 3' splice site impairs Rev function. The detrimental effect of a strong 3' splice site on the amount of Rev-dependent intron-containing HIV-1 glycoprotein coding (env) mRNA is not compensatable by weakening the strength of the upstream 5' splice site. Swapping the HIV-1 3' splice sites in an RRE-containing minigene, we found a 3' splice site usage which was variably dependent on the presence of the usual downstream exonic sequence. The most evident activation of 3' splice site usage by its usual downstream exonic sequence was observed for 3' splice site A1 which was turned from an intrinsic very weak 3' splice site into the most active 3' splice site, even abolishing Rev activity. Performing pull-down experiments with nuclear extracts of HeLa cells we identified a novel ASF/SF2-dependent exonic splicing enhancer (ESE) within HIV-1 exon 2 consisting of a heptameric sequence motif occurring twice (M1 and M2) within this short non-coding leader exon. Single point mutation of M1 within an infectious molecular clone is detrimental for HIV-1 exon 2 recognition without affecting Rev

  12. Response to 'Comment on 'Continuum modes in rotating plasmas: General equations and continuous spectra for large aspect ratio tokamaks' '[Phys. Plasmas 19, 064701 (2012)

    SciTech Connect

    Lakhin, V. P.; Ilgisonis, V. I.

    2012-06-15

    The equations for the continuous spectra derived in our paper [V. P. Lakhin and V. I. Ilgisonis, Phys. Plasmas 18, 092103 (2011)] can be reduced to the matrix form used by Goedbloed et al.[Phys. Plasmas 11, 28 (2004)]. It is shown that the assumptions made in our paper provide the elliptic flow regime and guarantee the existence of plasma equilibrium with nested magnetic surfaces of circular cross-section. The new results on magnetohydrodynamic instabilities of such tokamak equilibria obtained in our paper but absent in the paper by Goedbloed et al. are emphasized.

  13. Interaction between the Rev1 C-terminal Domain and the PolD3 Subunit of Polζ Suggests a Mechanism of Polymerase Exchange upon Rev1/Polζ-Dependent Translesion Synthesis

    PubMed Central

    Pustovalova, Yulia; Magalhães, Mariana T. Q.; D’Souza, Sanjay; Rizzo, Alessandro A.; Korza, George; Walker, Graham C.; Korzhnev, Dmitry M.

    2016-01-01

    Translesion synthesis (TLS) is a mutagenic branch of cellular DNA damage tolerance that enables bypass replication over DNA lesions carried out by specialized low-fidelity DNA polymerases. The replicative bypass of most types of DNA damage is performed in a two-step process of Rev1/Polζ-dependent TLS. In the first step, a Y-family TLS enzyme, typically Polη, Polι or Polκ, inserts a nucleotide across DNA lesion. In the second step, a four-subunit B-family DNA polymerase Polζ (Rev3/Rev7/PolD2/PolD3 complex) extends the distorted DNA primer-template. The coordinated action of error-prone TLS enzymes is regulated through their interactions with the two scaffold proteins, the sliding clamp PCNA and the TLS polymerase Rev1. Rev1 interactions with all other TLS enzymes are mediated by its C-terminal domain (Rev1-CT), which can simultaneously bind the Rev7 subunit of Polζ and Rev1-interacting regions (RIRs) from Polη, Polι or Polκ. In this work, we identified a previously unknown RIR motif in the C-terminal part of PolD3 subunit of Polζ whose interaction with the Rev1-CT is among the tightest mediated by RIR motifs. Three-dimensional structure of the Rev1-CT/PolD3-RIR complex determined by NMR spectroscopy revealed a structural basis for the relatively high affinity of this interaction. The unexpected discovery of PolD3-RIR motif suggests a mechanism of 'inserter' to 'extender' DNA polymerase switch upon Rev1/Polζ-dependent TLS, in which the PolD3-RIR binding to the Rev1-CT (i) helps displace the 'inserter' Polη, Polι or Polκ from its complex with Rev1, and (ii) facilitates assembly of the four-subunit 'extender' Polζ through simultaneous interaction of Rev1-CT with Rev7 and PolD3 subunits. PMID:26982350

  14. Interaction between the Rev1 C-Terminal Domain and the PolD3 Subunit of Polζ Suggests a Mechanism of Polymerase Exchange upon Rev1/Polζ-Dependent Translesion Synthesis.

    PubMed

    Pustovalova, Yulia; Magalhães, Mariana T Q; D'Souza, Sanjay; Rizzo, Alessandro A; Korza, George; Walker, Graham C; Korzhnev, Dmitry M

    2016-04-01

    Translesion synthesis (TLS) is a mutagenic branch of cellular DNA damage tolerance that enables bypass replication over DNA lesions carried out by specialized low-fidelity DNA polymerases. The replicative bypass of most types of DNA damage is performed in a two-step process of Rev1/Polζ-dependent TLS. In the first step, a Y-family TLS enzyme, typically Polη, Polι, or Polκ, inserts a nucleotide across a DNA lesion. In the second step, a four-subunit B-family DNA polymerase Polζ (Rev3/Rev7/PolD2/PolD3 complex) extends the distorted DNA primer-template. The coordinated action of error-prone TLS enzymes is regulated through their interactions with the two scaffold proteins, the sliding clamp PCNA and the TLS polymerase Rev1. Rev1 interactions with all other TLS enzymes are mediated by its C-terminal domain (Rev1-CT), which can simultaneously bind the Rev7 subunit of Polζ and Rev1-interacting regions (RIRs) from Polη, Polι, or Polκ. In this work, we identified a previously unknown RIR motif in the C-terminal part of PolD3 subunit of Polζ whose interaction with the Rev1-CT is among the tightest mediated by RIR motifs. Three-dimensional structure of the Rev1-CT/PolD3-RIR complex determined by NMR spectroscopy revealed a structural basis for the relatively high affinity of this interaction. The unexpected discovery of PolD3-RIR motif suggests a mechanism of "inserter" to "extender" DNA polymerase switch upon Rev1/Polζ-dependent TLS, in which the PolD3-RIR binding to the Rev1-CT (i) helps displace the "inserter" Polη, Polι, or Polκ from its complex with Rev1, and (ii) facilitates assembly of the four-subunit "extender" Polζ through simultaneous interaction of Rev1-CT with Rev7 and PolD3 subunits.

  15. Unprecedented NES non-antagonistic inhibitor for nuclear export of Rev from Sida cordifolia.

    PubMed

    Tamura, Satoru; Kaneko, Masafumi; Shiomi, Atsushi; Yang, Guang-Ming; Yamaura, Toshiaki; Murakami, Nobutoshi

    2010-03-15

    Bioassay-guided separation from the MeOH extract of the South American medicinal plant Sida cordifolia resulted in isolation of (10E,12Z)-9-hydroxyoctadeca-10,12-dienoic acid (1) as an unprecedented NES non-antagonistic inhibitor for nuclear export of Rev. This mechanism of action was established by competitive experiment by the biotinylated probe derived from leptomycin B, the known NES antagonistic inhibitor. Additionally, structure-activity relationship analysis by use of the synthesized analogs clarified cooperation of several functionalities in the Rev-export inhibitory activity of 1.

  16. Comment on ``Barut-Girardello and Klauder-Perelomov coherent states for the Kravchuk functions'' [J. Math. Phys. 48, 112106 (2007)

    NASA Astrophysics Data System (ADS)

    Fakhri, H.; Dehghani, A.

    2008-04-01

    We call attention to the misconstructions in a paper recently published in this journal [A. Chenaghlou and O. Faizy, J. Math. Phys. 48, 112106 (2007)]. It is shown that the constructed Barut-Girardello coherent states are problematic from the view points of the definition and the measure. The claimed coherencies for the Kravchuk functions cannot actually exist.

  17. Comment on ``The effects of Si doping on dislocation movement and tensile stress in GaN films'' [J. Appl. Phys. 109, 073509 (2011)

    NASA Astrophysics Data System (ADS)

    Dadgar, A.; Krost, A.

    2011-11-01

    In the publication by Moram et al. [J. Appl. Phys. 109, 073509 (2011)], some statements were made which disagree with the measurements presented by the authors of the article. In particular, silicon doping is claimed to suppress dislocation movement in GaN epitaxy hampering stress reduction during growth. We show that the data indeed prove the opposite, in agreement with prior publications.

  18. Note: Derivation of two-photon circular dichroism--Addendum to "Two-photon circular dichroism" [J. Chem. Phys. 62, 1006 (1975)].

    PubMed

    Friese, Daniel H

    2015-09-01

    This addendum shows the detailed derivation of the fundamental equations for two-photon circular dichroism which are given in a very condensed form in the original publication [I. Tinoco, J. Chem. Phys. 62, 1006 (1975)]. In addition, some minor errors are corrected and some of the derivations in the original publication are commented.

  19. Response to ``Comment on `Slow Debye-type peak observed in the dielectric response of polyalcohols' '' [J. Chem. Phys. 134, 037101 (2011)

    NASA Astrophysics Data System (ADS)

    Bergman, R.; Jansson, H.; Swenson, J.

    2011-01-01

    In our recent article [R. Bergman et al., J. Chem. Phys. 132, 044504 (2010)] we investigated some polyalcohols, i.e., glycerol, xylitol, and sorbitol by dielectric spectroscopy. In the study, a low-frequency peak of Debye character that normally is hidden by the large low-frequency dispersion due to conductivity was revealed by analyzing the real part of the permittivity and by using a thin Teflon film to suppress the low-frequency dispersion. We agree with the comment by Paluch et al. [J. Chem. Phys. 134, 037101 (2011)] that the Teflon film setup will indeed create a peak due to the dc conductivity. However, due to the fact that the location of the peak was almost identical in measurement with and without Teflon, we unfortunately mainly showed the data measured with Teflon, despite that it could also be observed in the real part of the permittivity without using the Teflon setup, as shown in our original article [R. Bergman et al., J. Chem. Phys. 132, 044504 (2010)]. Here, we show that the low-frequency peak of Debye character can also be observed by subtracting the dc conductivity. Furthermore, we show that the modulus representation used in Paluch et al. [J. Chem. Phys. 134, 037101 (2011).] is also not suitable for detecting processes hidden by the conductivity.

  20. Note: Derivation of two-photon circular dichroism—Addendum to “Two-photon circular dichroism” [J. Chem. Phys. 62, 1006 (1975)

    SciTech Connect

    Friese, Daniel H.

    2015-09-07

    This addendum shows the detailed derivation of the fundamental equations for two-photon circular dichroism which are given in a very condensed form in the original publication [I. Tinoco, J. Chem. Phys. 62, 1006 (1975)]. In addition, some minor errors are corrected and some of the derivations in the original publication are commented.

  1. Comment on 'Wave functions for a Duffin-Kemmer-Petiau particle in a time-dependent potential' [J. Math. Phys. 48, 073515 (2007)

    SciTech Connect

    Castro, L. B.; Castro, A. S. de

    2010-03-15

    It is shown that the paper 'Wave functions for a Duffin-Kemmer-Petiau particle in a time-dependent potential' by Merad and Bensaid [J. Math. Phys. 48, 073515 (2007)] is not correct in using inadvertently a non-Hermitian Hamiltonian in a formalism that does require Hermitian Hamiltonians.

  2. Bioavailable inhibitors of HIV-1 RNA biogenesis identified through a Rev-based screen.

    PubMed

    Prado, Silvia; Beltrán, Manuela; Coiras, Mayte; Bedoya, Luis M; Alcamí, José; Gallego, José

    2016-05-01

    New antiretroviral agents with alternative mechanisms are needed to complement the combination therapies used to treat HIV-1 infections. Here we report the identification of bioavailable molecules that interfere with the gene expression processes of HIV-1. The compounds were detected by screening a small library of FDA-approved drugs with an assay based on measuring the displacement of Rev, and essential virus-encoded protein, from its high-affinity RNA binding site. The antiretroviral activity of two hits was based on interference with post-integration steps of the HIV-1 cycle. Both hits inhibited RRE-Rev complex formation in vitro, and blocked LTR-dependent gene expression and viral transcription in cellular assays. The best compound altered the splicing pattern of HIV-1 transcripts in a manner consistent with Rev inhibition. This mechanism of action is different from those used by current antiretroviral agents. The screening hits recognized the Rev binding site in the viral RNA, and the best compound did so with substantial selectivity, allowing the identification of a new RNA-binding scaffold. These results may be used for developing novel antiretroviral drugs.

  3. Comparative proteome analysis of Brucella melitensis vaccine strain Rev 1 and a virulent strain, 16M.

    PubMed

    Eschenbrenner, Michel; Wagner, Mary Ann; Horn, Troy A; Kraycer, Jo Ann; Mujer, Cesar V; Hagius, Sue; Elzer, Philip; DelVecchio, Vito G

    2002-09-01

    The genus Brucella consists of bacterial pathogens that cause brucellosis, a major zoonotic disease characterized by undulant fever and neurological disorders in humans. Among the different Brucella species, Brucella melitensis is considered the most virulent. Despite successful use in animals, the vaccine strains remain infectious for humans. To understand the mechanism of virulence in B. melitensis, the proteome of vaccine strain Rev 1 was analyzed by two-dimensional gel electrophoresis and compared to that of virulent strain 16M. The two strains were grown under identical laboratory conditions. Computer-assisted analysis of the two B. melitensis proteomes revealed proteins expressed in either 16M or Rev 1, as well as up- or down-regulation of proteins specific for each of these strains. These proteins were identified by peptide mass fingerprinting. It was found that certain metabolic pathways may be deregulated in Rev 1. Expression of an immunogenic 31-kDa outer membrane protein, proteins utilized for iron acquisition, and those that play a role in sugar binding, lipid degradation, and amino acid binding was altered in Rev 1.

  4. De novo mutations in PLXND1 and REV3L cause Möbius syndrome

    PubMed Central

    Tomas-Roca, Laura; Tsaalbi-Shtylik, Anastasia; Jansen, Jacob G.; Singh, Manvendra K.; Epstein, Jonathan A.; Altunoglu, Umut; Verzijl, Harriette; Soria, Laura; van Beusekom, Ellen; Roscioli, Tony; Iqbal, Zafar; Gilissen, Christian; Hoischen, Alexander; de Brouwer, Arjan P. M.; Erasmus, Corrie; Schubert, Dirk; Brunner, Han; Pérez Aytés, Antonio; Marin, Faustino; Aroca, Pilar; Kayserili, Hülya; Carta, Arturo; de Wind, Niels; Padberg, George W.; van Bokhoven, Hans

    2015-01-01

    Möbius syndrome (MBS) is a neurological disorder that is characterized by paralysis of the facial nerves and variable other congenital anomalies. The aetiology of this syndrome has been enigmatic since the initial descriptions by von Graefe in 1880 and by Möbius in 1888, and it has been debated for decades whether MBS has a genetic or a non-genetic aetiology. Here, we report de novo mutations affecting two genes, PLXND1 and REV3L in MBS patients. PLXND1 and REV3L represent totally unrelated pathways involved in hindbrain development: neural migration and DNA translesion synthesis, essential for the replication of endogenously damaged DNA, respectively. Interestingly, analysis of Plxnd1 and Rev3l mutant mice shows that disruption of these separate pathways converge at the facial branchiomotor nucleus, affecting either motoneuron migration or proliferation. The finding that PLXND1 and REV3L mutations are responsible for a proportion of MBS patients suggests that de novo mutations in other genes might account for other MBS patients. PMID:26068067

  5. REV7 counteracts DNA double-strand break resection and affects PARP inhibition.

    PubMed

    Xu, Guotai; Chapman, J Ross; Brandsma, Inger; Yuan, Jingsong; Mistrik, Martin; Bouwman, Peter; Bartkova, Jirina; Gogola, Ewa; Warmerdam, Daniël; Barazas, Marco; Jaspers, Janneke E; Watanabe, Kenji; Pieterse, Mark; Kersbergen, Ariena; Sol, Wendy; Celie, Patrick H N; Schouten, Philip C; van den Broek, Bram; Salman, Ahmed; Nieuwland, Marja; de Rink, Iris; de Ronde, Jorma; Jalink, Kees; Boulton, Simon J; Chen, Junjie; van Gent, Dik C; Bartek, Jiri; Jonkers, Jos; Borst, Piet; Rottenberg, Sven

    2015-05-28

    Error-free repair of DNA double-strand breaks (DSBs) is achieved by homologous recombination (HR), and BRCA1 is an important factor for this repair pathway. In the absence of BRCA1-mediated HR, the administration of PARP inhibitors induces synthetic lethality of tumour cells of patients with breast or ovarian cancers. Despite the benefit of this tailored therapy, drug resistance can occur by HR restoration. Genetic reversion of BRCA1-inactivating mutations can be the underlying mechanism of drug resistance, but this does not explain resistance in all cases. In particular, little is known about BRCA1-independent restoration of HR. Here we show that loss of REV7 (also known as MAD2L2) in mouse and human cell lines re-establishes CTIP-dependent end resection of DSBs in BRCA1-deficient cells, leading to HR restoration and PARP inhibitor resistance, which is reversed by ATM kinase inhibition. REV7 is recruited to DSBs in a manner dependent on the H2AX-MDC1-RNF8-RNF168-53BP1 chromatin pathway, and seems to block HR and promote end joining in addition to its regulatory role in DNA damage tolerance. Finally, we establish that REV7 blocks DSB resection to promote non-homologous end-joining during immunoglobulin class switch recombination. Our results reveal an unexpected crucial function of REV7 downstream of 53BP1 in coordinating pathological DSB repair pathway choices in BRCA1-deficient cells.

  6. REV7 counteracts DNA double-strand break resection and impacts PARP inhibition

    PubMed Central

    Xu, Guotai; Yuan, Jingsong; Mistrik, Martin; Bouwman, Peter; Bartkova, Jirina; Gogola, Ewa; Warmerdam, Daniël; Barazas, Marco; Jaspers, Janneke E.; Watanabe, Kenji; Pieterse, Mark; Kersbergen, Ariena; Sol, Wendy; Celie, Patrick H. N.; Schouten, Philip C.; van den Broek, Bram; Salman, Ahmed; Nieuwland, Marja; de Rink, Iris; de Ronde, Jorma; Jalink, Kees; Boulton, Simon J.; Chen, Junjie; van Gent, Dik C.; Bartek, Jiri; Jonkers, Jos; Borst, Piet; Rottenberg, Sven

    2015-01-01

    Summary Error-free repair of DNA double-strand breaks (DSB) is achieved by homologous recombination (HR), and BRCA1 is an important factor for this repair pathway1. In the absence of BRCA1-mediated HR, administration of PARP inhibitors induces synthetic lethality of tumor cells of patients with breast or ovarian cancers2,3. Despite the benefit of this tailored therapy, drug resistance can occur by HR restoration4. Genetic reversion of BRCA1-inactivating mutations can be the underlying mechanism of drug resistance, but this does not explain resistance in all cases5. In particular, little is known about BRCA1-independent restoration of HR. Here, we show that loss of REV7 (also known as MAD2L2) re-establishes CtIP-dependent end resection of DSBs in BRCA1-deficient cells, leading to HR restoration and PARP inhibitor resistance, reversed by ATM kinase inhibition. REV7 is recruited to DSBs in a manner dependent on the H2AX-MDC1-RNF8-RNF168-53BP1 chromatin pathway, and appears to block HR and promote end joining in addition to its regulatory role in DNA damage tolerance6. Finally, we establish that REV7 blocks DSB resection to promote non-homologous end-joining (NHEJ) during immunoglobulin class switch recombination. Our results reveal an unexpected critical function of REV7 downstream of 53BP1 in coordinating pathological DSB repair pathway choices in BRCA1-deficient cells. PMID:25799992

  7. Athabaskan Stories from Anvik. Rev. John W. Chapman's "Ten'a Texts and Tales."

    ERIC Educational Resources Information Center

    Chapman, John W.; Kari, James, Ed.

    Sixteen Deg Hit'an (Ingalik) Athabaskan stories recorded by Rev. John W. Chapman during 1887-1905 in Anvik, Alaska, are presented. The stories are retranscribed with the help of current Deg Hit'an speakers, and are accompanied by both interlinear and free translations in English. The materials are intended to serve as reading material for students…

  8. De novo mutations in PLXND1 and REV3L cause Möbius syndrome.

    PubMed

    Tomas-Roca, Laura; Tsaalbi-Shtylik, Anastasia; Jansen, Jacob G; Singh, Manvendra K; Epstein, Jonathan A; Altunoglu, Umut; Verzijl, Harriette; Soria, Laura; van Beusekom, Ellen; Roscioli, Tony; Iqbal, Zafar; Gilissen, Christian; Hoischen, Alexander; de Brouwer, Arjan P M; Erasmus, Corrie; Schubert, Dirk; Brunner, Han; Pérez Aytés, Antonio; Marin, Faustino; Aroca, Pilar; Kayserili, Hülya; Carta, Arturo; de Wind, Niels; Padberg, George W; van Bokhoven, Hans

    2015-01-01

    Möbius syndrome (MBS) is a neurological disorder that is characterized by paralysis of the facial nerves and variable other congenital anomalies. The aetiology of this syndrome has been enigmatic since the initial descriptions by von Graefe in 1880 and by Möbius in 1888, and it has been debated for decades whether MBS has a genetic or a non-genetic aetiology. Here, we report de novo mutations affecting two genes, PLXND1 and REV3L in MBS patients. PLXND1 and REV3L represent totally unrelated pathways involved in hindbrain development: neural migration and DNA translesion synthesis, essential for the replication of endogenously damaged DNA, respectively. Interestingly, analysis of Plxnd1 and Rev3l mutant mice shows that disruption of these separate pathways converge at the facial branchiomotor nucleus, affecting either motoneuron migration or proliferation. The finding that PLXND1 and REV3L mutations are responsible for a proportion of MBS patients suggests that de novo mutations in other genes might account for other MBS patients. PMID:26068067

  9. 75 FR 53738 - Proposed Collection; Comment Request for Rev. Proc. 2007-35

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-01

    ... Internal Revenue Service Proposed Collection; Comment Request for Rev. Proc. 2007-35 AGENCY: Internal... 2007-35, Statistical Sampling for purposes of Section 199. DATES: Written comments should be received... 199. OMB Number: 1545-2072. Revenue Procedure Number: RP-2007-35. Abstract: This revenue...

  10. Borrelia burgdorferi RevA Significantly Affects Pathogenicity and Host Response in the Mouse Model of Lyme Disease

    PubMed Central

    Byram, Rebecca; Gaultney, Robert A.; Floden, Angela M.; Hellekson, Christopher; Stone, Brandee L.; Bowman, Amy; Stevenson, Brian; Johnson, Barbara J. B.

    2015-01-01

    The Lyme disease spirochete, Borrelia burgdorferi, expresses RevA and numerous outer surface lipoproteins during mammalian infection. As an adhesin that promotes bacterial interaction with fibronectin, RevA is poised to interact with the extracellular matrix of the host. To further define the role(s) of RevA during mammalian infection, we created a mutant that is unable to produce RevA. The mutant was still infectious to mice, although it was significantly less well able to infect cardiac tissues. Complementation of the mutant with a wild-type revA gene restored heart infectivity to wild-type levels. Additionally, revA mutants led to increased evidence of arthritis, with increased fibrotic collagen deposition in tibiotarsal joints. The mutants also induced increased levels of the chemokine CCL2, a monocyte chemoattractant, in serum, and this increase was abolished in the complemented strain. Therefore, while revA is not absolutely essential for infection, deletion of revA had distinct effects on dissemination, arthritis severity, and host response. PMID:26150536

  11. 75 FR 27840 - NUREG-0654/FEMA-REP-1, Rev. 1, Supplement 3, Guidance for Protective Action Recommendations for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-18

    ...: extension of comment period. SUMMARY: On March 8, 2010, (75 FR 10524), the Nuclear Regulatory Commission (NRC) published for public comment a document entitled: ``NUREG-0654/FEMA-REP-1, Rev. 1, Supplement 3... COMMISSION NUREG-0654/FEMA-REP-1, Rev. 1, Supplement 3, Guidance for Protective Action Recommendations...

  12. REV-ERB-ALPHA circadian gene variant associates with obesity in two independent populations: Mediterranean and North American

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Despite the solid connection between REV-ERB and obesity, the information about whether genetic variations at this locus may be associated with obesity traits is scarce. Therefore our objective was to study the association between REV-ERB-ALPHA1 rs2314339 and obesity in two independent populations. ...

  13. Borrelia burgdorferi RevA Significantly Affects Pathogenicity and Host Response in the Mouse Model of Lyme Disease.

    PubMed

    Byram, Rebecca; Gaultney, Robert A; Floden, Angela M; Hellekson, Christopher; Stone, Brandee L; Bowman, Amy; Stevenson, Brian; Johnson, Barbara J B; Brissette, Catherine A

    2015-09-01

    The Lyme disease spirochete, Borrelia burgdorferi, expresses RevA and numerous outer surface lipoproteins during mammalian infection. As an adhesin that promotes bacterial interaction with fibronectin, RevA is poised to interact with the extracellular matrix of the host. To further define the role(s) of RevA during mammalian infection, we created a mutant that is unable to produce RevA. The mutant was still infectious to mice, although it was significantly less well able to infect cardiac tissues. Complementation of the mutant with a wild-type revA gene restored heart infectivity to wild-type levels. Additionally, revA mutants led to increased evidence of arthritis, with increased fibrotic collagen deposition in tibiotarsal joints. The mutants also induced increased levels of the chemokine CCL2, a monocyte chemoattractant, in serum, and this increase was abolished in the complemented strain. Therefore, while revA is not absolutely essential for infection, deletion of revA had distinct effects on dissemination, arthritis severity, and host response.

  14. Rev-erbalpha gene expression in the mouse brain with special emphasis on its circadian profiles in the suprachiasmatic nucleus.

    PubMed

    Onishi, Hiroyasu; Yamaguchi, Shun; Yagita, Kazuhiro; Ishida, Yoshiki; Dong, Xin; Kimura, Hidehito; Jing, Zhang; Ohara, Hidefumi; Okamura, Hitoshi

    2002-06-01

    Rev-erbalpha is an orphan nuclear receptor that constitutively suppresses gene transcription. In the present study, the expression of Rev-erbalpha was investigated in the mouse brain by in situ hybridization using antisense cRNA probe. Positive Rev-erbalpha mRNA signals were detected widely in the brain with the highest expression in the suprachiasmatic nucleus (SCN). In the constant dark condition, the circadian expression profiles of Rev-erbalpha m RNA in the SCN showed a peak at early daytime (CT4) and a trough at early night time (CT16). The environmental lighting condition (light-dark environmental condition and exposure in the subjective night) did not alter the expression profiles. These findings indicate that Rev-erbalpha gene is a transcription factor intimately related to the circadian clock in the SCN.

  15. Identification of Brucella melitensis Rev.1 vaccine-strain genetic markers: Towards understanding the molecular mechanism behind virulence attenuation.

    PubMed

    Issa, Mohammad Nouh; Ashhab, Yaqoub

    2016-09-22

    Brucella melitensis Rev.1 is an avirulent strain that is widely used as a live vaccine to control brucellosis in small ruminants. Although an assembled draft version of Rev.1 genome has been available since 2009, this genome has not been investigated to characterize this important vaccine. In the present work, we used the draft genome of Rev.1 to perform a thorough genomic comparison and sequence analysis to identify and characterize the panel of its unique genetic markers. The draft genome of Rev.1 was compared with genome sequences of 36 different Brucella melitensis strains from the Brucella project of the Broad Institute of MIT and Harvard. The comparative analyses revealed 32 genetic alterations (30 SNPs, 1 single-bp insertion and 1 single-bp deletion) that are exclusively present in the Rev.1 genome. In silico analyses showed that 9 out of the 17 non-synonymous mutations are deleterious. Three ABC transporters are among the disrupted genes that can be linked to virulence attenuation. Out of the 32 mutations, 11 Rev.1 specific markers were selected to test their potential to discriminate Rev.1 using a bi-directional allele-specific PCR assay. Six markers were able to distinguish between Rev.1 and a set of control strains. We succeeded in identifying a panel of 32 genome-specific markers of the B. melitensis Rev.1 vaccine strain. Extensive in silico analysis showed that a considerable number of these mutations could severely affect the function of the associated genes. In addition, some of the discovered markers were able to discriminate Rev.1 strain from a group of control strains using practical PCR tests that can be applied in resource-limited settings. PMID:27595444

  16. A Naturally Occurring rev1-vpu Fusion Gene Does Not Confer a Fitness Advantage to HIV-1

    PubMed Central

    Langer, Simon M.; Hopfensperger, Kristina; Iyer, Shilpa S.; Kreider, Edward F.; Learn, Gerald H.; Lee, Lan-Hui; Hahn, Beatrice H.; Sauter, Daniel

    2015-01-01

    Background Pandemic strains of HIV-1 (group M) encode a total of nine structural (gag, pol, env), regulatory (rev, tat) and accessory (vif, vpr, vpu, nef) genes. However, some subtype A and C viruses exhibit an unusual gene arrangement in which the first exon of rev (rev1) and the vpu gene are placed in the same open reading frame. Although this rev1-vpu gene fusion is present in a considerable fraction of HIV-1 strains, its functional significance is unknown. Results Examining infectious molecular clones (IMCs) of HIV-1 that encode the rev1-vpu polymorphism, we show that a fusion protein is expressed in infected cells. Due to the splicing pattern of viral mRNA, however, these same IMCs also express a regular Vpu protein, which is produced at much higher levels. To investigate the function of the fusion gene, we characterized isogenic IMC pairs differing only in their ability to express a Rev1-Vpu protein. Analysis in transfected HEK293T and infected CD4+ T cells showed that all of these viruses were equally active in known Vpu functions, such as down-modulation of CD4 or counteraction of tetherin. Furthermore, the polymorphism did not affect Vpu-mediated inhibition of NF-кB activation or Rev-dependent nuclear export of incompletely spliced viral mRNAs. There was also no evidence for enhanced replication of Rev1-Vpu expressing viruses in primary PBMCs or ex vivo infected human lymphoid tissues. Finally, the frequency of HIV-1 quasispecies members that encoded a rev1-vpu fusion gene did not change in HIV-1 infected individuals over time. Conclusions Expression of a rev1-vpu fusion gene does not affect regular Rev and Vpu functions or alter HIV-1 replication in primary target cells. Since there is no evidence for increased replication fitness of rev1-vpu encoding viruses, this polymorphism likely emerged in the context of other mutations within and/or outside the rev1-vpu intergenic region, and may have a neutral phenotype. PMID:26554585

  17. Response to “Comment on ‘Stationary self-focusing of Gaussian laser beam in relativistic thermal quantum plasma’” [Phys. Plasmas 21, 064701 (2014)

    SciTech Connect

    Patil, S. D.; Takale, M. V.

    2014-06-15

    Habibi and Ghamari have presented a Comment on our paper [Phys. Plasmas 20, 072703 (2013)] by examining quantum dielectric response in thermal quantum plasma. They have modeled the relativistic self-focusing of Gaussian laser beam in cold and warm quantum plasmas and reported that self-focusing length does not change in both situations. In this response, we have reached the following important conclusions about the comment itself.

  18. Response to 'Comment on 'Solitary waves and double layers in an ultra-relativistic degenerate dusty electron-positron-ion plasma' '[Phys. Plasmas 19, 064703 (2012)

    SciTech Connect

    Roy, N.

    2012-06-15

    The investigation of the occurrence of nonlinear electrostatic waves (viz., solitary waves and double layers) in degenerate plasmas was the main concern of the article presented by Roy et al.[Phys. Plasmas 19, 033705 (2012)]. The equations of state used in the article were the limits explained by Chandrasekhar [Mon. Not. R. Astron. Soc. 170, 405 (1935)]. It was designated as 'misleading' by some authors, which is opposed in this reply with explanation.

  19. Comment on “General rotating quantum vortex filaments in the low-temperature Svistunov model of the local induction approximation” [Phys. Fluids 26, 065105 (2014)

    SciTech Connect

    Hietala, Niklas Hänninen, Risto

    2014-11-15

    Van Gorder considers a formulation of the local induction approximation, which allows the vortex to move in the direction of the reference axis [“General rotating quantum vortex filaments in the low-temperature Svistunov model of the local induction approximation,” Phys. Fluids 26, 065105 (2014)]. However, in his analytical and numerical study he does not use it. A mistake in the torsion of a helical vortex is also corrected.

  20. Comment on ``Scattering length for fermionic alkali atoms". by S. Gautam and D. Angom, Eur. Phys. J. D 56, 173-179 (2010)

    NASA Astrophysics Data System (ADS)

    Ouerdane, H.; Jamieson, M. J.

    2010-04-01

    We suggest that Gautam and Angom [Eur. Phys. J. D 56, 173 (2010)] underestimated the influence of the van der Waals dispersion forces at long range on their calculated low energy scattering parameters and we provide numerical evidence in support. We also provide a simple proof of the relation between s-wave and p-wave scattering parameters and we comment briefly on the semiclassical formula derived by these authors.

  1. Mutational analysis of the human immunodeficiency virus type 1 Rev transactivator: essential residues near the amino terminus.

    PubMed Central

    Hope, T J; McDonald, D; Huang, X J; Low, J; Parslow, T G

    1990-01-01

    The expression of certain mRNAs from human immunodeficiency virus type 1 (HIV-1) is controlled by the viral transactivator Rev, a nucleolar protein that binds a cis-acting element in these mRNAs. Rev is encoded by two viral exons that specify amino acids 1 to 26 and 27 to 116, respectively. Earlier studies have mapped essential regions of the protein that are encoded in the second exon. By further mutational analysis of Rev, we have now identified a novel locus encoded by the first exon that also is essential for transactivation in vivo. Defined by mutations at residues 14 to 20, this locus coincides with a cluster of positively charged and nonpolar amino acids that is conserved in Rev proteins of all known primate immunodeficiency viruses. Rev proteins that contained mutations at this site were defective in both nuclear localization and transactivation and did not function as trans-dominant inhibitors of wild-type Rev. Fusion of these mutants to a heterologous nuclear protein complemented the defect in localization but did not restore biological activity. Our findings suggest that this N-terminal locus may play a direct role in transactivation, perhaps contributing to essential protein-protein interactions or forming part of the RNA-binding domain of Rev. Images PMID:2120472

  2. The REV-ERBs and RORs: molecular links between circadian rhythms and lipid homeostasis

    PubMed Central

    Solt, Laura A; Kojetin, Douglas J; Burris, Thomas P

    2011-01-01

    Research efforts spanning the past two decades have established a clear link between nuclear receptor function, regulation of the circadian clock and lipid homeostasis. As such, this family of receptors represents an important area of research. Recent advances in the field have identified two nuclear receptor subfamilies, the REV-ERBs and the ‘retinoic acid receptor-related orphan receptors’ (RORs), as critical regulators of the circadian clock with significant roles in lipid homeostasis. In this review, the latest information garnered from cutting-edge research on these two nuclear receptor subfamilies will be discussed. Through direct targeting of the REV-ERBs and RORs with synthetic ligands, generation of novel tools aimed at characterizing their function in vivo have been developed, which may lead to novel therapeutics for the treatment of metabolic disorders. PMID:21526899

  3. A Circular Motion Activity with Hot Wheels® Rev-Ups

    NASA Astrophysics Data System (ADS)

    Wagner, Glenn

    2009-02-01

    Hot Wheels® Rev-Ups provide a pedagogically engaging and inexpensive culminating activity for the application of circular motion with constant speed in introductory mechanics. The introductory Rev-Up, shown in Fig. 1, consists of a very durable car with two strong magnets built into the front and back of the car. The track is a piece of flexible plastic with a built-in metallic strip through its center that can then be formed into a circle. Pushing the car forward several times on a flat surface allows the car to move in a vertical circle when placed inside the track. What makes this toy attractive is that the gearing system allows the car to move at a relatively constant speed for about three to five seconds before slowing down appreciably.

  4. Haloarcula marismortui (Volcani) sp. nov., nom. rev., an extremely halophilic bacterium from the Dead Sea

    NASA Technical Reports Server (NTRS)

    Oren, A.; Ginzburg, M.; Ginzburg, B. Z.; Hochstein, L. I.; Volcani, B. E.

    1990-01-01

    An extremely halophilic red archaebacterium isolated from the Dead Sea (Ginzburg et al., J. Gen. Physiol. 55: 187-207, 1970) belongs to the genus Haloarcula and differs sufficiently from the previously described species of the genus to be designated a new species; we propose the name Haloarcula marismortui (Volcani) sp. nov., nom. rev. because of the close resemblance of this organism to "Halobacterium marismortui," which was first described by Volcani in 1940. The type strain is strain ATCC 43049.

  5. Potent Inhibition of Human Immunodeficiency Virus Type 1 Replication by an Intracellular Anti-Rev Single-Chain Antibody

    NASA Astrophysics Data System (ADS)

    Duan, Lingxun; Bagasra, Omar; Laughlin, Mark A.; Oakes, Joseph W.; Pomerantz, Roger J.

    1994-05-01

    Human immunodeficiency virus type 1 (HIV-1) has a complex life cycle, which has made it a difficult target for conventional therapeutic modalities. A single-chain antibody moiety, directed against the HIV-1 regulatory protein Rev, which rescues unspliced viral RNA from the nucleus of infected cells, has now been developed. This anti-Rev single-chain construct (SFv) consists of both light and heavy chain variable regions of an anti-Rev monoclonal antibody, which, when expressed intracellularly within human cells, potently inhibits HIV-1 replication. This intracellular SFv molecule is demonstrated to specifically antagonize Rev function. Thus, intracellular SFv expression, against a retroviral regulatory protein, may be useful as a gene therapeutic approach to combat HIV-1 infections.

  6. WBN-1 Cycle 10 TPBAR Tritium Release, Deduced From Analysis of RCS Data TTP-1-3046-00, Rev 0

    SciTech Connect

    Shaver, Mark W.; Niehus, Mark T.; Love, Edward F.

    2012-02-19

    This document contains the calculation of the TPBAR tritium release from the Mark 9.2 design TPBARs irradiated in WBN cycle 10. The calculation utilizes the generalized cycle analysis methodology given in TTP-1-3045 Rev. 0.

  7. XRCC1 interaction with the REV1 C-terminal domain suggests a role in post replication repair.

    PubMed

    Gabel, Scott A; DeRose, Eugene F; London, Robert E

    2013-12-01

    The function of X-ray cross complementing group 1 protein (XRCC1), a scaffold that binds to DNA repair enzymes involved in single-strand break and base excision repair, requires that it be recruited to sites of damaged DNA. However, structural insights into this recruitment are currently limited. Sequence analysis of the first unstructured linker domain of XRCC1 identifies a segment consistent with a possible REV1 interacting region (X1RIR) motif. The X1RIR motif is present in translesion polymerases that can be recruited to the pol /REV1 DNA repair complex via a specific interaction with the REV1 C-terminal domain. NMR and fluorescence titration studies were performed on XRCC1-derived peptides containing this putative RIR motif in order to evaluate the binding affinity for the REV1 C-terminal domain. These studies demonstrate an interaction of the XRCC1-derived peptide with the human REV1 C-terminal domain characterized by dissociation constants in the low micromolar range. Ligand competition studies comparing the XRCC1 RIR peptide with previously studied RIR peptides were found to be inconsistent with the NMR based Kd values. These discrepancies were resolved using a fluorescence assay for which the RIR–REV1 system is particularly well suited. The structure of a REV1-XRCC1 peptide complex was determined by using NOE restraints to dock the unlabeled XRCC1 peptide with a labeled REV1 C-terminal domain. The structure is generally homologous with previously determined complexes with the pol κ and pol η RIR peptides, although the helical segment in XRCC1 is shorter than was observed in these cases. These studies suggest the possible involvement of XRCC1 and its associated repair factors in post replication repair.

  8. HIV-1 Rev protein specifies the viral RNA export pathway by suppressing TAP/NXF1 recruitment

    PubMed Central

    Taniguchi, Ichiro; Mabuchi, Naoto; Ohno, Mutsuhito

    2014-01-01

    Nuclear RNA export pathways in eukaryotes are often linked to the fate of a given RNA. Therefore, the choice of export pathway should be well-controlled to avoid an unfavorable effect on gene expression. Although some RNAs could be exported by more than one pathway, little is known about how the choice is regulated. This issue is highlighted when the human immunodeficiency virus type 1 (HIV-1) Rev protein induces the export of singly spliced and unspliced HIV-1 transcripts. How these RNAs are exported is not well understood because such transcripts should have the possibility of utilizing CRM1-dependent export via Rev or cellular TAP/NXF1-dependent export via the transcription/export (TREX) complex, or both. Here we found that Rev suppressed TAP/NXF1-dependent export of model RNA substrates that recapitulated viral transcripts. In this effect, Rev interacted with the cap-binding complex and inhibited the recruitment of the TREX complex. Thus, Rev controls the identity of the factor occupying the cap-proximal region that determines the RNA export pathway. This ribonucleoprotein remodeling activity of Rev may favor viral gene expression. PMID:24753416

  9. Comment on “Two-dimensional positive column structure in a discharge tube with radius discontinuity” [Phys. Plasmas 21, 113503 (2014)

    SciTech Connect

    Demidova, M. V.; Kudryavtsev, A. A.; Kurlyandskaya, I. P.; Saifutdinov, A. I.; Stepanova, O. M.

    2015-09-15

    Zobnin et al. have published a paper [Phys. Plasmas, 21, 113503 (2014)] on a topic of discharge physics in the presence of a sharp change in cylindrical discharge geometry. In the comment it is pointed out that for untrapped electrons a full kinetic equation, which includes dependences on spatial coordinates and energies, has to be used for the electron velocity distribution function determination. It is also unclear what probe theories Zobnin et al. have used in their paper for the calculation of electron current to the discharge tube wall.

  10. Comment on “Shape transition of unstrained flattest single-walled carbon nanotubes under pressure” [J. Appl. Phys. 115, 044512 (2014)

    SciTech Connect

    Vassilev, Vassil M. Djondjorov, Peter A.; Mladenov, Ivaïlo M.

    2015-05-21

    Recently, Mu et al. [J. Appl. Phys. 115, 044512 (2014)] have developed an analytic approach to describe some special shapes of a single-wall carbon nanotube (SWCNT) under hydrostatic pressure. These authors have found approximate analytic expressions for the parametric equations of the tube cross section profile and its curvature at the convex-to-concave transition pressure using a shell-like 2D continuum model describing the shapes of such nanotubes. In this comment, we provide additional insight into this problem taking into account the exact analytic representation of the shapes that a SWCNT attains when subjected to hydrostatic pressure according to the very same continuum model.

  11. Response to "Comment on 'Rethinking first-principles electron transport theories with projection operators: the problems caused by partitioning the basis set'" [J. Chem. Phys. 140, 177103 (2014)].

    PubMed

    Reuter, Matthew G; Harrison, Robert J

    2014-05-01

    The thesis of Brandbyge's comment [J. Chem. Phys. 140, 177103 (2014)] is that our operator decoupling condition is immaterial to transport theories, and it appeals to discussions of nonorthogonal basis sets in transport calculations in its arguments. We maintain that the operator condition is to be preferred over the usual matrix conditions and subsequently detail problems in the existing approaches. From this operator perspective, we conclude that nonorthogonal projectors cannot be used and that the projectors must be selected to satisfy the operator decoupling condition. Because these conclusions pertain to operators, the choice of basis set is not germane.

  12. Comment on “Frequency-domain stimulated and spontaneous light emission signals at molecular junctions” [J. Chem. Phys. 141, 074107 (2014)

    SciTech Connect

    Galperin, Michael; Ratner, Mark A.; Nitzan, Abraham

    2015-04-07

    We discuss the derivation of the optical response in molecular junctions presented by U. Harbola et al. [J. Chem. Phys. 141, 074107 (2014)], which questions some terms in the theory of Raman scattering in molecular junctions developed in our earlier publications. We show that the terms considered in our theory represent the correct contribution to calculated Raman scattering and are in fact identical to those considered by Harbola et al. We also indicate drawbacks of the presented approach in treating the quantum transport part of the problem.

  13. Comment on "Dual resonating C-band with enhanced bandwidth and broad X-band metamaterial absorber" in Appl. Phys. A (2016) 122:166

    NASA Astrophysics Data System (ADS)

    Li, Bo; Chen, Qiang; Fu, Yunqi; Yang, Chun; Chen, Qi

    2016-10-01

    In a recent paper, Agarwa et al. (Appl Phys A 122:166, 2016) proposed a structure of metamaterial unit cell, which could realize dual-band absorption in C-band, and by altering its design parameters, broadband absorption in X-band could also be easily achieved, and its peak absorptivity is over 99 %. However, we find that the peak absorptivity is 40 % in C-band and 32 % in X-band, since the ostensible good return loss performance is caused by the polarization rotation rather than the absorption.

  14. Comment on “Competition between coherent emission and broadband spontaneous emission in the quantum free electron laser” [Phys. Plasmas 20, 033106 (2013)

    SciTech Connect

    Petrillo, V.; Rossi, A. R.; Serafini, L.

    2013-12-15

    We point out that in the equation for the electron distribution evolution during Thomson/Compton or undulator radiation used in the paper: “Competition between coherent emission and broadband spontaneous emission in the quantum free electron laser” by G. R. M. Robb and R. Bonifacio [Phys. Plasmas 20, 033106 (2013)], the weight function should be the distribution of the number of emitted photons and not the photon energy distribution. Nevertheless, the considerations expressed in this comment do not alter the conclusions drawn in the paper in object.

  15. Comment on ``Cleaning properties of atomic oxygen excited to metastable state 2s22p4(1S0) [J. Appl. Phys. 102, 083304 (2007)]''

    NASA Astrophysics Data System (ADS)

    Sadeghi, Nader

    2008-05-01

    It is shown that the spectrum attributed in the work of Shun'ko and Belkin [J. Appl. Phys. 102, 083304 (2007)] to the 557 nm forbidden transition of oxygen, O(S10→D12), induced by collision with argon atoms is probably the chemiluminescence from the O+NO reaction. Also, given the less than 0.1 ms lifetime of O(S10) atoms in the gas flow, they cannot survive during the transport to the surface, and hence they cannot be responsible for the observed cleaning effect.

  16. Comment on “The two dimensional motion of a particle in an inverse square potential: Classical and quantum aspects” [J. Math. Phys. 54, 053509 (2013)

    SciTech Connect

    Bietenholz, Wolfgang Chryssomalakos, Chryssomalis Salgado, Marcelo

    2015-10-15

    We comment on a fatal flaw in the analysis contained in the work of Martínez-y-Romero et al., [J. Math. Phys. 54, 053509 (2013)], which concerns the motion of a point particle in an inverse square potential, and show that most conclusions reached there are wrong. In particular, the manifestly senseless claim that, in the attractive potential case, no bounded orbits exist for negative energies, is traced to a sign error. Several more mistakes, both in the classical and the quantum cases, are pointed out.

  17. Comment on ``The two dimensional motion of a particle in an inverse square potential: Classical and quantum aspects'' [J. Math. Phys. 54, 053509 (2013)

    NASA Astrophysics Data System (ADS)

    Bietenholz, Wolfgang; Chryssomalakos, Chryssomalis; Salgado, Marcelo

    2015-10-01

    We comment on a fatal flaw in the analysis contained in the work of Martínez-y-Romero et al., [J. Math. Phys. 54, 053509 (2013)], which concerns the motion of a point particle in an inverse square potential, and show that most conclusions reached there are wrong. In particular, the manifestly senseless claim that, in the attractive potential case, no bounded orbits exist for negative energies, is traced to a sign error. Several more mistakes, both in the classical and the quantum cases, are pointed out.

  18. Response to "Comment on `A large volume uniform plasma generator for the experiments of electromagnetic wave propagation in plasma'" [Phys. Plasmas 23, 094701 (2016)

    NASA Astrophysics Data System (ADS)

    Yang, Min; Li, Xiaoping; Xie, Kai; Liu, yanming; Liu, Donglin

    2016-09-01

    We respond to the issues raised in the comment by Eliseev and Kudryavtsev [Phys. Plasmas 23, 094701 (2016)]. We re-examine the principle of plasma generation and the operating situations in our plasma device, and some simplified models are founded to illustrate the qualitative relations between the pressure and the magnitude and uniformity of ne. We stand by our original conclusions in our plasma device that the magnitude and uniformity of ne are in roughly reverse proportion to the gas pressure in the chamber, as observed in the experiment.

  19. Comment on 'Continuum modes in rotating plasmas: General equations and continuous spectra for large aspect ratio tokamaks'[Phys. Plasmas 18, 092103 (2011)

    SciTech Connect

    Goedbloed, J. P.

    2012-06-15

    It is shown that some of the main results of the recent paper by Lakhin and Ilgisonis [Phys. Plasmas 18, 092103 (2011)], viz. the derivation of the equations for the continuous spectra of poloidally and toroidally rotating plasmas and their special solution for large aspect ratio tokamaks with large parallel flows were obtained before by Goedbloed, Belieen, van der Holst, and Keppens [Phys. Plasmas 11, 28 (2004)]. A further rearrangement of the system of equations for the coupled Alfven and slow continuous spectra clearly exhibits: (a) coupling through a single tangential derivative, which is a generalization of the geodesic curvature; (b) the 'transonic' transitions of the equilibrium, which need to be carefully examined in order to avoid entering hyperbolic flow regimes where the stability formalism breaks down. A critical discussion is devoted to the implications of this failure, which is generally missed in the tokamak literature, possibly as a result of the wide-spread use of the sonic Mach number of gas dynamics, which is an irrelevant and misleading parameter in 'transonic' magnetohydrodynamics. Once this obstacle in understanding is removed, further application of the theory of trans-slow Alfven continuum instabilities to both tokamaks, with possible implications for the L-H transition, and astrophysical objects like 'fat' accretion disks, with a possible new route to magnetohydrodynamic turbulence, becomes feasible.

  20. Response to "Comment on 'A model for phosphate glass topology considering the modifying ion sub-network"' [J. Chem. Phys. 142, 107103 (2015)].

    PubMed

    Hermansen, Christian; Mauro, John C; Yue, Yuanzheng

    2015-03-14

    In our recent paper [C. Hermansen, J. C. Mauro, and Y.-Z. Yue, J. Chem. Phys. 140, 154501 (2014)], we applied temperature-dependent constraint theory to model the glass transition temperature (Tg) and liquid fragility index (m) of alkali phosphate glasses. Sidebottom commented on this paper concerning the m values obtained by differential scanning calorimetry (DSC) [D. L. Sidebottom, J. Chem. Phys. 142, ⬛ (2015)]. We have considered Sidebottom's comments carefully and conclude that the m values of phosphate liquids obtained by DSC are reliable, except for the NaPO3 and possibly P2O5 compositions. Based on his dynamic light scattering measurements, Sidebottom has found that P2O5 is a strong liquid with m ≈ 20. However, based on the heat capacity jump at Tg and the stretching exponent of the relaxation function, P2O5 should be classified as an intermediate fragile liquid with m ≈ 40. We also argue that m cannot be universally related to the average connectivity of the network and point out several inconsistencies with this view.

  1. A novel, mouse mammary tumor virus encoded protein with Rev-like properties

    SciTech Connect

    Indik, Stanislav; Guenzburg, Walter H.; Salmons, Brian . E-mail: salmons@austrianova.com; Rouault, Francoise

    2005-06-20

    We have identified a novel, multiple spliced, subgenomic mRNA species in MMTV producing cells of different origin containing an open reading frame encoding a 39-kDa Rev-like protein, Rem (regulator of expression of MMTV). An EGFP-Rem fusion protein is shown to be predominantly in the nucleolus. Further leptomycin B inhibits the nuclear export of nonspliced MMTV transcripts, implicating Rem in nuclear export by the Crm1 pathway in MMTV. Rem is thus reminiscent of the Rec protein from the related endogenous human retrovirus, HERV-K.

  2. Role of AtPolζ, AtRev1, and AtPolη in UV light-induced mutagenesis in Arabidopsis.

    PubMed

    Nakagawa, Mayu; Takahashi, Shinya; Tanaka, Atsushi; Narumi, Issay; Sakamoto, Ayako N

    2011-01-01

    Translesion synthesis (TLS) is a DNA damage tolerance mechanism in which DNA lesions are bypassed by specific polymerases. To investigate the role of TLS activities in ultraviolet light-induced somatic mutations, we analyzed Arabidopsis (Arabidopsis thaliana) disruptants of AtREV3, AtREV1, and/or AtPOLH genes that encode TLS-type polymerases. The mutation frequency in rev3-1 or rev1-1 mutants decreased compared with that in the wild type, suggesting that AtPolζ and AtRev1 perform mutagenic bypass events, whereas the mutation frequency in the polh-1 mutant increased, suggesting that AtPolη performs nonmutagenic bypass events with respect to ultraviolet light-induced lesions. The rev3-1 rev1-1 double mutant showed almost the same mutation frequency as the rev1-1 single mutant. The increased mutation frequency found in polh-1 was completely suppressed in the rev3-1 polh-1 double mutant, indicating that AtPolζ is responsible for the increased mutations found in polh-1. In summary, these results suggest that AtPolζ and AtRev1 are involved in the same (error-prone) TLS pathway that is independent from the other (error-free) TLS pathway mediated by AtPolη.

  3. An Intrabody Based on a Llama Single-domain Antibody Targeting the N-terminal α-Helical Multimerization Domain of HIV-1 Rev Prevents Viral Production*

    PubMed Central

    Vercruysse, Thomas; Pardon, Els; Vanstreels, Els; Steyaert, Jan; Daelemans, Dirk

    2010-01-01

    The human immunodeficiency virus, type 1 (HIV-1)-encoded Rev protein is essential for the expression of late viral mRNAs. Rev forms a large organized multimeric protein-protein complex on the Rev response element of these viral mRNA species and transports them from the nucleus to the cytoplasm, exploiting the CRM1-mediated cellular machinery. Here we report the selection of a nanobody, derived from a llama heavy-chain only antibody, that efficiently blocks the assembly of Rev multimers. The nanobody inhibits HIV-1 replication in cells and specifically suppresses the Rev-dependent expression of partially spliced and unspliced HIV-1 RNA. In HIV-susceptible cells, this nanobody thus has potential as an effective anti-HIV agent using genetic immunization strategies. Its binding site was mapped to Rev residues Lys-20 and Tyr-23 located in the N-terminal α-helical multimerization domain. In the presence of this nanobody, we observed an accumulation of dimeric Rev species, supporting a head-to-head/tail-to-tail molecular model for Rev assembly. The results indicate that the oligomeric assembly of Rev follows an ordered stepwise process and identify a new epitope within Rev that could guide strategies for the development of novel HIV inhibitors. PMID:20406803

  4. REV-ERB-ALPHA circadian gene variant associates with obesity in two independent populations: Mediterranean and North American

    PubMed Central

    Garaulet, Marta; Smith, Caren E.; Gomez-Abellán, Purificación; Ordovás-Montañés, María; Lee, Yu-Chi; Parnell, Laurence D.; Arnett, Donna K.; Ordovás, José M.

    2014-01-01

    Scope Despite the solid connection between REV-ERB and obesity, the information about whether genetic variations at this locus may be associated with obesity traits is scarce. Therefore our objective was to study the association between REV-ERB-ALPHA1 rs2314339 and obesity in two independent populations. Methods and results Participants were 2214 subjects from Spanish Mediterranean (n = 1404) and North American (n = 810) populations. Anthropometric, biochemical, dietary, and genotype analyses were performed. We found novel associations between the REV-ERB-ALPHA1 rs2314339 genotype and obesity in two independent populations: in Spanish Mediterranean and North American groups, the frequency of the minor-allele-carriers (AA+ AG) was significantly lower in the “abdominally obese” group than in those of the “nonabdominally obese” group (p < 0.05). Minor allele carriers had lower probability of abdominal obesity than noncarriers, and the effect was of similar magnitude for both populations (OR ≈ 1.50). There were consistent associations between REV-ERB-ALPHA1 genotype and obesity-related traits (p < 0.05). Energy intake was not significantly associated with REV-ERB-ALPHA1 rs2314339. However, physical activity significantly differed by genotype. A significant interaction between the REV-ERB-ALPHA1 variant and monounsaturated-fatty-acids (MUFA) intake for obesity was also detected in the Mediterranean population. Conclusion This new discovery highlights the importance of REV-ERB-ALPHA1 in obesity and provides evidence for the connection between our biological clock and obesity-related traits. PMID:24173768

  5. Determinants of G quadruplex-induced epigenetic instability in REV1-deficient cells

    PubMed Central

    Schiavone, Davide; Guilbaud, Guillaume; Murat, Pierre; Papadopoulou, Charikleia; Sarkies, Peter; Prioleau, Marie-Noëlle; Balasubramanian, Shankar; Sale, Julian E

    2014-01-01

    REV1-deficient chicken DT40 cells are compromised in replicating G quadruplex (G4)-forming DNA. This results in localised, stochastic loss of parental chromatin marks and changes in gene expression. We previously proposed that this epigenetic instability arises from G4-induced replication fork stalls disrupting the accurate propagation of chromatin structure through replication. Here, we test this model by showing that a single G4 motif is responsible for the epigenetic instability of the BU-1 locus in REV1-deficient cells, despite its location 3.5 kb from the transcription start site (TSS). The effect of the G4 is dependent on it residing on the leading strand template, but is independent of its in vitro thermal stability. Moving the motif to more than 4 kb from the TSS stabilises expression of the gene. However, loss of histone modifications (H3K4me3 and H3K9/14ac) around the transcription start site correlates with the position of the G4 motif, expression being lost only when the promoter is affected. This supports the idea that processive replication is required to maintain the histone modification pattern and full transcription of this model locus. PMID:25190518

  6. Synthesis and in Vitro Anticancer Activity of the First Class of Dual Inhibitors of REV-ERBβ and Autophagy.

    PubMed

    Torrente, Esther; Parodi, Chiara; Ercolani, Luisa; De Mei, Claudia; Ferrari, Alessio; Scarpelli, Rita; Grimaldi, Benedetto

    2015-08-13

    Autophagy inhibition is emerging as a promising anticancer strategy. We recently reported that the circadian nuclear receptor REV-ERBβ plays an unexpected role in sustaining cancer cell survival when the autophagy flux is compromised. We also identified 4-[[[1-(2-fluorophenyl)cyclopentyl]amino]methyl]-2-[(4-methylpiperazin-1-yl)methyl]phenol, 1 (ARN5187), as a novel dual inhibitor of REV-ERBβ and autophagy. 1 had improved cytotoxicity against BT-474 breast cancer cells compared to chloroquine, a clinically relevant autophagy inhibitor. Here, we present the results of structure-activity studies, based around 1, that disclose the first class of dual inhibitors of REV-ERBβ and autophagy. This study led to identification of 18 and 28, which were more effective REV-ERBβ antagonists than 1 and were more cytotoxic to BT-474. The combination of optimal chemical and structural moieties of these analogs generated 30, which elicited 15-fold greater REV-ERBβ inhibitory and cytotoxic activities compared to 1. Furthermore, 30 induced death in a panel of tumor cell lines at doses 5-50 times lower than an equitoxic amount of chloroquine but did not affect the viability of normal mammary epithelial cells.

  7. Development of a real-time quantitative RT-PCR to detect REV contamination in live vaccine.

    PubMed

    Luan, Huaibiao; Wang, Yixin; Li, Yang; Cui, Zhizhong; Chang, Shuang; Zhao, Peng

    2016-09-01

    Based on the published Avian reticuloendotheliosis virus (REV) whole genome sequence, primers and TaqMan probes were designed and synthesized, and the TaqMan probe fluorescence real-time quantitative RT-PCR (qRT-PCR) method for detecting the REV pol gene was established by optimizing the reaction conditions. Sensitivity analysis showed that the qRT-PCR method had a sensitivity that was 1,000-fold higher than conventional PCR. Additionally, no amplification signals were obtained when we attempted to detect DNA or cDNA of ALV-A/B/J, MDV, CIAV, IBDV, ARV, NDV, AIV, or other viruses, suggesting a high specificity for our method. Various titers of REV were artificially "spiked" into the FPV and MDV vaccines to simulate REV contamination in attenuated vaccines to validate this qRT-PCR method. Our findings indicated that this qRT-PCR method could detect REV contamination at a dose of 1 TCID50/1,000 feathers, which was 10,000-fold more sensitive than the regular RT-PCR detection (10(4) TCID50/1000 feathers).

  8. Deletion of the GI-2 integrase and the wbkA flanking transposase improves the stability of Brucella melitensis Rev 1 vaccine

    PubMed Central

    2013-01-01

    Brucella melitensis Rev 1 is the best vaccine available for the prophylaxis of small ruminant brucellosis and, indirectly, for reducing human brucellosis. However, Rev 1 shows anomalously high rates of spontaneous dissociation from smooth (S) to rough (R) bacteria, the latter being inefficacious as vaccines. This S-R instability results from the loss of the O-polysaccharide. To overcome this problem, we investigated whether some recently described mechanisms promoting mutations in O-polysaccharide genes were involved in Rev 1 S-R dissociation. We found that a proportion of Rev 1 R mutants result from genome rearrangements affecting the wbo O-polysaccharide loci of genomic island GI-2 and the wbkA O-polysaccharide glycosyltransferase gene of the wbk region. Accordingly, we mutated the GI-2 int gene and the wbk IS transposase involved in those arrangements, and found that these Rev 1 mutants maintained the S phenotype and showed lower dissociation levels. Combining these two mutations resulted in a strain (Rev 2) displaying a 95% decrease in dissociation with respect to parental Rev 1 under conditions promoting dissociation. Rev 2 did not differ from Rev 1 in the characteristics used in Rev 1 typing (growth rate, colonial size, reactivity with O-polysaccharide antibodies, phage, dye and antibiotic susceptibility). Moreover, Rev 2 and Rev 1 showed similar attenuation and afforded similar protection in the mouse model of brucellosis vaccines. We conclude that mutations targeting genes and DNA sequences involved in spontaneous O-polysaccharide loss enhance the stability of a critical vaccine phenotype and complement the empirical stabilization precautions taken during S Brucella vaccine production. PMID:24176078

  9. Response to “Comment on ‘Twin symmetry texture of energetically condensed niobium thin films on sapphire substrate’ ” [J. Appl. Phys. 112, 016101 (2012)

    DOE PAGES

    Zhao, X.; Philips, L.; Reece, C. E.; Seo, Kang; Krishnan, M.; Valderrama, E.

    2012-07-01

    Welander is correct about the misidentified crystal-directions in the top-view sapphire lattice (Fig. 4 [Zhao et al., J. Appl. Phys. 110, 033523 (2011)]). He is also correct about the misorientation of the pole figures in Fig. 4. In Fig. 1 of this response, we have corrected these errors. Perhaps because of these errors, Welander misconstrued our discussion of the Nbcrystal growth as claiming a new 3D registry. That was not our intention. Rather, we wished to highlight the role of energetic condensation that drives low-defect crystal growth by a combination of non-equilibrium sub-plantation that disturbs the substrate lattice and thermalmore » annealing that annihilates defects and promotes large-grain crystal growth.« less

  10. Response to "Comment on `Application of the extended Lie group analysis to the Hopf functional formulation of the Burgers equation'" [J. Math. Phys. 57, 034102 (2016)

    NASA Astrophysics Data System (ADS)

    Wacławczyk, Marta; Oberlack, Martin

    2016-03-01

    We address the criticism of Frewer et al. concerning the paper "Application of the extended Lie group analysis to the Hopf functional formulation of the Burgers equation" [J. Math. Phys. 54, 072901 (2013)]. Most importantly, we stress that we never claimed that any new statistical symmetries were found in this paper. The aim of this paper was to apply the Lie group analysis to an equation with functional derivatives and derive invariant solutions for this equation. These results still stand as they are, most important, mathematically correct. We address also other critical statements of Frewer et al. and show that there is a connection between the translational invariance of statistics and transformations of the functional Φ. To sum up, key ideas and fundamental result in the work of Wacławczyk and Oberlack are still unaffected.

  11. Comment on: "Disentangling density and temperature effects in the viscous slowing down of glass forming liquids" [J. Chem. Phys. 120, 6135 (2004)].

    PubMed

    Roland, C M; Casalini, R

    2004-12-01

    Recently, Tarjus et al. [G. Tarjus, D. Kivelson, S. Mossa, and C. Alba-Simionesco, J. Chem. Phys. 120, 6135 (2004)] concluded from a review of data for a variety of glass formers that the supercooled dynamics are almost invariably dominated by temperature T, rather than by density rho. By including additional published data into such a compilation, we show that for van der Waals molecular liquids, the dynamics near T(g) are in fact governed as much by density as by temperature. Moreover, relaxation times measured at various temperatures and pressures can be superimposed by plotting as a function rho(gamma)/T. This scaling form can arise from an assumed inverse power law for the intermolecular repulsive potential, with gamma a material constant. (c) 2004 American Institute of Physics.

  12. Comment on ``The effects of Bohm potential on ion-acoustic solitary waves interaction in a nonplanar quantum plasma'' [Phys. Plasmas 17, 082307 (2010)

    NASA Astrophysics Data System (ADS)

    Akbari-Moghanjoughi, M.

    2010-11-01

    Recently, Li [Phys. Plasmas 17, 082307 (2010)] has studied the effects of Bohm potential on interaction of nonplanar ion-acoustic solitary waves in an unmagnetized electron-positron-ion quantum plasma. In his work the extended reductive perturbation technique has been employed to reduce the basic quantum hydrodynamics plasma equations to Korteweg-de Vries evolution equations (one for each wave) as well as other coupled differential equations describing the phase variation of the resulting solitary waves. The calculated collisional phase-shifts are then numerically evaluated in terms of plasma parameters such as the fractional positron to ion number-density p, relative electron to positron Fermi-temperature σ and the quantum diffraction parameter H. We show that in the chosen plasma model, the parameters p and σ are not independent quantum plasma parameters which has important consequences on the graphical interpretations presented in the mentioned article.

  13. Comment on 'The effects of Bohm potential on ion-acoustic solitary waves interaction in a nonplanar quantum plasma' [Phys. Plasmas 17, 082307 (2010)

    SciTech Connect

    Akbari-Moghanjoughi, M.

    2010-11-15

    Recently, Li [Phys. Plasmas 17, 082307 (2010)] has studied the effects of Bohm potential on interaction of nonplanar ion-acoustic solitary waves in an unmagnetized electron-positron-ion quantum plasma. In his work the extended reductive perturbation technique has been employed to reduce the basic quantum hydrodynamics plasma equations to Korteweg-de Vries evolution equations (one for each wave) as well as other coupled differential equations describing the phase variation of the resulting solitary waves. The calculated collisional phase-shifts are then numerically evaluated in terms of plasma parameters such as the fractional positron to ion number-density p, relative electron to positron Fermi-temperature {sigma} and the quantum diffraction parameter H. We show that in the chosen plasma model, the parameters p and {sigma} are not independent quantum plasma parameters which has important consequences on the graphical interpretations presented in the mentioned article.

  14. Comment on: ``Disentangling density and temperature effects in the viscous slowing down of glass forming liquids'' [J. Chem. Phys. 120, 6135 (2004)

    NASA Astrophysics Data System (ADS)

    Roland, C. M.; Casalini, R.

    2004-12-01

    Recently, Tarjus et al. [G. Tarjus, D. Kivelson, S. Mossa, and C. Alba-Simionesco, J. Chem. Phys. 120, 6135 (2004)] concluded from a review of data for a variety of glass formers that the supercooled dynamics are almost invariably dominated by temperature T, rather than by density ρ. By including additional published data into such a compilation, we show that for van der Waals molecular liquids, the dynamics near Tg are in fact governed as much by density as by temperature. Moreover, relaxation times measured at various temperatures and pressures can be superimposed by plotting as a function ργ/T. This scaling form can arise from an assumed inverse power law for the intermolecular repulsive potential, with γ a material constant.

  15. Comment on ``Photonic bands in two-dimensional microplasma array. I. Theoretical derivation of band structures of electromagnetic waves'' [J. Appl. Phys. 101, 073304 (2007)

    NASA Astrophysics Data System (ADS)

    Zhang, Hai-feng; Liu, Shao-bin; Kong, Xiang-kun; Zhou, Liang; Li, Chun-zao; Bian, Bo-rui

    2011-07-01

    Recently, theoretical derivation of band structures of electromagnetic waves in two-dimensional microplasma array has been induced by Osamu Sakai et al. [J. Appl. Phys. 101, 073304 (2007)] using a modified plane wave expansion (PWE) method and a frequency-dependent finite difference time-domain (FDTD) method. This report reveals band diagrams with the effects of plasma electron collision frequency, especially focuses on the TE wave by nonmagnetized plasma. Although the band diagrams of TE wave and formulas of calculation look correct at first glance, there are some mistakes in the report which are unfortunately ignored by the authors. The correct formulas of the modified PWE method and FDTD method will be proposed.

  16. Comment on "High-pressure synthesis of orthorhombic SrIrO3 perovskite and its positive magnetoresistance" [J. Appl. Phys. 103, 103706 (2008)

    NASA Astrophysics Data System (ADS)

    Puggioni, D.; Rondinelli, J. M.

    2016-02-01

    In their article, Zhao et al. report the synthesis of SrIrO3 at high temperature and high pressure [J. Appl. Phys. 103, 103706 (2008)]. Under these conditions, the crystal structure of SrIrO3 can be stabilized as an orthorhombic perovskite with space group Pnma. They refine the lattice parameters and list the Wyckoff orbits and atomic coordinates. We believe that Zhao and coworkers made an unintentional error in reporting the crystal structure, which may adversely affect the description of the electronic structure. Indeed, we show the reported structure does not define a standard perovskite with nearly rigid IrO6 octahedral tilts and rather exhibits a structural discrepancy with respect to the equilibrium structure obtained from density functional calculations.

  17. Comment on "Rethinking first-principles electron transport theories with projection operators: The problems caused by partitioning the basis set" [J. Chem. Phys. 139, 114104 (2013)

    NASA Astrophysics Data System (ADS)

    Brandbyge, Mads

    2014-05-01

    In a recent paper Reuter and Harrison [J. Chem. Phys. 139, 114104 (2013)] question the widely used mean-field electron transport theories, which employ nonorthogonal localized basis sets. They claim these can violate an "implicit decoupling assumption," leading to wrong results for the current, different from what would be obtained by using an orthogonal basis, and dividing surfaces defined in real-space. We argue that this assumption is not required to be fulfilled to get exact results. We show how the current/transmission calculated by the standard Greens function method is independent of whether or not the chosen basis set is nonorthogonal, and that the current for a given basis set is consistent with divisions in real space. The ambiguity known from charge population analysis for nonorthogonal bases does not carry over to calculations of charge flux.

  18. Reduced viral load and lack of CD4 depletion in SCID-hu mice infected with Rev-independent clones of human immunodeficiency virus type 1.

    PubMed Central

    Valentin, A; Aldrovandi, G; Zolotukhin, A S; Cole, S W; Zack, J A; Pavlakis, G N; Felber, B K

    1997-01-01

    The posttranscriptional control element CTE of the simian type D retrovirus has been shown to support replication of Rev-Rev-responsive-element (RRE)-deficient molecular clones of human immunodeficiency virus type 1 (HIV-1). Upon infection of peripheral blood mononuclear cells in vitro, these CTE-containing Rev-independent viruses that are nef+ or nef-minus showed lower replicative capacity and infectivity than the wild-type HIV-1. We studied the effects of Rev-RRE replacement by the CTE on HIV-1 expression with SCID-hu mice. The nef+ and nef-minus Rev-independent viruses established infection with kinetics slower than that of the nef-minus NL4-3. Most importantly, no depletion of CD4-bearing thymocytes was observed after 6 weeks for mice infected with these Rev-independent viruses. This is in contrast to the infection with both wild-type and nef-minus viruses, which led to varying depletion of thymocytes. These data suggest an attenuated phenotype for growth and cytotoxicity of the Rev-independent HIV-1 clones in SCID-hu mice, independent of the presence of Nef. The mutant viruses, which have the essential Rev-RRE regulatory system eliminated, display a distinct phenotype not previously observed with HIV mutant viruses having deletions of accessory genes. Therefore, replacement of the Rev-RRE regulatory axis may generate viruses with altered biological properties in vivo. PMID:9371653

  19. The Protein Level of Rev1, a TLS Polymerase in Fission Yeast, Is Strictly Regulated during the Cell Cycle and after DNA Damage.

    PubMed

    Uchiyama, Masashi; Terunuma, Junko; Hanaoka, Fumio

    2015-01-01

    Translesion DNA synthesis provides an alternative DNA replication mechanism when template DNA is damaged. In fission yeast, Eso1 (polη), Kpa1/DinB (polκ), Rev1, and Polζ (a complex of Rev3 and Rev7) have been identified as translesion synthesis polymerases. The enzymatic characteristics and protein-protein interactions of these polymerases have been intensively characterized; however, how these proteins are regulated during the cell cycle remains unclear. Therefore, we examined the cell cycle oscillation of translesion polymerases. Interestingly, the protein levels of Rev1 peaked during G1 phase and then decreased dramatically at the entry of S phase; this regulation was dependent on the proteasome. Temperature-sensitive proteasome mutants, such as mts2-U31 and mts3-U32, stabilized Rev1 protein when the temperature was shifted to the restrictive condition. In addition, deletion of pop1 or pop2, subunits of SCF ubiquitin ligase complexes, upregulated Rev1 protein levels. Besides these effects during the cell cycle, we also observed upregulation of Rev1 protein upon DNA damage. This upregulation was abolished when rad3, a checkpoint protein, was deleted or when the Rev1 promoter was replaced with a constitutive promoter. From these results, we hypothesize that translesion DNA synthesis is strictly controlled through Rev1 protein levels in order to avoid unwanted mutagenesis.

  20. The Protein Level of Rev1, a TLS Polymerase in Fission Yeast, Is Strictly Regulated during the Cell Cycle and after DNA Damage

    PubMed Central

    Uchiyama, Masashi; Terunuma, Junko; Hanaoka, Fumio

    2015-01-01

    Translesion DNA synthesis provides an alternative DNA replication mechanism when template DNA is damaged. In fission yeast, Eso1 (polη), Kpa1/DinB (polκ), Rev1, and Polζ (a complex of Rev3 and Rev7) have been identified as translesion synthesis polymerases. The enzymatic characteristics and protein-protein interactions of these polymerases have been intensively characterized; however, how these proteins are regulated during the cell cycle remains unclear. Therefore, we examined the cell cycle oscillation of translesion polymerases. Interestingly, the protein levels of Rev1 peaked during G1 phase and then decreased dramatically at the entry of S phase; this regulation was dependent on the proteasome. Temperature-sensitive proteasome mutants, such as mts2-U31 and mts3-U32, stabilized Rev1 protein when the temperature was shifted to the restrictive condition. In addition, deletion of pop1 or pop2, subunits of SCF ubiquitin ligase complexes, upregulated Rev1 protein levels. Besides these effects during the cell cycle, we also observed upregulation of Rev1 protein upon DNA damage. This upregulation was abolished when rad3, a checkpoint protein, was deleted or when the Rev1 promoter was replaced with a constitutive promoter. From these results, we hypothesize that translesion DNA synthesis is strictly controlled through Rev1 protein levels in order to avoid unwanted mutagenesis. PMID:26147350

  1. Temperature inducible β-sheet structure in the transactivation domains of retroviral regulatory proteins of the Rev family

    NASA Astrophysics Data System (ADS)

    Thumb, Werner; Graf, Christine; Parslow, Tristram; Schneider, Rainer; Auer, Manfred

    1999-11-01

    The interaction of the human immunodeficiency virus type 1 (HIV-1) regulatory protein Rev with cellular cofactors is crucial for the viral life cycle. The HIV-1 Rev transactivation domain is functionally interchangeable with analog regions of Rev proteins of other retroviruses suggesting common folding patterns. In order to obtain experimental evidence for similar structural features mediating protein-protein contacts we investigated activation domain peptides from HIV-1, HIV-2, VISNA virus, feline immunodeficiency virus (FIV) and equine infectious anemia virus (EIAV) by CD spectroscopy, secondary structure prediction and sequence analysis. Although different in polarity and hydrophobicity, all peptides showed a similar behavior with respect to solution conformation, concentration dependence and variations in ionic strength and pH. Temperature studies revealed an unusual induction of β-structure with rising temperatures in all activation domain peptides. The high stability of β-structure in this region was demonstrated in three different peptides of the activation domain of HIV-1 Rev in solutions containing 40% hexafluoropropanol, a reagent usually known to induce α-helix into amino acid sequences. Sequence alignments revealed similarities between the polar effector domains from FIV and EIAV and the leucine rich (hydrophobic) effector domains found in HIV-1, HIV-2 and VISNA. Studies on activation domain peptides of two dominant negative HIV-1 Rev mutants, M10 and M32, pointed towards different reasons for the biological behavior. Whereas the peptide containing the M10 mutation (L 78E 79→D 78L 79) showed wild-type structure, the M32 mutant peptide (L 78L 81L 83→A 78A 81A 83) revealed a different protein fold to be the reason for the disturbed binding to cellular cofactors. From our data, we conclude, that the activation domain of Rev proteins from different viral origins adopt a similar fold and that a β-structural element is involved in binding to a

  2. Cloning and characterization of cDNAs encoding equine infectious anemia virus tat and putative Rev proteins.

    PubMed Central

    Stephens, R M; Derse, D; Rice, N R

    1990-01-01

    We isolated and characterized six cDNA clones from an equine infectious anemia virus-infected cell line that displays a Rev-defective phenotype. With the exception of one splice site in one of the clones, all six cDNAs exhibited the same splicing pattern and consisted of four exons. Exon 1 contained the 5' end of the genome; exon 2 contained the tat gene from mid-genome; exon 3 consisted of a small section of env, near the 5' end of the env gene; and exon 4 contained the putative rev open reading frame from the 3' end of the genome. The structures of the cDNAs predict a bicistronic message in which Tat is encoded by exons 1 and 2 and the presumptive Rev protein is encoded by exons 3 and 4. tat translation appears to be initiated at a non-AUG codon within the first 15 codons of exon 1. Equine infectious anemia virus-specific tat activity was expressed in transient transfections with cDNA expression plasmids. The predicted wild-type Rev protein contains 30 env-derived amino acids and 135 rev open reading frame residues. All of the cDNAs had a frameshift in exon 4, leading to a truncated protein and thus providing a plausible explanation for the Rev-defective phenotype of the original cells. We used peptide antisera to detect the faulty protein, thus confirming the cDNA sequence, and to detect the normal protein in productively infected cells. Images PMID:2164593

  3. HIV-1 Suppressive Sequences Are Modulated by Rev Transport of Unspliced RNA and Are Required for Efficient HIV-1 Production

    PubMed Central

    Noguchi, Kousei; Ishibashi, Keisuke; Miyokawa, Kaori; Hokari, Manami; Kanno, Tomoyuki; Hirano, Tomoya; Yamamoto, Norio; Takaku, Hiroshi

    2012-01-01

    The unspliced human immunodeficiency virus type 1 (HIV-1) RNAs are translated as Gag and Gag-Pol polyproteins or packaged as genomes into viral particles. Efficient translation is necessary before the transition to produce infective virions. The viral protein Rev exports all intron-containing viral RNAs; however, it also appears to enhance translation. Cellular microRNAs target cellular and viral mRNAs to silence their translation and enrich them at discrete cytoplasmic loci that overlap with the putative interim site of Gag and the genome. Here, we analyzed how Rev-mediated transport and the splicing status of the mRNA influenced the silencing status imposed by microRNA. Through identification and mutational analysis of the silencing sites in the HIV-1 genome, we elucidated the effect of silencing on virus production. Renilla luciferase mRNA, which contains a let-7 targeting site in its 3′ untranslated region, was mediated when it was transported by Rev and not spliced, but it was either not mediated when it was spliced even in a partial way or it was Rev-independent. The silencing sites in the pol and env-nef regions of the HIV-1 genome, which were repressed in T cells and other cell lines, were Drosha-dependent and could also be modulated by Rev in an unspliced state. Mutant viruses that contained genomic mutations that reflect alterations to show more derepressive effects in the 3′ untranslated region of the Renilla luciferase gene replicated more slowly than wild-type virus. These findings yield insights into the HIV-1 silencing sites that might allow the genome to avoid translational machinery and that might be utilized in coordinating virus production during initial virus replication. However, the function of Rev to modulate the silencing sites of unspliced RNAs would be advantageous for the efficient translation that is required to support protein production prior to viral packaging and particle production. PMID:23251516

  4. Cloning and sequencing of 28 kDa outer membrane protein gene of Brucella melitensis Rev. 1.

    PubMed

    Chaudhuri, Pallab; Kumar, S Vinoth; Prasad, Rajeev; Srivastava, S K; Yadav, M P

    2005-09-01

    Brucella melitensis is an organism of paramount zoonotic importance. The 28 kDa outer membrane protein (OMP) is one of the immunodominant antigens of B. melitensis. The gene encoding 28 kDa OMP (omp28) has been amplified from B. melitensis Rev. 1 strain. A PCR product of 753 bp, encoding complete omp28 gene of B. melitensis, was obtained. The gene was further cloned and sequenced. The nucleotide sequence of B. melitensis Rev. 1 strain showed substitution of 2 nucleotides from that of 16M strain.

  5. Safeguards Summary Event List (SSEL), January 1, 1990--December 31, 1996, Vol. 2, Rev. 5

    SciTech Connect

    1997-07-01

    The Safeguards Summary Event List (SSEL), Vol. 2, Rev. 5, provides brief summaries of several hundred safeguards-related events involving nuclear material or facilities regulated by the US Nuclear Regulatory Commission (NRC) which occurred and were reported from January 1, 1990, through December 31, 1996. Because of public interest, the Miscellaneous category includes a few events which involve either source material, byproduct material, or natural uranium which are exempt from safeguards requirements. Events are described under the categories of Bomb-related, Intrusion, Missing and/or Allegedly Stolen, Transportation-related, Tampering/Vandalism, Arson, Firearms, Radiological Sabotage, Nonradiological Sabotage, and Miscellaneous. The information contained in the event descriptions is derived primarily from official NRC reporting channels.

  6. Targeted site-specific cleavage of HIV-1 viral Rev responsive element by copper aminoglycosides.

    PubMed

    Sreedhara, A; Cowan, J A

    2001-02-01

    Site-specific cleavage of the HIV-1 viral Rev responsive element by copper aminoglycosides is reported under physiological conditions. This bubble and stem-loop RNA structure is efficiently targeted at micromolar concentrations of complex. The specificity of cleavage of structured viral RNA relative to a non-cognate tRNAPhe of well-defined secondary and tertiary structure is demonstrated. Cleavage products from simpler substrates [diribonucleotide (ApA) and 2',3'-cyclic monophosphate ester (cAMP)] were analyzed by 31P NMR and demonstrate a hydrolytic mechanism in the absence of external redox agents. These results demonstrate copper aminoglycosides to be highly efficient chemical nucleases with a targeting capability for viral RNA and suggest a novel methodology to counter RNA viruses.

  7. Modelling one row of Horns Rev wind farm with the Actuator Line Model with coarse resolution

    NASA Astrophysics Data System (ADS)

    Draper, M.; Guggeri, A.; Usera, G.

    2016-09-01

    Actuator models have been used to represent the presence of wind turbines in a simulation in the past few years. The Actuator Line Model (ALM) has shown to reproduce with reasonable accuracy the wind flow through wind turbines under different operational conditions. Nevertheless, there are not many simulations of wind farms performed with the ALM mainly because of its computational cost. The aim of the present paper is to evaluate the ALM in spatial resolutions coarser than what is generally recommended, also using larger time steps, in a simulation of a real wind farm. To accomplish this, simulations of one row of Horns Rev wind farm are performed, for different wind directions. It is concluded that the ALM is able to capture the main features of the interaction between wind turbines relaxing its resolution requirements. A sensitivity analysis is performed to assess the influence of the smearing factor and the spatial resolution.

  8. Erratum: Evidence of b-jet quenching in PbPb collisions at sNN=2.76TeV [Phys. Rev. Lett. 113 , 132301 (2014)

    SciTech Connect

    Chatrchyan, S.

    2015-07-10

    In our Letter, there was a component of the statistical uncertainty from the simulated PbPb Monte Carlo samples. This uncertainty was not propagated to all of the results. Figures 3 and 4 have been updated to reflect this source of uncertainty. In this case, the statistical uncertainties remain smaller than the systematic uncertainties in all cases such that the conclusions of the Letter are unaltered.

  9. 78 FR 27971 - Determination That REV-EYES (Dapiprazole Hydrochloride Ophthalmic Solution), 0.5%, Was Not...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-13

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration Determination That REV-EYES (Dapiprazole Hydrochloride Ophthalmic Solution), 0.5%, Was Not Withdrawn From Sale for Reasons of Safety or Effectiveness AGENCY:...

  10. Solution structures and characterization of human immunodeficiency virus Rev responsive element IIB RNA targeting zinc finger proteins.

    PubMed

    Mishra, Subrata H; Shelley, Christopher M; Barrow, Doyle J; Darby, Martyn K; Germann, Markus W

    2006-11-01

    The Rev responsive element (RRE), a part of unspliced human immunodeficiency virus (HIV) RNA, serves a crucial role in the production of infectious HIV virions. The viral protein Rev binds to RRE and facilitates transport of mRNA to the cytoplasm. Inhibition of the Rev-RRE interaction disrupts the viral life cycle. Using a phage display protocol, dual zinc finger proteins (ZNFs) were generated that bind specifically to RREIIB at the high affinity Rev binding site. These proteins were further shortened and simplified, and they still retained their RNA binding affinity. The solution structures of ZNF29 and a mutant, ZNF29G29R, have been determined by nuclear magnetic resonance (NMR) spectroscopy. Both proteins form C(2)H(2)-type zinc fingers with essentially identical structures. RNA protein interactions were evaluated quantitatively by isothermal titration calorimetry, which revealed dissociation constants (K(d)'s) in the nanomolar range. The interaction with the RNA is dependent upon the zinc finger structure; in the presence of EDTA, RNA binding is abolished. For both proteins, RNA binding is mediated by the alpha-helical portion of the zinc fingers and target the bulge region of RREIIB-TR. However, ZNF29G29R exhibits significantly stronger binding to the RNA target than ZNF29; this illustrates that the binding of the zinc finger scaffold is amenable to further improvements.

  11. 75 FR 32493 - NUREG-0654/FEMA-REP-, Rev. 1, Supplement 3, Guidance for Protective Action Recommendations for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-08

    ... Preparedness Program Manual and Supplement 4 to NUREG-0654/FEMA-REP-1, Rev.1 (74 FR 23198 published on May 18... comments, see the ``Announcement of Issuance for Public Comment, Availability'' (at 75 FR 10524, on March 8... of availability, titled ``Announcement of Issuance for Public Comment, Availability'' (75 FR...

  12. 76 FR 13449 - Proposed Collection; Comment Request for Revenue Procedure 2009-41 (Rev. Proc. 2002-59 Is...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-11

    .... 2002-59 Is Superseded) AGENCY: Internal Revenue Service (IRS), Treasury. ACTION: Notice and request for... 1995, Public Law 104-13 (44 U.S.C. 3506(c)(2)(A)). Currently, the IRS is soliciting comments concerning.... Revenue Procedure Number: Revenue Procedure 2009-41. (Rev. Proc. 2002-59 is superseded.) Abstract:...

  13. Rev1 is essential in generating G to C transversions downstream of the Ung2 pathway but not the Msh2+Ung2 hybrid pathway.

    PubMed

    Krijger, Peter Hugo Lodewijk; Tsaalbi-Shtylik, Anastasia; Wit, Niek; van den Berk, Paul Cornelius Maria; de Wind, Niels; Jacobs, Heinz

    2013-10-01

    Somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin (Ig) genes are initiated by the enzymatic deamination of cytosine (C) to uracil (U). Uracil-DNA-glycosylase (Ung2) converts uracils into apyrimidinic (AP) sites, which is essential for the generation of transversions (TVs) at G/C basepairs during SHM and for efficient DNA break formation during CSR. Besides Ung2, the mismatch repair protein Msh2 and the translesion synthesis (TLS) DNA polymerase (Pol) Rev1 are implicated in SHM and CSR. To further unravel the role of Rev1, we studied WT, Rev1-deficient, Msh2-deficient, and Rev1, Msh2 double-deficient B cells. Loss of Rev1 only slightly reduced CSR. During SHM G/C to C/G TVs are generated in both Ung2- and Ung+Msh2-dependent fashions. We found that Rev1 is essential for the Msh2-independent generation of these TVs downstream of Ung2-induced AP sites. In the Ung+Msh2 hybrid pathway, Rev1 is not essential and can be substituted by an alternative TLS Pol, especially when Rev1 is lacking. PMID:23857323

  14. Public Data Set: Erratum: "Multi-point, high-speed passive ion velocity distribution diagnostic on the Pegasus Toroidal Experiment" [Rev. Sci. Instrum. 83, 10D516 (2012)

    DOE Data Explorer

    Burke, Marcus G. [University of Wisconsin-Madison] (ORCID:0000000176193724); Fonck, Raymond J. [University of Wisconsin-Madison] (ORCID:0000000294386762); Bongard, Michael W. [University of Wisconsin-Madison] (ORCID:0000000231609746); Schlossberg, David J. [University of Wisconsin-Madison] (ORCID:0000000287139448); Winz, Gregory R. [University of Wisconsin-Madison] (ORCID:0000000177627184)

    2016-07-18

    This data set contains openly-documented, machine readable digital research data corresponding to figures published in M.G. Burke et al., 'Erratum: "Multi-point, high-speed passive ion velocity distribution diagnostic on the Pegasus Toroidal Experiment" [Rev. Sci. Instrum. 83, 10D516 (2012)],' Rev. Sci. Instrum. 87, 079902 (2016).

  15. Rev1 promotes replication through UV lesions in conjunction with DNA polymerases η, ι, and κ but not DNA polymerase ζ

    PubMed Central

    Yoon, Jung-Hoon; Park, Jeseong; Conde, Juan; Wakamiya, Maki; Prakash, Louise; Prakash, Satya

    2015-01-01

    Translesion synthesis (TLS) DNA polymerases (Pols) promote replication through DNA lesions; however, little is known about the protein factors that affect their function in human cells. In yeast, Rev1 plays a noncatalytic role as an indispensable component of Polζ, and Polζ together with Rev1 mediates a highly mutagenic mode of TLS. However, how Rev1 functions in TLS and mutagenesis in human cells has remained unclear. Here we determined the role of Rev1 in TLS opposite UV lesions in human and mouse fibroblasts and showed that Rev1 is indispensable for TLS mediated by Polη, Polι, and Polκ but is not required for TLS by Polζ. In contrast to its role in mutagenic TLS in yeast, Rev1 promotes predominantly error-free TLS opposite UV lesions in humans. The identification of Rev1 as an indispensable scaffolding component for Polη, Polι, and Polκ, which function in TLS in highly specialized ways opposite a diverse array of DNA lesions and act in a predominantly error-free manner, implicates a crucial role for Rev1 in the maintenance of genome stability in humans. PMID:26680302

  16. 75 FR 29358 - Maritime Security Directive 104-6 (Rev 2 and 3); Guidelines for U.S. Vessels Operating in High...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-25

    ... announced the release of MARSEC Directive 104-6 (71 FR 7054) for those owners and operators of vessels... robbery against ships are prevalent. MARSEC Directive 104-6 (Rev 2 and 3) also includes an annex that... areas where acts of piracy and armed robbery against ships is prevalent. MARSEC Directive 104-6 (Rev...

  17. Comment on "A model for phosphate glass topology considering the modifying ion sub-network" [J. Chem. Phys. 140, 154501 (2014)].

    PubMed

    Sidebottom, David L

    2015-03-14

    In a recent paper, Hermansen, Mauro, and Yue [J. Chem. Phys. 140, 154501 (2014)] applied the temperature-dependent constraint theory to model both the glass transition temperature, Tg, and fragility, m, of a series of binary alkali phosphate glasses of the form R2OxP2O5 1-x, where R represents an alkali species. Key to their success seems to be the retention of linear constraints between the alkali ion (R(+)) and the non-bridging oxygens near Tg, which allows the model to mimic a supposed minimum for both Tg(x) and m(x) located near x = 0.2. However, the authors have overlooked several recent studies that clearly show there is no minimum in m(x). We argue that the retention of the alkali ion constraints at these temperatures is unjustified and question whether the model calculations can be revised to meet the actual experimental data. We also discuss alternative interpretations for the fragility based on two-state thermodynamics that can accurately account for its compositional dependence.

  18. Comment on "Magnetic geometry and physics of advanced divertors: The X-divertor and the snowflake" [Phys. Plasmas 20, 102507 (2013)

    NASA Astrophysics Data System (ADS)

    Ryutov, D. D.; Cohen, R. H.; Rognlien, T. D.; Soukhanovskii, V. A.; Umansky, M. V.

    2014-05-01

    In the recently published paper "Magnetic geometry and physics of advanced divertors: The X-divertor and the snowflake" [Phys. Plasmas 20, 102507 (2013)], the authors raise interesting and important issues concerning divertor physics and design. However, the paper contains significant errors: (a) The conceptual framework used in it for the evaluation of divertor "quality" is reduced to the assessment of the magnetic field structure in the outer Scrape-Off Layer. This framework is incorrect because processes affecting the pedestal, the private flux region and all of the divertor legs (four, in the case of a snowflake) are an inseparable part of divertor operation. (b) The concept of the divertor index focuses on only one feature of the magnetic field structure and can be quite misleading when applied to divertor design. (c) The suggestion to rename the divertor configurations experimentally realized on NSTX (National Spherical Torus Experiment) and DIII-D (Doublet III-D) from snowflakes to X-divertors is not justified: it is not based on comparison of these configurations with the prototypical X-divertor, and it ignores the fact that the NSTX and DIII-D poloidal magnetic field geometries fit very well into the snowflake "two-null" prescription.

  19. Response to Comment on '#28;Twin Symmetry Texture of Energetically Condensed 2 Niobium Thin Films on Sapphire Substrate' #29; [J. Appl. Phys. 110, 033523(2011)

    SciTech Connect

    Xin Zhao, Charles Reece, Phillips Larry, Mahadevan Krishnan, Kang Seo

    2012-07-01

    Welander commented that in our article [J. Appl. Phys. 110, 033523(2011)] , Zhao et al claim to have found a new three-dimensional (3D) relationship for niobium-on-sapphire epitaxy”. Welander might have misunderstood the purpose of our article, which was to show that energetic condensation of Nb on sapphire drives crystal growth that is quite distinct from the type of epitaxy encountered in lower energy deposition. Welander is correct about the misidentified crystal-directions in the top-view sapphire lattice (Fig.4[ref.1]). He is also correct about the misorientation of the pole figures in Fig4[ref.1]. In Fig.1 of this response, we have corrected these errors. Perhaps because of these errors, Welander misconstrued our discussion of the Nb crystal growth as claiming a new 3D registry. That was not our intention. Rather, we wished to highlight the role of energetic condensation that drives low-defect crystal growth by a combination of non-equilibrium sub-plantation that disturbs the substrate lattice and thermal annealing that annihilates defects and promotes large-grain crystal growth.

  20. Comment on “A model for phosphate glass topology considering the modifying ion sub-network” [J. Chem. Phys. 140, 154501 (2014)

    SciTech Connect

    Sidebottom, David L.

    2015-03-14

    In a recent paper, Hermansen, Mauro, and Yue [J. Chem. Phys. 140, 154501 (2014)] applied the temperature-dependent constraint theory to model both the glass transition temperature, T{sub g}, and fragility, m, of a series of binary alkali phosphate glasses of the form (R{sub 2}O){sub x}(P{sub 2}O{sub 5}){sub 1−x}, where R represents an alkali species. Key to their success seems to be the retention of linear constraints between the alkali ion (R{sup +}) and the non-bridging oxygens near T{sub g}, which allows the model to mimic a supposed minimum for both T{sub g}(x) and m(x) located near x = 0.2. However, the authors have overlooked several recent studies that clearly show there is no minimum in m(x). We argue that the retention of the alkali ion constraints at these temperatures is unjustified and question whether the model calculations can be revised to meet the actual experimental data. We also discuss alternative interpretations for the fragility based on two-state thermodynamics that can accurately account for its compositional dependence.

  1. Reply to "Comment on `Generalized exclusion processes: Transport coefficients' "

    NASA Astrophysics Data System (ADS)

    Arita, Chikashi; Krapivsky, P. L.; Mallick, Kirone

    2016-07-01

    We reply to the Comment of Becker, Nelissen, Cleuren, Partoens, and Van den Broeck [Phys. Rev. E 93, 046101 (2016), 10.1103/PhysRevE.93.046101] on our article [Arita, Krapivsky, and Mallick, Phys. Rev. E 90, 052108 (2014), 10.1103/PhysRevE.90.052108] about the transport properties of a class of generalized exclusion processes.

  2. REVS: a radar-based enhanced vision system for degraded visual environments

    NASA Astrophysics Data System (ADS)

    Brailovsky, Alexander; Bode, Justin; Cariani, Pete; Cross, Jack; Gleason, Josh; Khodos, Victor; Macias, Gary; Merrill, Rahn; Randall, Chuck; Rudy, Dean

    2014-06-01

    Sierra Nevada Corporation (SNC) has developed an enhanced vision system utilizing fast-scanning 94 GHz radar technology to provide three-dimensional measurements of an aircraft's forward external scene topography. This threedimensional data is rendered as terrain imagery, from the pilot's perspective, on a Head-Up Display (HUD). The image provides the requisite "enhanced vision" to continue a safe approach along the flight path below the Decision Height (DH) in Instrument Meteorological Conditions (IMC) that would otherwise be cause for a missed approach. Terrain imagery is optionally fused with digital elevation model (DEM) data of terrain outside the radar field of view, giving the pilot additional situational awareness. Flight tests conducted in 2013 show that REVS™ has sufficient resolution and sensitivity performance to allow identification of requisite visual references well above decision height in dense fog. This paper provides an overview of the Enhanced Flight Vision System (EFVS) concept, of the technology underlying REVS, and a detailed discussion of the flight test results.

  3. Domain- and nucleotide-specific Rev response element regulation of feline immunodeficiency virus production

    PubMed Central

    Na, Hong; Huisman, Willem; Ellestad, Kristofor K.; Phillips, Tom R.; Power, Christopher

    2010-01-01

    Computational analysis of feline immunodeficiency virus (FIV) RNA sequences indicated that common FIV strains contain a rev response element (RRE) defined by a long unbranched hairpin with 6 stem-loop sub-domains, termed stem-loop A (SLA). To examine the role of the RNA secondary structure of the RRE, mutational analyses were performed in both an infectious FIV molecular clone and a FIV CAT-RRE reporter system. These studies disclosed that the stems within SLA (SA1, 2, 3, 4, and 5) of the RRE were critical but SA6 was not essential for FIV replication and CAT expression. These studies also revealed that the secondary structure rather than an antisense protein (ASP) mediates virus expression and replication in vitro. In addition, a single synonymous mutation within the FIV-RRE, SA3/45, reduced viral reverse transcriptase activity and p24 expression after transfection but in addition also showed a marked reduction in viral expression and production following infection. PMID:20570310

  4. Dynamical mechanism of Bmal 1 / Rev- erbα loop in circadian clock

    NASA Astrophysics Data System (ADS)

    Li, Ying; Liu, Zengrong

    2015-07-01

    In mammals, the circadian clock is driven by multiple integrated transcriptional feedback loops involving three kinds of central clock-controlled elements (CCEs): E-boxes, D-boxes and ROR-elements. With the aid of CCEs, the concentrations of the active proteins are approximated by the delayed concentrations of mRNAs, which simplifies the circadian system drastically. The regulatory loop composed by BMAL1 and REV-ERB- α plays important roles in circadian clock. With delay differential equations, we gave a mathematical model of this loop and investigated its dynamical mechanisms. Specially, we theoretically provided the sufficient conditions for sustained oscillation of the loop with Hopf bifurcation theory. The total of delays determines the emergence of oscillators, which explains the crucial roles of delays in circadian clock revealed by biological experiments. Numerically, we studied the amplitude and period against the variations of delays and the degradation rates. The different sensitivities of amplitude and period on these factors provide ideas to adjust the amplitude or period of circadian oscillators.

  5. Estimating the elastic modulus and REV of Inada Granite using a homogenization analysis method

    NASA Astrophysics Data System (ADS)

    Chae, B.; Choi, J.; Seo, Y.

    2013-12-01

    The elastic behavior of granite, which is a composite of various minerals, was calculated with consideration of fracture distribution using the homogenization theory. Microscopic and photographic analyses were conducted to measure the random distribution of the minerals and microcracks in Inada granite. A modal analysis was conducted simultaneously with the photographic analysis. The elastic homogenization theory was applied to calculate the elastic modulus of Inada granite using the results of the modal analysis. The elastic modulus that was determined using the homogenization analysis became constant when the size of the model was larger than 254.3 mm2 (1,156 elements). The elastic modulus, which was calculated as 94.1 GPa, was lower than the experimental value by 7.3 GPa. After the distribution of the rock-forming elements and the elastic modulus were calculated, the representative elementary volume (REV) of the fine-grained Inada granite was estimated to be 254.3 mm2 (1,156 elements).

  6. In Vitro Metabolic Studies of REV-ERB Agonists SR9009 and SR9011

    PubMed Central

    Geldof, Lore; Deventer, Koen; Roels, Kris; Tudela, Eva; Van Eenoo, Peter

    2016-01-01

    SR9009 and SR9011 are attractive as performance-enhancing substances due to their REV-ERB agonist effects and thus circadian rhythm modulation activity. Although no pharmaceutical preparations are available yet, illicit use of SR9009 and SR9011 for doping purposes can be anticipated, especially since SR9009 is marketed in illicit products. Therefore, the aim was to identify potential diagnostic metabolites via in vitro metabolic studies to ensure effective (doping) control. The presence of SR9009 could be demonstrated in a black market product purchased over the Internet. Via human liver microsomal metabolic assays, eight metabolites were detected for SR9009 and fourteen metabolites for SR9011 by liquid chromatography–high resolution mass spectrometry (LC–HRMS). Structure elucidation was performed for all metabolites by LC–HRMS product ion scans in both positive and negative ionization mode. Retrospective data analysis was applied to 1511 doping control samples previously analyzed by a full-scan LC–HRMS screening method to verify the presence of SR9009, SR9011 and their metabolites. So far, the presence of neither the parent compound nor the metabolites could be detected in routine urine samples. However, to further discourage use of these potentially harmful compounds, incorporation of SR9009 and SR9011 into screening methods is highly recommended. PMID:27706103

  7. Association of Rev-erbα in adipose tissues with Type 2 diabetes mellitus amelioration after gastric bypass surgery in Goto-Kakizaki rats.

    PubMed

    Zhang, Rui; Yan, Caifeng; Zhou, Xinrong; Qian, Bangguo; Li, Fuqiang; Sun, Yidan; Shi, Chen; Li, Bing; Saito, Shigeru; Horimoto, Katsuhisa; Zhou, Huarong

    2013-07-15

    We estimated the key molecules related to Type 2 diabetes mellitus (T2DM) in adipose, liver, and muscle tissues, from nonobese diabetic Goto-Kakizaki (GK) rats and their Wistar controls, by computationally analyzing the expression profiles in open source data. With the aid of information from previous reports, Rev-erbα in adipose tissue emerged as one of the most plausible candidates. Here, in animal models, including GK rats surgically treated to ameliorate T2DM, we examined the association of Rev-erbα in adipose tissue with T2DM progression. After analyses of the Rev-erbα mRNA expression in the adipose tissue of our animal models, we compared the Rev-erbα protein expression levels in the adipose, liver, and muscle tissues of GK and Wistar controls at the ages of 1 mo (M), 3M, and 6M. The Rev-erbα protein levels in adipose tissue showed a distinctive pattern, with the negative correlation of an increasing trend in GK rats, and a decreasing trend in Wistar rats during aging, from those in liver and muscle tissues. Moreover, dysregulation of the circadian Rev-erbα expression in the adipose tissue of 6-mo-old GK rats was also observed. In particular, we ameliorated T2DM in GK rats by gastric bypass surgery, and revealed that T2DM amelioration in diabetic GK rats was associated with improved circadian Rev-erbα expression, in a comparison between the surgically treated and untreated GK rats. The roles of Rev-erbα in adipose tissue were further investigated by observations of Rev-erbα-related molecules, with reference to previous reports.

  8. Growth-inhibitory Activity and Downregulation of the Class II Tumor-suppressor Gene H-rev107 in Tumor Cell Lines and Experimental Tumors

    PubMed Central

    Sers, Christine; Emmenegger, Urban; Husmann, Knut; Bucher, Katharina; Andres, Ann-Catherine; Schäfer, Reinhold

    1997-01-01

    The H-rev107 gene is a new class II tumor suppressor, as defined by its reversible downregulation and growth-inhibiting capacity in HRAS transformed cell lines. Overexpression of the H-rev107 cDNA in HRAS-transformed ANR4 hepatoma cells or in FE-8 fibroblasts resulted in 75% reduction of colony formation. Cell populations of H-rev107 transfectants showed an attenuated tumor formation in nude mice. Cells explanted from tumors or maintained in cell culture for an extended period of time no longer exhibited detectable levels of the H-rev107 protein, suggesting strong selection against H-rev107 expression in vitro and in vivo. Expression of the truncated form of H-rev107 lacking the COOH-terminal membrane associated domain of 25 amino acids, had a weaker inhibitory effect on proliferation in vitro and was unable to attenuate tumor growth in nude mice. The H-rev107 mRNA is expressed in most adult rat tissues, and immunohistochemical analysis showed expression of the protein in differentiated epithelial cells of stomach, of colon and small intestine, in kidney, bladder, esophagus, and in tracheal and bronchial epithelium. H-rev107 gene transcription is downregulated in rat cell lines derived from liver, kidney, and pancreatic tumors and also in experimental mammary tumors expressing a RAS transgene. In colon carcinoma cell lines only minute amounts of protein were detectable. Thus, downregulation of H-rev107 expression may occur at the level of mRNA or protein. PMID:9049257

  9. Final Report - Sulfate Solubility in RPP-WTP HLW Glasses, VSL-06R6780-1, Rev. 0

    SciTech Connect

    Kruger, Albert A.; Pegg, I. L.; Feng, A.; Gan, H.; Kot, W. K.

    2013-12-03

    This report describes the results of work and testing specified by Test Specifications 24590-HLW-TSP-RT-01-006 Rev 1, Test Plans VSL-02T7800-1 Rev 1 and Test Exceptions 24590-HLW-TEF-RT-05-00007. The work and any associated testing followed established quality assurance requirements and were conducted as authorized. The descriptions provided in this report are an accurate account of both the conduct of the work and the data collected. Results required by the Test Plans are reported. Also reported are any unusual or anomalous occurrences that are different from the starting hypotheses. The test results and this report have been reviewed and verified.

  10. Nuclear receptor REV-ERBα mediates circadian sensitivity to mortality in murine vesicular stomatitis virus-induced encephalitis.

    PubMed

    Gagnidze, Khatuna; Hajdarovic, Kaitlyn H; Moskalenko, Marina; Karatsoreos, Ilia N; McEwen, Bruce S; Bulloch, Karen

    2016-05-17

    Certain components and functions of the immune system, most notably cytokine production and immune cell migration, are under circadian regulation. Such regulation suggests that circadian rhythms may have an effect on disease onset, progression, and resolution. In the vesicular stomatitis virus (VSV)-induced encephalitis model, the replication, caudal penetration, and survivability of intranasally applied VSV depends on both innate and adaptive immune mechanisms. In the current study, we investigated the effect of circadian time of infection on the progression and outcome of VSV-induced encephalitis and demonstrated a significant decrease in the survival rate in mice infected at the start of the rest cycle, zeitgeber time 0 (ZT0). The lower survival rate in these mice was associated with higher levels of circulating chemokine (C-C motif) ligand 2 (CCL2), a greater number of peripherally derived immune cells accumulating in the olfactory bulb (OB), and increased production of proinflammatory cytokines, indicating an immune-mediated pathology. We also found that the acrophase of molecular circadian clock component REV-ERBα mRNA expression in the OB coincides with the start of the active cycle, ZT12, when VSV infection results in a more favorable outcome. This result led us to hypothesize that REV-ERBα may mediate the circadian effect on survival following VSV infection. Blocking REV-ERBα activity before VSV administration resulted in a significant increase in the expression of CCL2 and decreased survival in mice infected at the start of the active cycle. These data demonstrate that REV-ERBα-mediated inhibition of CCL2 expression during viral-induced encephalitis may have a protective effect. PMID:27143721

  11. Cooperativity among Rev-Associated Nuclear Export Signals Regulates HIV-1 Gene Expression and Is a Determinant of Virus Species Tropism

    PubMed Central

    Aligeti, Mounavya; Behrens, Ryan T.; Pocock, Ginger M.; Schindelin, Johannes; Dietz, Christian; Eliceiri, Kevin W.; Swanson, Chad M.; Malim, Michael H.; Ahlquist, Paul

    2014-01-01

    ABSTRACT Murine cells exhibit a profound block to HIV-1 virion production that was recently mapped to a species-specific structural attribute of the murine version of the chromosomal region maintenance 1 (mCRM1) nuclear export receptor and rescued by the expression of human CRM1 (hCRM1). In human cells, the HIV-1 Rev protein recruits hCRM1 to intron-containing viral mRNAs encoding the Rev response element (RRE), thereby facilitating viral late gene expression. Here we exploited murine 3T3 fibroblasts as a gain-of-function system to study hCRM1's species-specific role in regulating Rev's effector functions. We show that Rev is rapidly exported from the nucleus by mCRM1 despite only weak contributions to HIV-1's posttranscriptional stages. Indeed, Rev preferentially accumulates in the cytoplasm of murine 3T3 cells with or without hCRM1 expression, in contrast to human HeLa cells, where Rev exhibits striking en masse transitions between the nuclear and cytoplasmic compartments. Efforts to bias Rev's trafficking either into or out of the nucleus revealed that Rev encoding a second CRM1 binding domain (Rev-2xNES) or Rev-dependent viral gag-pol mRNAs bearing tandem RREs (GP-2xRRE), rescue virus particle production in murine cells even in the absence of hCRM1. Combined, these results suggest a model wherein Rev-associated nuclear export signals cooperate to regulate the number or quality of CRM1's interactions with viral Rev/RRE ribonucleoprotein complexes in the nucleus. This mechanism regulates CRM1-dependent viral gene expression and is a determinant of HIV-1's capacity to produce virions in nonhuman cell types. IMPORTANCE Cells derived from mice and other nonhuman species exhibit profound blocks to HIV-1 replication. Here we elucidate a block to HIV-1 gene expression attributable to the murine version of the CRM1 (mCRM1) nuclear export receptor. In human cells, hCRM1 regulates the nuclear export of viral intron-containing mRNAs through the activity of the viral Rev

  12. Response to {open_quotes}Comment on {open_quote}Reversible work of formation of an embryo of a new phase within a uniform macroscopic mother phase{close_quote}thinsp{close_quotes} [J. Chem. Phys. {bold 111}, 3769 (1999)

    SciTech Connect

    Debenedetti, P.G.; Reiss, H.

    1999-08-01

    External constraints are necessary in order to calculate the energetics of embryo formation when the embryo is not a critical nucleus. The expression for the reversible work of formation obtained in by Debenedetti and Reiss [J. Chem. Phys. {bold 108}, 5498 (1998)] is rigorous and valid regardless of the relative densities of the embryo and mother phase. {copyright} {ital 1999 American Institute of Physics.}

  13. Suppression of Rev3, the catalytic subunit of Pol{zeta}, sensitizes drug-resistant lung tumors to chemotherapy.

    PubMed

    Doles, Jason; Oliver, Trudy G; Cameron, Eleanor R; Hsu, Gerald; Jacks, Tyler; Walker, Graham C; Hemann, Michael T

    2010-11-30

    Platinum-based chemotherapeutic drugs are front-line therapies for the treatment of non-small cell lung cancer. However, intrinsic drug resistance limits the clinical efficacy of these agents. Recent evidence suggests that loss of the translesion polymerase, Polζ, can sensitize tumor cell lines to cisplatin, although the relevance of these findings to the treatment of chemoresistant tumors in vivo has remained unclear. Here, we describe a tumor transplantation approach that enables the rapid introduction of defined genetic lesions into a preclinical model of lung adenocarcinoma. Using this approach, we examined the effect of impaired translesion DNA synthesis on cisplatin response in aggressive late-stage lung cancers. In the presence of reduced levels of Rev3, an essential component of Polζ, tumors exhibited pronounced sensitivity to cisplatin, leading to a significant extension in overall survival of treated recipient mice. Additionally, treated Rev3-deficient cells exhibited reduced cisplatin-induced mutation, a process that has been implicated in the induction of secondary malignancies following chemotherapy. Taken together, our data illustrate the potential of Rev3 inhibition as an adjuvant therapy for the treatment of chemoresistant malignancies, and highlight the utility of rapid transplantation methodologies for evaluating mechanisms of chemotherapeutic resistance in preclinical settings.

  14. Exome sequencing reveals recurrent REV3L mutations in cisplatin-resistant squamous cell carcinoma of head and neck

    PubMed Central

    Huang, Kie Kyon; Jang, Kang Won; Kim, Sangwoo; Kim, Han Sang; Kim, Sung-Moo; Kwon, Hyeong Ju; Kim, Hye Ryun; Yun, Hwan Jung; Ahn, Myung Ju; Park, Keon Uk; Ramnarayanan, Kalpana; McPherson, John R.; Zhang, Shenli; Rhee, Je-Keun; Vettore, André L.; Das, Kakoli; Ishimoto, Takatsugu; Kim, Joo Hang; Koh, Yoon Woo; Kim, Se Hun; Choi, Eun Chang; Teh, Bin Tean; Rozen, Steven G.; Kim, Tae-Min; Tan, Patrick; Cho, Byoung Chul

    2016-01-01

    Dacomitinib, an irreversible pan-HER inhibitor, had shown modest clinical activity in squamous cell carcinoma of head and neck (SCCHN) patients. Therefore, validated predictive biomarkers are required to identify patients most likely to benefit from this therapeutic option. To characterize the genetic landscape of cisplatin-treated SCCHN genomes and identify potential predictive biomarkers for dacomitinib sensitivity, we performed whole exome sequencing on 18 cisplatin-resistant metastatic SCCHN tumors and their matched germline DNA. Platinum-based chemotherapy elevated the mutation rates of SCCHN compared to chemotherapy-naïve SCCHNs. Cisplatin-treated SCCHN genomes uniquely exhibited a novel mutational signature characterized by C:G to A:T transversions at CCR sequence contexts that may have arisen due to error-prone translesional synthesis. Somatic mutations in REV3L, the gene encoding the catalytic subunit of DNA polymerase ζ involved in translesional synthesis, are significantly enriched in a subset of patients who derived extended clinical benefit to dacomitinib (P = 0.04). Functional assays showed that loss-of-function of REV3L dramatically enhanced the sensitivity of SCCHN cells to dacomitinib by the loss of both translesion synthesis and homologous recombination pathways. Our data suggest that the ‘platinum’ mutational signature and inactivation of REV3L may inform treatment options in patients of recurrent SCCHN. PMID:26790612

  15. Protein-Template-Directed Synthesis across an Acrolein-Derived DNA Adduct by Yeast Rev1 DNA Polymerase

    SciTech Connect

    Nair, Deepak T.; Johnson, Robert E.; Prakash, Louise; Prakash, Satya; Aggarwal, Aneel K.

    2008-07-08

    Acrolein is generated as the end product of lipid peroxidation and is also a ubiquitous environmental pollutant. Its reaction with the N{sup 2} of guanine leads to a cyclic {gamma}-HOPdG adduct that presents a block to normal replication. We show here the yeast Rev1 incorporates the correct nucleotide C opposite a permanently ring-closed form of {gamma}-HOPdG (PdG) with nearly the same efficiency as opposite an undamaged G. The structural bais of this action lies in the eviction of PdG adduct from the Rev1 active site, and the pairing of incoming dCTP with a surrogate' arginine residue. We also show that yeast Pol{zeta} can carry out the subsequent extension reaction. Together, our studies reveal how the exocyclic PdG adduct is accommodated in a DNA polymerase active site, and they show that the combined action of Rev1 and Pol{zeta} provides for accurate and efficient synthesis through this potentially carcinogenic DNA lesion.

  16. Re(V) and Re(III) complexes with sal2phen and triphenylphosphine: rearrangement, oxidation and reduction.

    PubMed

    Lane, Stephanie Renee; Sisay, Nebiat; Carney, Brett; Dannoon, Shorouk; Williams, Stephen; Engelbrecht, Hendrik Petrus; Barnes, Charles Leslie; Jurisson, Silvia Sabine

    2011-01-01

    Reactions of Re(V), tetradentate Schiff base complexes with tertiary phosphines have previously yielded both rearranged Re(V) and reduced Re(III) complexes. To further understand this chemistry, the rigid diiminediphenol (N(2)O(2)) Schiff base ligand sal(2)phen (N,N'-o-phenylenebis(salicylaldimine)) was reacted with (n-Bu(4)N)[ReOCl(4)] to yield trans-[ReOCl(sal(2)phen)] (1). On reaction with triphenylphosphine (PPh(3)), a rearranged Re(V) product cis-[ReO(PPh(3))(sal(2)phen*)]PF(6) (2), in which one of the imines was reduced to an amine during the reaction, and the reduced Re(III) products trans-[ReCl(PPh(3))(sal(2)phen)] (4) and trans-[Re(PPh(3))(2)(sal(2)phen)](+) (5) were isolated. Reaction of sal(2)phen with [ReCl(3)(PPh(3))(2)(CH(3)CN)] resulted in the isolation of [ReCl(2)(PPh(3))(2)(salphen)] (3). The compounds were characterized using standard spectroscopic methods, elemental analyses and single crystal X-ray crystallography. PMID:21079821

  17. Re(V) and Re(III) Complexes with Sal2phen and Triphenylphosphine: Rearrangement, Oxidation and Reduction

    PubMed Central

    Lane, Stephanie Renee; Sisay, Nebiat; Carney, Brett; Dannoon, Shorouk; Williams, Stephen; Engelbrecht, Hendrik Petrus; Barnes, Charles Leslie; Jurisson, Silvia Sabine

    2010-01-01

    Reactions of ReV, tetradentate Schiff base complexes with tertiary phosphines have previously yielded both rearranged ReV and reduced ReIII complexes. To further understand this chemistry, the rigid diiminediphenol (N2O2) Schiff base ligand sal2phen (N,N’-o-phenylenebis(salicylaldimine)) was reacted with (n-Bu4N)[ReOCl4] to yield trans-[ReOCl(sal2phen)] (1). On reaction with triphenylphosphine (PPh3), a rearranged ReV product cis-[ReO(PPh3)(sal2phen*)]PF6 (2), in which one of the imines was reduced to an amine during the reaction, and the reduced ReIII products trans-[ReCl(PPh3)(sal2phen)] (4) and trans- [Re(PPh3)2(sal2phen)]+ (5) were isolated. Reaction of sal2phen with [ReCl3(PPh3)2(CH3CN)] resulted in the isolation of [ReCl2(PPh3)2(salphen)] (3). The compounds were characterized using standard spectroscopic methods, elemental analyses and single crystal X-ray crystallography. PMID:21079821

  18. Epitopes of human immunodeficiency virus regulatory proteins tat, nef, and rev are expressed in normal human tissue.

    PubMed Central

    Parmentier, H. K.; van Wichen, D. F.; Meyling, F. H.; Goudsmit, J.; Schuurman, H. J.

    1992-01-01

    The expression of regulatory proteins tat, rev, and nef of human immunodeficiency virus type-1 (HIV-1) and tat of HIV-2 was studied in frozen sections of lymph nodes from HIV-1-infected individuals, and various tissues from uninfected persons. In HIV-1-positive lymph nodes, monoclonal antibodies to HIV-1-tat stained solitary cells in the germinal centers and interfollicular zones, and vascular endothelium. Staining by an anti-nef monoclonal antibody was restricted to follicular dendritic cells, whereas anti-rev antibody bound to fibriohistiocytes and high endothelial venules. The antibodies used labeled several cell types in tissues from uninfected individuals. Anti-HIV-1-tat antibodies labeled blood vessels and Hassall's corpuscles in skin and thymus; goblet cells in intestinal tissue and trachea; neural cells in brain and spinal cord; and zymogen-producing cells in pancreas. Anti-rev antibody stained high endothelial venules, Hassall's corpuscles and histiocytes. One anti-nef antibody solely stained follicular dendritic cells in spleen, tonsil, lymph node and Peyer's patches, whereas two other anti-nef antibodies bound to astrocytes, solitary cells in the interfollicular zones of lymph nodes, and skin cells. The current results hamper the immunohistochemical study for pathogenetic and diagnostic use of HIV regulatory protein expression in infected tissue specimens or cells. Images Figure 1 Figure 3 Figure 4 Figure 5 Figure 6 PMID:1279980

  19. Electronic spectra of oxocomplexes of Re(V) with thiolato ligands

    NASA Astrophysics Data System (ADS)

    Gancheff, Jorge S.; Denis, Pablo A.; Hahn, F. Ekkehardt

    2010-08-01

    The electronic spectra of monooxo complexes of rhenium(V) with 1,2-benzenedithiolato (bdt 2-), 3,4-toluenenedithiolato (tdt 2-), maleonitriledithiolato (mnt 2-), and 1,2-dithiooxalato (dto 2-) ligands were investigated at the TD-DFT level employing several functionals and basis sets. The most important transitions are due to ligand-to-metal charge transfer (LMCT) with some minor contribution of ligand-to-metal-ligand charge transfer (LMLCT). However, for [ReO(dto) 2] - this statement does not hold because the transitions are due to metal-ligand-to-metal-ligand charge transfer (MLMLCT). This observation arises from the presence of the oxalate groups. These substituents increase the flexibility of this complex with respect to the complexes containing bdt 2-, mnt 2- and tdt 2-. In these complexes, the C-C backbone imposes a rigid geometry, which leads to the occupied rhenium-orbitals lying energetically below the sulfur-based orbitals. For the complexes [ReO(bdt) 2] -, [ReO(mnt) 2] - and [ReO(tdt) 2] -, the HOMO is a sulfur-based out-of-plane molecular orbital. However, the HOMO of [ReO(dto) 2] - shows a high contribution of the rhenium dx2- y2 and in-plane sulfur-centered orbitals. The comparison of the results obtained with several functionals clearly point to the PBE1PBE/LANL2DZ method as the best TD-DFT method to investigate the electronic spectra of monooxo complexes of Re(V) with thiolato ligands. The results obtained with larger basis sets suggest that the agreement between experiment and theory was due to an error cancellation between basis set incompleteness and deficiencies in the DFT methods.

  20. Dinuclear triple-stranded complexes of ReV with bis(benzene-o-dithiolato) ligands

    NASA Astrophysics Data System (ADS)

    Gancheff, Jorge S.; Hahn, F. Ekkehardt

    2012-12-01

    The reaction of K2ReCl6 with 1,2-bis(2,3-dimercaptobenzamido)ethane (H4-1), and 1,2-bis(2,3-dimercaptobenzamido)benzene (H4-2) in the presence of Na2CO3 in methanol affords dinuclear complexes of ReV. Experimental evidence supports the presence of self-assembled complexes with two {Re(S2C6H3)3} units connected in a triple-stranded fashion. Density Functional Theory (DFT) studies on geometry and electronic properties were conducted employing the hybrid B3LYP and PBE1PBE functionals. The helical (ΔΔ and ΛΛ) and meso-helical (ΔΛ) isomers were considered. For the helicate complexes included in this study, differences in the stability of the isomers were observed originating in different steric and strain interactions between the three ligand strands. The geometries at the minimum exhibit a distorted trigonal-prismatic coordination environment at the metal centers. Natural bond orbitals (NBO) analysis indicates the presence of Re-S bonds which are strongly polarized toward the non-metal. Time-Dependent DFT (TD-DFT) calculations were performed for a further understanding of the optical spectra. The calculations show the occupied 5d orbitals of the rhenium lying beneath occupied sulfur-based MOs. The general features of the electronic spectra in the visible region are reasonably reproduced by the calculations. The analysis of molecular orbitals also allows the assignment of the origin for all experimentally detected absorption bands. In the high-energy region of the spectrum the absorptions are attributed to ligand-to-metal-ligand charge transfer (LMLCT), in which sulfur-based orbitals and unoccupied orbitals at the rhenium atom and the benzene-o-dithiolato groups are involved. Also in the blue region, shoulders originating from LMLCT are observed.

  1. Mapping Wind Farm Loads and Power Production - A Case Study on Horns Rev 1

    NASA Astrophysics Data System (ADS)

    Galinos, Christos; Dimitrov, Nikolay; Larsen, Torben J.; Natarajan, Anand; Hansen, Kurt S.

    2016-09-01

    This paper describes the development of a wind turbine (WT) component lifetime fatigue load variation map within an offshore wind farm. A case study on the offshore wind farm Horns Rev I is conducted with this purpose, by quantifying wake effects using the Dynamic Wake Meandering (DWM) method, which has previously been validated based on CFD, Lidar and full scale load measurements. Fully coupled aeroelastic load simulations using turbulent wind conditions are conducted for all wind directions and mean wind speeds between cut-in and cut-out using site specific turbulence level measurements. Based on the mean wind speed and direction distribution, the representative 20-year lifetime fatigue loads are calculated. It is found that the heaviest loaded WT is not the same when looking at blade root, tower top or tower base components. The blade loads are mainly dominated by the wake situations above rated wind speed and the highest loaded blades are in the easternmost row as the dominating wind direction is from West. Regarding the tower components, the highest loaded WTs are also located towards the eastern central location. The turbines with highest power production are, not surprisingly, the ones facing a free sector towards west and south. The power production results of few turbines are compared with SCADA data. The results of this paper are expected to have significance for operation and maintenance planning, where the schedules for inspection and service activities can be adjusted to the requirements arising from the varying fatigue levels. Furthermore, the results can be used in the context of remaining fatigue lifetime assessment and planning of decommissioning.

  2. High energy neutrinos from astrophysical accelerators of cosmic ray nuclei

    NASA Astrophysics Data System (ADS)

    Anchordoqui, Luis A.; Hooper, Dan; Sarkar, Subir; Taylor, Andrew M.

    2008-02-01

    . Rev. Lett.6619912697(Erratum-ibid. 69 (1992) 2738)F.W.SteckerPhys. Rev. D722005107301A.AtoyanC.D.DermerPhys. Rev. Lett.872001221102L.A.AnchordoquiH.GoldbergF.HalzenT.J.WeilerPhys. Lett. B6002004202E.WaxmanJ.N.BahcallPhys. Rev. Lett.7819972292C.D.DermerA.AtoyanPhys. Rev. Lett.912003071102D.GuettaD.HooperJ.Alvarez-MunizF.HalzenE.ReuveniAstropart. Phys.202004429J.Alvarez-MunizF.HalzenD.W.HooperPhys. Rev. D622000093015A.LoebE.WaxmanJCAP06052006003S. Inoue, G. Sigl, F. Miniati, E. Armengaud, arXiv:astro-ph/0701167.E.WaxmanJ.N.BahcallPhys. Rev. D591999023002Phys. Rev. D642001023002K.MannheimR.J.ProtheroeJ.P.RachenPhys. Rev. D632001023003arXiv:astro-ph/9908031M.AhlersL.A.AnchordoquiH.GoldbergF.HalzenA.RingwaldT.J.WeilerPhys. Rev. D722005023001E.WaxmanAstrophys. J.4521995L1Note that the neutrino spectral shape can deviate from that for protons if the Feynman plateau is not flat in pseudo-rapidity space;L.AnchordoquiH.GoldbergC.NunezPhys. Rev. D712005065014This is in fact suggested by Tevatron data;F.AbeCDF CollaborationPhys. Rev. D4119902330J.G.LearnedS.PakvasaAstropart. Phys.31995267F.HalzenD.SaltzbergPhys. Rev. Lett.8119984305J.F.BeacomN.F.BellD.HooperS.PakvasaT.J.WeilerPhys. Rev. D682003093005(Erratum-ibid. D 72 (2005) 019901)L.A.AnchordoquiH.GoldbergF.HalzenT.J.WeilerPhys. Lett. B593200442L.A.AnchordoquiH.GoldbergF.HalzenT.J.WeilerPhys. Lett. B621200518A.M.HillasAnn. Rev. Astron. Astrophys.221984425For a general discussion on the acceleration time-scale in these sources see, e.g.,D.F.TorresL.A.AnchordoquiRep. Prog. Phys.6720041663M.C.BegelmanB.RudakM.SikoraAstrophys. J.362199038M.J.ChodorowskiA.A.ZdziarskiM.SikoraAstrophys. J.4001992181S.MichalowskiD.AndrewsJ.EickmeyerT.GentileN.MistryR.TalmanK.UenoPhys. Rev. Lett.391977737J.L.PugetF.W.SteckerJ.H.BredekampAstrophys. J.2051976638D.HooperS.SarkarA.M.TaylorAstropart. Phys.272007199The non-thermal energy release in GRBs is much smaller than that output by AGN.P.L.BiermannP.A.StrittmatterAstrophys. J.3221987643R.J.ProtheroeA.P.SzaboPhys

  3. Tissue damage drives co-localization of NF-κB, Smad3, and Nrf2 to direct Rev-erb sensitive wound repair in mouse macrophages

    PubMed Central

    Eichenfield, Dawn Z; Troutman, Ty Dale; Link, Verena M; Lam, Michael T; Cho, Han; Gosselin, David; Spann, Nathanael J; Lesch, Hanna P; Tao, Jenhan; Muto, Jun; Gallo, Richard L; Evans, Ronald M; Glass, Christopher K

    2016-01-01

    Although macrophages can be polarized to distinct phenotypes in vitro with individual ligands, in vivo they encounter multiple signals that control their varied functions in homeostasis, immunity, and disease. Here, we identify roles of Rev-erb nuclear receptors in regulating responses of mouse macrophages to complex tissue damage signals and wound repair. Rather than reinforcing a specific program of macrophage polarization, Rev-erbs repress subsets of genes that are activated by TLR ligands, IL4, TGFβ, and damage-associated molecular patterns (DAMPS). Unexpectedly, a complex damage signal promotes co-localization of NF-κB, Smad3, and Nrf2 at Rev-erb-sensitive enhancers and drives expression of genes characteristic of multiple polarization states in the same cells. Rev-erb-sensitive enhancers thereby integrate multiple damage-activated signaling pathways to promote a wound repair phenotype. DOI: http://dx.doi.org/10.7554/eLife.13024.001 PMID:27462873

  4. 76 FR 2402 - Maritime Security Directive 104-6 (Rev 5); Guidelines for U.S. Vessels Operating in High Risk Waters

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-13

    ... Indian Ocean. With the issuance of (Rev 5), MARSEC Directive 104-6 (Rev 4) is no longer valid. To support... pirates operate along a 2,300 mile coast and in 2.5 million square miles of ocean. Given the size and... Directive 104-6 (71 FR 7054) for those owners and operators of vessels subject to 33 CFR parts 101 and...

  5. Production of HIV Particles Is Regulated by Altering Sub-Cellular Localization and Dynamics of Rev Induced by Double-Strand RNA Binding Protein

    PubMed Central

    Urcuqui-Inchima, Silvio; Patiño, Claudia; Zapata, Ximena; García, María Patricia; Arteaga, José; Chamot, Christophe; Kumar, Ajit; Hernandez-Verdun, Danièle

    2011-01-01

    Human immunodeficiency virus (HIV)-1 encoded Rev is essential for export from the nucleus to the cytoplasm, of unspliced and singly spliced transcripts coding for structural and nonstructural viral proteins. This process is spatially and temporally coordinated resulting from the interactions between cellular and viral proteins. Here we examined the effects of the sub-cellular localization and dynamics of Rev on the efficiency of nucleocytoplasmic transport of HIV-1 Gag transcripts and virus particle production. Using confocal microscopy and fluorescence recovery after bleaching (FRAP), we report that NF90ctv, a cellular protein involved in Rev function, alters both the sub-cellular localization and dynamics of Rev in vivo, which drastically affects the accumulation of the viral protein p24. The CRM1–dependent nuclear export of Gag mRNA linked to the Rev Response Element (RRE) is dependent on specific domains of the NF90ctv protein. Taken together, our results demonstrate that the appropriate intracellular localization and dynamics of Rev could regulate Gag assembly and HIV-1 replication. PMID:21364984

  6. Soil hydraulic properties and REV study using X-ray microtomography and pore-scale modelling: saturated hydraulic conductivity

    NASA Astrophysics Data System (ADS)

    Gerke, Kirill; Khirevich, Siarhei; Sizonenko, Timofey; Karsanina, Marina; Umarova, Aminat; Korost, Dmitry; Matthai, Stephan; Mallants, Dirk

    2016-04-01

    To verify pore-scale modelling approach for determination of soil saturated hydraulic conductivity properties we scanned three cylindrical soil samples taken from A, Ah and B horizons using X-ray microtomography method. Resulting 3D soil images with resolutions of 15.25-20.96 μm were segmented into pores and solids and their maximum inscribed cube subvolumes were used as input data for three major pore-scale modelling methods to simulate saturated flow - lattice-Boltzmann method, finite-difference solution of the Stokes problem, and pore-network model. Provided that imaging resolution is high enough to capture the backbone of effective porosity and the main conducting pores all three methods resulted in simulated soil permeabilities close to experimental values for Ah and B samples. The resolution of A sample was not enough for an accurate modelling and we concluded that this soil requires multi-scale imaging to cover all relevant heterogeneities. We demonstrate that popular SWV method to choose segmentation threshold resulted in oversegmentation and order of magnitude higher permeability values. Careful manual thresholding combined with local segmentation algorithm provided much more accurate results. Detailed analysis of water retention curves showed that air-filled porosity at relevant pressure stages cannot be used for verification of the segmentation results. Representativity analysis by simulating flow in increasing soil volume up to 2.8 cm3 revealed no representative elementary volume (REV) within Ah sample and non-uniqueness of REV for B sample. The latter was explained by soil structure non-stationarity. We further speculate that structures soil horizons can exhibit no REV at all. We discuss numerous advantages of coupled imaging and pore-scale modelling approach and show how it can become a successor of the conventional soil coring method to parametrize large scale continuum models.

  7. Erratum to “Axial and transverse acoustic radiation forces on a fluid sphere placed arbitrarily in Bessel beam standing wave tweezers” [Ann. Phys. 342 (3) (2014) 158-170

    NASA Astrophysics Data System (ADS)

    Mitri, F. G.

    2014-09-01

    A typographical error is corrected in three equations in the article [Ann. Phys. 342 (3) (2014) 158-170, http://dx.doi.org/10.1016/j.aop.2013.12.009]. They are Eqs. (12)-(14), where the factor (1+Sp,q) should have been printed as (1+sp(ka)). The numerical computations and plots used the correct factor (1+sp(ka)) in the related equations.

  8. The therapeutic potential of nuclear receptor modulators for treatment of metabolic disorders: PPARγ, RORs, and Rev-erbs.

    PubMed

    Marciano, David P; Chang, Mi Ra; Corzo, Cesar A; Goswami, Devrishi; Lam, Vinh Q; Pascal, Bruce D; Griffin, Patrick R

    2014-02-01

    Nuclear receptors (NRs) play central roles in metabolic syndrome, making them attractive drug targets despite the challenge of achieving functional selectivity. For instance, members of the thiazolidinedione class of insulin sensitizers offer robust efficacy but have been limited due to adverse effects linked to activation of genes not involved in insulin sensitization. Studies reviewed here provide strategies for targeting subsets of PPARγ target genes, enabling development of next-generation modulators with improved therapeutic index. Additionally, emerging evidence suggests that targeting the NRs ROR and Rev-erb holds promise for treating metabolic syndrome based on their involvement in circadian rhythm and metabolism.

  9. Halogenated analogs of 1'-acetoxychavicol acetate, Rev-export inhibitor from Alpinia galanga, designed from mechanism of action.

    PubMed

    Tamura, Satoru; Shiomi, Atsushi; Kimura, Tominori; Murakami, Nobutoshi

    2010-04-01

    In the course of search for the robust analogs of 1'-acetoxychavicol acetate (ACA, 1), the Rev-export inhibitor from the medicinal plant Alpinia galanga, we clarified formation of the quinone methide intermediate ii to be essential for exerting the inhibitory activity of 1. Based on this mechanism of action, the rational design from the MO calculation of the conclusive activation energy to ii resulted in the four halogenated analogs with more potent activity than ACA (1). In particular, the difluoroanalog 20d exhibited approximately four-fold potent activity as compared with 1.

  10. Response to “Comment on ‘General rotating quantum vortex filaments in the low-temperature Svistunov model of the local induction approximation’” [Phys. Fluids 26, 119101 (2014)

    SciTech Connect

    Van Gorder, Robert A.

    2014-11-15

    In R. A. Van Gorder, “General rotating quantum vortex filaments in the low-temperature Svistunov model of the local induction approximation,” Phys. Fluids 26, 065105 (2014) I discussed properties of generalized vortex filaments exhibiting purely rotational motion under the low-temperature Svistunov model of the local induction approximation. Such solutions are stationary in terms of translational motion. In the Comment [N. Hietala, “Comment on ‘General rotating quantum vortex filaments in the low-temperature Svistunov model of the local induction approximation’ [Phys. Fluids 26, 065105 (2014)],” Phys. Fluids 26, 119101 (2014)], the author criticizes my paper for not including translational motion (although it was clearly stated that the filament motion was assumed rotational). As it turns out, if one is interested in studying the geometric structure of solutions (which was the point of my paper), one obtains the needed qualitative results on the structure of such solutions by studying the purely rotational case. Nevertheless, in this Response I shall discuss the vortex filaments that have both rotational and translational motions. I then briefly discuss why one might want to study such generalized rotating filament solutions, in contrast to simple the standard helical or planar examples (which are really special cases). I also discuss how one can study the time evolution of filaments which exhibit more complicated dynamics than pure translation and rotation. Doing this, one can study non-stationary solutions which initially appear purely rotational and gradually display other dynamics as the filaments evolve.

  11. Evolutionary constraints acting on DDX3X protein potentially interferes with Rev-mediated nuclear export of HIV-1 RNA.

    PubMed

    Sharma, Deepak; Bhattacharya, Jayanta

    2010-01-01

    Differential host-pathogen interactions direct viral replication in infected cells. In HIV-1 infected cells, nuclear export of viral RNA transcripts into cellular cytoplasm is governed by interaction of HIV-1 Rev, Exportin-1 (CRM-1) and DDX3X. Knock down of DDX3X has been shown to drastically impair HIV replication. Here we show that evolutionary forces are responsible for demarking previously unidentified critical functionally important residues on the surface of DDX3X. Using computational approaches, we show that these functional residues, depending on their location, are capable of regulating ATPase and RNA helicase functions of DDX3X. The potential of these residues in designing better blockers against HIV-1 replication was also assessed. Also, using stepwise docking simulations, we could identify DDX3X-CRM-1 interface and its critical functional residues. Our data would help explain the role of DDX3X in HIV-1 Rev function with potential to design new intervention strategies against HIV-1 replication.

  12. A threading approach to protein structure prediction: Studies on TNF-like molecules, Rev proteins, and protein kinases

    NASA Astrophysics Data System (ADS)

    Ihm, Yungok

    The main focus of this dissertation is the application of the threading approach to specific biological problems. The threading scheme developed in our group targets incorporating important structural features necessary for detecting structural similarity between the target sequence and the template structure. This enables us to use our threading method to solve problems for which sequence-based methods are not very much useful. We applied our threading method to predict the three-dimensional structures of lentivirus (EIAV, HIV-1, FIV, SIV) Rev proteins. Predicted structures of Rev proteins suggest that they share a structural similarity among themselves (four-helix bundle). Also, the threading approach has been utilized for screening for potential TNF-like molecules in Arabidopsis. The threading approach identified 35 potential TNF-like proteins in Arabidopsis, six of which are particularly interesting to be tested for the receptor kinase ligand activity. Threading method has also been used to identify potentially new protein kinases, which are not included in the protein kinase data base of C. elegans and Arabidopis. We identified eleven potentially new protein kinases and an additional protein worth investigating for protein kinase activity in C. elegans. Further, we identified ten potentially new protein kinases and additional four proteins worth investigating for the protein kinase activity in Arabidopsis.

  13. Characterization of possible correlates of protective response against Brucella ovis infection in rams immunized with the B. melitensis Rev 1 vaccine.

    PubMed

    Galindo, Ruth C; Muñoz, Pilar M; de Miguel, María J; Marin, Clara M; Blasco, José M; Gortazar, Christian; Kocan, Katherine M; de la Fuente, José

    2009-05-18

    Vaccination with the live attenuated Brucella melitensis Rev 1 vaccine is used to control ovine brucellosis caused by Brucella ovis in sheep. The objective of this study was to identify possible correlates of protective response to B. ovis infection through the characterization by microarray hybridization and real-time RT-PCR of inflammatory and immune response genes differentially expressed in rams previously immunized with B. melitensis Rev 1 and experimentally challenged with B. ovis. Gene expression profiles were compared before and after challenge with B. ovis between rams protected and those vaccinated but found infected after challenge. The TLR10, Bak and ANXI genes were expressed at higher levels in vaccinated and protected rams. These genes provide possible correlates of protective response to B. ovis infection in rams immunized with the B. melitensis Rev 1 vaccine.

  14. Inhibition of Rev-mediated HIV-1 expression by an RNA binding protein encoded by the interferon-inducible 9-27 gene

    SciTech Connect

    Constantoulakis, P.; Campbell, M.; Felber, B.K.; Nasioulas, G.; Afonina, E.; Pavlakis, G.N. )

    1993-02-26

    Interferon inhibits expression of human immunodeficiency virus type-1 (HIV-1) through unknown mechanisms. A gene inducible by interferon-[alpha] (IFN-[alpha]) and interferon-[gamma] (IFN-[gamma]) was isolated by screening of a human complementary DNA library for proteins binding to the Rev-responsive element (RRE) of HIV-1. The product of this gene, RBP9-27, was shown to bind RNA in vitro and to inhibit HIV-1 expression after transfection into human cells. RBP9-27 primarily inhibited Rev-dependent posttransscriptional steps of viral gene expression. Thus, RBP9-27 is a cellular factor that antagonizes Rev function. These results suggest an inteferon-induced antiviral mechanism operating through the induction of RNA binding proteins such as RBP9-27. Elucidation of RBP9-27 function may lead to a better understanding of the mechanism of interferon action during HIV-1 infection. 29 refs., 4 figs.

  15. Effects of Twelve Germline Missense Variations on DNA Lesion and G-Quadruplex Bypass Activities of Human DNA Polymerase REV1.

    PubMed

    Yeom, Mina; Kim, In-Hyeok; Kim, Jae-Kwon; Kang, KyeongJin; Eoff, Robert L; Guengerich, F Peter; Choi, Jeong-Yun

    2016-03-21

    The Y-family DNA polymerase REV1 is involved in replicative bypass of damaged DNA and G-quadruplex (G4) DNA. In addition to a scaffolding role in the replicative bypass, REV1 acts in a catalytic role as a deoxycytidyl transferase opposite some replication stall sites, e.g., apurinic/apyrimidinic (AP) sites, N(2)-guanyl lesions, and G4 sites. We characterized the biochemical properties of 12 reported germline missense variants of human REV1, including the N373S variant associated with high risk of cervical cancer, using the recombinant REV1 (residues 330-833) proteins and DNA templates containing a G, AP site, N(2)-CH2(2-naphthyl)G (N(2)-NaphG), or G4. In steady-state kinetic analyses, the F427L, R434Q, M656V, D700N, R704Q, and P831L variants displayed 2- to 8-fold decreases in kcat/Km for dCTP insertion opposite all four templates, compared to that of wild-type, while the N373S, M407L, and N497S showed 2- to 3-fold increases with all four and the former three or two templates, respectively. The F427L, R434Q, M656V, and R704Q variants also had 2- to 3-fold lower binding affinities to DNA substrates containing G, an AP site, and/or N(2)-NaphG than wild-type. Distinctively, the N373S variant had a 3-fold higher binding affinity to G4 DNA than the wild-type, as well as a 2-fold higher catalytic activity opposite the first tetrad G, suggesting a facilitating effect of this variation on replication of G4 DNA sequences in certain human papillomavirus genomes. Our results suggest that the catalytic function of REV1 is moderately or slightly altered by at least nine genetic variations, and the G4 DNA processing function of REV1 is slightly enhanced by the N373S variation, which might provide the possibility that certain germline missense REV1 variations affect the individual susceptibility to carcinogenesis by modifying the capability of REV1 for replicative bypass past DNA lesions and G4 motifs derived from chemical and viral carcinogens.

  16. Mathematical model of the Tat-Rev regulation of HIV-1 replication in an activated cell predicts the existence of oscillatory dynamics in the synthesis of viral components

    PubMed Central

    2014-01-01

    Background The life cycle of human immunodeficiency virus type-1 (HIV-1) makes possible the realization of regulatory strategies that can lead to complex dynamical behavior of the system. We analyze the strategy which is based on two feedback mechanisms, one mediating a positive regulation of the virus replication by Tat protein via the antitermination of the genomic RNAs transcription on TAR (transactivation responsive) element of the proviral DNA and the second mechanism providing a negative regulation of the splicing of the full-length (9 kb) RNAs and incompletely spliced (4 kb) RNAs via their transport from the nucleus to the cytoplasm. Although the existence of these two regulatory feedback loops has been considered in other mathematical models, none of them examined the conditions for the emergence of complex oscillatory patterns in the intracellular dynamics of viral components. Results We developed a mechanistic mathematical model for the Tat-Rev mediated regulation of HIV-1 replication, which considers the activation of proviral DNA transcription, the Tat-specific antitermination of transcription on TAR-element, resulting in the synthesis of the full-length 9 kb RNA, the splicing of the 9 kb RNA down to the 4 kb RNA and the 4 kb RNA to 2 kb RNA, the transport of 2 kb mRNAs from the nucleus to the cytoplasm by the intracellular mechanisms, the multiple binding of the Rev protein to RRE (Rev Response Element) sites on 9 kb and 4 kb RNA resulting in their export to the cytoplasm and the synthesis of Tat and Rev proteins in the cytoplasm followed by their transport into the nucleus. The degradation of all viral proteins and RNAs both in the cytoplasm and the nucleus is described. The model parameters values were derived from the published literature data. The model was used to examine the dynamics of the synthesis of the viral proteins Tat and Rev, the mRNAs under the intracellular conditions specific for activated HIV-1 infected macrophages. In addition, we

  17. Comment on: "Fundamental flows with nonlinear slip conditions: exact solutions", by R. Ellahi, T. Hayat, F. M. Mahomed and A. Zeeshan, Z. Angew. Math. Phys. 61 (2010) 877-888

    NASA Astrophysics Data System (ADS)

    El-Mistikawy, Tarek M. A.

    2011-12-01

    In their article (Fundamental flows with nonlinear slip conditions: exact solutions, R. Ellahi, T. Hayat, F. M. Mahomed and A. Zeeshan, Z. Angew. Math. Phys. 61 (2010) 877-888.), the authors considered three simple cases of the steady flow of a third grade fluid between parallel plates with slip conditions; namely, Couette flow, Poiseuille flow, and generalized Couette flow. They obtained exact solutions, which were utilized in a way that did not lead to useful results. Their conclusion that the Couette flow cannot be obtained from the generalized Couette flow, by dropping the pressure gradient, is incorrect. Meaningful results based on their solution are herein presented.

  18. Amchitka Mud Pit Sites 2006 Post-Closure Monitoring and Inspection Report, Amchitka Island, Alaska, Rev. No.: 0

    SciTech Connect

    Matthews, Patrick

    2006-09-01

    In 2001, the U.S. Department of Energy (DOE), National Nuclear Security Administration (NNSA/NSO) remediated six areas associated with Amchitka mud pit release sites located on Amchitka Island, Alaska. This included the construction of seven closure caps. To ensure the integrity and effectiveness of remedial action, the mud pit sites are to be inspected every five years as part of DOE's long-term monitoring and surveillance program. In August of 2006, the closure caps were inspected in accordance with the ''Post-Closure Monitoring and Inspection Plan for Amchitka Island Mud Pit Release Sites'' (Rev. 0, November 2005). This post-closure monitoring report provides the 2006 cap inspection results.

  19. X-33 (Rev-F) Aeroheating Results of Test 6770 in NASA Langley 20-Inch Mach 6 Air Tunnel

    NASA Technical Reports Server (NTRS)

    Berry, Scott A.; Horvath, Thomas J.; Kowalkowski, Matthew K.; Liechty, Derek S.

    1999-01-01

    Aeroheating characteristics of the X-33 Rev-F configuration have been experimentally examined in the Langley 20-Inch Mach 6 Air Tunnel (Test 6770). Global surface heat transfer distributions, surface streamline patterns, and shock shapes were measured on a 0.013-scale model at Mach 6 in air. Parametric variations include angles-of-attack of 20-deg, 30-deg, and 40-deg; Reynolds numbers based on model length of 0.9 to 4.9 million; and body-flap deflections of 10-deg and 20-deg. The effects of discrete roughness elements on boundary layer transition, which included trip height, size, and location, both on and off the windward centerline, were investigated. This document is intended to serve as a quick release of preliminary data to the X-33 program; analysis is limited to observations of the experimental trends in order to expedite dissemination.

  20. 1'S-1'-acetoxychavicol acetate isolated from Alpinia galanga inhibits human immunodeficiency virus type 1 replication by blocking Rev transport.

    PubMed

    Ye, Ying; Li, Baoan

    2006-07-01

    AIDS remains a major global health concern. Despite a number of therapeutic advancements, there is still an urgent need to develop a new class of therapy for human immunodeficiency virus (HIV). Here, it was shown that 1'S-1'-acetoxychavicol acetate (ACA), a small molecular compound isolated from the rhizomes of Alpinia galanga, inhibited Rev transport at a low concentration by binding to chromosomal region maintenance 1 and accumulating full-length HIV-1 RNA in the nucleus, resulting in a block in HIV-1 replication in peripheral blood mononuclear cells. Additionally, ACA and didanosine acted synergistically to inhibit HIV-1 replication. Thus, ACA may represent a novel treatment for HIV-1 infection, especially in combination with other anti-HIV drugs.

  1. Erratum: “Multi-point, high-speed passive ion velocity distribution diagnostic on the Pegasus Toroidal Experiment” [Rev. Sci. Instrum. 83, 10D516 (2012)

    DOE PAGES

    Burke, Marcus G.; Fonck, Raymond J.; Bongard, Michael W.; Schlossberg, David J.; Winz, Gregory R.

    2016-07-18

    This article corrects an error in M.G. Burke et al., 'Multi-point, high-speed passive ion velocity distribution diagnostic on the Pegasus Toroidal Experiment,' Rev. Sci. Instrum. 83, 10D516 (2012) pertaining to ion temperature. The conclusions of this paper are not altered by the revised ion temperature measurements.

  2. High frequency of defective vpu compared with tat and rev genes in brain from patients with HIV type 1-associated dementia.

    PubMed

    Thomas, Elaine R; Dunfee, Rebecca L; Stanton, Jennifer; Bogdan, Derek; Kunstman, Kevin; Wolinsky, Steven M; Gabuzda, Dana

    2007-04-01

    Human immunodeficiency virus type 1 (HIV) infection of the central nervous system frequently causes HIV-associated dementia (HAD) and other neurological disorders. The role of HIV regulatory and accessory proteins in the pathogenesis of these disorders is unclear. Here we analyzed sequences of tat, rev, and vpu genes in 55 subgenomic clones previously shown to encode functional env genes from brain and lymphoid tissues of four AIDS patients with HAD. Phylogenetic analysis showed distinct compartmentalization of tat, rev, and vpu genes in brain versus lymphoid tissues. Nine of 19 vpu sequences from brain of two patients had premature stop codons at positions between amino acids 2 and 30, compared with 0 of 8 from lymphoid tissues. Tat sequences from brain (n = 8 of 8) but not lymphoid (n = 0 of 6) tissue from one patient had a 35 amino acid truncation at the C-terminus. Rev sequences from the brain of one patient (n = 6 of 8) had a 5 amino acid truncation. These results demonstrate a high frequency of defective vpu compared with tat and rev genes in brain from HAD patients, and identify sequence variants of these regulatory/accessory genes that may influence the pathogenesis of HIV-associated neurological disease.

  3. Comparative Analysis of in vivo Interactions Between Rev1 Protein and Other Y-Family DNA Polymerases in Animals and Yeasts

    PubMed Central

    Kosarek, J. Nicole; Woodruff, Rachel V.; Rivera-Begeman, Amanda; Guo, Caixia; D’Souza, Sanjay; Koonin, Eugene V.; Walker, Graham C.; Friedberg, Errol C.

    2008-01-01

    Summary Eukaryotes are endowed with multiple specialized DNA polymerases, some (if not all) of which are believed to play important roles in the tolerance of base damage during DNA replication. Among these DNA polymerases, Rev1 protein (a deoxycytidyl transferase) from vertebrates interacts with several other specialized polymerases via a highly conserved C-terminal region. The present studies assessed whether these interactions are retained in more experimentally tractable model systems, including yeasts, flies, and the nematode C. elegans. We observed a physical interaction between Rev1 protein and other Y-family polymerases in the fruit fly Drosophila melanogaster. However, despite the fact that the C-terminal region of Drosophila and yeast Rev1 are conserved from vertebrates to a similar extent, such interactions were not observed in S. cerevisiae or S. pombe. With respect to regions in specialized DNA polymerases that are required for interaction with Rev1, we find predicted disorder to be an underlying structural commonality. The results of this study suggest that special consideration should be exercised when making mechanistic extrapolations regarding translesion DNA synthesis from one eukaryotic system to another. PMID:18242152

  4. Translational regulation of HIV-1 replication by HIV-1 Rev cellular cofactors Sam68, eIF5A, hRIP, and DDX3.

    PubMed

    Liu, Jinfeng; Henao-Mejia, Jorge; Liu, Hao; Zhao, Yingren; He, Johnny J

    2011-06-01

    Nuclear export and translation of HIV-1 RNA are two important posttranscriptional events for HIV-1 gene expression and replication. HIV-1 Rev functions to export unspliced and incompletely spliced HIV-1 RNA from the nucleus to the cytoplasm; it requires interaction with several cellular cofactors such as Sam68, eIF5A, hRIP, and DDX3. Meanwhile, some studies have also implicated Rev and some of its cofactors such as Sam68 in HIV-1 RNA translation. Thus, in this study, we aimed to characterize the potential function of all these four Rev cofactors in HIV-1 RNA translation. Ectopic expression, siRNA knockdown, and trans-complementation assays confirmed that all these cofactors were very important for HIV-1 gene expression and production through Rev and, accordingly, Rev-dependent reporter gene expression. Importantly, these studies revealed for the first time that each of these cofactors also regulated Rev-independent reporter gene expression. To directly determine the roles of these cofactors in HIV-1 RNA translation, we designed and synthesized a full-length capped HIV-1 RNA in vitro, transfected it into cells to bypass the RNA nuclear export step, and determined HIV-1 Gag expression from the cytoplasmic RNA in the cells that had ectopically expressed or siRNA knocked down cofactors. Gag expression was found to closely correlate with the expression levels of all these cofactors. Furthermore, we took advantage of a HIV-1 internal ribosomal entry site (IRES)-based bicistronic reporter gene assay and determined the effects of these cofactors on cap-independent IRES-mediated HIV-1 translation. The results showed that DDX3, eIF5A, and hRIP enhanced HIV-1 IRES-mediated translation, whereas Sam68 did not. Taken together, these results show that HIV-1 Rev cofactors Sam68, eIF5A, hRIP, and DDX3 also function in the translation of HIV-1 RNA and suggest that the regulatory mechanisms of HIV-1 RNA translation are likely different among these cofactors.

  5. RevM10-expressing T cells derived in vivo from transduced human hematopoietic stem-progenitor cells inhibit human immunodeficiency virus replication.

    PubMed Central

    Bonyhadi, M L; Moss, K; Voytovich, A; Auten, J; Kalfoglou, C; Plavec, I; Forestell, S; Su, L; Böhnlein, E; Kaneshima, H

    1997-01-01

    A key feature of the pathogenesis of human immunodeficiency virus type 1 (HIV-1) infection is the gradual loss of CD4-positive T cells. A number of gene therapy strategies have been designed with the intent of inhibiting HIV replication in mature T cells. As T cells are products of hematolymphoid differentiation, insertion of antiviral genes into hematopoietic stem cells could serve as a vehicle to confer long-term protection in progeny T cells derived from transduced stem cells. One such "cellular immunization" strategy utilizes the gene coding for the HIV-1 rev trans-dominant mutant protein RevM10 which has been demonstrated to inhibit HIV-1 replication in T-cell lines and in primary T cells. In this study, we used a Moloney murine leukemia virus-based retrovirus encoding a bicistronic message coexpressing RevM10 and the murine CD8-alpha' chain (Lyt2). This vector allows rapid selection of transgene-expressing cells as well as quantitation of transgene expression. We demonstrate that RevM10-transduced CD34-enriched hematopoietic progenitor-stem cells (HPSC) isolated from human umbilical cord blood or from granulocyte colony-stimulating factor-mobilized peripheral blood can give rise to mature thymocytes in the SCID-hu thymus/liver mouse model. The phenotypic distribution of HPSC-derived thymocytes is normal, and expression of the transgene can be detected by flow cytometric analysis. Moreover, we demonstrate that RevM10 can inhibit HIV replication in T cells derived from transduced HPSC after expansion in vitro. This is the first demonstration of anti-HIV efficacy in T cells derived from transduced human HPSC. PMID:9151864

  6. Comment on “Motion of a helical vortex filament in superfluid {sup 4}He under the extrinsic form of the local induction approximation” [Phys. Fluids 25, 085101 (2013)

    SciTech Connect

    Hietala, Niklas Hänninen, Risto

    2014-01-15

    We comment on the paper by Van Gorder [“Motion of a helical vortex filament in superfluid {sup 4}He under the extrinsic form of the local induction approximation,” Phys. Fluids 25, 085101 (2013)]. We point out that the flow of the normal fluid component parallel to the vortex will often lead into the Donnelly–Glaberson instability, which will cause the amplification of the Kelvin wave. We explain why the comparison to local nonlinear equation is unreasonable, and remark that neglecting the motion in the x-direction is not reasonable for a Kelvin wave with an arbitrary wavelength and amplitude. The correct equations in the general case are also derived.

  7. Response to "Comment on `Construction of the landscape for multi-stable systems: Potential landscape, quasi-potential, A-type integral and beyond"' [J. Chem. Phys. 145, 147104 (2016)

    NASA Astrophysics Data System (ADS)

    Zhou, Peijie; Li, Tiejun

    2016-10-01

    The uniqueness issue of SDE decomposition theory proposed by Ao and his co-workers has recently been discussed. A comprehensive study to investigate connections among different landscape theories [J. Chem. Phys. 144, 094109 (2016)] has pointed out that the decomposition is generally not unique, while Ao et al. recently argue that such conclusions are "incorrect" because the uniqueness of the decomposition for Ornstein-Uhlenbeck (O-U) process has been claimed before. In this response, we will demonstrate that the claimed "uniqueness" of the O-U process decomposition is invalid to serve as a counterexample according to the original definition of SDE decomposition. The absence of effective and concrete boundary conditions in previous SDE decomposition papers will be pointed out, and some other issues in the comment will also be responded.

  8. Response to 'Comment on 'Resonant dissociative electron transfer of the presolvated electron to CCl{sub 4} in liquid: Direct observation and lifetime of the CCl{sub 4}*{sup -} transition state' [J. Chem. Phys. 129, 027101 (2008)]'

    SciTech Connect

    Wang, C.-R.; Drew, K.; Luo, T.; Lu, M.-J.; Lu, Q.-B.

    2008-07-14

    In our recent paper [J. Chem. Phys.128, 041102 (2008)], we reported a femtosecond time-resolved laser spectroscopic study of the electron transfer reaction of CCl{sub 4} in liquid ethanol. Our results provide direct evidence of the resonant dissociative electron transfer (RDET) of the presolvated electron to CCl{sub 4}, and indicate that RDET can be an efficient process in an aqueous environment. In a recent Comment, the author argues that the relevance of diethanolamine (DEA) induced destruction of chlorofluorocarbons (CFCs) in the polar stratosphere as a possible pathway for chemical ozone destruction should not be a motivation for further studies of DEA on CFC molecules, as no correlation is observed between polar chemical ozone loss and cosmic ray activity. Here, we show that this claim is misleading: it is made by using inconclusive and ambiguous data while ignoring pronounced and well-documented data.

  9. PHYS-MA-TECH. An Integrated Partnership.

    ERIC Educational Resources Information Center

    Scarborough, Jule Dee

    This document contains 45 integrated physics, mathematics, and technology curriculum modules developed by teachers at 5 Illinois schools. An introduction discusses the collaborative project, in which teams of one mathematics, physics, and technology teacher from each school developed innovative instructional delivery models that enabled the three…

  10. Numerical modelling of the flow in the resin infusion process on the REV scale: A feasibility study

    NASA Astrophysics Data System (ADS)

    Jabbari, M.; Jambhekar, V. A.; Gersborg, A. R.; Spangenberg, J.; Hattel, J. H.; Helmig, R.

    2016-06-01

    The resin infusion process (RIP) has developed as a low cost method for manufacturing large fibre reinforced plastic parts. However, the process still presents some challenges to industry with regards to reliability and repeatability, resulting in expensive and inefficient trial and error development. In this paper, we show the implementation of 2D numerical models for the RIP using the open source simulator DuMuX. The idea of this study is to present a model which accounts for the interfacial forces coming from the capillary pressure on the so-called representative elementary volume (REV) scale. The model is described in detail and three different test cases — a constant and a tensorial permeability as well as a preform/Balsa domain — are investigated. The results show that the developed model is very applicable for the RIP for manufacturing of composite parts. The idea behind this study is to test the developed model for later use in a real application, in which the preform medium has numerous layers with different material properties.

  11. Reply to "Comment on `Self-assembly of magnetic balls: From chains to tubes' "

    NASA Astrophysics Data System (ADS)

    Messina, René; Stanković, Igor

    2015-05-01

    The authors of the Comment [Phys. Rev. E 91, 057201 (2015), 10.1103/PhysRevE.91.057201] propose compact round clusters as, energetically, better candidates than stacked rings found in Messina et al. [Phys. Rev. E 89, 011202 (2014), 10.1103/PhysRevE.89.011202] (forming open tubes) at a pretty large number of constitutive magnets, typically for N ≳1300 . Our new findings show that elongated rodlike structures can even outmatch the reported structures in Friedrich et al. [Phys. Rev. E 91, 057201 (2015), 10.1103/PhysRevE.91.057201] and in Messina et al. [Phys. Rev. E 89, 011202 (2014), 10.1103/PhysRevE.89.011202] from typically N ≳460 .

  12. High Affinity Heme Binding to a Heme Regulatory Motif on the Nuclear Receptor Rev-erbβ Leads to Its Degradation and Indirectly Regulates Its Interaction with Nuclear Receptor Corepressor.

    PubMed

    Carter, Eric L; Gupta, Nirupama; Ragsdale, Stephen W

    2016-01-29

    Rev-erbα and Rev-erbβ are heme-binding nuclear receptors (NR) that repress the transcription of genes involved in regulating metabolism, inflammation, and the circadian clock. Previous gene expression and co-immunoprecipitation studies led to a model in which heme binding to Rev-erbα recruits nuclear receptor corepressor 1 (NCoR1) into an active repressor complex. However, in contradiction, biochemical and crystallographic studies have shown that heme decreases the affinity of the ligand-binding domain of Rev-erb NRs for NCoR1 peptides. One explanation for this discrepancy is that the ligand-binding domain and NCoR1 peptides used for in vitro studies cannot replicate the key features of the full-length proteins used in cellular studies. However, the combined in vitro and cellular results described here demonstrate that heme does not directly promote interactions between full-length Rev-erbβ (FLRev-erbβ) and an NCoR1 construct encompassing all three NR interaction domains. NCoR1 tightly binds both apo- and heme-replete FLRev-erbβ·DNA complexes; furthermore, heme, at high concentrations, destabilizes the FLRev-erbβ·NCoR1 complex. The interaction between FLRev-erbβ and NCoR1 as well as Rev-erbβ repression at the Bmal1 promoter appear to be modulated by another cellular factor(s), at least one of which is related to the ubiquitin-proteasome pathway. Our studies suggest that heme is involved in regulating the degradation of Rev-erbβ in a manner consistent with its role in circadian rhythm maintenance. Finally, the very slow rate constant (10(-6) s(-1)) of heme dissociation from Rev-erbβ rules out a prior proposal that Rev-erbβ acts as an intracellular heme sensor.

  13. Final Report - DuraMelter 100 Tests to Support LAW Glass Formulation Correlation Development, VSL-06R6480-1, Rev. 0

    SciTech Connect

    Kruger, Albert A.; Muller, I. S.; Gong, W.; Pegg, I. L.; Matlack, K. S.

    2013-12-03

    This report describes the results of work and testing specified by Test Specifications 24590-LAW-TSP-RT-04-004, Rev. 0, Test Plans VSL-05T5480-1, Rev. 0 and Text Exceptions 24590-LAW-TEF-RT-05-00002. The work and any associated testing followed established quality assurance requirements and was conducted as authorized. The descriptions provided in this test report are an accurate account of both the conduct of the work and the data collected. Results required by the Test Plan are reported. Also reported are any unusual or anomalous occurences that are different from the starting hypotheses. The test results and this report have been reviewed and verified.

  14. Inhibitory role of REV-ERBα in the expression of bone morphogenetic protein gene family in rat uterus endometrium stromal cells.

    PubMed

    Tasaki, Hirotaka; Zhao, Lijia; Isayama, Keishiro; Chen, Huatao; Yamauchi, Nobuhiko; Shigeyoshi, Yasufumi; Hashimoto, Seiichi; Hattori, Masa-aki

    2015-04-01

    Uterus circadian rhythms have been implicated in the gestation processes of mammals through entraining of the clock proteins to numerous downstream genes. Bone morphogenetic proteins (BMPs), having clock-controlled regulatory sites in their gene promoters, are expressed in the uterus during decidualization, but the regulation of the Bmp gene expression is poorly understood. The present study was designed to dissect the physiological roles of the uterus oscillators in the Bmp expression using the uterus endometrial stromal cells (UESCs) isolated from Per2-dLuc transgenic rats on day 4.5 of gestation. The in vitro decidualization of UESCs was induced by medroxyprogesterone acetate and 2-O-dibutyryl cAMP. A significant decline of Per2-dLuc bioluminescence activity was induced in decidual cells, and concomitantly, the expression of canonical clock genes was downregulated. Conversely, the expression of the core Bmp genes Bmp2, Bmp4, Bmp6, and Bmp7 was upregulated. In UESCs transfected with Bmal1-specific siRNA, in which Rev-erbα expression was downregulated, Bmp genes, such as Bmp2, Bmp4, and Bmp6 were upregulated. However, Bmp1, Bmp7, and Bmp8a were not significantly affected by Bmal1 silencing. The expression of all Bmp genes was enhanced after treatment with the REV-ERBα antagonist (SR8278), although their rhythmic profiles were differed from each other. The binding of REV-ERBα to the proximal regions of the Bmp2 and Bmp4 promoters was revealed by chromatin immunoprecipitation-PCR analysis. Collectively, these results indicate that the Bmp genes are upregulated by the attenuation of the cellular circadian clock; in particular, its core component REV-ERBα functions as a transcriptional silencer in the Bmp gene family.

  15. Identification of a novel circadian clock modulator controlling BMAL1 expression through a ROR/REV-ERB-response element-dependent mechanism.

    PubMed

    Lee, Jiyeon; Lee, Seungbeom; Chung, Sooyoung; Park, Noheon; Son, Gi Hoon; An, Hongchan; Jang, Jaebong; Chang, Dong-Jo; Suh, Young-Ger; Kim, Kyungjin

    2016-01-15

    Circadian rhythms, biological oscillations with a period of about 24 h, are maintained by an innate genetically determined time-keeping system called the molecular circadian clockwork. Despite the physiological and clinical importance of the circadian clock, development of small molecule modulators targeting the core clock machinery has only recently been initiated. BMAL1, a core clock gene, is controlled by a ROR/REV-ERB-response element (RORE)-dependent mechanism, which plays an important role in stabilizing the period of the molecular circadian clock. Therefore, we aimed to identify a novel small molecule modulator that regulates Bmal1 gene expression in RORE-dependency, thereby influencing the molecular feedback loop of the circadian clock. For this purpose, we carried out a cell-based screen of more than 1000 drug-like compounds, using a luciferase reporter driven by the proximal region of the mouse Bmal1 promoter. One compound, designated KK-S6, repressed the RORE-dependent transcriptional activity of the mBmal1 promoter and reduced endogenous BMAL1 protein expression. More importantly, KK-S6 significantly altered the amplitude of circadian oscillations of Bmal1 and Per2 promoter activities in a dose-dependent manner, but barely affected the period length. KK-S6 effectively decreased mRNA expression of metabolic genes acting downstream of REV-ERBα, Pai-1 and Citrate synthase, that contain RORE cis-element in their promoter. KK-S6 likely acts in a RORE-dependent manner by reinforcing the REV-ERBα activity, though not by the same mechanism as known REV-ERB agonists. In conclusion, the present study demonstrates that KK-S6 functions as a novel modulator of the amplitude of molecular circadian rhythms by influencing RORE-mediated BMAL1 expression.

  16. Amphibian transcription factor IIIA proteins contain a sequence element functionally equivalent to the nuclear export signal of human immunodeficiency virus type 1 Rev.

    PubMed

    Fridell, R A; Fischer, U; Lührmann, R; Meyer, B E; Meinkoth, J L; Malim, M H; Cullen, B R

    1996-04-01

    The human immunodeficiency virus type 1 (HIV-1) Rev protein is required for nuclear export of late HIV-1 mRNAs. This function is dependent on the mutationally defined Rev activation domain, which also forms a potent nuclear export signal. Transcription factor IIIA (TFIIIA) binds to 5S rRNA transcripts and this interaction has been proposed to play a role in the efficient nuclear export of 5S rRNA in amphibian oocytes. Here it is reported that amphibian TFIIIA proteins contain a sequence element with homology to the Rev activation domain that effectively substitutes for this domain in inducing the nuclear export of late HIV-1 mRNAs. It is further demonstrated that this TFIIIA sequence element functions as a protein nuclear export signal in both human cells and frog oocytes. Thus, this shared protein motif may play an analogous role in mediating the nuclear export of both late HIV-1 RNAs and 5S rRNA transcripts. PMID:8610146

  17. Reply to "Comment on `Flow-induced arrest of spatiotemporal chaos and transition to a stationary pattern in the Gray-Scott model' "

    NASA Astrophysics Data System (ADS)

    Das, Debojyoti

    2016-10-01

    We reply to the Comment of Berenstein et al. [preceding paper, Phys. Rev. E 94, 046201 (2016), 10.1103/PhysRevE.94.046201] on our article [D. Das, Phys. Rev. E 92, 052914 (2015), 10.1103/PhysRevE.92.052914] about the effect of streamlined flow on the dynamics of the Gray-Scott model characterized by wave-induced spatiotemporal chaos.

  18. Making mission possible. A response to Rev. Richard A. McCormick's article on the preservation of Catholic hospitals.

    PubMed

    O'Rourke, K D

    1995-01-01

    In "The Catholic Hospital Today: Mission Impossible?" (Origins, March 16, 1995, pp. 648-653), Rev. Richard A. McCormick, SJ, STD, questions whether Catholic hospitals can continue their missions in a society with so many factors and influences that seem to oppose efforts to perpetuate the healing ministry of Christ. As Fr. McCormick states, the matrix of good medicine is centered on the good of the individual. But too often, the patient has been considered an individual isolated from others. The rights of families, people who belong to the same insurance program, and the society funding much of healthcare must also be considered. Fr. McCormick points out that an obstacle to the healing mission arises because healthcare is often treated as a business instead of a service. If not-for-profit healthcare facilities come to exist for the well-being of the shareholders, as do for-profit healthcare facilities, then a perversion of values results. This should lead us to renounce for-profit healthcare and the behavior that some Catholic health organizations have borrowed from the for-profit sector. In addition, Fr. McCormick calls attention to our society's denial of death and tendency to call on medicine to cure personal, social, or economic problems. This denial-of-death phenomenon helps us realize the need for the mission of Catholic hospitals. Continuing the mission of Catholic hospitals will require the attention of all involved in them-physicians, trustees, nurses, administrators, and ancillary personnel. These healthcare providers must not be distracted from the mission by joint ventures and economic issues.

  19. TRACKED VEHICLE Rev 75

    SciTech Connect

    Raby, Eric Y.

    2007-05-08

    Revision 75 of the Tracked Vehicle software is a soft real-time simulation of a differentially steered, tracked mobile robot, which, because of the track flippers, resembles the iRobot PackBot (http://www.irobot.com/). Open source libraries are used for the physics engine (http://www.ode.org/), the display and user interface (http://www.mathies.com/cpw/), and the program command line and configuration file parameters (http://www.boost.org/). The simulation can be controlled by a USB joystick or the keyboard. The configuration file contains demonstration model parameters of no particular vehicle. This simulation can be used as a starting point for those doing tracked vehicle simulations. This simulation software is essentially a research tool which can be modified and adapted for certain types of tracked vehicle research. An open source license allows an individual researchers to tailor the code to their specific research needs.

  20. Rev Your Engines!

    ERIC Educational Resources Information Center

    Blanchard, Margaret; Sharp, Jennifer; Grable, Lisa

    2009-01-01

    As part of the "Car Lab Project," students constructed rubber band cars, raced them, and worked through a number of automotive activities. The students engaged in this project certainly had fun, but they also used high-tech gear such as motion sensors and graphing calculators to gather data on the distance and time cars traveled and to generate…

  1. TRACKED VEHICLE Rev 75

    2007-05-08

    Revision 75 of the Tracked Vehicle software is a soft real-time simulation of a differentially steered, tracked mobile robot, which, because of the track flippers, resembles the iRobot PackBot (http://www.irobot.com/). Open source libraries are used for the physics engine (http://www.ode.org/), the display and user interface (http://www.mathies.com/cpw/), and the program command line and configuration file parameters (http://www.boost.org/). The simulation can be controlled by a USB joystick or the keyboard. The configuration file contains demonstration model parametersmore » of no particular vehicle. This simulation can be used as a starting point for those doing tracked vehicle simulations. This simulation software is essentially a research tool which can be modified and adapted for certain types of tracked vehicle research. An open source license allows an individual researchers to tailor the code to their specific research needs.« less

  2. Rev Up Your Veggies!

    ERIC Educational Resources Information Center

    King, Melissa DiGennaro

    2000-01-01

    Teaches concepts such as inertia, gravity, and friction using a "Lunch Box Derby" activity. Uses vegetables for the construction of race cars. Explains student approaches during the design and construction portion. Describes the rubrics used for student evaluation. (YDS)

  3. Comment on “Magnetic field mediated low-temperature resistivity upturn in electron-doped La{sub 1−x}Hf{sub x}MnO{sub 3} manganite oxides” [J. Appl. Phys. 112, 123710 (2012)

    SciTech Connect

    Rozenberg, E.

    2014-01-21

    In a recent paper, Guo et al. [J. Appl. Phys. 112, 123710 (2012)] reported on characteristic features of the temperature (T) and magnetic field (H) dependences of electrical resistivity (ρ) in polycrystalline La{sub 1−x}Hf{sub x}MnO{sub 3} (x = 0.2 and 0.3) manganites. In particular, shallow minima were observed at some T{sub min} below 100 K on ρ(T) curves. Application of an external H ≤ 5 T leads first to a decrease in the T{sub min} value, while this value increases notably at H > 0.75 T. The authors attributed this complex behavior to competitive electron-electron interaction and Kondo-like spin dependent scattering of carriers. It is shown in the comment that such interpretation is very questionable due to the fundamental inapplicability of this approach for analysis of low-T conductivity in polycrystalline manganites. It seems that the most likely reason for the appearance of the low temperature minima on ρ(T) curves and their evolution upon field application is the well known grain boundary effects in magnetically and structurally inhomogeneous samples.

  4. Model for roughening and ripple instability due to ion-induced mass redistribution [Addendum to H. Hofsäss, Appl. Phys. A 114 (2014) 401, "Surface instability and pattern formation by ion-induced erosion and mass redistribution"

    NASA Astrophysics Data System (ADS)

    Hofsäss, Hans

    2015-05-01

    Carter and Vishnyakov introduced a model (CV model) to describe roughening and ripple instability due to ion-induced mass redistribution. This model is based on the assumption that the irradiated surface layer on a static solid substrate is described by a viscous incompressible thin film bound to the substrate by a "no slip" and "no transport" kinematic boundary condition, i.e. similar to a thin film of viscous paint. However, this boundary condition is incomplete for a layer under ion irradiation. The boundary condition must allow exchange of atoms between the substrate and the irradiated film, so that the thickness of the film is always determined by the size of the collision cascade, independent of the evolution of the surface height profile. In addition, the film thickness depends on the local ion incidence angle, which leads to a time dependence of the film thickness at a given position. The equation of motion of the surface and interface profiles for these boundary conditions is introduced, and a new curvature-dependent coefficient is found which is absent in the CV model. This curvature coefficient depends on the angular derivative of the layer thickness and the atomic drift velocity at the film surface induced by recoil events. Such a stabilizing curvature coefficient was introduced in Appl. Phys. A 114 (2014) 401 and is most pronounced at intermediate angles.

  5. Comment on: Measurement of the force exerted on the surface of an object immersed in a plasma. Eur. Phys. J. D 69: 91 (2015), DOI: 10.1140/epjd/e2015-50743-2

    NASA Astrophysics Data System (ADS)

    Czarnetzki, Uwe; Tsankov, Tsanko V.

    2015-10-01

    Surfaces exposed to a plasma experience a certain pressure that pushes them away from the volume. This effect has been investigated experimentally in a recent article by Thomas Trottenberg, Thomas Richter, and Holger Kersten from Kiel University/Germany [Eur. Phys. J. D 69, 91 (2015)]. The experimental results are impressive and have actually drawn the attention of the community to an interesting question which so far has been largely ignored. In addition to their experimental results the Kiel group proposes also a rough concept in order to explain their findings which provides certainly a basic qualitative understanding of the physical processes involved. However, on a closer inspection the picture developed so far is not entirely satisfying and the problem seems to require a more fundamental approach. This comment shows that the effect of the wall pressure can be described exactly using only analytical methods. The physical situation is analyzed by three different approaches. First, the simple case of only one spatial dimension is presented in detail. Second, the case of spherical symmetry is analyzed by some simplifying assumptions in order to investigate the effect of higher dimensionality. Third, a formal derivation for arbitrary geometry is given. This general result includes the one-dimensional case but does not allow a convenient connection between the pressures at the wall and in the center. Finally, the results are summarized and some conclusions are drawn.

  6. A Bidirectional SF2/ASF- and SRp40-Dependent Splicing Enhancer Regulates Human Immunodeficiency Virus Type 1 rev, env, vpu, and nef Gene Expression

    PubMed Central

    Caputi, Massimo; Freund, Marcel; Kammler, Susanne; Asang, Corinna; Schaal, Heiner

    2004-01-01

    The integrated human immunodeficiency virus type 1 (HIV-1) genome is transcribed in a single pre-mRNA that is alternatively spliced into more than 40 mRNAs. We characterized a novel bidirectional exonic splicing enhancer (ESE) that regulates the expression of the HIV-1 env, vpu, rev, and nef mRNAs. The ESE is localized downstream of the vpu-, env-, and nef-specific 3′ splice site no. 5. SF2/ASF and SRp40 activate the ESE and are required for efficient 3′ splice site usage and binding of the U1 snRNP to the downstream 5′ splice site no. 4. U1 snRNP binding to the 5′ splice site no. 4 is required for splicing of the rev and nef mRNAs and to increase expression of the partially spliced env mRNA. Finally, our results indicate that this ESE is necessary for the recruitment of the U1 snRNP to the 5′ splice site no. 4, even when the 5′ splice site and the U1 snRNA have been mutated to obtain a perfect complementary match. The ESE characterized here is highly conserved in most viral subtypes. PMID:15163745

  7. The Rev protein of human immunodeficiency virus type 1 counteracts the effect of an AU-rich negative element in the human papillomavirus type 1 late 3' untranslated region.

    PubMed Central

    Tan, W; Schwartz, S

    1995-01-01

    We have identified a sequence in the late 3' untranslated region of human papillomavirus type 1 mRNAs that acts posttranscriptionally to repress gene expression. Deletion analysis localized the inhibitory element to an AU-rich sequence between nucleotides 6958 and 6984 on the human papillomavirus type 1 genome. This sequence inhibits gene expression in an orientation-dependent manner. Upon transfection of eucaryotic cells with plasmids containing this sequence, approximately 4-fold-lower cytoplasmic mRNA levels and 64- to 128-fold-lower protein levels were produced compared with those produced by plasmids lacking the inhibitory sequence. Interestingly, providing the constitutive transport element of simian retrovirus type 1 in sense orientation counteracted inhibition exerted by the human papillomavirus type 1 sequence. Inhibition could also be overcome by the presence of human immunodeficiency virus type 1 Rev protein in trans and its target sequence, the Rev-responsive element, in cis. Rev is a nuclear protein and acts by promoting nuclear export of human immunodeficiency virus type 1 mRNAs encoding structural proteins. Our results are consistent with a model for human papillomavirus type 1 late-gene expression in which mRNAs containing human papillomavirus type 1 inhibitory sequences enter a nonproductive route in the nucleus, resulting in inefficient mRNA utilization. Rev directs mRNA containing inhibitory sequences to a productive route by interacting with the Rev-responsive element. PMID:7707519

  8. Comment on "Calibration-independent measurement of complex permittivity of liquids using a coaxial transmission line" [Rev. Sci. Instrum. 86, 014704 (2015)

    NASA Astrophysics Data System (ADS)

    Hasar, U. C.; Barroso, J. J.

    2015-07-01

    In this letter, we comment on the applicability of the derived characteristic equation (Eq. (7)) in a recently published article of Guoxin [Rev. Sci. Instrum. 86, 014704 (2015)]. To validate our comment, we first derive another characteristic function for determination of complex permittivity of dielectric materials for the configurations considered in the above article using calibration-independent uncorrected S-parameters for transmission-line measurements (coaxial-line, waveguide, free-space, etc). Unlike the characteristic equation in this article, the characteristic equation derived here for determination of the complex permittivity of liquid samples does not require any knowledge about the complex permittivity of plugs, used for holding liquid samples in place. We then performed 3-D full-wave simulations for the measurement configurations presented in Guoxin's article for substantiation of the characteristic equation derived in this letter.

  9. Comment on ``Comments on the use of asymmetric monochromators for x-ray diffraction on a synchrotron source'' [Rev. Sci. Instrum. 66, 2174 (1995)

    NASA Astrophysics Data System (ADS)

    Sanchez del Rio, M.; Cerrina, F.

    1996-10-01

    In the article ``Comments on the use of asymmetric monochromators for x-ray diffraction on a synchrotron source,'' by Colin Nave, Ana Gonzalez, Graham Clark, Sean McSweeney, Stewart Cummings, and Michael Hart, Rev. Sci. Instrum. 66, 2174 (1995), paragraph II, the authors' unfamiliarity with our modeling codes leads them to claim that our approach to treat bent-asymmetrically cut crystals in ray tracing calculations is incorrect. Since SHADOW is a widely used code, it is important to correct any misunderstandings, and we give here arguments to demonstrate that our approach is perfectly valid, and the arguments used by the authors to criticize our method are based on an unwarranted conclusion extracted from one of our previous articles. We show that SHADOW, when properly run, treats the cases raised exactly. Indeed, their arguments provide a nice benchmark test for verifying the accuracy of SHADOW

  10. FANC Pathway Promotes UV-Induced Stalled Replication Forks Recovery by Acting Both Upstream and Downstream Polη and Rev1

    PubMed Central

    Renaud, Emilie; Rosselli, Filippo

    2013-01-01

    To cope with ultraviolet C (UVC)-stalled replication forks and restart DNA synthesis, cells either undergo DNA translesion synthesis (TLS) by specialised DNA polymerases or tolerate the lesions using homologous recombination (HR)-based mechanisms. To gain insight into how cells manage UVC-induced stalled replication forks, we analysed the molecular crosstalk between the TLS DNA polymerases Polη and Rev1, the double-strand break repair (DSB)-associated protein MDC1 and the FANC pathway. We describe three novel functional interactions that occur in response to UVC-induced DNA lesions. First, Polη and Rev1, whose optimal expression and/or relocalisation depend on the FANC core complex, act upstream of FANCD2 and are required for the proper relocalisation of monoubiquitinylated FANCD2 (Ub-FANCD2) to subnuclear foci. Second, during S-phase, Ub-FANCD2 and MDC1 relocalise to UVC-damaged nuclear areas or foci simultaneously but independently of each other. Third, Ub-FANCD2 and MDC1 are independently required for optimal BRCA1 relocalisation. While RPA32 phosphorylation (p-RPA32) and RPA foci formation were reduced in parallel with increasing levels of H2AX phosphorylation and MDC1 foci in UVC-irradiated FANC pathway-depleted cells, MDC1 depletion was associated with increased UVC-induced Ub-FANCD2 and FANCD2 foci as well as p-RPA32 levels and p-RPA32 foci. On the basis of the previous observations, we propose that the FANC pathway participates in the rescue of UVC-stalled replication forks in association with TLS by maintaining the integrity of ssDNA regions and by preserving genome stability and preventing the formation of DSBs, the resolution of which would require the intervention of MDC1. PMID:23365640

  11. FANC pathway promotes UV-induced stalled replication forks recovery by acting both upstream and downstream Polη and Rev1.

    PubMed

    Renaud, Emilie; Rosselli, Filippo

    2013-01-01

    To cope with ultraviolet C (UVC)-stalled replication forks and restart DNA synthesis, cells either undergo DNA translesion synthesis (TLS) by specialised DNA polymerases or tolerate the lesions using homologous recombination (HR)-based mechanisms. To gain insight into how cells manage UVC-induced stalled replication forks, we analysed the molecular crosstalk between the TLS DNA polymerases Polη and Rev1, the double-strand break repair (DSB)-associated protein MDC1 and the FANC pathway. We describe three novel functional interactions that occur in response to UVC-induced DNA lesions. First, Polη and Rev1, whose optimal expression and/or relocalisation depend on the FANC core complex, act upstream of FANCD2 and are required for the proper relocalisation of monoubiquitinylated FANCD2 (Ub-FANCD2) to subnuclear foci. Second, during S-phase, Ub-FANCD2 and MDC1 relocalise to UVC-damaged nuclear areas or foci simultaneously but independently of each other. Third, Ub-FANCD2 and MDC1 are independently required for optimal BRCA1 relocalisation. While RPA32 phosphorylation (p-RPA32) and RPA foci formation were reduced in parallel with increasing levels of H2AX phosphorylation and MDC1 foci in UVC-irradiated FANC pathway-depleted cells, MDC1 depletion was associated with increased UVC-induced Ub-FANCD2 and FANCD2 foci as well as p-RPA32 levels and p-RPA32 foci. On the basis of the previous observations, we propose that the FANC pathway participates in the rescue of UVC-stalled replication forks in association with TLS by maintaining the integrity of ssDNA regions and by preserving genome stability and preventing the formation of DSBs, the resolution of which would require the intervention of MDC1.

  12. Supplement to the paper "Quadratic Sagnac effect — the influence of the gravitational potential of the Coriolis force on the phase difference between the arms of a rotating Michelson interferometer (an explanation of D C Miller's experimental results, 1921 - 1926)" (Usp. Fiz. Nauk 185 431 (2015) [Phys. Usp. 58 398 (2015)])

    NASA Astrophysics Data System (ADS)

    Malykin, G. B.; Pozdnyakova, V. I.

    2015-08-01

    The paper "Quadratic Sagnac effect — the influence of the gravitational potential of the Coriolis force on the phase difference between the arms of a rotating Michelson interferometer (an explanation of D C Miller's experimental results, 1921 - 1926)" (Usp. Fiz. Nauk 185 431 (2015) [Phys. Usp. 58 398 (2015)]) is amended and supplemented with information concerning earlier work on the influence of rotation on Michelson - Morley's nonzero results.

  13. Interferon-induced HERC5 is evolving under positive selection and inhibits HIV-1 particle production by a novel mechanism targeting Rev/RRE-dependent RNA nuclear export

    PubMed Central

    2014-01-01

    Background Type I interferon (IFN) inhibits virus replication by activating multiple antiviral mechanisms and pathways. It has long been recognized that type I IFNs can potently block HIV-1 replication in vitro; as such, HIV-1 has been used as a system to identify and characterize IFN-induced antiviral proteins responsible for this block. IFN-induced HERC5 contains an amino-terminal Regulator of Chromosome Condensation 1 (RCC1)-like domain and a carboxyl-terminal Homologous to the E6-AP Carboxyl Terminus (HECT) domain. HERC5 is the main cellular E3 ligase that conjugates the IFN-induced protein ISG15 to proteins. This E3 ligase activity was previously shown to inhibit the replication of evolutionarily diverse viruses, including HIV-1. The contribution of the RCC1-like domain to the antiviral activity of HERC5 was previously unknown. Results In this study, we showed that HERC5 inhibits HIV-1 particle production by a second distinct mechanism that targets the nuclear export of Rev/RRE-dependent RNA. Unexpectedly, the E3 ligase activity of HERC5 was not required for this inhibition. Instead, this activity required the amino-terminal RCC1-like domain of HERC5. Inhibition correlated with a reduction in intracellular RanGTP protein levels and/or the ability of RanGTP to interact with RanBP1. Inhibition also correlated with altered subcellular localization of HIV-1 Rev. In addition, we demonstrated that positive evolutionary selection is operating on HERC5. We identified a region in the RCC1-like domain that exhibits an exceptionally high probability of having evolved under positive selection and showed that this region is required for HERC5-mediated inhibition of nuclear export. Conclusions We have identified a second distinct mechanism by which HERC5 inhibits HIV-1 replication and demonstrate that HERC5 is evolving under strong positive selection. Together, our findings contribute to a growing body of evidence suggesting that HERC5 is a novel host restriction factor

  14. Comment on ``Arrival time in quantum mechanics'' and ``Time of arrival in quantum mechanics''

    NASA Astrophysics Data System (ADS)

    Kijowski, Jerzy

    1999-01-01

    Contrary to claims contained in papers by Grot, Rovelli, and Tate [Phys. Rev. A 54, 4676 1996)] and Delgado and Muga [Phys. Rev. A 56, 3425 (1997)], the ``time operator,'' which I have constructed [Rep. Math. Phys. 6, 361 (1974)] in an axiomatic way, is a self-adjoint operator existing in a usual Hilbert space of (nonrelativistic or relativistic) quantum mechanics.

  15. Comment on ‘Time-resolved resonant photoionization of He using a time-dependent Feshbach method with ultrashort laser pulses’

    NASA Astrophysics Data System (ADS)

    Nicolaides, C. A.; Komninos, Y.; Mercouris, Th

    2014-07-01

    We compare the contents of the recent paper by Granados-Castro and Sanz-Vicario (2013 J.Phys. B 46 055601) to our previously published work on the same problem (Mercouris, Komninos and Nicolaides 2007 Phys. Rev. A 75 013407; 2013 Phys. Rev. A 87 069905(E)).

  16. Development of Lentiviral Vectors Simultaneously Expressing Multiple siRNAs Against CCR5, vif and tat/rev Genes for an HIV-1 Gene Therapy Approach.

    PubMed

    Spanevello, Francesca; Calistri, Arianna; Del Vecchio, Claudia; Mantelli, Barbara; Frasson, Chiara; Basso, Giuseppe; Palù, Giorgio; Cavazzana, Marina; Parolin, Cristina

    2016-04-19

    Gene therapy holds considerable promise for the functional cure of HIV-1 infection and, in this context, RNA interference (RNAi)-based approaches represent powerful strategies. Stable expression of small interfering RNAs (siRNAs) targeting HIV genes or cellular cofactors has the potential to render HIV-1 susceptible cells resistant to infection. To inhibit different steps of virus life cycle, self-inactivating lentiviral vectors expressing multiple siRNAs targeting the CCR5 cellular gene as well as vif and tat/rev viral transcripts, under the control of different RNA polymerase III promoters (U6, 7SK, H1) were developed. The use of a single RNA polymerase III promoter driving the expression of a sequence giving rise to three siRNAs directed against the selected targets (e-shRNA) was also investigated. Luciferase assay and inhibition of HIV-1 replication in human Jurkat T-cell line were adopted to select the best combination of promoter/siRNA. The efficacy of selected developed combinatorial vectors in interfering with viral replication was evaluated in human primary CD4(+) T lymphocytes. We identified two effective anti-HIV combinatorial vectors that conferred protection against R5- and X4- tropic viruses. Overall, our results showed that the antiviral effect is influenced by different factors, including the promoter used to express the RNAi molecules and the selected cassette combination. These findings contribute to gain further insights in the design of RNAi-based gene therapy approaches against HIV-1 for clinical application.

  17. [Genetically modified crops: promises and good intentions are not enough (refutation to Espinoza et aL 2004, Rev. Biol. Trop. 52 (3): 727-732)].

    PubMed

    García, Jaime E G

    2007-06-01

    The arguments presented by Espinoza et al. in their paper "Relationship of genetically modified crops with the environment and health of the Costa Rican human population" published in this journal (Rev. Biol. Trop. 52: 727-732, 2004) are questioned and refuted. The arguments are confronted with evidence offered by scientists and national and international independent organizations around the world (e.g. World Health Organization, Consumers International, Physicians and Scientists for Responsible Application of Science and Technology, International Union for Conservation of Nature and Natural Resources, the Council of the University of Costa Rica, and the Independent Science Panel) showing the current uncertainty and limitations of science in this area, as well as those of proposed and applied biosafety approaches. Environment, biodiversity and food security are so important and basic matters, that there is need of serious testing, particularly when promises seem to be based on environmentally dangerous ideas promoted half a century ago by the so called "green revolution". Debate should continue, based on a holistic analysis of facts and with ethical reasoning, avoiding emotional positions that can confuse virtual reality with reality.

  18. The human immunodeficiency virus (HIV) Rev-binding protein (HRB) is a co-factor for HIV-1 Nef-mediated CD4 downregulation.

    PubMed

    Landi, Alessia; Timermans, Cristina Garcia; Naessens, Evelien; Vanderstraeten, Hanne; Stove, Veronique; Verhasselt, Bruno

    2016-03-01

    Human immunodeficiency virus type 1 (HIV-1)-mediated CD4 downregulation is an important determinant of viral replication in vivo. Research on cellular co-factors involved in this process could lead to the identification of potential therapeutic targets. We found that CD4 surface levels were significantly higher in HIV-1-infected cells knocked-down for the HIV Rev-binding protein (HRB) compared with control cells. HRB knock-down affected CD4 downregulation induced by Nef but not by HIV-1 Vpu. Interestingly, the knock-down of the related protein HRBL (HRB-like), but not of the HRB interaction partner EPS15 (epidermal growth factor receptor pathway substrate 15), increased CD4 levels in Vpu-expressing cells significantly. Both of these proteins are known to be involved in HIV-1-mediated CD4 downregulation as co-factors of HIV-1 Nef. These results identify HRB as a previously unknown co-factor for HIV-1 Nef-mediated CD4 downregulation and highlight differences with the related protein HRBL, which affects the CD4 downregulation in a dual role as co-factor of both HIV-1 Nef and Vpu.

  19. Comment on ``Implementing of a precision fast thermoelectric cooler using a personal computer parallel port connection and ADN8830 controller'' [Rev. Sci. Instrum. 74, 3862 (2003)

    NASA Astrophysics Data System (ADS)

    Sloman, A. W.

    2004-03-01

    Eli Flaxer has described a feedback controlled circuit to drive a Peltier junction to control the temperature of a specimen in the range 0 to 50 °C in a room temperature environment [Rev. Sci. Instrum. 74, 3862 (2003)]. The amount of heat transferred per unit current by a Peltier junction varies substantially with the temperature difference across the Peltier junction. Flaxer's circuit does not provide any mechanism to compensate for this variation. This means that if the proportional-integral-differential control loop he uses is optimized at any particular temperature differential, the control loop with be over-damped at lower specimen temperatures, and under-damped at higher specimen temperatures. A circuit using a second thermistor to monitor the temperature of the exhaust side of the Peltier junction, and a digital control loop, can minimize this problem [A. W. Sloman, Paul Buggs, James Molloy, and Douglas Stewart, Meas. Sci. Technol. 7, 1653 (1996)]. This circuit has the incidental advantage of offering ten times better temperature stability.

  20. [Genetically modified crops: promises and good intentions are not enough (refutation to Espinoza et aL 2004, Rev. Biol. Trop. 52 (3): 727-732)].

    PubMed

    García, Jaime E G

    2007-06-01

    The arguments presented by Espinoza et al. in their paper "Relationship of genetically modified crops with the environment and health of the Costa Rican human population" published in this journal (Rev. Biol. Trop. 52: 727-732, 2004) are questioned and refuted. The arguments are confronted with evidence offered by scientists and national and international independent organizations around the world (e.g. World Health Organization, Consumers International, Physicians and Scientists for Responsible Application of Science and Technology, International Union for Conservation of Nature and Natural Resources, the Council of the University of Costa Rica, and the Independent Science Panel) showing the current uncertainty and limitations of science in this area, as well as those of proposed and applied biosafety approaches. Environment, biodiversity and food security are so important and basic matters, that there is need of serious testing, particularly when promises seem to be based on environmentally dangerous ideas promoted half a century ago by the so called "green revolution". Debate should continue, based on a holistic analysis of facts and with ethical reasoning, avoiding emotional positions that can confuse virtual reality with reality. PMID:19069750

  1. Erratum: Evolution of precipitate morphology during heat treatment and its implications for the superconductivity in KxFe1.6+ySe2 single crystals [Phys. Rev. B 86 , 144507 (2012)

    SciTech Connect

    Liu, Y.; Xing, Q.; Dennis, K. W.; McCallum, R. W.; Lograsso, T. A.

    2015-08-14

    In this article, we study the relationship between precipitate morphology and superconductivity in KxFe1.6+ySe2 single crystals grown by self-flux method. Scanning electron microscopy (SEM) measurements revealed that the superconducting phase forms a network in the samples quenched above iron vacancy order-disorder transition temperature Ts, whereas it aggregates into micrometer-sized rectangular bars and aligns as disconnected chains in the furnace-cooled samples.

  2. Spin resonance strength of a localized rf magnetic field

    NASA Astrophysics Data System (ADS)

    Lee, S. Y.

    2006-07-01

    Spin-resonance strength produced by a localized rf field has been a focus of recent publications [V. S. Morozov , Phys. Rev. ST Accel. Beams 7, 024002 (2004).PRABFM1098-440210.1103/PhysRevSTAB.7.024002; M. A. Leonova (to be published).; T. Roser, in Handbook of Accelerator Physics and Engineering, edited by A. W. Chao and M. Tigner (World Scientific, Singapore, 1999), p. 151.; M. Bai, W. W. MacKay, and T. Roser, Phys. Rev. ST Accel. Beams 8, 099001 (2005).PRABFM1098-440210.1103/PhysRevSTAB.8.099001; V. S. Morozov , Phys. Rev. ST Accel. Beams 8, 099002 (2005).PRABFM1098-440210.1103/PhysRevSTAB.8.099002]. This paper discusses the debated factor of 2, and provides a formula to calculate the component enhanced by the induced betatron motion.

  3. Comment on ``Vortex-assisted photon counts and their magnetic field dependence in single-photon superconducting detectors''

    NASA Astrophysics Data System (ADS)

    Gurevich, A.; Vinokur, V. M.

    2012-07-01

    We discuss the importance of the vortex core energy and realistic boundary conditions to the Fokker-Plank equation for the calculation of thermally activated hopping of vortices across narrow superconducting films. Disregard of these issues in the papers by Bulaevskii, Graf and Kogan, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.85.014505 85, 014505 (2012) and by Bulaevskii , Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.83.144526 83, 144526 (2011) in which an uncertain London vortex core cutoff was used, can produce large numerical errors and a significant discrepancy between their results and the results of the paper by Gurevich and Vinokur, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.100.227007 100, 227007 (2008) in which these issues were taken into account. This can be essential for the interpretation of experimental data on thin-film photon detectors and other superconducting nanostructures.

  4. Modifier genes as therapeutics: the nuclear hormone receptor Rev Erb alpha (Nr1d1) rescues Nr2e3 associated retinal disease.

    PubMed

    Cruz, Nelly M; Yuan, Yang; Leehy, Barrett D; Baid, Rinku; Kompella, Uday; DeAngelis, Margaret M; Escher, Pascal; Haider, Neena B

    2014-01-01

    Nuclear hormone receptors play a major role in many important biological processes. Most nuclear hormone receptors are ubiquitously expressed and regulate processes such as metabolism, circadian function, and development. They function in these processes to maintain homeostasis through modulation of transcriptional gene networks. In this study we evaluate the effectiveness of a nuclear hormone receptor gene to modulate retinal degeneration and restore the integrity of the retina. Currently, there are no effective treatment options for retinal degenerative diseases leading to progressive and irreversible blindness. In this study we demonstrate that the nuclear hormone receptor gene Nr1d1 (Rev-Erbα) rescues Nr2e3-associated retinal degeneration in the rd7 mouse, which lacks a functional Nr2e3 gene. Mutations in human NR2E3 are associated with several retinal degenerations including enhanced S cone syndrome and retinitis pigmentosa. The rd7 mouse, lacking Nr2e3, exhibits an increase in S cones and slow, progressive retinal degeneration. A traditional genetic mapping approach previously identified candidate modifier loci. Here, we demonstrate that in vivo delivery of the candidate modifier gene, Nr1d1 rescues Nr2e3 associated retinal degeneration. We observed clinical, histological, functional, and molecular restoration of the rd7 retina. Furthermore, we demonstrate that the mechanism of rescue at the molecular and functional level is through the re-regulation of key genes within the Nr2e3-directed transcriptional network. Together, these findings reveal the potency of nuclear receptors as modulators of disease and specifically of NR1D1 as a novel therapeutic for retinal degenerations.

  5. Development of Lentiviral Vectors Simultaneously Expressing Multiple siRNAs Against CCR5, vif and tat/rev Genes for an HIV-1 Gene Therapy Approach

    PubMed Central

    Spanevello, Francesca; Calistri, Arianna; Del Vecchio, Claudia; Mantelli, Barbara; Frasson, Chiara; Basso, Giuseppe; Palù, Giorgio; Cavazzana, Marina; Parolin, Cristina

    2016-01-01

    Gene therapy holds considerable promise for the functional cure of HIV-1 infection and, in this context, RNA interference (RNAi)-based approaches represent powerful strategies. Stable expression of small interfering RNAs (siRNAs) targeting HIV genes or cellular cofactors has the potential to render HIV-1 susceptible cells resistant to infection. To inhibit different steps of virus life cycle, self-inactivating lentiviral vectors expressing multiple siRNAs targeting the CCR5 cellular gene as well as vif and tat/rev viral transcripts, under the control of different RNA polymerase III promoters (U6, 7SK, H1) were developed. The use of a single RNA polymerase III promoter driving the expression of a sequence giving rise to three siRNAs directed against the selected targets (e-shRNA) was also investigated. Luciferase assay and inhibition of HIV-1 replication in human Jurkat T-cell line were adopted to select the best combination of promoter/siRNA. The efficacy of selected developed combinatorial vectors in interfering with viral replication was evaluated in human primary CD4+ T lymphocytes. We identified two effective anti-HIV combinatorial vectors that conferred protection against R5- and X4- tropic viruses. Overall, our results showed that the antiviral effect is influenced by different factors, including the promoter used to express the RNAi molecules and the selected cassette combination. These findings contribute to gain further insights in the design of RNAi-based gene therapy approaches against HIV-1 for clinical application. PMID:27093170

  6. Project Execution Plan, Rev. 3

    SciTech Connect

    IT Corporation, Las Vegas

    2002-08-01

    This plan addresses project activities encompassed by the U.S. Department of Energy's (DOE's), National Nuclear Security Administration Nevada Operations Office, Environmental Restoration Division and conforms to the requirements contained in the Life-Cycle Asset Management, DOE Order 430.1A; The Joint Program Office Policy on Project Management in Support of DOE Order 430.1; Program and Project Management for the Acquisition of Capital Assets, DOE Order 413.3; the Project Execution and Engineering Management Planning Guide, GPG-FM-010; and other applicable Good Practice Guides; and the FY 2001 Integrated Planning, Accountability, and Budgeting System Policy Guidance. The plan also reflects the milestone philosophies of the Federal Facility Agreement and Consent Order, as agreed to by the State of Nevada, the DOE, and the U.S. Department of Defense; and traditional project management philosophies such as the development of life-cycle costs, schedules, and work scope; identification o f roles and responsibilities; and baseline management and controls.

  7. ARAM-CI Rev. 1

    2008-07-30

    ARAM-CI provides the basic RAM framework process for conducting a security risk analysis (risk assessment and risk management) for different critical infrastructures. The user works through a step-by-step process which includes screening, facility characterization, identification of potential targets, detemine consequences, identify and characterize threat, conduct a vulnerability assessment, and detemining a relative risk. The ARAM-CI tool also allows the user address risk reduction measrues by developing upgrade packages and considering possible impacts.

  8. Determination of the 3He+α→7Be asymptotic normalization coefficients, the nuclear vertex constants, and their application for the extrapolation of the 3He(α,γ)7Be astrophysical S factors to the solar energy region

    NASA Astrophysics Data System (ADS)

    Tursunmahatov, Q. I.; Yarmukhamedov, R.

    2012-04-01

    A new analysis of the modern astrophysical S factors for the direct-capture 3He(α,γ)7Be reaction, precisely measured in recent works [B.S. Nara Singh , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.93.262503 93, 262503 (2004); D. Bemmerer , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.97.122502 97, 122502 (2006);F. Confortola , Phys. Rev. CPRVCAN0556-281310.1103/PhysRevC.75.065803 75, 065803 (2007), Gy. Gyürky , Phys. Rev. CPRVCAN0556-281310.1103/PhysRevC.75.035805 75, 035805 (2007), T. A. D. Brown , Phys. Rev. CPRVCAN0556-281310.1103/PhysRevC.76.055801 76, 055801 (2007), and A. Di Leva, , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.102.232502 102, 232502 (2009)], has been carried out within the modified two-body potential approach. New estimates are obtained for the “indirectly determined” values of the asymptotic normalization constants and the respective nuclear vertex constants for 3He+α→7Be(g.s.) and 3He+α→7Be(0.429 MeV) as well as the astrophysical S factors S34(E) at E≤90 keV, including E=0. The values of asymptotic normalization constants have been used to obtain the values of the ratio of the α-particle spectroscopic factors for the mirror (7Li7Be) pair.

  9. Wigner function and Schroedinger equation in phase-space representation

    SciTech Connect

    Chruscinski, Dariusz; Mlodawski, Krzysztof

    2005-05-15

    We discuss a family of quasidistributions (s-ordered Wigner functions of Agarwal and Wolf [Phys. Rev. D 2, 2161 (1970); Phys. Rev. D 2, 2187 (1970); Phys. Rev. D 2, 2206 (1970)]) and its connection to the so-called phase space representation of the Schroedinger equation. It turns out that although Wigner functions satisfy the Schroedinger equation in phase space, they have a completely different interpretation.

  10. Exotic quantum critical point on the surface of three-dimensional topological insulator

    NASA Astrophysics Data System (ADS)

    Bi, Zhen; You, Yi-Zhuang; Xu, Cenke

    2016-07-01

    In the last few years a lot of exotic and anomalous topological phases were constructed by proliferating the vortexlike topological defects on the surface of the 3 d topological insulator (TI) [Fidkowski et al., Phys. Rev. X 3, 041016 (2013), 10.1103/PhysRevX.3.041016; Chen et al., Phys. Rev. B 89, 165132 (2014), 10.1103/PhysRevB.89.165132; Bonderson et al., J. Stat. Mech. (2013) P09016, 10.1088/1742-5468/2013/09/P09016; Wang et al., Phys. Rev. B 88, 115137 (2013), 10.1103/PhysRevB.88.115137; Metlitski et al., Phys. Rev. B 92, 125111 (2015), 10.1103/PhysRevB.92.125111]. In this work, rather than considering topological phases at the boundary, we will study quantum critical points driven by vortexlike topological defects. In general, we will discuss a (2 +1 )d quantum phase transition described by the following field theory: L =ψ ¯γμ(∂μ-i aμ) ψ +| (∂μ-i k aμ) ϕ| 2+r|ϕ | 2+g |ϕ| 4 , with tuning parameter r , arbitrary integer k , Dirac fermion ψ , and complex scalar bosonic field ϕ , which both couple to the same (2 +1 )d dynamical noncompact U(1) gauge field aμ. The physical meaning of these quantities/fields will be explained in the text. Making use of the new duality formalism developed in [Metlitski et al., Phys. Rev. B 93, 245151 (2016), 10.1103/PhysRevB.93.245151; Wang et al., Phys. Rev. X 5, 041031 (2015), 10.1103/PhysRevX.5.041031; Wang et al., Phys. Rev. B 93, 085110 (2016), 10.1103/PhysRevB.93.085110; D. T. Son, Phys. Rev. X 5, 031027 (2015), 10.1103/PhysRevX.5.031027], we demonstrate that this quantum critical point has a quasi-self-dual nature. And at this quantum critical point, various universal quantities such as the electrical conductivity and scaling dimension of gauge-invariant operators, can be calculated systematically through a 1 /k2 expansion, based on the observation that the limit k →+∞ corresponds to an ordinary 3 d X Y transition.

  11. Corrective Action Decision Document/Closure Report for Corrective Action Unit 552: Area 12 Muckpile and Ponds, Nevada Test Site, Nevada, Rev. No.: 0 with Errata Sheet

    SciTech Connect

    Laura Pastor

    2005-09-01

    This Corrective Action Decision Document (CADD)/Closure Report (CR) has been prepared for Corrective Action Unit (CAU) 552, Area 12 Muckpile and Ponds, Nevada Test Site (NTS), Nevada. The corrective actions proposed in this document are in accordance with the ''Federal Facility Agreement and Consent Order'' (FFACO) that was agreed to by the State of Nevada, U.S. Department of Energy (DOE), and the U.S. Department of Defense (FFACO, 1996). The NTS is approximately 65 miles (mi) northwest of Las Vegas, Nevada (Figure 1-1). Corrective Action Unit 552 is comprised of the corrective action site (CAS) that is shown on Figure 1-2 and listed below: 12-23-05, Ponds. The ponds were originally constructed to catch runoff from the muckpile. As the muckpile continued to be extended to the north and to the east, it became impossible to ensure that all of the runoff from the muckpile was funneled into the pond. Some of the runoff from the muckpile continues to be caught in the upper pond, but portions of the muckpile have eroded, diverting much of the runoff away from the ponds. Regarding the other ponds, there is no evidence that any of the overflow ponds ever received runoff from overflow of the upper pond. The muckpile was removed from CAU 552 because an active leachfield exists within the muckpile and there are current activities at G-Tunnel. A detailed discussion of the history of this CAU is presented in the ''Corrective Action Investigation Plan (CAIP) for Corrective Action Unit 552: Area 12 Muckpile and Ponds, Nevada Test Site, Nevada'', Rev. 1 (NNSA/NSO, 2005). Corrective Action Unit 552, Area 12 Muckpile and Ponds, consists of one site located in the southern portion of Area 12. Corrective Action Site 12-23-05 consists of dry ponds adjacent to the G-Tunnel muckpile. The ponds were used to contain effluent from the G-Tunnel. The purpose of this CADD/CR is to provide justification for the closure of CAU 552 with no further corrective action. This justification is based on

  12. Comment on ``Adiabatic quantum computation with a one-dimensional projector Hamiltonian''

    NASA Astrophysics Data System (ADS)

    Kay, Alastair

    2013-10-01

    The partial adiabatic search algorithm was introduced in Tulsi's paper [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.80.052328 80, 052328 (2009)] as a modification of the usual adiabatic algorithm for a quantum search with the idea that most of the interesting computation only happens over a very short range of the adiabatic path. By focusing on that restricted range, one can potentially gain an advantage by reducing the control requirements on the system, enabling a uniform rate of evolution. In this Comment, we point out an oversight in Tulsi's paper [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.80.052328 80, 052328 (2009)] that invalidates its proof. However, the argument can be corrected, and the calculations in Tulsi's paper [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.80.052328 80, 052328 (2009)] are then sufficient to show that the scheme still works. Nevertheless, subsequent works [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.82.034304 82, 034304 (2010), Chin. Phys. BCPBHAJ1674-105610.1088/1674-1056/20/4/040309 20, 040309 (2011), Chin. Phys. BCPBHAJ1674-105610.1088/1674-1056/21/1/010306 21, 010306 (2012), AASRI Procedia 1, 5862 (2012), and Quantum Inf. Process.10.1007/s11128-013-0557-1 12, 2689 (2013)] cannot all be recovered in the same way.

  13. Editorial: phys. stat. sol. (b) 241/5

    NASA Astrophysics Data System (ADS)

    Stutzmann, Martin

    2004-04-01

    Physica status solidi was founded in 1961 by a number of eminent solid state physicists as an attempt to overcome the iron curtain, which then separated East and West, at least in the field of science. Since that time our world has changed quite a bit, and so have the boundary conditions of science publishing. However, one thing has not changed: then as now, the general policy and development of a respectable scientific journal should be determined by a board of independent scientists, who volunteer to assume responsibility for the scientific content of the journal, to assure a fair and critical peer review process for all submitted manuscripts, and, in cases of conflict, to finally decide which papers will be published and which will not.As a matter of fact, an international Board of Editors which consists of scientists coming from different countries and continents, with a good reputation in their respective community, and without any conflict of interest with the Publisher of the journal is, in my opinion, these days more important than ever. As our daily scientific work becomes increasingly specialized, but at the same time also increasingly interdisciplinary, we are more and more forced to trust the quality and reliability of published scientific results in the literature, without really having a chance to come to an independent opinion on our own. This is one of the reasons why the many recent cases of plagiarism, scientific misconduct, or outright fraud have caused such a high level of public awareness. It is quite clear that without a serious peer review there would be an even larger number of such cases in the literature, and that without the responsible action taken by concerned Journal Editors, many of the revealed cases probably would have remained under the carpet.It is, therefore, a particular pleasure for me to introduce to you on the following pages the current Editorial Board of physica status solidi (b) in the form of a brief curriculum vitae, a photograph, and an e-mail address (in case you want to contact our Editors directly!). Of course, since 1961 the Editorial Board of our journal has undergone many changes and will continue to do so, but we always have attempted to maintain a good balance between the different areas of solid state physics, between theory and experiment, and between different countries. And although nothing is perfect, I hope that you will find at least one or two board members, who are known to you through their contributions to the literature in solid state physics.For me, this is the perfect occasion to thank all Members of the Editorial Board, past and present, for their advice, continuing support, and dedication! Vielen herzlichen Dank!

  14. Editorial: phys. stat. sol. (a) 201/5

    NASA Astrophysics Data System (ADS)

    Stutzmann, Martin

    2004-04-01

    Physica status solidi was founded in 1961 by a number of eminent solid state physicists as an attempt to overcome the iron curtain, which then separated East and West, at least in the field of science. Since that time our world has changed quite a bit, and so have the boundary conditions of science publishing. However, one thing has not changed: then as now, the general policy and development of a respectable scientific journal should be determined by a board of independent scientists, who volunteer to assume responsibility for the scientific content of the journal, to assure a fair and critical peer review process for all submitted manuscripts, and, in cases of conflict, to finally decide which papers will be published and which will not.As a matter of fact, an international Board of Editors which consists of scientists coming from different countries and continents, with a good reputation in their respective community, and without any conflict of interest with the Publisher of the journal is, in my opinion, these days more important than ever. As our daily scientific work becomes increasingly specialized, but at the same time also increasingly interdisciplinary, we are more and more forced to trust the quality and reliability of published scientific results in the literature, without really having a chance to come to an independent opinion on our own. This is one of the reasons why the many recent cases of plagiarism, scientific misconduct, or outright fraud have caused such a high level of public awareness. It is quite clear that without a serious peer review there would be an even larger number of such cases in the literature, and that without the responsible action taken by concerned Journal Editors, many of the revealed cases probably would have remained under the carpet.It is, therefore, a particular pleasure for me to introduce to you on the following pages the current Editorial Board of physica status solidi (a) in the form of a brief curriculum vitae, a photograph, and an e-mail address (in case you want to contact our Editors directly!). Of course, since 1961 the Editorial Board of our journal has undergone many changes and will continue to do so, but we always have attempted to maintain a good balance between the different areas of solid state physics, between theory and experiment, and between different countries. And although nothing is perfect, I hope that you will find at least one or two board members, who are known to you through their contributions to the literature in solid state physics.For me, this is the perfect occasion to thank all Members of the Editorial Board, past and present, for their advice, continuing support, and dedication! Vielen herzlichen Dank!

  15. Preface: phys. stat. sol. (a) 202/7

    NASA Astrophysics Data System (ADS)

    Pollak, Fred H.; Misiewicz, Jan; Sitarek, Piotr

    2005-05-01

    We have recently observed a growing interest in using the powerful technique of optical modulation spectroscopy. These applications are related mostly to the characterization of low dimensional semiconductor structures and devices based on them.The International Workshop on Modulation Spectroscopy of Semiconductor Structures (MS3) at the beginning of July 2004 gathered in Wrocaw (in the southwest part of Poland) almost 40 participants, half of them from abroad. The 8 invited and 16 contributed talks were presented by the leaders of research teams from the USA, Japan, Taiwan, Canada, Germany, France, the Netherlands, Sweden, Ireland, Russia, Lithuania and Poland. Part of the MS3 workshop was held at the Laboratory of Advanced Optical Spectroscopy, Institute of Physics, Wrocaw University of Technology, where discussions on technical matter of the modulation spectroscopy were carried out in a relaxing atmosphere over a cup of coffee.The topics of the MS3 workshop included: advantages of photoreflectance, electroreflectance, contactless electroreflectance, thermoreflectance, differential reflectance and wavelength-modulated surface photovoltage spectroscopy. The applications of the above methods to investigate transistor, diode and laser structures including VCSELs, low dimensional structures of both wings of the spectrum, i.e. wide band gap materials like GaN, AlGaN, ZnO and low band gap materials such as GaInN(Sb)As, InAs, InSb, and FeSi2 were demonstrated.It is our great pleasure to publish the most interesting of the MS3 workshop presentations in this issue of physica status solidi (a).The organizers acknowledge Wrocaw University of Technology, the Center of Exellence CEPHONA from the Institute of Electron Technology in Warsaw and the Polish Committee for Scientific Research for financial support of the workshop.

  16. Preface: phys. stat. sol. (a) 203/12

    NASA Astrophysics Data System (ADS)

    Jackman, Richard B.; Nesládek, Milo; Haenen, Ken

    2006-09-01

    The 30 papers gathered in this issue of physica status solidi (a) give a thorough overview over different topics that were presented during the 11th edition of the International Workshop on Surface and Bulk Defects in CVD Diamond Films (SBDD), which took place from 22 to 24 February 2006, at the Hasselt University in Diepenbeek-Hasselt, Belgium. Since its start more than 10 years ago, the SBDD Workshop has grown into a well-established, yearly early bird meeting place, addressing new emerging science related to the progress in the CVD diamond field. The 10 invited lectures, 29 contributed oral presentations and 26 posters were presented in several sessions during an intense two and a half day long meeting.The number of participants reached 115 this year with participants coming from fifteen countries: Austria, Belgium, Czech Republic, France, Germany, Israel, Italy, Japan, Mexico, Poland, Russia, Singapore, Slovak Republic, Sweden, UK, and USA. The mixture of young and established scientists, including a great proportion of students, made this meeting a hot spot of lively discussions on a wide range of scientific subjects, not only during the meeting itself, but also at several occasions throughout many social events offered by the hospitality of the city of Hasselt.It stands for itself that the workshop would not have been possible without the support of many people and institutions. For financial aid we are especially indebted to the Scientific Research Community Surface Modification of Materials of the F.W.O.-Vlaanderen (Belgium), whose incessant support plays an important role in keeping this meeting going. We also thank the Hasselt University for offering the lecture hall and infrastructure facilities and Seki Technotron Corp. for sponsoring the poster reception and their presence with a table top exhibit. Finally we highly appreciate the active approach of the editorial staff of physica status solidi in this conference and would like to thank most notably Stefan Hildebrandt, Ron Schulz-Rheinländer, Christoph Lellig, and Julia Hübner, for their excellent and patient work, bringing the number of successfully published proceedings of SBDD in pss (a) up to 8 already!To finish, we would all like to invite you to the 12th edition of the SBDD series, newly renamed as Hasselt Diamond Workshop, to be held at its established location of Diepenbeek-Hasselt. We look forward meeting you again at SBDD XII in 2007:Hasselt Diamond Workshop - SBDD XII28 February-2 March 2007Hasselt University, Diepenbeek-Hasselt, Belgiumhttp://www.imo.uhasselt.be/SBDD2007London, Paris, Hasselt, August 2006

  17. Preface: phys. stat. sol. (a) 201/11

    NASA Astrophysics Data System (ADS)

    Bergonzo, Philippe; Haenen, Ken; Nebel, Christoph; Nesládek, Milo; Vanek, Milan

    2004-09-01

    The present issue of physica status solidi (a) contains a collection of 24 papers presented at the 9th International Workshop on Surface and Bulk Defects in CVD Diamond Films held in Diepen- beek-Hasselt, Belgium, 18-20 February 2004. The concept of this workshop originated in 1996 with the idea of bringing together scientists who are active and innovative in the field of electronic and optical properties of thin film diamond. Since then, this meeting have grown up to a regular conference devoted to new issues in CVD diamond research and related to diamond as a material for electronics and nanobioelectronics. This year the programme was spread over two and a half days, including 8 invited lectures from a total of 39 talks, and a poster session featuring 15 posters. In addition we were able to connect this meeting with a workshop on Defects and Impurities in Crystalline Boron Nitride Compounds, scientifically organized from the University of Antwerp and leading finally to a joint meeting lasting four days. The papers from the BN workshop are joining this proceeding issue on pages 2559-2598.At SBDD IX, topics ranged from homo- and heteroepitaxial growth, doping, hydrogen induced surface conductivity, defects and their characterization, to devices including bio-sensing applications. As usual, very intense and lively discussions took place among participants, from young students to established scientists, after talks, during breaks and in the evenings while enjoying the hospitality of the Limburgs Universitair Centrum and especially the city of Hasselt. The number of participants reached a record breaking 96 this year, with participants coming from fifteen different countries (Australia, Austria, Belgium, Czech Republic, France, Germany, Israel, Italy, Japan, Mexico, Romania, Russia, Sweden, UK, USA). This yearly increasing number indicates that this workshop is continuing to be very attractive to a large scientific community, as it summarizes the up-to-date research on diamond as a wide band gap semiconductor.The workshop would have not been possible without the support of many people and institutions. For financial aid we are especially indebted to the Scientific Research Community Surface Modification of Materials of the F. W. O.-Vlaanderen (Belgium) and its continuous support since starting this workshop 9 years ago. We also thank the Limburgs Universitair Centrum for offering the lecture hall and infrastructure facilities. Finally we highly appreciate the active approach of the editorial staff of physica status solidi in this conference and would like to thank most notably Stefan Hildebrandt and Katharina Fröhlich, for their excellent and patient work, making this already the sixth successfully published proceedings of SBDD in pss (a).To finish, we would all like to invite you for the 10th anniversary of the SBDD series in February 2005 in Diepenbeek-Hasselt and we look forward to seeing you at:Surface and Bulk Defects in CVD Diamond Films, X23-25 February 2005Limburgs Universitair Centrum, Diepenbeek - Hasselt, Belgiumhttp://www.imo.luc.ac.be/SBDD2005

  18. Preface: phys. stat. sol. (a) 203/4

    NASA Astrophysics Data System (ADS)

    Kittler, Martin; Yang, Deren

    2006-03-01

    This issue of physica status solidi (a) contains the majority of papers presented at the 2nd Sino-German Symposium The Silicon Age which was held at the Lindner Hotel Cottbus, Germany, 19-24 September 2005. This meeting followed the 1st Symposium Progress in Silicon Materials held in June 2002 in Hangzhou, P.R. China. 8 Chinese and 14 German scientists from universities, research institutes and industry were invited to present their views about different aspects of silicon.There was a continuous progress in silicon materials development during the last 40-50 years, driven by the need of the IC industry for better and larger monocrystalline silicon wafers. Moreover, low-cost crystalline silicon now dominates the world's production of solar cells in the photovoltaics industry. Furthermore, there are intensive research activities worldwide for on-chip integration of Si-based photonics in CMOS technology. In addition, new areas being connected with silicon are starting to appear, namely Si-based biochips and nanoelectronics. Silicon, one can reasonably argue, is already the most investigated of all materials. However, there is still a need for continuation of research and development regarding numerous aspects of Si and also SiGe, including related technologies, advanced diagnostics or the role of crystal defects, which are the working fields of many laboratories all over the world. This was also shown by the presentations at the symposium and can be found in the contributions contained in this issue.The organizers would like to thank the participants for their high level contributions and discussions during the symposium. This intensive and open communication allowed the participants to create synergies between the different fields of silicon research and also to build up relationships for cooperation between Chinese and German research groups.Finally, we would like to thank the Sino-German Science Center for the financial support of the symposium.

  19. Preface: phys. stat. sol. (c) 1/10

    NASA Astrophysics Data System (ADS)

    Suh, Eun-Kyung; Yoon, Euijoon; Lee, Hyung Jae

    2004-09-01

    The Fifth International Symposium on Blue Laser and Light Emitting Diodes (ISBLLED-2004) was held in Gyeongju, Korea from 15-19 March 2004. Gyeongju, the ancient capital of the thousand-year Silla kingdom (57 B.C. to 935 A.D.) provided additional pleasure to the participants as an exceptional open-air museum with antique treasures scattered all around the city.During the last decade we have witnessed remarkable developments in wide-gap semiconductors and light emitting devices in the spectral range from the visible to deep UV. The purpose of the Symposium was to provide a forum for intensive discussion on the issues and main progress especially in optoelectronic devices, material growth and characterization, and quantum structures of wide bandgap semiconductors. A total of 243 papers including 220 contributed and 23 invited ones were presented and discussed by 487 participants from 17 countries world-wide. Among them, 154 manuscripts were submitted and reviewed by the usual evaluation process of physica status solidi. Some were rejected or withdrawn, and finally 139 papers are published in the special issues of physica status solidi (a), (b), and (c). We gratefully acknowledge the referees for their careful review. The papers are grouped into 7 categories. The subheadings and the number of papers in each are as follows: Optoelectronic devices, 43; Growth and characterization, 45; Nano and quantum structures, 21; Contacts, 8; Zinc oxide, 9; Indium nitride and indium rich InGaN, 6; Others, 7. The special session of the Symposium, The LED Highlight, designed partially to meet the challenging targets of the technology, i.e., energy savings and clean environment preservation, drew much attention and is edited as a special coloured section in this issue.The next symposium is scheduled for Montpellier, France, in 2006. We wish the organizers of that symposium the best of luck and hope to see all of the ISBLLED-2004 participants again at ISBLLED-2006.ISBLLED-2004 was sponsored by The Research Society for the Wide-gap Semiconductors, Korean Physical Society, Office of Naval Research, Korea Science and Engineering Foundation, Korea Research Foundation, Korea Association for Photonics Industry Development, Asian Office of Aerospace Research and Development, and Korea Photonics Technology Institute. We would like to thank Ms. E. S. Hwang for her devotion to the preparation and the Proceedings of the symposium including the manuscript handling for publication.

  20. Preface: phys. stat. sol. (a) 201/8

    NASA Astrophysics Data System (ADS)

    Shin, Sung-Chul

    2004-06-01

    The KMS/SOMMA Meeting 2003 was held 3-6 December 2003 at Spapia Hotel, Daejeon, Korea. It was the 5th SOMMA (International Symposium on Magnetic Materials and Applications) organized by ReCAMM (Research Center for Advanced Magnetic Materials) of Chungnam National University. Since 2002, the Korean Magnetics Society (KMS) winter conference has been jointly held with SOMMA. This was the second time to have a KMS/SOMMA joint meeting. The main objective of the meeting was to provide an international forum to discuss up-to-date results on magnetism and magnetic materials. The conference brought together 360 participants from 12 countries. Sessions of the meeting were: Theory and Fundamentals, Magnetic Random Access Memory, Spintronics, Information Storage, Nanostructured Materials, Sensors, and Interdisciplinary. In these seven sessions, 325 papers were presented including 66 oral and 259 poster presentations. Since the symposium was held in Korea, this enabled a large number of Asian scientists to attend: 239 from Korea, 41 from Japan, 7 from Taiwan, and 5 from China.The conference program had 25 invited and plenary speakers. They were Y. Ando (Tohoku U.), M. Inoue (Toyohashi U. Tech), H. Kubota (Tohoku U.), K. Mohri (Nagoya U.), M. Sahashi, M. Takahashi, K. Takanashi, M. Tsunoda (Tohoku U.), and H. Yoda (Toshiba) from Japan; A. J. Freeman (Northwestern U.), A. T. Hanbicki (NRL), F. B. Humphrey (Boston U.), and S. Sun (IBM) from the USA; J. D. Boeck (IMEC, Belgium), B. Dieny (CEA, France), N. Garcia (CSIS, Spain), G. Reiss (Bielefeld U., Germany), T. Stobiecki (U. M. & M. Krakow, Poland), and M. Wolfram (Singulus Tech, Germany) from Europe; C. G. Kim, D. J. Kim (CNU), T. W. Kim (SAIT), S. H. Lim (KIST), Sung-Chul Shin (KAIST), and Yoon Hee Chung (POSTEC) from Korea.For the first time, the SOMMA Proceedings appear in physica status solidi. The Editors hope that the Proceedings could provide chances for deeper and wider understanding of the presentations as well as for enhanced relationship between all participants. We deeply appreciate the help of the editorial staff of physica status solidi for their efficient and kind help during the paper preparations and publications.Finally, we would like to take this opportunity to thank all members of the Advisory Committee, Organizing Committee, referees, and KMS staff for their effort before, during, and after the meeting.

  1. Preface: phys. stat. sol. (b) 241/7

    NASA Astrophysics Data System (ADS)

    Shin, Sung-Chul

    2004-06-01

    The KMS/SOMMA Meeting 2003 was held 3-6 December 2003 at Spapia Hotel, Daejeon, Korea. It was the 5th SOMMA (International Symposium on Magnetic Materials and Applications) organized by ReCAMM (Research Center for Advanced Magnetic Materials) of Chungnam National University. Since 2002, the Korean Magnetics Society (KMS) winter conference has been jointly held with SOMMA. This was the second time to have a KMS/SOMMA joint meeting.The main objective of the meeting was to provide an international forum to discuss up-to-date results on magnetism and magnetic materials. The conference brought together 360 participants from 12 countries. Sessions of the meeting were: Theory and Fundamentals, Magnetic Random Access Memory, Spintronics, Information Storage, Nanostructured Materials, Sensors, and Interdisciplinary. In these seven sessions, 325 papers were presented including 66 oral and 259 poster presentations. Since the symposium was held in Korea, this enabled a large number of Asian scientists to attend: 239 from Korea, 41 from Japan, 7 from Taiwan, and 5 from China.The conference program had 25 invited and plenary speakers. They were Y. Ando (Tohoku U.), M. Inoue (Toyohashi U. Tech), H. Kubota (Tohoku U.), K. Mohri (Nagoya U.), M. Sahashi, M. Takahashi, K. Takanashi, M. Tsunoda (Tohoku U.), and H. Yoda (Toshiba) from Japan; A. J. Freeman (Northwestern U.), A. T. Hanbicki (NRL), F. B. Humphrey (Boston U.), and S. Sun (IBM) from the USA; J. D. Boeck (IMEC, Belgium), B. Dieny (CEA, France), N. Garcia (CSIS, Spain), G. Reiss (Bielefeld U., Germany), T. Stobiecki (U. M. & M. Krakow, Poland), and M. Wolfram (Singulus Tech, Germany) from Europe; C. G. Kim, D. J. Kim (CNU), T. W. Kim (SAIT), S. H. Lim (KIST), Sung-Chul Shin (KAIST), and Yoon Hee Chung (POSTEC) from Korea.For the first time, the SOMMA Proceedings appear in physica status solidi. The Editors hope that the Proceedings could provide chances for deeper and wider understanding of the presentations as well as for enhanced relationship between all participants. We deeply appreciate the help of the editorial staff of physica status solidi for their efficient and kind help during the paper preparations and publications.Finally, we would like to take this opportunity to thank all members of the Advisory Committee, Organizing Committee, referees, and KMS staff for their effort before, during, and after the meeting.

  2. Preface: phys. stat. sol. (b) 242/1

    NASA Astrophysics Data System (ADS)

    Ginzburg, V. L.; Maksimov, E. G.

    2005-01-01

    We have accepted with great pleasure the suggestion of the Guest Editor Miodrag Kuli to write a short preface to the special issue of this journal, which is devoted to the role played by electron-phonon interaction (EPI) in high-temperature superconductors (HTSC). From the very beginning, it was absolutely clear to us that there is no metal in which the EPI could be ignored, and high-temperature superconducting compounds cannot be an exception in this respect. We expressed this opinion, in particular, in our early Review Article [1] and in the talk [2] given at the Grenoble M2S HTSC Conference in 1994. We would like to emphasize that we were not in isolation. There have been many other researchers, some authors of this issue among them, who have also considered the EPI as an essential part of the physics of high-temperature superconductors. However, a large part of researchers in the field, including a few famous scientists, have considered the EPI to be irrelevant to high-temperature superconductivity. Up to now, we do not understand the scientific basis for such an opinion. Moreover, that point of view has never been shared by some other famous scientists; in this respect mention should be made of J. Friedel and A. A. Abrikosov.Turning back to physics, we would like to point out some features of high-temperature superconducting cuprates, which should lead to the existence of a strong EPI in these materials. First of all, it is the proximity of these compounds, even in the optimally doped case, to the layered ionic crystals. This fact has been emphasized in our early publications as well as in many papers by other authors, and it is discussed in detail in the Review Article by C. Falter published in this issue. There are other approaches to the HTSC compounds, which allow to consider that a strong EPI exists. They are also based on some peculiarities in the crystalline and chemical structure of these compounds, in particular, on their multiphase nanoscale structure. This point is discussed by J. Phillips in this issue.There are also many experimental indications in favor of the existence of a strong EPI in the HTSC cuprates. For example, the behavior of the electron relaxation, the peculiarities of the phonon spectra, the interaction of the Josephson current with phonons, and the electron mass renormalization. All these phenomena have been discussed in the recent Review Articles [3, 4]. Currently, additional evidence was provided which has thrown new light on the role played by the EPI in HTSC systems. These are the ARPES experiments conducted by the Stanford group, which have given an unambiguous proof of the electron mass renormalization due to the EPI. A Review Article of this group by T. Cuk et al. is also presented in this issue. We should also mention the contribution of L. Pintschovius who presented new interesting results on the electron-phonon coupling effects observed by means of inelastic neutron scattering.A comprehensive discussion of a major part of the electron-phonon coupling effects presented in the Review Articles [1, 3] has been based on the traditional approach of the Eliashberg type. Up to now, we consider this approach to be quite suitable for pursuing a number of goals, mainly for describing properties of the normal state. Nevertheless, we do not disclaim the importance of more detailed investigations of the EPI, which take into account the strong anisotropy, the interplay between electron-phonon and electron-electron interaction, and the non-adiabatic effects. Four Review Articles in this issue, by Schneider, by Rösch, Han, Gunnarsson and Crespi, by Kuli and Dolgov, and by Cappelluti and Pietronero are devoted to different aspects of these problems.To conclude, we would like to emphasize that the main problem related to the mechanism of superconductivity in the HTSC cuprates is the interplay between the strong EPI and the electron exchange and correlation. Unfortunately, previous work did not crack this problem and much effort should be made in the future. We hope that the publication of this issue will aid to attract the attention of many researchers to the investigation of unsolved problems of the EPI in HTSC systems.

  3. Preface: phys. stat. sol. (a) 201/5

    NASA Astrophysics Data System (ADS)

    Avelino Pasa, André

    2004-04-01

    This issue contains scientific contributions to the 4th German/Brazilian Workshop on Applied Surface Science. The workshop was held in Germany at the beautiful Castle Ringberg conference site of the Max Planck Society, located 60 km from Munich, from 21-26 September 2003. The meeting was attended by about 50 participants, with 21 invited talks and 18 contributed presentations (8 oral and 10 posters) on relevant topics of surface science.As in previous meetings (1995 in Portobello, RJ, Brazil, 1998 in Döllnsee, Berlin, Germany, and 2001 in Itapema, SC, Brazil), a significant number of important questions in surface science were covered from both the theoretical and the experimental point of view. In the field of materials science, emphasis was given to the description of the structural, physical and chemical properties of nanostructures and films of inorganic (metals, alloys and oxides) and organic (polymers and biological molecules) materials.A substantial part of the success of the meeting can be attributed to the relaxed atmosphere at the castle, near the lake Tegernsee, where excellent scientific presentations were mixed with intense discussions among both senior and younger researchers. The event also led to the development of new and ongoing collaborations between partners from Brazil and Germany.The organizers of the Workshop, Israel J. R. Baumvol (Porto Alegre, Brazil), Hajo Freund (Berlin, Germany), Wolfgang H. P. Losch (Natal, Brazil), Horst Niehus (Berlin, Germany), André A. Pasa (Florianópolis, Brazil) and Eberhard Umbach (Würzburg, Germany), are greatly indebted to the following organizations for financial support: Deutsche Forschungsgemeinschaft (DFG), Fritz-Haber-Institut Berlin (FHI), Fundação Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Universidade Federal de Santa Catarina (UFSC) and the specially created intergovernmental agreement between CAPES and DFG to promote such meetings.

  4. Preface: phys. stat. sol. (b) 241/9

    NASA Astrophysics Data System (ADS)

    Morawetz, Klaus

    2004-07-01

    Modelling and Simulation in Molecular Systems, Mesoscopic Structures, and Material Science was the title of a workshop held at the University of Technology in Chemnitz from 21 to 23 April 2004. This workshop coincided with the 50th birthday of Michael Schreiber. Therefore, the idea to publish a special issue is supported by two good reasons. First, a topical collection is appropriate for giving an overview about a field and to initiate further studies. This is one intention of the present issue. Second, the birthday is a suitable occasion for reflecting on the status of the different fields where Michael Schreiber has been active himself. Motivated by the characteristic name of the workshop (MS4), which expresses the broad range of his activities, the contributions are grouped into three main chapters: Disorder and Interaction, Phase Transitions and Criticality, and Transport Properties.The first part starts with the currently intensively discussed topic of composite Fermions in the paper by B. Kramer et al. This method of rewriting correlations as new quasiparticles has amongst other things the merit of explaining such exciting phenomena as the fractional quantum Hall effect. The methodological questions of Ward identities, causality, and conservation laws are the focus of the systematic investiga-tion in the second article by V. Janis et al. which concentrates on the problem of disorder and configura-tional averaging. The interplay between disorder and correlation is treated in the third contribution by C. Schuster et al., where different theoretical methods are tested on the problem of Friedel oscillations within the one-dimensional Heisenberg and Hubbard model. In the next contribution, M. Berciu et al. focus on localization as one consequence of disorder. The localized and extended electronic states are treated, together with the magnetic degrees of freedom, like spin waves. One of the astonishing consequence of localiza-tion is the observation of resonant Rayleigh backscattering. This is investigated by random matrix theory in the next article by E. Runge et al. and extended to exciton transitions in semiconductor nanostructures. In order to characterize localization, A. Eilmes et al. consider the two-dimensional Anderson model in the following article with special focus on the critical exponents for the localization length. The chapter on disorder ends with a contribution by A. Aldea et al. where the disorder effects are investigated in twodimensional systems with perpendicular magnetic fields such that the interplay between Landau levels and localized states can be considered.The second chapter in the collection is devoted to critical phenomena and phase transitions. It starts with an overview of the most prominent example of critical phenomena, high-Tc superconductivity. A. Sherman presents a review on magnetic and spectral properties of cuprate perovskites within t - J models. The long-range hopping problem and the extraction of critical exponents are the topic of the contribution by E. Cuevas, who calculated the level spacing distribution as well as the correlation dimen-sion in the strong coupling limit. The critical points and the thermodynamics of quenched spatial disordered systems are then treated by T. Vojta et al. Here it is shown that different parts of a system might undergo phase transitions controlled by different parameter values. Different microstructures are important when phenomena like the growth of crystals are considered. Consequently the latter problem is treated in the next contribution by H. Emmrich et al., who develop an analytical solution and compare it to simulations in order to provide insights into the universality of diffusion-limited crystal growth. That the applications of critical phenomena are quite versatile is demonstrated in a short paper by J. Stäring et al. who show how statistical methods can be employed to optimize networks of wireless communication. This chapter on critical phenomena ends with a methodological investigation by U. Grimm. This concerns the often applied random matrix theory, and a method to calculate the level spacing distribution by using coupled differential equations.The third chapter is devoted to transport. It starts with an article about conductance fluctuations by M. Ortuno et al. These quantum fluctuations are considered in localized systems which is directly related to the topics in the first chapter. M. Schröder et al. present in the next article a method to propagate wave functions by approximating them by multi-dimensional wave packets. In contrast to variational methods, this method is based on stochastic calculus. In the case where only a few electrons are transferred, as in the reaction of donor-acceptor complexes and molecular wires, a unified description is presented in the contribution by V. May et al. The transfer rate and the stationary current are calculated and their depend-ence on the length of the molecular system is shown. The method of Green's functions based on local orbitals is used in the next article by M. Albrecht et al. to calculate molecular charge transport. This results into a Landauer theory for the calculation of the transmission coefficient. The special role of elec-tron-electron interaction in the transport properties of disordered wires is considered by H. Mori et al. Here the interplay of interaction and disorder is investigated and the different roles of interaction for the localization phenomena are discussed. We close this chapter on transport by an investigation of electronic transport through nanoparticle arrays. The self-assembled nanoparticle structures are considered within the contri-bution by K. Nicolic whose structures represent very promising nanoelectronic devices.The broad-range approaches and applications selected in these three chapters demonstrate the exciting interplay between structure, disorder, and correlations and suggest the kind of future developments which are to be expected within this field. Finally, in the name of all authors and workshop participants: Happy birthday to Michael Schreiber and all best wishes for exciting future scientific activities!

  5. Preface: phys. stat. sol (a) 203/9

    NASA Astrophysics Data System (ADS)

    Duewski, P.; Bristowe, P.; Maurice, J.-L.; Komninou, P.

    2006-07-01

    This special issue contains a selection of papers that were presented at a symposium on Interfacial Processes and Properties of Advanced Materials (IPAM05) held at the E-MRS Fall Meeting, Warsaw, Poland on 5-7 September 2005. The symposium was conceived and inspired by the success of its predecessor (IPAM04) held at the University of Caen, France in June 2004.The symposium attracted over sixty contributions and was organized around five areas: Interfaces and dislocations in compound semiconductors, Gate oxide interfaces, Interfaces and defects in electroceramics, Metal-metal interfaces and interfacial modeling, and Interfaces in nano-structured and amorphous thin-film systems. The focus was on the influence of buried interfaces on the functionality of various electronic and opto-electronic devices such as lasers, ferroelectric memories, CMOS and magnetic disks. Therefore the materials addressed at the symposium included compound semiconductors (e.g. GaN, CdTe, ZnO), perovskites (e.g. SrTiO3), dielectrics (e.g. HfO2, SiO2, Al2O3), and metals (e.g. Fe/V superlattices). The aim of the symposium was to bring together leading interface experts, both experimental and theoretical, to explore the connection between interfacial properties (atomic and electronic structure, segregation, diffusion, kinetics) and materials performance in a device application. Papers were presented that described the use of a variety of sophisticated experimental techniques to explore the interfacial properties including HRTEM, X-ray high-resolution diffraction, Raman spectroscopy, STM, AFM, PL spectroscopy, SIMS and electrical and magnetic measurements. The theoretical work included applications of density functional theory, atomistic simulations, dislocation theory and finite element modeling. The program stimulated many exciting and productive discussions between experimentalists and theorists. The ultimate objective was to improve our knowledge of the role of interfaces on the properties of current and emerging device materials. It is hoped that these proceedings represent a step towards that goal and will encourage further conferences in this area in the future.The organisers gratefully acknowledge funding from the US Office of Naval Research Global (ONRG) Conference Support Program. They also would like to thank E-MRS for their administrative support and the Institute of Physics, Polish Academy of Sciences and the Warsaw University of Technology for hosting the symposium.

  6. Preface: phys. stat. sol. (b) 242/9

    NASA Astrophysics Data System (ADS)

    Sánchez, Maria

    2005-07-01

    The XVII Latin American Symposium on Solid State Physics took place in the conference rooms of the Convent San Francisco de Asis, in the heart of the Old Havana. The sixteen previous editions were organized in eight different countries; the last two were in Colombia (Cartagena, 1999) and Venezuela (Merida, 2002). After eighteen years the meeting came back to Havana in 2004.The program topics included: Surfaces and interfaces analysis; Spintronics; Magnetism; Materials and energy; Ab-initio methods, simulations and modeling in solids; Nanophysics, nanomaterials and nanotechnology; New materials, properties and applications; Preparation of materials, thin films and characterization; High temperature superconductivity; Techniques of structural analysis in solids. The program included 6 plenary talks, 13 invited talks, 58 oral presentations (in eight sessions) and 200 poster contributions (in four poster sessions).The meeting attracted more than 200 participants from 14 countries. The physica status solidi Young Researcher Award sponsored by Wiley-VCH was conferred at the meeting. This prize was divided between two participants: Clara Calderón (Study of electrical transport properties of ZnO thin films used as front contact of solar cells) from Colombia and Aim?? Pelaiz Barranco (AC behavior in lanthanum modified PZT ferroelectric ceramics) from Cuba. Special Mentions went to Val??rie Halté (Femtosec-ond dynamics of transmission of gold arrays of sub-wavelength holes) from France, Erick Larramendi Cancio (Cd desorption induced by Zn exposure during atomic layer epitaxy of CdxZn1-xTe) and Julio Cesar Rimada Herrera (Quantum and conversion efficiency calculation of AlGaAs/GaAs multiple quantum well solar cells) from Cuba.Nanostructures and in general low dimensional physics related to different systems was a very hot topic during the meeting. Some talks and presentations were devoted to optoelectronic materials and devices. Characterization of solids by different structural and optical techniques together with modeling and simulations were also important subjects of the symposium.The XVIII Symposium will be held in Mexico in 2006.The editors wish to thank all the participants who contributed to the success of the meeting and hope that it helped to develop close links between researchers and institutions of Latin America.

  7. Preface: phys. stat. sol. (c) 1/6

    NASA Astrophysics Data System (ADS)

    Kavokin, Alexey

    2004-04-01

    This volume contains some of the papers presented at the Third International Conference on Physics of Light-Matter Coupling in Nanostructures (PLMCN3) which took place in Acireale, Sicily, from 1 to 4 October 2003. This meeting was fourth in the series started by PLMCN (St. Nectaire, 2000) and continued by PLMCN1 (Rome, 2001) and PLMCN2 (Rithymnon, 2002). All four conferences had the same format (about 70 participants), similar subject scope (interface between fundamental physics of light-matter coupling phenomena and applied research on new semiconductor materials and low-dimensional structures), and the proceedings of all of them have been published in physica status solidi.During these four years, a huge progress has been achieved in the understanding of exciton-polariton effects in microcavities. From the discovery of stimulated scattering of polaritons in 1999 to the first experimental reports of polariton Bose condensation and lasing, attention to this rapidly developing research area has been increased drastically. It is clear now that realization of a new generation of opto-electronic devices, referred to as polariton devices, is a realistic task for the coming decade. To achieve this target, much work has to be done both in fundamental research on dynamics of exciton-polaritons in microcavities and experimental realization of high-quality microcavities presumably based on wide-band gap semiconductors like GaN, ZnO, ZnSe, suitable for the observation of strong exciton-light coupling at room temperature. Forty nine research teams from twelve European countries have created a Polariton Consortium aimed at integration of the European research effort towards fabrication of polariton devices. PLMCN3 was not only an international conference devoted, in particular, to the research on polariton devices, but also the first scientific meeting of this community.The PLMCN meetings since the very first one have been sponsored by the US Army European Research Office (ERO). This time, with the initiative of Jim Harvey from ERO, a special session has been organized on the devices of 21st century, where a number of intriguing ideas have been proposed on new light sources, polariton lasers, and quantum memory elements based on microcavities. A special prize for the most crazy but realizable idea has been won by Misha Portnoi (Exeter) for the concept of a white diode based on a microcavity.Each PLMCN meeting brings participants from new countries. This time, the traditionally strong participation from Japan, Russia, the European Union and the USA has been enforced by a representative delegation from Israel and two speakers from Mexico. We are looking forward for new-comers from other countries not yet involved in the PLMCN community, to join us for the next meeting to be held in St. Petersburg on 29 June-3 July 2004. Sergey Ivanov from the A. F. Ioffe Institute chairs the local Organizing Committee of this future conference. We are going to keep a unique informal and creative atmosphere being characteristic of the PLMCN meetings. We invite all those who wish to know more about light-matter coupling in solids or to present any new interesting results in this area and at the same time to enjoy the beautiful city of St. Petersburg, to contact Sergey Ivanov (ivan@beam.ioffe.rssi.ru) or myself (kavokin@lasmea.univ-bpclermont.fr). We are looking forward to welcoming you in St. Petersburg!

  8. 75 FR 23729 - Orders Finding that the (1) Phys,1

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-04

    ... of liquidity is implicitly understood to be a relevant, if not fundamental factor, where material....3(c) promulgated thereunder. \\10\\ 74 FR 53724 (October 20, 2009). DATES: Effective Date: April 28... determined closing, settlement or other daily price of another contract. \\13\\ 74 FR 12178 (Mar. 23,...

  9. Preface: phys. stat. sol. (c) 1/7

    NASA Astrophysics Data System (ADS)

    Cheikhrouhou, Abdelwaheb

    2004-05-01

    The Third International Conference on Magnetic and Superconducting Materials (MSM03) belongs to a series of conferences, held biannually, aiming at providing a forum to the scientists in the magnetic and superconducting materials areas over the world.The first conference of the series (MSM99) was held in Iran with the proceedings published by World Scientific in 2000, and the second conference (MSM01) was held in Jordan with the proceedings published in Physica B 321 (2002).MSM03 was organized by the Materials Physics Laboratory, Sfax University (Laboratoire de Physique des Matériaux de la Faculté des Sciences de Sfax), with many domestic and international supporting institutions. It was held in Monastir (Tunisia), 1-4 September 2003, with over 150 participants and keynote lecturers attending from the following countries: Algeria, Austria, China, Czech Republic, Egypt, France, Germany, Hungary, Iran, Italy, Japan, Jordan, Morocco, Netherlands, Pakistan, Poland, Russia, Spain, Sudan, Sultanate of Oman, Taiwan, Tunisia, United Kingdom and United States of America.Altogether, about 170 papers on a variety of subjects relevant to the topic of the conference were presented, out of which 42 were keynote lectures. The submissions were peer-reviewed, and ultimately 115 articles were selected for publication in this journal. However, it must be noted that 13 of 39 keynote speakers did not submit their manuscripts for publication. Invited and other speakers were distinguished members of the international scientific community who are interested in pure sciences and materials research, and involved in the fabrication, characterization and investigation of the physical properties of magnetic and superconducting materials. High-caliber scientists attended the conference contributing to its success and the event resulted in new international relationships in research and cooperation. The Chairman of the Organizing Committee was Professor Abdelwaheb Cheikhrouhou, Materials Physics Laboratory, Sciences Faculty of Sfax (Tunisia) and the Co-Chairmen were Professor Sami Mahmood, Dean of Sciences at Yarmouk University (Jordan) and Professor Mohamed Akhavan from the Sharif University of Technology (Iran). The four-day conference consisted of several oral and poster sessions, followed by social programs in the evenings. The success of the event could be measured during the closing session on the last day, when several delegates emphasized the high-quality science that had been evident at the conference. A post conference three-day tour to the south of Tunisia (Matmata, Douz City: the gate of desert and the mountains oasis: Tamerza, Mides and Chebika) was also arranged. The conference was generously sponsored by: - The Tunisian Ministry of High Education, Scientific Research and Technology - The Tunisian Secretary of State for Scientific Research and Technology - The Tunisian National Office of Tourism - The Abdus Salam International Centre for Theoretical Physics (ICTP) - French Institute for Cooperation in Tunisia - Tunisian-Italian Scientific Partnership - British Gas - Tunisian Society for Electricity and Gas - Imex Olive Oil -Confiserie TRIKI Le Moulin The next MSM conference in 2005 will be held in Morocco.

  10. Preface: phys. stat. sol. (b) 242/13

    NASA Astrophysics Data System (ADS)

    Esser, Norbert; Zahn, Dietrich R. T.

    2005-11-01

    Wolfgang Richter celebrated his 65th birthday on 2 January 2005. On such an occasion, usually marking retirement, achievements and breakthroughs in research are reviewed. But Wolfgang Richter is not retiring: he has accepted an offer of a professorship at the University Rome II Tor Vergata. As he explained to us with his famous smile, he plans to concentrate his future efforts even more on his true love in science - the optical diagnostics of interfaces.Wolfgang Richter has been working in the field of optical spectroscopy of solids since his PhD studies at the University of Cologne. Having finished his PhD in 1969 in the field of infrared spectroscopy he decided to reduce the probed volume by increasing the energy of probing photons: Raman spectroscopy! During his postdoctoral and Habilitation periods (1970-1979) at Pennsylvania State University, Max-Planck-Institut für Festkörperforschung, and RWTH Aachen, he pursued his interest in resonance Raman spectroscopy on semiconductors.In 1979 he received his first appointment as full professor at the University of Ulm. He returned to RWTH Aachen in 1981 and discovered his true destiny: semiconductor interfaces. At that time in the Department of Semiconductor Technology, metal-organic vapour phase epitaxy (MOVPE) was under development as a new technique for growing semiconductor layers. The underlying processes in MOVPE were known to be complex and very difficult to analyse with available experimental techniques, due to the unfriendly, reactive gas phase environment. Optical diagnostics turned out to be the key to a better understanding of MOVPE processes. Wolfgang Richter moved from RWTH Aachen to TU Berlin at the end of 1988 and began building a strong research group concentrating on interface analysis from two complementary sides: on the one hand, tracking MOVPE growth processes online by in situ optics and, on the other hand, advancing the fundamental understanding of optical spectra of interfaces by relating the optical response to atomic structures. Combining both aspects has finally led to considerable progress in surface and interface optics, as well as in vapour phase epitaxy and, moreover, the in situ optical tools developed are nowadays available as standard options in commercial MOVPE machines.The advances largely concerned the development of reflectance anisotropy spectroscopy and spectroscopic ellipsometry as in situ optical tools. However, considerable progress in Raman spectroscopy was also made: analysis of surfaces, ultrathin layers down to a single monolayer or even sub-monolayer coverages, and sub-wavelength spatial resolution were demonstrated in recent years. Current challenges concern, in particular, organic materials, molecule-solid interfaces and bio-interfaces, which will help in the development of many new applications and devices. Interfaces will play a crucial role in many of these developments and optical spectroscopy offers promising capabilities for analysing such interfaces. Wolfgang Richter and his group at University of Rome II Tor Vergata are sure to be active in this emerging field for a long time to come.Based on a symposium on Optical Spectroscopy of Interfaces at the Spring Meeting of the German Physical Society in Berlin 2005, we have asked former and present colleagues of Wolfgang Richter to contribute to this special issue of physica status solidi (b) on Advanced Optical Diagnostics of Surfaces, Nanostructures and Ultrathin Films. We think that the collection of 26 papers gives an excellent overview on recent achievements and future developments in the field of linear optics. In addition to a number of Original Papers on experimental work and some Review Articles, the issue includes examples of the current approaches of computational theory to solid state optics and interface optics. We hope that this issue will stimulate the expansion of the growing field of optical analysis of interfaces, nanostructures and ultrathin layers into new areas of basic and applied science. After the success in characterising inorganic materials, it is

  11. Probing Quark Gluon Liquid Using Transverse Momentum Fluctuations

    NASA Astrophysics Data System (ADS)

    Abdel-Aziz, Mohamed; Gavin, Sean

    2006-08-01

    The onset of equilibration of partons in nuclear collisions may lead to related trends in the centrality dependence of , p fluctuations, and net charge fluctuations [S. Gavin, Phys. Rev. Lett. 92, 162301 (2004); J. Phys. G 30, S1385 (2004)]. We extend the transport description of ref. [S. Gavin, Phys. Rev. Lett. 92, 162301 (2004); J. Phys. G 30, S1385 (2004)] to include radial flow.

  12. Comment on ``Photoelectron spectroscopic studies of polyatomic molecules: Theory for spin polarization''

    NASA Astrophysics Data System (ADS)

    Cherepkov, N. A.; Kuznetsov, V. V.

    1991-08-01

    The relation between the theory developed recently by Chandra [Phys. Rev. A 40, 752 (1989)] and our theory, derived previously [N. A. Cherepkov, J. Phys. B 16, 1543 (1983); 14, 2165 (1981); Adv. At. Mol. Phys. 19, 395 (1983); N. A. Cherepkov and V. V. Kuznetsov, Z. Phys. D 7, 271 (1987)], is established.

  13. Evolution of the Antisense Overlap between Genes for Thyroid Hormone Receptor and Rev-erbα and Characterization of an Exonic G-Rich Element That Regulates Splicing of TRα2 mRNA

    PubMed Central

    Munroe, Stephen H.; Morales, Christopher H.; Duyck, Tessa H.; Waters, Paul D.

    2015-01-01

    The α-thyroid hormone receptor gene (TRα) codes for two functionally distinct proteins: TRα1, the α-thyroid hormone receptor; and TRα2, a non-hormone-binding variant. The final exon of TRα2 mRNA overlaps the 3’ end of Rev-erbα mRNA, which encodes another nuclear receptor on the opposite strand of DNA. To understand the evolution of this antisense overlap, we sequenced these genes and mRNAs in the platypus Orthorhynchus anatinus. Despite its strong homology with other mammals, the platypus TRα/Rev-erbα locus lacks elements essential for expression of TRα2. Comparative analysis suggests that alternative splicing of TRα2 mRNA expression evolved in a stepwise fashion before the divergence of eutherian and marsupial mammals. A short G-rich element (G30) located downstream of the alternative 3’splice site of TRα2 mRNA and antisense to the 3’UTR of Rev-erbα plays an important role in regulating TRα2 splicing. G30 is tightly conserved in eutherian mammals, but is absent in marsupials and monotremes. Systematic deletions and substitutions within G30 have dramatically different effects on TRα2 splicing, leading to either its inhibition or its enhancement. Mutations that disrupt one or more clusters of G residues enhance splicing two- to three-fold. These results suggest the G30 sequence can adopt a highly structured conformation, possibly a G-quadruplex, and that it is part of a complex splicing regulatory element which exerts both positive and negative effects on TRα2 expression. Since mutations that strongly enhance splicing in vivo have no effect on splicing in vitro, it is likely that the regulatory role of G30 is mediated through linkage of transcription and splicing. PMID:26368571

  14. Evolution of the Antisense Overlap between Genes for Thyroid Hormone Receptor and Rev-erbα and Characterization of an Exonic G-Rich Element That Regulates Splicing of TRα2 mRNA.

    PubMed

    Munroe, Stephen H; Morales, Christopher H; Duyck, Tessa H; Waters, Paul D

    2015-01-01

    The α-thyroid hormone receptor gene (TRα) codes for two functionally distinct proteins: TRα1, the α-thyroid hormone receptor; and TRα2, a non-hormone-binding variant. The final exon of TRα2 mRNA overlaps the 3' end of Rev-erbα mRNA, which encodes another nuclear receptor on the opposite strand of DNA. To understand the evolution of this antisense overlap, we sequenced these genes and mRNAs in the platypus Orthorhynchus anatinus. Despite its strong homology with other mammals, the platypus TRα/Rev-erbα locus lacks elements essential for expression of TRα2. Comparative analysis suggests that alternative splicing of TRα2 mRNA expression evolved in a stepwise fashion before the divergence of eutherian and marsupial mammals. A short G-rich element (G30) located downstream of the alternative 3'splice site of TRα2 mRNA and antisense to the 3'UTR of Rev-erbα plays an important role in regulating TRα2 splicing. G30 is tightly conserved in eutherian mammals, but is absent in marsupials and monotremes. Systematic deletions and substitutions within G30 have dramatically different effects on TRα2 splicing, leading to either its inhibition or its enhancement. Mutations that disrupt one or more clusters of G residues enhance splicing two- to three-fold. These results suggest the G30 sequence can adopt a highly structured conformation, possibly a G-quadruplex, and that it is part of a complex splicing regulatory element which exerts both positive and negative effects on TRα2 expression. Since mutations that strongly enhance splicing in vivo have no effect on splicing in vitro, it is likely that the regulatory role of G30 is mediated through linkage of transcription and splicing. PMID:26368571

  15. Mutational Analysis of the C8-Guanine Adduct of the Environmental Carcinogen 3-Nitrobenzanthrone in Human Cells: Critical Roles of DNA Polymerases η and κ and Rev1 in Error-Prone Translesion Synthesis

    PubMed Central

    2015-01-01

    3-Nitrobenzanthrone (3-NBA), a potent mutagen and suspected human carcinogen, is a common environmental pollutant. The genotoxicity of 3-NBA has been associated with its ability to form DNA adducts, including N-(2′-deoxyguanosin-8-yl)-3-aminobenzanthrone (C8-dG-ABA). To investigate the molecular mechanism of C8-dG-ABA mutagenesis in human cells, we have replicated a plasmid containing a single C8-dG-ABA in human embryonic kidney 293T (HEK293T) cells, which yielded 14% mutant progeny. The major types of mutations induced by C8-dG-ABA were G → T > G → A > G → C. siRNA knockdown of the translesion synthesis (TLS) DNA polymerases (pols) in HEK293T cells indicated that pol η, pol κ, pol ι, pol ζ, and Rev1 each have a role in replication across this adduct. The extent of TLS was reduced with each pol knockdown, but the largest decrease (of ∼55% reduction) in the level of TLS occurred in cells with knockdown of pol ζ. Pol η and pol κ were considered the major contributors of the mutagenic TLS, because the mutation frequency (MF) decreased by 70%, when these pols were simultaneously knocked down. Rev1 also is important for mutagenesis, as reflected by the 60% reduction in MF upon Rev1 knockdown, but it probably plays a noncatalytic role by physically interacting with the other two Y-family pols. In contrast, pol ζ appeared to be involved in the error-free bypass of the lesion, because MF increased by 60% in pol ζ knockdown cells. These results provide important mechanistic insight into the bypass of the C8-dG-ABA adduct. PMID:25080294

  16. Reclassification of Xanthomonas campestris pv. citri (ex Hasse 1915) Dye 1978 forms A, B/C/D, and E as X. smithii subsp. citri (ex Hasse) sp. nov. nom. rev. comb. nov., X. fuscans subsp. aurantifolii (ex Gabriel 1989) sp. nov. nom. rev. comb. nov., and X. alfalfae subsp. citrumelo (ex Riker and Jones) Gabriel et al., 1989 sp. nov. nom. rev. comb. nov.; X. campestris pv malvacearum (ex smith 1901) Dye 1978 as X. smithii subsp. smithii nov. comb. nov. nom. nov.; X. campestris pv. alfalfae (ex Riker and Jones, 1935) dye 1978 as X. alfalfae subsp. alfalfae (ex Riker et al., 1935) sp. nov. nom. rev.; and "var. fuscans" of X. campestris pv. phaseoli (ex Smith, 1987) Dye 1978 as X. fuscans subsp. fuscans sp. nov.

    PubMed

    Schaad, Norman W; Postnikova, Elena; Lacy, George H; Sechler, Aaron; Agarkova, Irina; Stromberg, Paul E; Stromberg, Verlyn K; Vidaver, Anne K

    2005-08-01

    , respectively, Xanthomonas smithii subsp. citri (ex Hasse, 1915) sp. nov. nom. rev. comb. nov., Xanthomonas fuscans subsp. aurantifolii (ex Gabriel et al., 1989) sp. nov. nom. rev. comb. nov., and Xanthomonas alfalfae subsp. citrumelo (ex Riker and Jones) Gabriel et al., 1989 nov. rev. comb. nov. Furthermore, based on the analysis of 40 strains of 19 other xanthomonads, we propose to reclassify X. campestris pv. malvacearum (ex Smith, 1901) Dye 1978 as X. smithii subsp. smithii sp. nov. comb. nov. nom. nov.; X. campestris pv. alfalfae (ex Riker and Jones) Dye 1978 as X. alfalfae subsp. alfalfae (ex Riker et al., 1935) sp. nov. nov. rev.; and "var. fuscans" (ex Burkholder 1930) of X. campestris pv. phaseoli (ex Smith, 1897) as X. fuscans subsp. fuscans sp. nov.

  17. Qualification of the Savannah River National Laboratories Coulometer, Model SRNL-Rev. 2 (Serial # SRNL-003 Coulometer) for use in Process 3401a, Plutonium Assay by Controlled Coulometer

    SciTech Connect

    Tandon, Lav; Colletti, Lisa M.; Drake, Lawrence R.; Lujan, Elmer J. W.; Garduno, Katherine

    2012-08-22

    This report discusses the process used to prove in the SRNL-Rev.2 coulometer for isotopic data analysis used in the special plutonium material project. In May of 2012, the PAR 173 coulometer system that had been the workhorse of the Plutonium Assay team since the early 1970s became inoperable. A new coulometer system had been purchased from Savannah River National Laboratory (SRNL) and installed in August of 2011. Due to funding issues the new system was not qualified at that time. Following the failure of the PAR 173, it became necessary to qualify the new system for use in Process 3401a, Plutonium Assay by Controlled Coulometry. A qualification plan similar to what is described in PQR -141a was followed. Experiments were performed to establish a statistical summary of the performance of the new system by monitoring the repetitive analysis of quality control sample, PEOL, and the assay of plutonium metals obtained from the Plutonium Exchange Program. The data for the experiments was acquired using work instructions ANC125 and ANC195. Figure 1 shows approximately 2 years of data for the PEOL material obtained using the PAR 173. The required acceptance criteria for the sample are that it returns the correct value for the quality control material of 88.00% within 2 sigma (95% Confidence Interval). It also must meet daily precision standards that are set from the historical data analysis of decades of data. The 2 sigma value that is currently used is 0.146 % as evaluated by the Statistical Science Group, CCS-6. The average value of the PEOL quality control material run in 10 separate days on the SRNL-03 coulometer is 87.98% with a relative standard deviation of 0.04 at the 95% Confidence interval. The date of data acquisition is between 5/23/2012 to 8/1/2012. The control samples are run every day experiments using the coulometer are carried out. It is also used to prove an instrument is in statistical control before any experiments are undertaken. The total number of

  18. Tevatron electron lenses: Design and operation

    NASA Astrophysics Data System (ADS)

    Shiltsev, Vladimir; Bishofberger, Kip; Kamerdzhiev, Vsevolod; Kozub, Sergei; Kufer, Matthew; Kuznetsov, Gennady; Martinez, Alexander; Olson, Marvin; Pfeffer, Howard; Saewert, Greg; Scarpine, Vic; Seryi, Andrey; Solyak, Nikolai; Sytnik, Veniamin; Tiunov, Mikhail; Tkachenko, Leonid; Wildman, David; Wolff, Daniel; Zhang, Xiao-Long

    2008-10-01

    The beam-beam effects have been the dominating sources of beam loss and lifetime limitations in the Tevatron proton-antiproton collider [V. Shiltsev , Phys. Rev. ST Accel. Beams 8, 101001 (2005)PRABFM1098-440210.1103/PhysRevSTAB.8.101001]. Electron lenses were originally proposed for compensation of electromagnetic long-range and head-on beam-beam interactions of proton and antiproton beams [V. Shiltsev , Phys. Rev. ST Accel. Beams 2, 071001 (1999).PRABFM1098-440210.1103/PhysRevSTAB.2.071001]. Results of successful employment of two electron lenses built and installed in the Tevatron are reported by Shiltsev et al. [Phys. Rev. Lett. 99, 244801 (2007)PRLTAO0031-900710.1103/PhysRevLett.99.244801; New J. Phys. 10, 043042 (2008)NJOPFM1367-263010.1088/1367-2630/10/4/043042] and by Zhang et al. [X.-L. Zhang , Phys. Rev. ST Accel. Beams 11, 051002 (2008)PRABFM1098-440210.1103/PhysRevSTAB.11.051002]. In this paper we present design features of the Tevatron electron lenses (TELs), discuss the generation of electron beams, describe different modes of operation, and outline the technical parameters of various subsystems.

  19. Guaranteed resonance enclosures and exclosures for atoms and molecules

    PubMed Central

    Bögli, Sabine; Brown, B. Malcolm; Marletta, Marco; Tretter, Christiane; Wagenhofer, Markus

    2014-01-01

    In this paper, we confirm, with absolute certainty, a conjecture on a certain oscillatory behaviour of higher auto-ionizing resonances of atoms and molecules beyond a threshold. These results not only definitely settle a more than 30 year old controversy in Rittby et al. (1981 Phys. Rev. A 24, 1636–1639 (doi:10.1103/PhysRevA.24.1636)) and Korsch et al. (1982 Phys. Rev. A 26, 1802–1803 (doi:10.1103/PhysRevA.26.1802)), but also provide new and reliable information on the threshold. Our interval-arithmetic-based method allows one, for the first time, to enclose and to exclude resonances with guaranteed certainty. The efficiency of our approach is demonstrated by the fact that we are able to show that the approximations in Rittby et al. (1981 Phys. Rev. A 24, 1636–1639 (doi:10.1103/PhysRevA.24.1636)) do lie near true resonances, whereas the approximations of higher resonances in Korsch et al. (1982 Phys. Rev. A 26, 1802–1803 (doi:10.1103/PhysRevA.26.1802)) do not, and further that there exist two new pairs of resonances as suggested in Abramov et al. (2001 J. Phys. A 34, 57–72 (doi:10.1088/0305-4470/34/1/304)). PMID:25383033

  20. Contiguous 2,2,4-triamino-5(2H)-oxazolone obstructs DNA synthesis by DNA polymerases α, β, η, ι, κ, REV1 and Klenow Fragment exo-, but not by DNA polymerase ζ.

    PubMed

    Suzuki, Masayo; Kino, Katsuhito; Kawada, Taishu; Oyoshi, Takanori; Morikawa, Masayuki; Kobayashi, Takanobu; Miyazawa, Hiroshi

    2016-03-01

    Guanine is the most easily oxidized of the four DNA bases, and contiguous guanines (GG) in a sequence are more readily oxidized than a single guanine in a sequence. Continued oxidation of GGs results in a contiguous oxidized guanine lesion. Two contiguous 2,5-diamino-4H-imidazol-4-ones, an oxidized form of guanine that hydrolyses to 2,2,4-triamino-5(2H)-oxazolone (Oz), are detected following the oxidation of GG. In this study, we analysed translesion synthesis (TLS) across two contiguous Oz molecules (OzOz) using Klenow Fragment exo(-) (KF exo(-)) and DNA polymerases (Pols) α, β, ζ, η, ι, κ and REV1. We found that KF exo(-) and Pols α, β, ι and REV1 inserted one nucleotide opposite the 3' Oz of OzOz and stalled at the subsequent extension, and that Pol κ incorporated no nucleotide. Pol η only inefficiently elongated the primer up to full-length across OzOz; the synthesis of most DNA strands stalled at the 3' or 5' Oz of OzOz. Surprisingly, however, Pol ζ efficiently extended the primer up to full-length across OzOz, unlike the other DNA polymerases, but catalysed error-prone nucleotide incorporation. We therefore believe that Pol ζ is required for efficient TLS of OzOz. These results show that OzOz obstructs DNA synthesis by DNA polymerases except Pol ζ.

  1. MMW radar enhanced vision systems: the Helicopter Autonomous Landing System (HALS) and Radar-Enhanced Vision System (REVS) are rotary and fixed wing enhanced flight vision systems that enable safe flight operations in degraded visual environments

    NASA Astrophysics Data System (ADS)

    Cross, Jack; Schneider, John; Cariani, Pete

    2013-05-01

    Sierra Nevada Corporation (SNC) has developed rotary and fixed wing millimeter wave radar enhanced vision systems. The Helicopter Autonomous Landing System (HALS) is a rotary-wing enhanced vision system that enables multi-ship landing, takeoff, and enroute flight in Degraded Visual Environments (DVE). HALS has been successfully flight tested in a variety of scenarios, from brown-out DVE landings, to enroute flight over mountainous terrain, to wire/cable detection during low-level flight. The Radar Enhanced Vision Systems (REVS) is a fixed-wing Enhanced Flight Vision System (EFVS) undergoing prototype development testing. Both systems are based on a fast-scanning, threedimensional 94 GHz radar that produces real-time terrain and obstacle imagery. The radar imagery is fused with synthetic imagery of the surrounding terrain to form a long-range, wide field-of-view display. A symbology overlay is added to provide aircraft state information and, for HALS, approach and landing command guidance cuing. The combination of see-through imagery and symbology provides the key information a pilot needs to perform safe flight operations in DVE conditions. This paper discusses the HALS and REVS systems and technology, presents imagery, and summarizes the recent flight test results.

  2. Translesion Synthesis of the N(2)-2'-Deoxyguanosine Adduct of the Dietary Mutagen IQ in Human Cells: Error-Free Replication by DNA Polymerase κ and Mutagenic Bypass by DNA Polymerases η, ζ, and Rev1.

    PubMed

    Bose, Arindam; Millsap, Amy D; DeLeon, Arnie; Rizzo, Carmelo J; Basu, Ashis K

    2016-09-19

    Translesion synthesis (TLS) of the N(2)-2'-deoxyguanosine (dG-N(2)-IQ) adduct of the carcinogen 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) was investigated in human embryonic kidney 293T cells by replicating plasmid constructs in which the adduct was individually placed at each guanine (G1, G2, or G3) of the NarI sequence (5'-CG1G2CG3CC-3'). TLS efficiency was 38%, 29%, and 25% for the dG-N(2)-IQ located at G1, G2, and G3, respectively, which suggests that dG-N(2)-IQ is bypassed more efficiently by one or more DNA polymerases at G1 than at either G2 or G3. TLS efficiency was decreased 8-35% in cells with knockdown of pol η, pol κ, pol ι, pol ζ, or Rev1. Up to 75% reduction in TLS occurred when pol η, pol ζ, and Rev1 were simultaneously knocked down, suggesting that these three polymerases play important roles in dG-N(2)-IQ bypass. Mutation frequencies (MFs) of dG-N(2)-IQ at G1, G2, and G3 were 23%, 17%, and 11%, respectively, exhibiting a completely reverse trend of the previously reported MF of the C8-dG adduct of IQ (dG-C8-IQ), which is most mutagenic at G3 ( ( 2015 ) Nucleic Acids Res. 43 , 8340 - 8351 ). The major type of mutation induced by dG-N(2)-IQ was targeted G → T, as was reported for dG-C8-IQ. In each site, knockdown of pol κ resulted in an increase in MF, whereas MF was reduced when pol η, pol ι, pol ζ, or Rev1 was knocked down. The reduction in MF was most pronounced when pol η, pol ζ, and Rev1 were simultaneously knocked down and especially when the adduct was located at G3, where MF was reduced by 90%. We conclude that pol κ predominantly performs error-free TLS of the dG-N(2)-IQ adduct, whereas pols η, pol ζ, and Rev1 cooperatively carry out the error-prone TLS. However, in vitro experiments using yeast pol ζ and κ showed that the former was inefficient in full-length primer extension on dG-N(2)-IQ templates, whereas the latter was efficient in both error-free and error-prone extensions. We believe that the observed differences

  3. Transcriptional repression by the orphan steroid receptor RVR/Rev-erb beta is dependent on the signature motif and helix 5 in the E region: functional evidence for a biological role of RVR in myogenesis.

    PubMed Central

    Burke, L; Downes, M; Carozzi, A; Giguère, V; Muscat, G E

    1996-01-01

    RVR/Rev-erb beta/BD73 is an orphan steroid receptor that has no known ligand in the "classical' sense. RVR binds as a monomer to an element which consists of an A/T-rich sequence upstream of the consensus hexameric half-site. However, RVR does not activate transcription and blocks transactivation of this element by ROR/RZR. The mechanism of RVR action remains obscure, hence we used the GAL4 hybrid system to identify and characterize an active transcriptional silencer in the ligand binding domain (LBD) of RVR. Rigorous deletion and mutational analysis demonstrated that this repressor domain is encoded by amino acids 416-449 of RVR. Furthermore, we demonstrated that efficient repression is dependent on the so-called LBD-specific signature motif, (F/W)AKxxxxFxxLxxxDQxxLL (which spans loop3-4 and helix 4) and helix 5 (H5; identified in the crystal structures of the steroid receptor LBDs). Although RVR is expressed in many adult tissues, including skeletal muscle, and during embryogenesis, its physiological function in differentiation and mammalian development remains unknown. Since other 'orphans', e.g. COUP-TF II and Rev-erbA alpha, have been demonstrated to regulate muscle and adipocyte differentiation, we investigated the expression and functional role of RVR during mouse myogenesis. In C2C12 myogenic cells, RVR mRNA was detected in proliferating myoblasts and was suppressed when the cells were induced to differentiate into post-mitotic, multinucleated myotubes by serum withdrawal. This decrease in RVR mRNA correlated with the appearance of muscle-specific markers (e.g. myogenin mRNA). RVR 'loss of function' studies by constitutive over-expression of a dominant negative RVR delta E resulted in increased levels of p21Cip1/Waf1 and myogenin mRNAs after serum withdrawal. Time course studies indicated that expression of RVR delta E mRNA results in the precocious induction and accumulation of myogenin and p21 mRNAs after serum withdrawal. In addition, we demonstrated

  4. Efficient progressive readout of a register of qubits

    NASA Astrophysics Data System (ADS)

    Tilloy, Antoine

    2016-05-01

    Recently, a series of papers by Combes et al. [J. Combes, H. M. Wiseman, and K. Jacobs, Phys. Rev. Lett. 100, 160503 (2008), 10.1103/PhysRevLett.100.160503; J. Combes, H. M. Wiseman, and A. J. Scott, Phys. Rev. A 81, 020301(R) (2010), 10.1103/PhysRevA.81.020301; J. Combes and H. M. Wiseman, Phys. Rev. X 1, 011012 (2011), 10.1103/PhysRevX.1.011012; J. Combes, A. Denney, and H. M. Wiseman, Phys. Rev. A 91, 022305 (2015), 10.1103/PhysRevA.91.022305] has shown that it is possible to greatly improve the measurement rate of a register of qubits for given detector resources by means of a clever feedback control scheme. However, this speedup came at an exponential cost in terms of complexity and memory use. In this paper, I propose a simple efficient algorithm—exponentially more frugal in memory and less complex to implement—which is asymptotically as fast. I use extensively the implicit classicality of the situation to provide a slightly more straightforward interpretation of the results. I compute the speedup rates exactly in the case of the proposed model and in the case of the open-loop scheme of Combes et al. and prove that they indeed provide the same asymptotic speedup.

  5. Comment on ``Relative locality and the soccer ball problem''

    NASA Astrophysics Data System (ADS)

    Hossenfelder, S.

    2013-07-01

    It is explained why the argument by Amelino-Camelia et al. [Phys. Rev. D 84, 087702 (2011)PRVDAQ1550-799810.1103/PhysRevD.84.087702] does not answer the question how to describe multiparticle states in models with a deformed Lorentz symmetry in momentum space.

  6. Construction of three-qubit genuine entanglement with bipartite positive partial transposes

    NASA Astrophysics Data System (ADS)

    Ha, Kil-Chan; Kye, Seung-Hyeok

    2016-03-01

    We construct triqubit genuinely entangled states which have positive partial transposes (PPTs) with respect to the bipartition of systems. These examples disprove a conjecture [Novo, Moroder, and Gühne, Phys. Rev A 88, 012305 (2013), 10.1103/PhysRevA.88.012305] which claims that PPT mixtures are necessary and sufficient for the biseparability of three qubits.

  7. Comment on ``Finite Size Corrections to the Radiation Reaction Force in Classical Electrodynamics''

    NASA Astrophysics Data System (ADS)

    Forgács, P.; Herpay, T.; Kovács, P.

    2012-07-01

    A Comment on the Letter by C. R. Galley, A. K. Leibovich, and I. Z. Rothstein, Phys. Rev. Lett. 105, 094802 (2010)PRLTAO0031-900710.1103/PhysRevLett.105.094802. The authors of the Letter offer a Reply.

  8. Comment on 'Full quantum reconstruction of vortex states'

    SciTech Connect

    Bizarro, Joao P. S.

    2010-01-15

    It is pointed out that the bona fide Wigner distribution recently introduced [Phys. Rev. A 78, 060101(R) (2008)] is in fact the rotational Wigner function earlier derived and thoroughly studied [Phys. Rev. A 49, 3255 (1994); 71, 069901(E) (2005)], so the latter remains indeed the natural phase-space representation for the rotation-angle and angular-momentum pair.

  9. Comment on ``Sodium Pyroxene NaTiSi2O6: Possible Haldane Spin-1 Chain System''

    NASA Astrophysics Data System (ADS)

    Streltsov, S. V.; Popova, O. A.; Khomskii, D. I.

    2006-06-01

    A Comment on the Letter by Zoran S. Popović, Zeljko V. Šlijivančanin, and Filip R. Vukajlović, Phys. Rev. Lett. 93, 036401 (2004).PRLTAO0031-900710.1103/PhysRevLett.93.036401. The authors of the Letter offer a Reply.

  10. Solving the liar detection problem using the four-qubit singlet state

    SciTech Connect

    Cabello, Adan

    2003-07-01

    A method for solving the Byzantine agreement problem [M. Fitzi, N. Gisin, and U. Maurer, Phys. Rev. Lett. 87, 217901 (2001)] and the liar detection problem [A. Cabello, Phys. Rev. Lett. 89, 100402 (2002)] is introduced. The main advantages of this protocol are that it is simpler and is based on a four-qubit singlet state already prepared in the laboratory.

  11. Reply to "comment on 'Monte Carlo simulations for a Lotka-type model with reactant surface diffusion and interactions' ".

    PubMed

    Kuzovkov, V N; Zvejnieks, G

    2002-03-01

    We reply to the Comment by Zhdanov [preceding paper, Phys. Rev. E 65, blacksquare, square, filled (2002)] on our recent paper [G. Zvejnieks and V. N. Kuzovkov, Phys. Rev. E 63, 051104 (2001)]. We demonstrate that our quite different viewpoints result, in fact, entirely from nonunique definitions of the master equation, which has nothing to do with neglecting important physical principles, as Zhdanov claims.

  12. Comment on ``Theoretical Description of Carrier Mediated Magnetism in Cobalt Doped ZnO''

    NASA Astrophysics Data System (ADS)

    Sanvito, Stefano; Pemmaraju, Chaitanya Das

    2009-04-01

    A Comment on the Letter by Aron Walsh, Juarez L. F. Da Silva, and Su-Huai Wei, Phys. Rev. Lett.PRLTAO0031-9007 100, 256401 (2008)10.1103/PhysRevLett.100.256401. The authors of the Letter offer a Reply.

  13. Comment on ``Subgraph centrality in complex networks''

    NASA Astrophysics Data System (ADS)

    Stevanović, Dragan

    2013-08-01

    We disprove a conjecture of Estrada and Rodríguez-Velázquez [Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.71.056103 71, 056103 (2005)] that if a graph has identical subgraph centrality for all nodes, then the closeness and betweenness centralities are also identical for all nodes.

  14. Reply to 'Comment on 'Quantum convolutional error-correcting codes''

    SciTech Connect

    Chau, H.F.

    2005-08-15

    In their Comment, de Almeida and Palazzo [Phys. Rev. A 72, 026301 (2005)] discovered an error in my earlier paper concerning the construction of quantum convolutional codes [Phys. Rev. A 58, 905 (1998)]. This error can be repaired by modifying the method of code construction.

  15. Comment on ``Nonlocal symmetry for QED'' and ``Relativistically covariant symmetry in QED''

    NASA Astrophysics Data System (ADS)

    Rivelles, Victor O.

    1995-11-01

    A Comment on the Letter by Martin Lavelle and David McMullan, Phys. Rev. Lett. 71, 3758 (1993). The authors of the Letter offer a Reply. A Comment on the Letter by Zhong Tang and David Finkelstein, Phys. Rev. Lett. 73, 3055 (1994). The authors of the Letter offer a Reply.

  16. Experimental observations of structural relaxation in granular matter

    NASA Astrophysics Data System (ADS)

    Massalska-Arodź, M.; Mayer, J.; Brańkowski, J.; Ostrowicz, A.; Lisiecki, E.

    1997-01-01

    The relaxational changes of the electrical capacitance of a system of grains poured abruptly into a vessel capacitor have been observed. Two power-law decays have been found. The faster relaxation at the beginning has been interpreted as being driven by independent-grain motion. The later slower process has been ascribed to the collective reorganization of the granular system. The observations seem to be an experimental illustration of the computer simulation predictions of Mehta and Barker [Rep. Prog. Phys. 57, 383 (1994); Phys. Rev. A 45, 3435 (1992); Phys. Rev. Lett. 67, 394 (1991); Nature 364, 486 (1993); Phys. Rev. E 47, 184 (1993)].

  17. Relativistically induced transparency acceleration of light ions by an ultrashort laser pulse interacting with a heavy-ion-plasma density gradient

    NASA Astrophysics Data System (ADS)

    Sahai, Aakash A.; Tsung, Frank S.; Tableman, Adam R.; Mori, Warren B.; Katsouleas, Thomas C.

    2013-10-01

    The relativistically induced transparency acceleration (RITA) scheme of proton and ion acceleration using laser-plasma interactions is introduced, modeled, and compared to the existing schemes. Protons are accelerated with femtosecond relativistic pulses to produce quasimonoenergetic bunches with controllable peak energy. The RITA scheme works by a relativistic laser inducing transparency [Akhiezer and Polovin, Zh. Eksp. Teor. Fiz 30, 915 (1956); Kaw and Dawson, Phys. FluidsPFLDAS0031-917110.1063/1.1692942 13, 472 (1970); Max and Perkins, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.27.1342 27, 1342 (1971)] to densities higher than the cold-electron critical density, while the background heavy ions are stationary. The rising laser pulse creates a traveling acceleration structure at the relativistic critical density by ponderomotively [Lindl and Kaw, Phys. FluidsPFLDAS0031-917110.1063/1.1693437 14, 371 (1971); Silva , Phys. Rev. E1063-651X10.1103/PhysRevE.59.2273 59, 2273 (1999)] driving a local electron density inflation, creating an electron snowplow and a co-propagating electrostatic potential. The snowplow advances with a velocity determined by the rate of the rise of the laser's intensity envelope and the heavy-ion-plasma density gradient scale length. The rising laser is incrementally rendered transparent to higher densities such that the relativistic-electron plasma frequency is resonant with the laser frequency. In the snowplow frame, trace density protons reflect off the electrostatic potential and get snowplowed, while the heavier background ions are relatively unperturbed. Quasimonoenergetic bunches of velocity equal to twice the snowplow velocity can be obtained and tuned by controlling the snowplow velocity using laser-plasma parameters. An analytical model for the proton energy as a function of laser intensity, rise time, and plasma density gradient is developed and compared to 1D and 2D PIC OSIRIS [Fonseca , Lect. Note Comput. Sci.9783

  18. The circadian clock regulates autophagy directly through the nuclear hormone receptor Nr1d1/Rev-erbα and indirectly via Cebpb/(C/ebpβ) in zebrafish

    PubMed Central

    Huang, Guodong; Zhang, Fanmiao; Ye, Qiang; Wang, Han

    2016-01-01

    ABSTRACT Autophagy is a highly conserved intracellular degradation system, and recently was shown to display circadian rhythms in mice. The mechanisms underlying circadian regulation of autophagy, however, are still unclear. Here, we observed that numbers of autophagosomes and autolysosomes exhibit daily rhythms in the zebrafish liver, and cebpb/(c/ebpβ) and various autophagy genes are rhythmically expressed in zebrafish larvae but significantly upregulated in per1b and TALEN-generated nr1d1/rev-erbα mutant fish, indicating that both Per1b and Nr1d1 play critical roles in autophagy rhythms. Luciferase reporter and ChIP assays show that the circadian clock directly regulates autophagy genes through Nr1d1, and also regulates transcription of cebpb through Per1b. We also found that fasting leads to altered expression of both circadian clock genes and autophagy genes in zebrafish adult peripheral organs. Further, transcriptome analysis reveals multiple functions of Nr1d1 in zebrafish. Taken together, these findings provide evidence for how the circadian clock regulates autophagy, imply that nutritional signaling affects both circadian regulation and autophagy activities in peripheral organs, and shed light on how circadian gene mutations act through autophagy to contribute to common metabolic diseases such as obesity. PMID:27171500

  19. Response to ``Comment on `Elastic incoherent neutron scattering operating by varying instrumental energy resolution: Principle, simulations, and experiments of the resolution elastic neutron scattering (RENS)''' [Rev. Sci. Instrum. 83, 107101 (2012)

    NASA Astrophysics Data System (ADS)

    Magazó, Salvatore; Migliardo, Federica; Benedetto, Antonio

    2012-10-01

    Recently [S. Magazù et al., Rev. Sci. Instrum. 82, 105115 (2011), 10.1063/1.3641870] we have proposed a new method for characterizing, by neutron scattering, the dynamical properties of complex material systems, such as, the ones of interest in the biophysical field. This approach called Resolution Elastic Neutron Scattering, in short RENS, is based on the detection of the elastically scattered neutron intensity as a function of the instrumental energy resolution. By experimental, theoretical, and numerical findings, we have pointed out that an inflection point occurs in the elastic intensity when the system relaxation time approaches the instrumental energy resolution time. This approach, differently from quasi-elastic neutron scattering (QENS), gives the chance to evaluate the system relaxation times without using pre-defined models that can be wrong and/or misleading. Here, we reply to a Comment on the above-mentioned main paper in which Wuttke proposes a different approach to evaluate the above-mentioned inflection point; on this regard, it should be noticed that the existence of the inflection point, which is the main topic of our work, is not questioned and that the approach proposed by Wuttke in the Comment, although valid for a class of dynamical processes, is not applicable when different and distinct processes occur simultaneously at different time scale.

  20. Quantum-Critical Dynamics of the Skyrmion Lattice.

    NASA Astrophysics Data System (ADS)

    Green, Andrew G.

    2002-03-01

    Slightly away from exact filling of the lowest Landau level, the quantum Hall ferromagnet contains a finite density of magnetic vortices or Skyrmions[1,2]. These Skyrmions are expected to form a square lattice[3], the low energy excitations of which (translation/phonon modes and rotation/breathing modes) lead to dramatically enhanced nuclear relaxation[4,5]. Upon changing the filling fraction, the rotational modes undergo a quantum phase transition where zero-point fluctuations destroy the orientational order of the Skyrmions[4,6]. I will discuss the effect of this quantum critical point upon nuclear spin relaxation[7]. [1]S. L. Sondhi et al., Phys. Rev. B47, 16419 (1993). [2]S. E. Barrett et al., Phys. Rev. Lett. 74, 5112 (1995), A. Schmeller et al., Phys. Rev. Lett. 75, 4290 (1995). [3]L. Brey et al, Phys. Rev. Lett. 75, 2562 (1995). [4]R. Côté et al., Phys. Rev. Lett. 78, 4825 (1997). [5]R. Tycko et al., Science 268, 1460 (1995). [6]Yu V. Nazarov and A. V. Khaetskii, Phys. Rev. Lett. 80, 576 (1998). [7]A. G. Green, Phys. Rev. B61, R16 299 (2000).

  1. Nonlinear phenomena in Bose-Einstein condensates

    NASA Astrophysics Data System (ADS)

    Carr, Lincoln D.

    2008-05-01

    We present a medley of results from the last three years on nonlinear phenomena in BECs [1]. These include exact dynamics of multi-component condensates in optical lattices [2], vortices and ring solitons [3], macroscopic quantum tunneling [4], nonlinear band theory [5], and a pulsed atomic soliton laser [6]. 1. Emergent Nonlinear Phenomena in Bose-Einstein Condensates: Theory and Experiment, ed. P. G. Kevrekidis, D. J. Frantzeskakis, and R. Carretero-Gonzalez (Springer-Verlag, 2008). 2. R. Mark Bradley, James E. Bernard, and L. D. Carr, e-print arXiv:0711.1896 (2007). 3. G. Herring, L. D. Carr, R. Carretero-Gonzalez, P. G. Kevrekidis, D. J. Frantzeskakis, Phys. Rev. A in press, e-print arXiv:0709.2193 (2007); L. D. Carr and C. W. Clark, Phys. Rev. A v. 74, p.043613 (2006); L. D. Carr and C. W. Clark, Phys. Rev. Lett. v. 97, p.010403 (2006). 4. L. D. Carr, M. J. Holland, and B. A. Malomed, J. Phys. B: At. Mol. Opt. Phys., v.38, p.3217 (2005) 5. B. T. Seaman, L. D. Carr, and M. J. Holland, Phys. Rev. A, v. 71, p.033622 (2005). 6. L. D. Carr and J. Brand, Phys. Rev. A, v.70, p.033607 (2004); L. D. Carr and J. Brand, Phys. Rev. Lett., v.92, p.040401 (2004).

  2. Ability of a low-dimensional model to predict geometry-dependent dynamics of large-scale coherent structures in turbulence.

    PubMed

    Bai, Kunlun; Ji, Dandan; Brown, Eric

    2016-02-01

    We test the ability of a general low-dimensional model for turbulence to predict geometry-dependent dynamics of large-scale coherent structures, such as convection rolls. The model consists of stochastic ordinary differential equations, which are derived as a function of boundary geometry from the Navier-Stokes equations [Brown and Ahlers, Phys. Fluids 20, 075101 (2008); Phys. Fluids 20, 105105 (2008)]. We test the model using Rayleigh-Bénard convection experiments in a cubic container. The model predicts a mode in which the alignment of a convection roll stochastically crosses a potential barrier to switch between diagonals. We observe this mode with a measured switching rate within 30% of the prediction. PMID:26986423

  3. Ability of a low-dimensional model to predict geometry-dependent dynamics of large-scale coherent structures in turbulence.

    PubMed

    Bai, Kunlun; Ji, Dandan; Brown, Eric

    2016-02-01

    We test the ability of a general low-dimensional model for turbulence to predict geometry-dependent dynamics of large-scale coherent structures, such as convection rolls. The model consists of stochastic ordinary differential equations, which are derived as a function of boundary geometry from the Navier-Stokes equations [Brown and Ahlers, Phys. Fluids 20, 075101 (2008); Phys. Fluids 20, 105105 (2008)]. We test the model using Rayleigh-Bénard convection experiments in a cubic container. The model predicts a mode in which the alignment of a convection roll stochastically crosses a potential barrier to switch between diagonals. We observe this mode with a measured switching rate within 30% of the prediction.

  4. Instructor Revs Up Ailing Motorcycle Program

    ERIC Educational Resources Information Center

    Stevenson, Roy

    2011-01-01

    Bob Monroig smiles every day on his way to work at Lake Washington Technical College (LWTC), high atop a hill overlooking the affluent Seattle suburb of Kirkland, Washington. He's created his own job within a job, where he's the Harley-Davidson University program coordinator and tenured faculty in the Motorcycle, Marine, & Power Equipment Service…

  5. The First Reactor, 40th Anniversary (rev.)

    SciTech Connect

    Allardice, Corbin; Trapnell, Edward R; Fermi, Enrico; Fermi, Laura; Williams, Robert C

    1982-12-01

    This booklet, an updated version of the original booklet describing the first nuclear reactor, was written in honor of the 40th anniversary of the first reactor or "pile". It is based on firsthand accounts told to Corbin Allardice and Edward R. Trapnell, and includes recollections of Enrico and Laura Fermi.

  6. Stimulus Law Revs up Research on Energy

    ERIC Educational Resources Information Center

    Basken, Paul

    2009-01-01

    When President Obama dreams out loud, as he did in a speech last week, of a future when solar panels are as "cheap as paint" and buildings produce their own energy, researchers like the physicist Yang Yang are dreaming right along with him. Mr. Yang's laboratory is among hundreds at colleges around the country that stand to benefit from a new…

  7. Volatile Components from Packing Matrials, Rev. 2

    SciTech Connect

    Smith, R. A.

    2006-03-01

    An outgassing study was conducted on five packing materials, comprising two experiments. These materials comprised 277-4 borated concrete, Borobond4 concrete, polyethylene bags, silica-filled silicone rubber seals, and silicone foam padding. The purpose was measure the volume of gases which diffuse from packaging materials when sealed in containers. Two heating profiles were used to study the offgassing quantities in a set of accelerated aging tests. It was determined that the concretes contain a large quantity of water. The plastic materials hold much less moisture, with the silicone materials even consuming water, possibly due to the presence of silica filler. Polyethylene tends to degrade as the temperature is elevated and the foam stiffens.

  8. Watching the World Rev its Heat Engine

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Absorption of solar energy heats up our planet's surface and the atmosphere and makes life for us possible. But the energy cannot stay bound up in the Earth's environment forever. If it did then the Earth would be as hot as the Sun. Instead, as the surface and the atmosphere warm, they emit thermal longwave radiation, some of which escapes into space and allows the Earth to cool. This false-color image of the Earth was produced on September 30, 2001, by the Clouds and the Earth's Radiant Energy System (CERES) instrument flying aboard NASA's Terra spacecraft. The image shows where more or less heat, in the form of longwave radiation, is emanating from the top of Earth's atmosphere. As one can see in the image, the thermal radiation leaving the oceans is fairly uniform. The blue swaths across the central Pacific represent thick clouds, the tops of which are so high they are among the coldest places on Earth. In the American Southwest, which can be seen in the upper righthand corner of the globe, there is often little cloud cover to block outgoing radiation and relatively little water to absorb solar energy. Consequently, the amount of outgoing radiation in the American Southwest exceeds that of the oceans. Also, that region was experiencing an extreme heatwave when these data were acquired. Recently, NASA researchers discovered that incoming solar radiation and outgoing thermal radiation increased in the tropics from the 1980s to the 1990s. (Click to read the press release.) They believe that the reason for the unexpected increase has to do with an apparent change in circulation patterns around the globe, which effectively reduced the amount of water vapor and cloud cover in the upper reaches of the atmosphere. Without the clouds, more sunlight was allowed to enter the tropical zones and more thermal energy was allowed to leave. The findings may have big implications for climate change and future global warming. 'This suggests that the tropical heat engine increased its speed,' observes Dr. Bruce Wielicki, of NASA Langley Research Center. 'It's as if the heat engine in the tropics has become less efficient, using more fuel in the 1990s than in the 1980s.' Image courtesy Barbara Summey, NASA Goddard Visualization Analysis Lab, based upon data processed by Takmeng Wong, CERES Science Team, NASA Langley Research Center

  9. ICDP Complex Groundwater Monitoring Plan REV 5

    SciTech Connect

    Cahn, L. S.

    2007-08-09

    This Groundwater Monitoring Plan, along with the Quality Assurance Project Plan for Waste Area Groups 1, 2, 3, 4, 5, 6, 7, 10, and Removal Actions, constitutes the sampling and analysis plan for groundwater and perched water monitoring at the Idaho CERCLA Disposal Facility (ICDF). A detection monitoring system was installed in the Snake River Plan Aquifer to comply with substantive requirements of "Releases from Solid Waste Management Units" of the Resource Conservation and Recovery Act. This detection monitoring wells constructed in the Snake River Plain Aquifer.

  10. Chandra High Resolution Camera (HRC). Rev. 59

    NASA Technical Reports Server (NTRS)

    Murray, Stephen

    2004-01-01

    This monthly report discusses management and general status, mission support and operations, and science activities. A technical memorandum entitled "Failure Analysis of HRC Flight Relay" is included with the report.

  11. The World Revs its Heat Engine

    NASA Technical Reports Server (NTRS)

    2001-01-01

    Absorption of solar energy heats up our planet's surface and atmosphere making life for us possible. But the energy carnot stay bound up in the Earth's environment forever. If it did, the Earth would be as hot as the sun. Instead, as the surface and atmosphere warm, they emit thermal long wave radiation, some of which escapes into space and allows the Earth to cool. This false color image of the Earth was produced by the Clouds and the Earth's Radiant Energy System (CERES) instrument flying aboard NASA's Terra spacecraft. The image shows where more or less heat, in the form of long-wave radiation, is emanating from the top of the Earth's atmosphere. As one can see in the image, the thermal radiation leaving the oceans is fairly uniform. The blue swaths represent thick clouds, the tops of which are so high they are among the coldest places on Earth. In the American Southwest, which can be seen in the upper right hand corner of the globe, there is often little cloud cover to block outgoing radiation and relatively little water to absorb solar energy making the amount of outgoing radiation in this area exceeding that of the oceans. Recently, NASA researchers discovered that incoming solar radiation and outgoing thermal radiation increased in the tropics from the 1980s to the 1990s. They believe the unexpected change has to do with apparent change in circulation patterns around the globe, which effectively reduce the amount of water vapor and cloud cover in the upper reaches of the atmosphere. Without the clouds, more sunlight was allowed to enter the tropical zones and more thermal energy was allowed to leave. The findings may have big implications for climate change and future global warming. (Image courtesy NASA Goddard)

  12. Comparison of methods for improving the 1/N expansion

    NASA Astrophysics Data System (ADS)

    Varshni, Y. P.

    1989-08-01

    The recently proposed method by Papp [Phys. Rev. A 36, 3550 (1987); 38, 2158 (1988)] for determining the shift parameter in the shifted 1/N expansion method has been applied in three approximations to calculate the eigenenergies for the static screened Coulomb potential (SSCP) and Lennard-Jones 12-6 potential. The results are compared with those obtained by the method of Imbo et al. [Phys. Rev. D 29, 1669 (1984)] and the exact values. For the SSCP, comparison is also made with the results obtained by two methods proposed by Doren and Herschbach [Phys. Rev. A 34, 2654 (1986); 34, 2665 (1986)].

  13. The Long-Range Model of High-L Rydberg Fine Structure: A Critical Comparison with Experimental Data..

    NASA Astrophysics Data System (ADS)

    Snow, Erica L.; Wright, Laura E.; Lundeen, Stephen R.

    2006-05-01

    A simple view of the fine structure of non-penetrating Rydberg levels, suggested over 70 years ago [1], was refined to treat the fine structure of helium, lithium [2], and other atoms with S-state ion cores [3]. In this view the ion polarizabilities determine the fine structure pattern. Current experimental techniques provide access to highly excited high-L states in He [4], Li [5], Mg, SiIII [6], and Ba[7], and a test of the long-range model is possible with the availability of independent theoretical calculations. A critical comparison of the data treated with the long-range model will be made to the a-priori calculations of the ionic polarizabilities. [1] Joseph E. Mayer and Maria Goeppert Mayer, Phys. Rev. 43 605 (1933). [2] Richard J. Drachman and A. K. Bhatia, Phys. Rev. A 51 2926 (1995). [3] C. Laughlin, J. Phys. B: At. Mol. Opt. Phys. 28 2787 (1995). [4] G. D. Stevens and S. R. Lundeen, Comments on At. and Mol. Phys., Comments on Mod. Phys. 1,D 207 (2000). [5] C. H. Storry, N. E. Rothery, and E. A. Hessels, Phys. Rev. A 55 128 (1997). [6] R. A. Komara et. al., J. Phys. B: At. Mol. Opt. Phys. 38 S87 (2005). [7] E.L. Snow, et. al. Phys. Rev. A 71, 022510 (2005)

  14. Reply to "Comment on `Kinetic theory for a mobile impurity in a degenerate Tonks-Girardeau gas' "

    NASA Astrophysics Data System (ADS)

    Gamayun, O.; Lychkovskiy, O.; Cheianov, V.

    2015-07-01

    In our recent paper [O. Gamayun, O. Lychkovskiy, and V. Cheianov, Phys. Rev. E 90, 032132 (2014), 10.1103/PhysRevE.90.032132] we studied the dynamics of a mobile impurity particle weakly interacting with the Tonks-Girardeau gas and pulled by a small external force F . Working in the regime when the thermodynamic limit is taken prior to the small force limit, we found that the Bloch oscillations of the impurity velocity are absent in the case of a light impurity. Further, we argued that for a light impurity the steady-state drift velocity VD remains finite in the limit F →0 . These results are in contradiction with earlier works by Gangardt and co-workers [D. M. Gangardt and A. Kamenev, Phys. Rev. Lett. 102, 070402 (2009), 10.1103/PhysRevLett.102.070402; M. Schecter, D. M. Gangardt, and A. Kamenev, Ann. Phys. (NY) 327, 639 (2012), 10.1016/j.aop.2011.10.001]. One of us has conjectured [O. Lychkovskiy, Phys. Rev. A 91, 040101 (2015), 10.1103/PhysRevA.91.040101] that the central assumption of these works, the adiabaticity of the dynamics, can break down in the thermodynamic limit. In the preceding Comment [M. Schecter, D. M. Gangardt, and A. Kamenev, Phys. Rev. E 92, 016101 (2015), 10.1103/PhysRevE.92.016101], Schecter et al. have argued against this conjecture and in support of the existence of Bloch oscillations and the linearity of VD(F ) . They have suggested that the ground state of the impurity-fluid system is a quasibound state and that this is sufficient to ensure adiabaticity in the thermodynamic limit. Their analytical argument is based on a certain truncation of the Hilbert space of the system. We argue that extending the results and intuition based on their truncated model on the original many-body problem lacks justification.

  15. Comment on "Coherent interference in the resonant dissociative electron attachment to carbon monoxide"

    NASA Astrophysics Data System (ADS)

    Nag, Pamir; Nandi, Dhananjay

    2015-05-01

    In a recent article [Phys. Rev. A 88, 012708 (2013), 10.1103/PhysRevA.88.012708], Tian et al. claimed coherent interference among the various negative ion resonant states involved in the dissociative electron attachment (DEA) to carbon monoxide (CO) by investigating O- angular distribution using the anion velocity time-sliced map imaging technique. However, our recent detailed study [Phys. Chem. Chem. Phys. 17, 7130 (2015), 10.1039/C4CP05678G] on DEA to CO using the identical technique shows that the above claim can be questioned.

  16. Usefulness of entanglement-assisted quantum metrology

    NASA Astrophysics Data System (ADS)

    Huang, Zixin; Macchiavello, Chiara; Maccone, Lorenzo

    2016-07-01

    Entanglement-assisted quantum communication employs preshared entanglement between sender and receiver as a resource. We apply the same framework to quantum metrology, introducing shared entanglement between the probe and the ancilla in the preparation stage and allowing entangling operations at the measurement stage, i.e., using some entangled ancillary system that does not interact with the system to be sampled. This is known to be useless in the noiseless case, but was recently shown to be useful in the presence of noise [R. Demkowicz-Dobrzanski and L. Maccone, Phys. Rev. Lett. 113, 250801 (2014), 10.1103/PhysRevLett.113.250801; W. Dür, M. Skotiniotis, F. Fröwis, and B. Kraus, Phys. Rev. Lett. 112, 080801 (2014), 10.1103/PhysRevLett.112.080801; E. M. Kessler, I. Lovchinsky, A. O. Sushkov, and M. D. Lukin, Phys. Rev. Lett. 112, 150802 (2014);, 10.1103/PhysRevLett.112.150802 R. Demkowicz-Dobrzański and J. Kolodynski, New J. Phys. 15, 073043 (2013), 10.1088/1367-2630/15/7/073043]. Here we detail how and when it can be of use. For example, surprisingly it is useful when two channels are randomly alternated, for both of which ancillas do not help (depolarizing). We show that it is useful for all levels of noise for many noise models and propose a simple optical experiment to test these results.

  17. B80 and B101-103 clusters: Remarkable stability of the core-shell structures established by validated density functionalsa)

    NASA Astrophysics Data System (ADS)

    Li, Fengyu; Jin, Peng; Jiang, De-en; Wang, Lu; Zhang, Shengbai B.; Zhao, Jijun; Chen, Zhongfang

    2012-02-01

    Prompted by the very recent claim that the volleyball-shaped B80 fullerene [X. Wang, Phys. Rev. B 82, 153409 (2010), 10.1103/PhysRevB.82.153409] is lower in energy than the B80 buckyball [N. G. Szwacki, A. Sadrzadeh, and B. I. Yakobson, Phys. Rev. Lett. 98, 166804 (2007), 10.1103/PhysRevLett.98.166804] and core-shell structure [J. Zhao, L. Wang, F. Li, and Z. Chen, J. Phys. Chem. A 114, 9969 (2010), 10.1021/jp1018873], and inspired by the most recent finding of another core-shell isomer as the lowest energy B80 isomer [S. De, A. Willand, M. Amsler, P. Pochet, L. Genovese, and S. Goedecher, Phys. Rev. Lett. 106, 225502 (2011), 10.1103/PhysRevLett.106.225502], we carefully evaluated the performance of the density functional methods in the energetics of boron clusters and confirmed that the core-shell construction (stuffed fullerene) is thermodynamically the most favorable structural pattern for B80. Our global minimum search showed that both B101 and B103 also prefer a core-shell structure and that B103 can reach the complete core-shell configuration. We called for great attention to the theoretical community when using density functionals to investigate boron-related nanomaterials.

  18. Ab initio quantum Monte Carlo simulations of the uniform electron gas without fixed nodes: The unpolarized case

    NASA Astrophysics Data System (ADS)

    Dornheim, T.; Groth, S.; Schoof, T.; Hann, C.; Bonitz, M.

    2016-05-01

    In a recent publication [S. Groth et al., Phys. Rev. B 93, 085102 (2016), 10.1103/PhysRevB.93.085102], we have shown that the combination of two complementary quantum Monte Carlo approaches, namely configuration path integral Monte Carlo [T. Schoof et al., Phys. Rev. Lett. 115, 130402 (2015), 10.1103/PhysRevLett.115.130402] and permutation blocking path integral Monte Carlo [T. Dornheim et al., New J. Phys. 17, 073017 (2015), 10.1088/1367-2630/17/7/073017], allows for the accurate computation of thermodynamic properties of the spin-polarized uniform electron gas over a wide range of temperatures and densities without the fixed-node approximation. In the present work, we extend this concept to the unpolarized case, which requires nontrivial enhancements that we describe in detail. We compare our simulation results with recent restricted path integral Monte Carlo data [E. W. Brown et al., Phys. Rev. Lett. 110, 146405 (2013), 10.1103/PhysRevLett.110.146405] for different energy contributions and pair distribution functions and find, for the exchange correlation energy, overall better agreement than for the spin-polarized case, while the separate kinetic and potential contributions substantially deviate.

  19. Generalized Wannier functions: A comparison of molecular electric dipole polarizabilities

    NASA Astrophysics Data System (ADS)

    O'Regan, David D.; Payne, Mike C.; Mostofi, Arash A.

    2012-05-01

    Localized Wannier functions provide an efficient and intuitive means by which to compute dielectric properties from first principles. They are most commonly constructed in a post-processing step, following total-energy minimization. Nonorthogonal generalized Wannier functions (NGWFs) [Skylaris , Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.66.035119 66, 035119 (2002); Skylaris , J. Chem. Phys.JCPSA60021-960610.1063/1.1839852 122, 084119 (2005)] may also be optimized in situ, in the process of solving for the ground-state density. We explore the relationship between NGWFs and orthonormal, maximally localized Wannier functions (MLWFs) [Marzari and Vanderbilt, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.56.12847 56, 12847 (1997); Souza, Marzari, and Vanderbilt, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.65.035109 65, 035109 (2001)], demonstrating that NGWFs may be used to compute electric dipole polarizabilities efficiently, with no necessity for post-processing optimization, and with an accuracy comparable to MLWFs.

  20. Resonant-state-expansion Born approximation with a correct eigen-mode normalisation

    NASA Astrophysics Data System (ADS)

    Doost, M. B.

    2016-08-01

    The Born approximation (Born 1926 Z. Phys. 38 802) is a fundamental result in physics, it allows the calculation of weak scattering via the Fourier transform of the scattering potential. As was done by previous authors (Ge et al 2014 New J. Phys. 16 113048) the Born approximation is extended by including in the formula the resonant-states (RSs) of the scatterer. However in this study unlike previous studies the included eigen-modes are correctly normalised with dramatic positive consequences for the accuracy of the method. The normalisation of RSs used in the previous RS expansion Born approximation or resonant-state expansion (RSE) Born approximation made in Ge et al (2014 New J. Phys. 16 113048) has been shown to be numerically unstable in Muljarov et al (2014 arXiv:1409.6877) and by analytics here. The RSs of the system can be calculated using my recently discovered RSE perturbation theory for dispersive electrodynamic scatterers (Muljarov et al 2010 Europhys. Lett. 92 50010; Doost et al 2012 Phys. Rev. A 85 023835; Doost et al 2013 Phys. Rev. A 87 043827; Armitage et al 2014 Phys. Rev. A 89; Doost et al 2014 Phys. Rev. A 90 013834) and normalised correctly to appear in spectral Green's functions and hence the RSE Born approximation via the flux-volume normalisation which I recently rigorously derived in Armitage et al (2014 Phys. Rev. A 89), Doost et al (2014 Phys. Rev. A 90 013834), Doost (2016 Phys. Rev. A 93 023835). In the case of effectively one-dimensional systems I find a RSE Born approximation alternative to the scattering matrix method.

  1. Comment on "How to interpret Onsager cross terms in mixed ionic electronic conductors" by I. Riess, Phys. Chem. Chem. Phys., 2014, 16, 22513.

    PubMed

    Yoo, Han-Ill; Martin, Manfred; Janek, Juergen

    2015-04-28

    Here we show that the Onsager cross terms for ion-electron interactions are not an artifact, but the necessity to phenomenologically and completely describe the mass/charge transport of a mixed ionic-electronic conductor in terms of mobile charged components which are the only experimentally operable species. The use of an appropriate comprehensive defect model may help to reduce the cross terms (which depend on the choice of formal charge of the mobile defects), but it cannot obviate them if long-range Coulombic interactions are in action among the defects.

  2. Teleportation via a mixture of a two qubit subsystem of a N-qubit W and GHZ state

    NASA Astrophysics Data System (ADS)

    Chakrabarty, I.

    2010-04-01

    In this work we study a state which is a random mixture of a two qubit subsystem of a N-qubit W state and GHZ state. We analyze several possibilities like separability criterion (Peres-Horodecki criterion [M. Horodecki, P. Horodecki, R. Horodecki, Phys. Lett. A 223, 1 (1996); A. Peres, Phys. Rev. Lett. 77, 1413 (1996)]), non violation of Bell’s inequality [J.F. Clauser, M.A. Horne, A. Shimony, R.A. Holt, Phys. Rev. Lett. 23, 80 (1969)] (M(ρ)<1) and teleportation fidelity [N. Gisin, Phys. Lett. A 210, 157 (1996); R. Horodecki, P. Horodecki, M. Horodecki, Phys. Lett. A 200, 340 (1995); S. Massar, S. Popescu, Phys. Rev. Lett. 74, 1259 (1995); S. Popescu, Phys. Rev. Lett. 72, 797 (1994); C.H. Bennett, G. Brassard, C. Crepeau, R. Jozsa, A. Peres, W.K. Wootters, Phys. Rev. Lett. 70, 1895 (1993)] (F_{max}>2/3) for this state. We also obtain a relationship between N (number of qubits) and p (the classical probability of random mixture) for each of these possibilities. Finally we present a detailed analysis of all these possibilities for N=3,4,5 qubit systems. We also report that for N=3 and pin(0.75,1], this entangled state can be used as a teleportation channel without violating Bell’s inequality.

  3. Fractional process as a unified model for subdiffusive dynamics in experimental data

    NASA Astrophysics Data System (ADS)

    Burnecki, Krzysztof; Sikora, Grzegorz; Weron, Aleksander

    2012-10-01

    We show how to use a fractional autoregressive integrated moving average (FARIMA) model to a statistical analysis of the subdiffusive dynamics. The discrete time FARIMA(1,d,1) model is applied in this paper to the random motion of an individual fluorescently labeled mRNA molecule inside live E. coli cells in the experiment described in detail by Golding and Cox [Phys. Rev. Lett.10.1103/PhysRevLett.96.098102 96, 098102 (2006)] as well as to the motion of fluorescently labeled telomeres in the nucleus of live human cells (U2OS cancer) in the experiment performed by Bronstein [Phys. Rev. Lett.10.1103/PhysRevLett.103.018102 103, 018102 (2009)]. It is found that only the memory parameter d of the FARIMA model completely detects an anomalous dynamics of the experimental data in both cases independently of the observed distribution of random noises.

  4. Critical Supercurrents and Self-Organization in Quantum Hall Bilayers

    NASA Astrophysics Data System (ADS)

    Eastham, P. R.; Cooper, N. R.; Lee, D. K. K.

    2010-12-01

    We present a theory of interlayer tunneling in a disordered quantum Hall bilayer at total filling factor one, allowing for the effect of static vortices. In agreement with recent experiments [Phys. Rev. BPRBMDO1098-0121 80, 165120 (2009)10.1103/PhysRevB.80.165120; Phys. Rev. B PRBMDO1098-012178, 075302 (2008)10.1103/PhysRevB.78.075302], we find that the critical current is proportional to the sample area and is comparable in magnitude to observed values. This reflects the formation of a Bean critical state as a result of current injection at the boundary. We predict a crossover to a critical current proportional to the square-root of the area in smaller samples. We also predict a peak in the critical current as the electron density varies at fixed layer separation.

  5. Comment on ``Systematic approach to generate near-perfect periodic continuous random network models: Application to amorphous Si3N4''

    NASA Astrophysics Data System (ADS)

    Mousseau, Normand

    1997-12-01

    Ouyang and Ching [Phys. Rev. B 54, R15 594 (1996)] have recently proposed a very elegant algorithm for building amorphous networks. Their algorithm, though, leaves strong remnants of cubic symmetry and cannot provide satisfactory amorphous models.

  6. Reply to "Comment on `Acoustical observation of bubble oscillations induced by bubble popping' "

    NASA Astrophysics Data System (ADS)

    Ding, Junqi

    2015-03-01

    We reported on the sound pressure generated by aqueous foam bursts in our paper [Ding et al., Phys. Rev. E 75, 041601 (2007), 10.1103/PhysRevE.75.041601]. Blanc et al., [Phys. Rev. E 91, 036401 (2015), 10.1103/PhysRevE.91.036401] found that sound from one of three mechanisms of bubble burst (the prepopping) actually results from an acausal artifact of the signal processing performed by their acquisition system which lies outside of its prescribed working frequency range. We examined the same hardware used in our paper and found that the frequency range is not the cause of the artifact. The prepopping sound was a result from a built-in finite impulse response filter of analog-to-digital converters in the Brüel & Kjær data acquisition system.

  7. Formation of molecules in an expanding Bose-Einstein condensate

    NASA Astrophysics Data System (ADS)

    Yurovsky, Vladimir; Ben-Reuven, Abraham

    2004-05-01

    A mean field theory [1] is extended to an inhomogeneous case of expanding hybrid atom-molecule Bose-Einstein condensates. This theory is applied to the recent MPI experiments [2] on ^87Rb demonstrating the formation of ultracold molecules due to Feshbach resonance. The subsequent dissociation of the molecules is treated using a non-mean-field parametric approximation [3]. The latter method is also used in determining optimal conditions for the formation of molecular BEC. [1] V. A. Yurovsky, A. Ben-Reuven, P. S. Julienne and C. J. Williams, Phys. Rev. A 60, R765 (1999); Phys. Rev. A 62, 043605 (2000). [2] S. Dürr, T. Volz, A. Marte, and G. Rempe, Phys. Rev. Lett. 92, 020406 (2004). [3] V. A. Yurovsky and A. Ben-Reuven, Phys. Rev. A 67, 043611 (2003).

  8. Creating number states in the micromaser using feedback

    NASA Astrophysics Data System (ADS)

    Liebman, Ariel; Milburn, G. J.

    1995-01-01

    We use the quantum theory of feedback developed by Wiseman and Milburn [Phys. Rev. Lett. 70, 548 (1993)] and Wiseman [Phys. Rev. A 49, 2133 (1994)] to investigate the photon-number noise properties of the micromaser with direct detection feedback. We find that the feedback can significantly reduce the amount of noise in the photon number. Under the right conditions the feedback locks the systems onto a number state. As opposed to other schemes in the past [P. Meystre, Opt. Lett. 12, 669 (1987); J. Krause, M. O. Scully, and H. Walther, Phys. Rev. A 36, 4547 (1987)], we can fix the number states to which the system evolves. We also simulate the micromaser using the quantum-trajectories method and show that these results agree with the quantum theory of feedback. We show that the noise of quantum island states [P. Bogar, J. A. Bergou, and M. Hillary, Phys. Rev. A 50, 754 (1994)] can be significantly reduced by the feedback.

  9. Generalizing a unified model of dark matter, dark energy, and inflation with a noncanonical kinetic term

    NASA Astrophysics Data System (ADS)

    de-Santiago, Josue; Cervantes-Cota, Jorge L.

    2011-03-01

    We study a unification model for dark energy, dark matter, and inflation with a single scalar field with noncanonical kinetic term. In this model, the kinetic term of the Lagrangian accounts for the dark matter and dark energy, and at early epochs, a quadratic potential accounts for slow roll inflation. The present work is an extension to the work by Bose and Majumdar [Phys. Rev. DPRVDAQ1550-7998 79, 103517 (2009).10.1103/PhysRevD.79.103517] with a more general kinetic term that was proposed by Chimento in Phys. Rev. DPRVDAQ0556-2821 69, 123517 (2004).10.1103/PhysRevD.69.123517 We demonstrate that the model is viable at the background and linear perturbation levels.

  10. Hawking radiation and near horizon universality of chiral Virasoro algebra

    NASA Astrophysics Data System (ADS)

    Banerjee, Rabin; Gangopadhyay, Sunandan; Kulkarni, Shailesh

    2010-12-01

    We show that the diffeomorphism anomaly together with the trace anomaly reveal a chiral Virasoro algebra near the event horizon of a black hole. This algebra is the same irrespective of whether the anomaly is covariant or consistent, thereby manifesting its universal character and the fact that only the outgoing modes are relevant near the horizon. Our analysis therefore clarifies the role of the trace anomaly in the diffeomorphism anomaly approach [Robinson and Wilczek in Phys. Rev. Lett. 95:011303, 2005; Iso et al. in Phys. Rev. Lett. 96:151302, 2006; Banerjee and Kulkarni in Phys. Rev. D 77:024018, 2008; Gangopadhyay and Kulkarni in Phys. Rev. D 77:024038, 2008] to the Hawking radiation.

  11. Polarization-dependent manipulation of optical properties in a tripod system

    NASA Astrophysics Data System (ADS)

    Kumar, Santosh; Lauprêtre, Thomas; Bretenaker, Fabien; Goldfarb, Fabienne; Ghosh, Rupamanjari

    2013-08-01

    We analyze the dependence of the transmission profiles of an atom in a tripod configuration on the polarizations of the coupling and the probe beams and use room-temperature metastable helium (4He*) as a model system. We show that, by rotating the orthogonally polarized coupling-probe beams with respect to an applied small magnetic field, one can manipulate the detuned peaks due to electromagnetically induced transparency [Kumar, Lauprêtre, Ghosh, Bretenaker, and Goldfarb, Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.84.023811 84, 023811 (2011)] and the central peak arising because of ground-state coherent population oscillations [Lauprêtre, Kumar, Berger, Faoro, Ghosh, Bretenaker, and Goldfarb, Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.85.051805 85, 051805(R) (2012)] observed earlier separately. Our experimental results match well with our numerical simulation using the Floquet method.

  12. Reanalysis of Rosenbluth measurements of the proton form factors

    NASA Astrophysics Data System (ADS)

    Gramolin, A. V.; Nikolenko, D. M.

    2016-05-01

    We present a reanalysis of the data from Stanford Linear Accelerator Center (SLAC) experiments E140 [R. C. Walker et al., Phys. Rev. D 49, 5671 (1994), 10.1103/PhysRevD.49.5671] and NE11 [L. Andivahis et al., Phys. Rev. D 50, 5491 (1994), 10.1103/PhysRevD.50.5491] on elastic electron-proton scattering. This work is motivated by recent progress in calculating the corresponding radiative corrections and by the apparent discrepancy between the Rosenbluth and polarization transfer measurements of the proton electromagnetic form factors. New, corrected values for the scattering cross sections are presented, as well as a new form factor fit in the Q2 range from 1 to 8.83 GeV2. We also provide a complete set of revised formulas to account for radiative corrections in single-arm measurements of unpolarized elastic electron-proton scattering.

  13. Vibrational and rotational excited states within a Bohr Hamiltonian with a deformation-dependent mass formalism

    NASA Astrophysics Data System (ADS)

    Chabab, M.; Lahbas, A.; Oulne, M.

    2015-06-01

    In a recent work [Phys. Rev. C 84, 044321 (2011), 10.1103/PhysRevC.84.044321] M. J. Ermamatov and P. R. Fraser have studied rotational and vibrational excited states of axially symmetric nuclei within the Bohr Hamiltonian with different mass parameters. However, the energy formula that the authors have used contains some inaccuracies. So the numerical results they obtained seem to be controversial. In this paper, we revisit all calculations related to this problem and determine the appropriate formula for the energy spectrum. Moreover, in order to improve such calculations, we reconsider this problem within the framework of the deformation-dependent mass formalism. Also, unlike the work of Bonatsos et al. [Phys. Rev. C 83, 044321 (2011), 10.1103/PhysRevC.83.044321], in which the mass parameter has not been considered, we will show the importance of this parameter and its effect on numerical predictions.

  14. Noise induces rare events in granular media

    NASA Astrophysics Data System (ADS)

    Khain, Evgeniy; Sander, Leonard M.

    2016-09-01

    The granular Leidenfrost effect [B. Meerson, et al., Phys. Rev. Lett. 91, 024301 (2003), 10.1103/PhysRevLett.91.024301; P. Eshuis et al., Phys. Rev. Lett. 95, 258001 (2005), 10.1103/PhysRevLett.95.258001] is the levitation of a mass of granular matter when a wall below the grains is vibrated, giving rise to a hot granular gas below the cluster. We find by simulation that for a range of parameters the system is bistable: the levitated cluster can occasionally break and give rise to two clusters and a hot granular gas above and below. We use techniques from the theory of rare events to compute the mean transition time for breaking to occur. This requires the introduction of a two-component reaction coordinate.

  15. Examination and experimental constraints of the stellar reaction rate factor NA<σv> of the 18Ne(α,p)21Na reaction at temperatures of x-ray bursts

    NASA Astrophysics Data System (ADS)

    Mohr, P.; Matic, A.

    2013-03-01

    The 18Ne(α,p)21Na reaction is one key for the breakout from the hot CNO cycles to the rp-process. Recent papers have provided reaction rate factors NA<σv> which are discrepant by at least one order of magnitude. The compatibility of the latest experimental results is tested, and a partial explanation for the discrepant NA<σv> is given. A new rate factor is derived from the combined analysis of all available data. The new rate factor is located slightly below the higher rate factor found by Matic [Phys. Rev. CPRVCAN0556-281310.1103/PhysRevC.80.055804 80, 055804 (2009)] at low temperatures and significantly below at higher temperatures whereas it is about a factor of 5 higher than the lower rate factor recently published by Salter [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.108.242701 108, 242701 (2012)].

  16. Comment on {open_quotes}Confirmation of the Sigma Meson{close_quote}{close_quote}

    SciTech Connect

    Harada, M.; Sannino, F.; Schechter, J.; Sannino, F.

    1997-02-01

    A Comment on the Letter by Nils A. Tornqvist and Matts Roos, Phys.Rev.Lett.{bold 76}, 1575 (1996). The authors of the Letter offer a Reply. {copyright} {ital 1997} {ital The American Physical Society}

  17. Comment on {open_quote}{open_quote}Confirmation of the Sigma Meson{close_quote}{close_quote}

    SciTech Connect

    Isgur, N.; Speth, J.

    1996-09-01

    A Comment on the Letter by Nils A. T{umlt o}rnqvist and Matts Roos, Phys. Rev. Lett. {bold 76}, 1575 (1996). The authors of the Letter offer a Reply. {copyright} {ital 1996 The American Physical Society.}

  18. Comment on ``Electron Mass Operator in a Strong Magnetic Field and Dynamical Chiral Symmetry Breaking''

    NASA Astrophysics Data System (ADS)

    Gusynin, V. P.; Miransky, V. A.; Shovkovy, I. A.

    2003-02-01

    A Comment on the Letter by A. V. Kuznetsov and N. V. Mikheev,

    Phys. Rev. Lett.PRLTAO0031-9007 89, 011601 (2002).
    The authors of the Letter offer a Reply.

  19. Violation of Bell inequality based on S4 symmetry

    NASA Astrophysics Data System (ADS)

    Bolonek-Lasoń, Katarzyna

    2016-08-01

    In two recent papers [Phys. Rev. A 90, 062121 (2014), 10.1103/PhysRevA.90.062121 and Phys. Rev. A, 91, 052110 (2015), 10.1103/PhysRevA.91.052110] an interesting method of analyzing the violation of Bell inequalities has been proposed which is based on the theory of finite group representations. Here we apply this method to more complicated examples of S4 symmetry. We show how the Bell inequality can be related to the symmetries of regular tetrahedron. By choosing the orbits of three-dimensional representations of S4 determined by the geometry of tetrahedron we find that the Bell inequality under consideration is violated in quantum theory. The corresponding nonlocal game is analyzed.

  20. Nonlinear fluid equations for fully toroidal electromagnetic waves for the core tokamak plasma

    NASA Astrophysics Data System (ADS)

    Weiland, J.; Liu, C. S.; Liu

    2013-12-01

    The rather general set of fluid equations with full curvature effects (Shukla and Weiland, Phys. Rev. A 40, 341 (1989)) has been modified to apply to the core and generalized to include also microtearing modes.

  1. Comment on "Controlling the spectral shape of nonlinear Thomson scattering with proper laser chirping"

    NASA Astrophysics Data System (ADS)

    Terzić, Balša; Krafft, Geoffrey A.

    2016-09-01

    Rykovanov, Geddes, Schroeder, Esarey and Leemans [Phys. Rev. Accel. Beams 19, 030701 (2016), 10.1103/PhysRevAccelBeams.19.030701; hereafter RGSEL] have recently reported on the analytic derivation for the laser pulse frequency modulation (chirping) which controls spectrum broadening for high laser pulse intensities. We demonstrate here that their results are the same as the exact solutions reported in Terzić, Deitrick, Hofler and Krafft [Phys. Rev. Lett. 112, 074801 (2014), 10.1103/PhysRevLett.112.074801; hereafter TDHK]. While the two papers deal with circularly and linearly polarized laser pulses, respectively, the difference in expressions for the two is just the usual factor of 1 /2 present from going from circular to linear polarization. In addition, we note the authors used an approximation to the number of subsidiary peaks in the unchirped spectrum when a better solution is given in TDHK.

  2. Calculating work in weakly driven quantum master equations: Backward and forward equations.

    PubMed

    Liu, Fei

    2016-01-01

    I present a technical report indicating that the two methods used for calculating characteristic functions for the work distribution in weakly driven quantum master equations are equivalent. One involves applying the notion of quantum jump trajectory [Phys. Rev. E 89, 042122 (2014)PLEEE81539-375510.1103/PhysRevE.89.042122], while the other is based on two energy measurements on the combined system and reservoir [Silaev et al., Phys. Rev. E 90, 022103 (2014)PLEEE81539-375510.1103/PhysRevE.90.022103]. These represent backward and forward methods, respectively, which adopt a very similar approach to that of the Kolmogorov backward and forward equations used in classical stochastic theory. The microscopic basis for the former method is also clarified. In addition, a previously unnoticed equality related to the heat is also revealed. PMID:26871044

  3. Calculating work in weakly driven quantum master equations: Backward and forward equations

    NASA Astrophysics Data System (ADS)

    Liu, Fei

    2016-01-01

    I present a technical report indicating that the two methods used for calculating characteristic functions for the work distribution in weakly driven quantum master equations are equivalent. One involves applying the notion of quantum jump trajectory [Phys. Rev. E 89, 042122 (2014), 10.1103/PhysRevE.89.042122], while the other is based on two energy measurements on the combined system and reservoir [Silaev et al., Phys. Rev. E 90, 022103 (2014), 10.1103/PhysRevE.90.022103]. These represent backward and forward methods, respectively, which adopt a very similar approach to that of the Kolmogorov backward and forward equations used in classical stochastic theory. The microscopic basis for the former method is also clarified. In addition, a previously unnoticed equality related to the heat is also revealed.

  4. Comment on "Generalized exclusion processes: Transport coefficients"

    NASA Astrophysics Data System (ADS)

    Becker, T.; Nelissen, K.; Cleuren, B.; Partoens, B.; Van den Broeck, C.

    2016-04-01

    In a recent paper, Arita et al. [Phys. Rev. E 90, 052108 (2014), 10.1103/PhysRevE.90.052108] consider the transport properties of a class of generalized exclusion processes. Analytical expressions for the transport-diffusion coefficient are derived by ignoring correlations. It is claimed that these expressions become exact in the hydrodynamic limit. In this Comment, we point out that (i) the influence of correlations upon the diffusion does not vanish in the hydrodynamic limit, and (ii) the expressions for the self- and transport diffusion derived by Arita et al. are special cases of results derived in Becker et al. [Phys. Rev. Lett. 111, 110601 (2013), 10.1103/PhysRevLett.111.110601].

  5. Dynamical overstability of radiative blast waves: the atomic physics of shock stability.

    PubMed

    Laming, J Martin; Grun, Jacob

    2002-09-16

    Atomic-physics calculations of radiative cooling are used to develop criteria for the overstability of radiating shocks. Our calculations explain the measurement of shock overstability by Grun et al. [Phys. Rev. Lett. 66, 2738 (1991)

  6. Symmetry-adapted Wannier functions in the maximal localization procedure

    NASA Astrophysics Data System (ADS)

    Sakuma, R.

    2013-06-01

    A procedure to construct symmetry-adapted Wannier functions in the framework of the maximally localized Wannier function approach [Marzari and Vanderbilt, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.56.12847 56, 12847 (1997); Souza, Marzari, and Vanderbilt, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.65.035109 65, 035109 (2001)] is presented. In this scheme, the minimization of the spread functional of the Wannier functions is performed with constraints that are derived from symmetry properties of the specified set of the Wannier functions and the Bloch functions used to construct them, therefore one can obtain a solution that does not necessarily yield the global minimum of the spread functional. As a test of this approach, results of atom-centered Wannier functions for GaAs and Cu are presented.

  7. Drag reduction by polymer additives from turbulent spectra.

    PubMed

    Calzetta, Esteban

    2010-12-01

    We extend the analysis of the friction factor for turbulent pipe flow reported by G. Gioia and P. Chakraborty [Phys. Rev. Lett. 96, 044502 (2006)] to the case where drag is reduced by polymer additives.

  8. Devil's staircases and continued fractions in Josephson junctions

    NASA Astrophysics Data System (ADS)

    Shukrinov, Yu. M.; Medvedeva, S. Yu.; Botha, A. E.; Kolahchi, M. R.; Irie, A.

    2013-12-01

    Detailed numerical simulations of the IV characteristics of a Josephson junction under external electromagnetic radiation show the devil's staircase within different bias current intervals. We have found that the observed steps form very precisely continued fractions. Increase of the amplitude of the radiation shifts the devil's staircase to higher Shapiro steps. An algorithm for the appearance and detection of subharmonics with increasing radiation amplitude is proposed. We demonstrate that the subharmonic steps registered in the well-known experiments by Dayem and Wiegand [Phys. Rev. 155, 419 (1967), 10.1103/PhysRev.155.419] and Clarke [Phys. Rev. B 4, 2963 (1971), 10.1103/PhysRevB.4.2963] also form continued fractions.

  9. Sum-of-squares decompositions for a family of Clauser-Horne-Shimony-Holt-like inequalities and their application to self-testing

    NASA Astrophysics Data System (ADS)

    Bamps, Cédric; Pironio, Stefano

    2015-05-01

    We introduce two families of sum-of-squares (SOS) decompositions for the Bell operators associated with the tilted Clauser-Horne-Shimony-Holt (CHSH) expressions introduced in Acín et al. [Phys. Rev. Lett. 108, 100402 (2012), 10.1103/PhysRevLett.108.100402]. These SOS decompositions provide tight upper bounds on the maximal quantum value of these Bell expressions. Moreover, they establish algebraic relations that are necessarily satisfied by any quantum state and observables yielding the optimal quantum value. These algebraic relations are then used to show that the tilted CHSH expressions provide robust self-tests for any partially entangled two-qubit state. This application to self-testing follows closely the approach of Yang and Navascués [Phys. Rev. A 87, 050102(R) (2013), 10.1103/PhysRevA.87.050102], where we identify and correct two nontrivial flaws.

  10. Estimation of shear viscosity based on transverse momentum correlations

    NASA Astrophysics Data System (ADS)

    STAR Collaboration; Sharma, Monika; STAR Collaboration

    2009-11-01

    Event anisotropy measurements at RHIC suggest the strongly interacting matter created in heavy ion collisions flows with very little shear viscosity. Precise determination of “shear viscosity-to-entropy” ratio is currently a subject of extensive study [S. Gavin and M. Abdel-Aziz, Phys. Rev. Lett. 97 (2006) 162302]. We present preliminary results of measurements of the evolution of transverse momentum correlation function with collision centrality of Au+Au interactions at s=200 GeV. We compare two differential correlation functions, namely inclusive [J. Adams et al. (STAR Collaboration), Phys. Rev. C 72 (2005) 044902] and a differential version of the correlation measure C˜ introduced by Gavin et al. [S. Gavin and M. Abdel-Aziz, Phys. Rev. Lett. 97 (2006) 162302; M. Sharma and C. A. Pruneau, Phys. Rev. C 79 (2009) 024905.]. These observables can be used for the experimental study of the shear viscosity per unit entropy.

  11. Dynamical phase transitions, time-integrated observables, and geometry of states

    NASA Astrophysics Data System (ADS)

    Hickey, James M.; Genway, Sam; Garrahan, Juan P.

    2014-02-01

    We show that there exist dynamical phase transitions (DPTs), as defined by Heyl et al. [Phys. Rev. Lett. 110, 135704 (2013), 10.1103/PhysRevLett.110.135704], in the transverse-field Ising model (TFIM) away from the static quantum critical points. We study a class of special states associated with singularities in the generating functions of time-integrated observables as found by Hickey et al. [Phys. Rev. B 87, 184303 (2013)], 10.1103/PhysRevB.87.184303. Studying the dynamics of these special states under the evolution of the TFIM Hamiltonian, we find temporal nonanalyticities in the initial-state return probability associated with dynamical phase transitions. By calculating the Berry phase and Chern number we show the set of special states have interesting geometric features similar to those associated with static quantum critical points.

  12. Comment on 'How macroscopic properties dictate microscopic probabilities'

    SciTech Connect

    Finkelstein, J.

    2003-02-01

    Aharonov and Reznik have argued [in Phys. Rev A 65, 052116 (2002)] that the form of the probabilistic predictions of quantum theory can be seen to follow from properties of macroscopic systems. An error in their argument is identified.

  13. Attosecond delay of xenon 4 d photoionization at the giant resonance and Cooper minimum

    NASA Astrophysics Data System (ADS)

    Magrakvelidze, Maia; Madjet, Mohamed El-Amine; Chakraborty, Himadri S.

    2016-07-01

    A Kohn-Sham time-dependent local-density-functional scheme is utilized to predict attosecond time delays of xenon 4 d photoionization that involves the 4 d giant dipole resonance and Cooper minimum. The fundamental effect of electron correlations to uniquely determine the delay at both regions is demonstrated. In particular, for the giant dipole resonance, the delay underpins strong collective effect, emulating the recent prediction at C60 giant plasmon resonance [T. Barillot et al., Phys. Rev. A 91, 033413 (2015), 10.1103/PhysRevA.91.033413]. For the Cooper minimum, a qualitative similarity with a photorecombination experiment near argon 3 p minimum [S. B. Schoun et al., Phys. Rev. Lett. 112, 153001 (2014), 10.1103/PhysRevLett.112.153001] is found. The result should encourage attosecond measurements of Xe 4 d photoemission.

  14. Rotating effects on the Landau quantization for an atom with a magnetic quadrupole moment.

    PubMed

    Fonseca, I C; Bakke, K

    2016-01-01

    Based on the single particle approximation [Dmitriev et al., Phys. Rev. C 50, 2358 (1994) and C.-C. Chen, Phys. Rev. A 51, 2611 (1995)], the Landau quantization associated with an atom with a magnetic quadrupole moment is introduced, and then, rotating effects on this analogue of the Landau quantization is investigated. It is shown that rotating effects can modify the cyclotron frequency and breaks the degeneracy of the analogue of the Landau levels.

  15. Reorientation dynamics of ferroelectric liquid-crystal molecules near the smectic-A-smectic-C* transition

    NASA Astrophysics Data System (ADS)

    O'brien, J. P.; Moses, T.; Chen, W.; Freysz, E.; Ouchi, Y.; Shen, Y. R.

    1993-04-01

    A transient optical Kerr measurement is used to study molecular reorientation about the long molecular axis of chiral and nonchiral smectic-A liquid crystals. Two relaxation components were identified, associated with individual and collective molecular motions. In contradiction with a recent report [J. R. Lalanne et al., Phys. Rev. Lett. 62, 3046 (1989); Phys. Rev. A 44, 6632 (1991)], no critical behavior of this reorientation was observed as the transition to the ferroelectric smectic-C* phase was approached.

  16. Comment on 'Connection between entanglement and the speed of quantum evolution' and on 'Entanglement and the lower bounds on the speed of quantum evolution'

    SciTech Connect

    Chau, H. F.

    2010-11-15

    Batle et al.[Phys. Rev. A 72, 032337 (2005)] and Borras et al.[Phys. Rev. A 74, 022326 (2006)] studied the connection between entanglement and speed of quantum evolution for certain low-dimensional bipartite quantum states. However, their studies did not cover all possible cases. And the relation between entanglement and the maximum possible quantum evolution speed for these uncovered cases can be very different from the ones that they have studied.

  17. Comment on ``Perfect imaging with positive refraction in three dimensions''

    NASA Astrophysics Data System (ADS)

    Merlin, R.

    2010-11-01

    Leonhardt and Philbin [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.81.011804 81, 011804(R) (2010)] have recently constructed a mathematical proof that the Maxwell's fish-eye lens provides perfect imaging of electromagnetic waves without negative refraction. In this comment, we argue that the unlimited resolution is an artifact of having introduced an unphysical drain at the position of the geometrical image. The correct solution gives focusing consistent with the standard diffraction limit.

  18. Hawking radiation from Garfinkle-Horowitz-Strominger and nonextremal D1-D5 black holes via covariant anomalies

    NASA Astrophysics Data System (ADS)

    Gangopadhyay, Sunandan; Kulkarni, Shailesh

    2008-01-01

    We apply the method of Banerjee and Kulkarni [R. Banerjee and S. Kulkarni, Phys. Rev. D 77, 024018 (2008).PRVDAQ0556-282110.1103/PhysRevD.77.024018] to provide a derivation of Hawking radiation from the Garfinkle-Horowitz-Strominger (stringy) black hole which falls in the class of the most general spherically symmetric black holes (-g≠1) and also the nonextremal D1-D5 black hole using only covariant gravitational anomalies.

  19. Proposed bell experiment with genuine energy-time entanglement.

    PubMed

    Cabello, Adán; Rossi, Alessandro; Vallone, Giuseppe; De Martini, Francesco; Mataloni, Paolo

    2009-01-30

    Franson's Bell experiment with energy-time entanglement [Phys. Rev. Lett. 62, 2205 (1989)10.1103/PhysRevLett.62.2205] does not rule out all local hidden variable models. This defect can be exploited to compromise the security of Bell inequality-based quantum cryptography. We introduce a novel Bell experiment using genuine energy-time entanglement, based on a novel interferometer, which rules out all local hidden variable models. The scheme is feasible with actual technology. PMID:19257405

  20. Quantum walks, deformed relativity and Hopf algebra symmetries.

    PubMed

    Bisio, Alessandro; D'Ariano, Giacomo Mauro; Perinotti, Paolo

    2016-05-28

    We show how the Weyl quantum walk derived from principles in D'Ariano & Perinotti (D'Ariano & Perinotti 2014Phys. Rev. A90, 062106. (doi:10.1103/PhysRevA.90.062106)), enjoying a nonlinear Lorentz symmetry of dynamics, allows one to introduce Hopf algebras for position and momentum of the emerging particle. We focus on two special models of Hopf algebras-the usual Poincaré and theκ-Poincaré algebras.

  1. Kitaev's Zd-code threshold estimates

    NASA Astrophysics Data System (ADS)

    Duclos-Cianci, Guillaume; Poulin, David

    2013-06-01

    We study the quantum error correction threshold of Kitaev's toric code over the group Zd subject to a generalized bit-flip noise. This problem requires special decoding techniques, and for this purpose we generalize the renormalization-group method we introduced previously [G. Duclos-Cianci and D. Poulin, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.104.050504 104, 050504 (2010) and IEEE Information Theory Workshop, Dublin (2010), p. 1] for Z2 topological codes.

  2. Reply to Analysis of the lifetimes and fractions of antiprotons trapped in metastable states of antiprotonic helium''

    SciTech Connect

    Yamazaki, T. ); Ohtsuki, K. )

    1994-12-01

    Shimamura and Kimura have submitted the preceding Comment [Phys. Rev. A 50, 5346 (1994)], (to be referred to as SK), which criticizes our recent paper [T. Yamazaki and K. Ohtsuki, Phys. Rev. A 45, 7782 (1992)] (to be referred to as YO). In this Reply the authors clarify the purpose of YO and complement its essential points, thus showing that the criticisms of SK are inappropriate.

  3. Comment on "Nonclassicality indicator for the real phase-space distribution functions"

    NASA Astrophysics Data System (ADS)

    Kenfack, Anatole

    2016-03-01

    We show in this Comment that the nonclassicality indicator proposed in Sadeghi et al. [Phys. Rev. A 82, 012102 (2010), 10.1103/PhysRevA.82.012102] is controversial. Defined in terms of the interferences displayed by the quasidistribution function of at least two superposition states, this indicator may logically lead to zero for any single quantum state irrespective to its nonclassicality, in contradiction with their results.

  4. A pointwise estimate for fractionary derivatives with applications to partial differential equations.

    PubMed

    Cordoba, Antonio; Cordoba, Diego

    2003-12-23

    This article emphasizes the role played by a remarkable pointwise inequality satisfied by fractionary derivatives in order to obtain maximum principles and Lp-decay of solutions of several interesting partial differential equations. In particular, there are applications to quasigeostrophic flows, in two space variables with critical viscosity, that model the Eckman pumping [see Baroud, Ch. N., Plapp, B. B., She, Z. S. & Swinney, H. L. (2002) Phys. Rev. Lett. 88, 114501 and Constantin, P. (2002) Phys. Rev. Lett. 89, 184501].

  5. Comment on "Third law of thermodynamics as a key test of generalized entropies"

    NASA Astrophysics Data System (ADS)

    Bagci, G. Baris; Oikonomou, Thomas

    2015-07-01

    Bento et al. [Phys. Rev. E 91, 022105 (2015), 10.1103/PhysRevE.91.022105] state that the Tsallis entropy violates the third law of thermodynamics for q ≤0 and 0

  6. Convex polytopes and quantum separability

    NASA Astrophysics Data System (ADS)

    Holik, F.; Plastino, A.

    2011-12-01

    We advance a perspective of the entanglement issue that appeals to the Schlienz-Mahler measure [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.52.4396 52, 4396 (1995)]. Related to it, we propose a criterium based on the consideration of convex subsets of quantum states. This criterium generalizes a property of product states to convex subsets (of the set of quantum states) that is able to uncover an interesting geometrical property of the separability property.

  7. Quantum walks, deformed relativity and Hopf algebra symmetries.

    PubMed

    Bisio, Alessandro; D'Ariano, Giacomo Mauro; Perinotti, Paolo

    2016-05-28

    We show how the Weyl quantum walk derived from principles in D'Ariano & Perinotti (D'Ariano & Perinotti 2014Phys. Rev. A90, 062106. (doi:10.1103/PhysRevA.90.062106)), enjoying a nonlinear Lorentz symmetry of dynamics, allows one to introduce Hopf algebras for position and momentum of the emerging particle. We focus on two special models of Hopf algebras-the usual Poincaré and theκ-Poincaré algebras. PMID:27091171

  8. Two-player quantum pseudotelepathy based on recent all-versus-nothing violations of local realism

    SciTech Connect

    Cabello, Adan

    2006-02-15

    We introduce two two-player quantum pseudotelepathy games based on two recently proposed all-versus-nothing (AVN) proofs of Bell's theorem [A. Cabello, Phys. Rev. Lett. 95, 210401 (2005); Phys. Rev. A 72, 050101(R) (2005)]. These games prove that Broadbent and Methot's claim that these AVN proofs do not rule out local-hidden-variable theories in which it is possible to exchange unlimited information inside the same light cone (quant-ph/0511047) is incorrect.

  9. Differential cross sections of double photoionization of lithium

    SciTech Connect

    Kheifets, A. S.; Fursa, D. V.; Bray, I.; Colgan, J.; Pindzola, M. S.

    2010-08-15

    We extend our previous application of the convergent close-coupling (CCC) and time-dependent close-coupling (TDCC) methods [Phys. Rev. A 81, 023418 (2010)] to describe energy and angular resolved double photoionization (DPI) of lithium at arbitrary energy sharing. By doing so, we are able to evaluate the recoil ion momentum distribution of DPI of Li and make a comparison with recent measurements of Zhu et al. [Phys. Rev. Lett. 103, 103008 (2009)].

  10. Reply to "Comment on "'Theoretical analysis of the force on the end face of a nanofilament exerted by an outgoing light pulse'"

    NASA Astrophysics Data System (ADS)

    Mansuripur, Masud; Zakharian, Armis R.

    2014-05-01

    We respond to a Comment on our paper [Phys. Rev. A 80, 023823 (2009), 10.1103/PhysRevA.80.023823], which appears to have stemmed from a misunderstanding of the various energy-momentum tensors of classical electrodynamics. It is shown that each stress tensor, when used in conjunction with the corresponding force-density and momentum-density expressions, yields results that are consistent with Maxwell's equations and with the conservation laws.

  11. Comment on "Bit-string oblivious transfer based on quantum state computational distinguishability"

    NASA Astrophysics Data System (ADS)

    He, Guang Ping

    2015-10-01

    We show that in the protocol proposed in Phys. Rev. A 91, 042306 (2015), 10.1103/PhysRevA.91.042306, a dishonest sender can always ensure with certainty that the receiver fails to get the secret message. Thus the security requirement of oblivious transfer is not met. This security problem also makes the protocol unsuitable for serving as a building block for 1-out-of-2 oblivious transfer.

  12. Introducing the Pietarinen expansion method into the single-channel pole extraction problem

    NASA Astrophysics Data System (ADS)

    Švarc, Alfred; Hadžimehmedović, Mirza; Osmanović, Hedim; Stahov, Jugoslav; Tiator, Lothar; Workman, Ron L.

    2013-09-01

    We present a new approach to quantifying pole parameters of single-channel processes based on a Laurent expansion of partial-wave T matrices in the vicinity of the real axis. Instead of using the conventional power-series description of the nonsingular part of the Laurent expansion, we represent this part by a convergent series of Pietarinen functions. As the analytic structure of the nonsingular part is usually very well known (physical cuts with branch points at inelastic thresholds, and unphysical cuts in the negative energy plane), we find that one Pietarinen series per cut represents the analytic structure fairly reliably. The number of terms in each Pietarinen series is determined by the quality of the fit. The method is tested in two ways: on a toy model constructed from two known poles, various background terms, and two physical cuts, and on several sets of realistic πN elastic energy-dependent partial-wave amplitudes (GWU/SAID [Arndt , Phys. Rev. CPRVCAN0556-281310.1103/PhysRevC.74.045205 74, 045205 (2006); Workman , Phys. Rev. CPRVCAN0556-281310.1103/PhysRevC.86.035202 86, 035202 (2012)], and Dubna-Mainz-Taipei [Chen , Phys. Rev. CPRVCAN0556-281310.1103/PhysRevC.76.035206 76, 035206 (2007); Tiator , Phys. Rev. CPRVCAN0556-281310.1103/PhysRevC.82.055203 82, 055203 (2010)]). We show that the method is robust and confident using up to three Pietarinen series, and is particularly convenient in fits to amplitudes, such as single-energy solutions, coming more directly from experiment: cases where the analytic structure of the regular part is a priori unknown.

  13. Critical-current diffraction pattern of annular Josephson junctions

    NASA Astrophysics Data System (ADS)

    Nappi, Ciro

    1997-01-01

    A derivation of the exact analytical expressions for the critical current versus magnetic-field-diffraction pattern of ``electrically'' small annular Josephson junctions is presented. These formulas have been recently used to fit experimental data [N. Martucciello and R. Monaco, Phys. Rev. B 54, 9050 (1996)]. They include, as a special case, the approximate analytical results previously published [N. Martucciello and R. Monaco, Phys. Rev. B 53 3471 (1996)].

  14. Comment on {open_quotes}Experimental Fusion Barrier Distributions Reflecting Projectile Octupole State Coupling to Prolate and Oblate Target Nuclei{close_quotes}

    SciTech Connect

    Dasso, C.H.; Dasso, C.H.; Fernandez-Niello, J.

    1997-05-01

    The authors comment on the Letter by J.D. Bierman et al., Phys. Rev. Lett. 76, 1587(1996), and show the method by which they have been constructed is not the most appropriate. A Comment on the Letter by J.D. Bierman, {ital et al. }, Phys.Rev.Lett.{bold 76}, 1587 (1996). The authors of the Letter offer a Reply. {copyright} {ital 1997} {ital The American Physical Society}

  15. Time delay in photoionization near Cooper minima

    NASA Astrophysics Data System (ADS)

    Jose, Jobin; Kannur, Sindhu; Kumar, Ashish; Varma, Hari R.; Deshmukh, Pranawa C.; Manson, Steven T.

    2012-06-01

    The connection between the energy dependence of the scattering phase shift and time delay is known [1]. With the developments of techniques in attosecond physics, it has become possible to measure the time delay between photoemission from different subshells [2, 3]. There have been several nonrelativistic calculations of the time delay between photoelectrons from different subshells [4, 5] that confirmed the need to include many-electron correlations. In the present work, the RRPA [6], which includes both relativity and many of the important electron correlation effects, is employed to calculate the time delay between photoelectrons from the valance ns, np3/2 and np1/2 subshells of noble gas atoms in the dipole approximation, and particularly dramatic variations occur in the vicinity of Cooper minimum [7] owing to the rapid variation of the scattering phase shift in the vicinity of Cooper minima, including effects that occur only due to relativistic splittings. These effects appear to be amenable to experimental investigation.[4pt] [1] E. P. Wigner, Phys. Rev. 98, 145 (1955). [2] M. Schultze et al, Science 328, 1658 (2010). [3] K. Klunder et al, Phys. Rev. Lett. 106, 143002 (2011). [4] A. S. Kheifets and I. A. Ivanov, Phys. Rev. Lett. 105, 233002 (2010). [5] C. H. Zhang and U. Thumm, Phys. Rev. A 82, 043405 (2010). [6] W. R. Johnson and C. D. Lin, Phys. Rev. A 20, 964 (1979). [7] J. W. Cooper, Phys. Rev. 128, 681 (1962).

  16. Reply to "Comment on 'Origin of tilted-phase generation in systems of ellipsoidal molecules with dipolar interactions' "

    NASA Astrophysics Data System (ADS)

    Bose, Tushar Kanti; Saha, Jayashree

    2014-04-01

    In a recent article [T. K. Bose and J. Saha, Phys. Rev. E 86, 050701 (2012), 10.1103/PhysRevE.86.050701], we have presented the results of a Monte Carlo simulation study of the systems of dipolar Gay-Berne ellipsoids where two terminal antiparallel dipoles are placed symmetrically on the long axis of each ellipsoid, and the results revealed the combined contribution of dipolar separation and transverse orientations in controlling the tilt angle in the tilted hexatic smectic phase. The tilt angle changed from zero to a significant value, in the case of transverse dipoles, with a change in the dipolar separation. In the related comment, Madhusudana [preceding Comment, Phys. Rev. E 89, 046501 (2014), 10.1103/PhysRevE.89.046501] has claimed that the physical origin of the molecular tilt in the significantly tilted phases found in the simulations is similar to that proposed by McMillan [Phys. Rev. A 8, 1921 (1973), 10.1103/PhysRevA.8.1921]. Here, we explain that the claim is not correct and make it clear that the two compared pictures are quite different. In the preceding Comment, Madhusudana has also suggested an alternative explanation for tilt generation in the simulations by criticizing the original one proposed by us. We argue here in support of the original explanation and clarify that his explanation does not follow the simulation results.

  17. How to upload a physical quantum state into correlation space

    NASA Astrophysics Data System (ADS)

    Morimae, Tomoyuki

    2011-04-01

    In the framework of the computational tensor network [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.98.220503 98, 220503 (2007)], the quantum computation is performed in a virtual linear space called the correlation space. It was recently shown [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.103.050503 103, 050503 (2009)] that a state in a correlation space can be downloaded to the real physical space. In this paper, conversely, we study how to upload a state from a real physical space to the correlation space. After showing the impossibility of cloning a state between a real physical space and the correlation space, we propose a simple teleportation-like method of uploading. This method also enables the Gottesman-Chuang gate teleportation trick and entanglement swapping in the virtual-real hybrid setting. Furthermore, compared with the inverse of the downloading method by Cai [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.103.050503 103, 050503 (2009)], which also works to upload, the proposed uploading method has several advantages.

  18. Response of quark condensate to the chemical potential

    NASA Astrophysics Data System (ADS)

    Jiang, Yu; Zhang, Yan-Bin; Sun, Wei-Min; Zong, Hong-Shi

    2008-07-01

    In this paper we propose a new method for calculating the response of the quark condensate to the chemical potential. Based on the method of calculating the dressed-quark propagator at finite chemical potential in the framework of the rainbow-ladder approximation of the Dyson-Schwinger approach proposed in [H. S. Zong, L. Chang, F. Y. Hou, W. M. Sun, and Y. X. Liu, Phys. Rev. C 71, 015205 (2005).PRVCAN0556-281310.1103/PhysRevC.71.015205] and adopting the meromorphic form of the quark propagator given in [R. Alkofer, W. Detmold, C. S. Fischer, and P. Maris, Phys. Rev. D 70, 014014 (2004).PRVDAQ0556-282110.1103/PhysRevD.70.014014][M. S. Bhagwat, M. A. Pichowsky, and P. C. Tandy, Phys. Rev. D 67, 054019 (2003).PRVDAQ0556-282110.1103/PhysRevD.67.054019], the quark condensate at finite chemical potential ⟨ qmacr q⟩[μ] is calculated analytically. The obtained expression for ⟨ qmacr q⟩[μ] is real, which is different from the results in the previous literature. In addition, it is found that when the chemical potential μ is less than a critical one ⟨ qmacr q⟩[μ] is kept unchanged from its vacuum value. A comparison is made between this behavior of the quark condensate and those reported in the previous literatures.

  19. Weak measurement combined with quantum delayed-choice experiment and implementation in optomechanical system

    NASA Astrophysics Data System (ADS)

    Li, Gang; Wang, Tao; Ye, Ming-Yong; Song, He-Shan

    2015-12-01

    Weak measurement [Y. Aharonov, D.Z. Albert, L. Vaidman, Phys. Rev. Lett. 60, 1351 (1988); C. Simon, E.S. Polzik, Phys. Rev. A 83, 040101(R) (2011)] combined with quantum delayed-choice experiment that use Controlled Hadamard gate instead of Hadamard gate in quantum networks give rise to a surprising amplification effect, i.e., counterintuitive negative amplification effect. We show that this effect is caused by the wave and particle behaviours of the system, and it can't be explained by a semiclassical wave theory [D. Suter, Phys. Rev. A 51, 45 (1995); J.C. Howell, D.J. Starling, P.B. Dixon, P.K. Vudyasetu, A.N. Jordan, Phys. Rev. A 81, 033813 (2010); N. Brunner, A. Acín, D. Collins, N. Gisin, V. Scarani, Phys. Rev. Lett. 91, 180402 (2003)] and by the statistical feature of preselection and postselection with disturbance [C. Ferrie, J. Combes, Phys. Rev. Lett. 113, 120404 (2014)], due to the entanglement of the system and the ancilla in Controlled Hadamard gate. The generation mechanism with wave-particle duality in quantum mechanics lead us to a scheme for implementation of weak measurement in optomechanical system.

  20. Spin squeezing a cold molecule

    NASA Astrophysics Data System (ADS)

    Bhattacharya, M.

    2015-12-01

    In this article we present a concrete proposal for spin squeezing the cold ground-state polar paramagnetic molecule OH, a system currently under fine control in the laboratory. In contrast to existing work, we consider a single, noninteracting molecule with angular momentum greater than 1 /2 . Starting from an experimentally relevant effective Hamiltonian, we identify an adiabatic regime where different combinations of static electric and magnetic fields can be used to realize the single-axis twisting Hamiltonian of Kitagawa and Ueda [M. Kitagawa and M. Ueda, Phys. Rev. A 47, 5138 (1993), 10.1103/PhysRevA.47.5138], the uniform field Hamiltonian proposed by Law et al. [C. K. Law, H. T. Ng, and P. T. Leung, Phys. Rev. A 63, 055601 (2001), 10.1103/PhysRevA.63.055601], and a model of field propagation in a Kerr medium considered by Agarwal and Puri [G. S. Agarwal and R. R. Puri, Phys. Rev. A 39, 2969 (1989), 10.1103/PhysRevA.39.2969]. We then consider the situation in which nonadiabatic effects are quite large and show that the effective Hamiltonian supports spin squeezing even in this case. We provide analytical expressions as well as numerical calculations, including optimization of field strengths and accounting for the effects of field misalignment. Our results have consequences for applications such as precision spectroscopy, techniques such as magnetometry, and stereochemical effects such as the orientation-to-alignment transition.

  1. Multistage Zeeman deceleration

    NASA Astrophysics Data System (ADS)

    Wiederkehr, A. W.; Hogan, S. D.; Andrist, M.; Schmutz, H.; Lambilotte, B.; Merkt, F.

    2009-05-01

    In recent years multistage Zeeman deceleration of open shell atoms and molecules has been developed as a possible method to produce cold (< 1 K) samples for applications in precision spectroscopy and studies of cold reactive collisions [1-7]. This contribution will present the strategy followed at ETH Zurich which relies on (i) the generation of strong magnetic field pulses (> 2 T) with rise and fall times of only a few microseconds, (ii) the deceleration and loading of samples into quadrupole magnetic traps, (iii) 3D particle trajectory simulations of the complete deceleration and trapping processes, and (iv) comparison of the simulations with measurements of the velocity and spatial distributions of the decelerated and trapped samples. The four generations of Zeeman deceleration and trapping devices developed in our group will be presented and compared using results obtained with different samples. [0pt] [1] N. Vanhaecke et al., Phys. Rev. A 75, 031402(R)(2007).[0pt] [2] S. D. Hogan et al., Phys. Rev. A 76, 023412 (2007).[0pt] [3] E. Narevicius et al., New. J. Phys. 9, 358 (2007).[0pt] [4] E. Narevicius et al., Phys. Rev. Lett. 100, 093003 (2008).[0pt] [5] E. Narevicius et al., Phys. Rev. A 77, 051401(R) (2008).[0pt] [6] S. D. Hogan et al., J. Phys. B 41, 081005 (2008).[0pt] [7] S. D. Hogan et al., Phys. Rev. Lett. 101, 143001 (2008).

  2. FINAL REPORT MELTER TESTS WITH AZ-101 HLW SIMULANT USING A DURAMELTER 100 VITRIFICATION SYSTEM VSL-01R10N0-1 REV 1 2/25/02

    SciTech Connect

    KRUGER AA; MATLACK KS; KOT WK; PEGG IL

    2011-12-29

    heat transfer in rate attainment and the much greater role of wall effects in heat transfer when the melt pool is not agitated. The DM100 melter used for the present tests has a surface area of 0.108 m{sup 2}, which is approximately 5 times larger than that of the DM10 (0.021 m{sup 2}) and approximately 11 times smaller than that of the DM1000 (1.2 m{sup 2}) (the DM1000 has since been replaced by a pilot-scale prototypical HLW melter, designated the DM1200, which has the same surface area as the DM1000). Testing on smaller melters is the most economical method for obtaining data over a wide range of operating conditions (particularly at extremes) and for guiding the more expensive tests that are performed at pilot-scale. Thus, one objective of these tests was to determine whether the DM100 melters are sufficiently large to reproduce the un-bubbled melt rates observed at the DM1000 scale, or to determine the extent of any off-set. DM100-scale tests can then be used to screen feed chemistry variations that may serve to increase the un-bubbled production rates prior to confirmation at pilot scale. Finally, extensive characterization data obtained on simulated HLW melter feeds formed from various glass forming additives indicated that there may be advantages in terms of feed rheology and stability to the replacement of some of the hydroxides by carbonates. A further objective of the present tests was therefore to identify any deleterious processing effects of such a change before adopting the carbonate feed as the baseline. Data from the WVDP melter using acidified (nitrated) feeds, and without bubbling, showed productions rates that are higher than those observed with the alkaline RPP feeds at the VSL. Therefore, the effect of feed acidification on production rate also was investigated. This work was performed under Test Specification, 'TSP-W375-00-00019, Rev 0, 'HLW-DM10 and DM100 Melter Tests' dated November 13, 2000 and the corresponding Test Plan. It should be noted

  3. Characterizing the Gender Gap in Introductory Physics

    ERIC Educational Resources Information Center

    Kost, Lauren E.; Pollock, Steven J.; Finkelstein, Noah D.

    2009-01-01

    Previous research [S. J. Pollock et al., Phys. Rev. ST Phys. Educ. Res. 3, 1 (2007)] showed that despite the use of interactive engagement techniques, the gap in performance between males and females on a conceptual learning survey persisted from pretest to post-test at the University of Colorado at Boulder. Such findings were counter to…

  4. Effects of Representation on Students Solving Physics Problems: A Fine-Grained Characterization

    ERIC Educational Resources Information Center

    Kohl, Patrick B.; Finkelstein, Noah D.

    2006-01-01

    Recent papers document that student problem-solving competence varies (often strongly) with representational format, and that there are significant differences between the effects that traditional and reform-based instructional environments have on these competences [Kohl and Finkelstein, Phys. Rev. ST Phys. Educ. Res. 1, 010104 (2005); Kohl and…

  5. Effect of Instructional Environment on Physics Students' Representational Skills

    ERIC Educational Resources Information Center

    Kohl, Patrick B.; Finkelstein, Noah D.

    2006-01-01

    In a recent study we showed that physics students' problem-solving performance can depend strongly on problem representation, and that giving students a choice of problem representation can have a significant impact on their performance [ P. B. Kohl and N. D. Finklestein, Phys. Rev. ST. Phys. Educ. Res. 1, 010104 (2005) ] In this paper, we…

  6. Gender Disparities in Second-Semester College Physics: The Incremental Effects of a "Smog of Bias"

    ERIC Educational Resources Information Center

    Kost-Smith, Lauren E.; Pollock, Steven J.; Finkelstein, Noah D.

    2010-01-01

    Our previous research [Kost et al., Phys. Rev. ST Phys. Educ. Res. 5, 010101 (2009)] examined gender differences in the first-semester, introductory physics class at the University of Colorado at Boulder. We found that: (1) there were gender differences in several aspects of the course, including conceptual survey performance, (2) these…

  7. Capacitance of a quantum dot from the channel-anisotropic two-channel Kondo model

    NASA Astrophysics Data System (ADS)

    Le Hur, Karyn; Seelig, Georg

    2002-04-01

    We investigate the charge fluctuations of a large quantum dot coupled to a two-dimensional electron gas via a quantum point contact following the work of Matveev [K. A. Matveev, Phys. Rev. B 51, 1743 (1995); Z. Éksp. Teor. Fiz. 98, 1598 (1990) [Sov. Phys. JETP 72, 892 (1991)

  8. Analogical Scaffolding and the Learning of Abstract Ideas in Physics: Empirical Studies

    ERIC Educational Resources Information Center

    Podolefsky, Noah S.; Finkelstein, Noah D.

    2007-01-01

    Previously, we proposed a model of student reasoning which combines the roles of representation, analogy, and layering of meaning--analogical scaffolding [Podolefsky and Finkelstein, Phys. Rev. ST Phys. Educ. Res. 3, 010109 (2007)]. The present empirical studies build on this model to examine its utility and demonstrate the vital intertwining of…

  9. Comment on 'Quantum teleportation of an arbitrary two-qubit state and its relation to multipartite entanglement'

    SciTech Connect

    Deng Fuguo

    2005-09-15

    The multipartite state in the Rigolin's protocol [Phys. Rev. A 71, 032303 (2005)] for teleporting an arbitrary two-qubit state is just a product state of N Einstein-Podolsky-Rosen pairs in essence, not a genuine multipartite entangled state, and this protocol in principle is equivalent to the Yang-Guo protocol [Chin. Phys. Lett. 17, 162 (2000)].

  10. Interpretation of the I-Regime and transport associated with relevant heavy particle modes

    SciTech Connect

    Coppi, B.; Zhou, T.

    2012-01-15

    The excitation of a novel kind of heavy particle [B. Coppi et al., Phys. Rev. Lett. 17, 377 (1966); B. Coppi and T. Zhou, MIT(LNS) Report HEP 09/04, 2009, Cambridge, MA [Phys. Lett. A 375, 2916 (2011)

  11. A Charged Particle in a Magnetic Field: A Review of Two Formalisms of Coherent States and the Husimi Function

    ERIC Educational Resources Information Center

    Herrera, D.; Valencia, A. M.; Pennini, F.; Curilef, S.

    2008-01-01

    In this work, we review two formalisms of coherent states for the case of a particle in a magnetic field. We focus our revision on both pioneering (Feldman and Kahn 1970 "Phys. Rev." B 1 4584) and recent (Kowalski and Rembielinski 2005 "J. Phys. A: Math. Gen." 38 8247) formulations of coherent states for this problem. We introduce a general…

  12. Erratum: Raman linewidths and rotationally inelastic collision rates in nitrogen [J. Chem. Phys. 98, 257 (1993)

    NASA Astrophysics Data System (ADS)

    Green, Sheldon

    1993-09-01

    A computer program error led to erroneous results in the titled paper. Corrected generalized IOS cross sections are significantly changed, especially at lower collision energies. These changes tend to cancel in predicted Raman linewidths; there is a systematic increase of 10-15 %, changing quantitative, but not qualitative, comparisons with experimental data.

  13. Addendum to "Updating neutrino magnetic moment constraints" [Phys. Lett. B 753 (2016) 191-198

    NASA Astrophysics Data System (ADS)

    Cañas, B. C.; Miranda, O. G.; Parada, A.; Tórtola, M.; Valle, J. W. F.

    2016-06-01

    After the publication of this work we noticed that the uncertainties in the considered backgrounds in Borexino may affect our reported limit on the neutrino magnetic moment from Borexino data. Indeed, we have found that a more precise treatment of the uncertainties in the total normalization of these backgrounds results in a weaker sensitivity on the neutrino magnetic moment. This point will be hopefully improved in the near future thanks to the purification processes carried out in the second phase of the Borexino experiment. Meanwhile, however, we think it would be more reliable to adopt the bound on the neutrino magnetic moment reported by Borexino: μν < 5.4 ×10-11μB[1].

  14. Physical fitness training in Subacute Stroke (PHYS-STROKE) - study protocol for a randomised controlled trial

    PubMed Central

    2014-01-01

    Background Given the rising number of strokes worldwide, and the large number of individuals left with disabilities after stroke, novel strategies to reduce disability, increase functions in the motor and the cognitive domains, and improve quality of life are of major importance. Physical activity is a promising intervention to address these challenges but, as yet, there is no study demonstrating definite outcomes. Our objective is to assess whether additional treatment in the form of physical fitness-based training for patients early after stroke will provide benefits in terms of functional outcomes, in particular gait speed and the Barthel Index (co-primary outcome measures) reflecting activities of daily living (ADL). We will gather secondary functional outcomes as well as mechanistic parameters in an exploratory approach. Methods/Design Our phase III randomised controlled trial will recruit 215 adults with moderate to severe limitations of walking and ADL 5 to 45 days after stroke onset. Participants will be stratified for the prognostic variables of “centre”, “age”, and “stroke severity”, and randomly assigned to one of two groups. The interventional group receives physical fitness training delivered as supported or unsupported treadmill training (cardiovascular active aerobic training; five times per week, over 4 weeks; each session 50 minutes; total of 20 additional physical fitness training sessions) in addition to standard rehabilitation treatment. The control intervention consists of relaxation sessions (non-cardiovascular active; five times per week week, over 4 weeks; each session 50 minutes) in addition to standard rehabilitation treatment. Co-primary efficacy endpoints will be gait speed (in m/s, 10 m walk) and the Barthel Index (100 points total) at 3 months post-stroke, compared to baseline measurements. Secondary outcomes include standard measures of quality of life, sleep and mood, cognition, arm function, maximal oxygen uptake, and cardiovascular risk factors including blood pressure, pulse, waist-to-hip ratio, markers of inflammation, immunity and the insulin-glucose pathway, lipid profile, and others. Discussion The goal of this endpoint-blinded, phase III randomised controlled trial is to provide evidence to guide post-stroke physical fitness-based rehabilitation programmes, and to elucidate the mechanisms underlying this intervention. Trial registration Registered in ClinicalTrials.gov with the Identifier NCT01953549. PMID:24491065

  15. Post PhysTEC at Arkansas, Graduation Numbers Stable, Student Enthusiasm High

    NASA Astrophysics Data System (ADS)

    Stewart, Gay

    2011-04-01

    At the University of Arkansas in Fayetteville, active learning in the content coursework has been key to the recruitment of MAJORS and TEACHERS. We have supported the process through the use of apprentice teachers, one learning assistant model. Master teachers have also aided in the recruitment, and true partnerships with local schools have allowed us to provide improved support to our graduates through the induction years. The topics of this talk will be how did we create these programs and how did we institutionalize them? Funded in part by the National Science Foundation

  16. The New Phys Ed.: Dodgeball Is Passe; Schools Are Teaching Lifelong Fitness

    ERIC Educational Resources Information Center

    Schachter, Ron

    2011-01-01

    A growing number of physical education teachers are introducing a new kind of P.E. in schools, emphasizing lifelong activities such as running, cycling, yoga, and skateboarding, in an attempt to make exercise more engaging--and lifelong--for elementary and middle school students. The new generation of P.E. classes is introducing youngsters to…

  17. Erratum: ``The 1989 James Clerk Maxwell Prize in Plasma Physics'' [Phys. Fluids B 2, 233 (1990)

    NASA Astrophysics Data System (ADS)

    1990-09-01

    As the result of an error in editing the third sentence in Ravindra Nath Sudan's biography should read: In 1984-1985 he helped Ken Wilson found the Cornell Center for Theory and Simulation, which was funded by the National Science Foundation and IBM Corporation.

  18. Sustainable and Scalable Reforms in Physics Education: Research studies from Colorado PhysTEC

    NASA Astrophysics Data System (ADS)

    Finkelstein, Noah

    2006-03-01

    and STEVEN POLLOCK University of Colorado at Boulder -- While many practices developed within the physics education research community have been demonstrated as successful, they respond to calls and employ practices that echo efforts from the early part of the 20th Century. Are we bound to the same limited success as these precursors? We examine what it means to replicate proven reforms and to develop models for sustainable implementation of these reforms. As part of the Colorado Physics Teacher Education Coalition, we have implemented the Tutorials in Introductory Physics, which were developed by researchers at the University of Washington. We present research on the successful implementation of these reforms at the University of Colorado and begin to answer the questions: What does it mean to replicate an educational program? and How might these educational transformations be sustained? We present empirical data on the success of reforms and the fidelity of implementation as well as theoretical frames for analyzing these data. We also present a model (the Learning Assistant program) designed for sustaining these reforms and for increasing student interest and retention in teaching.

  19. Response to ``Comment on `The swimming of animalcules''' [Phys. Fluids 19, 079101 (2007)

    NASA Astrophysics Data System (ADS)

    Felderhof, B. U.

    2007-07-01

    The proof of the statement that a two-bead structure with constant mobilities cannot swim is incorrect. A general expression for the swimming velocity of a two-bead structure with given periodic relative motion is derived in the form of a line integral. The net torque exerted on the fluid is also expressed as a line integral. It is shown that in the example given by Friedman a net torque is exerted on the fluid. Therefore it is not acceptable as a swimming motion. A more complicated periodic relative motion is constructed for which the net torque vanishes, but which leads to a nonvanishing swimming velocity. A dynamical formulation appears to restrict the possibility of swimming.

  20. The oscillation modes of large-scale circulation in turbulent Rayleigh-Bénard convection

    NASA Astrophysics Data System (ADS)

    Ji, Dandan; Bai, Kunlun; Brown, Eric

    2014-11-01

    We present measurement of the large-scale circulation (LSC) of turbulent Rayleigh-Bénard convection of cubic cell. We found the reorientation events by rotation through the LSC orientation θ0 with a multi-peaked probability distribution p (θ0) , as predicted by the model presented by Brown and Ahlers (Phys. Fluids, 2008). In contrast to the results of oscillation modes in cylindrical cell, when the LSC was confined into one corner, the flow didn't exhibit the twisting and sloshing oscillation with a well-defined periodicity. The phase relation of θ0 at different heights in the cell was not fixed, so LSC was not in a plane. The sloshing displacement of the LSC from a center plane exhibited random switching between two states.

  1. A low-dimensional model for large-scale coherent structures

    NASA Astrophysics Data System (ADS)

    Bai, Kunlun; Ji, Dandan; Brown, Eric

    2015-11-01

    We demonstrate a methodology to predict the dynamics of the large-scale coherent structures in turbulence using a simple low dimensional stochastic model proposed by Brown and Ahlers (Phys. Fluids, 2008). The model terms are derived from the Navier-Stokes equations, including a potential term depending on the geometry of the system. The model has previously described several dynamical modes of the large-scale circulation (LSC) in turbulent Rayleigh-Bénard convection. Here we test a model prediction for the existence of a new mode where the LSC stochastically changes direction to align with different diagonals of a cubic container. The model successfully predicts the switching rate of the LSC at different tilting conditions. The success of the prediction of the switching mode demonstrates that a low-dimensional turbulent model can quantitatively predict the existence and properties of different dynamical states that result from boundary geometry.

  2. Phase-field crystal approach for modeling the role of microstructure in multiferroic composite materials

    NASA Astrophysics Data System (ADS)

    Seymour, Matthew; Sanches, F.; Elder, Ken; Provatas, Nikolas

    2015-11-01

    This paper introduces a phase-field crystal (PFC) approach that couples the atomic-scale PFC density field to order parameters describing ferromagnetic and ferroelectric ordering, as well to a solute impurity field. This model extends the magnetic PFC model introduced by Faghihi et al. [N. Faghihi, Ph.D. Thesis, The University of Western Ontario, 2012; N. Faghihi, N. Provatas, K. R. Elder, M. Grant, and M. Karttunen, Phys. Rev. E 88, 032407 (2013), 10.1103/PhysRevE.88.032407] to incorporate polarization and concentration fields, as well as anisotropic ordering of the magnetization and polarization fields as determined by the local crystalline orientation. Magnetoelectric coupling is incorporated through the elastic coupling. Analytic calculations for a body centered-cubic (BCC) system are presented to illustrate that the model reduces to the standard multiferroic phase-field models when only a single crystal is considered. Two special cases of the model are then studied, the first focusing on magnetocrystalline interactions in a system described by the two-point correlation function of the XPFC model developed by Greenwood et al. [M. Greenwood, N. Provatas, and J. Rottler, Phys. Rev. Lett. 105, 045702 (2010), 10.1103/PhysRevLett.105.045702; M. Greenwood, J. Rottler, and N. Provatas, Phys. Rev. E 83, 031601 (2011), 10.1103/PhysRevE.83.031601], and the second focusing on electrocrystalline interactions in a system described by the original PFC kernel developed by Elder et al. K. R. Elder, M. Katakowski, M. Haataja, and M. Grant, Phys. Rev. Lett. 88, 245701 (2002), 10.1103/PhysRevLett.88.245701; K. R. Elder and M. Grant, Phys. Rev. E 70, 051605 (2004), 10.1103/PhysRevE.70.051605]. We examine the small deformation properties of these two realizations of the model . Numerical simulations are performed to illustrate how magnetocrystalline coupling can be exploited to design a preferential grain texture and how defects and grain boundaries influence the ferroelectric

  3. Study of the Multiorbital Hubbard Model for the Fe-Superconductors Beyond Weak Coupling

    NASA Astrophysics Data System (ADS)

    Dagotto, Elbio

    2012-02-01

    A variety of experimental and theoretical investigations indicate that the pnictides and chalcogenides are materials with on-site Hubbard repulsion intermediate between weak coupling, where simple nesting ideas apply, and strong coupling where the spins are localized. For this reason, it is desirable to broaden the range of couplings theoretically studied as well as the many-body models and techniques employed. In this talk, an extensive analysis of model Hamiltonians for the Fe-based superconductors is presented. The multiorbital Hubbard models with two, three, and five orbitals are studied, via the Hartree-Fock approximation and exact diagonalization techniques. The main topics to be discussed are: magnetic ordering tendencies [1], range of realistic Hubbard repulsion and Hund couplings [2], orbital-weight redistribution at the Fermi surface and comparison with photoemission data [3], low-temperature transport properties [4], and competing pairing channels [5]. The possible magnetic states of the √5x√5 Fe-vacancy arrangement will also be presented [6]. The experimental reports of local moments at room temperature leads to our most recent efforts employing a three-orbital spin-fermion model, analyzed via Monte Carlo simulations, to study the temperature dependence of the (anisotropic) conductance [7]. It is concluded that considerable progress has been made in the understanding of these materials in spite of their difficult range of intermediate couplings. However, the existence of several open problems will also be discussed.[4pt] [1] R. Yu et al., Phys. Rev. B 79, 104510 (2009); A. Moreo et al., Phys. Rev. B 79, 134502 (2009).[0pt] [2] Q. Luo et al., Phys. Rev. B 82, 104508 (2010); A. Nicholson et al., Phys. Rev. B 84, 094519 (2011).[0pt] [3] M. Daghofer et al., Phys. Rev. B 81, 180514(R) (2010).[0pt] [4] X. Zhang and E. Dagotto, Phys. Rev. B 84, 132505 (2011). See also Q. Luo et al., Phys. Rev. B 83, 174513 (2011).[0pt] [5] A. Nicholson et al., Phys. Rev

  4. Chaotic density fluctuations in L-mode plasmas of the DIII-D tokamak

    NASA Astrophysics Data System (ADS)

    Maggs, J. E.; Rhodes, T. L.; Morales, G. J.

    2015-04-01

    Analysis of the time series obtained with the Doppler backscattering system (Hillsheim et al 2009 Rev. Sci. Instrum. 80 0835070) in the DIII-D tokamak (Luxon 2005 Fusion Sci. Technol. 48 828) shows that intermediate wave number plasma density fluctuations in low confinement (L-mode) tokamak plasmas are chaotic. The supporting evidence is based on the shape of the power spectrum; the location of the signal in the complexity-entropy plane (C-H plane) (Rosso et al 2007 Phys. Rev. Lett. 99 154102); and the population of the corresponding Bandt-Pompe (Bandt and Pompe 2002 Phys. Rev. Lett. 88 174102) probability distributions.

  5. Thermoelectric cooler concepts and the limit for maximum cooling

    NASA Astrophysics Data System (ADS)

    Seifert, W.; Pluschke, V.; Hinsche, N. F.

    2014-06-01

    The conventional analysis of a Peltier cooler approximates the material properties as independent of temperature using a constant properties model (CPM). Alternative concepts have been published by Bian and Shakouri (2006 Appl. Phys. Lett. 89 212101), Bian (et al 2007 Phys. Rev. B 75 245208) and Snyder et al (2012 Phys. Rev. B 86 045202). While Snyder's Thomson cooler concept results from a consideration of compatibility, the method of Bian et al focuses on the redistribution of heat. Thus, both approaches are based on different principles. In this paper we compare the new concepts to CPM and we reconsider the limit for maximum cooling. The results provide a new perspective on maximum cooling.

  6. Optimal Universal Uncertainty Relations

    PubMed Central

    Li, Tao; Xiao, Yunlong; Ma, Teng; Fei, Shao-Ming; Jing, Naihuan; Li-Jost, Xianqing; Wang, Zhi-Xi

    2016-01-01

    We study universal uncertainty relations and present a method called joint probability distribution diagram to improve the majorization bounds constructed independently in [Phys. Rev. Lett. 111, 230401 (2013)] and [J. Phys. A. 46, 272002 (2013)]. The results give rise to state independent uncertainty relations satisfied by any nonnegative Schur-concave functions. On the other hand, a remarkable recent result of entropic uncertainty relation is the direct-sum majorization relation. In this paper, we illustrate our bounds by showing how they provide a complement to that in [Phys. Rev. A. 89, 052115 (2014)]. PMID:27775010

  7. A Mathematical Learning Model Including Interactions among Different Learnings

    NASA Astrophysics Data System (ADS)

    Nariyuki, Yasuhiro; Yamaguchi, Norikazu

    2015-03-01

    The mathematical learning model reported by Nitta [PhysRevSTPER.6.020105">Phys. Rev. ST Phys. Educ. Res. 6, 020105 (2010)], which describes the transition from pre test score (fraction of the correct answer) to the post score, is extended to include interactions among different learnings. Numerical solutions of the model suggest that the effects of loss due to the different learnings possibly conceal interactive learnings from observational data.

  8. Shape profile of acoustic radiation-induced static displacement pulses in solids

    NASA Astrophysics Data System (ADS)

    Cantrell, John H.; Yost, William T.

    2010-07-01

    In a recent article Narasimha et al. [J. Appl. Phys. 105, 073506 (2009)] claim to show that the shape of static displacement pulses generated by ultrasonic tone-bursts in nondispersive solids is that of a growing trapezoid in the spatial domain that leads to a flat-topped pulse shape in the time domain for a fixed spatial position. Flaws in their theoretical arguments are corrected to show that their model actually predicts a right-triangular pulse shape for nondispersive monocrystals in both the spatial and time domains as originally reported by Yost and Cantrell [Phys. Rev. B 30, 3221 (1984)] and Cantrell et al. [Phys. Rev. B 35, 9780 (1987)].

  9. Thermometry and refrigeration in a two-component Mott insulator of ultracold atoms

    SciTech Connect

    Weld, David M.; Miyake, Hirokazu; Medley, Patrick; Pritchard, David E.; Ketterle, Wolfgang

    2010-11-15

    Interesting spin Hamiltonians can be realized with ultracold atoms in a two-component Mott insulator (2CMI) [Adv. Phys. 56, 243 (2007); Rev. Mod. Phys. 80, 885 (2008)]. It was recently demonstrated that the application of a magnetic field gradient to the 2CMI enables new techniques of thermometry [Phys. Rev. Lett. 103, 245301 (2009)] and adiabatic cooling [e-print arXiv:1006.4674]. Here we present a theoretical description which provides quantitative analysis of these two techniques. We show that adiabatic reduction of the field gradient is capable of cooling below the Curie or Neel temperature of certain spin-ordered phases.

  10. Exact coupling threshold for structural transition reveals diversified behaviors in interconnected networks

    NASA Astrophysics Data System (ADS)

    Darabi Sahneh, Faryad; Scoglio, Caterina; Van Mieghem, Piet

    2015-10-01

    An interconnected network features a structural transition between two regimes [F. Radicchi and A. Arenas, Nat. Phys. 9, 717 (2013), 10.1038/nphys2761]: one where the network components are structurally distinguishable and one where the interconnected network functions as a whole. Our exact solution for the coupling threshold uncovers network topologies with unexpected behaviors. Specifically, we show conditions that superdiffusion, introduced by Gómez et al. [Phys. Rev. Lett. 110, 028701 (2013), 10.1103/PhysRevLett.110.028701], can occur despite the network components functioning distinctly. Moreover, we find that components of certain interconnected network topologies are indistinguishable despite very weak coupling between them.

  11. Fundamental measure density functional theory study of hard spheres solid-liquid interface

    NASA Astrophysics Data System (ADS)

    Warshavsky, Vadim

    2005-03-01

    Interfacial free energy is an important characteristic of solid-liquid interface as it is one of the crucial parameters in many formula of interface thermodynamics such the nucleation theory. Previously different aspects of crystal-melt interfaces were intensively studied with simulations [1,2,3], but theoretical studies with Density Functional Theories (DFT) are inconclusive [4,5]. In this report the structure of hard spheres fcc crystal-melt interfaces and the anisotropy of the interfacial free energies are studied using the Rosenfeld's Fundamental Measure DFT as such a functional leads to reliable coexistence results not only for the hard sphere system but also for the Lennard-Jones systems [6]. The parameters of interfacial density profile were calculated by a proper minimization procedure. For the equilibrium density profile the interfacial free energies were compared with simulation results. 1. R.L.Davidchak and B.B.Laird, Phys.Rev.Lett., 85, 4751(2000). 2. J.J. Hoyt, M. Asta and A. Karma, Phys.Rev.Lett., 86, 5530 (2001). 3. J.R.Morris and X.Song, J.Chem.Phys., 119, 3920 (2003). 4. W.A.Curtin, Phys.Rev.B, 39, 6775(1989). 5. R.Ohnesorge, H.Lowen, and H.Wagner, Phys.Rev.E, 50, 4801 (1994). 6. V.Warshavsky and X.Song, Phys.Rev.E, 69, 061113 (2004).

  12. Theoretical and numerical study of axisymmetric lattice Boltzmann models

    NASA Astrophysics Data System (ADS)

    Huang, Haibo; Lu, Xi-Yun

    2009-07-01

    The forcing term in the lattice Boltzmann equation (LBE) is usually used to mimic Navier-Stokes equations with a body force. To derive axisymmetric model, forcing terms are incorporated into the two-dimensional (2D) LBE to mimic the additional axisymmetric contributions in 2D Navier-Stokes equations in cylindrical coordinates. Many axisymmetric lattice Boltzmann D2Q9 models were obtained through the Chapman-Enskog expansion to recover the 2D Navier-Stokes equations in cylindrical coordinates [I. Halliday , Phys. Rev. E 64, 011208 (2001); K. N. Premnath and J. Abraham, Phys. Rev. E 71, 056706 (2005); T. S. Lee, H. Huang, and C. Shu, Int. J. Mod. Phys. C 17, 645 (2006); T. Reis and T. N. Phillips, Phys. Rev. E 75, 056703 (2007); J. G. Zhou, Phys. Rev. E 78, 036701 (2008)]. The theoretical differences between them are discussed in detail. Numerical studies were also carried out by simulating two different flows to make a comparison on these models’ accuracy and τ sensitivity. It is found all these models are able to obtain accurate results and have the second-order spatial accuracy. However, the model C [J. G. Zhou, Phys. Rev. E 78, 036701 (2008)] is the most stable one in terms of τ sensitivity. It is also found that if density of fluid is defined in its usual way and not directly relevant to source terms, the lattice Boltzmann model seems more stable.

  13. Questioning the observation of laser-assisted ionization in fast collisions of He(2 /sup 1,3/S) with He

    SciTech Connect

    Gillen, K.T.

    1989-02-15

    In four recent papers Pradel et al. (Phys. Rev. Lett. 54, 2600 (1985); Phys. Rev. A 35, 1062 (1987)) and Monchicourt et al. (Phys. Rev. A 33, 3515 (1986); Chem. Phys. Lett. 152, 336 (1988)) give arguments claiming the observation of laser-assisted ionization of the short-lived collision complex formed during collisions of He/sup */(2 /sup 1,3/S) with He. However, estimates of the relative sizes of the assisted and unassisted ion signals observed make it very unlikely that laser-assisted ionization has been observed in those experiments. Collisional excitation to higher He/sup */ states, followed by (single-photon) ionization of the excited states, seems a more likely explanation at all energies considered.

  14. Hall Viscosity I: Linear Response Theory for Viscosity

    NASA Astrophysics Data System (ADS)

    Bradlyn, Barry; Goldstein, Moshe; Read, Nicholas

    2012-02-01

    In two dimensional systems with broken time-reversal symmetry, there can exist a non-dissipative viscosity coefficient [1,2,3]. This Hall viscosity is similar in nature to the non-dissipative Hall conductivity. In order to investigate this phenomenon further, we develop a linear response formalism for viscosity. We derive a Kubo formula for the frequency dependent viscosity tensor in the long wavelength limit. We compute the viscosity tensor for the free electron gas, integer quantum Hall systems, and two-dimensional paired superfluids. In the zero frequency limit, we show how the known results [3,4] for the Hall viscosity are recovered.[4pt] [1] J. Avron, R. Seiler, and P. Zograf, Phys. Rev. Lett. 75, 697 (1995).[0pt] [2] P. Levay, J. Math. Phys. 36, 2792 (1995).[0pt] [3] N. Read, Phys. Rev. B 79, 045308 (2009).[0pt] [4] N. Read and E. Rezayi, Phys. Rev. B 84, 085316 (2011).

  15. A study of proton-deuteron scattering in configuration space

    NASA Astrophysics Data System (ADS)

    Suslov, Vladimir; Braun, Mikhail; Filikhin, Igor; Vlahovic, Branislav

    2007-10-01

    A new computational method for solving the configuration-space Faddeev equations for the breakup scattering problem [1] has been applied to consider the pd scattering below and above the deuteron threshold. To perform numerical calculations for arbitrary nuclear potential and with arbitrary number of partial waves retained we use approach proposed in [2]. The calculations of the inelasticity and phase-shift for various lab energies were performed with the charge independent AV14 potential. The results are compared with those of other authors [3, 4]. 1. V.M. Suslov and B. Vlahovic, Phys. Rev. C69, 044003 (2004). 2. S.P. Merkuriev, C. Gignoux and A. Laverne, Ann. Phys. 99, 30 (1976). 3. A.Kievsky, J.L Friar, G.L. Payne, S. Rosati, M. Viviani, Phys. Rev. C63, 064004 (2001). 4. A. Deltuva, A.C. Fonseca, A.Kievsky, S. Rosati, P.U. Sauer, and M. Viviani, Phys. Rev. C74, 064003 (2005).

  16. Solar System tests in f (T ) gravity

    NASA Astrophysics Data System (ADS)

    Farrugia, Gabriel; Said, Jackson Levi; Ruggiero, Matteo Luca

    2016-05-01

    We investigate the four solar system tests of gravity—perihelion precession, light bending, Shapiro time delay, gravitational redshift—in f (T ) gravity. In particular, we investigate the solution derived by Ruggiero and Radicella53 , Phys. Rev. D 91, 104014 (2015). for a nondiagonal vierbein field for a polynomial f (T )=T +α Tn , where α is a constant and |n |≠1 . In this paper, we derive the solutions for each test, in which Weinberg's, Bodenner and Will's, Cattani et al., and Rindler and Ishak's methods are applied55 , Gravitation and Cosmology: Principles and Applications of the General Theory of Relativity (Wiley, New York, 1972); 56 Am. J. Phys. 71 (2003); 57 Phys. Rev. D 87, 047503 (2013); 58 Phys. Rev. D 76, 043006 (2007). We set a constraint on α for n =2 , 3 by using data available from literature.

  17. Improvements to laser wakefield accelerated electron beam stability, divergence, and energy spread using three-dimensional printed two-stage gas cell targets

    SciTech Connect

    Vargas, M.; Schumaker, W.; He, Z.-H.; Zhao, Z.; Behm, K.; Chvykov, V.; Hou, B.; Krushelnick, K.; Maksimchuk, A.; Yanovsky, V.; Thomas, A. G. R.

    2014-04-28

    High intensity, short pulse lasers can be used to accelerate electrons to ultra-relativistic energies via laser wakefield acceleration (LWFA) [T. Tajima and J. M. Dawson, Phys. Rev. Lett. 43, 267 (1979)]. Recently, it was shown that separating the injection and acceleration processes into two distinct stages could prove beneficial in obtaining stable, high energy electron beams [Gonsalves et al., Nat. Phys. 7, 862 (2011); Liu et al., Phys. Rev. Lett. 107, 035001 (2011); Pollock et al., Phys. Rev. Lett. 107, 045001 (2011)]. Here, we use a stereolithography based 3D printer to produce two-stage gas targets for LWFA experiments on the HERCULES laser system at the University of Michigan. We demonstrate substantial improvements to the divergence, pointing stability, and energy spread of a laser wakefield accelerated electron beam compared with a single-stage gas cell or gas jet target.

  18. Measurements of the dielectric and viscoelastic constants in mixtures of 4,4'-n-octyl-cyanobiphenyl and biphenyl.

    PubMed

    Oswald, Patrick; Scalliet, Camille

    2014-03-01

    We performed measurements of the dielectric constants, splay elastic constant, and rotational viscosity of the nematic phase of mixtures of 4,4'-n-octyl-cyanobiphenyl (8CB) and biphenyl (BP). In contrast with previous results of DasGupta et al. [Phys. Rev. E 63, 041703 (2001); Phys. Lett. A 288, 323 (2001)], we do not find any anomaly of these constants when the smectic-A phase is approached at all concentrations of BP. These results are compatible with recent calorimetric measurements of Denolf et al. [Phys. Rev. Lett. 97, 107801 (2006); Phys. Rev. E 76, 051702 (2007)] and the absence of a tricritical point in the phase diagram. The origin of the anomalies observed by DasGupta et al. at large concentration of BP is also briefly discussed and a likely explanation in terms of biphenyl evaporation is proposed.

  19. Physics Beyond the Standard Model from Molecular Hydrogen Spectroscopy

    NASA Astrophysics Data System (ADS)

    Ubachs, Wim; Salumbides, Edcel John; Bagdonaite, Julija

    2015-06-01

    The spectrum of molecular hydrogen can be measured in the laboratory to very high precision using advanced laser and molecular beam techniques, as well as frequency-comb based calibration [1,2]. The quantum level structure of this smallest neutral molecule can now be calculated to very high precision, based on a very accurate (10-15 precision) Born-Oppenheimer potential [3] and including subtle non-adiabatic, relativistic and quantum electrodynamic effects [4]. Comparison between theory and experiment yields a test of QED, and in fact of the Standard Model of Physics, since the weak, strong and gravitational forces have a negligible effect. Even fifth forces beyond the Standard Model can be searched for [5]. Astronomical observation of molecular hydrogen spectra, using the largest telescopes on Earth and in space, may reveal possible variations of fundamental constants on a cosmological time scale [6]. A study has been performed at a 'look-back' time of 12.5 billion years [7]. In addition the possible dependence of a fundamental constant on a gravitational field has been investigated from observation of molecular hydrogen in the photospheres of white dwarfs [8]. The latter involves a test of the Einsteins equivalence principle. [1] E.J. Salumbides et al., Phys. Rev. Lett. 107, 143005 (2011). [2] G. Dickenson et al., Phys. Rev. Lett. 110, 193601 (2013). [3] K. Pachucki, Phys. Rev. A82, 032509 (2010). [4] J. Komasa et al., J. Chem. Theory Comp. 7, 3105 (2011). [5] E.J. Salumbides et al., Phys. Rev. D87, 112008 (2013). [6] F. van Weerdenburg et al., Phys. Rev. Lett. 106, 180802 (2011). [7] J. Badonaite et al., Phys. Rev. Lett. 114, 071301 (2015). [8] J. Bagdonaite et al., Phys. Rev. Lett. 113, 123002 (2014).

  20. Quantum cosmology: From hidden symmetries towards a new (supersymmetric) perspective

    NASA Astrophysics Data System (ADS)

    Jalalzadeh, S.; Rostami, T.; Moniz, P. V.

    2016-02-01

    We review pedagogically some of the basic essentials regarding recent results intertwining boundary conditions, the algebra of constraints and hidden symmetries in quantum cosmology. They were extensively published in Refs. [S. Jalalzadeh, S. M. M. Rasouli and P. V. Moniz, Phys. Rev. D 90 (2014) 023541, S. Jalalzadeh and P. V. Moniz, Phys. Rev. D 89 (2014), S. Jalalzadeh, T. Rostami and P. V. Moniz, Eur. Phys. J. C 75 (2015) 38, arXiv:gr-qc/1412.6439 and T. Rostami, S. Jalalzadeh and P. V. Moniz, Phys. Rev. D 92 (2015) 023526, arXiv:gr-qc/1507.04212], where complete discussions and full details can be found. More concretely, in Refs. [S. Jalalzadeh, S. M. M. Rasouli and P. V. Moniz, Phys. Rev. D 90 (2014) 023541, S. Jalalzadeh and P. V. Moniz, Phys. Rev. D 89 (2014) and S. Jalalzadeh, T. Rostami and P. V. Moniz, Eur. Phys. J. C 75 (2015) 38, arXiv:gr-qc/1412.6439] it has been shown that specific boundary conditions can be related to the algebra of Dirac observables. Moreover, a process afterwards associated to the algebra of existent hidden symmetries, from which the boundary conditions can be selected, was introduced. On the other hand, in Ref. [T. Rostami, S. Jalalzadeh and P. V. Moniz, Phys. Rev. D 92 (2015) 023526, arXiv:gr-qc/1507.04212] it was subsequently argued that some factor ordering choices can be extracted from the hidden symmetries structure of the minisuperspace model. In Refs. [S. Jalalzadeh, S. M. M. Rasouli and P. V. Moniz, Phys. Rev. D 90 (2014) 023541, S. Jalalzadeh and P. V. Moniz, Phys. Rev. D 89 (2014), S. Jalalzadeh, T. Rostami and P. V. Moniz, Eur. Phys. J. C 75 (2015) 38, arXiv:gr-qc/1412.6439 and T. Rostami, S. Jalalzadeh and P. V. Moniz, Phys. Rev. D 92 (2015) 023526, arXiv:gr-qc/1507.04212], we proceeded gradually towards less simple models, ranging from a FLRW model with a perfect fluid [S. Jalalzadeh, S. M. M. Rasouli and P. V. Moniz, Phys. Rev. D 90 (2014) 023541] up to a conformal scalar field content [T. Rostami, S. Jalalzadeh and

  1. Statistical mechanical theory for steady state systems. VI. Variational principles.

    PubMed

    Attard, Phil

    2006-12-01

    Several variational principles that have been proposed for nonequilibrium systems are analyzed. These include the principle of minimum rate of entropy production due to Prigogine [Introduction to Thermodynamics of Irreversible Processes (Interscience, New York, 1967)], the principle of maximum rate of entropy production, which is common on the internet and in the natural sciences, two principles of minimum dissipation due to Onsager [Phys. Rev. 37, 405 (1931)] and to Onsager and Machlup [Phys. Rev. 91, 1505 (1953)], and the principle of maximum second entropy due to Attard [J. Chem.. Phys. 122, 154101 (2005); Phys. Chem. Chem. Phys. 8, 3585 (2006)]. The approaches of Onsager and Attard are argued to be the only viable theories. These two are related, although their physical interpretation and mathematical approximations differ. A numerical comparison with computer simulation results indicates that Attard's expression is the only accurate theory. The implications for the Langevin and other stochastic differential equations are discussed.

  2. Oscillator-field model of moving mirrors in quantum optomechanics

    NASA Astrophysics Data System (ADS)

    Galley, Chad R.; Behunin, Ryan O.; Hu, B. L.

    2013-04-01

    We present a microphysics model for the kinematics and dynamics of optomechanics describing the coupling between an optical field, modeled here by a massless scalar field, and the internal and mechanical degrees of freedom of a movable mirror. Instead of implementing boundary conditions on the field, we introduce an internal degree of freedom and its dynamics to describe the mirror's reflectivity. Depending on parameter values, the internal degrees of freedom of the mirror in this model capture a range of its optical activities, from those exhibiting broadband reflective properties to those reflecting only in a narrow band. After establishing the model we show how appropriate parameter choices lead to other well-known optomechanical models, including those of Barton and Calogeracos [Ann. Phys. (NY)0003-491610.1006/aphy.1995.1021 238, 227 (1995)], Calogeracos and Barton, Ann. Phys. (NY)10.1006/aphy.1995.1022 238, 268 (1995), Law [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.51.2537 51, 2537 (1995)], and Golestanian and Kardar [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.78.3421 78, 3421 (1997); Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.58.1713 58, 1713 (1998)]. As a simple illustrative application we derive classical radiation pressure cooling from this model. We then connect our microphysics model to the common descriptions of a moving mirror coupled to radiation pressure (e.g., with Nx coupling, where N is the photon number and x is the mirror displacement), making explicit the underlying assumptions made in these phenomenological models. Our model is also applicable to the lesser explored case of small N, which existing models based on sideband approximations [Kimble , Phys. Rev. DPRVDAQ1550-799810.1103/PhysRevD.65.022002 65, 022002 (2001)] have not addressed. Interestingly, we also find that slow-moving mirrors in our model can be described by the ubiquitous Brownian motion model of quantum open systems. The scope of applications of this model ranges

  3. Nature of the metastable boron-oxygen complex formation in crystalline silicon

    NASA Astrophysics Data System (ADS)

    Crandall, Richard S.

    2010-11-01

    Transient capacitance measurements reveal new physics of metastable defect formation in boron-doped oxygen-containing crystalline silicon solar cells. These measurements demonstrate that holes are deeply trapped during defect formation and removed during thermal annealing with activation energy of 1.3 eV. Previous theoretical models {Du et al., [Phys. Rev. Lett. 97, 256602 (2006)] and Adey et al., [Phys. Rev. Lett. 93, 055504 (2004)]} are supported by present findings that defect formation is a slow two-stage process with activation energies of 0.17 eV and 0.4 eV at high and low temperature, respectively. Repulsive hole capture by a positive oxygen-dimer determines the defect formation rate at low temperature {Du et al., [Phys. Rev. Lett. 97, 256602 (2006)]}. The high temperature process is governed by a structural conversion of the dimer {Du et al., [Phys. Rev. Lett. 97, 256602 (2006)] and Adey et al., [Phys. Rev. Lett. 93, 055504 (2004)]}. An abnormally low rate prefactor allows this low-enthalpy reaction to be observed at the higher temperature. This dimer conversion presents an excellent example of an "entropy barrier" that explains the low conversion rate. Disparate formation and annealing results published here and in other publications are related by the Meyer-Neldel rule with an isokinetic temperature of 410 K.

  4. Surface Exciton-Plasmons in Carbon Nanotubes

    NASA Astrophysics Data System (ADS)

    Bondarev, Igor; Tatur, Kevin; Woods, Lilia

    2008-03-01

    We study theoretically the interactions of excitonic states with surface electromagnetic modes of a single-walled carbon nanotube. We use our previously developed Green's function formalism to quantize an electromagnetic field in the presence of quasi-1D absorbing bodies [1]. We show that these interactions result in the exciton-plasmon coupling that is significant in its strength due to the presence of weakly-dispersive low-energy (˜0.5-2eV) interband surface plasmon modes [2] and large exciton excitation energies ˜1eV in small-diameter nanotubes [3]. We estimate the exciton-plasmon Rabi splitting to be ˜0.01-0.1eV which is close to that observed in organic semiconductors [4] and much larger than that reported for hybrid semiconductor-metal nanoparticle molecules [5]. We calculate the exciton absorption lineshape and demonstrate a clear line splitting effect as the exciton energy is tuned to the closest interband surface plasmon resonance. [1] I.V.Bondarev and Ph.Lambin, Phys. Rev. B72, 035451 (2005). [2] T.Pichler, et al., Phys. Rev. Lett. 80, 4729 (1998). [3] D.Spataru, et al., Phys. Rev. Lett. 95, 247402 (2005). [4] J.Belessa, et al., Phys. Rev. Lett. 93, 036404 (2004). [5] W.Zhang, A.O.Govorov, G.W.Bryant, Phys. Rev. Lett. 97, 146804 (2006).

  5. Dissipative electronic transport through double quantum dots irradiated with microwaves

    NASA Astrophysics Data System (ADS)

    Brandes, Tobias; Aguado, Ramon; Platero, Gloria

    2003-03-01

    Double quantum dots in the strong Coulomb blockade regime are realizations of two-level systems defined from two tunnel--splitted ground states, which are separated by a large energy gap from the remaining many--particle states. The interactions between electrons and bosonic degrees of freedom (photons, phonons) in these systems can be tested and manipulated in electronic transport experiments [1]. Monochromatic classical radiation (AC fields, microwaves) gives rise to various non-linear effects such as photo-sidebands or dynamical localization (coherent supression of tunneling) that show up in the time-averaged, stationary electronic current [2]. On the other hand, quantum noise of a dissipative environment strongly influences the transport properties of coupled quantum dots [3,4]. In this contribution, we quantitatively investigate the combined influence of a classical, monochromatic time-dependent AC field and a dissipative boson environment on the non-linear transport through a double quantum dot. We develop a Floquet-like theory [5] that takes into account the effect of the electron reservoirs (leads) and can be numerically evaluated for arbitrary strong AC fields and arbitrary boson environment. In limiting cases we reproduce previous analytical results (polaron tunneling, Tien-Gordon formula). [1] T. Fujisawa, T. H. Oosterkamp, W. G. van der Wiel, B. W. Broer, R. Aguado, S. Tarucha, and L. P. Kouwenhoven, Science 282, 932 (1998); R. H. Blick, D. Pfannkuche, R. J. Haug, K. v. Klitzing, and K. Eberl, Phys. Rev. Lett. 80, 4032 (1998). [2] T. H. Stoof, Yu. V. Nazarov, Phys. Rev. B 53, 1050 (1996). [3] T. Brandes, B. Kramer, Phys. Rev. Lett. 83, 3021 (1999); T. Brandes, F. Renzoni, R. H. Blick, Phys. Rev. B 64, 035319 (2001); T. Brandes, T. Vorrath, Phys. Rev. B 66, 075341 (2002). [4] R. Aguado and L. P. Kouwenhoven, Phys. Rev. Lett, 84, 1986 (2000). [5] M. Grifoni, P. Hänggi, Phys. Rep. 304, 229 (1998).

  6. Nonperturbative relativistic calculation of the muonic hydrogen spectrum

    SciTech Connect

    Carroll, J. D.; Thomas, A. W.; Rafelski, J.; Miller, G. A.

    2011-07-15

    We investigate the muonic hydrogen 2P{sub 3/2}{sup F=2} to 2S{sub 1/2}{sup F=1} transition through a precise, nonperturbative numerical solution of the Dirac equation including the finite-size Coulomb force and finite-size vacuum polarization. The results are compared with earlier perturbative calculations of (primarily) [E. Borie, Phys. Rev. A 71, 032508 (2005); E. Borie and G. A. Rinker, Rev. Mod. Phys. 54, 67 (1982); E. Borie, Z. Phys. A 275, 347 (1975) and A. P. Martynenko, Phys. Rev. A 71, 022506 (2005); A. Martynenko, Phys. At. Nucl. 71, 125 (2008), and K. Pachucki, Phys. Rev. A 53, 2092 (1996)] and experimental results recently presented by Pohl et al.[Nature (London) 466, 213 (2010)], in which this very comparison is interpreted as requiring a modification of the proton charge radius from that obtained in electron scattering and electronic hydrogen analyses. We find no significant discrepancy between the perturbative and nonperturbative calculations, and we present our results as confirmation of the perturbative methods.

  7. Eigenvalue-based method and form-factor determinant representations for integrable XXZ Richardson-Gaudin models

    NASA Astrophysics Data System (ADS)

    Claeys, Pieter W.; De Baerdemacker, Stijn; Van Raemdonck, Mario; Van Neck, Dimitri

    2015-04-01

    We propose an extension of the numerical approach for integrable Richardson-Gaudin models based on a new set of eigenvalue-based variables [A. Faribault et al., Phys. Rev. B 83, 235124 (2011), 10.1103/PhysRevB.83.235124; O. El Araby et al., Phys. Rev. B 85, 115130 (2012), 10.1103/PhysRevB.85.115130]. Starting solely from the Gaudin algebra, the approach is generalized towards the full class of XXZ Richardson-Gaudin models. This allows for a fast and robust numerical determination of the spectral properties of these models, avoiding the singularities usually arising at the so-called singular points. We also provide different determinant expressions for the normalization of the Bethe ansatz states and form factors of local spin operators, opening up possibilities for the study of larger systems, both integrable and nonintegrable. These expressions can be written in terms of the new set of variables and generalize the results previously obtained for rational Richardson-Gaudin models [A. Faribault and D. Schuricht, J. Phys. A 45, 485202 (2012), 10.1088/1751-8113/45/48/485202] and Dicke-Jaynes-Cummings-Gaudin models [H. Tschirhart and A. Faribault, J. Phys. A 47, 405204 (2014), 10.1088/1751-8113/47/40/405204]. Remarkably, these results are independent of the explicit parametrization of the Gaudin algebra, exposing a universality in the properties of Richardson-Gaudin integrable systems deeply linked to the underlying algebraic structure.

  8. Band gap engineering via doping: A predictive approach

    NASA Astrophysics Data System (ADS)

    Andriotis, Antonis N.; Menon, Madhu

    2015-03-01

    We employ an extension of Harrison's theory at the tight binding level of approximation to develop a predictive approach for band gap engineering involving isovalent doping of wide band gap semiconductors. Our results indicate that reasonably accurate predictions can be achieved at qualitative as well as quantitative levels. The predictive results were checked against ab initio ones obtained at the level of DFT/SGGA + U approximation. The minor disagreements between predicted and ab initio results can be attributed to the electronic processes not incorporated in Harrison's theory. These include processes such as the conduction band anticrossing [Shan et al., Phys. Rev. Lett. 82, 1221 (1999); Walukiewicz et al., Phys. Rev. Lett. 85, 1552 (2000)] and valence band anticrossing [Alberi et al., Phys. Rev. B 77, 073202 (2008); Appl. Phys. Lett. 92, 162105 (2008); Appl. Phys. Lett. 91, 051909 (2007); Phys. Rev. B 75, 045203 (2007)], as well as the multiorbital rehybridization. Another cause of disagreement between the results of our predictive approach and the ab initio ones is shown to be the result of the shift of Fermi energy within the impurity band formed at the edge of the valence band maximum due to rehybridization. The validity of our approach is demonstrated with example applications for the systems GaN1-xSbx, GaP1-xSbx, AlSb1-xPx, AlP1-xSbx, and InP1-xSbx.

  9. Nondispersive wave packets -- control through chaos

    NASA Astrophysics Data System (ADS)

    Buchleitner, Andreas

    2005-05-01

    Nondispersive wave packets were predicted to emerge in periodically driven Rydberg atoms a little more than 10 years ago [1], and have now been observed in the laboratory [2]. I shall illustrate how these robust, generic ``quantum particles'' and their relatives naturally emerge from the theory of chaotic quantum systems [3], and thus open new perspectives for robust quantum control in various experimental settings -- from one and two-electron [4] atoms under periodic or impulsive [5] driving to cold atoms in flashing periodic potentials, possibly amended by harmonic confinement [6]. Besides the fundamental underlying (nonlinear) resonance phenomena also some more subtle properties will be discussed, including open questions within the realm of spectral theory. *[1] A. Buchleitner, thèse de doctorat, Universit'e Paris 6 (1993); I. Bialynicki-Birula, M. Kalinski, and J. H. Eberly, Phys. Rev. Lett. 73, 1777 (1994); D. Delande and A. Buchleitner, Adv. At. Mol. Opt. Phys. 34, 85 (1994). *[2] H. Maeda and T. F. Gallagher, Phys. Rev. Lett. 92, 133004 (2004). *[3] A. Buchleitner, D. Delande, and J. Zakrzewski, Phys. Rep. 386, 409 (2002). *[4] J. Madroñero, PhD thesis, Ludwig-Maximilians-Universität München (2004), http://edoc.ub.uni-muenchen.de/archive/00002187. *[5] D.G. Arb'o et al., Phys. Rev. A 67, 63401 (2003). *[6] A.R.R. de Carvalho and A. Buchleitner, Phys. Rev. Lett. 93, 204101 (2004).

  10. Investigation on hot electron generation and propagation in interaction of ultrashort laser pulses with solids

    NASA Astrophysics Data System (ADS)

    Zhang, Jie

    2002-04-01

    Hot electron generation and propagation have been investigated in the interaction of ultrashort laser pulses with solid targets. The hot election generation and absorption mechanisms of ultrashort laser pulses have been studied at intensities of 5¡Á1016 7¡Á1017 Wcm-2 [1,2]. The competition between vacuum heating and resonance absorption has been found to be the main reason for a double-temperature distribution of hot electrons [3,4]. The effects of charge-separation-potential have been found to play a main role in the interaction process [5]. The effects of laser polarization on the hot electron emission have also been studied [6]. Outgoing hot electrons collimated in the polarization direction has been observed for the s-polarized laser irradiation, whereas for the p-polarized irradiation, very directional emission of outgoing hot electrons has been found close to the normal direction of the target. Dependence of the jet emission of hot electrons on the plasma scale-length has been obtained. The angular distribution has been found to be dependent on the energy of hot electrons. Particle-in-Cell (PIC) simulations have confirmed most of the observations [1,3,7]. The propagation process of hot electrons through solids have also been investigated [8]. References [1] Q.L. Dong, J. Zhang and H. Teng, Phys. Rev. E64, 026411 (2001). [2] L.M Chen, J.Zhang, et al., Phys. Plasmas 8, 2925 (2001). [3] Q.L. Dong, J. Zhang, Phys. Plasmas 8,1025 (2001). [4] H. Lin, et al., Phys. Plasmas 8,1707 (2001). [5] L.M. Chen, J. Zhang, et al., Phys. Rev. E63,036403 (2001). [6] L. M. Chen, J. Zhang, et al., Phys. Rev. Lett. 87, 225001 (2001). [7] Z.M. Sheng, et al., Phys. Rev. Lett. 85, 5340 (2000). [8] Y.T. Li, J. Zhang, et al., Phys. Rev. E64, 046407 (2001).

  11. Fault-tolerant logical gates in quantum error-correcting codes

    NASA Astrophysics Data System (ADS)

    Pastawski, Fernando; Yoshida, Beni

    2015-01-01

    Recently, S. Bravyi and R. König [Phys. Rev. Lett. 110, 170503 (2013), 10.1103/PhysRevLett.110.170503] have shown that there is a trade-off between fault-tolerantly implementable logical gates and geometric locality of stabilizer codes. They consider locality-preserving operations which are implemented by a constant-depth geometrically local circuit and are thus fault tolerant by construction. In particular, they show that, for local stabilizer codes in D spatial dimensions, locality-preserving gates are restricted to a set of unitary gates known as the D th level of the Clifford hierarchy. In this paper, we explore this idea further by providing several extensions and applications of their characterization to qubit stabilizer and subsystem codes. First, we present a no-go theorem for self-correcting quantum memory. Namely, we prove that a three-dimensional stabilizer Hamiltonian with a locality-preserving implementation of a non-Clifford gate cannot have a macroscopic energy barrier. This result implies that non-Clifford gates do not admit such implementations in Haah's cubic code and Michnicki's welded code. Second, we prove that the code distance of a D -dimensional local stabilizer code with a nontrivial locality-preserving m th -level Clifford logical gate is upper bounded by O (LD +1 -m) . For codes with non-Clifford gates (m >2 ), this improves the previous best bound by S. Bravyi and B. Terhal [New. J. Phys. 11, 043029 (2009), 10.1088/1367-2630/11/4/043029]. Topological color codes, introduced by H. Bombin and M. A. Martin-Delgado [Phys. Rev. Lett. 97, 180501 (2006), 10.1103/PhysRevLett.97.180501; Phys. Rev. Lett. 98, 160502 (2007), 10.1103/PhysRevLett.98.160502; Phys. Rev. B 75, 075103 (2007), 10.1103/PhysRevB.75.075103], saturate the bound for m =D . Third, we prove that the qubit erasure threshold for codes with a nontrivial transversal m th -level Clifford logical gate is upper bounded by 1 /m . This implies that no family of fault-tolerant codes with

  12. Physics of Earthquakes and Faults

    NASA Astrophysics Data System (ADS)

    Ben-Zion, Yehuda

    2010-03-01

    Detailed observations and theoretical results on brittle failure events in individual fault zones point to three general dynamic regimes [1]. The first is associated with broad range of heterogeneities, little dynamic weakening during failure, power law frequency-size statistics, and temporal clustering of events. The second is associated with relatively-uniform localized structures, significant dynamic weakening, and quasi-periodic occurrence of characteristic system-size events. For a range of conditions, the response can switch back and forth between the forgoing two types of behavior. These dynamic regimes, geometrical properties of slip, and observed moment rate shapes can be explained by a simple model having two tuning parameters: dynamic weakening and conservation of elastic stress transfer during failure events [2]. The model can also explain multiple aspects of deformation in volumetric regions, including stress-strain curves, acoustic emissions and related power spectra, with a continuous transition from brittle to plastic behavior, and statistics of failure events in granular media [3]. The results from the latter studies are in good agreement with experimental data [4] and simulations with other frameworks [5]. An extension of the model to include cohesion changes during failure and healing phases of deformation may account for transitions between solid and granular phases of materials [6].[4pt] [1] Y. Ben-Zion, Rev. Geophys., 46, RG4006 (2008) and references therein. [0pt] [2] D.S. Fisher et al., Phys. Rev. Lett. 78, 4885 (1997); Y. Ben-Zion, and J.R. Rice, J. Geophys. Res., 98, 14109, (1993). K.A. Dahmen et al., Phys. Rev. E 58, 1494 (1998). A.P. Mehta et al., Phys. Rev. E 73, 056104 (2006). [0pt] [3] K.A. Dahmen, et al., Phys. Rev. Lett., 102, 175501, 2009. K.A.Dahmen, Y. Ben-Zion and J.T. Uhl, submitted, 2009. [0pt] [4] K.E. Daniels and N.W. Hayman, Journal of Geophysical Research, 113 B11411 (2008). H. Jaeger, S.R. Nagel, R.P. Behringer, Revs. Mod

  13. Fuel Summary Report: Shippingport Light Water Breeder Reactor - Rev. 2

    SciTech Connect

    Olson, Gail Lynn; Mc Cardell, Richard Keith; Illum, Douglas Brent

    2002-09-01

    The Shippingport Light Water Breeder Reactor (LWBR) was developed by Bettis Atomic Power Laboratory to demonstrate the potential of a water-cooled, thorium oxide fuel cycle breeder reactor. The LWBR core operated from 1977-82 without major incident. The fuel and fuel components suffered minimal damage during operation, and the reactor testing was deemed successful. Extensive destructive and nondestructive postirradiation examinations confirmed that the fuel was in good condition with minimal amounts of cladding deformities and fuel pellet cracks. Fuel was placed in wet storage upon arrival at the Expended Core Facility, then dried and sent to the Idaho Nuclear Technology and Engineering Center for underground dry storage. It is likely that the fuel remains in good condition at its current underground dry storage location at the Idaho Nuclear Technology and Engineering Center. Reports show no indication of damage to the core associated with shipping, loading, or storage.

  14. Hanford Soil Inventory Model (SIM) Rev. 1 Users Guide

    SciTech Connect

    Simpson, Brett C.; Corbin, Rob A.; Anderson, Michael J.; Kincaid, Charles T.

    2006-09-25

    The focus of the development and application of a soil inventory model as part of the Remediation and Closure Science (RCS) Project managed by PNNL was to develop a probabilistic approach to estimate comprehensive, mass balanced-based contaminant inventories for the Hanford Site post-closure setting. The outcome of this effort was the Hanford Soil Inventory Model (SIM). This document is a user's guide for the Hanford SIM. The principal project requirement for the SIM was to provide comprehensive quantitative estimates of contaminant inventory and its uncertainty for the various liquid waste sites, unplanned releases, and past tank farm leaks as a function of time and location at Hanford. The majority, but not all of these waste sites are in the 200 Areas of Hanford where chemical processing of spent fuel occurred. A computer model capable of performing these calculations and providing satisfactory quantitative output representing a robust description of contaminant inventory and uncertainty for use in other subsequent models was determined to be satisfactory to address the needs of the RCS Project. The ability to use familiar, commercially available software on high-performance personal computers for data input, modeling, and analysis, rather than custom software on a workstation or mainframe computer for modeling, was desired.

  15. Oak Ridge National Laboratory Waste Management Plan. Rev. 1

    SciTech Connect

    1991-12-01

    The goal of the Oak Ridge National Laboratory (ORNL) Waste Management Program is the protection of workers, the public, and the environment. A vital aspect of this goal is to comply with all applicable state, federal, and DOE requirements. Waste management requirements for DOE radioactive wastes are detailed in DOE Order 5820.2A, and the ORNL Waste Management Program encompasses all elements of this order. The requirements of this DOE order and other appropriate DOE orders, along with applicable Tennessee Department of Environment and Conservation (TDEC) and US Environmental Protection Agency (EPA) rules and regulations, provide the principal source of regulatory guidance for waste management operations at ORNL. The objective of the Oak Ridge National Laboratory Waste Management Plan is to compile and to consolidate information annually on how the ORNL Waste Management is to compile and to consolidate information annually on how the ORNL Waste Management Program is conducted, which waste management facilities are being used to manage wastes, what forces are acting to change current waste management systems, what activities are planned for the forthcoming fiscal year (FY), and how all of the activities are documented.

  16. Reference Model 2: %22Rev 0%22 Rotor Design.

    SciTech Connect

    Barone, Matthew F.; Berg, Jonathan Charles; Griffith, Daniel

    2011-12-01

    The preliminary design for a three-bladed cross-flow rotor for a reference marine hydrokinetic turbine is presented. A rotor performance design code is described, along with modifications to the code to allow prediction of blade support strut drag as well as interference between two counter-rotating rotors. The rotor is designed to operate in a reference site corresponding to a riverine environment. Basic rotor performance and rigid-body loads calculations are performed to size the rotor elements and select the operating speed range. The preliminary design is verified with a simple finite element model that provides estimates of bending stresses during operation. A concept for joining the blades and support struts is developed and analyzed with a separate finite element analysis. Rotor mass, production costs, and annual energy capture are estimated in order to allow calculations of system cost-of-energy. Evaluation Only. Created with Aspose.Pdf.Kit. Copyright 2002-2011 Aspose Pty Ltd Evaluation Only. Created with Aspose.Pdf.Kit. Copyright 2002-2011 Aspose Pty Ltd

  17. Bottom/Side Lift Gantry Conceptual Design Rev. 01

    SciTech Connect

    Bair, P.S.

    2000-04-11

    The purpose of this task is to update the existing bottom/side lift gantry analysis so that the design is consistent with Enhanced Design Alternative II (EDA II) design constraints listed in the Monitored Geologic Repository Project Description Document (CRWMS M and O 1999a, Section 2.2.1.1, p. 9a). This update is consistent with the requirements of the Technical Guidance Document for License Application Preparation (YMP 1999, Section 6.2.5.1). This update will also take into account the latest available equipment classification and Waste Emplacement/Retrieval System Description Document (SDD) (CRWMS M and O 2000c) requirements. The principal objective of this analysis is to verify that the newly developed bottom/side lift gantry concept continues to be a suitable design concept for the current Monitored Geologic Repository (MGR) design. This analysis includes an examination of the waste package (WP) transfer operation at the emplacement drift transfer dock. In addition, this analysis verifies that the gantry is compatible with the WP transporter, which has been redesigned to handle WPs sitting on pallets (CRWMS M and O 2000a). The scope of this work is to examine the existing analysis and to determine what, if any, modifications to the analysis may be required as a result of additional requirements imposed by the EDA II concept. Then, a revision will be made to the conceptual design accordingly. The analysis will also be revised to show the approximate sizes and locations of the electrical equipment and control cabinets, and to take into account the weight of that equipment in the total gantry weight. The analytical portions of the analysis are revised, as required, to address changes resulting from modifications to the conceptual design or from changes in classification and/or SDD requirements. Finally, the revised conceptual design is evaluated to verify that it continues to be a suitable method for handling the WPs within the emplacement drift. Except as noted, the scope of this work does not include any new analytical investigations or any detailed studies regarding the mechanical or electrical subsystems of the gantry beyond those in Revision 00 of this analysis. This analysis has been prepared in accordance with the requirements set forth in Bottom/Side Lift Gantry Analysis (CRWMS M and O 1999b). This analysis supports the MGR design that will be presented as part of the Site Recommendation.

  18. InterMine Webservices for Phytozome (Rev2)

    SciTech Connect

    Carlson, Joseph; Goodstein, David; Rokhsar, Dan

    2014-07-10

    A datawarehousing framework for information provides a useful infrastructure for providers and users of genomic data. For providers, the infrastructure give them a consistent mechanism for extracting raw data. While for the users, the web services supported by the software allows them to make complex, and often unique, queries of the data. Previously, phytozome.net used BioMart to provide the infrastructure. As the complexity, scale and diversity of the dataset as grown, we decided to implement an InterMine web service on our servers. This change was largely motivated by the ability to have a more complex table structure and richer web reporting mechanism than BioMart. For InterMine to achieve its more complex database schema it requires an XML description of the data and an appropriate loader. Unlimited one-to-many and many-to-many relationship between the tables can be enabled in the schema. We have implemented support for:1.) Genomes and annotations for the data in Phytozome. This set is the 48 organisms currently stored in a back end CHADO datastore. The data loaders are modified versions of the CHADO data adapters from FlyMine. 2.) Interproscan results from all proteins in the Phytozome database. 3.) Clusters of proteins into a grouped heirarchically by similarity. 4.) Cufflinks results from tissue-specific RNA-Seq data of Phytozome organisms. 5.) Diversity data (GATK and SnpEFF results) from a set of individual organism. The last two datatypes are new in this implementation of our web services. We anticipate that the scale of these data will increase considerably in the near future.

  19. Foreign Object Debris: FOD Prevention QS210LSK-REV

    NASA Technical Reports Server (NTRS)

    Randolph, Sherry; Seaman, John

    2004-01-01

    Housekeeping in the space industry? You may think the idea isn't technical enough for the shuttle program. Yet, eliminating Foreign Object Debris or FOD is an important goal for USA and NASA. The justification for this effort is based on data from the aeronautics industry. Experience has shown that if debris is not controlled, it may later cause a variety of in-flight issues. FOD can result in material damage, or make systems and equipment inoperable unsafe, or less efficient

  20. Multi-pack Disposal Concepts for Spent Fuel (Rev. 0)

    SciTech Connect

    Hadgu, Teklu; Hardin, Ernest; Matteo, Edward N.

    2015-12-01

    At the initiation of the Used Fuel Disposition (UFD) R&D campaign, international geologic disposal programs and past work in the U.S. were surveyed to identify viable disposal concepts for crystalline, clay/shale, and salt host media (Hardin et al., 2012). Concepts for disposal of commercial spent nuclear fuel (SNF) and high-level waste (HLW) from reprocessing are relatively advanced in countries such as Finland, France, and Sweden. The UFD work quickly showed that these international concepts are all “enclosed,” whereby waste packages are emplaced in direct or close contact with natural or engineered materials . Alternative “open” modes (emplacement tunnels are kept open after emplacement for extended ventilation) have been limited to the Yucca Mountain License Application Design (CRWMS M&O, 1999). Thermal analysis showed that, if “enclosed” concepts are constrained by peak package/buffer temperature, waste package capacity is limited to 4 PWR assemblies (or 9-BWR) in all media except salt. This information motivated separate studies: 1) extend the peak temperature tolerance of backfill materials, which is ongoing; and 2) develop small canisters (up to 4-PWR size) that can be grouped in larger multi-pack units for convenience of storage, transportation, and possibly disposal (should the disposal concept permit larger packages). A recent result from the second line of investigation is the Task Order 18 report: Generic Design for Small Standardized Transportation, Aging and Disposal Canister Systems (EnergySolution, 2015). This report identifies disposal concepts for the small canisters (4-PWR size) drawing heavily on previous work, and for the multi-pack (16-PWR or 36-BWR).