On the Statistical Analysis of X-ray Polarization Measurements

NASA Technical Reports Server (NTRS)

Strohmayer, T. E.; Kallman, T. R.

2013-01-01

In many polarimetry applications, including observations in the X-ray band, the measurement of a polarization signal can be reduced to the detection and quantification of a deviation from uniformity of a distribution of measured angles of the form alpha plus beta cosine (exp 2)(phi - phi(sub 0) (0 (is) less than phi is less than pi). We explore the statistics of such polarization measurements using both Monte Carlo simulations as well as analytic calculations based on the appropriate probability distributions. We derive relations for the number of counts required to reach a given detection level (parameterized by beta the "number of sigma's" of the measurement) appropriate for measuring the modulation amplitude alpha by itself (single interesting parameter case) or jointly with the position angle phi (two interesting parameters case). We show that for the former case when the intrinsic amplitude is equal to the well known minimum detectable polarization (MDP) it is, on average, detected at the 3sigma level. For the latter case, when one requires a joint measurement at the same confidence level, then more counts are needed, by a factor of approximately equal to 2.2, than that required to achieve the MDP level. We find that the position angle uncertainty at 1sigma confidence is well described by the relation sigma(sub pi) equals 28.5(degrees) divided by beta.

Structural Conservation of the Myoviridae Phage Tail Sheath Protein Fold

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

Aksyuk, Anastasia A.; Kurochkina, Lidia P.; Fokine, Andrei

2012-02-21

Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 {angstrom} diameter icosahedral head and a 2000 {angstrom}-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 {angstrom} resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 {angstrom} resolution. Despite low sequence identity between these proteins, all ofmore » these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.« less

TOPP4 Regulates the Stability of PHYTOCHROME INTERACTING FACTOR5 during Photomorphogenesis in Arabidopsis1

PubMed Central

Qin, Qianqian; Meng, Siyuan; Li, Jia; Hou, Suiwen

2015-01-01

In plants, photoreceptors transfer light signals to phytochrome-interacting factors (PIFs), inducing the rapid phosphorylation and degradation of PIFs to promote photomorphogenesis. However, the phosphatase responsible for PIF dephosphorylation remains unknown. In this study, we identified a type 1 protein phosphatase, TOPP4, that is essential for PIF5 protein stability in Arabidopsis (Arabidopsis thaliana). Compared with the wild type, the dominant-negative mutant, topp4-1, displayed reduced hypocotyl length and larger apical hook and cotyledon opening angle under red light. Overexpression of topp4-1 in the wild type led to defects that were similar to those in the topp4-1 mutant. Red light induced phytochrome B (phyB)-dependent TOPP4 expression in hypocotyls. The topp4-1 mutation weakened the closed cotyledon angle of phyB-9 and phyA-211 phyB-9, while overexpression of TOPP4 significantly repressed the short hypocotyls of phyB-green fluorescent protein seedlings, indicating that TOPP4 and phyB function in an antagonistic way during photomorphogenesis. Protein interaction assays and phosphorylation studies demonstrate that TOPP4 interacts directly with PIF5 and dephosphorylates it. Furthermore, TOPP4 inhibits the red light-induced ubiquitination and degradation of PIF5. These findings demonstrate that dephosphorylation of PIF5 by TOPP4 inhibits its ubiquitin-mediated degradation during photomorphogenesis. These data outline a novel phytochrome signaling mechanism by which TOPP4-mediated dephosphorylation of PIF5 attenuates phytochrome-dependent light responses. PMID:26704640

X-Phi and Carnapian Explication.

PubMed

Shepherd, Joshua; Justus, James

2015-04-01

The rise of experimental philosophy (x-phi) has placed metaphilosophical questions, particularly those concerning concepts, at the center of philosophical attention. X-phi offers empirically rigorous methods for identifying conceptual content, but what exactly it contributes towards evaluating conceptual content remains unclear. We show how x-phi complements Rudolf Carnap's underappreciated methodology for concept determination, explication. This clarifies and extends x-phi's positive philosophical import, and also exhibits explication's broad appeal. But there is a potential problem: Carnap's account of explication was limited to empirical and logical concepts, but many concepts of interest to philosophers (experimental and otherwise) are essentially normative. With formal epistemology as a case study, we show how x-phi assisted explication can apply to normative domains.

The 'shoulder' and the 'ridge' in PHENIX

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

McCumber, M. P.; Awes, Terry C; Cianciolo, Vince

2008-01-01

The observation of jet quenching in ultra-relativistic heavy ion collisions demonstrates significant energy loss of fast partons when passing through the created medium. Correlations between final-state particles at intermediate transverse momentum (1.0 {approx}< p{sub T} {approx}< 4.0 GeV/c) allow for study of the medium and its response to deposited energy. Comparison of these measurements in heavy ion collisions with measurements in proton collisions show strong modification of the correlation shape and particle yields. Two new structures are created, both extended in {Delta}{eta}, one centered at {Delta}{phi} = 0 ('ridge') and the other occurring at {Delta}{phi} {approx} {pi} {+-} 1.1 ('shoulder').more » In these proceedings, we describe the measurements of these structures that show consistency with a scenario of parton-medium interaction and response. We discuss a new analysis which selects on the angle of trigger particles relative to the reaction plane in Run7. New measurements of the centrality and p{sub T} dependencies of the structures raise the possibility that the same production mechanism may give rise to both phenomena.« less

Cellular reflectarray antenna and method of making same

NASA Technical Reports Server (NTRS)

Romanofsky, Robert R (Inventor)

2011-01-01

A method of manufacturing a cellular reflectarray antenna arranged in an m by n matrix of radiating elements for communication with a satellite includes steps of determining a delay .phi.m,n for each of said m by n matrix of elements of said cellular reflectarray antenna using sub-steps of: determining the longitude and latitude of operation, determining elevation and azimuth angles of the reflectarray with respect to the satellite and converting theta.sub.0 (.theta..sub.0) and phi.sub.0 (.phi..sub.0), determining .DELTA..beta..sub.m,n, the pointing vector correction, for a given inter-element spacing and wavelength, determining .DELTA..phi..sub.m,n, the spherical wave front correction factor, for a given radius from the central element and/or from measured data from the feed horn; and, determining a delay .phi.m,n for each of said m by n matrix of elements as a function of .DELTA..beta..sub.m,n and .DELTA..phi..sub.m,n.

Cellular reflectarray antenna and method of making same

NASA Technical Reports Server (NTRS)

Romanofsky, Robert R (Inventor)

2010-01-01

A method of manufacturing a cellular reflectarray antenna arranged in an m by n matrix of radiating elements for communication with a satellite includes steps of determining a delay .phi.m,n for each of said m by n matrix of elements of said cellular reflectarray antenna using sub-steps of: determining the longitude and latitude of operation, determining elevation and azimuth angles of the reflectarray with respect to the satellite and converting theta.sub.0 (.theta..sub.0) and phi.sub.0 (.phi..sub.0), determining .DELTA..beta..sub.m,n, the pointing vector correction, for a given inter-element spacing and wavelength, determining .DELTA..phi..sub.m,n, the spherical wave front correction factor, for a given radius from the central element and/or from measured data from the feed horn; and, determining a delay .phi.m,n for each of said m by n matrix of elements as a function of .DELTA..beta..sub.m,n and .DELTA..phi..sub.m,n..

Optimal future liver remnant in patients treated with extensive preoperative chemotherapy for colorectal liver metastases.

PubMed

Shindoh, Junichi; Tzeng, Ching-Wei D; Aloia, Thomas A; Curley, Steven A; Zimmitti, Giuseppe; Wei, Steven H; Huang, Steven Y; Mahvash, Armeen; Gupta, Sanjay; Wallace, Michael J; Vauthey, Jean-Nicolas

2013-08-01

Patients with colorectal liver metastases (CLM) are increasingly treated with preoperative chemotherapy. Chemotherapy associated liver injury is associated with postoperative hepatic insufficiency (PHI) and mortality. The adequate minimum future liver remnant (FLR) volume in patients treated with extensive chemotherapy remains unknown. All patients with standardized FLR > 20 %, who underwent extended right hepatectomy for CLM from 1993-2011, were divided into three cohorts by chemotherapy duration: no chemotherapy (NC, n = 30), short duration (SD, ≤12 weeks, n = 78), long duration (LD, >12 weeks, n = 86). PHI and mortality were compared by using uni-/multivariate analyses. Optimal FLR for LD chemotherapy was determined using a minimum p-value approach. A total of 194 patients met inclusion criteria. LD chemotherapy was significantly associated with PHI (NC + SD 3.7 vs. LD 16.3%, p = 0.006). Ninety-day mortality rates were 0 % in NC, 1.3 % in SD, and 2.3% in LD patients, respectively (p = 0.95). In patients with FLR > 30 %, PHI occurred in only two patients (both LD, 2/20, 10 %), but all patients with FLR > 30 % survived. The best cutoff of FLR for preventing PHI after chemotherapy >12 weeks was estimated as >30 %. Both LD chemotherapy (odds ratio [OR] 5.4, p = 0.004) and FLR ≤ 30 % (OR 6.3, p = 0.019) were independent predictors of PHI. Preoperative chemotherapy >12 weeks increases the risk of PHI after extended right hepatectomy. In patients treated with long-duration chemotherapy, FLR > 30 % reduces the rate of PHI and may provide enough functional reserve for clinical rescue if PHI develops.

Structure determination of a peptide model of the repeated helical domain in Samia cynthia ricini silk fibroin before spinning by a combination of advanced solid-state NMR methods.

PubMed

Nakazawa, Yasumoto; Asakura, Tetsuo

2003-06-18

Fibrous proteins unlike globular proteins, contain repetitive amino acid sequences, giving rise to very regular secondary protein structures. Silk fibroin from a wild silkworm, Samia cynthia ricini, consists of about 100 repeats of alternating polyalanine (poly-Ala) regions of 12-13 residues in length and Gly-rich regions. In this paper, the precise structure of the model peptide, GGAGGGYGGDGG(A)(12)GGAGDGYGAG, which is a typical repeated sequence of the silk fibroin, was determined using a combination of three kinds of solid-state NMR studies; a quantitative use of (13)C CP/MAS NMR chemical shift with conformation-dependent (13)C chemical shift contour plots, 2D spin diffusion (13)C solid-state NMR under off magic angle spinning and rotational echo double resonance. The structure of the model peptide corresponding to the silk fibroin structure before spinning was determined. The torsion angles of the central Ala residue, Ala(19), in the poly-Ala region were determined to be (phi, psi) = (-59 degrees, -48 degrees ) which are values typically associated with alpha-helical structures. However, the torsion angles of the Gly(25) residue adjacent to the C-terminal side of the poly-Ala chain were determined to be (phi, psi) = (-66 degrees, -22 degrees ) and those of Gly(12) and Ala(13) residues at the N-terminal of the poly-Ala chain to be (phi, psi) = (-70 degrees, -30 degrees ). In addition, REDOR experiments indicate that the torsion angles of the two C-terminal Ala residues, Ala(23) and Ala(24), are (phi, psi) = (-66 degrees, -22 degrees ) and those of N-terminal two Ala residues, Ala(13) and Ala(14) are (phi, psi) = (-70 degrees, -30 degrees ). Thus, the local structure of N-terminal and C-terminal residues, and also the neighboring residues of alpha-helical poly-Ala chain in the model peptide is a more strongly wound structure than found in typical alpha-helix structures.

Using Molecular Models To Show Steric Clash in Peptides: An Illustration of Two Disallowed Regions in the Ramachandran Diagram

ERIC Educational Resources Information Center

Halkides, Christopher J.

2013-01-01

In this activity, students manipulate three-dimensional molecular models of the Ala-Ala-Ala tripeptide, where Ala is alanine. They rotate bonds to show that the pairs of dihedral angles phi = 0 degrees, psi = 180 degrees, and phi = 0 degrees, psi = 0 degrees lead to unfavorable interactions among the main chain atoms of the tripeptide. This…

Molecular structures of Se(SCH3)2 and Te(SCH3)2 using gas-phase electron diffraction and ab initio and DFT geometry optimisations.

PubMed

Fleischer, Holger; Wann, Derek A; Hinchley, Sarah L; Borisenko, Konstantin B; Lewis, James R; Mawhorter, Richard J; Robertson, Heather E; Rankin, David W H

2005-10-07

The molecular structures of Se(SCH(3))(2) and Te(SCH(3))(2) were investigated using gas-phase electron diffraction (GED) and ab initio and DFT geometry optimisations. While parameters involving H atoms were refined using flexible restraints according to the SARACEN method, parameters that depended only on heavy atoms could be refined without restraints. The GED-determined geometric parameters (r(h1)) are: rSe-S 219.1(1), rS-C 183.2(1), rC-H 109.6(4) pm; angleS-Se-S 102.9(3), angleSe-S-C 100.6(2), angleS-C-H (mean) 107.4(5), phiS-Se-S-C 87.9(20), phiSe-S-C-H 178.8(19) degrees for Se(SCH(3))(2), and rTe-S 238.1(2), rS-C 184.1(3), rC-H 110.0(6) pm; angleS-Te-S 98.9(6), angleTe-S-C 99.7(4), angleS-C-H (mean) 109.2(9), phiS-Te-S-C 73.0(48), phiTe-S-C-H 180.1(19) degrees for Te(SCH(3))(2). Ab initio and DFT calculations were performed at the HF, MP2 and B3LYP levels, employing either full-electron basis sets [3-21G(d) or 6-31G(d)] or an effective core potential with a valence basis set [LanL2DZ(d)]. The best fit to the GED structures was achieved at the MP2 level. Differences between GED and MP2 results for rS-C and angleS-Te-S were explained by the thermal population of excited vibrational states under the experimental conditions. All theoretical models agreed that each compound exists as two stable conformers, one in which the methyl groups are on the same side (g(+)g(-) conformer) and one in which they are on different sides (g(+)g(+) conformer) of the S-Y-S plane (Y = Se, Te). The conformational composition under the experimental conditions could not be resolved from the GED data. Despite GED R-factors and ab initio and DFT energies favouring the g(+)g(+) conformer, it is likely that both conformers are present, for Se(SCH(3))(2) as well as for Te(SCH(3))(2).

DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs.

PubMed

Wang, Lin; Zhang, Min; Alexov, Emil

2016-02-15

A new pKa prediction web server is released, which implements DelPhi Gaussian dielectric function to calculate electrostatic potentials generated by charges of biomolecules. Topology parameters are extended to include atomic information of nucleotides of RNA and DNA, which extends the capability of pKa calculations beyond proteins. The web server allows the end-user to protonate the biomolecule at particular pH based on calculated pKa values and provides the downloadable file in PQR format. Several tests are performed to benchmark the accuracy and speed of the protocol. The web server follows a client-server architecture built on PHP and HTML and utilizes DelPhiPKa program. The computation is performed on the Palmetto supercomputer cluster and results/download links are given back to the end-user via http protocol. The web server takes advantage of MPI parallel implementation in DelPhiPKa and can run a single job on up to 24 CPUs. The DelPhiPKa web server is available at http://compbio.clemson.edu/pka_webserver. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

X-Phi and Carnapian Explication

PubMed Central

Shepherd, Joshua; Justus, James

2015-01-01

The rise of experimental philosophy (x-phi) has placed metaphilosophical questions, particularly those concerning concepts, at the center of philosophical attention. X-phi offers empirically rigorous methods for identifying conceptual content, but what exactly it contributes towards evaluating conceptual content remains unclear. We show how x-phi complements Rudolf Carnap’s underappreciated methodology for concept determination, explication. This clarifies and extends x-phi’s positive philosophical import, and also exhibits explication’s broad appeal. But there is a potential problem: Carnap’s account of explication was limited to empirical and logical concepts, but many concepts of interest to philosophers (experimental and otherwise) are essentially normative. With formal epistemology as a case study, we show how x-phi assisted explication can apply to normative domains. PMID:26345713

Emergency Multiengine Aircraft System for Lateral Control Using Differential Thrust Control of Wing Engines

NASA Technical Reports Server (NTRS)

Burken, John J. (Inventor); Burcham, Frank W., Jr. (Inventor); Bull, John (Inventor)

2000-01-01

Development of an emergency flight control system is disclosed for lateral control using only differential engine thrust modulation of multiengine aircraft is currently underway. The multiengine has at least two engines laterally displaced to the left and right from the axis of the aircraft. In response to a heading angle command psi(sub c) is to be tracked. By continually sensing the heading angle psi of the aircraft and computing a heading error signal psi(sub e) as a function of the difference between the heading angle command psi(sub c) and the sensed heading angle psi, a track control signal is developed with compensation as a function of sensed bank angle phi. Bank angle rate phi, or roll rate p, yaw rate tau, and true velocity produce an aircraft thrust control signal ATC(sub psi(L,R)). The thrust control signal is differentially applied to the left and right engines, with equal amplitude and opposite sign, such that a negative sign is applied to the control signal on the side of the aircraft. A turn is required to reduce the error signal until the heading feedback reduces the error to zero.

Structures Of Magnetically-Supported Filaments And Their Appearance In The Linear Polarization

NASA Astrophysics Data System (ADS)

Tomisaka, Kohji

2017-10-01

Dust thermal emissions observed with Herschel have revealed that interstellar molecular clouds consist of many filaments. Polarization observation of interstellar extinctions in the optical and near IR wavelengths shows that the dense filaments are extending perpendicular to the interstellar magnetic field. Magnetohydrostatic structures of such filaments are studied. It is well known that a hydrostatic filament without magnetic field has a maximum line mass of ¥lambda_max=2c_s^2/G (c_s:the isothermal sound speed and G: the gravitational constant). On the other hand, the magnetically-supported maximum line mass increases in proportion to the magnetic flux per unit length threading the filament (¥phi), as ¥lambda_max 2c_s^2/G + ¥phi/(2¥pi G^1/2). Comparison is made with 3D clouds. Stability of these magnetized filaments is studied using time-dependent 3D MHD simulations to discuss star formation in the filaments. Polarization pattern expected for the magnetically subcritical filaments is calculated. The distribution function of the angle between B-field and the axis of the filament, which is obtained with Planck Satellite, is compared with this mock observation.

FAST TRACK COMMUNICATION: A closer look at arrested spinodal decomposition in protein solutions

NASA Astrophysics Data System (ADS)

Gibaud, Thomas; Schurtenberger, Peter

2009-08-01

Concentrated aqueous solutions of the protein lysozyme undergo a liquid-solid transition upon a temperature quench into the unstable spinodal region below a characteristic arrest temperature of Tf = 15 °C. We use video microscopy and ultra-small angle light scattering in order to investigate the arrested structures as a function of initial concentration, quench temperature and rate of the temperature quench. We find that the solid-like samples show all the features of a bicontinuous network that is formed through an arrested spinodal decomposition process. We determine the correlation length ξ and demonstrate that ξ exhibits a temperature dependence that closely follows the critical scaling expected for density fluctuations during the early stages of spinodal decomposition. These findings are in agreement with an arrest scenario based on a state diagram where the arrest or gel line extends far into the unstable region below the spinodal line. Arrest then occurs when during the early stage of spinodal decomposition the volume fraction phi2 of the dense phase intersects the dynamical arrest threshold phi2,Glass, upon which phase separation gets pinned into a space-spanning gel network with a characteristic length ξ.

Anisotropic scattering of discrete particle arrays.

PubMed

Paul, Joseph S; Fu, Wai Chong; Dokos, Socrates; Box, Michael

2010-05-01

Far-field intensities of light scattered from a linear centro-symmetric array illuminated by a plane wave of incident light are estimated at a series of detector angles. The intensities are computed from the superposition of E-fields scattered by the individual array elements. An average scattering phase function is used to model the scattered fields of individual array elements. The nature of scattering from the array is investigated using an image (theta-phi plot) of the far-field intensities computed at a series of locations obtained by rotating the detector angle from 0 degrees to 360 degrees, corresponding to each angle of incidence in the interval [0 degrees 360 degrees]. The diffraction patterns observed from the theta-Phi plot are compared with those for isotropic scattering. In the absence of prior information on the array geometry, the intensities corresponding to theta-Phi pairs satisfying the Bragg condition are used to estimate the phase function. An algorithmic procedure is presented for this purpose and tested using synthetic data. The relative error between estimated and theoretical values of the phase function is shown to be determined by the mean spacing factor, the number of elements, and the far-field distance. An empirical relationship is presented to calculate the optimal far-field distance for a given specification of the percentage error.

Does Stevens's Power Law for Brightness Extend to Perceptual Brightness Averaging?

ERIC Educational Resources Information Center

Bauer, Ben

2009-01-01

Stevens's power law ([Psi][infinity][Phi][beta]) captures the relationship between physical ([Phi]) and perceived ([Psi]) magnitude for many stimulus continua (e.g., luminance and brightness, weight and heaviness, area and size). The exponent ([beta]) indicates whether perceptual magnitude grows more slowly than physical magnitude ([beta] less…

Field line twist and field-aligned currents in an axially symmetric equilibrium magnetosphere. [of Uranus

NASA Technical Reports Server (NTRS)

Voigt, Gerd-Hannes

1986-01-01

Field-aligned Birkeland currents and the angle of the magnetic line twist were calculated for an axially symmetric pole-on magnetosphere (assumed to be in MHD equilibrium). The angle of the field line twist was shown to have a strong radial dependence on the axisymmetric magnetotail as well as on the ionospheric conductivity and the amount of thermal plasma contained in closed magnetotail flux tubes. The field line twist results from the planetary rotation, which leads to the development of a toroidal magnetic B-sub-phi component and to differentially rotating magnetic field lines. It was shown that the time development of the toroidal magnetic B-sub-phi component and the rotation frequency are related through an induction equation.

Addition of a 5/cm Spectral Resolution Band Model Option to LOWTRAN5.

DTIC Science & Technology

1980-10-01

THETA-PHI CEO 880 SALP -RX*SPHI CEO 890 IF (SPHIl.GT.1 .E-10) DS-(RE+2)*SIN(BET*CA)ISPHI CEO 900 BETA-BETA+BET CEO 910 PSI-BETA+PHI-ANGLE CEO 920 PHI...9,I+1 )/EH(9,I) CEO 1250 SPHI-SPHI*RX/RN CEO 1260 IF (SALP.CE .RN) SFRI- SALP CEO 1270 -J75 CONTINUE CEO 1280 GO TO 190 CEO 1290 C HORIZONTAL PATH CEO...ABS(X2-NM).CT.1.OE-5) ALP-ASfI( SALP )/CA CEO 2120 IET-ALP-THET CEO 2130 17 (SPEI...-10) DS-(RE+X2)*SIN(BET*Ch)/SBI CEO 2140 THETAmI 80. 0-TE CEO 2150

Phi (Φ) and psi (Ψ) angles involved in malarial peptide bonds determine sterile protective immunity.

PubMed

Patarroyo, Manuel E; Moreno-Vranich, Armando; Bermúdez, Adriana

2012-12-07

Modified HABP (mHABP) regions interacting with HLA-DRβ1(∗) molecules have a more restricted conformation and/or sequence than other mHABPs which do not fit perfectly into their peptide binding regions (PBR) and do not induce an acceptable immune response due to the critical role of their Φ and Ψ torsion angles. These angle's critical role was determined in such highly immunogenic, protection-inducing response against experimental malaria using the conformers (mHABPs) obtained by (1)H-NMR and superimposed into HLA-DRβ1(∗)-like Aotus monkey molecules; their phi (Φ) and psi (Ψ) angles were measured and the H-bond formation between these molecules was evaluated. The aforementioned mHABP propensity to assume a regular conformation similar to a left-handed polyproline type II helix (PPII(L)) led to suggesting that favouring these conformations according to their amino acid sequence would lead to high antibody titre production and sterile protective immunity induction against malaria, thereby adding new principles or rules for vaccine development, malaria being one of them. Copyright © 2012 Elsevier Inc. All rights reserved.

Energetic distributions of interface states Dit(phi sub s) of MOS transistors in extension of Kuhn's quasistatic C(V)-method

NASA Astrophysics Data System (ADS)

Krautschneider, W.; Wagemann, H. G.

1983-10-01

Kuhn's quasi-static C(V)-method has been extended to MOS transistors by considering the capacitances of the source and drain p-n junctions additionally to the MOS varactor circuit model. The width of the space charge layers w(phi sub s) is calculated as a function of the surface potential phi sub s and applied to the MOS capacitance as a function of the gate voltage. Capacitance behavior for different channel length is presented as a model and compared to measurement results and evaluations of energetic distributions of interface states Dit(phi sub s) for MOS transistor and MOS varactor on the same chip.

Vacuum-polarization effects in global monopole space-times

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

Mazzitelli, F.D.; Lousto, C.O.

1991-01-15

The gravitational effect produced by a global monopole may be approximated by a solid deficit angle. As a consequence, the energy-momentum tensor of a quantum field will have a nonzero vacuum expectation value. Here we study this vacuum-polarization effect'' around the monopole. We find explicit expressions for both {l angle}{phi}{sup 2}{r angle}{sub ren} and {l angle}{ital T}{sub {mu}{nu}}{r angle}{sub ren} for a massless scalar field. The back reaction of the quantum field on the monopole metric is also investigated.

PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database

PubMed Central

Urban, Martin; Cuzick, Alayne; Rutherford, Kim; Irvine, Alistair; Pedro, Helder; Pant, Rashmi; Sadanadan, Vidyendra; Khamari, Lokanath; Billal, Santoshkumar; Mohanty, Sagar; Hammond-Kosack, Kim E.

2017-01-01

The pathogen–host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen–host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. The new release of PHI-base Version 4.2 (October 2016) has an increased data content containing information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species belong ∼70% to plants and 30% to other species of medical and/or environmental importance. Additional data types included into PHI-base 4 are the direct targets of pathogen effector proteins in experimental and natural host organisms. The curation problems encountered and the future directions of the PHI-base project are briefly discussed. PMID:27915230

Are supernova remnants quasi-parallel or quasi-perpendicular accelerators

NASA Technical Reports Server (NTRS)

Spangler, S. R.; Leckband, J. A.; Cairns, I. H.

1989-01-01

Observations of shock waves in the solar system which show a pronounced difference in the plasma wave and particle environment depending on whether the shock is propagating along or perpendicular to the interplanetary magnetic field are discussed. Theories for particle acceleration developed for quasi-parallel and quasi-perpendicular shocks, when extended to the interstellar medium suggest that the relativistic electrons in radio supernova remnants are accelerated by either the Q parallel or Q perpendicular mechanisms. A model for the galactic magnetic field and published maps of supernova remnants were used to search for a dependence of structure on the angle Phi. Results show no tendency for the remnants as a whole to favor the relationship expected for either mechanism, although individual sources resemble model remnants of one or the other acceleration process.

Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling.

PubMed

Perić-Hassler, Lovorka; Hansen, Halvor S; Baron, Riccardo; Hünenberger, Philippe H

2010-08-16

Explicit-solvent molecular dynamics (MD) simulations of the 11 glucose-based disaccharides in water at 300K and 1bar are reported. The simulations were carried out with the GROMOS 45A4 force-field and the sampling along the glycosidic dihedral angles phi and psi was artificially enhanced using the local elevation umbrella sampling (LEUS) method. The trajectories are analyzed in terms of free-energy maps, stable and metastable conformational states (relative free energies and estimated transition timescales), intramolecular H-bonds, single molecule configurational entropies, and agreement with experimental data. All disaccharides considered are found to be characterized either by a single stable (overwhelmingly populated) state ((1-->n)-linked disaccharides with n=1, 2, 3, or 4) or by two stable (comparably populated and differing in the third glycosidic dihedral angle omega ; gg or gt) states with a low interconversion barrier ((1-->6)-linked disaccharides). Metastable (anti-phi or anti-psi) states are also identified with relative free energies in the range of 8-22 kJ mol(-1). The 11 compounds can be classified into four families: (i) the alpha(1-->1)alpha-linked disaccharide trehalose (axial-axial linkage) presents no metastable state, the lowest configurational entropy, and no intramolecular H-bonds; (ii) the four alpha(1-->n)-linked disaccharides (n=1, 2, 3, or 4; axial-equatorial linkage) present one metastable (anti-psi) state, an intermediate configurational entropy, and two alternative intramolecular H-bonds; (iii) the four beta(1-->n)-linked disaccharides (n=1, 2, 3, or 4; equatorial-equatorial linkage) present two metastable (anti-phi and anti-psi) states, an intermediate configurational entropy, and one intramolecular H-bond; (iv) the two (1-->6)-linked disaccharides (additional glycosidic dihedral angle) present no (isomaltose) or a pair of (gentiobiose) metastable (anti-phi) states, the highest configurational entropy, and no intramolecular H-bonds. The observed conformational preferences appear to be dictated by four main driving forces (ring conformational preferences, exo-anomeric effect, steric constraints, and possible presence of a third glycosidic dihedral angle), leaving a secondary role to intramolecular H-bonding and specific solvation effects. In spite of the weak conformational driving force attributed to solvent-exposed H-bonds in water (highly polar protic solvent), intramolecular H-bonds may still have a significant influence on the physico-chemical properties of the disaccharide by decreasing its hydrophilicity. Along with previous work, the results also complete the suggestion of a spectrum of approximate transition timescales for carbohydrates up to the disaccharide level, namely: approximately 30 ps (hydroxyl groups), approximately 1 ns (free lactol group, free hydroxymethyl groups, glycosidic dihedral angleomega in (1-->6)-linked disaccharides), approximately 10 ns to 2 micros (ring conformation, glycosidic dihedral angles phi and psi). The calculated average values of the glycosidic torsional angles agree well with the available experimental data, providing validation for the force-field and simulation methodology employed. Copyright 2010 Elsevier Ltd. All rights reserved.

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

Acosta, D.; Affolder, Anthony A.; Albrow, M.G.

The authors have measured the azimuthal angular correlation of b{bar b} production, using 86.5 pb{sup -1} of data collected by Collider Detector at Fermilab (CDF) in p{bar p} collisions at {radical}s = 1.8 TeV during 1994-1995. In high-energy p{bar p} collisions, such as at the Tevatron, b{bar b} production can be schematically categorized into three mechanisms. The leading-order (LO) process is ''flavor creation'', where both b and {bar b} quarks substantially participate in the hard scattering and result in a distinct back-to-back signal in final state. The ''flavor excitation'' and the ''gluon splitting'' processes, which appear at next-leading-order (NLO), aremore » known to make a comparable contribution to total b{bar b} cross section, while providing very different opening angle distributions from the LO process. An azimuthal opening angle between bottom and anti-bottom, {Delta}{phi}, has been used for the correlation measurement to probe the interaction creating b{bar b} pairs. The {Delta}{phi} distribution has been obtained from two different methods. one method measures the {Delta}{phi} between bottom hadrons using events with two reconstructed secondary vertex tags. The other method uses b{bar b} {yields} (J/{psi}X)({ell}X') events, where the charged lepton ({ell}) is an electron (e) or a muon ({mu}), to measure {Delta}{phi} between bottom quarks. The b{bar b} purity is determined as a function of {Delta}{phi} by fitting the decay length of the J/{psi} and the impact parameter of the {ell}. Both methods quantify the contribution from higher-order production mechanisms by the fraction of the b{bar b} pairs produced in the same azimuthal hemisphere, f{sub toward}. The measured f{sub toward} values are consistent with both parton shower Monte Carlo and NLO QCD predictions.« less

The Physics of the B Factories

NASA Astrophysics Data System (ADS)

Bevan, A. J.; Golob, B.; Mannel, Th.; Prell, S.; Yabsley, B. D.; Aihara, H.; Anulli, F.; Arnaud, N.; Aushev, T.; Beneke, M.; Beringer, J.; Bianchi, F.; Bigi, I. I.; Bona, M.; Brambilla, N.; Brodzicka, J.; Chang, P.; Charles, M. J.; Cheng, C. H.; Cheng, H.-Y.; Chistov, R.; Colangelo, P.; Coleman, J. P.; Drutskoy, A.; Druzhinin, V. P.; Eidelman, S.; Eigen, G.; Eisner, A. M.; Faccini, R.; Flood, K. T.; Gambino, P.; Gaz, A.; Gradl, W.; Hayashii, H.; Higuchi, T.; Hulsbergen, W. D.; Hurth, T.; Iijima, T.; Itoh, R.; Jackson, P. D.; Kass, R.; Kolomensky, Yu. G.; Kou, E.; Križan, P.; Kronfeld, A.; Kumano, S.; Kwon, Y. J.; Latham, T. E.; Leith, D. W. G. S.; Lüth, V.; Martinez-Vidal, F.; Meadows, B. T.; Mussa, R.; Nakao, M.; Nishida, S.; Ocariz, J.; Olsen, S. L.; Pakhlov, P.; Pakhlova, G.; Palano, A.; Pich, A.; Playfer, S.; Poluektov, A.; Porter, F. C.; Robertson, S. H.; Roney, J. M.; Roodman, A.; Sakai, Y.; Schwanda, C.; Schwartz, A. J.; Seidl, R.; Sekula, S. J.; Steinhauser, M.; Sumisawa, K.; Swanson, E. S.; Tackmann, F.; Trabelsi, K.; Uehara, S.; Uno, S.; van de Water, R.; Vasseur, G.; Verkerke, W.; Waldi, R.; Wang, M. Z.; Wilson, F. F.; Zupan, J.; Zupanc, A.; Adachi, I.; Albert, J.; Banerjee, Sw.; Bellis, M.; Ben-Haim, E.; Biassoni, P.; Cahn, R. N.; Cartaro, C.; Chauveau, J.; Chen, C.; Chiang, C. C.; Cowan, R.; Dalseno, J.; Davier, M.; Davies, C.; Dingfelder, J. C.; Echenard, B.; Epifanov, D.; Fulsom, B. G.; Gabareen, A. M.; Gary, J. W.; Godang, R.; Graham, M. T.; Hafner, A.; Hamilton, B.; Hartmann, T.; Hayasaka, K.; Hearty, C.; Iwasaki, Y.; Khodjamirian, A.; Kusaka, A.; Kuzmin, A.; Lafferty, G. D.; Lazzaro, A.; Li, J.; Lindemann, D.; Long, O.; Lusiani, A.; Marchiori, G.; Martinelli, M.; Miyabayashi, K.; Mizuk, R.; Mohanty, G. B.; Muller, D. R.; Nakazawa, H.; Ongmongkolkul, P.; Pacetti, S.; Palombo, F.; Pedlar, T. K.; Piilonen, L. E.; Pilloni, A.; Poireau, V.; Prothmann, K.; Pulliam, T.; Rama, M.; Ratcliff, B. N.; Roudeau, P.; Schrenk, S.; Schroeder, T.; Schubert, K. R.; Shen, C. P.; Shwartz, B.; Soffer, A.; Solodov, E. P.; Somov, A.; Starič, M.; Stracka, S.; Telnov, A. V.; Todyshev, K. Yu.; Tsuboyama, T.; Uglov, T.; Vinokurova, A.; Walsh, J. J.; Watanabe, Y.; Won, E.; Wormser, G.; Wright, D. H.; Ye, S.; Zhang, C. C.; Abachi, S.; Abashian, A.; Abe, K.; Abe, N.; Abe, R.; Abe, T.; Abrams, G. S.; Adam, I.; Adamczyk, K.; Adametz, A.; Adye, T.; Agarwal, A.; Ahmed, H.; Ahmed, M.; Ahmed, S.; Ahn, B. S.; Ahn, H. S.; Aitchison, I. J. R.; Akai, K.; Akar, S.; Akatsu, M.; Akemoto, M.; Akhmetshin, R.; Akre, R.; Alam, M. S.; Albert, J. N.; Aleksan, R.; Alexander, J. P.; Alimonti, G.; Allen, M. T.; Allison, J.; Allmendinger, T.; Alsmiller, J. R. G.; Altenburg, D.; Alwyn, K. E.; An, Q.; Anderson, J.; Andreassen, R.; Andreotti, D.; Andreotti, M.; Andress, J. C.; Angelini, C.; Anipko, D.; Anjomshoaa, A.; Anthony, P. L.; Antillon, E. A.; Antonioli, E.; Aoki, K.; Arguin, J. 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N.; Browne, M.; Bruinsma, M.; Brunet, S.; Bucci, F.; Buchanan, C.; Buchmueller, O. L.; Bünger, C.; Bugg, W.; Bukin, A. D.; Bula, R.; Bulten, H.; Burchat, P. R.; Burgess, W.; Burke, J. P.; Button-Shafer, J.; Buzykaev, A. R.; Buzzo, A.; Cai, Y.; Calabrese, R.; Calcaterra, A.; Calderini, G.; Camanzi, B.; Campagna, E.; Campagnari, C.; Capra, R.; Carassiti, V.; Carpinelli, M.; Carroll, M.; Casarosa, G.; Casey, B. C. K.; Cason, N. M.; Castelli, G.; Cavallo, N.; Cavoto, G.; Cecchi, A.; Cenci, R.; Cerizza, G.; Cervelli, A.; Ceseracciu, A.; Chai, X.; Chaisanguanthum, K. S.; Chang, M. C.; Chang, Y. H.; Chang, Y. W.; Chao, D. S.; Chao, M.; Chao, Y.; Charles, E.; Chavez, C. A.; Cheaib, R.; Chekelian, V.; Chen, A.; Chen, E.; Chen, G. P.; Chen, H. F.; Chen, J.-H.; Chen, J. C.; Chen, K. F.; Chen, P.; Chen, S.; Chen, W. T.; Chen, X.; Chen, X. R.; Chen, Y. Q.; Cheng, B.; Cheon, B. G.; Chevalier, N.; Chia, Y. M.; Chidzik, S.; Chilikin, K.; Chistiakova, M. V.; Cizeron, R.; Cho, I. S.; Cho, K.; Chobanova, V.; Choi, H. H. F.; Choi, K. S.; Choi, S. K.; Choi, Y.; Choi, Y. K.; Christ, S.; Chu, P. H.; Chun, S.; Chuvikov, A.; Cibinetto, G.; Cinabro, D.; Clark, A. R.; Clark, P. J.; Clarke, C. K.; Claus, R.; Claxton, B.; Clifton, Z. C.; Cochran, J.; Cohen-Tanugi, J.; Cohn, H.; Colberg, T.; Cole, S.; Colecchia, F.; Condurache, C.; Contri, R.; Convert, P.; Convery, M. R.; Cooke, P.; Copty, N.; Cormack, C. M.; Dal Corso, F.; Corwin, L. A.; Cossutti, F.; Cote, D.; Cotta Ramusino, A.; Cottingham, W. N.; Couderc, F.; Coupal, D. P.; Covarelli, R.; Cowan, G.; Craddock, W. W.; Crane, G.; Crawley, H. B.; Cremaldi, L.; Crescente, A.; Cristinziani, M.; Crnkovic, J.; Crosetti, G.; Cuhadar-Donszelmann, T.; Cunha, A.; Curry, S.; D'Orazio, A.; Dû, S.; Dahlinger, G.; Dahmes, B.; Dallapiccola, C.; Danielson, N.; Danilov, M.; Das, A.; Dash, M.; Dasu, S.; Datta, M.; Daudo, F.; Dauncey, P. D.; David, P.; Davis, C. L.; Day, C. T.; De Mori, F.; De Domenico, G.; De Groot, N.; De la Vaissière, C.; de la Vaissière, Ch.; de Lesquen, A.; De Nardo, G.; de Sangro, R.; De Silva, A.; DeBarger, S.; Decker, F. J.; del Amo Sanchez, P.; Del Buono, L.; Del Gamba, V.; del Re, D.; Della Ricca, G.; Denig, A. G.; Derkach, D.; Derrington, I. M.; DeStaebler, H.; Destree, J.; Devmal, S.; Dey, B.; Di Girolamo, B.; Marco, E. Di; Dickopp, M.; Dima, M. O.; Dittrich, S.; Dittongo, S.; Dixon, P.; Dneprovsky, L.; Dohou, F.; Doi, Y.; Doležal, Z.; Doll, D. A.; Donald, M.; Dong, L.; Dong, L. Y.; Dorfan, J.; Dorigo, A.; Dorsten, M. P.; Dowd, R.; Dowdell, J.; Drásal, Z.; Dragic, J.; Drummond, B. W.; Dubitzky, R. S.; Dubois-Felsmann, G. P.; Dubrovin, M. S.; Duh, Y. C.; Duh, Y. T.; Dujmic, D.; Dungel, W.; Dunwoodie, W.; Dutta, D.; Dvoretskii, A.; Dyce, N.; Ebert, M.; Eckhart, E. A.; Ecklund, S.; Eckmann, R.; Eckstein, P.; Edgar, C. L.; Edwards, A. J.; Egede, U.; Eichenbaum, A. M.; Elmer, P.; Emery, S.; Enari, Y.; Enomoto, R.; Erdos, E.; Erickson, R.; Ernst, J. A.; Erwin, R. J.; Escalier, M.; Eschenburg, V.; Eschrich, I.; Esen, S.; Esteve, L.; Evangelisti, F.; Everton, C. W.; Eyges, V.; Fabby, C.; Fabozzi, F.; Fahey, S.; Falbo, M.; Fan, S.; Fang, F.; Fanin, C.; Farbin, A.; Farhat, H.; Fast, J. E.; Feindt, M.; Fella, A.; Feltresi, E.; Ferber, T.; Fernholz, R. E.; Ferrag, S.; Ferrarotto, F.; Ferroni, F.; Field, R. C.; Filippi, A.; Finocchiaro, G.; Fioravanti, E.; Firmino da Costa, J.; Fischer, P.-A.; Fisher, A. S.; Fisher, P. H.; Flacco, C. J.; Flack, R. L.; Flaecher, H. U.; Flanagan, J.; Flanigan, J. M.; Ford, K. E.; Ford, W. T.; Forster, I. J.; Forti, A. C.; Forti, F.; Fortin, D.; Foster, B.; Foulkes, S. D.; Fouque, G.; Fox, J.; Franchini, P.; Franco Sevilla, M.; Franek, B.; Frank, E. D.; Fransham, K. B.; Fratina, S.; Fratini, K.; Frey, A.; Frey, R.; Friedl, M.; Fritsch, M.; Fry, J. R.; Fujii, H.; Fujikawa, M.; Fujita, Y.; Fujiyama, Y.; Fukunaga, C.; Fukushima, M.; Fullwood, J.; Funahashi, Y.; Funakoshi, Y.; Furano, F.; Furman, M.; Furukawa, K.; Futterschneider, H.; Gabathuler, E.; Gabriel, T. A.; Gabyshev, N.; Gaede, F.; Gagliardi, N.; Gaidot, A.; Gaillard, J.-M.; Gaillard, J. R.; Galagedera, S.; Galeazzi, F.; Gallo, F.; Gamba, D.; Gamet, R.; Gan, K. K.; Gandini, P.; Ganguly, S.; Ganzhur, S. F.; Gao, Y. Y.; Gaponenko, I.; Garmash, A.; Garra Tico, J.; Garzia, I.; Gaspero, M.; Gastaldi, F.; Gatto, C.; Gaur, V.; Geddes, N. I.; Geld, T. L.; Genat, J.-F.; George, K. A.; George, M.; George, S.; Georgette, Z.; Gershon, T. J.; Gill, M. S.; Gillard, R.; Gilman, J. D.; Giordano, F.; Giorgi, M. A.; Giraud, P.-F.; Gladney, L.; Glanzman, T.; Glattauer, R.; Go, A.; Goetzen, K.; Goh, Y. M.; Gokhroo, G.; Goldenzweig, P.; Golubev, V. B.; Gopal, G. P.; Gordon, A.; Gorišek, A.; Goriletsky, V. I.; Gorodeisky, R.; Gosset, L.; Gotow, K.; Gowdy, S. J.; Graffin, P.; Grancagnolo, S.; Grauges, E.; Graziani, G.; Green, M. G.; Greene, M. G.; Grenier, G. J.; Grenier, P.; Griessinger, K.; Grillo, A. A.; Grinyov, B. V.; Gritsan, A. V.; Grosdidier, G.; Grosse Perdekamp, M.; Grosso, P.; Grothe, M.; Groysman, Y.; Grünberg, O.; Guido, E.; Guler, H.; Gunawardane, N. J. W.; Guo, Q. H.; Guo, R. S.; Guo, Z. J.; Guttman, N.; Ha, H.; Ha, H. C.; Haas, T.; Haba, J.; Hachtel, J.; Hadavand, H. K.; Hadig, T.; Hagner, C.; Haire, M.; Haitani, F.; Haji, T.; Haller, G.; Halyo, V.; Hamano, K.; Hamasaki, H.; Hamel de Monchenault, G.; Hamilton, J.; Hamilton, R.; Hamon, O.; Han, B. Y.; Han, Y. L.; Hanada, H.; Hanagaki, K.; Handa, F.; Hanson, J. E.; Hanushevsky, A.; Hara, K.; Hara, T.; Harada, Y.; Harrison, P. F.; Harrison, T. J.; Harrop, B.; Hart, A. J.; Hart, P. A.; Hartfiel, B. L.; Harton, J. L.; Haruyama, T.; Hasan, A.; Hasegawa, Y.; Hast, C.; Hastings, N. C.; Hasuko, K.; Hauke, A.; Hawkes, C. M.; Hayashi, K.; Hazumi, M.; Hee, C.; Heenan, E. M.; Heffernan, D.; Held, T.; Henderson, R.; Henderson, S. W.; Hertzbach, S. S.; Hervé, S.; Heß, M.; Heusch, C. A.; Hicheur, A.; Higashi, Y.; Higasino, Y.; Higuchi, I.; Hikita, S.; Hill, E. J.; Himel, T.; Hinz, L.; Hirai, T.; Hirano, H.; Hirschauer, J. F.; Hitlin, D. G.; Hitomi, N.; Hodgkinson, M. C.; Höcker, A.; Hoi, C. T.; Hojo, T.; Hokuue, T.; Hollar, J. J.; Hong, T. M.; Honscheid, K.; Hooberman, B.; Hopkins, D. A.; Horii, Y.; Hoshi, Y.; Hoshina, K.; Hou, S.; Hou, W. S.; Hryn'ova, T.; Hsiung, Y. B.; Hsu, C. L.; Hsu, S. C.; Hu, H.; Hu, T.; Huang, H. C.; Huang, T. J.; Huang, Y. C.; Huard, Z.; Huffer, M. E.; Hufnagel, D.; Hung, T.; Hutchcroft, D. E.; Hyun, H. J.; Ichizawa, S.; Igaki, T.; Igarashi, A.; Igarashi, S.; Igarashi, Y.; Igonkina, O.; Ikado, K.; Ikeda, H.; Ikeda, H.; Ikeda, K.; Ilic, J.; Inami, K.; Innes, W. R.; Inoue, Y.; Ishikawa, A.; Ishino, H.; Itagaki, K.; Itami, S.; Itoh, K.; Ivanchenko, V. N.; Iverson, R.; Iwabuchi, M.; Iwai, G.; Iwai, M.; Iwaida, S.; Iwamoto, M.; Iwasaki, H.; Iwasaki, M.; Iwashita, T.; Izen, J. M.; Jackson, D. J.; Jackson, F.; Jackson, G.; Jackson, P. S.; Jacobsen, R. G.; Jacoby, C.; Jaegle, I.; Jain, V.; Jalocha, P.; Jang, H. K.; Jasper, H.; Jawahery, A.; Jayatilleke, S.; Jen, C. M.; Jensen, F.; Jessop, C. P.; Ji, X. B.; John, M. J. J.; Johnson, D. R.; Johnson, J. R.; Jolly, S.; Jones, M.; Joo, K. K.; Joshi, N.; Joshi, N. J.; Judd, D.; Julius, T.; Kadel, R. W.; Kadyk, J. A.; Kagan, H.; Kagan, R.; Kah, D. H.; Kaiser, S.; Kaji, H.; Kajiwara, S.; Kakuno, H.; Kameshima, T.; Kaminski, J.; Kamitani, T.; Kaneko, J.; Kang, J. H.; Kang, J. S.; Kani, T.; Kapusta, P.; Karbach, T. M.; Karolak, M.; Karyotakis, Y.; Kasami, K.; Katano, G.; Kataoka, S. U.; Katayama, N.; Kato, E.; Kato, Y.; Kawai, H.; Kawai, M.; Kawamura, N.; Kawasaki, T.; Kay, J.; Kay, M.; Kelly, M. P.; Kelsey, M. H.; Kent, N.; Kerth, L. T.; Khan, A.; Khan, H. R.; Kharakh, D.; Kibayashi, A.; Kichimi, H.; Kiesling, C.; Kikuchi, M.; Kikutani, E.; Kim, B. H.; Kim, C. H.; Kim, D. W.; Kim, H.; Kim, H. J.; Kim, H. O.; Kim, H. W.; Kim, J. B.; Kim, J. H.; Kim, K. T.; Kim, M. J.; Kim, P.; Kim, S. K.; Kim, S. M.; Kim, T. H.; Kim, Y. I.; Kim, Y. J.; King, G. J.; Kinoshita, K.; Kirk, A.; Kirkby, D.; Kitayama, I.; Klemetti, M.; Klose, V.; Klucar, J.; Knecht, N. S.; Knoepfel, K. J.; Knowles, D. J.; Ko, B. R.; Kobayashi, N.; Kobayashi, S.; Kobayashi, T.; Kobel, M. J.; Koblitz, S.; Koch, H.; Kocian, M. L.; Kodyš, P.; Koeneke, K.; Kofler, R.; Koike, S.; Koishi, S.; Koiso, H.; Kolb, J. A.; Kolya, S. D.; Kondo, Y.; Konishi, H.; Koppenburg, P.; Koptchev, V. B.; Kordich, T. M. B.; Korol, A. A.; Korotushenko, K.; Korpar, S.; Kouzes, R. T.; Kovalskyi, D.; Kowalewski, R.; Kozakai, Y.; Kozanecki, W.; Kral, J. F.; Krasnykh, A.; Krause, R.; Kravchenko, E. A.; Krebs, J.; Kreisel, A.; Kreps, M.; Krishnamurthy, M.; Kroeger, R.; Kroeger, W.; Krokovny, P.; Kronenbitter, B.; Kroseberg, J.; Kubo, T.; Kuhr, T.; Kukartsev, G.; Kulasiri, R.; Kulikov, A.; Kumar, R.; Kumar, S.; Kumita, T.; Kuniya, T.; Kunze, M.; Kuo, C. C.; Kuo, T.-L.; Kurashiro, H.; Kurihara, E.; Kurita, N.; Kuroki, Y.; Kurup, A.; Kutter, P. E.; Kuznetsova, N.; Kvasnička, P.; Kyberd, P.; Kyeong, S. H.; Lacker, H. M.; Lae, C. K.; Lamanna, E.; Lamsa, J.; Lanceri, L.; Landi, L.; Lang, M. I.; Lange, D. J.; Lange, J. S.; Langenegger, U.; Langer, M.; Lankford, A. J.; Lanni, F.; Laplace, S.; Latour, E.; Lau, Y. P.; Lavin, D. R.; Layter, J.; Lebbolo, H.; LeClerc, C.; Leddig, T.; Leder, G.; Le Diberder, F.; Lee, C. L.; Lee, J.; Lee, J. S.; Lee, M. C.; Lee, M. H.; Lee, M. J.; Lee, S.-J.; Lee, S. E.; Lee, S. H.; Lee, Y. J.; Lees, J. P.; Legendre, M.; Leitgab, M.; Leitner, R.; Leonardi, E.; Leonidopoulos, C.; Lepeltier, V.; Leruste, Ph.; Lesiak, T.; Levi, M. E.; Levy, S. L.; Lewandowski, B.; Lewczuk, M. J.; Lewis, P.; Li, H.; Li, H. B.; Li, S.; Li, X.; Li, Y.; Gioi, L. Li; Libby, J.; Lidbury, J.; Lillard, V.; Lim, C. L.; Limosani, A.; Lin, C. S.; Lin, J. Y.; Lin, S. W.; Lin, Y. S.; Lindquist, B.; Lindsay, C.; Lista, L.; Liu, C.; Liu, F.; Liu, H.; Liu, H. M.; Liu, J.; Liu, R.; Liu, T.; Liu, Y.; Liu, Z. Q.; Liventsev, D.; Lo Vetere, M.; Locke, C. B.; Lockman, W. S.; Di Lodovico, F.; Lombardo, V.; London, G. W.; Lopes Pegna, D.; Lopez, L.; Lopez-March, N.; Lory, J.; LoSecco, J. M.; Lou, X. C.; Louvot, R.; Lu, A.; Lu, C.; Lu, M.; Lu, R. S.; Lueck, T.; Luitz, S.; Lukin, P.; Lund, P.; Luppi, E.; Lutz, A. M.; Lutz, O.; Lynch, G.; Lynch, H. L.; Lyon, A. J.; Lyubinsky, V. R.; MacFarlane, D. B.; Mackay, C.; MacNaughton, J.; Macri, M. M.; Madani, S.; Mader, W. F.; Majewski, S. A.; Majumder, G.; Makida, Y.; Malaescu, B.; Malaguti, R.; Malclés, J.; Mallik, U.; Maly, E.; Mamada, H.; Manabe, A.; Mancinelli, G.; Mandelkern, M.; Mandl, F.; Manfredi, P. F.; Mangeol, D. J. J.; Manoni, E.; Mao, Z. P.; Margoni, M.; Marker, C. E.; Markey, G.; Marks, J.; Marlow, D.; Marques, V.; Marsiske, H.; Martellotti, S.; Martin, E. C.; Martin, J. P.; Martin, L.; Martinez, A. J.; Marzolla, M.; Mass, A.; Masuzawa, M.; Mathieu, A.; Matricon, P.; Matsubara, T.; Matsuda, T.; Matsuda, T.; Matsumoto, H.; Matsumoto, S.; Matsumoto, T.; Matsuo, H.; Mattison, T. S.; Matvienko, D.; Matyja, A.; Mayer, B.; Mazur, M. A.; Mazzoni, M. A.; McCulloch, M.; McDonald, J.; McFall, J. D.; McGrath, P.; McKemey, A. K.; McKenna, J. A.; Mclachlin, S. E.; McMahon, S.; McMahon, T. R.; McOnie, S.; Medvedeva, T.; Melen, R.; Mellado, B.; Menges, W.; Menke, S.; Merchant, A. M.; Merkel, J.; Messner, R.; Metcalfe, S.; Metzler, S.; Meyer, N. T.; Meyer, T. I.; Meyer, W. T.; Michael, A. K.; Michelon, G.; Michizono, S.; Micout, P.; Miftakov, V.; Mihalyi, A.; Mikami, Y.; Milanes, D. A.; Milek, M.; Mimashi, T.; Minamora, J. S.; Mindas, C.; Minutoli, S.; Mir, L. M.; Mishra, K.; Mitaroff, W.; Miyake, H.; Miyashita, T. S.; Miyata, H.; Miyazaki, Y.; Moffitt, L. C.; Mohanty, G. B.; Mohapatra, A.; Mohapatra, A. K.; Mohapatra, D.; Moll, A.; Moloney, G. R.; Mols, J. P.; Mommsen, R. K.; Monge, M. R.; Monorchio, D.; Moore, T. B.; Moorhead, G. F.; Mora de Freitas, P.; Morandin, M.; Morgan, N.; Morgan, S. E.; Morganti, M.; Morganti, S.; Mori, S.; Mori, T.; Morii, M.; Morris, J. P.; Morsani, F.; Morton, G. W.; Moss, L. J.; Mouly, J. P.; Mount, R.; Mueller, J.; Müller-Pfefferkorn, R.; Mugge, M.; Muheim, F.; Muir, A.; Mullin, E.; Munerato, M.; Murakami, A.; Murakami, T.; Muramatsu, N.; Musico, P.; Nagai, I.; Nagamine, T.; Nagasaka, Y.; Nagashima, Y.; Nagayama, S.; Nagel, M.; Naisbit, M. T.; Nakadaira, T.; Nakahama, Y.; Nakajima, M.; Nakajima, T.; Nakamura, I.; Nakamura, T.; Nakamura, T. T.; Nakano, E.; Nakayama, H.; Nam, J. W.; Narita, S.; Narsky, I.; Nash, J. A.; Natkaniec, Z.; Nauenberg, U.; Nayak, M.; Neal, H.; Nedelkovska, E.; Negrini, M.; Neichi, K.; Nelson, D.; Nelson, S.; Neri, N.; Nesom, G.; Neubauer, S.; Newman-Coburn, D.; Ng, C.; Nguyen, X.; Nicholson, H.; Niebuhr, C.; Nief, J. Y.; Niiyama, M.; Nikolich, M. B.; Nisar, N. K.; Nishimura, K.; Nishio, Y.; Nitoh, O.; Nogowski, R.; Noguchi, S.; Nomura, T.; Nordby, M.; Nosochkov, Y.; Novokhatski, A.; Nozaki, S.; Nozaki, T.; Nugent, I. M.; O'Grady, C. P.; O'Neale, S. W.; O'Neill, F. G.; Oberhof, B.; Oddone, P. J.; Ofte, I.; Ogawa, A.; Ogawa, K.; Ogawa, S.; Ogawa, Y.; Ohkubo, R.; Ohmi, K.; Ohnishi, Y.; Ohno, F.; Ohshima, T.; Ohshima, Y.; Ohuchi, N.; Oide, K.; Oishi, N.; Okabe, T.; Okazaki, N.; Okazaki, T.; Okuno, S.; Olaiya, E. O.; Olivas, A.; Olley, P.; Olsen, J.; Ono, S.; Onorato, G.; Onuchin, A. P.; Onuki, Y.; Ooba, T.; Orimoto, T. J.; Oshima, T.; Osipenkov, I. L.; Ostrowicz, W.; Oswald, C.; Otto, S.; Oyang, J.; Oyanguren, A.; Ozaki, H.; Ozcan, V. E.; Paar, H. P.; Padoan, C.; Paick, K.; Palka, H.; Pan, B.; Pan, Y.; Panduro Vazquez, W.; Panetta, J.; Panova, A. I.; Panvini, R. S.; Panzenböck, E.; Paoloni, E.; Paolucci, P.; Pappagallo, M.; Paramesvaran, S.; Park, C. S.; Park, C. W.; Park, H.; Park, H. K.; Park, K. S.; Park, W.; Parry, R. J.; Parslow, N.; Passaggio, S.; Pastore, F. C.; Patel, P. M.; Patrignani, C.; Patteri, P.; Pavel, T.; Pavlovich, J.; Payne, D. J.; Peak, L. S.; Peimer, D. R.; Pelizaeus, M.; Pellegrini, R.; Pelliccioni, M.; Peng, C. C.; Peng, J. C.; Peng, K. C.; Peng, T.; Penichot, Y.; Pennazzi, S.; Pennington, M. R.; Penny, R. C.; Penzkofer, A.; Perazzo, A.; Perez, A.; Perl, M.; Pernicka, M.; Perroud, J.-P.; Peruzzi, I. M.; Pestotnik, R.; Peters, K.; Peters, M.; Petersen, B. A.; Petersen, T. C.; Petigura, E.; Petrak, S.; Petrella, A.; Petrič, M.; Petzold, A.; Pia, M. G.; Piatenko, T.; Piccolo, D.; Piccolo, M.; Piemontese, L.; Piemontese, M.; Pierini, M.; Pierson, S.; Pioppi, M.; Piredda, G.; Pivk, M.; Plaszczynski, S.; Polci, F.; Pompili, A.; Poropat, P.; Posocco, M.; Potter, C. T.; Potter, R. J. L.; Prasad, V.; Prebys, E.; Prencipe, E.; Prendki, J.; Prepost, R.; Prest, M.; Prim, M.; Pripstein, M.; Prudent, X.; Pruvot, S.; Puccio, E. M. T.; Purohit, M. V.; Qi, N. D.; Quinn, H.; Raaf, J.; Rabberman, R.; Raffaelli, F.; Ragghianti, G.; Rahatlou, S.; Rahimi, A. M.; Rahmat, R.; Rakitin, A. Y.; Randle-Conde, A.; Rankin, P.; Rashevskaya, I.; Ratkovsky, S.; Raven, G.; Re, V.; Reep, M.; Regensburger, J. J.; Reidy, J.; Reif, R.; Reisert, B.; Renard, C.; Renga, F.; Ricciardi, S.; Richman, J. D.; Ritchie, J. L.; Ritter, M.; Rivetta, C.; Rizzo, G.; Roat, C.; Robbe, P.; Roberts, D. A.; Robertson, A. I.; Robutti, E.; Rodier, S.; Rodriguez, D. M.; Rodriguez, J. L.; Rodriguez, R.; Roe, N. A.; Röhrken, M.; Roethel, W.; Rolquin, J.; Romanov, L.; Romosan, A.; Ronan, M. T.; Rong, G.; Ronga, F. J.; Roos, L.; Root, N.; Rosen, M.; Rosenberg, E. I.; Rossi, A.; Rostomyan, A.; Rotondo, M.; Roussot, E.; Roy, J.; Rozanska, M.; Rozen, Y.; Rozen, Y.; Rubin, A. E.; Ruddick, W. O.; Ruland, A. M.; Rybicki, K.; Ryd, A.; Ryu, S.; Ryuko, J.; Sabik, S.; Sacco, R.; Saeed, M. A.; Safai Tehrani, F.; Sagawa, H.; Sahoo, H.; Sahu, S.; Saigo, M.; Saito, T.; Saitoh, S.; Sakai, K.; Sakamoto, H.; Sakaue, H.; Saleem, M.; Salnikov, A. A.; Salvati, E.; Salvatore, F.; Samuel, A.; Sanders, D. A.; Sanders, P.; Sandilya, S.; Sandrelli, F.; Sands, W.; Sands, W. R.; Sanpei, M.; Santel, D.; Santelj, L.; Santoro, V.; Santroni, A.; Sanuki, T.; Sarangi, T. R.; Saremi, S.; Sarti, A.; Sasaki, T.; Sasao, N.; Satapathy, M.; Sato, Nobuhiko; Sato, Noriaki; Sato, Y.; Satoyama, N.; Satpathy, A.; Savinov, V.; Savvas, N.; Saxton, O. H.; Sayeed, K.; Schaffner, S. F.; Schalk, T.; Schenk, S.; Schieck, J. R.; Schietinger, T.; Schilling, C. J.; Schindler, R. H.; Schmid, S.; Schmitz, R. E.; Schmuecker, H.; Schneider, O.; Schnell, G.; Schönmeier, P.; Schofield, K. C.; Schott, G.; Schröder, H.; Schram, M.; Schubert, J.; Schümann, J.; Schultz, J.; Schumm, B. A.; Schune, M. H.; Schwanke, U.; Schwarz, H.; Schwiening, J.; Schwierz, R.; Schwitters, R. F.; Sciacca, C.; Sciolla, G.; Scott, I. J.; Seeman, J.; Seiden, A.; Seitz, R.; Seki, T.; Sekiya, A. I.; Semenov, S.; Semmler, D.; Sen, S.; Senyo, K.; Seon, O.; Serbo, V. V.; Serednyakov, S. I.; Serfass, B.; Serra, M.; Serrano, J.; Settai, Y.; Seuster, R.; Sevior, M. E.; Shakhova, K. V.; Shang, L.; Shapkin, M.; Sharma, V.; Shebalin, V.; Shelkov, V. G.; Shen, B. C.; Shen, D. Z.; Shen, Y. T.; Sherwood, D. J.; Shibata, T.; Shibata, T. A.; Shibuya, H.; Shidara, T.; Shimada, K.; Shimoyama, M.; Shinomiya, S.; Shiu, J. G.; Shorthouse, H. W.; Shpilinskaya, L. I.; Sibidanov, A.; Sicard, E.; Sidorov, A.; Sidorov, V.; Siegle, V.; Sigamani, M.; Simani, M. C.; Simard, M.; Simi, G.; Simon, F.; Simonetto, F.; Sinev, N. B.; Singh, H.; Singh, J. B.; Sinha, R.; Sitt, S.; Skovpen, Yu. I.; Sloane, R. J.; Smerkol, P.; Smith, A. J. S.; Smith, D.; Smith, D. S.; Smith, J. G.; Smol, A.; Snoek, H. L.; Snyder, A.; So, R. Y.; Sobie, R. J.; Soderstrom, E.; Soha, A.; Sohn, Y. S.; Sokoloff, M. D.; Sokolov, A.; Solagna, P.; Solovieva, E.; Soni, N.; Sonnek, P.; Sordini, V.; Spaan, B.; Spanier, S. M.; Spencer, E.; Speziali, V.; Spitznagel, M.; Spradlin, P.; Staengle, H.; Stamen, R.; Stanek, M.; Stanič, S.; Stark, J.; Steder, M.; Steininger, H.; Steinke, M.; Stelzer, J.; Stevanato, E.; Stocchi, A.; Stock, R.; Stoeck, H.; Stoker, D. P.; Stroili, R.; Strom, D.; Strother, P.; Strube, J.; Stugu, B.; Stypula, J.; Su, D.; Suda, R.; Sugahara, R.; Sugi, A.; Sugimura, T.; Sugiyama, A.; Suitoh, S.; Sullivan, M. K.; Sumihama, M.; Sumiyoshi, T.; Summers, D. J.; Sun, L.; Sun, S.; Sundermann, J. E.; Sung, H. F.; Susaki, Y.; Sutcliffe, P.; Suzuki, A.; Suzuki, J.; Suzuki, J. I.; Suzuki, K.; Suzuki, S.; Suzuki, S. Y.; Swain, J. E.; Swain, S. K.; T'Jampens, S.; Tabata, M.; Tackmann, K.; Tajima, H.; Tajima, O.; Takahashi, K.; Takahashi, S.; Takahashi, T.; Takasaki, F.; Takayama, T.; Takita, M.; Tamai, K.; Tamponi, U.; Tamura, N.; Tan, N.; Tan, P.; Tanabe, K.; Tanabe, T.; Tanaka, H. A.; Tanaka, J.; Tanaka, M.; Tanaka, S.; Tanaka, Y.; Tanida, K.; Taniguchi, N.; Taras, P.; Tasneem, N.; Tatishvili, G.; Tatomi, T.; Tawada, M.; Taylor, F.; Taylor, G. N.; Taylor, G. P.; Telnov, V. I.; Teodorescu, L.; Ter-Antonyan, R.; Teramoto, Y.; Teytelman, D.; Thérin, G.; Thiebaux, Ch.; Thiessen, D.; Thomas, E. W.; Thompson, J. M.; Thorne, F.; Tian, X. C.; Tibbetts, M.; Tikhomirov, I.; Tinslay, J. S.; Tiozzo, G.; Tisserand, V.; Tocut, V.; Toki, W. H.; Tomassini, E. W.; Tomoto, M.; Tomura, T.; Torassa, E.; Torrence, E.; Tosi, S.; Touramanis, C.; Toussaint, J. C.; Tovey, S. N.; Trapani, P. P.; Treadwell, E.; Triggiani, G.; Trincaz-Duvoid, S.; Trischuk, W.; Troost, D.; Trunov, A.; Tsai, K. L.; Tsai, Y. T.; Tsujita, Y.; Tsukada, K.; Tsukamoto, T.; Tuggle, J. M.; Tumanov, A.; Tung, Y. W.; Turnbull, L.; Turner, J.; Turri, M.; Uchida, K.; Uchida, M.; Uchida, Y.; Ueki, M.; Ueno, K.; Ujiie, N.; Ulmer, K. A.; Unno, Y.; Urquijo, P.; Ushiroda, Y.; Usov, Y.; Usseglio, M.; Usuki, Y.; Uwer, U.; Va'vra, J.; Vahsen, S. E.; Vaitsas, G.; Valassi, A.; Vallazza, E.; Vallereau, A.; Vanhoefer, P.; van Hoek, W. C.; Van Hulse, C.; van Winkle, D.; Varner, G.; Varnes, E. W.; Varvell, K. E.; Vasileiadis, G.; Velikzhanin, Y. S.; Verderi, M.; Versillé, S.; Vervink, K.; Viaud, B.; Vidal, P. B.; Villa, S.; Villanueva-Perez, P.; Vinograd, E. L.; Vitale, L.; Vitug, G. M.; Voß, C.; Voci, C.; Voena, C.; Volk, A.; von Wimmersperg-Toeller, J. H.; Vorobyev, V.; Vossen, A.; Vuagnin, G.; Vuosalo, C. O.; Wacker, K.; Wagner, A. P.; Wagner, D. L.; Wagner, G.; Wagner, M. N.; Wagner, S. R.; Wagoner, D. E.; Walker, D.; Walkowiak, W.; Wallom, D.; Wang, C. C.; Wang, C. H.; Wang, J.; Wang, J. G.; Wang, K.; Wang, L.; Wang, L. L.; Wang, P.; Wang, T. J.; Wang, W. F.; Wang, X. L.; Wang, Y. F.; Wappler, F. R.; Watanabe, M.; Watson, A. T.; Watson, J. E.; Watson, N. K.; Watt, M.; Weatherall, J. H.; Weaver, M.; Weber, T.; Wedd, R.; Wei, J. T.; Weidemann, A. W.; Weinstein, A. J. R.; Wenzel, W. A.; West, C. A.; West, C. G.; West, T. J.; White, E.; White, R. M.; Wicht, J.; Widhalm, L.; Wiechczynski, J.; Wienands, U.; Wilden, L.; Wilder, M.; Williams, D. C.; Williams, G.; Williams, J. C.; Williams, K. M.; Williams, M. I.; Willocq, S. Y.; Wilson, J. R.; Wilson, M. G.; Wilson, R. J.; Winklmeier, F.; Winstrom, L. O.; Winter, M. A.; Wisniewski, W. J.; Wittgen, M.; Wittlin, J.; Wittmer, W.; Wixted, R.; Woch, A.; Wogsland, B. J.; Won, E.; Wong, Q. K.; Wray, B. C.; Wren, A. C.; Wright, D. M.; Wu, C. H.; Wu, J.; Wu, S. L.; Wulsin, H. W.; Xella, S. M.; Xie, Q. L.; Xie, Y.; Xu, Z. Z.; Yéche, Ch.; Yamada, Y.; Yamaga, M.; Yamaguchi, A.; Yamaguchi, H.; Yamaki, T.; Yamamoto, H.; Yamamoto, N.; Yamamoto, R. K.; Yamamoto, S.; Yamanaka, T.; Yamaoka, H.; Yamaoka, J.; Yamaoka, Y.; Yamashita, Y.; Yamauchi, M.; Yan, D. S.; Yan, Y.; Yanai, H.; Yanaka, S.; Yang, H.; Yang, R.; Yang, S.; Yarritu, A. K.; Yashchenko, S.; Yashima, J.; Yasin, Z.; Yasu, Y.; Ye, S. W.; Yeh, P.; Yi, J. I.; Yi, K.; Yi, M.; Yin, Z. W.; Ying, J.; Yocky, G.; Yokoyama, K.; Yokoyama, M.; Yokoyama, T.; Yoshida, K.; Yoshida, M.; Yoshimura, Y.; Young, C. C.; Yu, C. X.; Yu, Z.; Yuan, C. Z.; Yuan, Y.; Yumiceva, F. X.; Yusa, Y.; Yushkov, A. N.; Yuta, H.; Zacek, V.; Zain, S. B.; Zallo, A.; Zambito, S.; Zander, D.; Zang, S. L.; Zanin, D.; Zaslavsky, B. G.; Zeng, Q. L.; Zghiche, A.; Zhang, B.; Zhang, J.; Zhang, J.; Zhang, L.; Zhang, L. M.; Zhang, S. Q.; Zhang, Z. P.; Zhao, H. W.; Zhao, M.; Zhao, Z. G.; Zheng, Y.; Zheng, Y. H.; Zheng, Z. P.; Zhilich, V.; Zhou, P.; Zhu, R. Y.; Zhu, Y. S.; Zhu, Z. M.; Zhulanov, V.; Ziegler, T.; Ziegler, V.; Zioulas, G.; Zisman, M.; Zito, M.; Zürcher, D.; Zwahlen, N.; Zyukova, O.; Živko, T.; Žontar, D.

2014-11-01

This work is on the Physics of the B Factories. Part A of this book contains a brief description of the SLAC and KEK B Factories as well as their detectors, BaBar and Belle, and data taking related issues. Part B discusses tools and methods used by the experiments in order to obtain results. The results themselves can be found in Part C. Please note that version 3 on the archive is the auxiliary version of the Physics of the B Factories book. This uses the notation alpha, beta, gamma for the angles of the Unitarity Triangle. The nominal version uses the notation phi_1, phi_2 and phi_3. Please cite this work as Eur. Phys. J. C74 (2014) 3026.

PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database.

PubMed

Urban, Martin; Cuzick, Alayne; Rutherford, Kim; Irvine, Alistair; Pedro, Helder; Pant, Rashmi; Sadanadan, Vidyendra; Khamari, Lokanath; Billal, Santoshkumar; Mohanty, Sagar; Hammond-Kosack, Kim E

2017-01-04

The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. The new release of PHI-base Version 4.2 (October 2016) has an increased data content containing information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species belong ∼70% to plants and 30% to other species of medical and/or environmental importance. Additional data types included into PHI-base 4 are the direct targets of pathogen effector proteins in experimental and natural host organisms. The curation problems encountered and the future directions of the PHI-base project are briefly discussed. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Focusers of obliquely incident laser radiation

NASA Astrophysics Data System (ADS)

Goncharskiy, A. V.; Danilov, V. A.; Popov, V. V.; Prokhorov, A. M.; Sisakyan, I. N.; Sayfer, V. A.; Stepanov, V. V.

1984-08-01

Focusing obliquely incident laser radiation along a given line in space with a given intensity distribution is treated as a problem of synthesizing a mirror surface. The intricate shape of such a surface, characterized by a function z= z (u,v) in the approximation of geometrical optics, is determined from the equation phi (u,v,z) - phi O(u,v,z)=O, which expresses that the incident field and the reflected field have identical eikonals. Further calculations are facilitated by replacing continuous mirror with a more easily manufactured piecewise continuous one. The problem is solved for the simple case of a plane incident wave with a typical iconal phi O(u,v,z)= -z cos0 at a large angle to a focus mirror in the z-plane region. Mirrors constructed on the basis of the theoretical solution were tested in an experiment with a CO2 laser. A light beam with Gaussian intensity distribution was, upon incidence at a 45 deg angle, focused into a circle or into an ellipse with uniform intensity distribution. Improvements in amplitudinal masking and selective tanning technology should reduce energy losses at the surface which results in efficient laser focusing mirrors.

Bacteriophage phi 6 RNA-dependent RNA polymerase: molecular details of initiating nucleic acid synthesis without primer.

PubMed

Laurila, Minni R L; Makeyev, Eugene V; Bamford, Dennis H

2002-05-10

Like most RNA polymerases, the polymerase of double-strand RNA bacteriophage phi6 (phi6pol) is capable of primer-independent initiation. Based on the recently solved phi6pol initiation complex structure, a four-amino acid-long loop (amino acids 630-633) has been suggested to stabilize the first two incoming NTPs through stacking interactions with tyrosine, Tyr(630). A similar loop is also present in the hepatitis C virus polymerase, another enzyme capable of de novo initiation. Here, we use a series of phi6pol mutants to address the role of this element. As predicted, mutants at the Tyr(630) position are inefficient in initiation de novo. Unexpectedly, when the loop is disordered by changing Tyr(630)-Lys(631)-Trp(632) to GSG, phi6pol becomes a primer-dependent enzyme, either extending complementary oligonucleotide or, when the template 3' terminus can adopt a hairpin-like conformation, utilizing a "copy-back" initiation mechanism. In contrast to the wild-type phi6pol, the GSG mutant does not require high GTP concentration for its optimal activity. These findings suggest a general model for the initiation of de novo RNA synthesis.

Fluorescence X-ray absorption spectroscopy using a Ge pixel array detector: application to high-temperature superconducting thin-film single crystals.

PubMed

Oyanagi, H; Tsukada, A; Naito, M; Saini, N L; Lampert, M O; Gutknecht, D; Dressler, P; Ogawa, S; Kasai, K; Mohamed, S; Fukano, A

2006-07-01

A Ge pixel array detector with 100 segments was applied to fluorescence X-ray absorption spectroscopy, probing the local structure of high-temperature superconducting thin-film single crystals (100 nm in thickness). Independent monitoring of pixel signals allows real-time inspection of artifacts owing to substrate diffractions. By optimizing the grazing-incidence angle theta and adjusting the azimuthal angle phi, smooth extended X-ray absorption fine structure (EXAFS) oscillations were obtained for strained (La,Sr)2CuO4 thin-film single crystals grown by molecular beam epitaxy. The results of EXAFS data analysis show that the local structure (CuO6 octahedron) in (La,Sr)2CuO4 thin films grown on LaSrAlO4 and SrTiO3 substrates is uniaxially distorted changing the tetragonality by approximately 5 x 10(-3) in accordance with the crystallographic lattice mismatch. It is demonstrated that the local structure of thin-film single crystals can be probed with high accuracy at low temperature without interference from substrates.

Multistep modeling of protein structure: application towards refinement of tyr-tRNA synthetase

NASA Technical Reports Server (NTRS)

Srinivasan, S.; Shibata, M.; Roychoudhury, M.; Rein, R.

1987-01-01

The scope of multistep modeling (MSM) is expanding by adding a least-squares minimization step in the procedure to fit backbone reconstruction consistent with a set of C-alpha coordinates. The analytical solution of Phi and Psi angles, that fits a C-alpha x-ray coordinate is used for tyr-tRNA synthetase. Phi and Psi angles for the region where the above mentioned method fails, are obtained by minimizing the difference in C-alpha distances between the computed model and the crystal structure in a least-squares sense. We present a stepwise application of this part of MSM to the determination of the complete backbone geometry of the 321 N terminal residues of tyrosine tRNA synthetase to a root mean square deviation of 0.47 angstroms from the crystallographic C-alpha coordinates.

Mathematical modeling of acid-base physiology

PubMed Central

Occhipinti, Rossana; Boron, Walter F.

2015-01-01

pH is one of the most important parameters in life, influencing virtually every biological process at the cellular, tissue, and whole-body level. Thus, for cells, it is critical to regulate intracellular pH (pHi) and, for multicellular organisms, to regulate extracellular pH (pHo). pHi regulation depends on the opposing actions of plasma-membrane transporters that tend to increase pHi, and others that tend to decrease pHi. In addition, passive fluxes of uncharged species (e.g., CO2, NH3) and charged species (e.g., HCO3− , NH4+) perturb pHi. These movements not only influence one another, but also perturb the equilibria of a multitude of intracellular and extracellular buffers. Thus, even at the level of a single cell, perturbations in acid-base reactions, diffusion, and transport are so complex that it is impossible to understand them without a quantitative model. Here we summarize some mathematical models developed to shed light onto the complex interconnected events triggered by acids-base movements. We then describe a mathematical model of a spherical cell–which to our knowledge is the first one capable of handling a multitude of buffer reaction–that our team has recently developed to simulate changes in pHi and pHo caused by movements of acid-base equivalents across the plasma membrane of a Xenopus oocyte. Finally, we extend our work to a consideration of the effects of simultaneous CO2 and HCO3− influx into a cell, and envision how future models might extend to other cell types (e.g., erythrocytes) or tissues (e.g., renal proximal-tubule epithelium) important for whole-body pH homeostasis. PMID:25617697

Acetylcholinesterase inhibition and anti-Soman efficacy of homologs of physostigmine. (Reannouncement with new availability information)

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

Harris, L.W.; Anderson, D.R.; Pastelak, A.M.

1992-12-31

Inhibition of acetylcholinesterase (AChE) activity by physostigmine (PHY) is reversible due to spontaneous decarbamylation. Physostigmine has been shown to be effective as a pretreatment against potent anticholinesterase poisons (e.g., soman) in experimental animals, yet it is short acting and causes undesirable side effects in mammals. The two-fold purpose of this study was (1) to determine whether extension of the N-substituted alkyl chain (N-SAC) of PHY from N-methyl to N-ethyl (1), N-propyl (2), N-isopropyl (3), N-butyl (4) or N-heptyl (5) affects anti-AChE potency and spontaneous decarbamylation of inhibited AChE of guinea pig blood in vitro and in vivo and (2) tomore » see whether chain extension affects efficacy as pretreatment in poisoning by soman. The in vitro AChE inhibition studies were done using whole blood incubated at 37 deg C for 30 min. All 5 homologs possessed anti-AChE activity with I50s ranging from 1.1 to 27.6 x l0(-7)M; compound III was the least potent in vitro and in vivo. Lengthening of the N-SAC of PHY markedly extended the duration of anti-AChE activity when compared to PHY, but rendered the modified compounds ineffective as pretreatments against soman. These data support the premise that the decrease in decarbamylation rates observed upon extending the N-SAC of PHY is responsible for the loss of effectiveness of pretreatment regimens against soman. Perhaps, these homologs of PHY may have potential use in instances where sustained action of acetylcholine is required at cholinergic junctions because of disease conditions or drug overdosage.... Physostigmine, Nerve agent pretreatment, Soman, Acetylcholinesterase inhibition.« less

Relative evolutionary rate inference in HyPhy with LEISR.

PubMed

Spielman, Stephanie J; Kosakovsky Pond, Sergei L

2018-01-01

We introduce LEISR (Likehood Estimation of Individual Site Rates, pronounced "laser"), a tool to infer relative evolutionary rates from protein and nucleotide data, implemented in HyPhy. LEISR is based on the popular Rate4Site (Pupko et al., 2002) approach for inferring relative site-wise evolutionary rates, primarily from protein data. We extend the original method for more general use in several key ways: (i) we increase the support for nucleotide data with additional models, (ii) we allow for datasets of arbitrary size, (iii) we support analysis of site-partitioned datasets to correct for the presence of recombination breakpoints, (iv) we produce rate estimates at all sites rather than at just a subset of sites, and (v) we implemented LEISR as MPI-enabled to support rapid, high-throughput analysis. LEISR is available in HyPhy starting with version 2.3.8, and it is accessible as an option in the HyPhy analysis menu ("Relative evolutionary rate inference"), which calls the HyPhy batchfile LEISR.bf.

Effect of gravity on liquid plug transport through an airway bifurcation model.

PubMed

Zheng, Y; Anderson, J C; Suresh, V; Grotberg, J B

2005-10-01

Many medical therapies require liquid plugs to be instilled into and delivered throughout the pulmonary airways. Improving these treatments requires a better understanding of how liquid distributes throughout these airways. In this study, gravitational and surface mechanisms determining the distribution of instilled liquids are examined experimentally using a bench-top model of a symmetrically bifurcating airway. A liquid plug was instilled into the parent tube and driven through the bifurcation by a syringe pump. The effect of gravity was adjusted by changing the roll angle (phi) and pitch angle (gamma) of the bifurcation (phi = gamma =0 deg was isogravitational). Phi determines the relative gravitational orientation of the two daughter tubes: when phi not equal to 0 deg, one daughter tube was lower (gravitationally favored) compared to the other. Gamma determines the component of gravity acting along the axial direction of the parent tube: when gamma not equal to 0 deg, a nonzero component of gravity acts along the axial direction of the parent tube. A splitting ratio Rs, is defined as the ratio of the liquid volume in the upper daughter to the lower just after plug splitting. We measured the splitting ratio, Rs, as a function of: the parent-tube capillary number (Cap); the Bond number (Bo); phi; gamma; and the presence of pre-existing plugs initially blocking either daughter tube. A critical capillary number (Cac) was found to exist below which no liquid entered the upper daughter (Rs = 0), and above which Rs increased and leveled off with Cap. Cac increased while Rs decreased with increasing phi, gamma, and Bo for blocked and unblocked cases at a given Cap > Ca,. Compared to the nonblockage cases, Rs decreased (increased) at a given Cap while Cac increased (decreased) with an upper (lower) liquid blockage. More liquid entered the unblocked daughter with a blockage in one daughter tube, and this effect was larger with larger gravity effect. A simple theoretical model that predicts Rs and Cac is in qualitative agreement with the experiments over a wide range of parameters.

Electrostatic persistence length.

PubMed

Fixman, Marshall

2010-03-11

The persistence length is calculated for polyelectrolyte chains with fixed bond lengths and bond angles (pi-theta), and a potential energy consisting of the screened Coulomb interaction between beads, potential wells alpha phi(i)2 for the dihedral angles phi(i), and coupling terms beta phi(i) phi(i+/-1). This model defines a librating chain that reduces in appropriate limits to the freely rotating or wormlike chains, it can accommodate local crumpling or extreme stiffness, and it is easy to simulate. A planar-quadratic (pq), analytic approximation is based on an expansion of the electrostatic energy in eigenfunctions of the quadratic form that describes the backbone energy, and on the assumption that the quadratic form not only is positive but also adequately confines the chain in an infinite phase space of dihedral angles to the physically unique part with all |phi(i)| < pi. The pq approximation is available under these weak constraints, but the simulations confirm its quantitative accuracy only under the expected condition that alpha is large, that is, for very stiff chains. Stiff chains can also be simulated with small alpha and small theta and compared to an OSF approximation suitably generalized to chains with finite rather than vanishing theta, and increasing agreement with OSF is found the smaller is theta. The two approximations, one becoming exact as alpha --> infinity with fixed theta, the other as theta --> 0 with fixed alpha, are quantitatively similar in behavior, both giving a persistence length P = P0 + aD2 for stiff chains, where D is the Debye length. However, the coefficient apq is about twice the value of aOSF. Under other conditions the simulations show that P may or not be linear in D2 at small or moderate D, depending on the magnitudes of alpha, beta, theta, and the charge density but always becomes linear at large D. Even at a moderately low charge density, corresponding to fewer than 20% of the beads being charged, and with strong crumpling induced by large beta, increasing D dissolves blobs and recovers a linear dependence of P on D2, although a lower power of D gives an adequate fit at moderate D. For the class of models considered, it is concluded that the only universal feature is the asymptotic linearity of P in D2, regardless of flexibility or stiffness.

The Enhancement of Phototropin-Induced Phototropic Curvature in Arabidopsis Occurs via a Photoreversible Phytochrome A-Dependent Modulation of Auxin Responsiveness1

PubMed Central

Stowe-Evans, Emily L.; Luesse, Darron R.; Liscum, Emmanuel

2001-01-01

The induction of phototropism in etiolated (dark-grown) seedlings exposed to an unidirectional pulse or extended irradiation with low fluence rate blue light (BL) requires the action of the phototropin (nph1) BL receptor. Although cryptochromes and phytochromes are not required for phototropic induction, these photoreceptors do modulate the magnitude of curvature resulting from phototropin activation. Modulatory increases in the magnitude of phototropic curvature have been termed “enhancement.” Here, we show that phototropic enhancement is primarily a phytochrome A (phyA)-dependent red/far-red-reversible low fluence response. This phyA-dependent response is genetically separable from the basal phototropin-dependent response, as demonstrated by its retention under extended irradiation conditions in the nph4 mutant background, which normally lacks the basal BL-induced response. It is interesting that the nph4 mutants fail to exhibit the basal phototropin-dependent and phyA-dependent enhancement responses under limiting light conditions. Given that NPH4 encodes a transcriptional activator, auxin response factor 7 (ARF7), we hypothesize that the ultimate target(s) of phyA action during the phototropic enhancement response is a rate-limiting ARF-containing transcriptional complex in which the constituent ARFs can vary in identity or activity depending upon the irradiation condition. PMID:11402210

Conversion of the magnetic field measured in three components on the magnetic sensor body's random coordinate system into three components on geographical coordinate system through quaternion rotation.

NASA Astrophysics Data System (ADS)

LIM, M.; PARK, Y.; Jung, H.; SHIN, Y.; Rim, H.; PARK, C.

2017-12-01

To measure all components of a physical property, for example the magnetic field, is more useful than to measure its magnitude only in interpretation and application thereafter. To convert the physical property measured in 3 components on a random coordinate system, for example on moving magnetic sensor body's coordinate system, into 3 components on a fixed coordinate system, for example on geographical coordinate system, by the rotations of coordinate system around Euler angles for example, we should have the attitude values of the sensor body in time series, which could be acquired by an INS-GNSS system of which the axes are installed coincident with those of the sensor body. But if we want to install some magnetic sensors in array at sea floor but without attitude acquisition facility of the magnetic sensors and to monitor the variation of magnetic fields in time, we should have also some way to estimate the relation between the geographical coordinate system and each sensor body's coordinate system by comparison of the vectors only measured on both coordinate systems on the assumption that the directions of the measured magnetic field on both coordinate systems are the same. For that estimation, we have at least 3 ways. The first one is to calculate 3 Euler angles phi, theta, psi from the equation Vgeograph = Rx(phi) Ry(theta) Rz(psi) Vrandom, where Vgeograph is the vector on geographical coordinate system etc. and Rx(phi) is the rotation matrix around the x axis by the angle phi etc. The second one is to calculate the difference of inclination and declination between the 2 vectors on spherical coordinate system. The third one, used by us for this study, is to calculate the angle of rotation along a great circle around the rotation axis, and the direction of the rotation axis. We installed no. 1 and no. 2 FVM-400 fluxgate magnetometers in array near Cheongyang Geomagnetic Observatory (IAGA code CYG) and acquired time series of magnetic fields for CYG and for the two magnetometers. Once the angle of rotation and the direction of the rotation axis for each couple of CYG and no. 1 and of CYG and no. 2 estimated, we rotated the measured time series of vectors using quaternion rotation to get 3 time series of magnetic fields all on geographical coordinate system, which were used for tracing the moving magnetic bodies along time in that area.

Modular low-aspect-ratio high-beta torsatron

DOEpatents

Sheffield, G.V.

1982-04-01

A fusion-reactor device is described which the toroidal magnetic field and at least a portion of the poloidal magnetic field are provided by a single set of modular coils. The coils are arranged on the surface of a low-aspect-ratio toroid in planed having the cylindrical coordinate relationship phi = phi/sub i/ + kz, where k is a constant equal to each coil's pitch and phi/sub i/ is the toroidal angle at which the i'th coil intersects the z = o plane. The toroid defined by the modular coils preferably has a race track minor cross section. When vertical field coils and, preferably, a toroidal plasma current are provided for magnetic-field-surface closure within the toroid, a vacuum magnetic field of racetrack-shaped minor cross section with improved stability and beta valves is obtained.

An Integrative Model for Phytochrome B Mediated Photomorphogenesis: From Protein Dynamics to Physiology

PubMed Central

Kircher, Stefan; Kirchenbauer, Daniel; Timmer, Jens; Nagy, Ferenc; Schäfer, Eberhard; Fleck, Christian

2010-01-01

Background Plants have evolved various sophisticated mechanisms to respond and adapt to changes of abiotic factors in their natural environment. Light is one of the most important abiotic environmental factors and it regulates plant growth and development throughout their entire life cycle. To monitor the intensity and spectral composition of the ambient light environment, plants have evolved multiple photoreceptors, including the red/far-red light-sensing phytochromes. Methodology/Principal Findings We have developed an integrative mathematical model that describes how phytochrome B (phyB), an essential receptor in Arabidopsis thaliana, controls growth. Our model is based on a multiscale approach and connects the mesoscopic intracellular phyB protein dynamics to the macroscopic growth phenotype. To establish reliable and relevant parameters for the model phyB regulated growth we measured: accumulation and degradation, dark reversion kinetics and the dynamic behavior of different nuclear phyB pools using in vivo spectroscopy, western blotting and Fluorescence Recovery After Photobleaching (FRAP) technique, respectively. Conclusions/Significance The newly developed model predicts that the phyB-containing nuclear bodies (NBs) (i) serve as storage sites for phyB and (ii) control prolonged dark reversion kinetics as well as partial reversibility of phyB Pfr in extended darkness. The predictive power of this mathematical model is further validated by the fact that we are able to formalize a basic photobiological observation, namely that in light-grown seedlings hypocotyl length depends on the total amount of phyB. In addition, we demonstrate that our theoretical predictions are in excellent agreement with quantitative data concerning phyB levels and the corresponding hypocotyl lengths. Hence, we conclude that the integrative model suggested in this study captures the main features of phyB-mediated photomorphogenesis in Arabidopsis. PMID:20502669

Characterization of Martian near-subsurface materials by determination of cohesion and angle of internal friction

NASA Technical Reports Server (NTRS)

Sullivan, R. J.

1992-01-01

Back-analysis (reconstruction) of the stability of thirty avalanche chutes was performed in the very limited areas where high resolution imaging overlapped with available 1:500 K topographic map coverage. A new technique was developed to incorporate the third dimension (width) of an avalanche chute in stability back-analysis in order to yield unambiguous values of cohesion and angle of internal friction. The procedure is based upon extending the ordinary method of slices to three dimensions, in order to construct avalanche chute cross-sections whose widths and depths vary as a function of gradient, gravity, density of material, and phi and c. Applying the technique to the well documented slide at Lodalen, Norway as a test produces excellent correspondence with reality. Generally, the technique reveals that the width:depth ratio of any avalanche chute decreases with increasing contrast between the average slope angle and the angle of internal friction. Applying this technique to the martian avalanche chute yields results consistent with indications from earlier work, but with greater certainty. Values of cohesion and angle of internal friction identify the materials at the time of failure as moderately cohesive debris. If Sharp's identification of these features as avalanche chutes is correct, then the results here imply that weathering processes have had a significant effect to depths of tens of meters (where failure has occured) below the martian surface. It is also implied that on relatively steep slopes within Valles Marineris, sizable, unaltered, unmantled bedrock exposures for high resolution spectral and spatial scanning by Mars Observer may be scarce.

Physicochemically Tunable Polyfunctionalized RNA Square Architecture with Fluorogenic and Ribozymatic Properties

PubMed Central

2015-01-01

Recent advances in RNA nanotechnology allow the rational design of various nanoarchitectures. Previous methods utilized conserved angles from natural RNA motifs to form geometries with specific sizes. However, the feasibility of producing RNA architecture with variable sizes using native motifs featuring fixed sizes and angles is limited. It would be advantageous to display RNA nanoparticles of diverse shape and size derived from a given primary sequence. Here, we report an approach to construct RNA nanoparticles with tunable size and stability. Multifunctional RNA squares with a 90° angle were constructed by tuning the 60° angle of the three-way junction (3WJ) motif from the packaging RNA (pRNA) of the bacteriophage phi29 DNA packaging motor. The physicochemical properties and size of the RNA square were also easily tuned by modulating the “core” strand and adjusting the length of the sides of the square via predictable design. Squares of 5, 10, and 20 nm were constructed, each showing diverse thermodynamic and chemical stabilities. Four “arms” extending from the corners of the square were used to incorporate siRNA, ribozyme, and fluorogenic RNA motifs. Unique intramolecular contact using the pre-existing intricacy of the 3WJ avoids relatively weaker intermolecular interactions via kissing loops or sticky ends. Utilizing the 3WJ motif, we have employed a modular design technique to construct variable-size RNA squares with controllable properties and functionalities for diverse and versatile applications with engineering, pharmaceutical, and medical potential. This technique for simple design to finely tune physicochemical properties adds a new angle to RNA nanotechnology. PMID:24971772

Preliminary evidence for the influence of physiography and scale upon the autocorrelation function of remotely sensed data

NASA Technical Reports Server (NTRS)

Labovitz, M. L.; Toll, D. L.; Kennard, R. E.

1980-01-01

Previously established results demonstrate that LANDSAT data are autocorrelated and can be described by a univariate linear stochastic process known as auto-regressive-integrated-moving-average model of degree 1, 0, 1 or ARIMA (1, 0, 1). This model has two coefficients of interest for interpretation phi(1) and theta(1). In a comparison of LANDSAT thematic mapper simulator (TMS) data and LANDSAT MSS data several results were established: (1) The form of the relatedness as described by this model is not dependent upon system look angle or pixel size. (2) The phi(1) coefficient increases with decreasing pixel size and increasing topographic complexity. (3) Changes in topography have a greater influence upon phi(1) than changes in land cover class. (4) The theta(1) seems to vary with the amount of atmospheric haze. These patterns of variation in phi(1) and theta(1) are potentially exploitable by the remote sensing community to yield stochastically independent sets of observations, characterize topography, and reduce the number of bytes needed to store remotely sensed data.

Differential cross sections and spin density matrix elements for gamma p -> phi p from CLAS

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

Biplab Dey, Curtis A. Meyer

2011-10-01

Preliminary differential cross-sections and the {rho}{sub MM'}{sup 0} spin density matrix elements (SDME) for the reaction {gamma}p {yields} {phi} for both charged- ({phi} {yields} K{sup +}K{sup -}) and neutral-mode ({phi} {yields} K{sub L}{sup 0}K{sub S}{sup 0}) topologies obtained from CLAS are presented. Our kinematic coverage is from near production threshold ({radical}s {approx} 1.97more » $$ GeV) to {radical}s = 2.84$$ GeV, with a wide coverage in the production angle. As seen in previous LEPS results, the differential cross-sections show a localized 'bump' between {radical}s {approx} 2 and 2.2 GeV that is not expected from a simple Pomeron exchange picture. Comparisons between the charged- and neutral-mode results and possible effects from the K{sup +} {Lambda}(1520) channel are discussed. Our SDME results confirm the well-known deviations from t-channel helicity conservation (TCHC) for Pomeron exchange, but s-channel helicity conservation (SCHC) is also seen to be broken.« less

Relating polarization phase difference of SAR signals to scene properties

NASA Technical Reports Server (NTRS)

Ulaby, Fawwaz T.; Dobson, Myron C.; Mcdonald, Kyle C.; Senior, Thomas B. A.; Held, Daniel

1987-01-01

This paper examines the statistical behavior of the phase difference Delta-phi between the HH-polarized and VV-polarized backscattered signals recorded by an L-band SAR over an agricultural test site in Illinois. Polarization-phase difference distributions were generated for about 200 agricultural fields for which ground information had been acquired in conjunction with the SAR mission. For the overwhelming majority of cases, the Delta-phi distribution is symmetric and has a single major lobe centered at the mean value of the distribution Delta-phi. Whereas the mean Delta-phi was found to be close to zero degrees for bare soil, cut vegetation, alfalfa, soybeans, and clover, a different pattern was observed for the corn fields; the mean Delta-phi increased with increasing incidence angle Theta = 35 deg. The explanation proposed for this variation is that the corn canopy, most of whose mass is contained in its vertical stalks, acts like a uniaxial crystal characterized by different velocities of propagation for waves with horizontal and vertical polarization. Thus, it is hypothesized that the observed backscatter is contributed by a combination of propagation delay, forward scatter by the soil surface, and specular bistatic reflection by the stalks. Model calculations based on this assumption were found to be in general agreement with the phase observations.

Systematic Redaction for Neuroimage Data

PubMed Central

Matlock, Matt; Schimke, Nakeisha; Kong, Liang; Macke, Stephen; Hale, John

2013-01-01

In neuroscience, collaboration and data sharing are undermined by concerns over the management of protected health information (PHI) and personal identifying information (PII) in neuroimage datasets. The HIPAA Privacy Rule mandates measures for the preservation of subject privacy in neuroimaging studies. Unfortunately for the researcher, the management of information privacy is a burdensome task. Wide scale data sharing of neuroimages is challenging for three primary reasons: (i) A dearth of tools to systematically expunge PHI/PII from neuroimage data sets, (ii) a facility for tracking patient identities in redacted datasets has not been produced, and (iii) a sanitization workflow remains conspicuously absent. This article describes the XNAT Redaction Toolkit—an integrated redaction workflow which extends a popular neuroimage data management toolkit to remove PHI/PII from neuroimages. Quickshear defacing is also presented as a complementary technique for deidentifying the image data itself. Together, these tools improve subject privacy through systematic removal of PII/PHI. PMID:24179597

Experimentally observed conformation-dependent geometry and hidden strain in proteins.

PubMed Central

Karplus, P. A.

1996-01-01

A database has been compiled documenting the peptide conformations and geometries from 70 diverse proteins refined at 1.75 A or better. Analysis of the well-ordered residues within the database shows phi, psi-distributions that have more fine structure than is generally observed. Also, clear evidence is presented that the peptide covalent geometry depends on conformation, with the interpeptide N-C alpha-C bond angle varying by nearly +/-5 degrees from its standard value. The observed deviations from standard peptide geometry are greatest near the edges of well-populated regions, consistent with strain occurring in these conformations. Minimization of such hidden strain could be an important factor in thermostability of proteins. These empirical data describing how equilibrium peptide geometry varies as a function of conformation confirm and extend quantum mechanics calculations, and have predictive value that will aid both theoretical and experimental analyses of protein structure. PMID:8819173

Study of high speed complex number algorithms. [for determining antenna for field radiation patterns

NASA Technical Reports Server (NTRS)

Heisler, R.

1981-01-01

A method of evaluating the radiation integral on the curved surface of a reflecting antenna is presented. A three dimensional Fourier transform approach is used to generate a two dimensional radiation cross-section along a planer cut at any angle phi through the far field pattern. Salient to the method is an algorithm for evaluating a subset of the total three dimensional discrete Fourier transform results. The subset elements are selectively evaluated to yield data along a geometric plane of constant. The algorithm is extremely efficient so that computation of the induced surface currents via the physical optics approximation dominates the computer time required to compute a radiation pattern. Application to paraboloid reflectors with off-focus feeds in presented, but the method is easily extended to offset antenna systems and reflectors of arbitrary shapes. Numerical results were computed for both gain and phase and are compared with other published work.

β Pictoris' inner disk in polarized light and new orbital parameters for β Pictoris b

DOE PAGES

Millar-Blanchaer, Maxwell A.; Graham, James R.; Pueyo, Laurent; ...

2015-09-16

Here, we present H-band observations of β Pic with the Gemini Planet Imager's (GPI's) polarimetry mode that reveal the debris disk between ~0farcs3 (6 AU) and ~1farcs7 (33 AU), while simultaneously detecting β Pic b. The polarized disk image was fit with a dust density model combined with a Henyey–Greenstein scattering phase function. The best-fit model indicates a disk inclined to the line of sight (more » $$\\phi =85\\buildrel{\\circ}\\over{.} {27}_{-0.19}^{+0.26}$$) with a position angle (PA) $${\\theta }_{\\mathrm{PA}}=30\\buildrel{\\circ}\\over{.} {35}_{-0.28}^{+0.29}$$ (slightly offset from the main outer disk, $${\\theta }_{\\mathrm{PA}}\\approx 29^\\circ $$), that extends from an inner disk radius of $${23.6}_{-0.6}^{+0.9}\\;\\mathrm{AU}$$ to well outside GPI's field of view.« less

Public health intelligence and the detection of potential pandemics.

PubMed

French, Martin; Mykhalovskiy, Eric

2013-02-01

This article considers contemporary developments in public health intelligence (PHI), especially their focus on health events of pandemic potential. It argues that the sociological study of PHI can yield important insights for the sociology of pandemics. PHI aims to detect health events as (or even before) they unfold. Whilst its apparatuses envelope traditional public health activities, such as epidemiological surveillance, they increasingly extend to non-traditional public health activities such as data-mining in electronically mediated social networks. With a focus on non-traditional PHI activities, the article first situates the study of PHI in relation to the sociology of public health. It then discusses the conceptualisation and actualisation of pandemics, reflecting on how public health professionals and organisations must equip themselves with diverse allies in order to realise the claims they make about pandemic phenomena. Finally, using the analytic tools of actor-network theory, sites for future empirical research that can contribute to the sociology of pandemics are suggested. © 2012 The Authors. Sociology of Health & Illness © 2012 Foundation for the Sociology of Health & Illness/Blackwell Publishing Ltd.

Modular low aspect ratio-high beta torsatron

DOEpatents

Sheffield, George V.; Furth, Harold P.

1984-02-07

A fusion reactor device in which the toroidal magnetic field and at least a portion of the poloidal magnetic field are provided by a single set of modular coils. The coils are arranged on the surface of a low aspect ratio toroid in planes having the cylindrical coordinate relationship .phi.=.phi..sub.i +kz where k is a constant equal to each coil's pitch and .phi..sub.i is the toroidal angle at which the i'th coil intersects the z=o plane. The device may be described as a modular, high beta torsation whose screw symmetry is pointed along the systems major (z) axis. The toroid defined by the modular coils preferably has a racetrack minor cross section. When vertical field coils and preferably a toroidal plasma current are provided for magnetic field surface closure within the toroid, a vacuum magnetic field of racetrack shaped minor cross section with improved stability and beta valves is obtained.

A Partially Saturated Constitutive Theory for Compacted Fills

DTIC Science & Technology

2004-06-01

degree of Doctor of Philosophy. COL James R. Rowan, EN , was Commander and Executive Director of ERDC, and Dr. James R. Houston was Director. CHAPTER...Reconsolidation Index CR Slope of the reconsolidation line Maximum Friction Angle of3 Friction Angle PHILIM traMaterial Ratio of minimum to maximum4 Phi Ratio PH ...Josa, A., (1988). "Un modelo elastoplastico para suelos no saturados," Tesis Doctorae, Universitat Politecnica de Catalunya, Barcelons, Spain. Lawton

Investigations of flowfields found in typical combustor geometries

NASA Technical Reports Server (NTRS)

Lilley, D. G.

1982-01-01

Experimental and theoretical research undertaken on 2-D axisymmetric geometries under low speed, nonreacting, turbulent, swirling flow conditions is reported. The flow enters the test section and proceeds into a larger chamber (the expansion ratio D/d = 2) via a sudden or gradual expansion (sidewall angle alpha = 90 and 45 degrees). Inlet swirl vanes are adjustable to a variety of vane angles with values of phi = 0, 38, 45, 60 and 70 degrees being emphasized.

Planar Poincare chart - A planar graphic representation of the state of light polarization

NASA Technical Reports Server (NTRS)

Tedjojuwono, Ken K.; Hunter, William W., Jr.; Ocheltree, Stewart L.

1989-01-01

The planar Poincare chart, which represents the complete planar equivalence of the Poincare sphere, is proposed. The four sets of basic lines are drawn on two separate charts for the generalization and convenience of reading the scale. The chart indicates the rotation of the principal axes of linear birefringent material. The relationships between parameters of the two charts are given as 2xi-2phi (orientation angle of the major axis-ellipticity angle) pair and 2alpha-delta (angle of amplitude ratio-phase difference angle) pair. The results are useful for designing and analyzing polarization properties of optical components with birefringent properties.

Phase-Array Approach to Optical Whispering Gallery Modulators

NASA Technical Reports Server (NTRS)

Strekalov, Dmitry

2010-01-01

This technology leverages the well-defined orbital number of a whispering gallery modulator (WGM) to expand the range of applications for such resonators. This property rigidly connects the phase variation of the field in this mode with the azimuthal angle between the coupling locations. A WGM with orbital momentum L has exactly L instant nodes around the circumference of the WGM resonator supporting such a mode. Therefore, in two locations separated by the arc alpha, the phase difference of such a field will be equal to phi= alpha L. Coupling the field out of such locations, and into a balanced interferometer, once can observe a complete constructive or distractive interference (or have any situation in between) depending on the angle alpha. Similarly, a mode L + delta L will pick up the phase phi + alpha delta L. In all applications of a WGM resonator as a modulator, the orbital numbers for the carrier and sidebands are different, and their differences delta L are known (usually, but not necessarily, delta L = 1). Therefore, the choice of the angle alpha, and of the interferometer arms difference, allows one to control the relative phase between different modes and to perform the conversion, separation, and filtering tasks necessary.

Practical implications of theoretical consideration of capsule filling by the dosator nozzle system.

PubMed

Jolliffe, I G; Newton, J M

1982-05-01

Eight lactose size fractions with mean particle sizes ranging from 15.6 to 155.2 micrometers were characterized by their failure properties using a Jenike shear cell. The effective angle of internal friction was found to be constant for all size fractions, with a mean value of 36.2 degrees. Jenike flow factors could only be obtained for the two most cohesive size fractions presumably due to limitations of the shear cell. Angles of wall friction, phi, were determined for all size fractions on face ground and turned stainless steel surfaces. These decreased with increasing particle size up to around 40 micrometers, above which they became effectively constant for both surfaces. The rougher turned plate gave consistently higher values of phi for each particle size. Simple retention experiments with a dosator nozzle and a range of powder bed bulk densities showed good retention was possible only up to a particle size of around 40 micrometers. Retention was difficult or impossible above this size. Values of phi were applied to equations derived in the theoretical approach described previously (Jolliffe et al 1980). This showed that the strength required within a powder to ensure arching increases with increasing particle size up to around 40 micrometers. Above this size, this strength requirement becomes constant. This is related to the powder retention observations. Finally, the failure data was used to calculate the minimum compressive stresses required to ensure powder retention within the dosator nozzle, by employing the equations described by Jolliffe et al (1980). This suggested that, as powders became more free flowing, a larger compressive stress is necessary and that the angle of wall friction should be lower to ensure stress is transmitted to the arching zone.

Evaluating the Applicability of Phi Coefficient in Indicating Habitat Preferences of Forest Soil Fauna Based on a Single Field Study in Subtropical China.

PubMed

Cui, Yang; Wang, Silong; Yan, Shaokui

2016-01-01

Phi coefficient directly depends on the frequencies of occurrence of organisms and has been widely used in vegetation ecology to analyse the associations of organisms with site groups, providing a characterization of ecological preference, but its application in soil ecology remains rare. Based on a single field experiment, this study assessed the applicability of phi coefficient in indicating the habitat preferences of soil fauna, through comparing phi coefficient-induced results with those of ordination methods in charactering soil fauna-habitat(factors) relationships. Eight different habitats of soil fauna were implemented by reciprocal transfer of defaunated soil cores between two types of subtropical forests. Canonical correlation analysis (CCorA) showed that ecological patterns of fauna-habitat relationships and inter-fauna taxa relationships expressed, respectively, by phi coefficients and predicted abundances calculated from partial redundancy analysis (RDA), were extremely similar, and a highly significant relationship between the two datasets was observed (Pillai's trace statistic = 1.998, P = 0.007). In addition, highly positive correlations between phi coefficients and predicted abundances for Acari, Collembola, Nematode and Hemiptera were observed using linear regression analysis. Quantitative relationships between habitat preferences and soil chemical variables were also obtained by linear regression, which were analogous to the results displayed in a partial RDA biplot. Our results suggest that phi coefficient could be applicable on a local scale in evaluating habitat preferences of soil fauna at coarse taxonomic levels, and that the phi coefficient-induced information, such as ecological preferences and the associated quantitative relationships with habitat factors, will be largely complementary to the results of ordination methods. The application of phi coefficient in soil ecology may extend our knowledge about habitat preferences and distribution-abundance relationships, which will benefit the understanding of biodistributions and variations in community compositions in the soil. Similar studies in other places and scales apart from our local site will be need for further evaluation of phi coefficient.

Evaluating the Applicability of Phi Coefficient in Indicating Habitat Preferences of Forest Soil Fauna Based on a Single Field Study in Subtropical China

PubMed Central

Cui, Yang; Wang, Silong; Yan, Shaokui

2016-01-01

Phi coefficient directly depends on the frequencies of occurrence of organisms and has been widely used in vegetation ecology to analyse the associations of organisms with site groups, providing a characterization of ecological preference, but its application in soil ecology remains rare. Based on a single field experiment, this study assessed the applicability of phi coefficient in indicating the habitat preferences of soil fauna, through comparing phi coefficient-induced results with those of ordination methods in charactering soil fauna-habitat(factors) relationships. Eight different habitats of soil fauna were implemented by reciprocal transfer of defaunated soil cores between two types of subtropical forests. Canonical correlation analysis (CCorA) showed that ecological patterns of fauna-habitat relationships and inter-fauna taxa relationships expressed, respectively, by phi coefficients and predicted abundances calculated from partial redundancy analysis (RDA), were extremely similar, and a highly significant relationship between the two datasets was observed (Pillai's trace statistic = 1.998, P = 0.007). In addition, highly positive correlations between phi coefficients and predicted abundances for Acari, Collembola, Nematode and Hemiptera were observed using linear regression analysis. Quantitative relationships between habitat preferences and soil chemical variables were also obtained by linear regression, which were analogous to the results displayed in a partial RDA biplot. Our results suggest that phi coefficient could be applicable on a local scale in evaluating habitat preferences of soil fauna at coarse taxonomic levels, and that the phi coefficient-induced information, such as ecological preferences and the associated quantitative relationships with habitat factors, will be largely complementary to the results of ordination methods. The application of phi coefficient in soil ecology may extend our knowledge about habitat preferences and distribution-abundance relationships, which will benefit the understanding of biodistributions and variations in community compositions in the soil. Similar studies in other places and scales apart from our local site will be need for further evaluation of phi coefficient. PMID:26930593

KLOE results on light meson spectroscopy and prospects for KLOE-2

NASA Astrophysics Data System (ADS)

Gauzzi, Paolo; KLOE-2 Collaboration

2012-03-01

The results obtained by the KLOE Collaboration on light meson spectroscopy are presented. The radiative decay phi → ηγ have been used to study several η decay channels. The Dalitz plot distributions of the η → 3π decays, both in charged and neutral final states have been measured. The box anomaly contribution in η → π+ π-γ has been investigated in, and the rare decays η → π0γγ, η → π+π-e+e- and η → e+e-e+e- have been measured. Also the strategy for the measurement of the transition form factor of phi → ηe+e- is described. The radiateve process phi → η'γ has been used to study the η' → ηππ decay channels, obtaining a measurement of the pseudoscalar mixing angle, and finding an evidence for a gluonium content of η'. The decays phi → PPγ where P means a pseudoscalar meson, have been exploited to investigate the light scalar mesons, f0(980), a0(980), and σ(600). The couplings of the scalar mesons to Kbar K, ππ or ππ0, and to the phi resonance have been measured. The prospects for the new KLOE-2 data-taking just started at the upgraded DAΦNE with an upgraded detector are described.

Optimizing X-Ray Optical Prescriptions for Wide-Field Applications

NASA Technical Reports Server (NTRS)

Elsner, R. F.; O'Dell, S. L.; Ramsey, B. D.; Weisskopf, M. C.

2010-01-01

X-ray telescopes with spatial resolution optimized over the field of view (FOV) are of special interest for missions, such as WFXT, focused on moderately deep and deep surveys of the x-ray sky, and for solar x-ray observations. Here we report on the present status of an on-going study of the properties of Wolter I and polynominal grazing incidence designs with a view to gain a deeper insight into their properties and simply the design process. With these goals in mind, we present some results in the complementary topics of (1) properties of Wolter I x-ray optics and polynominal x-ray optic ray tracing. Of crucial importance for the design of wide-field x-ray optics is the optimization criteria. Here we have adopted the minimization of a merit function, M, which measures the spatial resolution averaged over the FOV: M= ((integral of d phi) between the limits of 0 and 2 pi) (integral of d theta theta w(theta) sigma square (theta,phi) between the limits of 0 and theta(sub FOV)) (integral of d phi between the limits of 0 and phi/4) (Integral of d theta theta w(theta) between the limits of 0 and theta(sub FOV) where w(theta(sub 1) is a weighting function and Merit function: sigma-square (theta, phi) = summation of (x,y,z) [-<(x,y,z)> (exp 2)] is the spatial variance for a point source on the sky at polar and azimuthal off-axis angles (theta,phi).

On a new coordinate system with astrophysical application: Spiral coordinates

NASA Astrophysics Data System (ADS)

Campos, L. M. B. C.; Gil, P. J. S.

In this presentation are introduced spiral coordinates, which are a particular case of conformal coordinates, i.e. orthogonal curvelinear coordinates with equal factors along all coordinate axis. The spiral coordinates in the plane have as coordinate curves two families of logarithmic spirals, making a constant angle, respectively phi and pi / 2-phi, with all radial lines, where phi is a parameter. They can be obtained from a complex function, representing a spiral potential flow, due to the superposition of a source/sink with a vortex; the parameter phi in this case specifies the ratio of the ass flux of source/sink to the circulation of the vortex. Regardless of hydrodynamical or other interpretations, spiral coordinates are particulary convenient in situation where physical quantities vary only along a logarithmicspiral. The example chosen is the propagation of Alfven waves along a logarithmic spiral, as an approximation to Parker's spiral. The equation of dissipative MHD are written in spiral coordinates, and eliminated to specify the Alfven wave equation in spiral coordinates; the latter is solved exactly in terms of Bessel functions, and the results analyzed for values of the parameters corresponding to the solar wind.

N.m.r. studies of the conformation of analogues of methyl beta-lactoside in methyl sulfoxide-d6.

PubMed

Rivera-Sagredo, A; Jiménez-Barbero, J; Martín-Lomas, M

1991-12-16

The 1H- and 13C-n.m.r. spectra of solutions of methyl beta-lactoside (1), all of its monodeoxy derivatives (2, 3, 6-10), the 3-O-methyl derivative (4), and methyl 4-O-beta-D-galactopyranosyl-D-xylopyranoside (5) in methyl sulfoxide-d6 have been analysed. The n.O.e.'s and specific desheildings indicate similar distributions of low-energy conformers, comparable to those in aqueous solution. The major conformer has torsion angles phi H and psi H of 49 degrees and 5 degrees, respectively, with contributions of conformers with phi/psi 24 degrees/-59 degrees, 22 degrees/32 degrees, and 6 degrees/44 degrees.

Experimental study of turbulent flow heat transfer and pressure drop in plate heat exchanger with chevron plates

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

Muley, A.; Manglik, R.M.

1999-02-01

Experimental heat transfer and isothermal pressure drop data for single-phase water flows in a plate heat exchanger (PHE) with chevron plates are presented. In a single-pass U-type counterflow PHE, three different chevron plate arrangements are considered: two symmetric plate arrangements with {beta} = 30 deg/30 deg and 60 deg/60 deg, and one mixed-plate arrangement with {beta} = 30 deg/60 deg. For water (2 < Pr < 6) flow rates in the 600 < Re < 10{sup 4} regime, data for Nu and f are presented. The results show significant effects of both the chevron angle {beta} and surface area enlargementmore » factor {phi}. As {beta} increases, and compared to a flat-plate pack, up to two to five times higher Nu are obtained; the concomitant f, however, are 13 to 44 times higher. Increasing {phi} also has a similar, though smaller effect. Based on experimental data for Re {ge} 1000 and 30 deg {le} {beta} {le} 60 deg, predictive correlations of the form Nu = C{sub 1}({beta}) D{sub 1}({phi}) Re{sup p1({beta})} Pr{sup 1/3} ({mu}/{mu}{sub w}){sup 0.14} and f = C{sub 2}({beta}) D{sub 2}({phi}) Re{sup p2({beta})} are devised. Finally, at constant pumping power, and depending upon Re, {beta}, and {phi}, the heat transfer is found to be enhanced by up to 2.8 times that in an equivalent flat-plate channel.« less

Integrated information in discrete dynamical systems: motivation and theoretical framework.

PubMed

Balduzzi, David; Tononi, Giulio

2008-06-13

This paper introduces a time- and state-dependent measure of integrated information, phi, which captures the repertoire of causal states available to a system as a whole. Specifically, phi quantifies how much information is generated (uncertainty is reduced) when a system enters a particular state through causal interactions among its elements, above and beyond the information generated independently by its parts. Such mathematical characterization is motivated by the observation that integrated information captures two key phenomenological properties of consciousness: (i) there is a large repertoire of conscious experiences so that, when one particular experience occurs, it generates a large amount of information by ruling out all the others; and (ii) this information is integrated, in that each experience appears as a whole that cannot be decomposed into independent parts. This paper extends previous work on stationary systems and applies integrated information to discrete networks as a function of their dynamics and causal architecture. An analysis of basic examples indicates the following: (i) phi varies depending on the state entered by a network, being higher if active and inactive elements are balanced and lower if the network is inactive or hyperactive. (ii) phi varies for systems with identical or similar surface dynamics depending on the underlying causal architecture, being low for systems that merely copy or replay activity states. (iii) phi varies as a function of network architecture. High phi values can be obtained by architectures that conjoin functional specialization with functional integration. Strictly modular and homogeneous systems cannot generate high phi because the former lack integration, whereas the latter lack information. Feedforward and lattice architectures are capable of generating high phi but are inefficient. (iv) In Hopfield networks, phi is low for attractor states and neutral states, but increases if the networks are optimized to achieve tension between local and global interactions. These basic examples appear to match well against neurobiological evidence concerning the neural substrates of consciousness. More generally, phi appears to be a useful metric to characterize the capacity of any physical system to integrate information.

Application of geometric algebra for the description of polymer conformations.

PubMed

Chys, Pieter

2008-03-14

In this paper a Clifford algebra-based method is applied to calculate polymer chain conformations. The approach enables the calculation of the position of an atom in space with the knowledge of the bond length (l), valence angle (theta), and rotation angle (phi) of each of the preceding bonds in the chain. Hence, the set of geometrical parameters {l(i),theta(i),phi(i)} yields all the position coordinates p(i) of the main chain atoms. Moreover, the method allows the calculation of side chain conformations and the computation of rotations of chain segments. With these features it is, in principle, possible to generate conformations of any type of chemical structure. This method is proposed as an alternative for the classical approach by matrix algebra. It is more straightforward and its final symbolic representation considerably simpler than that of matrix algebra. Approaches for realistic modeling by means of incorporation of energetic considerations can be combined with it. This article, however, is entirely focused at showing the suitable mathematical framework on which further developments and applications can be built.

Study of Quantum Chaos in the Framework of Triaxial Rotator Models

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

Proskurins, J.; Bavrins, K.; Andrejevs, A.

2009-01-28

Dynamical quantum chaos criteria--a perturbed wave function entropy W({psi}{sub i}) and a fragmentation width {kappa}({phi}{sub k}) of basis states were studied in two cases of nuclear rigid triaxial rotator models. The first model is characterized by deformation angle {gamma} only, while the second model depends on both quadrupole deformation parameters ({beta},{gamma}). The degree of chaoticity has been determined in the studies of the dependence of criteria W({psi}{sub i}) and {kappa}({phi}{sub k}) from nuclear spin values up to I{<=}101 for model parameters {gamma} and ({beta},{gamma}) correspondingly. The transition from librational to rotational type energy spectra has been considered for both modelsmore » as well.« less

Long period perturbations of earth satellite orbits. [Von Zeipel method and zonal harmonics

NASA Technical Reports Server (NTRS)

Wang, K. C.

1979-01-01

All the equations involved in extending the PS phi solution to include the long periodic and second order secular effects of the zonal harmonics are presented. Topics covered include DSphi elements and relations for their conconical transformation into the PS phi elements; the solution algorithm based on the Von Zeipel method; and the elimination of long periodic terms and analytical integration of primed variables. The equations were entered into the ASOP program, checked out, and verified. Comparisons with numerical integrations show the long period theory to be accurate within several meters after 800 revolutions.

Potts glass reflection of the decoding threshold for qudit quantum error correcting codes

NASA Astrophysics Data System (ADS)

Jiang, Yi; Kovalev, Alexey A.; Pryadko, Leonid P.

We map the maximum likelihood decoding threshold for qudit quantum error correcting codes to the multicritical point in generalized Potts gauge glass models, extending the map constructed previously for qubit codes. An n-qudit quantum LDPC code, where a qudit can be involved in up to m stabilizer generators, corresponds to a ℤd Potts model with n interaction terms which can couple up to m spins each. We analyze general properties of the phase diagram of the constructed model, give several bounds on the location of the transitions, bounds on the energy density of extended defects (non-local analogs of domain walls), and discuss the correlation functions which can be used to distinguish different phases in the original and the dual models. This research was supported in part by the Grants: NSF PHY-1415600 (AAK), NSF PHY-1416578 (LPP), and ARO W911NF-14-1-0272 (LPP).

Constraints on Dark Energy from Baryon Acoustic Peak and Galaxy Cluster Gas Mass Measurements

NASA Astrophysics Data System (ADS)

Samushia, Lado; Ratra, Bharat

2009-10-01

We use baryon acoustic peak measurements by Eisenstein et al. and Percival et al., together with the Wilkinson Microwave Anisotropy Probe (WMAP) measurement of the apparent acoustic horizon angle, and galaxy cluster gas mass fraction measurements of Allen et al., to constrain a slowly rolling scalar field dark energy model, phiCDM, in which dark energy's energy density changes in time. We also compare our phiCDM results with those derived for two more common dark energy models: the time-independent cosmological constant model, ΛCDM, and the XCDM parameterization of dark energy's equation of state. For time-independent dark energy, the Percival et al. measurements effectively constrain spatial curvature and favor a close to the spatially flat model, mostly due to the WMAP cosmic microwave background prior used in the analysis. In a spatially flat model the Percival et al. data less effectively constrain time-varying dark energy. The joint baryon acoustic peak and galaxy cluster gas mass constraints on the phiCDM model are consistent with but tighter than those derived from other data. A time-independent cosmological constant in a spatially flat model provides a good fit to the joint data, while the α parameter in the inverse power-law potential phiCDM model is constrained to be less than about 4 at 3σ confidence level.

Calculated X-ray Intensities Using Monte Carlo Algorithms: A Comparison to Experimental EPMA Data

NASA Technical Reports Server (NTRS)

Carpenter, P. K.

2005-01-01

Monte Carlo (MC) modeling has been used extensively to simulate electron scattering and x-ray emission from complex geometries. Here are presented comparisons between MC results and experimental electron-probe microanalysis (EPMA) measurements as well as phi(rhoz) correction algorithms. Experimental EPMA measurements made on NIST SRM 481 (AgAu) and 482 (CuAu) alloys, at a range of accelerating potential and instrument take-off angles, represent a formal microanalysis data set that has been widely used to develop phi(rhoz) correction algorithms. X-ray intensity data produced by MC simulations represents an independent test of both experimental and phi(rhoz) correction algorithms. The alpha-factor method has previously been used to evaluate systematic errors in the analysis of semiconductor and silicate minerals, and is used here to compare the accuracy of experimental and MC-calculated x-ray data. X-ray intensities calculated by MC are used to generate a-factors using the certificated compositions in the CuAu binary relative to pure Cu and Au standards. MC simulations are obtained using the NIST, WinCasino, and WinXray algorithms; derived x-ray intensities have a built-in atomic number correction, and are further corrected for absorption and characteristic fluorescence using the PAP phi(rhoz) correction algorithm. The Penelope code additionally simulates both characteristic and continuum x-ray fluorescence and thus requires no further correction for use in calculating alpha-factors.

Frictionless bead packs have macroscopic friction, but no dilatancy.

PubMed

Peyneau, Pierre-Emmanuel; Roux, Jean-Noël

2008-07-01

The statement of the title is shown by numerical simulation of homogeneously sheared assemblies of frictionless, nearly rigid beads in the quasistatic limit. Results coincide for steady flows at constant shear rate gamma[over ] in the limit of small gamma[over ] and static approaches, in which packings are equilibrated under growing deviator stresses. The internal friction angle phi , equal to 5.76 degrees +/-0.22 degrees in simple shear, is independent of average pressure P in the rigid limit and stems from the ability of stable frictionless contact networks to form stress-induced anisotropic fabrics. No enduring strain localization is observed. Dissipation at the macroscopic level results from repeated network rearrangements, similar to the effective friction of a frictionless slider on a bumpy surface. Solid fraction Phi remains equal to the random close packing value approximately 0.64 in slowly or statically sheared systems. Fluctuations of stresses and volume are observed to regress in the large system limit. Defining the inertial number as I=gamma radical m/(aP), with m the grain mass and a its diameter, both internal friction coefficient mu*=tan phi and volume 1/Phi increase as powers of I in the quasistatic limit of vanishing I , in which all mechanical properties are determined by contact network geometry. The microstructure of the sheared material is characterized with a suitable parametrization of the fabric tensor and measurements of coordination numbers.

A Lightweight Encryption Scheme Combined with Trust Management for Privacy-Preserving in Body Sensor Networks.

PubMed

Guo, Ping; Wang, Jin; Ji, Sai; Geng, Xue Hua; Xiong, Neal N

2015-12-01

With the pervasiveness of smart phones and the advance of wireless body sensor network (BSN), mobile Healthcare (m-Healthcare), which extends the operation of Healthcare provider into a pervasive environment for better health monitoring, has attracted considerable interest recently. However, the flourish of m-Healthcare still faces many challenges including information security and privacy preservation. In this paper, we propose a secure and privacy-preserving framework combining with multilevel trust management. In our scheme, smart phone resources including computing power and energy can be opportunistically gathered to process the computing-intensive PHI (personal health information) during m-Healthcare emergency with minimal privacy disclosure. In specific, to leverage the PHI privacy disclosure and the high reliability of PHI process and transmission in m-Healthcare emergency, we introduce an efficient lightweight encryption for those users whose trust level is low, which is based on mix cipher algorithms and pair of plain text and cipher texts, and allow a medical user to decide who can participate in the opportunistic computing to assist in processing his overwhelming PHI data. Detailed security analysis and simulations show that the proposed framework can efficiently achieve user-centric privacy protection in m-Healthcare system.

A FORTRAN technique for correlating a circular environmental variable with a linear physiological variable in the sugar maple.

PubMed

Pease, J M; Morselli, M F

1987-01-01

This paper deals with a computer program adapted to a statistical method for analyzing an unlimited quantity of binary recorded data of an independent circular variable (e.g. wind direction), and a linear variable (e.g. maple sap flow volume). Circular variables cannot be statistically analyzed with linear methods, unless they have been transformed. The program calculates a critical quantity, the acrophase angle (PHI, phi o). The technique is adapted from original mathematics [1] and is written in Fortran 77 for easier conversion between computer networks. Correlation analysis can be performed following the program or regression which, because of the circular nature of the independent variable, becomes periodic regression. The technique was tested on a file of approximately 4050 data pairs.

An inverse inviscid method for the design of quasi-three dimensional rotating turbomachinery cascades

NASA Technical Reports Server (NTRS)

Bonataki, E.; Chaviaropoulos, P.; Papailiou, K. D.

1991-01-01

A new inverse inviscid method suitable for the design of rotating blade sections lying on an arbitrary axisymmetric stream-surface with varying streamtube width is presented. The geometry of the axisymmetric stream-surface and the streamtube width variation with meridional distance, the number of blades, the inlet flow conditions, the rotational speed and the suction and pressure side velocity distributions as functions of the normalized arc-length are given. The flow is considered irrotational in the absolute frame of reference and compressible. The output of the computation is the blade section that satisfies the above data. The method solves the flow equations on a (phi 1, psi) potential function-streamfunction plane for the velocity modulus, W and the flow angle beta; the blade section shape can then be obtained as part of the physical plane geometry by integrating the flow angle distribution along streamlines. The (phi 1, psi) plane is defined so that the monotonic behavior of the potential function is guaranteed, even in cases with high peripheral velocities. The method is validated on a rotating turbine case and used to design new blades. To obtain a closed blade, a set of closure conditions were developed and referred.

Boron neutrino flux and the MSW solution of the solar neutrino problem

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

Krastev, P.I.; Smirnov, A.Y.

1994-10-01

There are large uncertainties in the predictions of the boron neutrino flux from the Sun which cannot be considered as being of purely statistical origin. We treat the magnitude of this flux, {Phi}{sub B}, as a parameter to be found from experiment. The properties of the, MSW solution to the solar neutrino problem for different values of {Phi}{sub B} are studied. Present, data give the bounds: 0.38 < {Phi}{sub B}/{Phi}{sub B}{sup O} < 3.1 (2{sigma}), where {Phi}{sub B}{sup O} {identical_to} 5.7 {center_dot} 10{sup 6} cm{sup {minus}2}s{sup {minus}1} is the flux in the reference SSM. The variations of the flux inmore » this interval enlarge the allowed region of mixing angles: sin{sup 2} 2{theta} = 0.2 {divided_by} 2 {center_dot} 10{sup {minus}4} {divided_by} 2 {center_dot} 10{sup {minus}2} (small mixing solutions) and sin{sup 2} 2{theta} = 0.2 {divided_by} 0.85 (large mixing solution). If the value of the original boron neutrino flux is about that measured by Kamiokande, a consistent description of the data is achieved for sin{sup 2} 2{theta} {approximately} (0.8 {divided_by} 2) {center_dot} 10{sup {minus}3} (``very small mixing solution``). The solution is characterized by a strong suppression of the beryllium neutrino line, a weak distortion of the high energy part of the baron neutrino spectrum and a value of the double ratio (CC/NC){sup exp}/(CC/NC){sup SSM} at E > 5 MeV close to 1. We comment on the possibility to measure the neutrino parameters and the original boron neutrino flux in future experiments.« less

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

PubMed

Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent; Anisimova, Maria; Hordijk, Wim; Gascuel, Olivier

2010-05-01

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

Expanded turn conformations: characterization and sequence-structure correspondence in alpha-turns with implications in helix folding.

PubMed

Dasgupta, Bhaskar; Pal, Lipika; Basu, Gautam; Chakrabarti, Pinak

2004-05-01

Like the beta-turns, which are characterized by a limiting distance between residues two positions apart (i, i+3), a distance criterion (involving residues at positions i and i+4) is used here to identify alpha-turns from a database of known protein structures. At least 15 classes of alpha-turns have been enumerated based on the location in the phi,psi space of the three central residues (i+1 to i+3)-one of the major being the class AAA, where the residues occupy the conventional helical backbone torsion angles. However, moving towards the C-terminal end of the turn, there is a shift in the phi,psi angles towards more negative phi, such that the electrostatic repulsion between two consecutive carbonyl oxygen atoms is reduced. Except for the last position (i+4), there is not much similarity in residue composition at different positions of hydrogen and non-hydrogen bonded AAA turns. The presence or absence of Pro at i+1 position of alpha- and beta-turns has a bearing on whether the turn is hydrogen-bonded or without a hydrogen bond. In the tertiary structure, alpha-turns are more likely to be found in beta-hairpin loops. The residue composition at the beginning of the hydrogen bonded AAA alpha-turn has similarity with type I beta-turn and N-terminal positions of helices, but the last position matches with the C-terminal capping position of helices, suggesting that the existence of a "helix cap signal" at i+4 position prevents alpha-turns from growing into helices. Our results also provide new insights into alpha-helix nucleation and folding. Copyright 2004 Wiley-Liss, Inc.

Techniques for measurement of thoracoabdominal asynchrony

NASA Technical Reports Server (NTRS)

Prisk, G. Kim; Hammer, J.; Newth, Christopher J L.

2002-01-01

Respiratory motion measured by respiratory inductance plethysmography often deviates from the sinusoidal pattern assumed in the traditional Lissajous figure (loop) analysis used to determine thoraco-abdominal asynchrony, or phase angle phi. We investigated six different time-domain methods of measuring phi, using simulated data with sinusoidal and triangular waveforms, phase shifts of 0-135 degrees, and 10% noise. The techniques were then used on data from 11 lightly anesthetized rhesus monkeys (Macaca mulatta; 7.6 +/- 0.8 kg; 5.7 +/- 0.5 years old), instrumented with a respiratory inductive plethysmograph, and subjected to increasing levels of inspiratory resistive loading ranging from 5-1,000 cmH(2)O. L(-1). sec(-1).The best results were obtained from cross-correlation and maximum linear correlation, with errors less than approximately 5 degrees from the actual phase angle in the simulated data. The worst performance was produced by the loop analysis, which in some cases was in error by more than 30 degrees. Compared to correlation, other analysis techniques performed at an intermediate level. Maximum linear correlation and cross-correlation produced similar results on the data collected from monkeys (SD of the difference, 4.1 degrees ) but all other techniques had a high SD of the difference compared to the correlation techniques.We conclude that phase angles are best measured using cross-correlation or maximum linear correlation, techniques that are independent of waveform shape, and robust in the presence of noise. Copyright 2002 Wiley-Liss, Inc.

Characterization of tail sheath protein of giant bacteriophage phiKZ Pseudomonas aeruginosa

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

Kurochkina, Lidia P., E-mail: lpk@ibch.r; Aksyuk, Anastasia A.; Sachkova, Maria Yu.

2009-12-20

The tail sheath protein of giant bacteriophage phiKZ Pseudomonas aeruginosa encoded by gene 29 was identified and its expression system was developed. Localization of the protein on the virion was confirmed by immunoelectron microscopy. Properties of gene product (gp) 29 were studied by electron microscopy, immunoblotting and limited trypsinolysis. Recombinant gp29 assembles into the regular tubular structures (polysheaths) of variable length. Trypsin digestion of gp29 within polysheaths or extended sheath of virion results in specific cleavage of the peptide bond between Arg135 and Asp136. However, this cleavage does not affect polymeric structure of polysheaths, sheaths and viral infectivity. Digestion bymore » trypsin of the C-truncated gp29 mutant, lacking the ability to self-assemble, results in formation of a stable protease-resistant fragment. Although there is no sequence homology of phiKZ proteins to proteins of other bacteriophages, some characteristic biochemical properties of gp29 revealed similarities to the tail sheath protein of bacteriophage T4.« less

Simultaneous ionization-excitation of helium to the 3s, 3p, and 3d states of He+

NASA Astrophysics Data System (ADS)

Zatsarinny, Oleg; Bartschat, Klaus

2015-05-01

We extended our work on ionization of helium with simultaneous excitation to the n = 2 states to include the n = 3 manifold of the residual ion. This requires the inclusion of pseudo-states constructed on the 3s, 3p, and 3d ionic core. We used a parallelized version of the B-spline R-matrix (BSR) package to perform a calculation with 1,254 target states, resulting in up to 3,027 coupled channels and matrices of rank up to 200,000 to be diagonalized. The triple-differential cross section (TDCS) was extracted by the projection method. We obtain excellent agreement with experiment regarding the angular dependence of the TDCS for all kinematical situations available for comparison. Some discrepancies remain for the absolute magnitude. Results for the n = 2 states are stable and closely agree with previous predictions. Work supported by the United States National Science Foundation under grants No. PHY-1212450, PHY-1430245 and the XSEDE allocation PHY-090031.

Bandpass of microwave signals in a system of orthogonal magnetostatic-wave antennas

NASA Astrophysics Data System (ADS)

Zavisliak, I. V.; Zagorodnii, V. V.

1990-12-01

Experimental results are presented on a system consisting of MSW receive and transmit antennas integrated with a 36.7-micron-thick epitaxial YIG film. The amplitude-frequency response of this system was investigated for different values of magnetization parameters, and it was shown that the system has the property of selective transmittivity only in a narrow band of angles, phi = 48-53 deg.

Ultrastable pRNA hexameric ring gearing hexameric phi29 DNA-packaging motor by revolving without rotating and coiling

PubMed Central

Schwartz, Chad; Guo, Peixuan

2013-01-01

Biomotors have previously been classified into two categories: linear and rotational motors. It has long been popularly believed that viral DNA packaging motors are rotation motors. We have recently found that the DNA-packaging motor of bacteriophage phi29 uses a third mechanism: revolution without rotation. phi29 motor consists of three-coaxial rings of hexameric RNA, a hexameric ATPase, and a dodecameric channel. The motor uses six ATP to revolve one helical turn of dsDNA around the hexameric ring of ATPase gp16. Each dodecameric segment tilts at a 30°-angle and runs anti-parallel to the dsDNA helix to facilitate translation in one direction. The negatively charged phosphate backbone interacts with four positively charged lysine rings, resulting in four steps of transition. This review will discuss how the novel pRNA meets motor requirements for translocation concerning structure, stoichiometry, and thermostability; how pRNA studies have led to the generation of the concept of RNA nanotechnology; and how pRNA is fabricated into nanoparticles to deliver siRNA, miRNA, and ribozymes to cancer and virus-infected cells. PMID:23683853

Ray-splitting correction to the Weyl formula: Experiment versus theory

NASA Astrophysics Data System (ADS)

Blumel, Reinhold

2004-03-01

Ray splitting is a phenomenon we are all familiar with: A light ray hitting a water surface at an angle is split into a transmitted and a reflected ray. Ray splitting is not restricted to light and water, but occurs generally in all wave systems in which the properties of the propagation medium change rapidly on the scale of a wave length. It was predicted by Prange et al. [Phys. Rev. E 53, 207 (1996)] that ray splitting produces universal corrections to the Weyl formula, i.e. the average density of states. Following a brief review of Weyl's theory and the theory of ray splitting, this talk presents recent results of a first experimental confirmation of the existence of ray-splitting corrections to the Weyl formula. The experiment, a quasi two-dimensional microwave cavity loaded with two dielectric bars, has been carried out by Corrie Vaa and Peter Koch at the State University of New York at Stony Brook [C. Vaa, P. M. Koch, and R. Blumel, Phys. Rev. Lett. 90, 194102 (2003)]. This research is supported by the NSF under Grant Numbers PHY-9732443, PHY-0099398 and PHY-9984075.

Large Magellanic Cloud Distance and Structure from Near-Infrared Red Clump Observations

NASA Astrophysics Data System (ADS)

Koerwer, Joel F.

2009-07-01

We have applied the Infrared Survey Facility Magellanic Clouds Point-Source Catalog to the mapping of the red clump (RC) distance modulus across the Large Magellanic Cloud (LMC). Using the J- (1.25 μm) and H- (1.63 μm) band data to derive a reddening free luminosity function and a theoretical RC absolute magnitude from stellar evolution libraries, we estimate a distance modulus to the LMC of μ = 18.54 ± 0.06. The best fitting plane inclination, i, and the position angle of the line of nodes, phi, have little dependence on the assumed RC absolute magnitude; we find i = 23fdg5 ± 0fdg4 and phi = 154fdg6 ± 1fdg2. It was also noted that many fields included a significant asymptotic giant branch bump population that must be accounted for.

Slow-roll k-essence

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

Chiba, Takeshi; Dutta, Sourish; Scherrer, Robert J.

We derive slow-roll conditions for thawing k-essence with a separable Lagrangian p(X,{phi})=F(X)V({phi}). We examine the evolution of the equation of state parameter, w, as a function of the scale factor a, for the case where w is close to -1. We find two distinct cases, corresponding to X{approx_equal}0 and F{sub X}{approx_equal}0, respectively. For the case where X{approx_equal}0 the evolution of {phi} and hence w is described by only two parameters, and w(a) is model independent and coincides with similar behavior seen in thawing quintessence models. This result also extends to nonseparable Lagrangians where X{approx_equal}0. For the case F{sub X}{approx_equal}0, anmore » expression is derived for w(a), but this expression depends on the potential V({phi}), so there is no model-independent limiting behavior. For the X{approx_equal}0 case, we derive observational constraints on the two parameters of the model, w{sub 0} (the present-day value of w), and the K, which parametrizes the curvature of the potential. We find that the observations sharply constrain w{sub 0} to be close to -1, but provide very poor constraints on K.« less

Compartment-specific pH monitoring in Bacillus subtilis using fluorescent sensor proteins: a tool to analyze the antibacterial effect of weak organic acids.

PubMed

van Beilen, Johan W A; Brul, Stanley

2013-01-01

The internal pH (pHi) of a living cell is one of its most important physiological parameters. To monitor the pH inside Bacillus subtilis during various stages of its life cycle, we constructed an improved version (IpHluorin) of the ratiometric, pH-sensitive fluorescent protein pHluorin by extending it at the 5' end with the first 24 bp of comGA. The new version, which showed an approximate 40% increase in fluorescence intensity, was expressed from developmental phase-specific, native promoters of B. subtilis that are specifically active during vegetative growth on glucose (PptsG) or during sporulation (PspoIIA, PspoIIID, and PsspE). Our results show strong, compartment-specific expression of IpHluorin that allowed accurate pHi measurements of live cultures during exponential growth, early and late sporulation, spore germination, and during subsequent spore outgrowth. Dormant spores were characterized by an pHi of 6.0 ± 0.3. Upon full germination the pHi rose dependent on the medium to 7.0-7.4. The presence of sorbic acid in the germination medium inhibited a rise in the intracellular pH of germinating spores and inhibited germination. Such effects were absent when acetic was added at identical concentrations.

Scattering from arbitrarily shaped microstrip patch antennas

NASA Technical Reports Server (NTRS)

Shively, David G.; Deshpande, Manohar D.; Cockrell, Capers R.

1992-01-01

The scattering properties of arbitrarily shaped microstrip patch antennas are examined. The electric field integral equation for a current element on a grounded dielectric slab is developed for a rectangular geometry based on Galerkin's technique with subdomain rooftop basis functions. A shape function is introduced that allows a rectangular grid approximation to the arbitrarily shaped patch. The incident field on the patch is expressed as a function of incidence angle theta(i), phi(i). The resulting system of equations is then solved for the unknown current modes on the patch, and the electromagnetic scattering is calculated for a given angle. Comparisons are made with other calculated results as well as with measurements.

Investigations of flowfields found in typical combustor geometries

NASA Technical Reports Server (NTRS)

Lilley, D. G.; Mclaughlin, D. K.

1981-01-01

The flowfields of gas turbine combustion chambers were investigated. Six flowfield configurations with sidewall angles alpha = 90 and 45 deg. and swirl vane angles phi = 0, 45 and 70 deg. are characterized. Photography of neutrally-buoyant helium-filled soap bubbles, tufts, and injected smoke helps to characterize the time-mean streamlines, recirculation zones and regions of highly turbulent flow. Five-hole pitot probe pressure measurements allow the determination of time-mean velocities u, v and w. An advanced computer code equipped with a standard two-equation kappa-epsilon turbulence model was used to predict corresponding flow situations and to compare results with the experimental data.

AK-cut crystal resonators

NASA Technical Reports Server (NTRS)

Kahan, A.; Euler, F. K.

1983-01-01

Calculations have predicted the existence of crystallographically doubly rotated quartz orientations with turnover temperatures which are considerably less sensitive to angular misorientation then comparable AT- or BT-cuts. These crystals are arbitrarily designated as the AK-cut. Experimental data is given for seven orientations, phi-angle variations between 30-46 deg and theta-angle variations between 21-28 deg measured on 3.3-3.4 MHz fundamental mode resonators vibrating in the thickness shear c-mode. The experimental turnover temperatures of these resonators are between 80 C and 150 C, in general agreement with calculated values. The normalized frequency change as a function of temperature has been fitted with a cubic equation.

An enhanced mobile-healthcare emergency system based on extended chaotic maps.

PubMed

Lee, Cheng-Chi; Hsu, Che-Wei; Lai, Yan-Ming; Vasilakos, Athanasios

2013-10-01

Mobile Healthcare (m-Healthcare) systems, namely smartphone applications of pervasive computing that utilize wireless body sensor networks (BSNs), have recently been proposed to provide smartphone users with health monitoring services and received great attentions. An m-Healthcare system with flaws, however, may leak out the smartphone user's personal information and cause security, privacy preservation, or user anonymity problems. In 2012, Lu et al. proposed a secure and privacy-preserving opportunistic computing (SPOC) framework for mobile-Healthcare emergency. The brilliant SPOC framework can opportunistically gather resources on the smartphone such as computing power and energy to process the computing-intensive personal health information (PHI) in case of an m-Healthcare emergency with minimal privacy disclosure. To balance between the hazard of PHI privacy disclosure and the necessity of PHI processing and transmission in m-Healthcare emergency, in their SPOC framework, Lu et al. introduced an efficient user-centric privacy access control system which they built on the basis of an attribute-based access control mechanism and a new privacy-preserving scalar product computation (PPSPC) technique. However, we found out that Lu et al.'s protocol still has some secure flaws such as user anonymity and mutual authentication. To fix those problems and further enhance the computation efficiency of Lu et al.'s protocol, in this article, the authors will present an improved mobile-Healthcare emergency system based on extended chaotic maps. The new system is capable of not only providing flawless user anonymity and mutual authentication but also reducing the computation cost.

Proportional drift tubes for large area muon detectors

NASA Technical Reports Server (NTRS)

Cho, C.; Higashi, S.; Hiraoka, N.; Maruyama, A.; Okusawa, T.; Sato, T.; Suwada, T.; Takahashi, T.; Umeda, H.

1985-01-01

A proportional drift chamber which consists of eight rectangular drift tubes with cross section of 10 cm x 5 cm, a sense wire of 100 micron phi gold-plated tungsten wire and the length of 6 m, was tested using cosmic ray muons. Spatial resolution (rms) is between 0.5 and 1 mm over drift space of 50 mm, depending on incident angle and distance from sense wire.

Conformation of glycomimetics in the free and protein-bound state: structural and binding features of the C-glycosyl analogue of the core trisaccharide alpha-D-Man-(1 --> 3)-[alpha-D-Man-(1 --> 6)]-D-Man.

PubMed

Mikkelsen, Lise Munch; Hernáiz, María José; Martín-Pastor, M; Skrydstrup, Troels; Jiménez-Barbero, Jesús

2002-12-18

The conformational properties of the C-glycosyl analogue of the core trisaccharide alpha-D-Man-(1 --> 3)-[alpha-D-Man-(1 --> 6)]-D-Man in solution have been carefully analyzed by a combination of NMR spectroscopy and time-averaged restrained molecular dynamics. It has been found that both the alpha-1,3- and the alpha-1,6-glycosidic linkages show a major conformational averaging. Unusual Phi ca. 60 degrees orientations for both Phi torsion angles are found. Moreover, a major conformational distinction between the natural compound and the glycomimetic affects to the behavior of the omega(16) torsion angle around the alpha-1 --> 6-linkage. Despite this increased flexibility, the C-glycosyl analogue is recognized by three mannose binding lectins, as shown by NMR (line broadening, TR-NOE, and STD) and surface plasmon resonance (SPR) methods. Moreover, a process of conformational selection takes place, so that these lectins probably bind the glycomimetic similarly to the way they recognize the natural analogue. Depending upon the architecture and extension of the binding site of the lectin, loss or gain of binding affinity with respect to the natural analogue is found.

B cell helper factors. II. Synergy among three helper factors in the response of T cell- and macrophage-depleted B cells.

PubMed

Liebson, H J; Marrack, P; Kappler, J

1982-10-01

The concanavalin A- (Con A) stimulated supernatant of normal spleen cells (normal Con A SN) was shown to contain a set of helper factors sufficient to allow T cell- and macrophage- (M phi) depleted murine splenic B cells to produce a plaque-forming cell response to the antigen sheep red blood cells (SRBC). The activity of normal Con A SN could be reconstituted by a mixture of three helper factor preparations. The first was the interleukin 2- (IL 2) containing Con A SN of the T cell hybridoma, FS6-14.13. The second was a normal Con A SN depleted of IL 2 by extended culture with T cell blasts from which the 30,000 to 50,000 m.w. factors were isolated (interleukin X, IL X). The third was a SN either from the M phi tumor cell line P388D1 or from normal M phi taken from Corynebacterium parvum-immune mice. The combination of all three helper factor preparations was required to equal the activity of normal Con A SN; however, the M phi SN had the least overall effect. The M phi SN and IL 2 had to be added at the initiation of the culture period for a maximal effect, but the IL X preparation was most effective when added 24 hr after the initiation of culture. These results indicate that at least three nonspecific helper factors contribute to the helper activity in normal Con A SN.

Method of Generating X-Ray Diffraction Data for Integral Detection of Twin Defects in Super-Hetero-Epitaxial Materials

NASA Technical Reports Server (NTRS)

Park, Yeonjoon (Inventor); Choi, Sang Hyouk (Inventor); King, Glen C. (Inventor); Elliott, James R. (Inventor)

2009-01-01

A method provides X-ray diffraction (XRD) data suitable for integral detection of a twin defect in a strained or lattice-matched epitaxial material made from components having crystal structures having symme try belonging to different space groups. The material is mounted in a n X-ray diffraction (XRD) system. In one embodiment, the XRD system's goniometer angle Omega is set equal to (Theta(sub B)-Beta) where The ta(sub B) is a Bragg angle for a designated crystal plane of the allo y that is disposed at a non-perpendicular orientation with respect to the {111) crystal plane, and Beta is the angle between the designate d crystal plane and a { 111 } crystal plane of one of the epitaxial components. The XRD system's detector angle is set equal to (Theta(su b B)+Beta). The material can be rotated through an angle of azimuthal rotation Phi about the axis aligned with the material. Using the det ector, the intensity of the X-ray diffraction is recorded at least at the angle at which the twin defect occurs.

Analytical phase diagrams for colloids and non-adsorbing polymer.

PubMed

Fleer, Gerard J; Tuinier, Remco

2008-11-04

We review the free-volume theory (FVT) of Lekkerkerker et al. [Europhys. Lett. 20 (1992) 559] for the phase behavior of colloids in the presence of non-adsorbing polymer and we extend this theory in several aspects: (i) We take the solvent into account as a separate component and show that the natural thermodynamic parameter for the polymer properties is the insertion work Pi(v), where Pi is the osmotic pressure of the (external) polymer solution and v the volume of a colloid particle. (ii) Curvature effects are included along the lines of Aarts et al. [J. Phys.: Condens. Matt. 14 (2002) 7551] but we find accurate simple power laws which simplify the mathematical procedure considerably. (iii) We find analytical forms for the first, second, and third derivatives of the grand potential, needed for the calculation of the colloid chemical potential, the pressure, gas-liquid critical points and the critical endpoint (cep), where the (stable) critical line ends and then coincides with the triple point. This cep determines the boundary condition for a stable liquid. We first apply these modifications to the so-called colloid limit, where the size ratio q(R)=R/a between the radius of gyration R of the polymer and the particle radius a is small. In this limit the binodal polymer concentrations are below overlap: the depletion thickness delta is nearly equal to R, and Pi can be approximated by the ideal (van't Hoff) law Pi=Pi(0)=phi/N, where phi is the polymer volume fraction and N the number of segments per chain. The results are close to those of the original Lekkerkerker theory. However, our analysis enables very simple analytical expressions for the polymer and colloid concentrations in the critical and triple points and along the binodals as a function of q(R). Also the position of the cep is found analytically. In order to make the model applicable to higher size ratio's q(R) (including the so-called protein limit where q(R)>1) further extensions are needed. We introduce the size ratio q=delta/a, where the depletion thickness delta is no longer of order R. In the protein limit the binodal concentrations are above overlap. In such semidilute solutions delta approximately xi, where the De Gennes blob size (correlation length) xi scales as xi approximately phi(-gamma), with gamma=0.77 for good solvents and gamma=1 for a theta solvent. In this limit Pi=Pi(sd) approximately phi(3gamma). We now apply the following additional modifications: With these latter two modifications we obtain again a fully analytical model with simple equations for critical and triple points as a function of q(R). In the protein limit the binodal polymer concentrations scale as q(R)(1/gamma), and phase diagrams phiq(R)(-1/gamma) versus the colloid concentration eta become universal (i.e., independent of the size ratio q(R)). The predictions of this generalized free-volume theory (GFVT) are in excellent agreement with experiment and with computer simulations, not only for the colloid limit but also for the protein limit (and the crossover between these limits). The q(R)(1/gamma) scaling is accurately reproduced by both simulations and other theoretical models. The liquid window is the region between phi(c) (critical point) and phi(t) (triple point). In terms of the ratio phi(t)/phi(c) the liquid window extends from 1 in the cep (here phi(t)-phi(c)=0) to 2.2 in the protein limit. Hence, the liquid window is narrow: it covers at most a factor 2.2 in (external) polymer concentration.

Putting the Focus Back on the Patient: How Privacy Concerns Affect Personal Health Information Sharing Intentions

PubMed Central

Sanders, G Lawrence

2017-01-01

Background Health care providers are driven by greater participation and systemic cost savings irrespective of benefits to individual patients derived from sharing Personal Health Information (PHI). Protecting PHI is a critical issue in the sharing of health care information systems; yet, there is very little literature examining the topic of sharing PHI electronically. A good overview of the regulatory, privacy, and societal barriers to sharing PHI can be found in the 2009 Health Information Technology for Economic and Clinical Health Act. Objective This study investigated the factors that influence individuals’ intentions to share their PHI electronically with health care providers, creating an understanding of how we can represent a patient’s interests more accurately in sharing settings, instead of treating patients like predetermined subjects. Unlike privacy concern and trust, patient activation is a stable trait that is not subject to change in the short term and, thus, is a useful factor in predicting sharing behavior. We apply the extended privacy model in the health information sharing context and adapt this model to include patient activation and issue involvement to predict individuals’ intentions. Methods This was a survey-based study with 1600+ participants using the Health Information National Trends Survey (HINTS) data to validate a model through various statistical techniques. The research method included an assessment of both the measurement and structural models with post hoc analysis. Results We find that privacy concern has the most influence on individuals’ intentions to share. Patient activation, issue involvement, and patient-physician relationship are significant predictors of sharing intention. We contribute to theory by introducing patient activation and issue involvement as proxies for personal interest factors in the health care context. Conclusions Overall, this study found that although patients are open to sharing their PHI, they still have concerns over the privacy of their PHI during the sharing process. It is paramount to address this factor to increase information flow and identify how patients can assure that their privacy is protected. The outcome of this study is a set of recommendations for motivating the sharing of PHI. The goal of this research is to increase the health profile of the patients by integrating the testing and diagnoses of various doctors across health care providers and, thus, bring patients closer to the physicians. PMID:28903895

Inhibitory effects of thymus-independent type 2 antigens on MHC class II-restricted antigen presentation: comparative analysis of carbohydrate structures and the antigen presenting cell.

PubMed

González-Fernández, M; Carrasco-Marín, E; Alvarez-Domínguez, C; Outschoorn, I M; Leyva-Cobián, F

1997-02-25

The role of thymus-independent type 2 (TI-2) antigens (polysaccharides) on the MHC-II-restricted processing of protein antigens was studied in vitro. In general, antigen presentation is inhibited when both peritoneal and splenic macrophages (M phi) as well as Küpffer cells (KC) are preincubated with acidic polysaccharides or branched dextrans. However, the inhibitory effect of neutral polysaccharides was minimal when KC were used as antigen presenting cells (APC). Morphological evaluation of the uptake of fluoresceinated polysaccharides clearly correlates with this selective and differential interference. Polysaccharides do not block MHC-I-restricted antigen presentation. Some chemical characteristics shared by different saccharides seem to be specially related to their potential inhibitory abilities: (i) those where two anomeric carbon atoms of two interlinked sugars and (ii) those containing several sulfate groups per disaccharide repeating unit. No polysaccharide being inhibitory in M phi abrogated antigen processing in other APC: lipopolysaccharide-activated B cells, B lymphoma cells, or dendritic cells (DC). Using radiolabeled polysaccharides it was observed that DC and B cells incorporated less radioactivity as a function of time than M phi. Morphological evaluation of these different APC incubated for extended periods of time with inhibitory concentrations of polysaccharides revealed intense cytoplasmic vacuolization in M phi but not in B cells or DC. The large majority of M phi lysosomes containing polysaccharides fail to fuse with incoming endocytic vesicles and delivery of fluid-phase tracers was reduced, suggesting that indigestible carbohydrates reduced the fusion of these loaded lysosomes with endosomes containing recently internalized tracers. It is suggested that the main causes of this antigen presentation blockade are (i) the chemical characteristics of certain carbohydrates and whether the specific enzymatic machinery for their intracellular degradation exists; and (ii) the different phagocytic abilities of distinct APC populations, fluid-phase pinocytosis and receptor-mediated saccharide uptake, and existence of a differential antigen-processing pathway in M phi and DC or B cells, which could be based on a polysaccharide-inhibited step present in M phi but unaffected or irrelevant in both B cells and DC.

Prostate health index and prostate cancer gene 3 score but not percent-free Prostate Specific Antigen have a predictive role in differentiating histological prostatitis from PCa and other nonneoplastic lesions (BPH and HG-PIN) at repeat biopsy.

PubMed

De Luca, Stefano; Passera, Roberto; Fiori, Cristian; Bollito, Enrico; Cappia, Susanna; Mario Scarpa, Roberto; Sottile, Antonino; Franco Randone, Donato; Porpiglia, Francesco

2015-10-01

To determine if prostate health index (PHI), prostate cancer antigen gene 3 (PCA3) score, and percentage of free prostate-specific antigen (%fPSA) may be used to differentiate asymptomatic acute and chronic prostatitis from prostate cancer (PCa), benign prostatic hyperplasia (BPH), and high-grade prostate intraepithelial neoplasia (HG-PIN) in patients with elevated PSA levels and negative findings on digital rectal examination at repeat biopsy (re-Bx). In this prospective study, 252 patients were enrolled, undergoing PHI, PCA3 score, and %fPSA assessments before re-Bx. We used 3 multivariate logistic regression models to test the PHI, PCA3 score, and %fPSA as risk factors for prostatitis vs. PCa, vs. BPH, and vs. HG-PIN. All the analyses were performed for the whole patient cohort and for the "gray zone" of PSA (4-10ng/ml) cohort (171 individuals). Of the 252 patients, 43 (17.1%) had diagnosis of PCa. The median PHI was significantly different between men with a negative biopsy and those with a positive biopsy (34.9 vs. 48.1, P<0.001), as for the PCA3 score (24 vs. 54, P<0.001) and %fPSA (11.8% vs. 15.8%, P = 0.012). The net benefit of using PCA3 and PHI to differentiate prostatitis and PCa was moderate, although it extended to a good range of threshold probabilities (40%-100%), whereas that from using %fPSA was negligible: this pattern was reported for the whole population as for the "gray zone" PSA cohort. In front of a good diagnostic performance of all the 3 biomarkers in distinguishing negative biopsy vs. positive biopsy, the clinical benefit of using the PCA3 score and PHI to estimate prostatitis vs. PCa was comparable. PHI was the only determinant for prostatitis vs. BPH, whereas no biomarkers could differentiate prostate inflammation from HG-PIN. Copyright © 2015 Elsevier Inc. All rights reserved.

Structural changes of bacteriophage [phi]29 upon DNA packaging and release

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

Xiang, Y.; Morais, M.C.; Battisti, A.J.

2008-04-24

Cryo-electron microscopy three-dimensional reconstructions have been made of mature and of emptied bacteriophage {phi}29 particles without making symmetry assumptions. Comparisons of these structures with each other and with the {phi}29 prohead indicate how conformational changes might initiate successive steps of assembly and infection. The 12 adsorption capable 'appendages' were found to have a structure homologous to the bacteriophage P22 tailspikes. Two of the appendages are extended radially outwards, away from the long axis of the virus, whereas the others are around and parallel to the phage axis. The appendage orientations are correlated with the symmetry-mismatched positions of the five-fold relatedmore » head fibers, suggesting a mechanism for partial cell wall digestion upon rotation of the head about the tail when initiating infection. The narrow end of the head-tail connector is expanded in the mature virus. Gene product 3, bound to the 5-foot ends of the genome, appears to be positioned within the expanded connector, which may potentiate the release of DNA-packaging machine components, creating a binding site for attachment of the tail.« less

Shock-tube measurements of carbon to oxygen atom ratios for incipient soot formation with C2H2, C2H4 and C2H6 fuels

NASA Technical Reports Server (NTRS)

Radcliffe, S. W.; Appleton, J. P.

1971-01-01

The critical atomic carbon to oxygen ratios, Phi sub C, for incipient soot formation in shock heated acetylene, ethylene, ethane/oxygen/ argon mixtures was measured over the temperature range 2000 K to 2500 K for reactant partial pressures between 0.1 and 0.4 atoms. Absorption of light from a He-Ne laser at 6328A was was used to detect soot. It was observed that the values of Phi sub C for all three fuels increased uniformly with temperature such that at the highest temperatures Phi sub C was considerably greater than unity, i.e. greater than the value of about unity at which solid carbon should have been precipitated on a thermochemical equilibrium basis. Observations were made over periods extending up to about one millisecond, which was well in excess of the time required for the major heat release of the combustion reactions. The relevance of these experimental findings to the problem of soot formation in gas turbine combustion chambers is discussed.

Investigations of flowfields found in typical combustor geometries

NASA Technical Reports Server (NTRS)

Lilley, D. G.

1982-01-01

Measurements and computations are being applied to an axisymmetric swirling flow, emerging from swirl vanes at angle phi, entering a large chamber test section via a sudden expansion of various side-wall angles alpha. New features are: the turbulence measurements are being performed on swirling as well as nonswirling flow; and all measurements and computations are also being performed on a confined jet flowfield with realistic downstream blockage. Recent activity falls into three categories: (1) Time-mean flowfield characterization by five-hole pitot probe measurements and by flow visualization; (2) Turbulence measurements by a variety of single- and multi-wire hot-wire probe techniques; and (3) Flowfield computations using the computer code developed during the previous year's research program.

The effects of nonuniform magnetic field strength on density flux and test particle transport in drift wave turbulence

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

Dewhurst, J. M.; Hnat, B.; Dendy, R. O.

2009-07-15

The extended Hasegawa-Wakatani equations generate fully nonlinear self-consistent solutions for coupled density n and vorticity {nabla}{sup 2}{phi}, where {phi} is electrostatic potential, in a plasma with background density inhomogeneity {kappa}=-{partial_derivative} ln n{sub 0}/{partial_derivative}x and magnetic field strength inhomogeneity C=-{partial_derivative} ln B/{partial_derivative}x. Finite C introduces interchange effects and {nabla}B drifts into the framework of drift turbulence through compressibility of the ExB and diamagnetic drifts. This paper addresses the direct computation of the radial ExB density flux {gamma}{sub n}=-n{partial_derivative}{phi}/{partial_derivative}y, tracer particle transport, the statistical properties of the turbulent fluctuations that drive {gamma}{sub n} and tracer motion, and analytical underpinnings. Systematic trends emergemore » in the dependence on C of the skewness of the distribution of pointwise {gamma}{sub n} and in the relative phase of density-velocity and density-potential pairings. It is shown how these effects, together with conservation of potential vorticity {pi}={nabla}{sup 2}{phi}-n+({kappa}-C)x, account for much of the transport phenomenology. Simple analytical arguments yield a Fickian relation {gamma}{sub n}=({kappa}-C)D{sub x} between the radial density flux {gamma}{sub n} and the radial tracer diffusivity D{sub x}, which is shown to explain key trends in the simulations.« less

Compartment-specific pH monitoring in Bacillus subtilis using fluorescent sensor proteins: a tool to analyze the antibacterial effect of weak organic acids

PubMed Central

van Beilen, Johan W. A.; Brul, Stanley

2013-01-01

The internal pH (pHi) of a living cell is one of its most important physiological parameters. To monitor the pH inside Bacillus subtilis during various stages of its life cycle, we constructed an improved version (IpHluorin) of the ratiometric, pH-sensitive fluorescent protein pHluorin by extending it at the 5′ end with the first 24 bp of comGA. The new version, which showed an approximate 40% increase in fluorescence intensity, was expressed from developmental phase-specific, native promoters of B. subtilis that are specifically active during vegetative growth on glucose (PptsG) or during sporulation (PspoIIA, PspoIIID, and PsspE). Our results show strong, compartment-specific expression of IpHluorin that allowed accurate pHi measurements of live cultures during exponential growth, early and late sporulation, spore germination, and during subsequent spore outgrowth. Dormant spores were characterized by an pHi of 6.0 ± 0.3. Upon full germination the pHi rose dependent on the medium to 7.0–7.4. The presence of sorbic acid in the germination medium inhibited a rise in the intracellular pH of germinating spores and inhibited germination. Such effects were absent when acetic was added at identical concentrations. PMID:23785365

High-Speed Measurements on a Swept-Back Wing (Sweepback Angle phi = 35 Deg)

NASA Technical Reports Server (NTRS)

Goethert, B.

1947-01-01

In the following, high-speed measurements on a swept-back wing are reported. The curves of lift, moment, and drag have been determined up to Mach numbers of M = 0.87, and they are compared to a rectangular wing. Through measurements of the total-head loss behind the wing and through schlieren pictures, an insight into the formation of the compression shock at high Mach numbers has been obtained.

Deriving high-resolution protein backbone structure propensities from all crystal data using the information maximization device.

PubMed

Solis, Armando D

2014-01-01

The most informative probability distribution functions (PDFs) describing the Ramachandran phi-psi dihedral angle pair, a fundamental descriptor of backbone conformation of protein molecules, are derived from high-resolution X-ray crystal structures using an information-theoretic approach. The Information Maximization Device (IMD) is established, based on fundamental information-theoretic concepts, and then applied specifically to derive highly resolved phi-psi maps for all 20 single amino acid and all 8000 triplet sequences at an optimal resolution determined by the volume of current data. The paper shows that utilizing the latent information contained in all viable high-resolution crystal structures found in the Protein Data Bank (PDB), totaling more than 77,000 chains, permits the derivation of a large number of optimized sequence-dependent PDFs. This work demonstrates the effectiveness of the IMD and the superiority of the resulting PDFs by extensive fold recognition experiments and rigorous comparisons with previously published triplet PDFs. Because it automatically optimizes PDFs, IMD results in improved performance of knowledge-based potentials, which rely on such PDFs. Furthermore, it provides an easy computational recipe for empirically deriving other kinds of sequence-dependent structural PDFs with greater detail and precision. The high-resolution phi-psi maps derived in this work are available for download.

phyA-GFP is spectroscopically and photochemically similar to phyA and comprises both its native types, phyA' and phyA''.

PubMed

Sineshchekov, Vitaly; Sudnitsin, Artem; Ádám, Éva; Schäfer, Eberhard; Viczián, András

2014-12-01

Low-temperature fluorescence investigations of phyA-GFP used in experiments on its nuclear-cytoplasmic partitioning were carried out. In etiolated hypocotyls of phyA-deficient Arabidopsis thaliana expressing phyA-GFP, it was found that it is similar to phyA in spectroscopic parameters with both its native types, phyA' and phyA'', present and their ratio shifted towards phyA'. In transgenic tobacco hypocotyls, native phyA and rice phyA-GFP were also identical to phyA in the wild type whereas phyA-GFP belonged primarily to the phyA' type. Finally, truncated oat Δ6-12 phyA-GFP expressed in phyA-deficient Arabidopsis was represented by the phyA' type in contrast to full-length oat phyA-GFP with an approximately equal proportion of the two phyA types. This correlates with a previous observation that Δ6-12 phyA-GFP can form only numerous tiny subnuclear speckles while its wild-type counterpart can also localize into bigger and fewer subnuclear protein complexes. Thus, phyA-GFP is spectroscopically and photochemically similar or identical to the native phyA, suggesting that the GFP tag does not affect the chromophore. phyA-GFP comprises phyA'-GFP and phyA''-GFP, suggesting that both of them are potential participants in nuclear-cytoplasmic partitioning, which may contribute to its complexity.

Directivity and trends of noise generated by a propeller in a wake

NASA Technical Reports Server (NTRS)

Block, P. J. W.; Gentry, C. L., Jr.

1986-01-01

An experimental study of the effects on far-field propeller noise of a pylon wake interaction was conducted with a scale model of a single-rotation propeller in a low-speed anechoic wind tunnel. A detailed mapping of the noise directivity was obtained at 10 test conditions covering a wide range of propeller power landings at several subsonic tip speeds. Two types of noise penalties were investigated-pulser and spacing. The pusher noise penalty is the difference in the average overall sound pressure level, OASPL, for pusher and tractor installations. (In a pusher installation, the propeller disk is downstream of a pylon or another aerodynamic surface.) The spacing noise penalty is the difference in the average OASPL for different distances between the pylon trailing edge and the propeller. The variations of these noise penalties with axial, or flyover, angle theta and circumferential angle phi are presented, and the trends in these noise penalties with tip Mach number and power loading are given for selected values of theta and phi. The circumferential directivity of the noise from a pusher installation showed that the addition noise due to the interaction of the pylon wake with the propeller had a broad peak over a wide range of circumferential angles approximately perpendicular to the pylon with a sharp minimum 90 deg. to the pylon for the majority of cases tested. The variation of the pusher noise penalty with theta had a minimum occurring near the propeller plane and maximum values of as much as 20 dB occurring toward the propeller axes. The magnitude of the pusher noise penalty generally decreased as propeller tip Mach number or power loading was increased.

The determination of interplanetary magnetic field polarities around sector boundaries using E greater than 2 keV electrons

NASA Technical Reports Server (NTRS)

Kahler, S.; Lin, R. P.

1994-01-01

The determination of the polarities of interplanetary magnetic fields (whether the field direction is outward from or inward toward the sun) has been based on a comparison of observed field directions with the nominal Parker spiral angle. These polarities can be mapped back to the solar source field polarities. This technique fails when field directions deviate substantially from the Parker angle or when fields are substantially kinked. We introduce a simple new technique to determine the polarities of interplanetary fields using E greater than 2 keV interplanetary electrons which stream along field lines away from the sun. Those electrons usually show distinct unidirectional pitch-angle anisotropies either parallel or anti-parallel to the field. Since the electron flow direction is known to be outward from the sun, the anisotropies parallel to the field indicate outward-pointing, positive-polarity fields, and those anti-parallel indicate inward-pointing, negative-polarity fields. We use data from the UC Berkeley electron experiment on the International Sun Earth Explorer 3 (ISSE-3) spacecraft to compare the field polarities deduced from the electron data, Pe (outward or inward), with the polarities inferred from field directions, Pd, around two sector boundaries in 1979. We show examples of large (greater than 100 deg) changes in azimuthal field direction Phi over short (less than 1 hr) time scales, some with and some without reversals in Pe. The latter cases indicate that such large directional changes can occur in unipolar structures. On the other hand, we found an example of a change in Pe during which the rotation in Phi was less than 30 deg, indicating polarity changes in nearly unidirectional structures. The field directions are poor guides to the polarities in these cases.

Natural polypeptide scaffolds: beta-sheets, beta-turns, and beta-hairpins.

PubMed

Rotondi, Kenneth S; Gierasch, Lila M

2006-01-01

This paper provides an introduction to fundamental conformational states of polypeptides in the beta-region of phi,psi space, in which the backbone is extended near to its maximal length, and to more complex architectures in which extended segments are linked by turns and loops. There are several variants on these conformations, and they comprise versatile scaffolds for presentation of side chains and backbone amides for molecular recognition and designed catalysts. In addition, the geometry of these fundamental folds can be readily mimicked in peptidomimetics. Copyright 2005 Wiley Periodicals, Inc.

Putting the Focus Back on the Patient: How Privacy Concerns Affect Personal Health Information Sharing Intentions.

PubMed

Abdelhamid, Mohamed; Gaia, Joana; Sanders, G Lawrence

2017-09-13

Health care providers are driven by greater participation and systemic cost savings irrespective of benefits to individual patients derived from sharing Personal Health Information (PHI). Protecting PHI is a critical issue in the sharing of health care information systems; yet, there is very little literature examining the topic of sharing PHI electronically. A good overview of the regulatory, privacy, and societal barriers to sharing PHI can be found in the 2009 Health Information Technology for Economic and Clinical Health Act. This study investigated the factors that influence individuals' intentions to share their PHI electronically with health care providers, creating an understanding of how we can represent a patient's interests more accurately in sharing settings, instead of treating patients like predetermined subjects. Unlike privacy concern and trust, patient activation is a stable trait that is not subject to change in the short term and, thus, is a useful factor in predicting sharing behavior. We apply the extended privacy model in the health information sharing context and adapt this model to include patient activation and issue involvement to predict individuals' intentions. This was a survey-based study with 1600+ participants using the Health Information National Trends Survey (HINTS) data to validate a model through various statistical techniques. The research method included an assessment of both the measurement and structural models with post hoc analysis. We find that privacy concern has the most influence on individuals' intentions to share. Patient activation, issue involvement, and patient-physician relationship are significant predictors of sharing intention. We contribute to theory by introducing patient activation and issue involvement as proxies for personal interest factors in the health care context. Overall, this study found that although patients are open to sharing their PHI, they still have concerns over the privacy of their PHI during the sharing process. It is paramount to address this factor to increase information flow and identify how patients can assure that their privacy is protected. The outcome of this study is a set of recommendations for motivating the sharing of PHI. The goal of this research is to increase the health profile of the patients by integrating the testing and diagnoses of various doctors across health care providers and, thus, bring patients closer to the physicians. ©Mohamed Abdelhamid, Joana Gaia, G Lawrence Sanders. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 13.09.2017.

Nicotine can skew the characterization of the macrophage type-1 (M{Phi}1) phenotype differentiated with granulocyte-macrophage colony-stimulating factor to the M{Phi}2 phenotype

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

Yanagita, Manabu; Kobayashi, Ryohei; Murakami, Shinya, E-mail: ipshinya@dent.osaka-u.ac.jp

Macrophages (M{Phi}s) exhibit functional heterogeneity and plasticity in the local microenvironment. Recently, it was reported that M{Phi}s can be divided into proinflammatory M{Phi}s (M{Phi}1) and anti-inflammatory M{Phi}s (M{Phi}2) based on their polarized functional properties. Here, we report that nicotine, the major ingredient of cigarette smoke, can modulate the characteristics of M{Phi}1. Granulocyte-macrophage colony-stimulating factor-driven M{Phi}1 with nicotine (Ni-M{Phi}1) showed the phenotypic characteristics of M{Phi}2. Like M{Phi}2, Ni-M{Phi}1 exhibited antigen-uptake activities. Ni-M{Phi}1 suppressed IL-12, but maintained IL-10 and produced high amounts of MCP-1 upon lipopolysaccharide stimulation compared with M{Phi}1. Moreover, we observed strong proliferative responses of T cells to lipopolysaccharide-stimulated M{Phi}1,more » whereas Ni-M{Phi}1 reduced T cell proliferation and inhibited IFN-{gamma} production by T cells. These results suggest that nicotine can change the functional characteristics of M{Phi} and skew the M{Phi}1 phenotype to M{Phi}2. We propose that nicotine is a potent regulator that modulates immune responses in microenvironments.« less

Pusher propeller noise directivity and trends

NASA Technical Reports Server (NTRS)

Block, P. J. W.

1986-01-01

The effects of pylon wake interaction on far-field propeller noise are studied using a model scale SR-2 propeller in a low-speed anechoic wind tunnel. The variation in the pusher noise penalty with axial angle theta and circumferential angle phi is compared to that of the tractor noise penalty; and the former exhibits minima occurring in the propeller plane and maxima occurring toward the propeller axis. The magnitude of the pusher installation noise penalty decreased with in increase in shaft horsepower and tip Mach number. Directivity comparisons revealed that both a noise reduction and a directivity pattern change resulted when the pylon was moved farther from the propeller. Noise emerging from the wake interaction was distinguished from that of the propeller by means of a modal decomposition.

Linearity of the Faraday-rotation-type ac magnetic-field sensor with a ferrimagnetic or ferromagnetic rotator film

NASA Astrophysics Data System (ADS)

Mori, Hiroshi; Asahara, Yousuke

1996-03-01

We analyze the linearity and modulation depth of ac magnetic-field sensors or current sensors, using a ferrimagnetic or ferromagnetic film as the Faraday rotator and employing the detection of only the zeroth-order optical diffraction component from the rotator. It is theoretically shown that for this class of sensor the condition of a constant modulation depth and that of a constant ratio error give an identical series of curves for the relationship between Faraday rotation angle greater than or equals V and polarizer/analyzer relative angle Phi . We give some numerical examples to demonstrate the usefulness of the result with reference to a rare-earth iron garnet film as the rotator.

Summing up the Euler [phi] Function

ERIC Educational Resources Information Center

Loomis, Paul; Plytage, Michael; Polhill, John

2008-01-01

The Euler [phi] function counts the number of positive integers less than and relatively prime to a positive integer n. Here we look at perfect totient numbers, number for which [phi](n) + [phi]([phi](n)) + [phi]([phi]([phi](n))) + ... + 1 = n.

Reducing adaptive optics latency using Xeon Phi many-core processors

NASA Astrophysics Data System (ADS)

Barr, David; Basden, Alastair; Dipper, Nigel; Schwartz, Noah

2015-11-01

The next generation of Extremely Large Telescopes (ELTs) for astronomy will rely heavily on the performance of their adaptive optics (AO) systems. Real-time control is at the heart of the critical technologies that will enable telescopes to deliver the best possible science and will require a very significant extrapolation from current AO hardware existing for 4-10 m telescopes. Investigating novel real-time computing architectures and testing their eligibility against anticipated challenges is one of the main priorities of technology development for the ELTs. This paper investigates the suitability of the Intel Xeon Phi, which is a commercial off-the-shelf hardware accelerator. We focus on wavefront reconstruction performance, implementing a straightforward matrix-vector multiplication (MVM) algorithm. We present benchmarking results of the Xeon Phi on a real-time Linux platform, both as a standalone processor and integrated into an existing real-time controller (RTC). Performance of single and multiple Xeon Phis are investigated. We show that this technology has the potential of greatly reducing the mean latency and variations in execution time (jitter) of large AO systems. We present both a detailed performance analysis of the Xeon Phi for a typical E-ELT first-light instrument along with a more general approach that enables us to extend to any AO system size. We show that systematic and detailed performance analysis is an essential part of testing novel real-time control hardware to guarantee optimal science results.

Minimal-scan filtered backpropagation algorithms for diffraction tomography.

PubMed

Pan, X; Anastasio, M A

1999-12-01

The filtered backpropagation (FBPP) algorithm, originally developed by Devaney [Ultrason. Imaging 4, 336 (1982)], has been widely used for reconstructing images in diffraction tomography. It is generally known that the FBPP algorithm requires scattered data from a full angular range of 2 pi for exact reconstruction of a generally complex-valued object function. However, we reveal that one needs scattered data only over the angular range 0 < or = phi < or = 3 pi/2 for exact reconstruction of a generally complex-valued object function. Using this insight, we develop and analyze a family of minimal-scan filtered backpropagation (MS-FBPP) algorithms, which, unlike the FBPP algorithm, use scattered data acquired from view angles over the range 0 < or = phi < or = 3 pi/2. We show analytically that these MS-FBPP algorithms are mathematically identical to the FBPP algorithm. We also perform computer simulation studies for validation, demonstration, and comparison of these MS-FBPP algorithms. The numerical results in these simulation studies corroborate our theoretical assertions.

VERA-CS User Support Activities for PoR 14

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

Kochunas, Brendan

2017-11-01

The purpose of this milestone is to document the user support activities that took place between 10/1/2016 and 3/31/2017 (PoR 14). In the normal PHI workflow, that also extends to several activities within RTM, a Kanban process is followed. This involves creating tickets for specific work items and track the progress to complete these specific work items.

Understanding the branching ratios of {chi}{sub c1{yields}{phi}{phi}}, {omega}{omega}, {omega}{phi} observed at BES-III

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

Chen Dianyong; He Jun; Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000

In this work, we discuss the contribution of the mesonic loops to the decay rates of {chi}{sub c1{yields}{phi}{phi}}, {omega}{omega}, which are suppressed by the helicity selection rules and {chi}{sub c1{yields}{phi}{omega}}, which is a double-Okubo-Zweig-Iizuka forbidden process. We find that the mesonic loop effects naturally explain the clear signals of {chi}{sub c1{yields}{phi}{phi}}, {omega}{omega} decay modes observed by the BES Collaboration. Moreover, we investigate the effects of the {omega}-{phi} mixing, which may result in the order of magnitude of the branching ratio BR({chi}{sub c1{yields}{omega}{phi}}) being 10{sup -7}. Thus, we are waiting for the accurate measurements of the BR({chi}{sub c1{yields}{omega}{omega}}), BR({chi}{sub c1{yields}{phi}{phi}}), andmore » BR({chi}{sub c1{yields}{omega}{phi}}), which may be very helpful for testing the long-distant contribution and the {omega}-{phi} mixing in {chi}{sub c1{yields}{phi}{phi}}, {omega}{omega}, {omega}{phi} decays.« less

Differences in unwinding of supercoiled DNA induced by the two enantiomers of anti-benzo[a]pyrene diol epoxide.

PubMed Central

Xu, R; Birke, S; Carberry, S E; Geacintov, N E; Swenberg, C E; Harvey, R G

1992-01-01

The unwinding of supercoiled phi X174 RFI DNA induced by the tumorigenic (+) and non-tumorigenic (-) enantiomers of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) has been investigated by agarose slab-gel and ethidium titration tube gel electrophoresis. The differences in adduct conformations were verified by flow linear dichroism techniques. Both enantiomers cause a reversible unwinding by the formation of noncovalent intercalative complexes. The effects of covalently bound BPDE residues on the electrophoretic mobilities of the RF I DNA form in agarose gels were investigated in detail in the range of binding ratios rb approximately 0.0-0.06 (covalently bound BPDE residues/nucleotide). In this range of rb values, there is a striking difference in the mobilities of (+)-BPDE- and (-)-BPDE-adducted phi X174 DNA in agarose slab-gels, the covalently bound (+)-BPDE residues causing a significantly greater retardation than (-)-BPDE residues. Increasing the level of covalent adducts beyond rb approximately 0.06 in the case of the (+)-BPDE enantiomer, leads to further unwinding and a minimum in the mobilities (corresponding to comigration of the nicked form and the covalently closed relaxed modified form) at rb 0.10 +/- 0.01; at still higher rb values, rewinding of the modified DNA in the opposite sense is observed. From the minimum in the mobility, a mean unwinding angle (per BPDE residue) of theta = 12 +/- 1.5 degrees is determined, which is in good agreement the value of theta = 11 +/- 1.8 degrees obtained by the tube gel titration method. Using this latter method, values of theta = 6.8 +/- 1.7 degrees for (-)-BPDE-phi X174 adducts are observed. It is concluded that agarose slab gel techniques are not suitable for determining unwinding angles for (-)-BPDE-modified phi X174 DNA because the alterations in the tertiary structures for rb < 0.06 are too small to cause sufficiently large changes in the electrophoretic mobilities. The major trans (+)-BPDE-N2-guanosine covalent adduct is situated at external binding sites and the mechanisms of unwinding are therefore different from those relevant to noncovalent intercalative BPDE-DNA complexes or to classical intercalating drug molecules; a flexible hinge joint and a widening of the minor groove at the site of the lesion may account for the observed unwinding effects. The more heterogeneous (-)-BPDE-nucleoside adducts (involving cis and trans N2-guanosine, and adenosine adducts) are less effective in causing unwinding of supercoiled DNA for reasons which remain to be elucidated. Images PMID:1475180

Simple Method for Constructing RNA Triangle, Square, Pentagon by Tuning Interior RNA 3WJ Angle from 60° to 90° or 108°.

PubMed

Khisamutdinov, Emil F; Bui, My Nguyen Hoan; Jasinski, Daniel; Zhao, Zhengyi; Cui, Zheng; Guo, Peixuan

2015-01-01

Precise shape control of architectures at the nanometer scale is an intriguing but extremely challenging facet. RNA has recently emerged as a unique material and thermostable building block for use in nanoparticle construction. Here, we describe a simple method from design to synthesis of RNA triangle, square, and pentagon by stretching RNA 3WJ native angle from 60° to 90° and 108°, using the three-way junction (3WJ) of the pRNA from bacteriophage phi29 dsDNA packaging motor. These methods for the construction of elegant polygons can be applied to other RNA building blocks including the utilization and application of RNA 4-way, 5-way, and other multi-way junctions.

Gastric band slippage: a case-controlled study comparing new and old radiographic signs of this important surgical complication.

PubMed

Swenson, David W; Pietryga, Jason A; Grand, David J; Chang, Kevin J; Murphy, Brian L; Egglin, Thomas K

2014-07-01

The purpose of this study was to compare the diagnostic performance of four radiographic signs of gastric band slippage: abnormal phi angle, the "O sign," inferior displacement of the superolateral gastric band margin, and presence of an air-fluid level above the gastric band. A search of the electronic medical record identified 21 patients with a surgically proven slipped gastric band and 63 randomly-selected asymptomatic gastric band patients who had undergone barium swallow studies. These studies were evaluated for the four signs of band slippage by two independent radiologists who were blinded to clinical data. Sensitivity, specificity, and positive and negative predictive values were calculated for each radiographic sign of band slippage. Interobserver agreement between radiologists was assessed using the Fleiss kappa statistic. In evaluating for gastric band slippage, an abnormal phi angle greater than 58° was 91-95% sensitive and 52-62% specific (κ = 0.78), the O sign was 33-48% sensitive but 97% specific (κ = 0.84), inferior displacement of the superolateral band margin by more than 2.4 cm from the diaphragm was 95% sensitive and 97-98% specific (κ = 0.97), and the presence of an air-fluid level was 95% sensitive and 100% specific (κ = 1.00). We report two previously undescribed radiographic signs of gastric band slippage that are both sensitive and specific for this important surgical complication and recommend that these signs should be incorporated into the imaging evaluation of gastric band patients.

High-energy Variability of PSR J1311-3430

DOE PAGES

An, Hongjun; Romani, Roger W.; Johnson, Tyrel; ...

2017-11-21

Here, we have studied the variability of the black-widow-type binary millisecond pulsar PSR J1311–3430 from optical to gamma-ray energies. We confirm evidence for orbital modulation in the weak off-pulse ≳200 MeV emission, with a peak atmore » $${\\phi }_{B}\\approx 0.8$$, following pulsar inferior conjunction. The peak has a relatively hard spectrum, extending above ~1 GeV. XMM-Newton and Swift UV observations also show that this source's strong X-ray flaring activity is associated with optical/UV flares. With a duty cycle of ~7%–19%, this flaring is quite prominent with an apparent power-law intensity distribution. Flares are present at all orbital phases, with a slight preference for $${\\phi }_{B}=0.5\\mbox{--}0.7$$. We explore possible connections of these variabilities with the intrabinary shock and magnetic activity on the low-mass secondary.« less

The development of two postnatal health instruments: one for mothers (M-PHI) and one for fathers (F-PHI) to measure health during the first year of parenting.

PubMed

Jones, G L; Morrell, C J; Cooke, J M; Speier, D; Anumba, D; Stewart-Brown, S

2011-09-01

To develop and psychometrically evaluate two questionnaires measuring both positive and negative postnatal health of mothers (M-PHI) and fathers (F-PHI) during the first year of parenting. The M-PHI and the F-PHI were developed in four stages. Stage 1: Postnatal women's focus group (M-PHI) and postnatal fathers' postal questionnaire (F-PHI); Stage 2: Qualitative interviews; Stage 3: Pilot postal survey and main postal survey; and Stage 4: Test-retest postal survey. The M-PHI consisted of a 29-item core questionnaire with six main scales and five conditional scales. The F-PHI consisted of a 27-item questionnaire with six main scales. All scales achieved good internal reliability (Cronbach's α 0.66-0.87 for M-PHI, 0.72-0.90 for F-PHI). Intraclass correlation coefficients demonstrated high test-retest reliability (0.60-0.88). Correlation coefficients supported the criterion validity of the M-PHI and the F-PHI when tested against the Short-Form-12 (SF-12), Edinburgh Postnatal Depression Scale (EPDS) and the Warwick and Edinburgh Mental Well-Being Scale (WEMWBS). The M-PHI and F-PHI are valid, reliable, parent-generated instruments. These unique instruments will be invaluable for practitioners wishing to promote family-centred care and for trialists and other researchers requiring a validated instrument to measure both positive and negative health during the first postnatal year, as to date no such measurement has existed.

PKS1 plays a role in red-light-based positive phototropism in roots.

PubMed

Molas, Maria Lia; Kiss, John Z

2008-06-01

Aerial parts of plants curve towards the light (i.e. positive phototropism), and roots typically grow away from the light (i.e. negative phototropism). In addition, Arabidopsis roots exhibit positive phototropism relative to red light (RL), and this response is mediated by phytochromes A and B (phyA and phyB). Upon light stimulation, phyA and phyB interact with the phytochrome kinase substrate (PKS1) in the cytoplasm. In this study, we investigated the role of PKS1, along with phyA and phyB, in the positive phototropic responses to RL in roots. Using a high-resolution feedback system, we studied the phenotypic responses of roots of phyA, phyB, pks1, phyA pks1 and phyB pks1 null mutants as well as the PKS1-overexpressing line in response to RL. PKS1 emerged as an intermediary in the signalling pathways and appears to promote a negative curvature to RL in roots. In addition, phyA and phyB were both essential for a positive response to RL and act in a complementary fashion. However, either photoreceptor acting without the other results in negative curvature in response to red illumination so that the mode of action differs depending on whether phyA and phyB act independently or together. Our results suggest that PKS1 is part of a signalling pathway independent of phyA and phyB and that PKS1 modulates RL-based root phototropism.

A temporal forecast of radiation environments for future space exploration missions.

PubMed

Kim, Myung-Hee Y; Cucinotta, Francis A; Wilson, John W

2007-06-01

The understanding of future space radiation environments is an important goal for space mission operations, design, and risk assessment. We have developed a solar cycle statistical model in which sunspot number is coupled to space-related quantities, such as the galactic cosmic radiation (GCR) deceleration potential (phi) and the mean occurrence frequency of solar particle events (SPEs). Future GCR fluxes were derived from a predictive model, in which the temporal dependence represented by phi was derived from GCR flux and ground-based Climax neutron monitor rate measurements over the last four decades. These results showed that the point dose equivalent inside a typical spacecraft in interplanetary space was influenced by solar modulation by up to a factor of three. It also has been shown that a strong relationship exists between large SPE occurrences and phi. For future space exploration missions, cumulative probabilities of SPEs at various integral fluence levels during short-period missions were defined using a database of proton fluences of past SPEs. Analytic energy spectra of SPEs at different ranks of the integral fluences for energies greater than 30 MeV were constructed over broad energy ranges extending out to GeV for the analysis of representative exposure levels at those fluences. Results will guide the design of protection systems for astronauts during future space exploration missions.

General dynamical properties of cosmological models with nonminimal kinetic coupling

NASA Astrophysics Data System (ADS)

Matsumoto, Jiro; Sushkov, Sergey V.

2018-01-01

We consider cosmological dynamics in the theory of gravity with the scalar field possessing the nonminimal kinetic coupling to curvature given as η Gμνphi,μphi,ν, where η is an arbitrary coupling parameter, and the scalar potential V(phi) which assumed to be as general as possible. With an appropriate dimensionless parametrization we represent the field equations as an autonomous dynamical system which contains ultimately only one arbitrary function χ (x)= 8 π | η | V(x/√8 π) with x=√8 πphi. Then, assuming the rather general properties of χ(x), we analyze stationary points and their stability, as well as all possible asymptotical regimes of the dynamical system. It has been shown that for a broad class of χ(x) there exist attractors representing three accelerated regimes of the Universe evolution, including de Sitter expansion (or late-time inflation), the Little Rip scenario, and the Big Rip scenario. As the specific examples, we consider a power-law potential V(phi)=M4(phi/phi0)σ, Higgs-like potential V(phi)=λ/4(phi2‑phi02)2, and exponential potential V(phi)=M4 e‑phi/phi0.

Lysine 206 in Arabidopsis phytochrome A is the major site for ubiquitin-dependent protein degradation.

PubMed

Rattanapisit, Kaewta; Cho, Man-Ho; Bhoo, Seong Hee

2016-02-01

Phytochrome A (phyA) is a light labile phytochrome that mediates plant development under red/far-red light condition. Degradation of phyA is initiated by red light-induced phyA-ubiquitin conjugation through the 26S proteasome pathway. The N-terminal of phyA is known to be important in phyA degradation. To determine the specific lysine residues in the N-terminal domain of phyA involved in light-induced ubiquitination and protein degradation, we aligned the amino acid sequence of the N-terminal domain of Arabidopsis phyA with those of phyA from other plant species. Based on the alignment results, phytochrome over-expressing Arabidopsis plants were generated. In particular, wild-type and mutant (substitutions of conserved lysines by arginines) phytochromes fused with GFP were expressed in phyA(-)211 Arabidopsis plants. Degradation kinetics of over-expressed phyA proteins revealed that degradation of the K206R phyA mutant protein was delayed. Delayed phyA degradation of the K206R phyA mutant protein resulted in reduction of red-light-induced phyA-ubiquitin conjugation. Furthermore, seedlings expressing the K206R phyA mutant protein showed an enhanced phyA response under far-red light, resulting in inhibition of hypocotyl elongation as well as cotyledon opening. Together, these results suggest that lysine 206 is the main lysine for rapid ubiquitination and protein degradation of Arabidopsis phytochrome A. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Control of the Polarity of the Interplanetary Magnetic Field on the Dawn-Dusk Symmetry of the Magnetopause

NASA Astrophysics Data System (ADS)

Shue, J.; Jhuang, B.; Song, P.; Safrankova, J.; Nemecek, Z.; Russell, C. T.; Chen, S.

2008-12-01

The solar wind dynamic pressure is reduced when the solar wind flows around the magnetosphere due to the diversion of the flows. The magnetopause is the boundary where the reduced dynamic pressure is balanced with the magnetic pressure of the compressed magnetosphere by the solar wind. The size and shape of the magnetopause have long been considered among the most important parameters in Solar Terrestrial physics. Previous models of the size and shape of the magnetopause often assumed the axis- symmetry of the magnetopause with respect to the Sun-Earth line. With a large number of magnetopause crossings by ISEE-1 and -2, AMPTE/IRM, Hawkeye, Geotail, Interball-1, and Magion-4, we are able to consider the asymmetry of the magnetopuase. In the Shue et al. [1997] model, the magnetopause was modeled by two parameters, r0 and alpha, representing the subsolar standoff distance and the flaring level of the magnetopause, respectively. Parameter alpha was assumed to be independent of phi in the Shue et al. [1997] model, where phi is the angle between the Z axis and the mapping of the radial vector of the magnetopause on the YZ plane. In the present study we allow alpha to be a function of phi. We separate crossings with different phis and fit them in each bin to the new functional form proposed by Shue et al. [1997]. We find that the magnetopause is symmetric in the dawn-dusk direction for northward IMF. However, its size on the dawnside becomes larger when the IMF is southward. The function of alpha in terms of phi can be combined with the 2-D Shue et al. [1997] model into a 3-D magnetopause model. (Shue, J.-H., J. K. Chao, H. C. Fu, C. T. Russell, P. Song, K. K. Khurana, and H. J. Singer, A new functional form to study the solar wind control of the magnetopause size and shape, J. Geophys. Res., 102, 9497, 1997.)

PHyTIR - A Prototype Thermal Infrared Radiometer

NASA Technical Reports Server (NTRS)

Jau, Bruno M.; Hook, Simon J.; Johnson, William R.; Foote, Marc C.; Paine, Christopher G.; Pannell, Zack W.; Smythe, Robert F.; Kuan, Gary M.; Jakoboski, Julie K.; Eng, Bjorn T.

2013-01-01

This paper describes the PHyTIR (Prototype HyspIRI Thermal Infrared Radiometer) instrument, which is the engineering model for the proposed HyspIRI (Hyperspectral Infrared Imager) earth observing instrument. The HyspIRI mission would be comprised of the HyspIRI TIR (Thermal Infrared Imager), and a VSWIR (Visible Short-Wave Infra-Red Imaging Spectrometer). Both instruments would be used to address key science questions related to the earth's carbon cycle, ecosystems, climate, and solid earth properties. Data gathering of volcanic activities, earthquakes, wildfires, water use and availability, urbanization, and land surface compositions and changes, would aid the predictions and evaluations of such events and the impact they create. Even though the proposed technology for the HyspIRI imager is mature, the PHyTIR prototype is needed to advance the technology levels for several of the instrument's key components, and to reduce risks, in particular to validate 1) the higher sensitivity, spatial resolution, and higher throughput required for this focal plane array, 2) the pointing accuracy, 2) the characteristics of several spectral channels, and 4) the use of ambient temperature optics. The PHyTIR telescope consists of the focal plane assembly that is housed within a cold housing located inside a vacuum enclosure; all mounted to a bulkhead, and an optical train that consists of 3 powered mirrors; extending to both sides of the bulkhead. A yoke connects the telescope to a scan mirror. The rotating mirror enables to scan- a large track on the ground. This structure is supported by kinematic mounts, linking the telescope assembly to a base plate that would also become the spacecraft interface for HyspIRI. The focal plane's cooling units are also mounted to the base plate, as is an overall enclosure that has two viewing ports with large exterior baffles, shielding the focal plane from incoming stray light. PHyTIR's electronics is distributed inside and near the vacuum enclosure, and in a nearby rack. The data acquisition technique would be to take measurements over a 51deg wide swath in the cross spacecraft velocity direction, which is brought into view through the rotating scan mirror. A landscape mosaic thus can be assembled by overlaying rows of measurements. The paper briefly outlines the proposed HyspIRI mission and its data acquisition technique; it then describes the prototype PHyTIR instrument.

Free energy landscapes of peptides by enhanced conformational sampling.

PubMed

Nakajima, N; Higo, J; Kidera, A; Nakamura, H

2000-02-11

The free energy landscapes of peptide conformations in water have been observed by the enhanced conformational sampling method, applying the selectively enhanced multicanonical molecular dynamics simulations. The conformations of the peptide dimers, -Gly-Gly-, -Gly-Ala-, -Gly-Ser-, -Ala-Gly-, -Asn-Gly-, -Pro-Gly-, -Pro-Ala-, and -Ala-Ala-, which were all blocked with N-terminal acetyl and C-terminal N-methyl groups, were individually sampled with the explicit TIP3P water molecules. From each simulation trajectory, we obtained the canonical ensemble at 300 K, from which the individual three-dimensional landscape was drawn by the potential of mean force using the three reaction coordinates: the backbone dihedral angle, psi, of the first amino acid, the backbone dihedral angle, phi, of the second amino acid, and the distance between the carbonyl oxygen of the N-terminal acetyl group and the C-terminal amide proton. The most stable state and several meta-stable states correspond to extended conformations and typical beta-turn conformations, and their free energy values were accounted for from the potentials of mean force at the states. In addition, the contributions from the intra-molecular energies of peptides and those from the hydration effects were analyzed. Consequently, the stable beta-turn conformations in the free energy landscape were consistent with the empirically preferred beta-turn types for each amino acid sequence. The thermodynamic values for the hydration effect were decomposed and they correlated well with the empirical values estimated from the solvent accessible surface area of each molecular conformation during the trajectories. The origin of the architecture of protein local fragments was analyzed from the viewpoint of the free energy and its decomposed factors. Copyright 2000 Academic Press.

Bacteriophage phi11 lysin: physicochemical characterization and comparison with phage phi80a lysin

USDA-ARS?s Scientific Manuscript database

Phage lytic enzymes are promising antimicrobial agents. Lysins of phage phi11 (LysPhi11) and phi80a (LysPhi80a) can lyse (destroy) biofilms and cells of antibiotic-resistant strains of Staphylococcus aureus. Stability of enzymes is one of the parameters making their practical use possible. The obj...

Arabidopsis fhl/fhy1 double mutant reveals a distinct cytoplasmic action of phytochrome A

PubMed Central

Rösler, Jutta; Klein, Ilse; Zeidler, Mathias

2007-01-01

Phytochrome A (phyA) plays an important role during germination and early seedling development. Because phyA is the primary photoreceptor for the high-irradiance response and the very-low-fluence response, it can trigger development not only in red and far-red (FR) light but also in a wider range of light qualities. Although phyA action is generally associated with translocation to the nucleus and regulation of transcription, there is evidence for additional cytoplasmic functions. Because nuclear accumulation of phyA has been shown to depend on far-red-elongated hypocotyl 1 (FHY1) and FHL (FHY1-like), investigation of phyA function in a double fhl/fhy1 mutant might be valuable in revealing the mechanism of phyA translocation and possible cytoplasmic functions. In fhl/fhy1, the FR-triggered nuclear translocation of phyA could no longer be detected but could be restored by transgenic expression of CFP:FHY1. Whereas the fhl/fhy1 mutant showed a phyA phenotype in respect to hypocotyl elongation and cotyledon opening under high-irradiance response conditions as well as a typical phyA germination phenotype under very-low-fluence response conditions, fhl/fhy1 showed no phenotype with respect to the phyA-dependent abrogation of negative gravitropism in blue light and in red-enhanced phototropism, demonstrating clear cytoplasmic functions of phyA. Disturbance of phyA nuclear import in fhl/fhy1 led to formation of FR-induced phyA:GFP cytoplasmic foci resembling the sequestered areas of phytochrome. FHY1 and FHL play crucial roles in phyA nuclear translocation and signaling. Thus the double-mutant fhl/fhy1 allows nuclear and cytoplasmic phyA functions to be separated, leading to the novel identification of cytoplasmic phyA responses. PMID:17566111

Interactions of phytochromes A, B1 and B2 in light-induced competence for adventitious shoot formation in hypocotyl of tomato (Solanum lycopersicum L.).

PubMed

Lercari, B; Bertram, L

2004-02-01

The interactions of phytochrome A (phyA), phytochrome B1 (phyB1) and phytochrome B2 (phyB2) in light-dependent shoot regeneration from the hypocotyl of tomato was analysed using all eight possible homozygous allelic combinations of the null mutants. The donor plants were pre-grown either in the dark or under red or far-red light for 8 days after sowing; thereafter hypocotyl segments (apical, middle and basal portions) were transferred onto hormone-free medium for culture under different light qualities. Etiolated apical segments cultured in vitro under white light showed a very high frequency of regeneration for all of the genotypes tested besides phyB1phyB2, phyAphyB1 and phyAphyB1phyB2 mutants. Evidence is provided of a specific interference of phyB2 with phyA-mediated HIR to far-red and blue light in etiolated explants. Pre-treatment of donor plants by growth under red light enhanced the competence of phyB1phyB2, phyAphyB1 and phyAphyB1phyB2 mutants for shoot regeneration, whereas pre-irradiation with far-red light enhanced the frequency of regeneration only in the phyAphyB1 mutant. Multiple phytochromes are involved in red light- and far-red light-dependent acquisition of competence for shoot regeneration. The position of the segments along the hypocotyl influenced the role of the various phytochromes and the interactions between them. The culture of competent hypocotyl segments under red, far-red or blue light reduced the frequency of explants forming shoots compared to those cultured under white light, with different genotypes having different response patterns.

Canonical single field slow-roll inflation with a non-monotonic tensor-to-scalar ratio

NASA Astrophysics Data System (ADS)

Germán, Gabriel; Herrera-Aguilar, Alfredo; Hidalgo, Juan Carlos; Sussman, Roberto A.

2016-05-01

We take a pragmatic, model independent approach to single field slow-roll canonical inflation by imposing conditions, not on the potential, but on the slow-roll parameter epsilon(phi) and its derivatives epsilon'(phi) and epsilon''(phi), thereby extracting general conditions on the tensor-to-scalar ratio r and the running nsk at phiH where the perturbations are produced, some 50-60 e-folds before the end of inflation. We find quite generally that for models where epsilon(phi) develops a maximum, a relatively large r is most likely accompanied by a positive running while a negligible tensor-to-scalar ratio implies negative running. The definitive answer, however, is given in terms of the slow-roll parameter ξ2(phi). To accommodate a large tensor-to-scalar ratio that meets the limiting values allowed by the Planck data, we study a non-monotonic epsilon(phi) decreasing during most part of inflation. Since at phiH the slow-roll parameter epsilon(phi) is increasing, we thus require that epsilon(phi) develops a maximum for phi > phiH after which epsilon(phi) decrease to small values where most e-folds are produced. The end of inflation might occur trough a hybrid mechanism and a small field excursion Δphie ≡ |phiH-phie| is obtained with a sufficiently thin profile for epsilon(phi) which, however, should not conflict with the second slow-roll parameter η(phi). As a consequence of this analysis we find bounds for Δphie, rH and for the scalar spectral index nsH. Finally we provide examples where these considerations are explicitly realised.

Storage of red blood cells with improved maintenance of 2,3-bisphosphoglycerate.

PubMed

Högman, Claes F; Löf, Helena; Meryman, Harold T

2006-09-01

During storage, red blood cells (RBCs) rapidly lose 2,3-bisphosphoglycerate (2,3-DPG) leading to an increase in the affinity for O(2) and a temporary impairment of O(2) transport. Recent clinical evaluations indicate that the quality of transfused RBCs may be more important for patient survival than previously recognized. Glucose-free additive solutions (ASs) were prepared with sodium citrate, sodium gluconate, adenine, mannitol, and phosphates at high pH, a solution that can be heat-sterilized. CP2D was used as an anticoagulant. Additional CP2D was added to the AS to supply glucose. RBCs were stored at 4 degrees C and assayed periodically for intracellular pH (pHi), extracellular pH, glucose, lactate, phosphate, ATP, 2,3-DPG, hemolysis, and morphology. Storage in 175 mL of the chloride-free, hypotonic medium at a hematocrit (Hct) level of 59 to 60 percent resulted in an elevated pHi and the maintenance of 2,3-DPG at or above the initial value for 2 weeks without loss of ATP. The addition of 400 mL of storage solution followed by centrifugation and removal of 300 mL of excess solution to a Hct level of 60 to 66 percent further reduced the chloride concentration, resulting in the maintenance of 2,3-DPG for 4 weeks. Hemolysis was at 0.1 percent at 6 weeks. Improvements in the maintenance of 2,3-DPG were achieved with 175 mL of a chloride-free storage solution with familiar additives at nontoxic concentrations to increase pHi. Adding, instead, 400 mL of storage solution followed by the removal of 300 mL reduced the chloride concentration, increasing the pHi and extending the maintenance of 2,3-DPG to 4 weeks.

Incentive Spirometry after Lung Resection: A Randomized Controlled Trial.

PubMed

Malik, Peter Ra; Fahim, Christine; Vernon, Jordyn; Thomas, Priya; Schieman, Colin; Finley, Christian J; Agzarian, John; Shargall, Yaron; Farrokhyar, Forough; Hanna, Wael C

2018-04-24

Incentive spirometry (IS) is thought to reduce the incidence of postoperative pulmonary complications (PPC) after lung resection. We sought to determine whether the addition of IS to routine physiotherapy following lung resection results in a lower rate of PPC, as compared to physiotherapy alone. A single-blind prospective randomized controlled trial was conducted in adults undergoing lung resection. Individuals with previous lung surgery or home oxygen were excluded. Participants randomized to the control arm (PHY) received routine physiotherapy alone (deep breathing, ambulation and shoulder exercises). Those randomized to the intervention arm (PHY/IS) received IS in addition to routine physiotherapy. The trial was powered to detect a 10% difference in the rate of PPC (beta=80%). Student's t-test and chi-square were utilized for continuous and categorical variables respectively, with a significance level of p=0.05. A total of 387 participants (n=195 PHY/IS; n=192 PHY) were randomized between 2014-2017. Baseline characteristics were comparable for both arms. The majority of patients underwent a pulmonary lobectomy (PHY/IS=59.5%, PHY=61.0%, p=0.84), with no difference in the rates of minimally invasive and open procedures. There were no differences in the incidence of PPC at 30 days postoperatively (PHY/IS=12.3%, PHY=13.0%, p=0.88). There were no differences in rates of pneumonia (PHY/IS=4.6%, PHY=7.8%, p=0.21), mechanical ventilation (PHY/IS=2.1%, PHY=1.0%, p=0.41), home-oxygen (PHY/IS=13.8%, PHY=14.6%, p=0.89), hospital length of stay (PHY/IS=4 days, PHY=4 days, p=0.34), or rate of readmission to hospital (PHY/IS=10.3%, PH=9.9%, p=1.00). The addition of IS to routine postoperative physiotherapy does not reduce the incidence of PPC after lung resection. Copyright © 2018. Published by Elsevier Inc.

Purification and characterization of two distinct acidic phytases with broad pH stability from Aspergillus niger NCIM 563.

PubMed

Soni, S K; Magdum, A; Khire, J M

2010-11-01

Aspergillus niger NCIM 563 produced two different extracellular phytases (Phy I and Phy II) under submerged fermentation conditions at 30°C in medium containing dextrin-glucose-sodium nitrate-salts. Both the enzymes were purified to homogeneity using Rotavapor concentration, Phenyl-Sepharose column chromatography and Sephacryl S-200 gel filtration. The molecular mass of Phy I and II as determined by SDS-PAGE and gel filtration were 66, 264, 150 and 148 kDa respectively, indicating that Phy I consists of four identical subunits and Phy II is a monomer. The pI values of Phy I and II were 3.55 and 3.91, respectively. Phy I was highly acidic with optimum pH of 2.5 and was stable over a broad pH range (1.5-9.0) while Phy II showed a pH optimum of 5.0 with stability in the range of pH 3.5-9.0. Phy I exhibited very broad substrate specificity while Phy II was more specific for sodium phytate. Similarly Phy II was strongly inhibited by Ag(+), Hg(2+) (1 mM) metal ions and Phy I was partially inhibited. Peptide analysis by Mass Spectrometry (MS) MALDI-TOF also indicated that both the proteins were totally different. The K(m) for Phy I and II for sodium phytate was 2.01 and 0.145 mM while V(max) was 5,018 and 1,671 μmol min(-1) mg(-1), respectively. The N-terminal amino acid sequences of Phy I and Phy II were FSYGAAIPQQ and GVDERFPYTG, respectively. Phy II showed no homology with Phy I and any other known phytases from the literature suggesting its unique nature. This, according to us, is the first report of two distinct novel phytases from Aspergillus niger.

Phytochrome B Requires PIF Degradation and Sequestration to Induce Light Responses Across a Wide Range of Light Conditions.

PubMed

Park, Eunae; Kim, Yeojae; Choi, Giltsu

2018-05-15

Phytochrome B (phyB) inhibits the function of phytochrome-interacting factors (PIFs) by inducing their degradation and sequestration, but the relative physiological importance of these two phyB activities is unclear. In an analysis of published Arabidopsis thaliana phyB mutations, we identified a point mutation in the N-terminal half of phyB (phyBG111D) that abolishes its PIF sequestration activity without affecting its PIF degradation activity. We also identified a point mutation in the phyB C-terminal domain, which, when combined with a deletion of the C-terminal end (phyB990G767R), does the opposite; it blocks PIF degradation without affecting PIF sequestration. The resulting phyB proteins, phyB990G767R and phyBG111D, are equally capable of inducing light responses under continuous red light. However, phyBG111D, which exhibits only the PIF degradation activity, induces stronger light responses than phyB990G767R under white light with prolonged dark periods (i.e., diurnal cycles). In contrast, phyB990G767R, which exhibits only the PIF sequestration activity, induces stronger light responses in flickering light (a condition that mimics sunflecks). Together, our results indicate that both of these separable phyB activities are required for light responses in varying light conditions. © 2018 American Society of Plant Biologists. All rights reserved.

In-Plane Anisotropic Photoconduction in Nonpolar Epitaxial a-Plane GaN.

PubMed

Pant, Rohit; Shetty, Arjun; Chandan, Greeshma; Roul, Basanta; Nanda, K K; Krupanidhi, S B

2018-05-16

Nonpolar a-plane GaN epitaxial films were grown on an r-plane sapphire using the plasma-assisted molecular beam epitaxy system, with various nitrogen plasma power conditions. The crystallinity of the films was characterized by high-resolution X-ray diffraction and reciprocal space mapping. Using the X-ray "rocking curve-phi scan", [0002], [1-100], and [1-102] azimuth angles were identified, and interdigitated electrodes along these directions were fabricated to evaluate the direction-dependent UV photoresponses. UV responsivity ( R) and internal gain ( G) were found to be dependent on the azimuth angle and in the order of [0002] > [1-102] > [1-100], which has been attributed to the enhanced crystallinity and lowest defect density along [0002] azimuth. The temporal response was very stable irrespective of growth conditions and azimuth angles. Importantly, response time, responsivity, and internal gain were 210 ms, 1.88 A W -1 , and 648.9%, respectively, even at a bias as low as 1 V. The results were validated using the Silvaco Atlas device simulator, and experimental observations were consistent with simulated results. Overall, the photoresponse is dependent on azimuth angles and requires further optimization, especially for materials with in-plane crystal anisotropy.

Discrete Haar transform and protein structure.

PubMed

Morosetti, S

1997-12-01

The discrete Haar transform of the sequence of the backbone dihedral angles (phi and psi) was performed over a set of X-ray protein structures of high resolution from the Brookhaven Protein Data Bank. Afterwards, the new dihedral angles were calculated by the inverse transform, using a growing number of Haar functions, from the lower to the higher degree. New structures were obtained using these dihedral angles, with standard values for bond lengths and angles, and with omega = 0 degree. The reconstructed structures were compared with the experimental ones, and analyzed by visual inspection and statistical analysis. When half of the Haar coefficients were used, all the reconstructed structures were not yet collapsed to a tertiary folding, but they showed yet realized most of the secondary motifs. These results indicate a substantial separation of structural information in the space of Haar transform, with the secondary structural information mainly present in the Haar coefficients of lower degrees, and the tertiary one present in the higher degree coefficients. Because of this separation, the representation of the folded structures in the space of Haar transform seems a promising candidate to encompass the problem of premature convergence in genetic algorithms.

Experimental determination of torsion angles in the polypeptide backbone of the gramicidin A channel by solid state nuclear magnetic resonance.

PubMed

Teng, Q; Nicholson, L K; Cross, T A

1991-04-05

An analytical method for the determination of torsion angles from solid state 15N nuclear magnetic resonance (n.m.r.) spectroscopic data is demonstrated. Advantage is taken of the 15N-1H and 15N-13C dipolar interactions as well as the 15N chemical shift interaction in oriented samples. The membrane-bound channel conformation of gramicidin A has eluded an atomic resolution structure determination by more traditional approaches. Here, the torsion angles for the Ala3 site are determined by obtaining the n.m.r. data for both the Gly2-Ala3 and Ala3-Leu4 peptide linkages. Complete utilization of the orientational constraints derived from these orientation-dependent nuclear spin interactions in restricting the conformational space is most effectively achieved by utilizing spherical trigonometry. Two possible sets of torsion angles for the Ala3 site are obtained (phi, psi = -129 degrees, 153 degrees and -129 degrees, 122 degrees), both of which are consistent with a right-handed beta-helix. Other functional and computational evidence strongly supports the set for which the carbonyl oxygen atom of the Ala3-Leu4 linkage is rotated into the channel lumen.

Role of the N*(1535) in pp{yields}pp{phi} and {pi}{sup -}p{yields}n{phi} reactions

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

Xie Jujun; Graduate University of Chinese Academy of Sciences, Beijing 100049; Zou Bingsong

2008-01-15

The near-threshold {phi}-meson production in proton-proton and {pi}{sup -}p collisions is studied with the assumption that the production mechanism is due to the sub-N{phi}-threshold N*(1535) resonance. The {pi}{sup 0}-,{eta}-, and {rho}{sup 0}-meson exchanges for proton-proton collisions are considered. It is shown that the contribution to the pp{yields}pp{phi} reaction from the t-channel {pi}{sup 0}-meson exchange is dominant. With a significant N*(1535)N{phi} coupling [g{sub N*(1535)N{phi}}{sup 2}/4{pi}=0.13], both pp{yields}pp{phi} and {pi}{sup -}p{yields}n{phi} data are very well reproduced. The significant coupling of the N*(1535) resonance to N{phi} is compatible with previous indications of a large ss component in the quark wave function of themore » N*(1535) resonance and may be the real origin of the significant enhancement of the {phi} production over the naive OZI-rule predictions.« less

The differential production cross section of the $$\\phi $$ (1020) meson in $$\\sqrt{s}$$ TeV $pp$ collisions measured with the ATLAS detector

DOE PAGES

Aad, G.; Abajyan, T.; Abbott, B.; ...

2014-07-01

Ameasurement is presented of themore » $$\\phi $$×BR($$\\phi $$ →K < sup > + < /sup > K < sup > - < /sup > ) production cross section at √s = 7 TeV using pp collision data corresponding to an integrated luminosity of 383 μb -1, collected with the ATLAS experiment at the HC. Selection of $$\\phi $$(1020) mesons is based on the identification of charged kaons by their energy loss in the pixel detector. The differential cross section ismeasured as a function of the transverse momentum, pT,$$\\phi $$ , and rapidity, y$$\\phi $$, of the $$\\phi $$(1020) meson in the fiducial region 500 < pT,$$\\phi $$ < 1200MeV, |y$$\\phi $$ | < 0.8, kaon p T,K > 230 MeV and kaon momentum p K < 800 MeV. The integrated $$\\phi $$(1020)-meson production cross section in this fiducial range is measured to be sφ×BR($$\\phi $$ →K < sup > + < /sup > K < sup > - < /sup > ) = 570 ± 8 (stat) ± 66 (syst) ± 20 (lumi) μb.« less

Chiral mutagenesis of insulin. Contribution of the B20-B23 beta-turn to activity and stability.

PubMed

Nakagawa, Satoe H; Hua, Qing-xin; Hu, Shi-Quan; Jia, Wenhua; Wang, Shuhua; Katsoyannis, Panayotis G; Weiss, Michael A

2006-08-04

Insulin contains a beta-turn (residues B20-B23) interposed between two receptor-binding elements, the central alpha-helix of the B chain (B9-B19) and its C-terminal beta-strand (B24-B28). The turn contains conserved glycines at B20 and B23. Although insulin exhibits marked conformational variability among crystal forms, these glycines consistently maintain positive phi dihedral angles within a classic type-I beta-turn. Because the Ramachandran conformations of GlyB20 and GlyB23 are ordinarily forbidden to L-amino acids, turn architecture may contribute to structure or function. Here, we employ "chiral mutagenesis," comparison of corresponding D- and L-Ala substitutions, to investigate this turn. Control substitutions are introduced at GluB21, a neighboring residue exhibiting a conventional (negative) phi angle. The D- and L-Ala substitutions at B23 are associated with a marked stereospecific difference in activity. Whereas the D-AlaB23 analog retains native activity, the L analog exhibits a 20-fold decrease in receptor binding. By contrast, D- and L-AlaB20 analogs each exhibit high activity. Stereospecific differences between the thermodynamic stabilities of the analogs are nonetheless more pronounced at B20 (delta deltaG(u) 2.0 kcal/mole) than at B23 (delta deltaG(u) 0.7 kcal/mole). Control substitutions at B21 are well tolerated without significant stereospecificity. Chiral mutagenesis thus defines the complementary contributions of these conserved glycines to protein stability (GlyB20) or receptor recognition (GlyB23).

Extended bidirectional reflectance distribution function for polarized light scattering from subsurface defects under a smooth surface.

PubMed

Shen, Jian; Deng, Degang; Kong, Weijin; Liu, Shijie; Shen, Zicai; Wei, Chaoyang; He, Hongbo; Shao, Jianda; Fan, Zhengxiu

2006-11-01

By introducing the scattering probability of a subsurface defect (SSD) and statistical distribution functions of SSD radius, refractive index, and position, we derive an extended bidirectional reflectance distribution function (BRDF) from the Jones scattering matrix. This function is applicable to the calculation for comparison with measurement of polarized light-scattering resulting from a SSD. A numerical calculation of the extended BRDF for the case of p-polarized incident light was performed by means of the Monte Carlo method. Our numerical results indicate that the extended BRDF strongly depends on the light incidence angle, the light scattering angle, and the out-of-plane azimuth angle. We observe a 180 degrees symmetry with respect to the azimuth angle. We further investigate the influence of the SSD density, the substrate refractive index, and the statistical distributions of the SSD radius and refractive index on the extended BRDF. For transparent substrates, we also find the dependence of the extended BRDF on the SSD positions.

Measurement of the decays B--> phiK and B--> phiK*.

PubMed

Aubert, B; Boutigny, D; Gaillard, J M; Hicheur, A; Karyotakis, Y; Lees, J P; Robbe, P; Tisserand, V; Palano, A; Chen, G P; Chen, J C; Qi, N D; Rong, G; Wang, P; Zhu, Y S; Eigen, G; Reinertsen, P L; Stugu, B; Abbott, B; Abrams, G S; Borgland, A W; Breon, A B; Brown, D N; Button-Shafer, J; Cahn, R N; Clark, A R; Fan, Q; Gill, M S; Gowdy, S J; Gritsan, A; Groysman, Y; Jacobsen, R G; Kadel, R W; Kadyk, J; Kerth, L T; Kluth, S; Kolomensky, Y G; Kral, J F; LeClerc, C; Levi, M E; Liu, T; Lynch, G; Meyer, A B; Momayezi, M; Oddone, P J; Perazzo, A; Pripstein, M; Roe, N A; Romosan, A; Ronan, M T; Shelkov, V G; Telnov, A V; Wenzel, W A; Bright-Thomas, P G; Harrison, T J; Hawkes, C M; Kirk, A; Knowles, D J; O'Neale, S W; Penny, R C; Watson, A T; Watson, N K; Deppermann, T; Koch, H; Krug, J; Kunze, M; Lewandowski, B; Peters, K; Schmuecker, H; Steinke, M; Andress, J C; Barlow, N R; Bhimji, W; Chevalier, N; Clark, P J; Cottingham, W N; De Groot, N; Dyce, N; Foster, B; Mass, A; McFall, J D; Wallom, D; Wilson, F F; Abe, K; Hearty, C; Mattison, T S; McKenna, J A; Thiessen, D; Camanzi, B; Jolly, S; McKemey, A K; Tinslay, J; Blinov, V E; Bukin, A D; Bukin, D A; Buzykaev, A R; Dubrovin, M S; Golubev, V B; Ivanchenko, V N; Korol, A A; Kravchenko, E A; Onuchin, A P; Salnikov, A A; Serednyakov, S I; Skovpen, Y I; Telnov, V I; Yushkov, A N; Lankford, A J; Mandelkern, M; McMahon, S; Stoker, D P; Ahsan, A; Arisaka, K; Buchanan, C; Chun, S; Branson, J G; MacFarlane, D B; Prell, S; Rahatlou, S; Raven, G; Sharma, V; Campagnari, C; Dahmes, B; Hart, P A; Kuznetsova, N; Levy, S L; Long, O; Lu, A; Richman, J D; Verkerke, W; Witherell, M; Yellin, S; Beringer, J; Dorfan, D E; Eisner, A M; Frey, A; Grillo, A A; Grothe, M; Heusch, C A; Johnson, R P; Kroeger, W; Lockman, W S; Pulliam, T; Sadrozinski, H; Schalk, T; Schmitz, R E; Schumm, B A; Seiden, A; Turri, M; Walkowiak, W; Williams, D C; Wilson, M G; Chen, E; Dubois-Felsmann, G P; Dvoretskii, A; Hitlin, D G; Metzler, S; Oyang, J; Porter, F C; Ryd, A; Samuel, A; Weaver, M; Yang, S; Zhu, R Y; Devmal, S; Geld, T L; Jayatilleke, S; Mancinelli, G; Meadows, B T; Sokoloff, M D; Bloom, P; Fahey, S; Ford, W T; Gaede, F; Johnson, D R; Michael, A K; Nauenberg, U; Olivas, A; Park, H; Rankin, P; Roy, J; Sen, S; Smith, J G; van Hoek, W C; Wagner, D L; Blouw, J; Harton, J L; Krishnamurthy, M; Soffer, A; Toki, W H; Wilson, R J; Zhang, J; Brandt, T; Brose, J; Colberg, T; Dahlinger, G; Dickopp, M; Dubitzky, R S; Maly, E; Müller-Pfefferkorn, R; Otto, S; Schubert, K R; Schwierz, R; Spaan, B; Wilden, L; Behr, L; Bernard, D; Bonneaud, G R; Brochard, F; Cohen-Tanugi, J; Ferrag, S; Roussot, E; T'Jampens, S; Thiebaux, C; Vasileiadis, G; Verderi, M; Anjomshoaa, A; Bernet, R; Di Lodovico, F; Khan, A; Muheim, F; Playfer, S; Swain, J E; Falbo, M; Bozzi, C; Dittongo, S; Folegani, M; Piemontese, L; Treadwell, E; Anulli, F; Baldini-Ferroli, R; Calcaterra, A; de Sangro, R; Falciai, D; Finocchiaro, G; Patteri, P; Peruzzi, I M; Piccolo, M; Xie, Y; Zallo, A; Bagnasco, S; Buzzo, A; Contri, R; Crosetti, G; Fabbricatore, P; Farinon, S; Lo Vetere, M; Macri, M; Monge, M R; Musenich, R; Pallavicini, M; Parodi, R; Passaggio, S; Pastore, F C; Patrignani, C; Pia, M G; Priano, C; Robutti, E; Santroni, A; Morii, M; Bartoldus, R; Dignan, T; Hamilton, R; Mallik, U; Cochran, J; Crawley, H B; Fischer, P A; Lamsa, J; Meyer, W T; Rosenberg, E I; Benkebil, M; Grosdidier, G; Hast, C; Höcker, A; Lacker, H M; LePeltier, V; Lutz, A M; Plaszczynski, S; Schune, M H; Trincaz-Duvoid, S; Valassi, A; Wormser, G; Bionta, R M; Brigljevic, V; Fackler, O; Fujino, D; Lange, D J; Mugge, M; Shi, X; van Bibber, K; Wenaus, T J; Wright, D M; Wuest, C R; Carroll, M; Fry, J R; Gabathuler, E; Gamet, R; George, M; Kay, M; Payne, D J; Sloane, R J; Touramanis, C; Aspinwall, M L; Bowerman, D A; Dauncey, P D; Egede, U; Eschrich, I; Gunawardane, N J; Martin, R; Nash, J A; Sanders, P; Smith, D; Azzopardi, D E; Back, J J; Dixon, P; Harrison, P F; Potter, R J; Shorthouse, H W; Strother, P; Vidal, P B; Williams, M I; Cowan, G; George, S; Green, M G; Kurup, A; Marker, C E; McGrath, P; McMahon, T R; Ricciardi, S; Salvatore, F; Scott, I; Vaitsas, G; Brown, D; Davis, C L; Allison, J; Barlow, R J; Boyd, J T; Forti, A; Fullwood, J; Jackson, F; Lafferty, G D; Savvas, N; Simopoulos, E T; Weatherall, J H; Farbin, A; Jawahery, A; Lillard, V; Olsen, J; Roberts, D A; Schieck, J R; Blaylock, G; Dallapiccola, C; Flood, K T; Hertzbach, S S; Kofler, R; Lin, C S; Moore, T B; Staengle, H; Willocq, S; Wittlin, J; Brau, B; Cowan, R; Sciolla, G; Taylor, F; Yamamoto, R K; Britton, D I; Milek, M; Patel, P M; Trischuk, J; Lanni, F; Palombo, F; Bauer, J M; Booke, M; Cremaldi, L; Eschenburg, V; Kroeger, R; Reidy, J; Sanders, D A; Summers, D J; Martin, J P; Nief, J Y; Seitz, R; Taras, P; Zacek, V; Nicholson, H; Sutton, C S; Cartaro, C; Cavallo, N; De Nardo, G; Fabozzi, F; Gatto, C; Lista, L; Paolucci, P; Piccolo, D; Sciacca, C; LoSecco, J M; Alsmiller, J R; Gabriel, T A; Handler, T; Brau, J; Frey, R; Iwasaki, M; Sinev, N B; Strom, D; Colecchia, F; Dal Corso, F; Dorigo, A; Galeazzi, F; Margoni, M; Michelon, G; Morandin, M; Posocco, M; Rotondo, M; Simonetto, F; Stroili, R; Torassa, E; Voci, C; Benayoun, M; Briand, H; Chauveau, J; David, P; De La Vaissière, C; Del Buono, L; Hamon, O; Le Diberder, F; Leruste, P; Lory, J; Roos, L; Stark, J; Versillé, S; Manfredi, P F; Re, V; Speziali, V; Frank, E D; Gladney, L; Guo, Q H; Panetta, J H; Angelini, C; Batignani, G; Bettarini, S; Bondioli, M; Carpinelli, M; Forti, F; Giorgi, M A; Lusiani, A; Martinez-Vidal, F; Morganti, M; Neri, N; Paoloni, E; Rama, M; Rizzo, G; Sandrelli, F; Simi, G; Triggiani, G; Walsh, J; Haire, M; Judd, D; Paick, K; Turnbull, L; Wagoner, D E; Albert, J; Bula, C; Lu, C; McDonald, K T; Miftakov, V; Schaffner, S F; Smith, A J; Tumanov, A; Varnes, E W; Cavoto, G; del Re, D; Faccini, R; Ferrarotto, F; Ferroni, F; Fratini, K; Lamanna, E; Leonardi, E; Mazzoni, M A; Morganti, S; Piredda, G; Safai Tehrani, F; Serra, M; Voena, C; Christ, S; Waldi, R; Adye, T; Franek, B; Geddes, N I; Gopal, G P; Xella, S M; Aleksan, R; De Domenico, G; Emery, S; Gaidot, A; Ganzhur, S F; Giraud, P F; Hamel De Monchenault, G; Kozanecki, W; Langer, M; London, G W; Mayer, B; Serfass, B; Vasseur, G; Yeche, C; Zito, M; Copty, N; Purohit, M V; Singh, H; Yumiceva, F X; Adam, I; Anthony, P L; Aston, D; Baird, K; Bartelt, J; Bloom, E; Boyarski, A M; Bulos, F; Calderini, G; Claus, R; Convery, M R; Coupal, D P; Coward, D H; Dorfan, J; Doser, M; Dunwoodie, W; Field, R C; Glanzman, T; Godfrey, G L; Grosso, P; Himel, T; Huffer, M E; Innes, W R; Jessop, C P; Kelsey, M H; Kim, P; Kocian, M L; Langenegger, U; Leith, D W; Luitz, S; Luth, V; Lynch, H L; Manzin, G; Marsiske, H; Menke, S; Messner, R; Moffeit, K C; Mount, R; Muller, D R; O'Grady, C P; Petrak, S; Quinn, H; Ratcliff, B N; Robertson, S H; Rochester, L S; Roodman, A; Schietinger, T; Schindler, R H; Schwiening, J; Serbo, V V; Snyder, A; Soha, A; Spanier, S M; Stahl, A; Stelzer, J; Su, D; Sullivan, M K; Talby, M; Tanaka, H A; Trunov, A; Va'vra, J; Wagner, S R; Weinstein, A J; Wisniewski, W J; Young, C C; Burchat, P R; Cheng, C H; Kirkby, D; Meyer, T I; Roat, C; De Silva, A; Henderson, R; Bugg, W; Cohn, H; Hart, E; Weidemann, A W; Benninger, T; Izen, J M; Kitayama, I; Lou, X C; Turcotte, M; Bianchi, F; Bona, M; Di Girolamo, B; Gamba, D; Smol, A; Zanin, D; Bosisio, L; Della Ricca, G; Lanceri, L; Pompili, A; Poropat, P; Prest, M; Vallazza, E; Vuagnin, G; Panvini, R S; Brown, C M; Kowalewski, R; Roney, J M; Band, H R; Charles, E; Dasu, S; Elmer, P; Hu, H; Johnson, J R; Liu, R; Nielsen, J; Orejudos, W; Pan, Y; Prepost, R; Scott, I J; Sekula, S J; von Wimmersperg-Toeller, J H; Wu, S L; Yu, Z; Zobering, H; Kordich, T M; Neal, H

2001-10-08

We have observed the decays B--> phiK and phiK(*) in a sample of over 45 million B mesons collected with the BABAR detector at the PEP-II collider. The measured branching fractions are B(B+--> phiK+) = (7.7(+1.6)(-1.4)+/-0.8)x10(-6), B(B0--> phiK0) = (8.1(+3.1)(-2.5)+/-0.8)x10(-6), B(B+--> phiK(*+)) = (9.7(+4.2)(-3.4)+/-1.7)x10(-6), and B(B0--> phiK(*0)) = (8.7(+2.5)(-2.1)+/-1.1)x10(-6). We also report the upper limit B(B+--> phipi(+))<1.4x10(-6) ( 90% C.L.).

Effects of structural deformations on optical properties of tetrabenzoporphyrins: free-bases and Pd complexes.

PubMed

Lebedev, Artem Y; Filatov, Mikhail A; Cheprakov, Andrei V; Vinogradov, Sergei A

2008-08-21

A recently developed method of synthesis of pi-extended porphyrins made it possible to prepare a series of tetrabenzoporphyrins (TBP) with different numbers of meso-aryl substituents. The photophysical parameters of free-bases and Pd complexes of meso-unsubstituted TBP's, 5,15-diaryl-TBP's (Ar2TBP's) and 5,10,15,20-tetraaryl-TBP's (Ar4TBP's) were measured. For comparison, similarly meso-arylsubstituted porphyrins fused with nonaromatic cyclohexeno-rings, i.e. Ar(n)-tetracyclohexenoporphyrins (Ar(n)TCHP's, n = 0, 2, 4), were also synthesized and studied. Structural information was obtained by ab initio (DFT) calculations and X-ray crystallography. It was found that: 1) Free-base Ar4TBP's are strongly distorted out-of-plane (saddled), possess broadened, red-shifted spectra, short excited-state lifetimes and low fluorescence quantum yields (tau(fl) = 2-3 ns, phi(fl) = 0.02-0.03). These features are characteristic of other nonplanar free-base porphyrins, including Ar4TCHP's. 2) Ar2TBP free-bases possess completely planar geometries, although with significant in-plane deformations. These deformations have practically no effect on the singlet excited-state properties of Ar2TBP's as compared to planar meso-unsubstituted TBP's. Both types of porphyrins retain strong fluorescence (tau(fl) = 10-12 ns, phi(fl) = 0.3-0.4), and their radiative rate constants (k(r)) are 3-4 times higher than those of planar H2TCHP's. 3) Nonplanar deformations dramatically enhance nonradiative decay of triplet states of regular Pd porphyrins. For example, planar PdTCHP phosphoresces with high quantum yield (phi(phos) = 0.45, tau(phos) = 1118 micros), while saddled PdPh4TCHP is practically nonemissive. In contrast, both ruffled and saddled PdAr(n)TBP's retain strong phosphorescence at ambient temperatures (PdPh2TBP: tau(phos) = 496 micros, phi(phos) = 0.15; PdPh4TBP: tau(phos) = 258 micros, phi(phos) = 0.08). It appears that pi-extension is capable of counterbalancing deleterious effects of nonplanar deformations on triplet emissivity of Pd porphyrins.

Effect of dietary phosphorus, phytase, and 25-hydroxycholecalciferol on broiler chicken bone mineralization, litter phosphorus, and processing yields.

PubMed

Angel, R; Saylor, W W; Mitchell, A D; Powers, W; Applegate, T J

2006-07-01

Three floor pen experiments (Exp) were conducted to evaluate low nonphytin P (NPP) concentrations and the NPP sparing effect of phytase (PHY) and 25-hydroxycholecalciferol (25D) on bone mineralization, bone breaking during commercial processing, litter P, and water-soluble P (WSP) concentrations. Tested treatments (TRT) were control, National Research Council NPP; University of Maryland (UMD) NPP; UMD + PHY, UMD NPP reduced by 0.064% NPP + 600 U of PHY/kg; UMD + PHY + 25D, UMD NPP reduced by 0.090% NPP + 600 U of PHY and 70 microg of 25D/kg; control + PHY mimicked the industry practice of diets by 0.1% when PHY is added; and negative control with 90% UMD NPP concentrations. UMD + PHY and control + PHY diets contained 600 U of PHY/kg, and UMD + PHY + 25D contained 600 U of PHY + 70 microg of 25D/kg. Performance results were presented separately. After each Exp, litter P and WSP were determined, and bone measurements were obtained on 8 or 10 broilers per pen. Tested TRT did not affect broiler BW. Femur ash weight of broilers fed the UMD and UMD + PHY + 25D was lower in all Exp compared with that of broilers fed the control diet. Femur ash was similar for control and UMD + PHY broilers, yet averaged over all Exp, UMD + PHY broilers consumed 39% less NPP and required less NPP per gram of femur ash than those on the control (4.87 and 7.77 g of NPP/g of ash, Exp 3). At the end of Exp 3, broilers were processed in a commercial facility. Despite reductions in NPP intake and bone mineralization, no differences were observed in measurements of economic importance (parts lost, carcass yield, and incidence of broken bones). The P excretion per bird was lowest for birds fed the UMD + PHY + 25D diet followed by those fed the UMD + PHY and negative control diets (10.44, 12.00, and 13.78 g of P/bird, respectively) and were highest for those fed the control diet (19.55 g of P/bird). These results suggest that feeding diets low in P together with PHY and 25D will not affect performance or increase losses at processing while resulting in improved P retention and reductions in P and WSP excreted.

Centrality dependence of dihadron correlations and azimuthal anisotropy harmonics in PbPb collisions at $$\\sqrt{s_{NN}}= 2.76\\ \\mbox{TeV}$$

DOE PAGES

Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.; ...

2012-05-30

Measurements from the CMS experiment at the LHC of dihadron correlations for charged particles produced in PbPb collisions at a nucleon-nucleon centre-of-mass energy of 2. 76 TeV are presented. The results are reported as a function of the particle transverse momenta (p T ) and collision centrality over a broad range in relative pseudorapidity (Δη) and the full range of relative azimuthal angle (Δmore » $$\\phi$$). The observed two-dimensional correlation structure in Δη and Δ$$\\phi$$ is characterised by a narrow peak at (Δη,Δ$$\\phi$$)≈(0,0) from jet-like correlations and a long-range structure that persists up to at least |Δη|=4. An enhancement of the magnitude of the short-range jet peak is observed with increasing centrality, especially for particles of p T around 1-2 GeV/c. The long-range azimuthal dihadron correlations are extensively studied using a Fourier decomposition analysis. The extracted Fourier coefficients are found to factorise into a product of single-particle azimuthal anisotropies up to p T ≈3-3. 5 GeV/c for at least one particle from each pair, except for the second-order harmonics in the most central PbPb events. Various orders of the single-particle azimuthal anisotropy harmonics are extracted for associated particle p T of 1-3 GeV/c, as a function of the trigger particle p T up to 20 GeV/c and over the full centrality range.« less

Observation of {chi}{sub c1} Decays into Vector Meson Pairs {phi}{phi}, {omega}{omega}, and {omega}{phi}

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

Ablikim, M.; An, Z. H.; Bai, J. Z.

Using (106{+-}4)x10{sup 6} {psi}(3686) events accumulated with the BESIII detector at the BEPCII e{sup +}e{sup -} collider, we present the first measurement of decays of {chi}{sub c1} to vector meson pairs {phi}{phi}, {omega}{omega}, and {omega}{phi}. The branching fractions are measured to be (4.4{+-}0.3{+-}0.5)x10{sup -4}, (6.0{+-}0.3{+-}0.7)x10{sup -4}, and (2.2{+-}0.6{+-}0.2)x10{sup -5}, for {chi}{sub c1}{yields}{phi}{phi}, {omega}{omega}, and {omega}{phi}, respectively, which indicates that the hadron helicity selection rule is significantly violated in {chi}{sub cJ} decays. In addition, the measurement of {chi}{sub cJ}{yields}{omega}{phi} provides the first indication of the rate of doubly OZI-suppressed {chi}{sub cJ} decay. Finally, we present improved measurements for the branching fractionsmore » of {chi}{sub c0} and {chi}{sub c2} to vector meson pairs.« less

A documentation of two- and three-dimensional shock-separated turbulent boundary layers

NASA Technical Reports Server (NTRS)

Brown, J. D.; Brown, J. L.; Kussoy, M. I.

1988-01-01

A shock-related separation of a turbulent boundary layer has been studied and documented. The flow was that of an axisymmetric turbulent boundary layer over a 5.02-cm-diam cylinder that was aligned with the wind tunnel axis. The boundary layer was compressed by a 30 deg half-angle conical flare, with the cone axis inclined at an angle alpha to the cylinder axis. Nominal test conditions were P sub tau equals 1.7 atm and M sub infinity equals 2.85. Measurements were confined to the upper-symmetry, phi equals 0 deg, plane. Data are presented for the cases of alpha equal to 0. 5. and 10 deg and include mean surface pressures, streamwise and normal mean velocities, kinematic turbulent stresses and kinetic energies, as well as reverse-flow intermittencies. All data are given in tabular form; pressures, streamwise velocities, turbulent shear stresses, and kinetic energies are also presented graphically.

Triple Differential Cross Sections for Ionization of Laser-Aligned Mg Atoms by electron impact

NASA Astrophysics Data System (ADS)

Amami, Sadek; Madison, Don; Nixon, Kate; Murray, Andrew

2013-09-01

3DW (3-body distorted wave) triple differential cross sections have been calculated for electron impact ionization of magnesium atoms aligned by lasers. Calculations have been performed for the kinematics of the experiment performed by Kate Nixon and Andrew Murray at Manchester, England [K. L. Nixon and A. J. Murray 2011 Phys. Rev. Lett. 106, 123201]. An incident projectile was produced with energy of 41.91eV, scattered and ejected electrons were detected with equal energies (E1 =E2 =20eV), the scattered projectile was detected at a fixed angle of 30deg, and the ejected electrons were detected at angles ranging between 0circ; - 180circ; . The theoretical 3DW results will be compared with the experimental data. This work is supported by the US National Science Foundation under Grant.No.PHY-1068237.

Coupling system to a microsphere cavity

NASA Technical Reports Server (NTRS)

Iltchenko, Vladimir (Inventor); Maleki, Lute (Inventor); Yao, Steve (Inventor); Wu, Chi (Inventor)

2002-01-01

A system of coupling optical energy in a waveguide mode, into a resonator that operates in a whispering gallery mode. A first part of the operation uses a fiber in its waveguide mode to couple information into a resonator e.g. a microsphere. The fiber is cleaved at an angle .PHI. which causes total internal reflection within the fiber. The energy in the fiber then forms an evanescent field and a microsphere is placed in the area of the evanescent field. If the microsphere resonance is resonant with energy in the fiber, then the information in the fiber is effectively transferred to the microsphere.

Visual Navigation for an Autonomous Mobile Vehicle

DTIC Science & Technology

1992-03-26

Group 1 Angle Group 2 1 41 10- 0 80 60 0 20 11 1 9 o30 18 20 17 1 5 1 16-20 -17 -10 -110 -14 -40 -15 1350-30 -12 60 -1 1- 5 -1 -80 -111 70 Figure 6.2...A, M X . 0 .34 y= 267.42 - 220.59- 5 P- -C.7022 nr verify matches= 0 :, A, x- . :4 y= 266. 64 2: 2 81.8 8 .-. 8255 nr verify matches= 0 ,,. x " y...Returns 0 oiherv. ic. / 5 --------------- I--------------------------- int verticaIIr! EDGE ’r: return <(lbs~r->a\\ _phi, VERTCONSTRAINT) 1I

J/psi Polarization in pp collisions at s = 7 TeV

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

Abelev, B.; Awes, Terry C; Ganoti, P.

The ALICE Collaboration has studied J/{Psi} production in pp collisions at {radical}s = 7 TeV at the LHC through its muon pair decay. The polar and azimuthal angle distributions of the decay muons were measured, and results on the J/{Psi} polarization parameters {lambda}{sub {theta}} and {lambda}{sub {phi}} were obtained. The study was performed in the kinematic region 2.5 < y < 4, 2 < p{sub t} < 8 GeV/c, in the helicity and Collins-Soper reference frames. In both frames, the polarization parameters are compatible with zero, within uncertainties.

Inertial Pointing and Positioning System

NASA Technical Reports Server (NTRS)

Yee, Robert (Inventor); Robbins, Fred (Inventor)

1998-01-01

An inertial pointing and control system and method for pointing to a designated target with known coordinates from a platform to provide accurate position, steering, and command information. The system continuously receives GPS signals and corrects Inertial Navigation System (INS) dead reckoning or drift errors. An INS is mounted directly on a pointing instrument rather than in a remote location on the platform for-monitoring the terrestrial position and instrument attitude. and for pointing the instrument at designated celestial targets or ground based landmarks. As a result. the pointing instrument and die INS move independently in inertial space from the platform since the INS is decoupled from the platform. Another important characteristic of the present system is that selected INS measurements are combined with predefined coordinate transformation equations and control logic algorithms under computer control in order to generate inertial pointing commands to the pointing instrument. More specifically. the computer calculates the desired instrument angles (Phi, Theta. Psi). which are then compared to the Euler angles measured by the instrument- mounted INS. and forms the pointing command error angles as a result of the compared difference.

Phosphite, an analog of phosphate, suppresses the coordinated expression of genes under phosphate starvation.

PubMed

Varadarajan, Deepa K; Karthikeyan, Athikkattuvalasu S; Matilda, Paino Durzo; Raghothama, Kashchandra G

2002-07-01

Phosphate (Pi) and its analog phosphite (Phi) are acquired by plants via Pi transporters. Although the uptake and mobility of Phi and Pi are similar, there is no evidence suggesting that plants can utilize Phi as a sole source of phosphorus. Phi is also known to interfere with many of the Pi starvation responses in plants and yeast (Saccharomyces cerevisiae). In this study, effects of Phi on plant growth and coordinated expression of genes induced by Pi starvation were analyzed. Phi suppressed many of the Pi starvation responses that are commonly observed in plants. Enhanced root growth and root to shoot ratio, a hallmark of Pi stress response, was strongly inhibited by Phi. The negative effects of Phi were not obvious in plants supplemented with Pi. The expression of Pi starvation-induced genes such as LePT1, LePT2, AtPT1, and AtPT2 (high-affinity Pi transporters); LePS2 (a novel acid phosphatase); LePS3 and TPSI1 (novel genes); and PAP1 (purple acid phosphatase) was suppressed by Phi in plants and cell cultures. Expression of luciferase reporter gene driven by the Pi starvation-induced AtPT2 promoter was also suppressed by Phi. These analyses showed that suppression of Pi starvation-induced genes is an early response to addition of Phi. These data also provide evidence that Phi interferes with gene expression at the level of transcription. Synchronized suppression of multiple Pi starvation-induced genes by Phi points to its action on the early molecular events, probably signal transduction, in Pi starvation response.

USE OF THE PROSTATE HEALTH INDEX FOR DETECTION OF PROSTATE CANCER: RESULTS FROM A LARGE ACADEMIC PRACTICE

PubMed Central

Tosoian, Jeffrey J.; Druskin, Sasha C.; Andreas, Darian; Mullane, Patrick; Chappidi, Meera; Joo, Sarah; Ghabili, Kamyar; Agostino, Joseph; Macura, Katarzyna J.; Carter, H. Ballentine; Schaeffer, Edward M.; Partin, Alan W.; Sokoll, Lori J.; Ross, Ashley E.

2016-01-01

BACKGROUND The Prostate Health Index (phi) outperforms PSA and other PSA derivatives for the diagnosis of prostate cancer (PCa). The impact of phi testing in the real-world clinical setting has not been previously assessed. METHODS In a single, large, academic center, phi was tested in 345 patients presenting for diagnostic evaluation for PCa. Findings on prostate biopsy (including Grade Group [GG], defined as GG1: Gleason score [GS] 6, GG2: GS 3+4=7, GG3: GS 4+3=7, GG4: GS 8, and GG5: GS 9-10), magnetic resonance imaging (MRI), and radical prostatectomy (RP) were prospectively recorded. Biopsy rates and outcomes were compared to a contemporary cohort that did not undergo phi testing (n=1318). RESULTS Overall, 39% of men with phi testing underwent prostate biopsy. No men with phi<19.6 were diagnosed with PCa, and only 3 men with phi<27 had cancer of GG≥2. Phi was superior to PSA for the prediction of any PCa (AUC 0.72 vs. 0.47) and GG≥2 PCa (AUC 0.77 vs. 0.53) on prostate biopsy. Among men undergoing MRI and phi, no men with phi<27 and PI-RADS≤3 had GG≥2 cancer. For those men proceeding to RP, increasing phi was associated with higher pathologic GG (p=0.002) and stage (p=0.001). Compared to patients who did not undergo phi testing, the use of phi was associated with a 9% reduction in the rate of prostate biopsy (39% vs. 48%; p<0.001). Importantly, the reduction in biopsy among the phi population was secondary to decreased incidence of negative (8%) and GG1 (1%) biopsies, while the proportion of biopsies detecting GG≥2 cancers remained unchanged. CONCLUSIONS In this large, real-time clinical experience, phi outperformed PSA alone, was associated with high-grade PCa, and provided complementary information to MRI. Incorporation of phi into clinical practice reduced the rate of unnecessary biopsies without changing the frequency of detection of higher grade cancers. PMID:28117387

Phytochromes play a role in phototropism and gravitropism in Arabidopsis roots

NASA Astrophysics Data System (ADS)

Correll, Melanie J.; Coveney, Katrina M.; Raines, Steven V.; Mullen, Jack L.; Hangarter, Roger P.; Kiss, John Z.

2003-05-01

Phototropism as well as gravitropism plays a role in the oriented growth of roots in flowering plants. In blue or white light, roots exhibit negative phototropism, but red light induces positive phototropism in Arabidopsis roots. Phytochrome A (phyA) and phyB mediate the positive red-light-based photoresponse in roots since single mutants (and the double phyAB mutant) were severely impaired in this response. In blue-light-based negative phototropism, phyA and phyAB (but not phyB) were inhibited in the response relative to the WT. In root gravitropism, phyB and phyAB (but not phyA) were inhibited in the response compared to the WT. The differences observed in tropistic responses were not due to growth limitations since the growth rates among all the mutants tested were not significantly different from that of the WT. Thus, our study shows that the blue-light and red-light systems interact in roots and that phytochrome plays a key role in plant development by integrating multiple environmental stimuli.

Kinematics of reflections in subsurface offset and angle-domain image gathers

NASA Astrophysics Data System (ADS)

Dafni, Raanan; Symes, William W.

2018-05-01

Seismic migration in the angle-domain generates multiple images of the earth's interior in which reflection takes place at different scattering-angles. Mechanically, the angle-dependent reflection is restricted to happen instantaneously and at a fixed point in space: Incident wave hits a discontinuity in the subsurface media and instantly generates a scattered wave at the same common point of interaction. Alternatively, the angle-domain image may be associated with space-shift (regarded as subsurface offset) extended migration that artificially splits the reflection geometry. Meaning that, incident and scattered waves interact at some offset distance. The geometric differences between the two approaches amount to a contradictory angle-domain behaviour, and unlike kinematic description. We present a phase space depiction of migration methods extended by the peculiar subsurface offset split and stress its profound dissimilarity. In spite of being in radical contradiction with the general physics, the subsurface offset reveals a link to some valuable angle-domain quantities, via post-migration transformations. The angle quantities are indicated by the direction normal to the subsurface offset extended image. They specifically define the local dip and scattering angles if the velocity at the split reflection coordinates is the same for incident and scattered wave pairs. Otherwise, the reflector normal is not a bisector of the opening angle, but of the corresponding slowness vectors. This evidence, together with the distinguished geometry configuration, fundamentally differentiates the angle-domain decomposition based on the subsurface offset split from the conventional decomposition at a common reflection point. An asymptotic simulation of angle-domain moveout curves in layered media exposes the notion of split versus common reflection point geometry. Traveltime inversion methods that involve the subsurface offset extended migration must accommodate the split geometry in the inversion scheme for a robust and successful convergence at the optimal velocity model.

Direct detection of RNA in vitro and in situ by target-primed RCA: The impact of E. coli RNase III on the detection efficiency of RNA sequences distanced far from the 3'-end.

PubMed

Merkiene, Egle; Gaidamaviciute, Edita; Riauba, Laurynas; Janulaitis, Arvydas; Lagunavicius, Arunas

2010-08-01

We improved the target RNA-primed RCA technique for direct detection and analysis of RNA in vitro and in situ. Previously we showed that the 3' --> 5' single-stranded RNA exonucleolytic activity of Phi29 DNA polymerase converts the target RNA into a primer and uses it for RCA initiation. However, in some cases, the single-stranded RNA exoribonucleolytic activity of the polymerase is hindered by strong double-stranded structures at the 3'-end of target RNAs. We demonstrate that in such hampered cases, the double-stranded RNA-specific Escherichia coli RNase III efficiently assists Phi29 DNA polymerase in converting the target RNA into a primer. These observations extend the target RNA-primed RCA possibilities to test RNA sequences distanced far from the 3'-end and customize this technique for the inner RNA sequence analysis.

Statistical nature of infrared dynamics on de Sitter background

NASA Astrophysics Data System (ADS)

Tokuda, Junsei; Tanaka, Takahiro

2018-02-01

In this study, we formulate a systematic way of deriving an effective equation of motion(EoM) for long wavelength modes of a massless scalar field with a general potential V(phi) on de Sitter background, and investigate whether or not the effective EoM can be described as a classical stochastic process. Our formulation gives an extension of the usual stochastic formalism to including sub-leading secular growth coming from the nonlinearity of short wavelength modes. Applying our formalism to λ phi4 theory, we explicitly derive an effective EoM which correctly recovers the next-to-leading secularly growing part at a late time, and show that this effective EoM can be seen as a classical stochastic process. Our extended stochastic formalism can describe all secularly growing terms which appear in all correlation functions with a specific operator ordering. The restriction of the operator ordering will not be a big drawback because the commutator of a light scalar field becomes negligible at large scales owing to the squeezing.

Multiple phytochromes are involved in red-light-induced enhancement of first-positive phototropism in arabidopsis thaliana

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

Janoudi, A.K.; Gordon, W.R.; Poff, K.L.

1997-03-01

The amplitude of phototropic curvature to blue light is enhanced by a prior exposure of seedlings to red light. This enhancement is mediated by phytochrome. Fluence-response relationships have been constructed for red-light-induced enhancement in the phytochrome A (phyA) null mutant, the phytochrome B- (phyB) deficient mutant, and in two transgenic lines of Arabidopsis thaliana that overexpress either phyA or phyB. These fluence-response relationships demonstrate the existence of two responses in enhancement, a response in the very-low-to-low-fluence range, and a response in the high-fluence range. Only the response in the high-fluence range is present in the phyA null mutant. In contrast,more » the phyB-deficient mutant is indistinguishable from the wild-type parent in red-light responsiveness. These data indicate that phyA is necessary for the very-low-to-low but not the high-fluence response, and that phyB is not necessary for either response range. Based on these results, the high-fluence response, if controlled by a single phytochrome, must be controlled by a phytochrome other than phyA or phyB. Overexpression of phyA has a negative effect and overexpression of phyB has an enhancing effect in the high fluence range. These results suggest that overexpression of either phytochrome perturbs the function of the endogenous photoreceptor system in unpreditable fashion. 25 refs., 3 figs.« less

SUMOylation of phytochrome-B negatively regulates light-induced signaling in Arabidopsis thaliana

PubMed Central

Sadanandom, Ari; Ádám, Éva; Orosa, Beatriz; Viczián, András; Klose, Cornelia; Zhang, Cunjin; Josse, Eve-Marie; Kozma-Bognár, László; Nagy, Ferenc

2015-01-01

The red/far red light absorbing photoreceptor phytochrome-B (phyB) cycles between the biologically inactive (Pr, λmax, 660 nm) and active (Pfr; λmax, 730 nm) forms and functions as a light quality and quantity controlled switch to regulate photomorphogenesis in Arabidopsis. At the molecular level, phyB interacts in a conformation-dependent fashion with a battery of downstream regulatory proteins, including PHYTOCHROME INTERACTING FACTOR transcription factors, and by modulating their activity/abundance, it alters expression patterns of genes underlying photomorphogenesis. Here we report that the small ubiquitin-like modifier (SUMO) is conjugated (SUMOylation) to the C terminus of phyB; the accumulation of SUMOylated phyB is enhanced by red light and displays a diurnal pattern in plants grown under light/dark cycles. Our data demonstrate that (i) transgenic plants expressing the mutant phyBLys996Arg-YFP photoreceptor are hypersensitive to red light, (ii) light-induced SUMOylation of the mutant phyB is drastically decreased compared with phyB-YFP, and (iii) SUMOylation of phyB inhibits binding of PHYTOCHROME INTERACTING FACTOR 5 to phyB Pfr. In addition, we show that OVERLY TOLERANT TO SALT 1 (OTS1) de-SUMOylates phyB in vitro, it interacts with phyB in vivo, and the ots1/ots2 mutant is hyposensitive to red light. Taken together, we conclude that SUMOylation of phyB negatively regulates light signaling and it is mediated, at least partly, by the action of OTS SUMO proteases. PMID:26283376

New records of mosquitoes (Diptera: Culicidae) found in phytotelmata in Northern Argentina.

PubMed

Stein, Marina; Alvarez, Carla N; Alonso, Ana C; Bangher, DÉbora N; Willener, Juana A; Campos, RaÚl E

2018-03-20

The geographical distributions of Culex (Carrollia) secundus, Cx. (Microculex) davisi, Cx. (Phytotelmatomyia) castroi, Cx. (Phy.) renatoi, Lutzia (Lutzia) allostigma, Sabethes (Peytonulus) undosus, Sa. (Sabethoides) glaucodaemon, Toxorhynchites (Lynchiella) bambusicola, Tx. (Lyn.) theobaldi, Wyeomyia (Dodecamyia) aphobema, Wy. (Miamyia) codiocampa and Wy. serratoria (subgenus uncertain) are extended, including new records for four provinces in Argentina and four new records for the country, increasing the number of species known to occur in Argentina from 242 to 246.

Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis

USDA-ARS?s Scientific Manuscript database

Plants constantly monitor informational light signals using sensory photoreceptors, which include the phytochrome (phy) family (phyA to phyE), and adjust their growth and development accordingly. Following light-induced nuclear translocation, photoactivated phy molecules bind to and induce rapid pho...

[Genetic study of bacteriophage phi81. I. Isolation, study of complementation and preliminary mapping of amber-mutants of bacteriophage phi81].

PubMed

Sineokiĭ, S P; Pogosov, V Z; Iankovskiĭ, N K; Krylov, V N

1976-01-01

123 Amber mutants of lambdoid bacteriophage phi81 are isolated and distributed into 19 complementation groups. Deletion mapping made possible to locate 5 gene groups on the genetic map of bacteriophage phi81 and to determine a region of possible location of mm' sticky ends on the prophage genetic map. A gene of phage phi81 is localized, which controls the adsorption specificity, and which functional similarity to a respective gene of phage phi80 is demonstrated.

Evaluation of PHI Hunter in Natural Language Processing Research.

PubMed

Redd, Andrew; Pickard, Steve; Meystre, Stephane; Scehnet, Jeffrey; Bolton, Dan; Heavirland, Julia; Weaver, Allison Lynn; Hope, Carol; Garvin, Jennifer Hornung

2015-01-01

We introduce and evaluate a new, easily accessible tool using a common statistical analysis and business analytics software suite, SAS, which can be programmed to remove specific protected health information (PHI) from a text document. Removal of PHI is important because the quantity of text documents used for research with natural language processing (NLP) is increasing. When using existing data for research, an investigator must remove all PHI not needed for the research to comply with human subjects' right to privacy. This process is similar, but not identical, to de-identification of a given set of documents. PHI Hunter removes PHI from free-form text. It is a set of rules to identify and remove patterns in text. PHI Hunter was applied to 473 Department of Veterans Affairs (VA) text documents randomly drawn from a research corpus stored as unstructured text in VA files. PHI Hunter performed well with PHI in the form of identification numbers such as Social Security numbers, phone numbers, and medical record numbers. The most commonly missed PHI items were names and locations. Incorrect removal of information occurred with text that looked like identification numbers. PHI Hunter fills a niche role that is related to but not equal to the role of de-identification tools. It gives research staff a tool to reasonably increase patient privacy. It performs well for highly sensitive PHI categories that are rarely used in research, but still shows possible areas for improvement. More development for patterns of text and linked demographic tables from electronic health records (EHRs) would improve the program so that more precise identifiable information can be removed. PHI Hunter is an accessible tool that can flexibly remove PHI not needed for research. If it can be tailored to the specific data set via linked demographic tables, its performance will improve in each new document set.

Contribution of elevated intracellular calcium to pulmonary arterial myocyte alkalinization during chronic hypoxia

PubMed Central

Luke, Trevor; Shimoda, Larissa A.

2016-01-01

Abstract In the lung, exposure to chronic hypoxia (CH) causes pulmonary hypertension, a debilitating disease. Development of this condition arises from increased muscularity and contraction of pulmonary vessels, associated with increases in pulmonary arterial smooth muscle cell (PASMC) intracellular pH (pHi) and Ca2+ concentration ([Ca2+]i). In this study, we explored the interaction between pHi and [Ca2+]i in PASMCs from rats exposed to normoxia or CH (3 weeks, 10% O2). PASMC pHi and [Ca2+]i were measured with fluorescent microscopy and the dyes BCECF and Fura-2. Both pHi and [Ca2+]i levels were elevated in PASMCs from hypoxic rats. Exposure to KCl increased [Ca2+]i and pHi to a similar extent in normoxic and hypoxic PASMCs. Conversely, removal of extracellular Ca2+ or blockade of Ca2+ entry with NiCl2 or SKF 96365 decreased [Ca2+]i and pHi only in hypoxic cells. Neither increasing pHi with NH4Cl nor decreasing pHi by removal of bicarbonate impacted PASMC [Ca2+]i. We also examined the roles of Na+/Ca2+ exchange (NCX) and Na+/H+ exchange (NHE) in mediating the elevated basal [Ca2+]i and Ca2+-dependent changes in PASMC pHi. Bepridil, dichlorobenzamil, and KB-R7943, which are NCX inhibitors, decreased resting [Ca2+]i and pHi only in hypoxic PASMCs and blocked the changes in pHi induced by altering [Ca2+]i. Exposure to ethyl isopropyl amiloride, an NHE inhibitor, decreased resting pHi and prevented changes in pHi due to changing [Ca2+]i. Our findings indicate that, during CH, the elevation in basal [Ca2+]i may contribute to the alkaline shift in pHi in PASMCs, likely via mechanisms involving reverse-mode NCX and NHE. PMID:27076907

Clinical utility of the Prostate Health Index (phi) for biopsy decision management in a large group urology practice setting.

PubMed

White, Jay; Shenoy, B Vittal; Tutrone, Ronald F; Karsh, Lawrence I; Saltzstein, Daniel R; Harmon, William J; Broyles, Dennis L; Roddy, Tamra E; Lofaro, Lori R; Paoli, Carly J; Denham, Dwight; Reynolds, Mark A

2018-04-01

Deciding when to biopsy a man with non-suspicious DRE findings and tPSA in the 4-10 ng/ml range can be challenging, because two-thirds of such biopsies are typically found to be benign. The Prostate Health Index (phi) exhibits significantly improved diagnostic accuracy for prostate cancer detection when compared to tPSA and %fPSA, however only one published study to date has investigated its impact on biopsy decisions in clinical practice. An IRB approved observational study was conducted at four large urology group practices using a physician reported two-part questionnaire. Physician recommendations were recorded before and after receiving the phi test result. A historical control group was queried from each site's electronic medical records for eligible men who were seen by the same participating urologists prior to the implementation of the phi test in their practice. 506 men receiving a phi test were prospectively enrolled and 683 men were identified for the historical control group (without phi). Biopsy and pathological findings were also recorded for both groups. Men receiving a phi test showed a significant reduction in biopsy procedures performed when compared to the historical control group (36.4% vs. 60.3%, respectively, P < 0.0001). Based on questionnaire responses, the phi score impacted the physician's patient management plan in 73% of cases, including biopsy deferrals when the phi score was low, and decisions to perform biopsies when the phi score indicated an intermediate or high probability of prostate cancer (phi ≥36). phi testing significantly impacted the physician's biopsy decision for men with tPSA in the 4-10 ng/ml range and non-suspicious DRE findings. Appropriate utilization of phi resulted in a significant reduction in biopsy procedures performed compared to historical patients seen by the same participating urologists who would have met enrollment eligibility but did not receive a phi test.

Evaluation of PHI Hunter in Natural Language Processing Research

PubMed Central

Redd, Andrew; Pickard, Steve; Meystre, Stephane; Scehnet, Jeffrey; Bolton, Dan; Heavirland, Julia; Weaver, Allison Lynn; Hope, Carol; Garvin, Jennifer Hornung

2015-01-01

Objectives We introduce and evaluate a new, easily accessible tool using a common statistical analysis and business analytics software suite, SAS, which can be programmed to remove specific protected health information (PHI) from a text document. Removal of PHI is important because the quantity of text documents used for research with natural language processing (NLP) is increasing. When using existing data for research, an investigator must remove all PHI not needed for the research to comply with human subjects’ right to privacy. This process is similar, but not identical, to de-identification of a given set of documents. Materials and methods PHI Hunter removes PHI from free-form text. It is a set of rules to identify and remove patterns in text. PHI Hunter was applied to 473 Department of Veterans Affairs (VA) text documents randomly drawn from a research corpus stored as unstructured text in VA files. Results PHI Hunter performed well with PHI in the form of identification numbers such as Social Security numbers, phone numbers, and medical record numbers. The most commonly missed PHI items were names and locations. Incorrect removal of information occurred with text that looked like identification numbers. Discussion PHI Hunter fills a niche role that is related to but not equal to the role of de-identification tools. It gives research staff a tool to reasonably increase patient privacy. It performs well for highly sensitive PHI categories that are rarely used in research, but still shows possible areas for improvement. More development for patterns of text and linked demographic tables from electronic health records (EHRs) would improve the program so that more precise identifiable information can be removed. Conclusions PHI Hunter is an accessible tool that can flexibly remove PHI not needed for research. If it can be tailored to the specific data set via linked demographic tables, its performance will improve in each new document set. PMID:26807078

Nuclear phytochrome A signaling promotes phototropism in Arabidopsis.

PubMed

Kami, Chitose; Hersch, Micha; Trevisan, Martine; Genoud, Thierry; Hiltbrunner, Andreas; Bergmann, Sven; Fankhauser, Christian

2012-02-01

Phototropin photoreceptors (phot1 and phot2 in Arabidopsis thaliana) enable responses to directional light cues (e.g., positive phototropism in the hypocotyl). In Arabidopsis, phot1 is essential for phototropism in response to low light, a response that is also modulated by phytochrome A (phyA), representing a classical example of photoreceptor coaction. The molecular mechanisms underlying promotion of phototropism by phyA remain unclear. Most phyA responses require nuclear accumulation of the photoreceptor, but interestingly, it has been proposed that cytosolic phyA promotes phototropism. By comparing the kinetics of phototropism in seedlings with different subcellular localizations of phyA, we show that nuclear phyA accelerates the phototropic response, whereas in the fhy1 fhl mutant, in which phyA remains in the cytosol, phototropic bending is slower than in the wild type. Consistent with this data, we find that transcription factors needed for full phyA responses are needed for normal phototropism. Moreover, we show that phyA is the primary photoreceptor promoting the expression of phototropism regulators in low light (e.g., PHYTOCHROME KINASE SUBSTRATE1 [PKS1] and ROOT PHOTO TROPISM2 [RPT2]). Although phyA remains cytosolic in fhy1 fhl, induction of PKS1 and RPT2 expression still occurs in fhy1 fhl, indicating that a low level of nuclear phyA signaling is still present in fhy1 fhl.

Nuclear Phytochrome A Signaling Promotes Phototropism in Arabidopsis[W][OA

PubMed Central

Kami, Chitose; Hersch, Micha; Trevisan, Martine; Genoud, Thierry; Hiltbrunner, Andreas; Bergmann, Sven; Fankhauser, Christian

2012-01-01

Phototropin photoreceptors (phot1 and phot2 in Arabidopsis thaliana) enable responses to directional light cues (e.g., positive phototropism in the hypocotyl). In Arabidopsis, phot1 is essential for phototropism in response to low light, a response that is also modulated by phytochrome A (phyA), representing a classical example of photoreceptor coaction. The molecular mechanisms underlying promotion of phototropism by phyA remain unclear. Most phyA responses require nuclear accumulation of the photoreceptor, but interestingly, it has been proposed that cytosolic phyA promotes phototropism. By comparing the kinetics of phototropism in seedlings with different subcellular localizations of phyA, we show that nuclear phyA accelerates the phototropic response, whereas in the fhy1 fhl mutant, in which phyA remains in the cytosol, phototropic bending is slower than in the wild type. Consistent with this data, we find that transcription factors needed for full phyA responses are needed for normal phototropism. Moreover, we show that phyA is the primary photoreceptor promoting the expression of phototropism regulators in low light (e.g., PHYTOCHROME KINASE SUBSTRATE1 [PKS1] and ROOT PHOTO TROPISM2 [RPT2]). Although phyA remains cytosolic in fhy1 fhl, induction of PKS1 and RPT2 expression still occurs in fhy1 fhl, indicating that a low level of nuclear phyA signaling is still present in fhy1 fhl. PMID:22374392

How does gravity save or kill Q-balls?

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

Tamaki, Takashi; Sakai, Nobuyuki; Department of Education, Yamagata University, Yamagata 990-8560

2011-02-15

We explore stability of gravitating Q-balls with potential V{sub 4}({phi})=(m{sup 2}/2){phi}{sup 2}-{lambda}{phi}{sup 4}+({phi}{sup 6}/M{sup 2}) via catastrophe theory, as an extension of our previous work on Q-balls with potential V{sub 3}({phi})=(m{sup 2}/2){phi}{sup 2}-{mu}{phi}{sup 3}+{lambda}{phi}{sup 4}. In flat spacetime Q-balls with V{sub 4} in the thick-wall limit are unstable and there is a minimum charge Q{sub min}, where Q-balls with Q

Implications of Gamma-Ray Transparency Constraints in Blazars: Minimum Distances and Gamma-Ray Collimation

NASA Technical Reports Server (NTRS)

Becker, Peter A.; Kafatos, Menas

1995-01-01

We develop a general expression for the gamma - gamma absorption coefficient, alpha(sub gamma(gamma)) for gamma-rays propagating in an arbitrary direction at an arbitrary point in space above an X-ray-emitting accretion disk. The X-ray intensity is assumed to vary as a power law in energy and radius between the outer disk radius, R(sub 0), and the inner radius, R(sub ms) which is the radius of marginal stability for a Schwarzschild black hole. We use our result for alpha(sub gamma(gamma)) to calculate the gamma - gamma optical depth, tau(sub gamma(gamma)) for gamma - rays created at height z and propagating at angle Phi relative to the disk axis, and we show that for Phi = 0 and z greater than or approx equal to R(sub 0), tau(sub gamma(gamma)) proportional to Epsilon(sup alpha)z(sup -2(alpha) - 3), where alpha is the X-ray spectral index and Epsilon is the gamma - ray energy. As an application, we use our formalism to compute the minimum distance between the central black hole and the site of production of the gamma-rays detected by EGRET during the 1991 June flare of 3C 279. In order to obtain an upper limit, we assume that all of the X-rays observed contemporaneously by Ginga were emitted by the disk. Our results suggest that the observed gamma - rays may have originated within less than or approx equal to 45 GM/sq c from a black hole of mass greater than or approx equal to 10(exp 9) solar mass, perhaps in active plasma located above the central funnel of the accretion disk. This raises the possibility of establishing a direct connection between the production of the observed gamma - rays and the accretion of material onto the black hole. We also consider the variation of the optical depth as a function of the angle of propagation Phi. Our results indicate that the "focusing" of the gamma - rays along the disk axis due to pair production is strong enough to explain the observed degree of alignment in blazar sources. If the gamma - rays are produced isotropically in gamma - ray blazars, then these objects should appear as bright MeV sources when viewed along off-axis lines of sight.

Interaction between physostigmine and soman on brain regional cholinesterase activity and /sup 3/H-physostigmine distribution

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

Hallak, M.E.; Woodruff, E.; Giacobini, E.

1986-03-05

Physostigmine (Phy) concentrations (as radioactivity) were studied in various brain areas after /sup 3/H-Phy administration as a function of time. Five min after 500 ..mu..g/kg i.m., cortex (CX) and total brain showed similar concentrations (370 ng/g) which were 50-90% higher than those of other brain regions (striatum, hippocampus, and medulla oblongata). Soman did not affect Phy levels in whole brain after pretreatment with Phy (100 or 500 ..mu..g/kg), however, the regional distribution of Phy was altered by soman as was ChE inhibition. A significant increase in Phy concentration was seen in HC (22 and 45% at 5 and 30 min,more » respectively) and CX (21% at 30 min). ChE activity in total brain was 12, 30, and 24% (5, 15 and 30 min after soman administration) lower than after Phy alone. If the pretreatment dose of Phy was increased to 500 ..mu..g/kg /sup 3/H-Phy, ChE activity was further reduced to 4, 13 and 19%. This might indicate that higher doses of Phy provide more protection of the enzyme from soman than lower doses. The protective role of Phy seen in total brain was not consistent for all brain regions. Soman alone produced a 95% ChE inhibition and there were no differences in its effect between total brain or brain areas. Pretreatment of the rat with Phy produced a protective effect upon ChE activity up to 30 min. However, no protective effect on survival was observed.« less

Phytochromes play a role in phototropism and gravitropism in Arabidopsis roots.

PubMed

Correll, Melanie J; Coveney, Katrina M; Raines, Steven V; Mullen, Jack L; Hangarter, Roger P; Kiss, John Z

2003-01-01

Phototropism as well as gravitropism plays a role in the oriented growth of roots in flowering plants. In blue or white light, roots exhibit negative phototropism, but red light induces positive phototropism in Arabidopsis roots. Phytochrome A (phyA) and phyB mediate the positive red-light-based photoresponse in roots since single mutants (and the double phyAB mutant) were severely impaired in this response. In blue-light-based negative phototropism, phyA and phyAB (but not phyB) were inhibited in the response relative to the WT. In root gravitropism, phyB and phyAB (but not phyA) were inhibited in the response compared to the WT. The differences observed in tropistic responses were not due to growth limitations since the growth rates among all the mutants tested were not significantly different from that of the WT. Thus, our study shows that the blue-light and red-light systems interact in roots and that phytochrome plays a key role in plant development by integrating multiple environmental stimuli. c2003 COSPAR. Published by Elsevier Ltd. All rights reserved.

Phytochromes play a role in phototropism and gravitropism in Arabidopsis roots

NASA Technical Reports Server (NTRS)

Correll, Melanie J.; Coveney, Katrina M.; Raines, Steven V.; Mullen, Jack L.; Hangarter, Roger P.; Kiss, John Z.

2003-01-01

Phototropism as well as gravitropism plays a role in the oriented growth of roots in flowering plants. In blue or white light, roots exhibit negative phototropism, but red light induces positive phototropism in Arabidopsis roots. Phytochrome A (phyA) and phyB mediate the positive red-light-based photoresponse in roots since single mutants (and the double phyAB mutant) were severely impaired in this response. In blue-light-based negative phototropism, phyA and phyAB (but not phyB) were inhibited in the response relative to the WT. In root gravitropism, phyB and phyAB (but not phyA) were inhibited in the response compared to the WT. The differences observed in tropistic responses were not due to growth limitations since the growth rates among all the mutants tested were not significantly different from that of the WT. Thus, our study shows that the blue-light and red-light systems interact in roots and that phytochrome plays a key role in plant development by integrating multiple environmental stimuli. c2003 COSPAR. Published by Elsevier Ltd. All rights reserved.

Sequential and coordinated action of phytochromes A and B during Arabidopsis stem growth revealed by kinetic analysis

NASA Technical Reports Server (NTRS)

Parks, B. M.; Spalding, E. P.; Evans, M. L. (Principal Investigator)

1999-01-01

Photoreceptor proteins of the phytochrome family mediate light-induced inhibition of stem (hypocotyl) elongation during the development of photoautotrophy in seedlings. Analyses of overt mutant phenotypes have established the importance of phytochromes A and B (phyA and phyB) in this developmental process, but kinetic information that would augment emerging molecular models of phytochrome signal transduction is absent. We have addressed this deficiency by genetically dissecting phytochrome-response kinetics, after having solved the technical issues that previously limited growth studies of small Arabidopsis seedlings. We show here, with resolution on the order of minutes, that phyA initiated hypocotyl growth inhibition upon the onset of continuous red light. This primary contribution of phyA began to decrease after 3 hr of irradiation, the same time at which immunochemically detectable phyA disappeared and an exclusively phyB-dependent phase of inhibition began. The sequential and coordinated actions of phyA and phyB in red light were not observed in far-red light, which inhibited growth persistently through an exclusively phyA-mediated pathway.

Theory of flux cutting and flux transport at the critical current of a type-II superconducting cylindrical wire

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

Clem, John R.

2011-02-17

I introduce a critical-state theory incorporating both flux cutting and flux transport to calculate the magnetic-field and current-density distributions inside a type-II superconducting cylinder at its critical current in a longitudinal applied magnetic field. The theory is an extension of the elliptic critical-state model introduced by Romero-Salazar and Perez-Rodriguez. The vortex dynamics depend in detail on two nonlinear effective resistivities for flux cutting ({rho}{parallel}) and flux flow ({rho}{perpendicular}), and their ratio r = {rho}{parallel}/{rho}{perpendicular}. When r < 1, the low relative efficiency of flux cutting in reducing the magnitude of the internal magnetic-flux density leads to a paramagnetic longitudinal magneticmore » moment. As a model for understanding the experimentally observed interrelationship between the critical currents for flux cutting and depinning, I calculate the forces on a helical vortex arc stretched between two pinning centers when the vortex is subjected to a current density of arbitrary angle {phi}. Simultaneous initiation of flux cutting and flux transport occurs at the critical current density J{sub c}({phi}) that makes the vortex arc unstable.« less

Intracellular pH Regulation in Cultured Astrocytes from Rat Hippocampus

PubMed Central

Bevensee, Mark O.; Weed, Regina A.; Boron, Walter F.

1997-01-01

We studied the regulation of intracellular pH (pHi) in single cultured astrocytes passaged once from the hippocampus of the rat, using the dye 2′,7′-biscarboxyethyl-5,6-carboxyfluorescein (BCECF) to monitor pHi. Intrinsic buffering power (βI) was 10.5 mM (pH unit)−1 at pHi 7.0, and decreased linearly with pHi; the best-fit line to the data had a slope of −10.0 mM (pH unit)−2. In the absence of HCO3 −, pHi recovery from an acid load was mediated predominantly by a Na-H exchanger because the recovery was inhibited 88% by amiloride and 79% by ethylisopropylamiloride (EIPA) at pHi 6.05. The ethylisopropylamiloride-sensitive component of acid extrusion fell linearly with pHi. Acid extrusion was inhibited 68% (pHi 6.23) by substituting Li+ for Na+ in the bath solution. Switching from a CO2/HCO3 −-free to a CO2/HCO3 −-containing bath solution caused mean steady state pHi to increase from 6.82 to 6.90, due to a Na+-driven HCO3 − transporter. The HCO3 −-induced pHi increase was unaffected by amiloride, but was inhibited 75% (pHi 6.85) by 400 μM 4,4′-diisothiocyanatostilbene-2,2′-disulfonic acid (DIDS), and 65% (pHi 6.55–6.75) by pretreating astrocytes for up to ∼6.3 h with 400 μM 4-acetamide-4′-isothiocyanatostilbene-2,2′-disulfonic acid (SITS). The CO2/HCO3 −-induced pHi increase was blocked when external Na+ was replaced with N-methyl-d-glucammonium (NMDG+). In the presence of HCO3 −, the Na+-driven HCO3 − transporter contributed to the pHi recovery from an acid load. For example, HCO3 − shifted the plot of acid-extrusion rate vs. pHi by 0.15–0.3 pH units in the alkaline direction. Also, with Na-H exchange inhibited by amiloride, HCO3 − increased acid extrusion 3.8-fold (pHi 6.20). When astrocytes were acid loaded in amiloride, with Li+ as the major cation, HCO3 − failed to elicit a substantial increase in pHi. Thus, Li+ does not appear to substitute well for Na+ on the HCO3 − transporter. We conclude that an amiloride-sensitive Na-H exchanger and a Na+-driven HCO3 − transporter are the predominant acid extruders in astrocytes. PMID:9379175

76 FR 63342 - Petition for Exemption; Summary of Petition Received

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-12

...-1039. Petitioner: PHI, Inc. Section of 14 CFR Affected: Sec. 91.9(a). Description of Relief Sought: PHI, Inc. (PHI), requests an exemption from 91.9(a) to allow PHI to operate S-92A helicopters in accordance...

Intracellular pH change does not accompany egg activation in the mouse.

PubMed

Phillips, K P; Baltz, J M

1996-09-01

In the sea urchin, some other marine invertebrates, and the frog, Xenopus, egg activation at fertilization is accompanied by an increase in intracellular pH (pHi). We measured pHi in germinal vesicle (GV)-intact mouse oocytes, ovulated eggs, and in vivo fertilized zygotes using the pH indicator dye, SNARF-1. The mean pH, was 6.96 +/- 0.004 (+/- SEM) in GV-intact oocytes, 7.00 +/- 0.01 in ovulated, unfertilized eggs, and 7.02 +/- 0.01 in fertilized zygotes, indicating no sustained changes in pHi after germinal vesicle breakdown (GVBD) or fertilization. To examine whether transient changes in pHi occur shortly after egg activation, mouse eggs were parthenogenetically activated by 7% ethanol in phosphate buffered saline (PBS); no significant change in pHi followed ethanol activation. Since increased Na+/H+ antiporter activity is responsible for pHi increase in the sea urchin, pHi was measured in the absence of added bicarbonate or CO2 (a condition under which the antiporter would be the only major pHi regulatory mechanism able to operate, since the others were bicarbonate-dependent) in GV-intact oocytes, ovulated eggs, and in vivo fertilized zygotes to determine whether a Na+/H+ antiporter was activated. There was no physiologically significant difference in pHi after GVBD or fertilization, when pHi was measured in bicarbonate-free medium, nor any change upon parthenogenetic activation. Thus, a change in pHi is not a feature of egg activation in the mouse.

[Application study on PHI and 16PF and SCL-90 for freshman's psychology inspection].

PubMed

Niu, Peng

2009-07-01

To explore the effect of application of the measurement table of PHI and 16PF and SCL-90 for freshmen psychology inspection. The measurement tables of PHI and 16PF for psychology inspection of freshmen of 2004-2007 years were used to sift crisis intervention objects. Continuous four years test showed certain stability, in addition to excited factors,the scores of Freshmen's PHI factors were more lower than normal. The incidence rates of mental problems screened by PHI table were very low and 3-5 serious-mental-problem students weren't detected. The problem can be resolved by the application of PHI combined with 16PF through remesuring the suspected cases by SCL-90. The combinative application of PHI, 16PF and SCL-90 would be better.

Molecular characterization of a genomic region in a Lactococcus bacteriophage that is involved in its sensitivity to the phage defense mechanism AbiA.

PubMed

Dinsmore, P K; Klaenhammer, T R

1997-05-01

A spontaneous mutant of the lactococcal phage phi31 that is insensitive to the phage defense mechanism AbiA was characterized in an effort to identify the phage factor(s) involved in sensitivity of phi31 to AbiA. A point mutation was localized in the genome of the AbiA-insensitive phage (phi31A) by heteroduplex analysis of a 9-kb region. The mutation (G to T) was within a 738-bp open reading frame (ORF245) and resulted in an arginine-to-leucine change in the predicted amino acid sequence of the protein. The mutant phi31A-ORF245 reduced the sensitivity of phi31 to AbiA when present in trans, indicating that the mutation in ORF245 is responsible for the AbiA insensitivity of phi31A. Transcription of ORF245 occurs early in the phage infection cycles of phi31 and phi31A and is unaffected by AbiA. Expansion of the phi31 sequence revealed ORF169 (immediately upstream of ORF245) and ORF71 (which ends 84 bp upstream of ORF169). Two inverted repeats lie within the 84-bp region between ORF71 and ORF169. Sequence analysis of an independently isolated AbiA-insensitive phage, phi31B, identified a mutation (G to A) in one of the inverted repeats. A 118-bp fragment from phi31, encompassing the 84-bp region between ORF71 and ORF169, eliminates AbiA activity against phi31 when present in trans, establishing a relationship between AbiA and this fragment. The study of this region of phage phi31 has identified an open reading frame (ORF245) and a 118-bp DNA fragment that interact with AbiA and are likely to be involved in the sensitivity of this phage to AbiA.

[Improvement of Phi bodies stain and its clinical significance].

PubMed

Gong, Xu-Bo; Lu, Xing-Guo; Yan, Li-Juan; Xiao, Xi-Bin; Wu, Dong; Xu, Gen-Bo; Zhang, Xiao-Hong; Zhao, Xiao-Ying

2009-02-01

The aim of this study was to improve the dyeing method of hydroperoxidase (HPO), to analyze the morphologic features of Phi bodies and to evaluate the clinical application of this method. 128 bone marrow or peripheral blood smears from patients with myeloid and lymphoid malignancies were stained by improved HPO staining. The Phi bodies were observed with detection rate of Phi bodies in different leukemias. 69 acute myeloid leukemia (AML) specimens were chosen randomly, the positive rate and the number of Phi bodies between the improved HPO and POX stain based on the same substrate of 3, 3'diaminobenzidine were compared. The results showed that the shape of bundle-like Phi bodies was variable, long or short. while the nubbly Phi bodies often presented oval and smooth. Club-like Phi bodies were found in M(3). The detection rates of bundle-like Phi bodies in AML M(1)-M(5) were 42.9% (6/14), 83.3% (15/18), 92.0% (23/25), 52.3% (11/21), 33.3% (5/15) respectively, and those of nubbly Phi bodies were 28.6% (4/14), 66.7% (12/18), 11.1% (3/25), 33.3% (7/21), 20.0% (3/15) respectively. The detection rate of bundle-like Phi bodies in M(3) was significantly higher than that in (M(1) + M(2)) or (M(4) + M(5)) groups. The detection rate of nubbly Phi bodies in (M(1) + M(2)) group was higher than that in M(3) group. In conclusion, after improvement of staining method, the HPO stain becomes simple, the detection rate of Phi bodies is higher than that by the previous method, the positive granules are more obvious, and the results become stable. This improved method plays an important role in differentiating AML from ALL, subtyping AML, and evaluating the therapeutic results.

The role and uptake of private health insurance in different health care systems: are there lessons for developing countries?

PubMed

Odeyemi, Isaac Ao; Nixon, John

2013-01-01

Social and national health insurance schemes are being introduced in many developing countries in moving towards universal health care. However, gaps in coverage are common and can only be met by out-of-pocket payments, general taxation, or private health insurance (PHI). This study provides an overview of PHI in different health care systems and discusses factors that affect its uptake and equity. A representative sample of countries was identified (United States, United Kingdom, The Netherlands, France, Australia, and Latvia) that illustrates the principal forms and roles of PHI. Literature describing each country's health care system was used to summarize how PHI is utilized and the factors that affect its uptake and equity. In the United States, PHI is a primary source of funding in conjunction with tax-based programs to support vulnerable groups; in the UK and Latvia, PHI is used in a supplementary role to universal tax-based systems; in France and Latvia, complementary PHI is utilized to cover gaps in public funding; in The Netherlands, PHI is supplementary to statutory private and social health insurance; in Australia, the government incentivizes the uptake of complementary PHI through tax rebates and penalties. The uptake of PHI is influenced by age, income, education, health care system typology, and the incentives or disincentives applied by governments. The effect on equity can either be positive or negative depending on the type of PHI adopted and its role within the wider health care system. PHI has many manifestations depending on the type of health care system used and its role within that system. This study has illustrated its common applications and the factors that affect its uptake and equity in different health care systems. The results are anticipated to be helpful in informing how developing countries may utilize PHI to meet the aim of achieving universal health care.

Density perturbations in general modified gravitational theories

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

De Felice, Antonio; Tsujikawa, Shinji; Mukohyama, Shinji

2010-07-15

We derive the equations of linear cosmological perturbations for the general Lagrangian density f(R,{phi},X)/2+L{sub c}, where R is a Ricci scalar, {phi} is a scalar field, and X=-{partial_derivative}{sup {mu}{phi}{partial_derivative}}{sub {mu}{phi}/}2 is a field kinetic energy. We take into account a nonlinear self-interaction term L{sub c}={xi}({phi}) {open_square}{phi}({partial_derivative}{sup {mu}{phi}{partial_derivative}}{sub {mu}{phi}}) recently studied in the context of ''Galileon'' cosmology, which keeps the field equations at second order. Taking into account a scalar-field mass explicitly, the equations of matter density perturbations and gravitational potentials are obtained under a quasistatic approximation on subhorizon scales. We also derive conditions for the avoidance of ghosts and Laplacianmore » instabilities associated with propagation speeds. Our analysis includes most of modified gravity models of dark energy proposed in literature; and thus it is convenient to test the viability of such models from both theoretical and observational points of view.« less

P2P Watch: Personal Health Information Detection in Peer-to-Peer File-Sharing Networks

PubMed Central

El Emam, Khaled; Arbuckle, Luk; Neri, Emilio; Rose, Sean; Jonker, Elizabeth

2012-01-01

Background Users of peer-to-peer (P2P) file-sharing networks risk the inadvertent disclosure of personal health information (PHI). In addition to potentially causing harm to the affected individuals, this can heighten the risk of data breaches for health information custodians. Automated PHI detection tools that crawl the P2P networks can identify PHI and alert custodians. While there has been previous work on the detection of personal information in electronic health records, there has been a dearth of research on the automated detection of PHI in heterogeneous user files. Objective To build a system that accurately detects PHI in files sent through P2P file-sharing networks. The system, which we call P2P Watch, uses a pipeline of text processing techniques to automatically detect PHI in files exchanged through P2P networks. P2P Watch processes unstructured texts regardless of the file format, document type, and content. Methods We developed P2P Watch to extract and analyze PHI in text files exchanged on P2P networks. We labeled texts as PHI if they contained identifiable information about a person (eg, name and date of birth) and specifics of the person’s health (eg, diagnosis, prescriptions, and medical procedures). We evaluated the system’s performance through its efficiency and effectiveness on 3924 files gathered from three P2P networks. Results P2P Watch successfully processed 3924 P2P files of unknown content. A manual examination of 1578 randomly selected files marked by the system as non-PHI confirmed that these files indeed did not contain PHI, making the false-negative detection rate equal to zero. Of 57 files marked by the system as PHI, all contained both personally identifiable information and health information: 11 files were PHI disclosures, and 46 files contained organizational materials such as unfilled insurance forms, job applications by medical professionals, and essays. Conclusions PHI can be successfully detected in free-form textual files exchanged through P2P networks. Once the files with PHI are detected, affected individuals or data custodians can be alerted to take remedial action. PMID:22776692

P2P watch: personal health information detection in peer-to-peer file-sharing networks.

PubMed

Sokolova, Marina; El Emam, Khaled; Arbuckle, Luk; Neri, Emilio; Rose, Sean; Jonker, Elizabeth

2012-07-09

Users of peer-to-peer (P2P) file-sharing networks risk the inadvertent disclosure of personal health information (PHI). In addition to potentially causing harm to the affected individuals, this can heighten the risk of data breaches for health information custodians. Automated PHI detection tools that crawl the P2P networks can identify PHI and alert custodians. While there has been previous work on the detection of personal information in electronic health records, there has been a dearth of research on the automated detection of PHI in heterogeneous user files. To build a system that accurately detects PHI in files sent through P2P file-sharing networks. The system, which we call P2P Watch, uses a pipeline of text processing techniques to automatically detect PHI in files exchanged through P2P networks. P2P Watch processes unstructured texts regardless of the file format, document type, and content. We developed P2P Watch to extract and analyze PHI in text files exchanged on P2P networks. We labeled texts as PHI if they contained identifiable information about a person (eg, name and date of birth) and specifics of the person's health (eg, diagnosis, prescriptions, and medical procedures). We evaluated the system's performance through its efficiency and effectiveness on 3924 files gathered from three P2P networks. P2P Watch successfully processed 3924 P2P files of unknown content. A manual examination of 1578 randomly selected files marked by the system as non-PHI confirmed that these files indeed did not contain PHI, making the false-negative detection rate equal to zero. Of 57 files marked by the system as PHI, all contained both personally identifiable information and health information: 11 files were PHI disclosures, and 46 files contained organizational materials such as unfilled insurance forms, job applications by medical professionals, and essays. PHI can be successfully detected in free-form textual files exchanged through P2P networks. Once the files with PHI are detected, affected individuals or data custodians can be alerted to take remedial action.

Tonometry revisited: perfusion-related, metabolic, and respiratory components of gastric mucosal acidosis in acute cardiorespiratory failure.

PubMed

Jakob, Stephan M; Parviainen, Ilkka; Ruokonen, Esko; Kogan, Alexander; Takala, Jukka

2008-05-01

Mucosal pH (pHi) is influenced by local perfusion and metabolism (mucosal-arterial pCO2 gradient, DeltapCO2), systemic metabolic acidosis (arterial bicarbonate), and respiration (arterial pCO2). We determined these components of pHi and their relation to outcome during the first 24 h of intensive care. We studied 103 patients with acute respiratory or circulatory failure (age, 63+/-2 [mean+/-SEM]; Acute Physiology and Chronic Health Evaluation II score, 20+/-1; Sequential Organ Failure Assessment score, 8+/-0). pHi, and the effects of bicarbonate and arterial and mucosal pCO2 on pHi, were assessed at admission, 6, and 24 h. pHi was reduced (at admission, 7.27+/-0.01) due to low arterial bicarbonate and increased DeltapCO2. Low pHi (<7.32) at admission (n=58; mortality, 29% vs. 13% in those with pHi>or=7.32 at admission; P=0.061) was associated with an increased DeltapCO2 in 59% of patients (mortality, 47% vs. 4% for patients with low pHi and normal DeltapCO2; P=0.0003). An increased versus normal DeltapCO2, regardless of pHi, was associated with increased mortality at admission (51% vs. 5%; P<0.0001; n=39) and at 6 h (34% vs. 13%; P=0.016; n=45). A delayed normalization or persistently low pHi (n=47) or high DeltapCO2 (n=25) was associated with high mortality (low pHi [34%] vs. high DeltapCO2 [60%]; P=0.046). In nonsurvivors, hypocapnia increased pHi at baseline, 6, and 24 h (all P

Symplectic approach to calculation of magnetic field line trajectories in physical space with realistic magnetic geometry in divertor tokamaks

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

Punjabi, Alkesh; Ali, Halima

A new approach to integration of magnetic field lines in divertor tokamaks is proposed. In this approach, an analytic equilibrium generating function (EGF) is constructed in natural canonical coordinates ({psi},{theta}) from experimental data from a Grad-Shafranov equilibrium solver for a tokamak. {psi} is the toroidal magnetic flux and {theta} is the poloidal angle. Natural canonical coordinates ({psi},{theta},{phi}) can be transformed to physical position (R,Z,{phi}) using a canonical transformation. (R,Z,{phi}) are cylindrical coordinates. Another canonical transformation is used to construct a symplectic map for integration of magnetic field lines. Trajectories of field lines calculated from this symplectic map in natural canonicalmore » coordinates can be transformed to trajectories in real physical space. Unlike in magnetic coordinates [O. Kerwin, A. Punjabi, and H. Ali, Phys. Plasmas 15, 072504 (2008)], the symplectic map in natural canonical coordinates can integrate trajectories across the separatrix surface, and at the same time, give trajectories in physical space. Unlike symplectic maps in physical coordinates (x,y) or (R,Z), the continuous analog of a symplectic map in natural canonical coordinates does not distort trajectories in toroidal planes intervening the discrete map. This approach is applied to the DIII-D tokamak [J. L. Luxon and L. E. Davis, Fusion Technol. 8, 441 (1985)]. The EGF for the DIII-D gives quite an accurate representation of equilibrium magnetic surfaces close to the separatrix surface. This new approach is applied to demonstrate the sensitivity of stochastic broadening using a set of perturbations that generically approximate the size of the field errors and statistical topological noise expected in a poloidally diverted tokamak. Plans for future application of this approach are discussed.« less

The application of A.C. impedance spectroscopy on the durability of hydrated cement paste subjected to various environmental conditions

NASA Astrophysics Data System (ADS)

Perron, Stacey

Harsh Canadian winters cause many problems in reinforced concrete structures due to damaging freezing-thawing cycles which is exacerbated by the heavy use of de-icing salts on roadways. Evaluation of concrete durability with current ASTM methods may give unreliable results and are destructive to the structure. A relatively new and novel approach to evaluating the durability of concrete uses A. C. Impedance Spectroscopy (ACIS). Hydrated cement paste (hcp), mortar, brick and vycor glass were evaluated using ACIS during drying-rewetting and freezing-thawing cycles. Thermal mechanical analysis (TMA), and differential scanning calorimetry (DSC) tests were also conducted and used as references. Results indicate that ACIS can be used to successfully evaluate the pore structure of hcp. The results from the drying-rewetting cycles are consistent with the pore coarsening theory. ACIS revealed pore structure changes consistent with the mechanical strains and pore solution chemistry. Increased pore continuity with each drying-rewetting cycle was indicated by a reduction in sample resistance. Unique tests were conducted on hydrated cement paste, mortar, brick and vycor glass that measured the ACIS and mechanical strains simultaneously while undergoing temperature changes. The temperature was lowered from 5°C to -80°C and then raised to +20°C. The ACIS results indicate that durability of the material can be assessed using the parameters R, material resistance, and phi, indicative of the frequency dispersion angle. The resistance on freezing values correlates with the amount of pore water freezing. The phi values on freezing are representative of the pore size distribution of the test sample. Resistance and phi data from freezing-thawing tests can be analyzed to assess durability of the sample. A material that is durable to freezing-thawing cycles can be described as having a high resistance at room temperature, a low freezing resistance and small changes in phi. Results were consistent among all the materials tested. Freezing-thawing tests were also conducted on specimens resaturated with salt solutions (5%, 10%, 15%). The results of these tests indicated a lower incipient freezing temperature, increase in pore blockage temperatures, and increased mobility of the pore water during freezing (increase in the change to phi). A series of test were conducted to evaluate the electrode polarization effects associated with the permittivity values at low frequencies. Teflon sheets were used to minimize the electrode polarization effects. It is shown that electrode polarization effects dominate over bulk polarization effects. Effects vary with the porosity of the material.

Some demographic issues affecting private health insurance.

PubMed

Hanning, Brian

2004-01-01

There will be significant changes in the demography of persons with Private Health Insurance (PHI). Two methods of projecting PHI coverage are discussed in this paper. The first assumes the only factors affecting PHI coverage are demographic change and mortality and facilitates comparisons between actual and projected PHI coverage. The second projects the percentage of the population insured in each five year age cohort, and makes allowance for changes in PHI coverage due to all factors. Demographic change will increase Registered Health Benefit Organization (RHBO) premiums by 1.7% per annum. The role of these projections in analysing the effect of future premium increases on PHI retention rates is also discussed.

Independent regulation of reovirus membrane penetration and apoptosis by the mu1 phi domain.

PubMed

Danthi, Pranav; Coffey, Caroline M; Parker, John S L; Abel, Ty W; Dermody, Terence S

2008-12-01

Apoptosis plays an important role in the pathogenesis of reovirus encephalitis. Reovirus outer-capsid protein mu1, which functions to penetrate host cell membranes during viral entry, is the primary regulator of apoptosis following reovirus infection. Ectopic expression of full-length and truncated forms of mu1 indicates that the mu1 phi domain is sufficient to elicit a cell death response. To evaluate the contribution of the mu1 phi domain to the induction of apoptosis following reovirus infection, phi mutant viruses were generated by reverse genetics and analyzed for the capacity to penetrate cell membranes and elicit apoptosis. We found that mutations in phi diminish reovirus membrane penetration efficiency by preventing conformational changes that lead to generation of key reovirus entry intermediates. Independent of effects on membrane penetration, amino acid substitutions in phi affect the apoptotic potential of reovirus, suggesting that phi initiates apoptosis subsequent to cytosolic delivery. In comparison to wild-type virus, apoptosis-defective phi mutant viruses display diminished neurovirulence following intracranial inoculation of newborn mice. These results indicate that the phi domain of mu1 plays an important regulatory role in reovirus-induced apoptosis and disease.

Phi is not beta, and why Wertheimer's discovery launched the Gestalt revolution.

PubMed

Steinman, R M; Pizlo, Z; Pizlo, F J

2000-01-01

Max Wertheimer (1880-1943), the founder of the Gestalt School of Psychology, published a monograph on the perception of apparent motion in 1912, which initiated a new direction for a great deal of subsequent perceptual theory and research. Wertheimer's research was inspired by a serendipitous observation of a pure apparent movement, which he called the phi-phenomenon to distinguish it from optimal apparent movement (beta), which resembles real movement. Wertheimer called his novel observation 'pure' because it was perceived in the absence of any object being seen to change its position in space. The phi-phenomenon, as well as the best conditions for seeing it, were not described clearly in this monograph, leading to considerable subsequent confusion about its appearance and occurrence. We review the history leading to the discovery of the phi-phenomenon, and then describe: (i) a likely source for the confusion evident in most contemporary research on the phi-phenomenon; (ii) the best conditions for seeing the phi-phenomenon; (iii) new conditions that provide a particularly vivid phi-phenomenon; and (iv) two lines of thought that may provide explanations of the phi-phenomenon and also distinguish phi from beta.

Self-reproduction in k-inflation

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

Helmer, Ferdinand; Winitzki, Sergei

2006-09-15

We study cosmological self-reproduction in models of inflation driven by a scalar field {phi} with a noncanonical kinetic term (k-inflation). We develop a general criterion for the existence of attractors and establish conditions selecting a class of k-inflation models that admit a unique attractor solution. We then consider quantum fluctuations on the attractor background. We show that the correlation length of the fluctuations is of order c{sub s}H{sup -1}, where c{sub s} is the speed of sound. By computing the magnitude of field fluctuations, we determine the coefficients of Fokker-Planck equations describing the probability distribution of the spatially averaged fieldmore » {phi}. The field fluctuations are generally large in the inflationary attractor regime; hence, eternal self-reproduction is a generic feature of k-inflation. This is established more formally by demonstrating the existence of stationary solutions of the relevant Fokker-Planck equations. We also show that there exists a (model-dependent) range {phi}{sub R}<{phi}<{phi}{sub max} within which large fluctuations are likely to drive the field towards the upper boundary {phi}={phi}{sub max}, where the semiclassical consideration breaks down. An exit from inflation into reheating without reaching {phi}{sub max} will occur almost surely (with probability 1) only if the initial value of {phi} is below {phi}{sub R}. In this way, strong self-reproduction effects constrain models of k-inflation.« less

The prostate health index PHI predicts oncological outcome and biochemical recurrence after radical prostatectomy - analysis in 437 patients

PubMed Central

Maxeiner, Andreas; Kilic, Ergin; Matalon, Julia; Friedersdorff, Frank; Miller, Kurt; Jung, Klaus; Stephan, Carsten; Busch, Jonas

2017-01-01

The purpose of this study was to investigate the Prostate-Health-Index (PHI) for pathological outcome prediction following radical prostatectomy and also for biochemical recurrence prediction in comparison to established parameters such as Gleason-score, pathological tumor stage, resection status (R0/1) and prostate-specific antigen (PSA). Out of a cohort of 460 cases with preoperative PHI-measurements (World Health Organization calibration: Beckman Coulter Access-2-Immunoassay) between 2001 and 2014, 437 patients with complete follow up data were included. From these 437 patients, 87 (19.9%) developed a biochemical recurrence. Patient characteristics were compared by using chi-square test. Predictors were analyzed by multivariate adjusted logistic and Cox regression. The median follow up for a biochemical recurrence was 65 (range 3-161) months. PHI, PSA, [-2]proPSA, PHI- and PSA-density performed as significant variables (p < 0.05) for cancer aggressiveness: Gleason-score <7 or ≥7 (ISUP grade 1 or ≥2) . Concerning pathological tumor stage discrimination and prediction, variables as PHI, PSA, %fPSA, [-2]proPSA, PHI- and PSA-density significantly discriminated between stages

The prostate health index PHI predicts oncological outcome and biochemical recurrence after radical prostatectomy - analysis in 437 patients.

PubMed

Maxeiner, Andreas; Kilic, Ergin; Matalon, Julia; Friedersdorff, Frank; Miller, Kurt; Jung, Klaus; Stephan, Carsten; Busch, Jonas

2017-10-03

The purpose of this study was to investigate the Prostate-Health-Index (PHI) for pathological outcome prediction following radical prostatectomy and also for biochemical recurrence prediction in comparison to established parameters such as Gleason-score, pathological tumor stage, resection status (R0/1) and prostate-specific antigen (PSA). Out of a cohort of 460 cases with preoperative PHI-measurements (World Health Organization calibration: Beckman Coulter Access-2-Immunoassay) between 2001 and 2014, 437 patients with complete follow up data were included. From these 437 patients, 87 (19.9%) developed a biochemical recurrence. Patient characteristics were compared by using chi-square test. Predictors were analyzed by multivariate adjusted logistic and Cox regression. The median follow up for a biochemical recurrence was 65 (range 3-161) months. PHI, PSA, [-2]proPSA, PHI- and PSA-density performed as significant variables (p < 0.05) for cancer aggressiveness: Gleason-score <7 or ≥7 (ISUP grade 1 or ≥2) . Concerning pathological tumor stage discrimination and prediction, variables as PHI, PSA, %fPSA, [-2]proPSA, PHI- and PSA-density significantly discriminated between stages

Comparison of limb kinematics between collected and lengthened (medium/extended) trot in two groups of dressage horses on two different surfaces.

PubMed

Walker, V A; Tranquille, C A; Newton, J R; Dyson, S J; Brandham, J; Northrop, A J; Murray, R C

2017-09-01

Dressage horses are often asked to work in lengthened paces during training and competition, but to date there is limited information about the biomechanics of dressage-specific paces. Preliminary work has shown increased fetlock extension in extended compared with collected paces, but further investigation of the kinematic differences between collected, medium and extended trot in dressage horses is warranted. Investigation of the effect of collected vs. medium/extended trot on limb kinematics of dressage horses. Prospective kinematic evaluation. Twenty clinically sound horses in active dressage training were used. Group 1: Ten young horses (≤6 years) were assessed at collected and medium trot and Group 2: Ten mature horses (≥9 years) were assessed at collected and extended trot. All horses were evaluated on two different surfaces. High speed motion capture (240 Hz) was used to determine kinematic variables. Fore- and hindlimb angles were measured at mid-stance. Descriptive statistics and mixed effect multilevel regression analyses were performed. Speed and stride length were reduced and stride duration increased at collected compared with medium/extended trot. Lengthened trot (medium/extended trot) was associated with increased fetlock extension in both the fore- and hindlimbs in both groups of horses. Changes were greater in mature horses compared with young horses. Shoulder and carpus angles were associated with forelimb fetlock angle. Hock angle was not significantly influenced by pace. Surface had no effect on fetlock or hock angles. Only 2D motion analysis was carried out. Results may have differed in horses with more extreme gait characteristics. Medium/extended trot increases extension of the fore- and hindlimb fetlock joints compared with collected trot in both young and mature dressage horses, respectively. © 2017 EVJ Ltd.

phiGENOME: an integrative navigation throughout bacteriophage genomes.

PubMed

Stano, Matej; Klucar, Lubos

2011-11-01

phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

DNA conformational change induced by the bacteriophage phi 29 connector.

PubMed Central

Valpuesta, J M; Serrano, M; Donate, L E; Herranz, L; Carrascosa, J L

1992-01-01

Translocation of viral DNA inwards and outwards of the capsid of double-stranded DNA bacteriophages occurs through the connector, a key viral structure that is known to interact with DNA. It is shown here that phage phi 29 connector binds both linear and circular double-stranded DNA. However, DNA-mediated protection of phi 29 connectors against Staphylococcus aureus endoprotease V8 digestion suggests that binding to linear DNA is more stable than to circular DNA. Endoprotease V8-protection assays also suggest that the length of the linear DNA required to produce a stable phi 29 connector-DNA interaction is, at least, twice longer than the phi 29 connector channel. This result is confirmed by experiments of phi 29 connector-protection of DNA against DNase I digestion. Furthermore, DNA circularization assays indicate that phi 29 connectors restrain negative supercoiling when bound to linear DNA. This DNA conformational change is not observed upon binding to circular DNA and it could reflect the existence of some left-handed DNA coiling or DNA untwisting inside of the phi 29 connector channel. Images PMID:1454519

Scaling of ion expansion energy with laser flux in moderate-Z plasmas produced by lasers

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

Gupta, P.D.; Goel, S.K.; Uppal, J.S.

1982-09-01

Ion expansion energy measurements in plasmas created by focusing 1-GW, 5-nsec Nd:glass laser on plane solid targets of polythene, carbon, and aluminum are reported. It is observed that the scaling of ion expansion energy with laser flux Phi varies between Phi/sup 0.28/ and Phi/sup 0.66/ for polythene, Phi/sup 0.28/ and Phi/sup 0.70/ for carbon, and Phi/sup 0.51/ and Phi/sup 0.44/ for aluminum in the flux range 5 x 10/sup 10/--5 x 10/sup 12/ W/cm/sup 2/ of our experiment. The scaling is either much slower or faster than a scaling of Phi/sup 4/9/ expected from a self-regulating model for plasmas createdmore » in the low flux range. It is shown that this behavior, as well as results of experiments on similar plasmas reported by other authors, can be explained when radiation losses and the energy spent in ionization are also considered in the self-regulating model.« less

Defining, Describing, and Categorizing Public Health Infrastructure Priorities for Tropical Cyclone, Flood, Storm, Tornado, and Tsunami-Related Disasters.

PubMed

Ryan, Benjamin J; Franklin, Richard C; Burkle, Frederick M; Watt, Kerrianne; Aitken, Peter; Smith, Erin C; Leggat, Peter

2016-08-01

The study aim was to undertake a qualitative research literature review to analyze available databases to define, describe, and categorize public health infrastructure (PHI) priorities for tropical cyclone, flood, storm, tornado, and tsunami-related disasters. Five electronic publication databases were searched to define, describe, or categorize PHI and discuss tropical cyclone, flood, storm, tornado, and tsunami-related disasters and their impact on PHI. The data were analyzed through aggregation of individual articles to create an overall data description. The data were grouped into PHI themes, which were then prioritized on the basis of degree of interdependency. Sixty-seven relevant articles were identified. PHI was categorized into 13 themes with a total of 158 descriptors. The highest priority PHI identified was workforce. This was followed by water, sanitation, equipment, communication, physical structure, power, governance, prevention, supplies, service, transport, and surveillance. This review identified workforce as the most important of the 13 thematic areas related to PHI and disasters. If its functionality fails, workforce has the greatest impact on the performance of health services. If addressed post-disaster, the remaining forms of PHI will then be progressively addressed. These findings are a step toward providing an evidence base to inform PHI priorities in the disaster setting. (Disaster Med Public Health Preparedness. 2016;10:598-610).

The occurrence of phi in dento-facial beauty of fine art from antiquity through the Renaissance.

PubMed

Wiener, R Constance; Wiener Pla, Regina M

2012-01-01

External beauty is a complex construct that influences lives and may be impacted by dentists. Beauty is not easily quantified, but one cited anthropometric of beauty is the ratio phi, the number 1.618033(...). This study examined phi as a measure of female frontal facial beauty in classic Western art, using pre- Renaissance (N = 30), and Renaissance (N = 30) artwork. Four horizontal and five vertical ratios were determined in the works of art, which were then compared with the phi ratio. All horizontal ratios for both pre-Renaissance and Renaissance artwork were similar to each other, but did not contain the phi ratio (P < 0.001). Nevertheless, all vertical ratios for pre-Renaissance and Renaissance art-work did contain the phi ratio within their confidence intervals with the exception of the vertical ratio, "intereye point to soft tissue menton/ intereye point to stomion", that was found to be less than phi in the Renaissance group. The study provides evidence of the presence of the phi ratio in vertical aspect of females in artwork from pre-Renaissance through the Renaissance demonstrating consistent temporal preferences. Therefore, the phi ratio seems to be an important consideration in altering vertical facial dimensions in full mouth rehabilitation and reconstructive orthognathic surgery involving females.

Cytoplasmic pH influences cytoplasmic calcium in MC3T3-E1 osteoblast cells

NASA Technical Reports Server (NTRS)

Lin, H. S.; Hughes-Fulford, M.; Kumegawa, M.; Pitts, A. C.; Snowdowne, K. W.

1993-01-01

We found that the cytoplasmic concentration of calcium (Cai) of MC3T3-E1 osteoblasts was influenced by the type of pH buffer we used in the perfusing medium, suggesting that intracellular pH (pHi) might influence Cai. To study this effect, the Cai and pHi were monitored as we applied various experimental conditions known to change pHi. Exposure to NH4Cl caused a transient increase in both pHi and Cai without a change in extracellular pH (pHo). Decreasing pHo and pHi by lowering the bicarbonate concentration of the medium decreased Cai, and increasing pHi by the removal of 5% CO2 increased Cai. Clamping pHi to known values with 10 microM nigericin, a potassium proton ionophore, also influenced Cai: acid pHi lowered Cai, whereas alkaline pHi increased it. The rise in Cai appears to be very sensitive to the extracellular concentration of calcium, suggesting the existence of a pH-sensitive calcium influx mechanism. We conclude that physiologic changes in pH could modulate Cai by controlling the influx of calcium ions and could change the time course of the Cai transient associated with hormonal activation.

RNA packaging device of double-stranded RNA bacteriophages, possibly as simple as hexamer of P4 protein.

PubMed

Kainov, Denis E; Pirttimaa, Markus; Tuma, Roman; Butcher, Sarah J; Thomas, George J; Bamford, Dennis H; Makeyev, Eugene V

2003-11-28

Genomes of complex viruses have been demonstrated, in many cases, to be packaged into preformed empty capsids (procapsids). This reaction is performed by molecular motors translocating nucleic acid against the concentration gradient at the expense of NTP hydrolysis. At present, the molecular mechanisms of packaging remain elusive due to the complex nature of packaging motors. In the case of the double-stranded RNA bacteriophage phi 6 from the Cystoviridae family, packaging of single-stranded genomic precursors requires a hexameric NTPase, P4. In the present study, the purified P4 proteins from two other cystoviruses, phi 8 and phi 13, were characterized and compared with phi 6 P4. All three proteins are hexameric, single-stranded RNA-stimulated NTPases with alpha/beta folds. Using a direct motor assay, we found that phi 8 and phi 13 P4 hexamers translocate 5' to 3' along ssRNA, whereas the analogous activity of phi 6 P4 requires association with the procapsid. This difference is explained by the intrinsically high affinity of phi 8 and phi 13 P4s for nucleic acids. The unidirectional translocation results in RNA helicase activity. Thus, P4 proteins of Cystoviridae exhibit extensive similarity to hexameric helicases and are simple models for studying viral packaging motor mechanisms.

Measurements of CP Asymmetries in the Decay B --> {phi}K

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

Aubert, B

The authors present a preliminary measurement of the time-dependent CP asymmetry for the neutral B-meson decay B{sup 0} --> {phi}K{sup 0}. They use a sample of approximately 227 million B-meson pairs recorded at the {Upsilon}(4S) resonance with the BABAR detector at the PEP-II B-meson Factory at SLAC. They reconstruct the CP eigenstates {phi}K{sub s}{sup 0} and {phi}K{sub L}{sup 0} where {phi} --> K{sup +}K{sup -}, K{sub s}{sup 0} --> {pi}{sup +}{pi}{sup -}, and K{sub L}{sup 0} is observed via its hadronic interactions. The other B meson in the event is tagged as either a B{sup 0} or {bar B}{sup 0}more » from its decay products. The values of the CP-violation parameters deived from the combined {phi}K{sup 0} dataset are S{sub {phi}K} = +0.50 {+-} 0.25(stat.){sub -0.04}{sup +0.07}(syst.) and C{sub {phi}K} = 0.00 {+-} 0.23(stat.) {+-}0.05(syst.). In addition, the authors measure the CP-violating charge asymmetry A{sub CP}(B{sup +} --> {phi}K{sup +}) = 0.054 {+-} 0.056(stat.) {+-} 0.012(syst.). All results are preliminary.« less

Kinetics and metabolism of physostigmine in rat in the presence of soman

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

Khalique, A.; Somani, S.M.

1986-03-01

The effect of soman (105 ..mu..g/kg; 1.5 LD/sub 50/ s.c.) administration on pharmacokinetics and metabolism of /sup 3/H-physostigmine (Phy) was studied in rats. The rats were pretreated with either Phy 100 ..mu..g/kg i.v. or 500 ..mu..g/kg i.m., 5 or 15 min prior to soman administration. Phy and metabolites were determined in plasma and brain by HPLC. The half-life of Phy in plasma after i.v. administration was 15.5 min both in the presence and absence of soman, however the t/sub 1/2/ in brain was 11 min and 13 min, respectively. Clearance was 71.4 ml/min/kg in the Phy treated rat and 90more » ml/min/kg in the presence of soman. The half-life of Phy in plasma was 18 min and 17 min, and in brain 17 min and 15 min, respectively in the absence and presence of soman after i.m. dose of Phy. Clearance after Phy treatment was 85.2 mlmin/kg however in the presence of soman, it was 66.7 ml/min/kg. Phy was slightly less metabolized to eseroline and two other metabolites, M/sub 1/ and M/sub 2/, in the presence of soman after i.v. as well as after i.m. administration in plasma and brain. The soman administration does not change the pharmacokinetics of Phy by the two different dosages and routes of administration.« less

Novel phytochrome sequences in Arabidopsis thaliana: Structure, evolution, and differential expression of a plant regulatory photoreceptor family

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

Sharrock, R.A.; Quail, P.H.

1989-01-01

Phytochrome is a plant regulatory photoreceptor that mediates red light effects on a wide variety of physiological and molecular responses. DNA blot analysis indicates that the Arabidopsis thaliana genome contains four to five phytochrome-related gene sequences. The authors have isolated and sequenced cDNA clones corresponding to three of these genes and have deduced the amino acid sequence of the full-length polypeptide encoded in each case. One of these proteins (phyA) shows 65-80% amino acid sequence identity with the major, etiolated-tissue phytochrome apoproteins described previously in other plant species. The other two polypeptides (phyB and phyC) are unique in that theymore » have low sequence identity with each other, with phyA, and with all previously described phytochromes. The phyA, phyB, and phyC proteins are of similar molecular mass, have related hydropathic profiles, and contain a conserved chromophore attachment region. However, the sequence comparison data indicate that the three phy genes diverged early in plant evolution, well before the divergence of the two major groups of angiosperms, the monocots and dicots. The steady-state level of the phyA transcript is high in dark-grown A. thaliana seedlings and is down-regulated by light. In contrast, the phyB and phyC transcripts are present at lower levels and are not strongly light-regulated. These findings indicate that the red/far red light-responsive phytochrome photoreceptor system in A. thaliana, and perhaps in all higher plants, consists of a family of chromoproteins that are heterogeneous in structure and regulation.« less

Time course of cholinesterase activity in plasma, brain and muscle of rat pretreated with physostigmine, and then soman

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

Giacobini, E.; Boyer, A.; Somani, S.M.

1986-03-05

Time course of /sup 3/H-physostigmine (Phy) concentration and cholinesterase (ChE) activity in plasma and tissues was studied in rats pretreated with Phy and then soman. Rats were dosed with Phy (100 ..mu..g/kg, i.v.), 5 or 15 min prior to soman (105 ..mu..g/kg, 1.5 LD/sub 50/, s.c.) treatment and were sacrificed at various times; Phys conc. and ChE activity were determined. BuChE activity in plasma was 5% of control from 7-30 min after Phy i.v. pretreatment and soman or soman alone treatment. Plasma Phy conc. steadily declined (32.6 ng/ml at 7 min) to 15 ng/ml at 30 min. ChE activity inmore » muscle was 60-50% of control for Phy pretreated but soman alone gave 85-72% activity from 2-30 min. Brain ChE activity was about 5% of control within 2 min after soman treatment; however, with Phy pretreatment, the activity was about 52% at 7 min, 40% at 22 min, which recovered to 45% of control at 35 min, indicating that Phy protected brain ChE. Brain Phy conc. steadily declined (58.6 ng/g at 7 min) to 11.7 ng/g at 30 min. However, pretreatment of rat with a higher dose of Phy and then soman showed BuChE in plasma and ChE in brain and muscle to be about 25, 35 and 51%, in comparison to about 5% in plasma and brain with soman alone treatment, indicating higher protection of ChE enzyme with higher conc. of Phy in plasma and brain.« less

A phytochrome/phototropin chimeric photoreceptor of fern functions as a blue/far-red light-dependent photoreceptor for phototropism in Arabidopsis.

PubMed

Kanegae, Takeshi; Kimura, Izumi

2015-08-01

In the fern Adiantum capillus-veneris, the phototropic response of the protonemal cells is induced by blue light and partially inhibited by subsequent irradiation with far-red light. This observation strongly suggests the existence of a phytochrome that mediates this blue/far-red reversible response; however, the phytochrome responsible for this response has not been identified. PHY3/NEO1, one of the three phytochrome genes identified in Adiantum, encodes a chimeric photoreceptor composed of both a phytochrome and a phototropin domain. It was demonstrated that phy3 mediates the red light-dependent phototropic response of Adiantum, and that phy3 potentially functions as a phototropin. These findings suggest that phy3 is the phytochrome that mediates the blue/far-red response in Adiantum protonemata. In the present study, we expressed Adiantum phy3 in a phot1 phot2 phototropin-deficient Arabidopsis line, and investigated the ability of phy3 to induce phototropic responses under various light conditions. Blue light irradiation clearly induced a phototropic response in the phy3-expressing transgenic seedlings, and this effect was fully inhibited by simultaneous irradiation with far-red light. In addition, experiments using amino acid-substituted phy3 indicated that FMN-cysteinyl adduct formation in the light, oxygen, voltage (LOV) domain was not necessary for the induction of blue light-dependent phototropism by phy3. We thus demonstrate that phy3 is the phytochrome that mediates the blue/far-red reversible phototropic response in Adiantum. Furthermore, our results imply that phy3 can function as a phototropin, but that it acts principally as a phytochrome that mediates both the red/far-red and blue/far-red light responses. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Tumor-cytolytic human macrophages cultured as nonadherent cells: potential for the adoptive immunotherapy of cancer.

PubMed

Helinski, E H; Hurley, E L; Streck, R J; Bielat, K L; Pauly, J L

1990-01-01

Tumor-cytolytic lymphokine (e.g., interleukin-2; IL-2)-activated killer cells are currently being evaluated in IL-2/LAK cell adoptive immunotherapy regimens for the treatment of cancer. Monocyte-derived macrophages (M phi) are also known to be efficient tumor killer cells; accordingly, M phi that have been activated in vitro may also be of therapeutic merit. However, attempts to cultivate M phi for morphological and functional studies have often been compromised because M phi adhere rapidly and tenaciously to cultureware. Studies that we have conducted to address this problem have proven successful in developing procedures for the long-term cultivation of non-adherent immunocompetent M phi in serum-free medium using petri dishes containing a thin Teflon liner. The utility of this technology is documented by the results of studies presented herein in which light and scanning electron microscopy was used to analyze tumor-cytolytic human M phi. In these experiments, we demonstrated that nonadherent immunocompetent human M phi can be prepared for detailed examinations of their pleomorphic membrane architecture. Moreover, nonadherent human M phi could readily be collected for preparing conjugates of M phi and tumor cells. It is anticipated that this technology should prove useful for future structure-function studies defining the topographical location and spatial distribution of antigens and receptors on M phi membrane ultrastructures, particularly the microvilli-like projections that bridge together an immunocompetent effector M phi and target cell (e.g., tumor cells and microbial pathogens) and which provide the physical interaction required for the initial phases of a cellular immune response that includes antigen recognition and cell-to-cell adhesion.

Expression of Aspergillus nidulans phy Gene in Nicotiana benthamiana Produces Active Phytase with Broad Specificities

PubMed Central

Oh, Tae-Kyun; Oh, Sung; Kim, Seongdae; Park, Jae Sung; Vinod, Nagarajan; Jang, Kyung Min; Kim, Sei Chang; Choi, Chang Won; Ko, Suk-Min; Jeong, Dong Kee; Udayakumar, Rajangam

2014-01-01

A full-length phytase gene (phy) of Aspergillus nidulans was amplified from the cDNA library by polymerase chain reaction (PCR), and it was introduced into a bacterial expression vector, pET-28a. The recombinant protein (rPhy-E, 56 kDa) was overexpressed in the insoluble fraction of Escherichia coli culture, purified by Ni-NTA resin under denaturing conditions and injected into rats as an immunogen. To express A. nidulans phytase in a plant, the full-length of phy was cloned into a plant expression binary vector, pPZP212. The resultant construct was tested for its transient expression by Agrobacterium-infiltration into Nicotiana benthamiana leaves. Compared with a control, the agro-infiltrated leaf tissues showed the presence of phy mRNA and its high expression level in N. benthamiana. The recombinant phytase (rPhy-P, 62 kDa) was strongly reacted with the polyclonal antibody against the nonglycosylated rPhy-E. The rPhy-P showed glycosylation, two pH optima (pH 4.5 and pH 5.5), an optimum temperature at 45~55 °C, thermostability and broad substrate specificities. After deglycosylation by peptide-N-glycosidase F (PNGase-F), the rPhy-P significantly lost the phytase activity and retained 1/9 of the original activity after 10 min of incubation at 45 °C. Therefore, the deglycosylation caused a significant reduction in enzyme thermostability. In animal experiments, oral administration of the rPhy-P at 1500 U/kg body weight/day for seven days caused a significant reduction of phosphorus excretion by 16% in rat feces. Besides, the rPhy-P did not result in any toxicological changes and clinical signs. PMID:25192284

Genome of Enterobacteriophage Lula/phi80 and Insights into Its Ability To Spread in the Laboratory Environment

PubMed Central

Rotman, Ella; Kouzminova, Elena; Plunkett, Guy

2012-01-01

The novel temperate bacteriophage Lula, contaminating laboratory Escherichia coli strains, turned out to be the well-known lambdoid phage phi80. Our previous studies revealed that two characteristics of Lula/phi80 facilitate its spread in the laboratory environment: cryptic lysogen productivity and stealthy infectivity. To understand the genetics/genomics behind these traits, we sequenced and annotated the Lula/phi80 genome, encountering an E. coli-toxic gene revealed as a gap in the sequencing contig and analyzing a few genes in more detail. Lula/phi80's genome layout copies that of lambda, yet homology with other lambdoid phages is mostly limited to the capsid genes. Lula/phi80's DNA is resistant to cutting with several restriction enzymes, suggesting DNA modification, but deletion of the phage's damL gene, coding for DNA adenine methylase, did not make DNA cuttable. The damL mutation of Lula/phi80 also did not change the phage titer in lysogen cultures, whereas the host dam mutation did increase it almost 100-fold. Since the high phage titer in cultures of Lula/phi80 lysogens is apparently in response to endogenous DNA damage, we deleted the only Lula/phi80 SOS-controlled gene, dinL. We found that dinL mutant lysogens release fewer phage in response to endogenous DNA damage but are unchanged in their response to external DNA damage. The toxic gene of Lula/phi80, gamL, encodes an inhibitor of the host ATP-dependent exonucleases, RecBCD and SbcCD. Its own antidote, agt, apparently encoding a modifier protein, was found nearby. Interestingly, Lula/phi80 lysogens are recD and sbcCD phenocopies, so GamL and Agt are part of lysogenic conversion. PMID:23042999

Relationship between intracellular pH and proton mobility in rat and guinea-pig ventricular myocytes.

PubMed

Swietach, Pawel; Vaughan-Jones, Richard D

2005-08-01

Intracellular H+ ion mobility in eukaryotic cells is low because of intracellular buffering. We have investigated whether Hi+ mobility varies with pHi. A dual microperfusion apparatus was used to expose guinea-pig or rat myocytes to small localized doses (3-5 mm) of ammonium chloride (applied in Hepes-buffered solution). Intracellular pH (pHi) was monitored confocally using the fluorescent dye, carboxy-SNARF-1. Local ammonium exposure produced a stable, longitudinal pHi gradient. Its size was fed into a look-up table (LUT) to give an estimate of the apparent intracellular proton diffusion coefficient (D(app)H). LUTs were generated using a diffusion-reaction model of Hi+ mobility based on intracellular buffer diffusion. To examine the pHi sensitivity of D(app)H, whole-cell pHi was initially displaced using a whole-cell ammonium or acetate prepulse, before locally applying the low dose of ammonium. In both rat and guinea-pig, D(app)H decreased with pHi over the range 7.5-6.5. In separate pipette-loading experiments, the intracellular diffusion coefficient for carboxy-SNARF-1 (a mobile-buffer analogue) exhibited no significant pHi dependence. The pHi sensitivity of D(app)H is thus likely to be governed by the mobile fraction of intrinsic buffering capacity. These results reinforce the buffer hypothesis of Hi+ mobility. The pHi dependence of D(app)H was used to characterize the mobile and fixed buffer components, and to estimate D(mob) (the average diffusion coefficient for intracellular mobile buffer). One consequence of a decline in Hi+ mobility at low pHi is that it will predispose the myocardium to pHi nonuniformity. The physiological relevance of this is discussed.

Hydrogen ion dynamics in human red blood cells

PubMed Central

Swietach, Pawel; Tiffert, Teresa; Mauritz, Jakob M A; Seear, Rachel; Esposito, Alessandro; Kaminski, Clemens F; Lew, Virgilio L; Vaughan-Jones, Richard D

2010-01-01

Our understanding of pH regulation within red blood cells (RBCs) has been inferred mainly from indirect experiments rather than from in situ measurements of intracellular pH (pHi). The present work shows that carboxy-SNARF-1, a pH fluorophore, when used with confocal imaging or flow cytometry, reliably reports pHi in individual, human RBCs, provided intracellular fluorescence is calibrated using a ‘null-point’ procedure. Mean pHi was 7.25 in CO2/HCO3−-buffered medium and 7.15 in Hepes-buffered medium, and varied linearly with extracellular pH (slope of 0.77). Intrinsic (non-CO2/HCO3−-dependent) buffering power, estimated in the intact cell (85 mmol (l cell)−1 (pH unit)−1 at resting pHi), was somewhat higher than previous estimates from cell lysates (50–70 mmol (l cell)−1 (pH unit)−1). Acute displacement of pHi (superfusion of weak acids/bases) triggered rapid pHi recovery. This was mediated via membrane Cl−/HCO3− exchange (the AE1 gene product), irrespective of whether recovery was from an intracellular acid or base load, and with no evident contribution from other transporters such as Na+/H+ exchange. H+-equivalent flux through AE1 was a linear function of [H+]i and reversed at resting pHi, indicating that its activity is not allosterically regulated by pHi, in contrast to other AE isoforms. By simultaneously monitoring pHi and markers of cell volume, a functional link between membrane ion transport, volume and pHi was demonstrated. RBC pHi is therefore tightly regulated via AE1 activity, but modulated during changes of cell volume. A comparable volume–pHi link may also be important in other cell types expressing anion exchangers. Direct measurement of pHi should be useful in future investigations of RBC physiology and pathology. PMID:20962000

Prostate Health Index (Phi) and Prostate Cancer Antigen 3 (PCA3) Significantly Improve Prostate Cancer Detection at Initial Biopsy in a Total PSA Range of 2–10 ng/ml

PubMed Central

Perdonà, Sisto; Marino, Ada; Mazzarella, Claudia; Perruolo, Giuseppe; D’Esposito, Vittoria; Cosimato, Vincenzo; Buonerba, Carlo; Di Lorenzo, Giuseppe; Musi, Gennaro; De Cobelli, Ottavio; Chun, Felix K.; Terracciano, Daniela

2013-01-01

Many efforts to reduce prostate specific antigen (PSA) overdiagnosis and overtreatment have been made. To this aim, Prostate Health Index (Phi) and Prostate Cancer Antigen 3 (PCA3) have been proposed as new more specific biomarkers. We evaluated the ability of phi and PCA3 to identify prostate cancer (PCa) at initial prostate biopsy in men with total PSA range of 2–10 ng/ml. The performance of phi and PCA3 were evaluated in 300 patients undergoing first prostate biopsy. ROC curve analyses tested the accuracy (AUC) of phi and PCA3 in predicting PCa. Decision curve analyses (DCA) were used to compare the clinical benefit of the two biomarkers. We found that the AUC value of phi (0.77) was comparable to those of %p2PSA (0.76) and PCA3 (0.73) with no significant differences in pairwise comparison (%p2PSA vs phi p = 0.673, %p2PSA vs. PCA3 p = 0.417 and phi vs. PCA3 p = 0.247). These three biomarkers significantly outperformed fPSA (AUC = 0.60), % fPSA (AUC = 0.62) and p2PSA (AUC = 0.63). At DCA, phi and PCA3 exhibited a very close net benefit profile until the threshold probability of 25%, then phi index showed higher net benefit than PCA3. Multivariable analysis showed that the addition of phi and PCA3 to the base multivariable model (age, PSA, %fPSA, DRE, prostate volume) increased predictive accuracy, whereas no model improved single biomarker performance. Finally we showed that subjects with active surveillance (AS) compatible cancer had significantly lower phi and PCA3 values (p<0.001 and p = 0.01, respectively). In conclusion, both phi and PCA3 comparably increase the accuracy in predicting the presence of PCa in total PSA range 2–10 ng/ml at initial biopsy, outperforming currently used %fPSA. PMID:23861782

Prostate Health Index (Phi) and Prostate Cancer Antigen 3 (PCA3) significantly improve prostate cancer detection at initial biopsy in a total PSA range of 2-10 ng/ml.

PubMed

Ferro, Matteo; Bruzzese, Dario; Perdonà, Sisto; Marino, Ada; Mazzarella, Claudia; Perruolo, Giuseppe; D'Esposito, Vittoria; Cosimato, Vincenzo; Buonerba, Carlo; Di Lorenzo, Giuseppe; Musi, Gennaro; De Cobelli, Ottavio; Chun, Felix K; Terracciano, Daniela

2013-01-01

Many efforts to reduce prostate specific antigen (PSA) overdiagnosis and overtreatment have been made. To this aim, Prostate Health Index (Phi) and Prostate Cancer Antigen 3 (PCA3) have been proposed as new more specific biomarkers. We evaluated the ability of phi and PCA3 to identify prostate cancer (PCa) at initial prostate biopsy in men with total PSA range of 2-10 ng/ml. The performance of phi and PCA3 were evaluated in 300 patients undergoing first prostate biopsy. ROC curve analyses tested the accuracy (AUC) of phi and PCA3 in predicting PCa. Decision curve analyses (DCA) were used to compare the clinical benefit of the two biomarkers. We found that the AUC value of phi (0.77) was comparable to those of %p2PSA (0.76) and PCA3 (0.73) with no significant differences in pairwise comparison (%p2PSA vs phi p = 0.673, %p2PSA vs. PCA3 p = 0.417 and phi vs. PCA3 p = 0.247). These three biomarkers significantly outperformed fPSA (AUC = 0.60), % fPSA (AUC = 0.62) and p2PSA (AUC = 0.63). At DCA, phi and PCA3 exhibited a very close net benefit profile until the threshold probability of 25%, then phi index showed higher net benefit than PCA3. Multivariable analysis showed that the addition of phi and PCA3 to the base multivariable model (age, PSA, %fPSA, DRE, prostate volume) increased predictive accuracy, whereas no model improved single biomarker performance. Finally we showed that subjects with active surveillance (AS) compatible cancer had significantly lower phi and PCA3 values (p<0.001 and p = 0.01, respectively). In conclusion, both phi and PCA3 comparably increase the accuracy in predicting the presence of PCa in total PSA range 2-10 ng/ml at initial biopsy, outperforming currently used %fPSA.

A simplified model of the source channel of the Leksell GammaKnife tested with PENELOPE.

PubMed

Al-Dweri, Feras M O; Lallena, Antonio M; Vilches, Manuel

2004-06-21

Monte Carlo simulations using the code PENELOPE have been performed to test a simplified model of the source channel geometry of the Leksell GammaKnife. The characteristics of the radiation passing through the treatment helmets are analysed in detail. We have found that only primary particles emitted from the source with polar angles smaller than 3 degrees with respect to the beam axis are relevant for the dosimetry of the Gamma Knife. The photon trajectories reaching the output helmet collimators at (x, v, z = 236 mm) show strong correlations between rho = (x2 + y2)(1/2) and their polar angle theta, on one side, and between tan(-1)(y/x) and their azimuthal angle phi, on the other. This enables us to propose a simplified model which treats the full source channel as a mathematical collimator. This simplified model produces doses in good agreement with those found for the full geometry. In the region of maximal dose, the relative differences between both calculations are within 3%, for the 18 and 14 mm helmets, and 10%, for the 8 and 4 mm ones. Besides, the simplified model permits a strong reduction (larger than a factor 15) in the computational time.

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

Vdovin V.L.

In this report we describe theory and 3D full wave code description for the wave excitation, propagation and absorption in 3-dimensional (3D) stellarator equilibrium high beta plasma in ion cyclotron frequency range (ICRF). This theory forms a basis for a 3D code creation, urgently needed for the ICRF heating scenarios development for the operated LHD, constructed W7-X, NCSX and projected CSX3 stellarators, as well for re evaluation of ICRF scenarios in operated tokamaks and in the ITER . The theory solves the 3D Maxwell-Vlasov antenna-plasma-conducting shell boundary value problem in the non-orthogonal flux coordinates ({Psi}, {theta}, {var_phi}), {Psi} being magneticmore » flux function, {theta} and {var_phi} being the poloidal and toroidal angles, respectively. All basic physics, like wave refraction, reflection and diffraction are self consistently included, along with the fundamental ion and ion minority cyclotron resonances, two ion hybrid resonance, electron Landau and TTMP absorption. Antenna reactive impedance and loading resistance are also calculated and urgently needed for an antenna -generator matching. This is accomplished in a real confining magnetic field being varying in a plasma major radius direction, in toroidal and poloidal directions, through making use of the hot dense plasma wave induced currents with account to the finite Larmor radius effects. We expand the solution in Fourier series over the toroidal ({var_phi}) and poloidal ({theta}) angles and solve resulting ordinary differential equations in a radial like {Psi}-coordinate by finite difference method. The constructed discretization scheme is divergent-free one, thus retaining the basic properties of original equations. The Fourier expansion over the angle coordinates has given to us the possibility to correctly construct the ''parallel'' wave number k{sub //}, and thereby to correctly describe the ICRF waves absorption by a hot plasma. The toroidal harmonics are tightly coupled with each other due to magnetic field inhomogeneity of stellarators in toroidal direction. This is drastically different from axial symmetric plasma of the tokamaks. The inclusion in the problem major radius variation of magnetic field can strongly modify earlier results obtained for the straight helical, especially for high beta plasma, due to location modification of the two ion hybrid resonance layers. For the NCSX, LHD, W7-AS and W7-X like magnetic field topology inclusion in our theory of a major radius inhomogeneity of the magnetic field is a key element for correct description of RF power deposition profiles at all. The theory is developed in a manner that includes tokamaks and magnetic mirrors as the particular cases through general metric tensor (provided by an equilibrium solver) treatment of the wave equations. We describe that newly developed stellarator ICRF 3D full wave code PSTELION, based on theory described in this report. Applications to tokamaks, ITER, stellarators and benchmarking with 2D TORIC and 3D AORSA codes are given in included subreports« less

The phi-meson and Chiral-mass-meson production in heavy-ion collisions as potential probes of quark-gluon-plasma and Chiral symmetry transitions

NASA Technical Reports Server (NTRS)

Takahashi, Y.; Eby, P. B.

1985-01-01

Possibilities of observing abundances of phi mesons and narrow hadronic pairs, as results of QGP and Chiral transitions, are considered for nucleus-nucleus interactions. Kinematical requirements in forming close pairs are satisfied in K+K decays of S(975) and delta (980) mesons with small phi, and phi (91020) mesons with large PT, and in pi-pi decays of familiar resonance mesons only in a partially restored chiral symmetry. Gluon-gluon dominance in QGP can enhance phi meson production. High hadronization rates of primordial resonance mesons which form narrow hadronic pairs are not implausible. Past cosmic ray evidences of anomalous phi production and narrow pair abundances are considered.

Cross-couplings in the elaboration of luminescent bis-terpyridyl iridium complexes: the effect of extended or inhibited conjugation on emission.

PubMed

Leslie, Wendy; Batsanov, Andrei S; Howard, Judith A K; Williams, J A Gareth

2004-02-21

The utility of Suzuki cross-coupling methodology for the in situ elaboration of bromo-functionalised bis-terpyridyl iridium(III) complexes has been explored. The complex [Ir(tpy)(tpy-phi-Br)]3+ [tpy-phi-Br = 4'-(4-bromophenyl)-2,2':6',2''-terpyridine] undergoes palladium-catalysed cross-coupling with aryl boronic acids to yield biaryl-substituted complexes directly. The biphenyl and 4-cyanobiphenyl-substituted products display relatively intense, long-lived (tau > 100 mus) yellow emission in degassed aqueous solution at room temperature, assigned to a 3pi-pi* state. A 4-aminobiphenyl-substituted analogue displays an additional low energy absorbance band, attributed to an intraligand charge-transfer (ILCT) excited state, and is scarcely emissive under the same conditions. The iridium(III) complex of 4'-mesityl-terpyridine is also reported. Its emission is much shorter-lived, with a spectral profile resembling that of unsubstituted [Ir(tpy)2]3+, confirming the need for the attainment of a roughly coplanar geometry for stabilisation of the 3pi-pi* excited state.

Strangeness Production in Jets with ALICE at the LHC

NASA Astrophysics Data System (ADS)

Smith, Chrismond; Harton, Austin; Garcia, Edmundo; Alice Collaboration

2016-03-01

The study of strange particle production is an important tool for understanding the properties of the hot and dense QCD medium created in heavy-ion collisions at ultra-relativistic energies. The study of strange particles in these collisions provides information on parton fragmentation, a fundamental QCD process. While measurements at low and intermediate pT, are already in progress at the LHC, the study of high momentum observables is equally important for a complete understanding of the QCD matter, this can be achieved by studying jet interactions. We propose the measurement of the characteristics of the jets containing strange particles. Starting with proton-proton collisions, we have calculated the inclusive pTJet spectra and the spectra for jets containing strange particles (K-short or lambda), and we are extending this analysis to lead-lead collisions. In this talk the ALICE experiment will be described, the methodology used for the data analysis and the available results will be discussed. This material is based upon work supported by the National Science Foundation under Grants PHY-1305280 and PHY-1407051.

Finite-Length Diocotron Modes in a Non-neutral Plasma Column

NASA Astrophysics Data System (ADS)

Walsh, Daniel; Dubin, Daniel

2017-10-01

Diocotron modes are 2D distortions of a non-neutral plasma column that propagate azimuthally via E × B drifts. While the infinite-length theory of diocotron modes is well-understood for arbitrary azimuthal mode number l, the finite-length mode frequency is less developed (with some exceptions), and is naturally of relevance to experiments. In this poster, we present an approach to address finite length effects, such as temperature dependence of the mode frequency. We use a bounce-averaged solution to the Vlasov Equation, in which the Vlasov Equation is solved using action-angle variables of the unperturbed Hamiltonian. We write the distribution function as a Fourier series in the bounce-angle variable ψ, keeping only the bounce-averaged term. We demonstrate a numerical solution to this equation for a realistic plasma with a finite Debye Length, compare to the existing l = 1 theory, and discuss possible extensions of the existing theory to l ≠ 1 . Supported by NSF/DOE Partnership Grants PHY1414570 and DESC0002451.

Molecular Dynamics Simulations of Hydrophobic Residues

NASA Astrophysics Data System (ADS)

Caballero, Diego; Zhou, Alice; Regan, Lynne; O'Hern, Corey

2013-03-01

Molecular recognition and protein-protein interactions are involved in important biological processes. However, despite recent improvements in computational methods for protein design, we still lack a predictive understanding of protein structure and interactions. To begin to address these shortcomings, we performed molecular dynamics simulations of hydrophobic residues modeled as hard spheres with stereo-chemical constraints initially at high temperature, and then quenched to low temperature to obtain local energy minima. We find that there is a range of quench rates over which the probabilities of side-chain dihedral angles for hydrophobic residues match the probabilities obtained for known protein structures. In addition, we predict the side-chain dihedral angle propensities in the core region of the proteins T4, ROP, and several mutants. These studies serve as a first step in developing the ability to quantitatively rank the energies of designed protein constructs. The success of these studies suggests that only hard-sphere dynamics with geometrical constraints are needed for accurate protein structure prediction in hydrophobic cavities and binding interfaces. NSF Grant PHY-1019147

Extending the scanning angle of a phased array antenna by using a null-space medium.

PubMed

Sun, Fei; He, Sailing

2014-10-30

By introducing a columnar null-space region as the reference space, we design a radome that can extend the scanning angle of a phased array antenna (PAA) by a predetermined relationship (e.g. a linear relationship between the incident angle and steered output angle can be achieved). After some approximation, we only need two homogeneous materials to construct the proposed radome layer by layer. This kind of medium is called a null-space medium, which has been studied and fabricated for realizing hyper-lenses and some other devices. Numerical simulations verify the performance of our radome.

IRBIT plays an important role in NHE3-mediated pHi regulation in HSG cells.

PubMed

Tran, Tien Manh; Park, Moon-Yong; Lee, Jiyeon; Bae, Jun-Seok; Hwang, Sung-Min; Choi, Se-Young; Mikoshiba, Katsuhiko; Park, Kyungpyo

2013-07-19

Expression of inositol-1,4,5-trisphosphate (IP3) receptor-binding protein (IRBIT) has been reported in epithelial cells. However, its role in pHi regulation is not well understood. In this study, we investigated the role of IRBIT in pHi regulation, mediated by Na(+)/H(+) exchangers (NHEs), in salivary glands. We measured pHi recovery from cell acidification in BCECF-loaded salivary HSG cells. Western blot and co-immunoprecipitation (CO-IP) assays were also performed, showing that NHE1, 2 and 3 are expressed, and IRBIT binds to NHE3. HOE642, a specific NHE1 blocker, inhibited pHi recovery, but 40% pH(i) recovery was still observed even at the highest concentration of HOE642. Furthermore, pretreatment of the cells with siIRBIT significantly inhibited pHi recovery, indicating that NHE3 potentially plays a role in pHi recovery as well. The amount of membrane-localized NHE3 and its interaction with IRBIT are also significantly increased by cell acidification. In addition, we found that Ste20p-related proline alanine-rich kinase (SPAK) reverses the effect of IRBIT on membrane NHE3 translocation. Taken together, we conclude that IRBIT plays an important role in pHi regulation, mediated by NHE3, and further regulated by SPAK. Copyright © 2013 Elsevier Inc. All rights reserved.

Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values.

PubMed

Geierhaas, Christian D; Salvatella, Xavier; Clarke, Jane; Vendruscolo, Michele

2008-03-01

It has been suggested that Phi-values, which allow structural information about transition states (TSs) for protein folding to be obtained, are most reliably interpreted when divided into three classes (high, medium and low). High Phi-values indicate almost completely folded regions in the TS, intermediate Phi-values regions with a detectable amount of structure and low Phi-values indicate mostly unstructured regions. To explore the extent to which this classification can be used to characterise in detail the structure of TSs for protein folding, we used Phi-values divided into these classes as restraints in molecular dynamics simulations. This type of procedure is related to that used in NMR spectroscopy to define the structure of native proteins from the measurement of inter-proton distances derived from nuclear Overhauser effects. We illustrate this approach by determining the TS ensembles of five proteins and by showing that the results are similar to those obtained by using as restraints the actual numerical Phi-values measured experimentally. Our results indicate that the simultaneous consideration of a set of low-resolution Phi-values can provide sufficient information for characterising the architecture of a TS for folding of a protein.

A novel protein tyrosine phosphatase like phytase from Lactobacillus fermentum NKN51: Cloning, characterization and application in mineral release for food technology applications.

PubMed

Sharma, Rekha; Kumar, Piyush; Kaushal, Vandana; Das, Rahul; Kumar Navani, Naveen

2018-02-01

A novel protein tyrosine phosphatase like phytase (PTPLP), designated as PhyLf from probiotic bacterium Lactobacillus fermentum NKN51 was identified, cloned, expressed and characterized. The recombinant PhyLf showed specific activity of 174.5 U/mg. PhyLf exhibited strict specificity towards phytate and optimum temperature at 60 °C, pH 5.0 and ionic strength of 100 mM. K m and K cat of PhyLf for phytate were 0.773 mM and 84.31 s -1 , respectively. PhyLf exhibited high resistance against oxidative inactivation. PhyLf shares no homology, sans the active site with reported PTLPs, warranting classification as a new subclass. Dephytinization of durum wheat and finger millet under in vitro gastrointestinal conditions using PhyLf enhanced the bioaccessibility of mineral ions. Probiotic origin, phytate specificity, resistance to oxidative environment and gastric milieu coupled with ability to release micronutrients are unique properties of PhyLf which present a strong case for its use in ameliorating nutritional value of cereals and animal feed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ordovician and Silurian Phi Kappa and Trail Creek formations, Pioneer Mountains, central Idaho; stratigraphic and structural revisions, and new data on graptolite faunas

USGS Publications Warehouse

Dover, James H.; Berry, William B.N.; Ross, Reuben James

1980-01-01

Recent geologic mapping in the northern Pioneer Mountains combined with the identification of graptolites from 116 new collections indicate that the Ordovician and Silurian Phi Kappa and Trail Creek Formations occur in a series of thrust-bounded slices within a broad zone of imbricate thrust faulting. Though confirming a deformational style first reported in a 1963 study by Michael Churkin, our data suggest that the complexity and regional extent of the thrust zone were not previously recognized. Most previously published sections of the Phi Kappa and Trail Creek Formations were measured across unrecognized thrust faults and therefore include not only structural repetitions of graptolitic Ordovician and Silurian rocks but also other tectonically juxtaposed lithostratigraphic units of diverse ages as well. Because of this discovery, the need to reconsider the stratigraphic validity of these formations and their lithology, nomenclature, structural distribution, facies relations, and graptolite faunas has arisen. The Phi Kappa Formation in most thrust slices has internal stratigraphic continuity despite the intensity of deformation to which it was subjected. As revised herein, the Phi Kappa Formation is restricted to a structurally repeated succession of predominantly black, carbonaceous, graptolitic argillite and shale. Some limy, light-gray-weathering shale occurs in the middle part of the section, and fine-grained locally pebbly quartzite is present at the base. The basal quartzite is here named the Basin Gulch Quartzite Member of the Phi Kappa. The Phi Kappa redefined on a lithologic basis represents the span of Ordovician time from W. B. N. Berry's graptolite zones 2-4 through 15 and also includes approximately 17 m of lithologically identical shale of Early and Middle Silurian age at the top. The lower contact of the formation as revised is tectonic. The Phi Kappa is gradationally overlain by the Trail Creek Formation as restricted herein. Most of the coarser clastic rocks reported in previously measured sections of the Phi Kappa, as well as the sequence along Phi Kappa Creek from which the name originates, are excluded from the Phi Kappa as revised and are reassigned to two structural plates of Mississippian Copper Basin Formation; other strata now excluded from the formation are reassigned to the Trail Creek Formation and to an unnamed Silurian and Devonian unit. As redefined, the Phi Kappa Formation is only about 240 m thick, compared with the 3,860 m originally estimated, and it occupies only about 25 percent of the outcrop area previously mapped in 1930 by H. G. Westgate and C. P. Ross. Despite this drastic reduction in thickness and the exclusion of the rocks along Phi Kappa Creek, the name Phi Kappa is retained because of widely accepted prior usage to denote the Ordovician graptolitic shale facies of central Idaho, and because the Phi Kappa Formation as revised is present in thrust slices on Phi Kappa Mountain, at the head of Phi Kappa Creek. The lithic and faunal consistency of this unit throughout the area precludes the necessity for major facies telescoping along individual faults within the outcrop belt. However, tens of kilometers of tectonic shortening seems required to juxtapose the imbricated Phi Kappa shale facies with the Middle Ordovician part of the carbonate and quartzite shale sequence of east central Idaho. The shelf rocks are exposed in the Wildhorse structural window of the northeastern Pioneer Mountains, and attain a thickness of at least 1,500 m throughout the region north and east of the Pioneer Mountains. The Phi Kappa is in direct thrust contact on intensely deformed medium- to high-grade metamorphic equivalents of the same shelf sequence in the Pioneer window at the south end of the Phi Kappa-Trail Creek outcrop belt. Along East Pass, Big Lake, and Pine Creeks, north of the Pioneer Mountains, some rocks previously mapped as Ramshorn Slate are lithologically and faunally equivalent to the P

The extraction of Φ – N total cross section from d ( γ , p K + K - ) n

DOE PAGES

Qian, X.; Chen, W.; Gao, H.; ...

2009-10-01

We report on the first measurement of the differential cross section ofmore » $$\\phi$$-meson photoproduction for the $$d(\\gamma,pK^{+}K^{-})n$$ exclusive reaction channel. The experiment was performed using a \\textcolor{black}{tagged-photon} beam and the CEBAF Large Acceptance Spectrometer (CLAS) at Jefferson Lab. A combined analysis using data from the $$d(\\gamma,pK^{+}K^{-})n$$ channel and those from a previous publication on coherent $$\\phi$$ production on the deuteron has been carried out to extract the $$\\phi-N$$ total cross section, $$\\sigma_{\\phi N}$$. The extracted $$\\phi-N$$ total cross section favors a value above 20 mb. This value is larger than the value extracted using vector-meson dominance models for $$\\phi$$ photoproduction on the proton.« less

Re-entrant phase behavior of a concentrated anionic surfactant system with strongly binding counterions.

PubMed

Ghosh, Sajal Kumar; Rathee, Vikram; Krishnaswamy, Rema; Raghunathan, V A; Sood, A K

2009-08-04

The phase behavior of the anionic surfactant sodium dodecyl sulfate (SDS) in the presence of the strongly binding counterion p-toluidine hydrochloride (PTHC) has been examined using small-angle X-ray diffraction and polarizing microscopy. A hexagonal-to-lamellar transition on varying the PTHC to SDS molar ratio (alpha) occurs through a nematic phase of rodlike micelles (Nc) --> isotropic (I) --> nematic of disklike micelles (N(D)) at a fixed surfactant concentration (phi). The lamellar phase is found to coexist with an isotropic phase (I') over a large region of the phase diagram. Deuterium nuclear magnetic resonance investigations of the phase behavior at phi = 0.4 confirm the transition from N(C) to N(D) on varying alpha. The viscoelastic and flow behaviors of the different phases were examined. A decrease in the steady shear viscosity across the different phases with increasing alpha suggests a decrease in the aspect ratio of the micellar aggregates. From the transient shear stress response of the N() and N(D) nematic phases in step shear experiments, they were characterized to be tumbling and flow aligning, respectively. Our studies reveal that by tuning the morphology of the surfactant micelles strongly binding counterions modify the phase behavior and rheological properties of concentrated surfactant solutions.

The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile.

PubMed

Ramírez-Vargas, Gabriel; Goh, Shan; Rodríguez, César

2018-01-01

Until recently, Clostridium difficile phages were limited to Myoviruses and Siphoviruses of medium genome length (32-57 kb). Here we report the finding of phiCD5763, a Siphovirus with a large extrachromosomal circular genome (132.5 kb, 172 ORFs) and a large capsid (205.6 ± 25.6 nm in diameter) infecting MLST Clade 1 strains of C. difficile . Two subgroups of big phage genomes similar to phiCD5763 were identified in 32 NAP CR1 /RT012/ST-54 C. difficile isolates from Costa Rica and in whole genome sequences (WGS) of 41 C. difficile isolates of Clades 1, 2, 3, and 4 from Canada, USA, UK, Belgium, Iraq, and China. Through comparative genomics we discovered another putative big phage genome in a non-NAP CR1 isolate from Costa Rica, phiCD2955, which represents other big phage genomes found in 130 WGS of MLST Clade 1 and 2 isolates from Canada, USA, Hungary, France, Austria, and UK. phiCD2955 (131.6 kb, 172 ORFs) is related to a previously reported C. difficile phage genome, phiCD211/phiCDIF1296T. Detailed genome analyses of phiCD5763, phiCD2955, phiCD211/phiCDIF1296T, and seven other putative C. difficile big phage genome sequences of 131-136 kb reconstructed from publicly available WGS revealed a modular gene organization and high levels of sequence heterogeneity at several hotspots, suggesting that these genomes correspond to biological entities undergoing recombination. Compared to other C. difficile phages, these big phages have unique predicted terminase, capsid, portal, neck and tail proteins, receptor binding proteins (RBPs), recombinases, resolvases, primases, helicases, ligases, and hypothetical proteins. Moreover, their predicted gene load suggests a complex regulation of both phage and host functions. Overall, our results indicate that the prevalence of C. difficile big bacteriophages is more widespread than realized and open new avenues of research aiming to decipher how these viral elements influence the biology of this emerging pathogen.

Release and bioactivity of bone morphogenetic protein-2 are affected by scaffold binding techniques in vitro and in vivo.

PubMed

Suliman, Salwa; Xing, Zhe; Wu, Xujun; Xue, Ying; Pedersen, Torbjorn O; Sun, Yang; Døskeland, Anne P; Nickel, Joachim; Waag, Thilo; Lygre, Henning; Finne-Wistrand, Anna; Steinmüller-Nethl, Doris; Krueger, Anke; Mustafa, Kamal

2015-01-10

A low dose of 1μg rhBMP-2 was immobilised by four different functionalising techniques on recently developed poly(l-lactide)-co-(ε-caprolactone) [(poly(LLA-co-CL)] scaffolds. It was either (i) physisorbed on unmodified scaffolds [PHY], (ii) physisorbed onto scaffolds modified with nanodiamond particles [nDP-PHY], (iii) covalently linked onto nDPs that were used to modify the scaffolds [nDP-COV] or (iv) encapsulated in microspheres distributed on the scaffolds [MICS]. Release kinetics of BMP-2 from the different scaffolds was quantified using targeted mass spectrometry for up to 70days. PHY scaffolds had an initial burst of release while MICS showed a gradual and sustained increase in release. In contrast, NDP-PHY and nDP-COV scaffolds showed no significant release, although nDP-PHY scaffolds maintained bioactivity of BMP-2. Human mesenchymal stem cells cultured in vitro showed upregulated BMP-2 and osteocalcin gene expression at both week 1 and week 3 in the MICS and nDP-PHY scaffold groups. These groups also demonstrated the highest BMP-2 extracellular protein levels as assessed by ELISA, and mineralization confirmed by Alizarin red. Cells grown on the PHY scaffolds in vitro expressed collagen type 1 alpha 2 early but the scaffold could not sustain rhBMP-2 release to express mineralization. After 4weeks post-implantation using a rat mandible critical-sized defect model, micro-CT and Masson trichrome results showed accelerated bone regeneration in the PHY, nDP-PHY and MICS groups. The results demonstrate that PHY scaffolds may not be desirable for clinical use, since similar osteogenic potential was not seen under both in vitro and in vivo conditions, in contrast to nDP-PHY and MICS groups, where continuous low doses of BMP-2 induced satisfactory bone regeneration in both conditions. The nDP-PHY scaffolds used here in critical-sized bone defects for the first time appear to have promise compared to growth factors adsorbed onto a polymer alone and the short distance effect prevents adverse systemic side effects. Copyright © 2014. Published by Elsevier B.V.

Polarization in Vector-Vector Decay of B Mesons at CDF

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

Hans, Randal Milton

1996-01-01

The factorization assumption in bound state decays (splitting four-quark operators into the product of two two-quark operators) has proved to be a useful tool in B and D meson decays. The longitudinal polarization fraction,more » $,L/,,$ in the decays $$B_d \\to J/\\psi K^{*0}$$ and $$B_s \\to J/\\psi \\phi$$ can be calculated using various phenomenological models within the factorization assumption and, when compared to experimental measurements, provides a test of the factorization procedure when extended to color suppressed B decays....« less

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

Dorey, Patrick; Halavanau, Aliaksei; Mercer, James

Here, we study boundary scattering in themore » $$\\phi^4$$ model on a half-line with a one-parameter family of Neumann-type boundary conditions. A rich variety of phenomena is observed, which extends previously-studied behaviour on the full line to include regimes of near-elastic scattering, the restoration of a missing scattering window, and the creation of a kink or oscillon through the collision-induced decay of a metastable boundary state. We also study the decay of the vibrational boundary mode, and explore different scenarios for its relaxation and for the creation of kinks.« less

Intracellular pH in mammalian stages of Trypanosoma cruzi is K+-dependent and regulated by H+-ATPases.

PubMed

Van Der Heyden, N; Docampo, R

2000-02-05

Regulation of intracellular pH (pHi) was investigated in Trypanosoma cruzi amastigotes and trypomastigotes using 2',7'-bis-(carboxyethyl)-5(and-6)-carboxyfluorescein (BCECF). pHi was determined to be 7.33 +/- 0.08 and 7.35 +/- 0.07 in amastigotes and trypomastigotes, respectively, and there were no significant differences in the regulation of pH, between the two stages. Steady-state pHi, recovery of pHi from acidification, and H+-efflux were all decreased markedly by the H+-ATPase inhibitors N,N'-dicyclohexylcarbodi-imide (DCCD), diethylstilbestrol (DES) and N-ethylmaleimide (NEM) supporting a significant role for a plasma membrane H+-ATPase in the regulation of pHi. pHi was maintained at neutrality over a range of external pH (pHe) from 5-8 in parasites suspended in a buffer containing Na+ and K+ (standard buffer) but was acidified at low pHe in the absence of these cations (choline buffer). The pHi of trypomastigotes decreased significantly when they transformed into amastigotes. The rate of recovery of pHi by acidified parasites was similar in Na+-free buffer and standard buffer but was slower in the absence of K+ (K+-free or choline buffer) and parasites suspended in choline buffer were acidic by 0.25 pH units as compared with controls. Ba2+ and Cs+ decreased the pHi of parasites suspended in standard but not choline buffer suggesting the presence of an inward directed K+ channel. The pHi of amastigotes and trypomastigotes suspended in Cl(-)-free buffer was decreased by 0.13 and 0.2 pH units, respectively, supporting the presence of a chloride conductive channel. No evidence of pH regulation via a Na+/H+ or Cl-/HCO3- exchanger was found. These results are consistent with the presence of a plasma membrane H+-ATPase that regulates pHi and is supported by K+ and Cl- channels.

Medically Unexplained and Explained Physical Symptoms in the General Population: Association with Prevalent and Incident Mental Disorders

PubMed Central

van Eck van der Sluijs, Jonna; ten Have, Margreet; Rijnders, Cees; van Marwijk, Harm; de Graaf, Ron; van der Feltz-Cornelis, Christina

2015-01-01

Background Clinical studies have shown that Medically Unexplained Symptoms (MUS) are related to common mental disorders. It is unknown how often common mental disorders occur in subjects who have explained physical symptoms (PHY), MUS or both, in the general population, what the incidence rates are, and whether there is a difference between PHY and MUS in this respect. Aim To study the prevalence and incidence rates of mood, anxiety and substance use disorders in groups with PHY, MUS and combined MUS and PHY compared to a no-symptoms reference group in the general population. Method Data were derived from the Netherlands Mental Health Survey and Incidence Study-2 (NEMESIS-2), a nationally representative face-to-face survey of the general population aged 18-64 years. We selected subjects with explained physical symptoms only (n=1952), with MUS only (n=177), with both MUS and PHY (n=209), and a reference group with no physical symptoms (n=4168). The assessment of common mental disorders was through the Composite International Diagnostic Interview 3.0. Multivariate logistic regression analyses were used to examine the association between group membership and the prevalence and first-incidence rates of comorbid mental disorders, adjusted for socio-demographic characteristics. Results MUS were associated with the highest prevalence rates of mood and anxiety disorders, and combined MUS and PHY with the highest prevalence rates of substance disorder. Combined MUS and PHY were associated with a higher incidence rate of mood disorder only (OR 2.9 (95%CI:1.27,6.74)). Conclusion In the general population, PHY, MUS and the combination of both are related to mood and anxiety disorder, but odds are highest for combined MUS and PHY in relation to substance use disorder. Combined MUS and PHY are related to a greater incidence of mood disorder. These findings warrant further research into possibilities to improve recognition and early intervention in subjects with combined MUS and PHY. PMID:25853676

Anonymization of DICOM Electronic Medical Records for Radiation Therapy

PubMed Central

Newhauser, Wayne; Jones, Timothy; Swerdloff, Stuart; Newhauser, Warren; Cilia, Mark; Carver, Robert; Halloran, Andy; Zhang, Rui

2014-01-01

Electronic medical records (EMR) and treatment plans are used in research on patient outcomes and radiation effects. In many situations researchers must remove protected health information (PHI) from EMRs. The literature contains several studies describing the anonymization of generic Digital Imaging and Communication in Medicine (DICOM) files and DICOM image sets but no publications were found that discuss the anonymization of DICOM radiation therapy plans, a key component of an EMR in a cancer clinic. In addition to this we were unable to find a commercial software tool that met the minimum requirements for anonymization and preservation of data integrity for radiation therapy research. The purpose of this study was to develop a prototype software code to meet the requirements for the anonymization of radiation therapy treatment plans and to develop a way to validate that code and demonstrate that it properly anonymized treatment plans and preserved data integrity. We extended an open-source code to process all relevant PHI and to allow for the automatic anonymization of multiple EMRs. The prototype code successfully anonymized multiple treatment plans in less than 1 minute per patient. We also tested commercial optical character recognition (OCR) algorithms for the detection of burned-in text on the images, but they were unable to reliably recognize text. In addition, we developed and tested an image filtering algorithm that allowed us to isolate and redact alpha-numeric text from a test radiograph. Validation tests verified that PHI was anonymized and data integrity, such as the relationship between DICOM unique identifiers (UID) was preserved. PMID:25147130

Anonymization of DICOM electronic medical records for radiation therapy.

PubMed

Newhauser, Wayne; Jones, Timothy; Swerdloff, Stuart; Newhauser, Warren; Cilia, Mark; Carver, Robert; Halloran, Andy; Zhang, Rui

2014-10-01

Electronic medical records (EMR) and treatment plans are used in research on patient outcomes and radiation effects. In many situations researchers must remove protected health information (PHI) from EMRs. The literature contains several studies describing the anonymization of generic Digital Imaging and Communication in Medicine (DICOM) files and DICOM image sets but no publications were found that discuss the anonymization of DICOM radiation therapy plans, a key component of an EMR in a cancer clinic. In addition to this we were unable to find a commercial software tool that met the minimum requirements for anonymization and preservation of data integrity for radiation therapy research. The purpose of this study was to develop a prototype software code to meet the requirements for the anonymization of radiation therapy treatment plans and to develop a way to validate that code and demonstrate that it properly anonymized treatment plans and preserved data integrity. We extended an open-source code to process all relevant PHI and to allow for the automatic anonymization of multiple EMRs. The prototype code successfully anonymized multiple treatment plans in less than 1min/patient. We also tested commercial optical character recognition (OCR) algorithms for the detection of burned-in text on the images, but they were unable to reliably recognize text. In addition, we developed and tested an image filtering algorithm that allowed us to isolate and redact alpha-numeric text from a test radiograph. Validation tests verified that PHI was anonymized and data integrity, such as the relationship between DICOM unique identifiers (UID) was preserved. Copyright © 2014 Elsevier Ltd. All rights reserved.

Greater Patient Health Information Control to Improve the Sustainability of Health Information Exchanges.

PubMed

Abdelhamid, Mohamed

2018-06-09

Health information exchanges (HIEs) are multisided platforms that facilitate the sharing of patient health information (PHI) between providers and payers across organizations within a region, community or hospital system. The benefits of HIEs to payers and providers include lower cost, faster services, and better health outcome. However, most HIEs have configured the patient healthcare consent process to give all providers who sign up with the exchange access to PHI for all consenting patients, leaving no control to patients in customized what information to share and with who. This research investigates the impact of granting greater control to patients in sharing their personal health information on consent rates and making them active participants in the HIEs system. This research utilizes a randomized experimental survey design study. The study uses responses from 388 participants and structural equation modeling (SEM) to test the conceptual model. The main findings of this research include that patients consent rate increases significantly when greater control in sharing PHI is offered to the patient. In addition, greater control reduces the negative impact of privacy concern on the intention to consent. Similarly, trust in healthcare professionals leads to higher consent when greater control is offered to the patient. Thus, greater control empowers the role of trust in engaging patients and sustaining HIEs. The paper makes a theoretical contribution to research by extending the unified theory of acceptance and use of technology (UTAUT) model. The findings impact practice by providing insights that will help sustain HIEs. Copyright © 2018. Published by Elsevier Inc.

The potential cost-effectiveness of infant pneumococcal vaccines in Australia.

PubMed

Newall, Anthony T; Creighton, Prudence; Philp, David J; Wood, James G; MacIntyre, C Raina

2011-10-19

Over the last decade infant pneumococcal vaccination has been adopted as part of routine immunisation schedules in many developed countries. Although highly successful in many settings such as Australia and the United States, rapid serotype replacement has occurred in some European countries. Recently two pneumococcal conjugate vaccines (PCVs) with extended serotype coverage have been licensed for use, a 10-valent (PHiD-CV) and a 13-valent (PCV-13) vaccine, and offer potential replacements for the existing vaccine (PCV-7) in Australia. To evaluate the cost-effectiveness of PCV programs we developed a static, deterministic state-transition model. The perspective for costs included those to the government and healthcare system. When compared to current practice (PCV-7) both vaccines offered potential benefits, with those estimated for PHiD-CV due primarily to prevention of otitis media and PCV-13 due to a further reduction in invasive disease in Australia. At equivalent total cost to vaccinate an infant, compared to no PCV the base-case cost per QALY saved were estimated at A$64,900 (current practice, PCV-7; 3+0), A$50,200 (PHiD-CV; 3+1) and A$55,300 (PCV-13; 3+0), respectively. However, assumptions regarding herd protection, serotype protection, otitis media efficacy, and vaccination cost changed the relative cost-effectiveness of alternative PCV programs. The high proportion of current invasive disease caused by serotype 19A (as included in PCV-13) may be a decisive factor in determining vaccine policy in Australia. Copyright © 2011 Elsevier Ltd. All rights reserved.

Specific binding of (/sup 3/H-Tyr8)physalaemin to rat submaxillary gland substance P receptor

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

Bahouth, S.W.; Lazaro, D.M.; Brundish, D.E.

1985-01-01

(/sup 3/H)Physalaemin ((/sup 3/H)PHY) binds to a single class of noninteracting sites on rat submaxillary gland membranes suspended in high ionic strength media with a KD of 2.7 nM, a Bmax of 240 fmol/mg of protein, and low nonspecific binding. The relative potencies of substance P (SP) and its fragments in competing with (/sup 3/H)PHY correlate with their relative salivation potencies. This indicates that (/sup 3/H)PHY interacts with a physiologically relevant SP receptor. In low ionic strength media, the KD of (/sup 3/H)PHY does not change, but SP and some of its fragments are more potent than PHY in competingmore » with (/sup 3/H) PHY. Computer-assisted analysis of (/sup 3/H)PHY and (/sup 3/H)SP binding in high and low ionic strength media demonstrated that both peptides are equipotent in high ionic strength but that the affinity of SP increases by 70-fold in low ionic strength. The SP fragments that contain a basic residue in positions 1 and/or 3 also display an increased affinity in low ionic strength. These findings document that (/sup 3/H)PHY binding in high ionic strength (mu . 0.6) accurately reflects the pharmacological potencies of agonists on the SP-P receptor. The binding of (/sup 3/H)PHY, like that of (/sup 3/H)SP, increases by the addition of divalent cations (Mg2+ greater than Ca2+ greater than Mn2+). Guanine nucleotides decrease (/sup 3/H)PHY binding by decreasing the Bmax to the same level (160 fmol/mg of protein), in the presence or absence of Mg2+.« less

Evolutionary divergence of phytochrome protein function in Zea mays PIF3 signaling.

PubMed

Kumar, Indrajit; Swaminathan, Kankshita; Hudson, Karen; Hudson, Matthew E

2016-07-01

Two maize phytochrome-interacting factor (PIF) basic helix-loop-helix (bHLH) family members, ZmPIF3.1 and ZmPIF3.2, were identified, cloned and expressed in vitro to investigate light-signaling interactions. A phylogenetic analysis of sequences of the maize bHLH transcription factor gene family revealed the extent of the PIF family, and a total of seven predicted PIF-encoding genes were identified from genes encoding bHLH family VIIa/b proteins in the maize genome. To investigate the role of maize PIFs in phytochrome signaling, full-length cDNAs for phytochromes PhyA2, PhyB1, PhyB2 and PhyC1 from maize were cloned and expressed in vitro as chromophorylated holophytochromes. We showed that ZmPIF3.1 and ZmPIF3.2 interact specifically with the Pfr form of maize holophytochrome B1 (ZmphyB1), showing no detectable affinity for the Pr form. Maize holophytochrome B2 (ZmphyB2) showed no detectable binding affinity for PIFs in either Pr or Pfr forms, but phyB Pfr from Arabidopsis interacted with ZmPIF3.1 similarly to ZmphyB1 Pfr. We conclude that subfunctionalization at the protein-protein interaction level has altered the role of phyB2 relative to that of phyB1 in maize. Since the phyB2 mutant shows photomorphogenic defects, we conclude that maize phyB2 is an active photoreceptor, without the binding of PIF3 seen in other phyB family proteins. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Plasma HIV viral rebound following protocol-indicated cessation of ART commenced in primary and chronic HIV infection.

PubMed

Hamlyn, Elizabeth; Ewings, Fiona M; Porter, Kholoud; Cooper, David A; Tambussi, Giuseppe; Schechter, Mauro; Pedersen, Court; Okulicz, Jason F; McClure, Myra; Babiker, Abdel; Weber, Jonathan; Fidler, Sarah

2012-01-01

The magnitude of HIV viral rebound following ART cessation has consequences for clinical outcome and onward transmission. We compared plasma viral load (pVL) rebound after stopping ART initiated in primary (PHI) and chronic HIV infection (CHI). Two populations with protocol-indicated ART cessation from SPARTAC (PHI, n = 182) and SMART (CHI, n = 1450) trials. Time for pVL to reach pre-ART levels after stopping ART was assessed in PHI using survival analysis. Differences in pVL between PHI and CHI populations 4 weeks after stopping ART were examined using linear and logistic regression. Differences in pVL slopes up to 48 weeks were examined using linear mixed models and viral burden was estimated through a time-averaged area-under-pVL curve. CHI participants were categorised by nadir CD4 at ART stop. Of 171 PHI participants, 71 (41.5%) rebounded to pre-ART pVL levels, at a median of 50 (95% CI 48-51) weeks after stopping ART. Four weeks after stopping treatment, although the proportion with pVL ≥ 400 copies/ml was similar (78% PHI versus 79% CHI), levels were 0.45 (95% CI 0.26-0.64) log(10) copies/ml lower for PHI versus CHI, and remained lower up to 48 weeks. Lower CD4 nadir in CHI was associated with higher pVL after ART stop. Rebound for CHI participants with CD4 nadir >500 cells/mm(3) was comparable to that experienced by PHI participants. Stopping ART initiated in PHI and CHI was associated with viral rebound to levels conferring increased transmission risk, although the level of rebound was significantly lower and sustained in PHI compared to CHI.

A Systematic Review and Meta-analysis of the Diagnostic Accuracy of Prostate Health Index and 4-Kallikrein Panel Score in Predicting Overall and High-grade Prostate Cancer.

PubMed

Russo, Giorgio Ivan; Regis, Federica; Castelli, Tommaso; Favilla, Vincenzo; Privitera, Salvatore; Giardina, Raimondo; Cimino, Sebastiano; Morgia, Giuseppe

2017-08-01

Markers for prostate cancer (PCa) have progressed over recent years. In particular, the prostate health index (PHI) and the 4-kallikrein (4K) panel have been demonstrated to improve the diagnosis of PCa. We aimed to review the diagnostic accuracy of PHI and the 4K panel for PCa detection. We performed a systematic literature search of PubMed, EMBASE, Cochrane, and Academic One File databases until July 2016. We included diagnostic accuracy studies that used PHI or 4K panel for the diagnosis of PCa or high-grade PCa. The methodological quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. Twenty-eight studies including 16,762 patients have been included for the analysis. The pooled data showed a sensitivity of 0.89 and 0.74 for PHI and 4K panel, respectively, for PCa detection and a pooled specificity of 0.34 and 0.60 for PHI and 4K panel, respectively. The derived area under the curve (AUC) from the hierarchical summary receiver operating characteristic (HSROC) showed an accuracy of 0.76 and 0.72 for PHI and 4K panel respectively. For high-grade PCa detection, the pooled sensitivity was 0.93 and 0.87 for PHI and 4K panel, respectively, whereas the pooled specificity was 0.34 and 0.61 for PHI and 4K panel, respectively. The derived AUC from the HSROC showed an accuracy of 0.82 and 0.81 for PHI and 4K panel, respectively. Both PHI and the 4K panel provided good diagnostic accuracy in detecting overall and high-grade PCa. Copyright © 2016 Elsevier Inc. All rights reserved.

Evaluation of the Xeon phi processor as a technology for the acceleration of real-time control in high-order adaptive optics systems

NASA Astrophysics Data System (ADS)

Barr, David; Basden, Alastair; Dipper, Nigel; Schwartz, Noah; Vick, Andy; Schnetler, Hermine

2014-08-01

We present wavefront reconstruction acceleration of high-order AO systems using an Intel Xeon Phi processor. The Xeon Phi is a coprocessor providing many integrated cores and designed for accelerating compute intensive, numerical codes. Unlike other accelerator technologies, it allows virtually unchanged C/C++ to be recompiled to run on the Xeon Phi, giving the potential of making development, upgrade and maintenance faster and less complex. We benchmark the Xeon Phi in the context of AO real-time control by running a matrix vector multiply (MVM) algorithm. We investigate variability in execution time and demonstrate a substantial speed-up in loop frequency. We examine the integration of a Xeon Phi into an existing RTC system and show that performance improvements can be achieved with limited development effort.

A search for a doubly-charged Higgs boson in pp collisions at $$\\sqrt{s} = 7 \\ \\mbox{TeV}$$

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

Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.

A search for a doubly-charged Higgs boson in pp collisions atmore » $$ \\sqrt{s}=7 $$ TeV is presented. The data correspond to an integrated luminosity of 4.9 inverse femtobarns, collected by the CMS experiment at the LHC. The search is performed using events with three or more isolated charged leptons of any flavor, giving sensitivity to the decays of pair-produced triplet components Phi[++]Phi[--], and Phi[++]Phi[-] from associated production. No excess is observed compared to the background prediction, and upper limits at the 95% confidence level are set on the Phi[++] production cross section, under specific assumptions on its branching fractions. Lower bounds on the Phi[++] mass are reported, providing significantly more stringent constraints than previously published limits.« less

Effects of intracellular pH on the mitotic apparatus and mitotic stage in the sand dollar egg.

PubMed

Watanabe, K; Hamaguchi, M S; Hamaguchi, Y

1997-01-01

The effect of change in intracellular pH (pHi) on mitosis was investigated in the sand dollar egg. The pHi in the fertilized egg of Scaphechinus mirabilis and Clypeaster japonicus, which was 7.34 and 7.31, respectively, changed by means of treating the egg at nuclear envelope breakdown with sea water containing acetate and/or ammonia at various values of pH. The mitotic apparatus at pHi 6.70 became larger than that of normal fertilized eggs; that is, the mitotic spindle had the maximal size, especially in length at pHi 6.70. The spindle length linearly decreased when pHi increased from 6.70 to 7.84. By polarization microscopy, the increase in birefringence retardation was detected at slightly acidic pHi, suggesting that the increase in size of the spindle is caused by the increase in the amount of microtubules in the spindle. At pHi 6.30, the organization of the mitotic apparatus was inhibited. Furthermore, slightly acidic pHi caused cleavage retardation or inhibition. By counting the number of the eggs at various mitotic stages with time after treating them with the media, it is found that metaphase was persistent and most of the S. mirabilis eggs were arrested at metaphase under the condition of pHi 6.70. It is concluded that at slightly acidic pH, the microtubules in the spindle are stabilized and more microtubules assembled than those in the normal eggs.

Multisite Light-Induced Phosphorylation of the Transcription Factor PIF3 Is Necessary for Both Its Rapid Degradation and Concomitant Negative Feedback Modulation of Photoreceptor phyB Levels in Arabidopsis[C][W

PubMed Central

Ni, Weimin; Xu, Shou-Ling; Chalkley, Robert J.; Pham, Thao Nguyen D.; Guan, Shenheng; Maltby, Dave A.; Burlingame, Alma L.; Wang, Zhi-Yong; Quail, Peter H.

2013-01-01

Plants constantly monitor informational light signals using sensory photoreceptors, which include the phytochrome (phy) family (phyA to phyE), and adjust their growth and development accordingly. Following light-induced nuclear translocation, photoactivated phy molecules bind to and induce rapid phosphorylation and degradation of phy-interacting basic Helix Loop Helix (bHLH) transcription factors (PIFs), such as PIF3, thereby regulating the expression of target genes. However, the mechanisms underlying the signal-relay process are still not fully understood. Here, using mass spectrometry, we identify multiple, in vivo, light-induced Ser/Thr phosphorylation sites in PIF3. Using transgenic expression of site-directed mutants of PIF3, we provide evidence that a set of these phosphorylation events acts collectively to trigger rapid degradation of the PIF3 protein in response to initial exposure of dark-grown seedlings to light. In addition, we show that phyB-induced PIF3 phosphorylation is also required for the known negative feedback modulation of phyB levels in prolonged light, potentially through codegradation of phyB and PIF3. This mutually regulatory intermolecular transaction thus provides a mechanism with the dual capacity to promote early, graded, or threshold regulation of the primary, PIF3-controlled transcriptional network in response to initial light exposure, and later, to attenuate global sensitivity to the light signal through reductions in photoreceptor levels upon prolonged exposure. PMID:23903316

Elevated Prostate Health Index (phi) and Biopsy Reclassification During Active Surveillance of Prostate Cancer.

PubMed

Andreas, Darian; Tosoian, Jeffrey J; Landis, Patricia; Wolf, Sacha; Glavaris, Stephanie; Lotan, Tamara L; Schaeffer, Edward M; Sokoll, Lori J; Ross, Ashley E

2016-07-01

The Prostate Health Index (phi) has been FDA approved for decision-making regarding prostate biopsy. Phi has additionally been shown to positively correlate with tumor volume, extraprostatic disease and higher Gleason grade tumors. Here we describe a case in which an elevated phi encouraged biopsy of a gentleman undergoing active surveillance leading to reclassification of his disease as high risk prostate cancer.

Dye to use with virus challenge for testing barrier materials.

PubMed Central

Lytle, C D; Felten, R P; Truscott, W

1991-01-01

Can FD&C Blue no. 1 dye photoinactivate bacteriophages phi X174, T7, PRD1, and phi 6 under laboratory lighting conditions? At high levels of light, the dye (500 microM) photoinactivated only phi 6. Thus, this dye can be used at concentrations up to 500 microM with bacteriophages phi X174, T7, and PRD1 to test barrier material integrity. PMID:1872612

Tiny abortive initiation transcripts exert antitermination activity on an RNA hairpin-dependent intrinsic terminator.

PubMed

Lee, Sooncheol; Nguyen, Huong Minh; Kang, Changwon

2010-10-01

No biological function has been identified for tiny RNA transcripts that are abortively and repetitiously released from initiation complexes of RNA polymerase in vitro and in vivo to date. In this study, we show that abortive initiation affects termination in transcription of bacteriophage T7 gene 10. Specifically, abortive transcripts produced from promoter phi 10 exert trans-acting antitermination activity on terminator T phi both in vitro and in vivo. Following abortive initiation cycling of T7 RNA polymerase at phi 10, short G-rich and oligo(G) RNAs were produced and both specifically sequestered 5- and 6-nt C + U stretch sequences, consequently interfering with terminator hairpin formation. This antitermination activity depended on sequence-specific hybridization of abortive transcripts with the 5' but not 3' half of T phi RNA. Antitermination was abolished when T phi was mutated to lack a C + U stretch, but restored when abortive transcript sequence was additionally modified to complement the mutation in T phi, both in vitro and in vivo. Antitermination was enhanced in vivo when the abortive transcript concentration was increased via overproduction of RNA polymerase or ribonuclease deficiency. Accordingly, antitermination activity exerted on T phi by abortive transcripts should facilitate expression of T phi-downstream promoter-less genes 11 and 12 in T7 infection of Escherichia coli.

Estimation of Reconnection Flux Using Post-Eruption Arcades and Its Relevance to Magnetic Clouds at 1 AU

NASA Technical Reports Server (NTRS)

Gopalswamy, N.; Yashiro, S.; Akiyama, S.; Xie, H.

2017-01-01

We report on a new method to compute the flare reconnection (RC) flux from post-eruption arcades (PEAs) and the underlying photospheric magnetic fields. In previous works, the RC flux has been computed using the cumulative flare ribbon area. Here we obtain the RC flux as the flux in half of the area underlying the PEA in EUV imaged after the flare maximum. We apply this method to a set of 21 eruptions that originated near the solar disk center in Solar Cycle 23. We find that the RC flux from the arcade method ((Phi)rA) has excellent agreement with the flux from the flare-ribbon method ((Phi)rR) according to (Phi)rA = 1.24((Phi)rR)(sup 0.99). We also find (Phi)rA to be correlated with the poloidal flux ((Phi)P) of the associated magnetic cloud at 1 AU: (Phi)P = 1.20((Phi)rA)(sup 0.85). This relation is nearly identical to that obtained by Qiu et al. (Astrophys. J. 659, 758, 2007) using a set of only 9 eruptions. Our result supports the idea that flare reconnection results in the formation of the flux rope and PEA as a common process.

Role of phi cells and the endodermis under salt stress in Brassica oleracea.

PubMed

Fernandez-Garcia, N; Lopez-Perez, L; Hernandez, M; Olmos, E

2009-01-01

Phi cell layers were discovered in the 19th century in a small number of species, including members of the Brassicaceae family. A mechanical role was first suggested for this structure; however, this has never been demonstrated. The main objective of the present work was to analyse the ultrastructure of phi cells, their influence on ion movement from the cortex to the stele, and their contribution to salt stress tolerance in Brassica oleracea. Transmission electron microscopy and X-ray microanalysis studies were used to analyse the subcellular structure and distribution of ions in phi cells and the endodermis under salt stress. Ion movement was analysed using lanthanum as an apoplastic tracer. The ultrastructural results confirm that phi cells are specialized cells showing cell wall ingrowths in the inner tangential cell walls. X-ray microanalysis confirmed a build-up of sodium. Phi thickenings were lignified and lanthanum moved periplasmically at this level. To the best of our knowledge, this is the first study reporting the possible role of the phi cells as a barrier controlling the movement of ions from the cortex to the stele. Therefore, the phi cell layer and endodermis seem to be regulating ion transport in Brassica oleracea under salt stress.

Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis

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

Pletneva, Nadya V.; Pletnev, Vladimir Z., E-mail: vzpletnev@gmail.com; Souslova, Ekaterina

The yellow fluorescent protein phiYFPv with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium. The yellow fluorescent protein phiYFPv (λ{sub em}{sup max} ≃ 537 nm) with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium. The latter fluorescent protein is one of only two known cases of naturally occurring proteins that exhibit emission spectra in the yellow–orange range (535–555 nm). Here, the crystal structure of phiYFPv has been determined at 2.05 Å resolution. The ‘yellow’ chromophore formed from the sequence triad Thr65-Tyr66-Gly67 adoptsmore » the bicyclic structure typical of fluorophores emitting in the green spectral range. It was demonstrated that perfect antiparallel π-stacking of chromophore Tyr66 and the proximal Tyr203, as well as Val205, facing the chromophore phenolic ring are chiefly responsible for the observed yellow emission of phiYFPv at 537 nm. Structure-based site-directed mutagenesis has been used to identify the key functional residues in the chromophore environment. The obtained results have been utilized to improve the properties of phiYFPv and its homologous monomeric biomarker tagYFP.« less

Intracellular pH in sperm physiology.

PubMed

Nishigaki, Takuya; José, Omar; González-Cota, Ana Laura; Romero, Francisco; Treviño, Claudia L; Darszon, Alberto

2014-08-01

Intracellular pH (pHi) regulation is essential for cell function. Notably, several unique sperm ion transporters and enzymes whose elimination causes infertility are either pHi dependent or somehow related to pHi regulation. Amongst them are: CatSper, a Ca(2+) channel; Slo3, a K(+) channel; the sperm-specific Na(+)/H(+) exchanger and the soluble adenylyl cyclase. It is thus clear that pHi regulation is of the utmost importance for sperm physiology. This review briefly summarizes the key components involved in pHi regulation, their characteristics and participation in fundamental sperm functions such as motility, maturation and the acrosome reaction. Copyright © 2014 Elsevier Inc. All rights reserved.

On character amenability of Banach algebras

NASA Astrophysics Data System (ADS)

Kaniuth, E.; Lau, A. T.; Pym, J.

2008-08-01

We continue our work [E. Kaniuth, A.T. Lau, J. Pym, On [phi]-amenability of Banach algebras, Math. Proc. Cambridge Philos. Soc. 144 (2008) 85-96] in the study of amenability of a Banach algebra A defined with respect to a character [phi] of A. Various necessary and sufficient conditions of a global and a pointwise nature are found for a Banach algebra to possess a [phi]-mean of norm 1. We also completely determine the size of the set of [phi]-means for a separable weakly sequentially complete Banach algebra A with no [phi]-mean in A itself. A number of illustrative examples are discussed.

Extending the scanning angle of a phased array antenna by using a null-space medium

PubMed Central

Sun, Fei; He, Sailing

2014-01-01

By introducing a columnar null-space region as the reference space, we design a radome that can extend the scanning angle of a phased array antenna (PAA) by a predetermined relationship (e.g. a linear relationship between the incident angle and steered output angle can be achieved). After some approximation, we only need two homogeneous materials to construct the proposed radome layer by layer. This kind of medium is called a null-space medium, which has been studied and fabricated for realizing hyper-lenses and some other devices. Numerical simulations verify the performance of our radome. PMID:25355198

The genome of the Erwinia amylovora phage PhiEaH1 reveals greater diversity and broadens the applicability of phages for the treatment of fire blight.

PubMed

Meczker, Katalin; Dömötör, Dóra; Vass, János; Rákhely, Gábor; Schneider, György; Kovács, Tamás

2014-01-01

The enterobacterium Erwinia amylovora is the causal agent of fire blight. This study presents the analysis of the complete genome of phage PhiEaH1, isolated from the soil surrounding an E. amylovora-infected apple tree in Hungary. Its genome is 218 kb in size, containing 244 ORFs. PhiEaH1 is the second E. amylovora infecting phage from the Siphoviridae family whose complete genome sequence was determined. Beside PhiEaH2, PhiEaH1 is the other active component of Erwiphage, the first bacteriophage-based pesticide on the market against E. amylovora. Comparative genome analysis in this study has revealed that PhiEaH1 not only differs from the 10 formerly sequenced E. amylovora bacteriophages belonging to other phage families, but also from PhiEaH2. Sequencing of more Siphoviridae phage genomes might reveal further diversity, providing opportunities for the development of even more effective biological control agents, phage cocktails against Erwinia fire blight disease of commercial fruit crops.

[PHI regulates histone methylation and acetylation in Burkitt lymphoma Daudi cell line].

PubMed

Hong, Ling-Ling; Ma, Xu-Dong; Huang, Yi-Qun

2011-02-01

This study was purposed to investigate the effects of phenylhexyl isothiocyanate (PHI) on Burkitt lymphoma Daudi cell line and regulation of histone acetylation and methylation in Daudi cells, and to explore the potential mechanism. The apoptotic rate of Daudi cells treated with PHI was measured by flow cytometry, the changes of histone H3 and H4 acetylation, histone H3K9 and H3K4 methylation in Daudi cells treated with PHI were detected by Western blot. The results showed that PHI could induce apoptosis of Daudi cells, increased the acetylation level of H3 and H4, enhanced the methylation of H3K4, but reduced the methylation of H3K9. It is concluded that the PHI can up-regulate the acetylation level of histone H3 associated with transcription stimulation and the methylation of histone H3K4, down-regulate the methylation on histone H3K9 associated with transcription inhibition, promotes the apoptosis of Daudi cells. PHI may be a potential agent for target therapy of lymphoma.

The life of phi: the development of phi thickenings in roots of the orchids of the genus Miltoniopsis.

PubMed

Idris, Nurul A; Collings, David A

2015-02-01

Phi thickenings, bands of secondary wall thickenings that reinforce the primary wall of root cortical cells in a wide range of species, are described for the first time in the epiphytic orchid Miltoniopsis. As with phi thickenings found in other plants, the phi thickenings in Miltoniopsis contain highly aligned cellulose running along the lengths of the thickenings, and are lignified but not suberized. Using a combination of histological and immunocytochemical techniques, thickening development can be categorized into three different stages. Microtubules align lengthwise along the thickening during early and intermediate stages of development, and callose is deposited within the thickening in a pattern similar to the microtubules. These developing thickenings also label with the fluorescently tagged lectin wheat germ agglutinin (WGA). These associations with microtubules and callose, and the WGA labeling, all disappear when the phi thickenings are mature. This pattern of callose and WGA deposition show changes in the thickened cell wall composition and may shed light on the function of phi thickenings in plant roots, a role for which has yet to be established.

Particle-in-Cell laser-plasma simulation on Xeon Phi coprocessors

NASA Astrophysics Data System (ADS)

Surmin, I. A.; Bastrakov, S. I.; Efimenko, E. S.; Gonoskov, A. A.; Korzhimanov, A. V.; Meyerov, I. B.

2016-05-01

This paper concerns the development of a high-performance implementation of the Particle-in-Cell method for plasma simulation on Intel Xeon Phi coprocessors. We discuss the suitability of the method for Xeon Phi architecture and present our experience in the porting and optimization of the existing parallel Particle-in-Cell code PICADOR. Direct porting without code modification gives performance on Xeon Phi close to that of an 8-core CPU on a benchmark problem with 50 particles per cell. We demonstrate step-by-step optimization techniques, such as improving data locality, enhancing parallelization efficiency and vectorization leading to an overall 4.2 × speedup on CPU and 7.5 × on Xeon Phi compared to the baseline version. The optimized version achieves 16.9 ns per particle update on an Intel Xeon E5-2660 CPU and 9.3 ns per particle update on an Intel Xeon Phi 5110P. For a real problem of laser ion acceleration in targets with surface grating, where a large number of macroparticles per cell is required, the speedup of Xeon Phi compared to CPU is 1.6 ×.

Genome packaging in EL and Lin68, two giant phiKZ-like bacteriophages of P. aeruginosa.

PubMed

Sokolova, O S; Shaburova, O V; Pechnikova, E V; Shaytan, A K; Krylov, S V; Kiselev, N A; Krylov, V N

2014-11-01

A unique feature of the Pseudomonas aeruginosa giant phage phiKZ is its way of genome packaging onto a spool-like protein structure, the inner body. Until recently, no similar structures have been detected in other phages. We have studied DNA packaging in P. aeruginosa phages EL and Lin68 using cryo-electron microscopy and revealed the presence of inner bodies. The shape and positioning of the inner body and the density of the DNA packaging in EL are different from those found in phiKZ and Lin68. This internal organization explains how the shorter EL genome is packed into a large EL capsid, which has the same external dimensions as the capsids of phiKZ and Lin68. The similarity in the structural organization in EL and other phiKZ-like phages indicates that EL is phylogenetically related to other phiKZ-like phages, and, despite the lack of detectable DNA homology, EL, phiKZ, and Lin68 descend from a common ancestor. Copyright © 2014 Elsevier Inc. All rights reserved.

Developing Workforce Capacity in Public Health Informatics: Core Competencies and Curriculum Design

PubMed Central

Wholey, Douglas R.; LaVenture, Martin; Rajamani, Sripriya; Kreiger, Rob; Hedberg, Craig; Kenyon, Cynthia

2018-01-01

We describe a master’s level public health informatics (PHI) curriculum to support workforce development. Public health decision-making requires intensive information management to organize responses to health threats and develop effective health education and promotion. PHI competencies prepare the public health workforce to design and implement these information systems. The objective for a Master’s and Certificate in PHI is to prepare public health informaticians with the competencies to work collaboratively with colleagues in public health and other health professions to design and develop information systems that support population health improvement. The PHI competencies are drawn from computer, information, and organizational sciences. A curriculum is proposed to deliver the competencies and result of a pilot PHI program is presented. Since the public health workforce needs to use information technology effectively to improve population health, it is essential for public health academic institutions to develop and implement PHI workforce training programs. PMID:29770321

Intracellular pH of symbiotic dinoflagellates

NASA Astrophysics Data System (ADS)

Gibbin, E. M.; Davy, S. K.

2013-09-01

Intracellular pH (pHi) is likely to play a key role in maintaining the functional success of cnidarian-dinoflagellate symbiosis, yet until now the pHi of the symbiotic dinoflagellates (genus Symbiodinium) has never been quantified. Flow cytometry was used in conjunction with the ratiometric fluorescent dye BCECF to monitor changes in pHi over a daily light/dark cycle. The pHi of Symbiodinium type B1 freshly isolated from the model sea anemone Aiptasia pulchella was 7.25 ± 0.01 (mean ± SE) in the light and 7.10 ± 0.02 in the dark. A comparable effect of irradiance was seen across a variety of cultured Symbiodinium genotypes (types A1, B1, E1, E2, F1, and F5) which varied between pHi 7.21-7.39 in the light and 7.06-7.14 in the dark. Of note, there was a significant genotypic difference in pHi, irrespective of irradiance.

Macrophage tumoricidal mechanisms are selectively altered by prenatal chlordane exposure.

PubMed

Theus, S A; Tabor, D R; Soderberg, L S; Barnett, J B

1992-09-01

Macrophages (m phi) derived from mice treated in utero with chlordane show a significant delay of tumoricidal induction activity. In this study, m phi from chlordane-treated animals required a 48 h in vitro period of induction with interferon-gamma and lipopolysaccharide (IFN/LPS) before they could kill P815 targets. Similarly, m phi from chlordane-treated animals also failed to produce an immediate H2O2 burst upon perturbation. Conversely, their stimulated control m phi counterparts were tumoricidal by 2 h and exhibited a respiratory burst without any delay. Moreover, levels of the second messenger, inositol triphosphate (IP3), were significantly delayed in chlordane-treated animals following interaction with IFN/LPS. When nitrate/nitrite production was analyzed as an alternate mechanism for killing tumors, stimulated m phi from both normal and chlordane-treated animals responded equally. The data show that chlordane differentially introduces defects in m phi biochemical mechanisms associated with tumor killing.

Order and disorder in crystals of hexameric NTPases from dsRNA bacteriophages.

PubMed

Mancini, Erika J; Grimes, Jonathan M; Malby, Robyn; Sutton, Geoffrey C; Kainov, Denis E; Juuti, Jarmo T; Makeyev, Eugene V; Tuma, Roman; Bamford, Dennis H; Stuart, David I

2003-12-01

The packaging of genomic RNA in members of the Cystoviridae is performed by P4, a hexameric protein with NTPase activity. Across family members such as Phi6, Phi8 and Phi13, the P4 proteins show low levels of sequence identity, but presumably have similar atomic structures. Initial structure-determination efforts for P4 from Phi6 and Phi8 were hampered by difficulties in obtaining crystals that gave ordered diffraction. Diffraction from crystals of full-length P4 showed a variety of disorder and anisotropy. Subsequently, crystals of Phi13 P4 were obtained which yielded well ordered diffraction to 1.7 A. Comparison of the packing arrangements of P4 hexamers in different crystal forms and analysis of the disorder provides insights into the flexibility of this family of proteins, which might be an integral part of their biological function.

Measurement of differential cross sections in the $$\\phi^*$$ variable for inclusive Z boson production in pp collisions at $$\\sqrt{s}=$$ 8 TeV

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

Sirunyan, Albert M; et al.

Measurements of differential cross sections dmore » $$\\sigma$$/d$$\\phi^*$$ and double-differential cross sections d$$^2\\sigma$$/d$$\\phi^*\\,$$d$|y|$ for inclusive Z boson production are presented using the dielectron and dimuon final states. The kinematic observable $$\\phi^*$$ correlates with the dilepton transverse momentum but has better resolution, and $y$ is the dilepton rapidity. The analysis is based on data collected with the CMS experiment at a centre-of-mass energy of 8 TeV corresponding to an integrated luminosity of 19.7 fb$$^{-1}$$. The normalised cross section (1/$$\\sigma$$)$$\\,$$d$$\\sigma$$/d$$\\phi^*$$, within the fiducial kinematic region, is measured with a precision of better than 0.5% for $$\\phi^*$$<1. The measurements are compared to theoretical predictions and they agree, typically, within few percent.« less

Developing Workforce Capacity in Public Health Informatics: Core Competencies and Curriculum Design.

PubMed

Wholey, Douglas R; LaVenture, Martin; Rajamani, Sripriya; Kreiger, Rob; Hedberg, Craig; Kenyon, Cynthia

2018-01-01

We describe a master's level public health informatics (PHI) curriculum to support workforce development. Public health decision-making requires intensive information management to organize responses to health threats and develop effective health education and promotion. PHI competencies prepare the public health workforce to design and implement these information systems. The objective for a Master's and Certificate in PHI is to prepare public health informaticians with the competencies to work collaboratively with colleagues in public health and other health professions to design and develop information systems that support population health improvement. The PHI competencies are drawn from computer, information, and organizational sciences. A curriculum is proposed to deliver the competencies and result of a pilot PHI program is presented. Since the public health workforce needs to use information technology effectively to improve population health, it is essential for public health academic institutions to develop and implement PHI workforce training programs.

The polarization modulators based on liquid crystal variable retarders for the PHI and METIS instruments for the solar orbiter mission

NASA Astrophysics Data System (ADS)

Alvarez-Herrero, A.; García Parejo, P.; Laguna, H.; Villanueva, J.; Barandiarán, J.; Bastide, L.; Reina, M.; Royo, M.

2017-11-01

A technical development activity was carried out from 2009 to 2011 under ESA supervision to validate the Liquid Crystal Variable Retarders (LCVRs) as polarization modulators for the Solar Orbiter mission. After this, the technology achieved the Technology Readiness Level 5 (TRL5) corresponding to "Component Validation in Relevant Environment". Afterwards, additional tests and characterizations were performed in order to select the final specifications of the LCVRs cells to optimize their performances under the mission environmental conditions. The LCVRs will be used to measure the complete Stokes vector of the incoming light in PHI (The Polarimetric and Helioseismic Imager for Solar Orbiter) and the linear polarization in the case of METIS (Multi Element Telescope for Imaging and Spectroscopy). PHI is an imaging spectro-polarimeter that will acquire high resolution solar magnetograms. On the other hand, METIS is a solar coronagraph that will analyze the linear polarization for observations of the visible-light K-corona. The polarization modulators are described in this work including the optical, mechanical, thermal and electrical aspects. Both modulators will consist of two identical LCVRs with a relative azimuth orientation of 45° for PHI and parallel for the METIS modulator. In the first case, the configuration allows the analysis of the full Stockes vector with maximum polarimetric efficiencies. In the second setup, wide acceptance angles (<=+/-4°) are obtained. The polarization modulators will be thermal controlled to reach a stability better than +/-0.5°C during the measurement acquisition time (<=60s) under all the operational thermal conditions. This is required to fulfill the required polarimetric accuracy (<=10-3), because the LCVRs behavior has a dependence on temperature. The mechanical design has been conceived to minimize mass, volume and the thermal conductivity as well as the mechanical stress produced by the mounts to the cells, but taking into account the vibration environment due to the launch loads that the device shall withstand. Additionally, the optical clear aperture has been maximized and the design avoids breaks due to thermo-elastic deformations produced during the thermal cycling. Finally, the electrical cables and connections have been designed to obtain a very compact, modular and robust device.

Effect of dust charging and trapped electrons on nonlinear solitary structures in an inhomogeneous magnetized plasma

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

Kumar, Ravinder; Malik, Hitendra K.; Singh, Khushvant

2012-01-15

Main concerns of the present article are to investigate the effects of dust charging and trapped electrons on the solitary structures evolved in an inhomogeneous magnetized plasma. Such a plasma is found to support two types of waves, namely, fast wave and slow wave. Slow wave propagates in the plasma only when the wave propagation angle {theta} satisfies the condition {theta}{>=}tan{sup -1}{l_brace}({radical}((1+2{sigma})-[(n{sub dlh}({gamma}{sub 1}-1))/(1+n{sub dlh}{gamma}{sub 1})])-v{sub 0}/u{sub 0}){r_brace}, where v{sub 0}(u{sub 0}) is the z- (x-) component of ion drift velocity, {sigma} = T{sub i}/T{sub eff}, n{sub dlh} = n{sub d0}/(n{sub el0} + n{sub eh0}), and {gamma}{sub 1}=-(1/{Phi}{sub i0})[(1-{Phi}{sub i0}/1+{sigma}(1-{Phi}{submore » i0}))] together with T{sub i} as ion temperature, n{sub el0}(n{sub eh0}) as the density of trapped (isothermal) electrons, {Phi}{sub i0} as the dust grain (density n{sub d0}) surface potential relative to zero plasma potential, and T{sub eff}=(n{sub elo}+n{sub eho})T{sub el}T{sub eh}/(n{sub elo}T{sub eh}+n{sub eho}T{sub el}), where T{sub el}(T{sub eh}) is the temperature of trapped (isothermal) electrons. Both the waves evolve in the form of density hill type structures in the plasma, confirming that these solitary structures are compressive in nature. These structures are found to attain higher amplitude when the charge on the dust grains is fluctuated (in comparison with the case of fixed charge) and also when the dust grains and trapped electrons are more in number; the same is the case with higher temperature of ions and electrons. Slow solitary structures show weak dependence on the dust concentration. Both types of structures are found to become narrower under the application of stronger magnetic field. With regard to the charging of dust grains, it is observed that the charge gets reduced for the higher trapped electron density and temperature of ions and electrons, and dust charging shows weak dependence on the ion temperature.« less

Reusable design: A proposed approach to Public Health Informatics system design

PubMed Central

2011-01-01

Background Since it was first defined in 1995, Public Health Informatics (PHI) has become a recognized discipline, with a research agenda, defined domain-specific competencies and a specialized corpus of technical knowledge. Information systems form a cornerstone of PHI research and implementation, representing significant progress for the nascent field. However, PHI does not advocate or incorporate standard, domain-appropriate design methods for implementing public health information systems. Reusable design is generalized design advice that can be reused in a range of similar contexts. We propose that PHI create and reuse information design knowledge by taking a systems approach that incorporates design methods from the disciplines of Human-Computer Interaction, Interaction Design and other related disciplines. Discussion Although PHI operates in a domain with unique characteristics, many design problems in public health correspond to classic design problems, suggesting that existing design methods and solution approaches are applicable to the design of public health information systems. Among the numerous methodological frameworks used in other disciplines, we identify scenario-based design and participatory design as two widely-employed methodologies that are appropriate for adoption as PHI standards. We make the case that these methods show promise to create reusable design knowledge in PHI. Summary We propose the formalization of a set of standard design methods within PHI that can be used to pursue a strategy of design knowledge creation and reuse for cost-effective, interoperable public health information systems. We suggest that all public health informaticians should be able to use these design methods and the methods should be incorporated into PHI training. PMID:21333000

Direct CP Violation in Charmless Hadronic B-Meson Decays at the PEP-II Asymmetric B-Meson Factory

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

Telnov, Alexandre Valerievich; /UC, Berkeley

2005-05-06

The study of the quark transition b {yields} s{bar s}s, which is a pure loop-level (''penguin'') process leading to several B-meson-decay final states, most notably {phi}K, is arguably the hottest topic in B-meson physics today. The reason is the sensitivity of the amplitudes and the CP-violating asymmetries in such processes to physics beyond the Standard Model. By performing these measurements, we improve our understanding of the phenomenon of combined-parity (CP) violation, which is believed to be responsible for the dominance of matter over antimatter in our Universe. Here, we present measurements of branching fractions and charge asymmetries in the decaysmore » B{sup +} {yields} {phi}K{sup +} and B{sup 0} {yields} {phi}K{sup 0} in a sample of approximately 89 million B{bar B} pairs collected by the BABAR detector at the PEP-II asymmetric-energy B-meson Factory at SLAC. We determine {Beta}(B{sup +} {yields} {phi}K{sup +}) = (10.0{sub -0.8}{sup +0.9} {+-} 0.5) x 10{sup -6} and {Beta}(B{sup 0} {yields} {phi}K{sup 0}) = (8.4{sub -1.3}{sup +1.5} {+-} 0.5) x 10{sup -6}, where the first error is statistical and the second is systematic. Additionally, we measure the CP-violating charge asymmetry {Alpha}{sub CP}(B{sup {+-}} {yields} {phi}K{sup {+-}}) = 0.04 {+-} 0.09 {+-} 0.01, with a 90% confidence-level interval of [-0.10, 0.18], and set an upper limit on the CKM- and color-suppressed decay B{sup +} {yields} {phi}{pi}{sup +}, {Beta}(B{sup +} {yields} {phi}{pi}{sup +}) < 0.41 x 10{sup -6} (at the 90% confidence level). Our results are consistent with the Standard Model, which predicts {Alpha}{sub CP}(B{sup {+-}} {yields} {phi}K{sup {+-}}) {approx}< 1% and {Beta}(B {yields} {phi}{tau}) << 10{sup -7}. Since many models of physics beyond the Standard Model introduce additional loop diagrams with new heavy particles and new CP-violating phases that would contribute to these decays, potentially making {Alpha}{sub CP} (B{sup {+-}} {yields} {phi}K{sup {+-}}) and {Beta}(B {yields} {phi}{pi}) quite large, our results can be used to substantially constrain the parameter spaces of such models.« less

Is there a field-theoretic explanation for precursor biopolymers?

PubMed

Rosen, Gerald

2002-08-01

A Hu-Barkana-Gruzinov cold dark matter scalar field phi may enter a weak isospin invariant derivative interaction that causes the flow of right-handed electrons to align parallel to (inverted delta phi). Hence, in the outer regions of galaxies where (inverted delta phi) is large, as in galactic halos, the derivative interaction may induce a chirality-imbued quantum chemistry. Such a chirality-imbued chemistry would in turn be conducive to the formation of abundant precursor biopolymers on interstellar dust grains, comets and meteors in galactic halo regions, with subsequent delivery to planets in the inner galactic regions where phi and (inverted delta phi) are concomitantly near zero and left-right symmetric terrestrial quantum chemistry prevails.

Thermal performance testing of two Thales 9310 pulse-tube cryocoolers for PHyTIR

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

Paine, Christopher G.

2014-01-29

PHyTIR is a NASA-funded technology demonstration for a near-term earth-observing instrument in the thermal infrared spectrum, intended for use in the HyspIRI mission. PHyTIR will use two Thales 9310 single-stage pulse tube cryocoolers, one to directly cool the FPA, the other to simulate a passive radiator. We report performance measurements for the two Thales 9310 cryocoolers intended for inclusion in the PHyTIR demonstrator.

Genomic characterization of Ralstonia solanacearum phage phiRSB1, a T7-like wide-host-range phage.

PubMed

Kawasaki, Takeru; Shimizu, Mio; Satsuma, Hideki; Fujiwara, Akiko; Fujie, Makoto; Usami, Shoji; Yamada, Takashi

2009-01-01

PhiRSB1 is a wide-host-range, T7-like bacteriophage that infects and efficiently lyses the phytopathogenic bacterium Ralstonia solanacearum. The phiRSB1 genome comprises 43,079 bp of double-stranded DNA (61.7% G+C) with 325-bp terminal repeats and contains 47 open reading frames. Strong activity of tandem early promoters and wide specificity of phage promoters of phiRSB1 were demonstrated.

[The value of PHI/PCA3 in the early diagnosis of prostate cancer].

PubMed

Tan, S J; Xu, L W; Xu, Z; Wu, J P; Liang, K; Jia, R P

2016-01-12

To investigate the value of prostate health index (PHI) and prostate cancer gene 3 (PCA3) in the early diagnosis of prostate cancer (PCa). A total of 190 patients with abnormal serum prostate specific antigen (PSA) or abnormal digital rectal examination were enrolled. They were all underwent initial biopsy and 11 of them were also underwent repeated biopsy. In addition, 25 healthy cases (with normal digital rectal examination and PSA<4 ng/ml) were the control group.The PHI and PCA3 were detected by using immunofluorescence and Loop-Mediated Isothermal Amplification (LAMP). The sensitivity and specificity of diagnosis were determined by ROC curve.In addition, the relationship between PHI/PSA and the Gleason score and clinical stage were analyzed. A total of 89 patients were confirmed PCa by Pathological diagnosis. The other 101 patients were diagnosed as benign prostatic hyperplasia (BPH). The sensitivity and specificity of PCA3 test were 85.4% was 92.1%. Area under curve (AUC) of PHI is higher than AUC of PSA (0.727>0.699). The PHI in peripheral blood was positively correlated with Gleason score and clinical stage. The detection of PCA3 and PHI shows excellent detecting effectiveness. Compared with single PSA, the combined detection of PHI and PCA3 improved the diagnostic specificity. It can provide a new method for the early diagnosis in prostate cancer and avoid unnecessary biopsies.

Genome packaging in EL and Lin68, two giant phiKZ-like bacteriophages of P. aeruginosa

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

Sokolova, O.S., E-mail: sokolova@mail.bio.msu.ru; A.V. Shoubnikov Institute of Crystallography RAS, Moscow; Shaburova, O.V.

A unique feature of the Pseudomonas aeruginosa giant phage phiKZ is its way of genome packaging onto a spool-like protein structure, the inner body. Until recently, no similar structures have been detected in other phages. We have studied DNA packaging in P. aeruginosa phages EL and Lin68 using cryo-electron microscopy and revealed the presence of inner bodies. The shape and positioning of the inner body and the density of the DNA packaging in EL are different from those found in phiKZ and Lin68. This internal organization explains how the shorter EL genome is packed into a large EL capsid, whichmore » has the same external dimensions as the capsids of phiKZ and Lin68. The similarity in the structural organization in EL and other phiKZ-like phages indicates that EL is phylogenetically related to other phiKZ-like phages, and, despite the lack of detectable DNA homology, EL, phiKZ, and Lin68 descend from a common ancestor. - Highlights: • We performed a comparative structural study of giant P. aeruginosa phages: EL, Lin68 and phiKZ. • We revealed that the inner body is a common feature in giant phages. • The phage genome size correlates with the overall dimensions of the inner body.« less

Expression, purification and characterization of a phyAm-phyCs fusion phytase*

PubMed Central

Zou, Li-kou; Wang, Hong-ning; Pan, Xin; Tian, Guo-bao; Xie, Zi-wen; Wu, Qi; Chen, Hui; Xie, Tao; Yang, Zhi-rong

2008-01-01

The phyAm gene encoding acid phytase and optimized neutral phytase phyCs gene were inserted into expression vector pPIC9K in correct orientation and transformed into Pichia pastoris in order to expand the pH profile of phytase and decrease the cost of production. The fusion phytase phyAm-phyCs gene was successfully overexpressed in P. pastoris as an active and extracellular phytase. The yield of total extracellular fusion phytase activity is (25.4±0.53) U/ml at the flask scale and (159.1±2.92) U/ml for high cell-density fermentation, respectively. Purified fusion phytase exhibits an optimal temperature at 55 °C and an optimal pH at 5.5~6.0 and its relative activity remains at a relatively high level of above 70% in the range of pH 2.0 to 7.0. About 51% to 63% of its original activity remains after incubation at 75 °C to 95 °C for 10 min. Due to heavy glycosylation, the expressed fusion phytase shows a broad and diffuse band in SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis). After deglycosylation by endoglycosidase H (EndoHf), the enzyme has an apparent molecular size of 95 kDa. The characterization of the fusion phytase was compared with those of phyCs and phyAm. PMID:18600783

PhiC31 recombination system demonstrates heritable germinal transmission of site-specific excision from the Arabidopsis genome

PubMed Central

2010-01-01

Background The large serine recombinase phiC31 from broad host range Streptomyces temperate phage, catalyzes the site-specific recombination of two recognition sites that differ in sequence, typically known as attachment sites attB and attP. Previously, we characterized the phiC31 catalytic activity and modes of action in the fission yeast Schizosaccharomyces pombe. Results In this work, the phiC31 recombinase gene was placed under the control of the Arabidopsis OXS3 promoter and introduced into Arabidopsis harboring a chromosomally integrated attB and attP-flanked target sequence. The phiC31 recombinase excised the attB and attP-flanked DNA, and the excision event was detected in subsequent generations in the absence of the phiC31 gene, indicating germinal transmission was possible. We further verified that the genomic excision was conservative and that introduction of a functional recombinase can be achieved through secondary transformation as well as manual crossing. Conclusion The phiC31 system performs site-specific recombination in germinal tissue, a prerequisite for generating stable lines with unwanted DNA removed. The precise site-specific deletion by phiC31 in planta demonstrates that the recombinase can be used to remove selectable markers or other introduced transgenes that are no longer desired and therefore can be a useful tool for genome engineering in plants. PMID:20178628

Embryonic common snapping turtles (Chelydra serpentina) preferentially regulate intracellular tissue pH during acid-base challenges.

PubMed

Shartau, Ryan B; Crossley, Dane A; Kohl, Zachary F; Brauner, Colin J

2016-07-01

The nests of embryonic turtles naturally experience elevated CO2 (hypercarbia), which leads to increased blood PCO2  and a respiratory acidosis, resulting in reduced blood pH [extracellular pH (pHe)]. Some fishes preferentially regulate tissue pH [intracellular pH (pHi)] against changes in pHe; this has been proposed to be associated with exceptional CO2 tolerance and has never been identified in amniotes. As embryonic turtles may be CO2 tolerant based on nesting strategy, we hypothesized that they preferentially regulate pHi, conferring tolerance to severe acute acid-base challenges. This hypothesis was tested by investigating pH regulation in common snapping turtles (Chelydra serpentina) reared in normoxia then exposed to hypercarbia (13 kPa PCO2 ) for 1 h at three developmental ages: 70% and 90% of incubation, and yearlings. Hypercarbia reduced pHe but not pHi, at all developmental ages. At 70% of incubation, pHe was depressed by 0.324 pH units while pHi of brain, white muscle and lung increased; heart, liver and kidney pHi remained unchanged. At 90% of incubation, pHe was depressed by 0.352 pH units but heart pHi increased with no change in pHi of other tissues. Yearlings exhibited a pHe reduction of 0.235 pH units but had no changes in pHi of any tissues. The results indicate common snapping turtles preferentially regulate pHi during development, but the degree of response is reduced throughout development. This is the first time preferential pHi regulation has been identified in an amniote. These findings may provide insight into the evolution of acid-base homeostasis during development of amniotes, and vertebrates in general. © 2016. Published by The Company of Biologists Ltd.

Evidence for the role of a Na(+)/HCO(3)(-) cotransporter in trout hepatocyte pHi regulation.

PubMed

Furimsky, M; Moon, T W; Perry, S F

2000-07-01

The mechanisms of intracellular pH (pHi) regulation were examined in hepatocytes of the rainbow trout Oncorhynchus mykiss. pHi was monitored using the pH-sensitive fluorescent dye BCECF, and the effects of various media and pharmacological agents were examined for their influence on baseline pHi and recovery rates from acid and base loading. Rates of Na(+) uptake were measured using (22)Na, and changes in membrane potential were examined using the potentiometric fluorescent dye Oxonol VI. The rate of proton extrusion following acid loading was diminished by the blockade of either Na(+)/H(+) exchange (using amiloride) or anion transport (using DIDS). The removal of external HCO(3)(-) and the abolition of outward K(+) diffusion by the channel blocker Ba(2+) also decreased the rate of proton extrusion following acid load. Depolarization of the cell membrane with 50 mmol l(-)(1) K(+), however, did not affect pHi. The rate of recovery from base loading was significantly diminished by the blockade of anion transport, removal of external HCO(3)(-) and, to a lesser extent, by blocking Na(+)/H(+) exchange. The blockade of K(+) conductance had no effect. The decrease in Na(+) uptake rate observed in the presence of the anion transport blocker DIDS and the DIDS-sensitive hyperpolarization of membrane potential during recovery from acid loading suggest that a Na(+)-dependent electrogenic transport system is involved in the restoration of pHi after intracellular acidification. The effects on baseline pHi indicate that the different membrane exchangers are tonically active in the maintenance of steady-state pHi. This study confirms the roles of a Na(+)/H(+) exchanger and a Cl(-)/HCO(3)(-) exchanger in the regulation of trout hepatocyte pHi and provides new evidence that a Na(+)/HCO(3)(-) cotransporter contributes to pHi regulation.

Characterization of beta-turn and Asx-turns mimicry in a model peptide: stabilization via C--H . . . O interaction.

PubMed

Thakur, A K; Kishore, R

2006-04-15

The chemical synthesis and single-crystal X-ray diffraction analysis of a model peptide, Boc-Thr-Thr-NH2 (1) comprised of proteinogenic residues bearing an amphiphilic Cbeta -stereogenic center, has been described. Interestingly, the analysis of its molecular structure revealed the existence of a distinct conformation that mimics a typical beta-turn and Asx-turns, i.e., the two Thr residues occupy the left- and right-corner positions. The main-chain torsion angles of the N- and C-terminal residues i.e., semiextended: phi = -68.9 degrees , psi = 128.6 degrees ; semifolded: phi = -138.1 degrees , psi = 2.5 degrees conformations, respectively, in conjunction with a gauche- disposition of the obligatory C-terminus Thr CgammaH3 group, characterize the occurrence of the newly described beta-turn- and Asx-turns-like topology. The preferred molecular structure is suggested to be stabilized by an effective nonconventional main-chain to side-chain Ci=O . . . H--Cgamma(i+2)-type intraturn hydrogen bond. Noteworthy, the observed topology of the resulting 10-membered hydrogen-bonded ring is essentially similar to the one perceived for a classical beta-turn and the Asx-turns, stabilized by a conventional intraturn hydrogen bond. Considering the signs as well as magnitudes of the backbone torsion angles and the orientation of the central peptide bond, the overall mimicked topology resembles the type II beta-turn or type II Asx-turns. An analysis of Xaa-Thr sequences in high-resolution X-ray elucidated protein structures revealed the novel topology prevalence in functional proteins (unpublished). In view of indubitable structural as well as functional importance of nonconventional interactions in bioorganic and biomacromolecules, we intend to highlight the participation of Thr CgammaH in the creation of a short-range C=O . . . H--Cgamma -type interaction in peptides and proteins. Copyright 2006 Wiley Periodicals, Inc.

Intracellular pH regulation by acid-base transporters in mammalian neurons

PubMed Central

Ruffin, Vernon A.; Salameh, Ahlam I.; Boron, Walter F.; Parker, Mark D.

2014-01-01

Intracellular pH (pHi) regulation in the brain is important in both physiological and physiopathological conditions because changes in pHi generally result in altered neuronal excitability. In this review, we will cover 4 major areas: (1) The effect of pHi on cellular processes in the brain, including channel activity and neuronal excitability. (2) pHi homeostasis and how it is determined by the balance between rates of acid loading (JL) and extrusion (JE). The balance between JE and JL determine steady-state pHi, as well as the ability of the cell to defend pHi in the face of extracellular acid-base disturbances (e.g., metabolic acidosis). (3) The properties and importance of members of the SLC4 and SLC9 families of acid-base transporters expressed in the brain that contribute to JL (namely the Cl-HCO3 exchanger AE3) and JE (the Na-H exchangers NHE1, NHE3, and NHE5 as well as the Na+- coupled HCO3− transporters NBCe1, NBCn1, NDCBE, and NBCn2). (4) The effect of acid-base disturbances on neuronal function and the roles of acid-base transporters in defending neuronal pHi under physiopathologic conditions. PMID:24592239

Comparative evaluation of urinary PCA3 and TMPRSS2: ERG scores and serum PHI in predicting prostate cancer aggressiveness.

PubMed

Tallon, Lucile; Luangphakdy, Devillier; Ruffion, Alain; Colombel, Marc; Devonec, Marian; Champetier, Denis; Paparel, Philippe; Decaussin-Petrucci, Myriam; Perrin, Paul; Vlaeminck-Guillem, Virginie

2014-07-30

It has been suggested that urinary PCA3 and TMPRSS2:ERG fusion tests and serum PHI correlate to cancer aggressiveness-related pathological criteria at prostatectomy. To evaluate and compare their ability in predicting prostate cancer aggressiveness, PHI and urinary PCA3 and TMPRSS2:ERG (T2) scores were assessed in 154 patients who underwent radical prostatectomy for biopsy-proven prostate cancer. Univariate and multivariate analyses using logistic regression and decision curve analyses were performed. All three markers were predictors of a tumor volume≥0.5 mL. Only PHI predicted Gleason score≥7. T2 score and PHI were both independent predictors of extracapsular extension(≥pT3), while multifocality was only predicted by PCA3 score. Moreover, when compared to a base model (age, digital rectal examination, serum PSA, and Gleason sum at biopsy), the addition of both PCA3 score and PHI to the base model induced a significant increase (+12%) when predicting tumor volume>0.5 mL. PHI and urinary PCA3 and T2 scores can be considered as complementary predictors of cancer aggressiveness at prostatectomy.

Imaging of Intracellular pH in Tumor Spheroids Using Genetically Encoded Sensor SypHer2.

PubMed

Zagaynova, Elena V; Druzhkova, Irina N; Mishina, Natalia M; Ignatova, Nadezhda I; Dudenkova, Varvara V; Shirmanova, Marina V

2017-01-01

Intracellular pH (pHi) is one of the most important parameters that regulate the physiological state of cells and tissues. pHi homeostasis is crucial for normal cell functioning. Cancer cells are characterized by having a higher (neutral to slightly alkaline) pHi and lower (acidic) extracellular pH (pHe) compared to normal cells. This is referred to as a "reversed" pH gradient, and is essential in supporting their accelerated growth rate, invasion and migration, and in suppressing anti-tumor immunity, the promotion of metabolic coupling with fibroblasts and in preventing apoptosis. Moreover, abnormal pH, both pHi and pHe, contribute to drug resistance in cancers. Therefore, the development of methods for measuring pH in living tumor cells is likely to lead to better understanding of tumor biology and to open new ways for cancer treatment. Genetically encoded, fluorescent, pH-sensitive probes represent promising instruments enabling the subcellular measurement of pHi with unrivaled specificity and high accuracy. Here, we describe a protocol for pHi imaging at a microscopic level in HeLa tumor spheroids, using the genetically encoded ratiometric (dual-excitation) pHi indicator, SypHer2.

77 FR 71172 - Proposed Collection; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-29

... beneficiaries on their TRICARE benefits. Personal health information (PHI) and personally identifiable.../PHI to obtain and verify TRICARE eligibility, treatment, payment, and other healthcare operations... during the case resolution process, individuals may object to the collection of PHI and PII via verbal or...

Spectral observations of Be stars in the visible range. I - Phi Per, Psi Per, 11 Cam, and Phi And

NASA Astrophysics Data System (ADS)

Krugov, V. D.

1986-02-01

Phi Per was found to display considerable variations of emission in H-alpha and H-beta. The H-alpha and H-beta emission profiles of Psi Per appeared to vary with a period of several years. A complete disappearance of H-alpha emission was observed for 11 Cam. Finally, the H-alpha emission for Phi And did not display intensity variations during the entire period of observations in 1983.

The Effects of Exercise on Pharmacokinetics and Pharmacodynamics of Physostigmine in Rats

DTIC Science & Technology

1989-02-15

Phy ( cholinesterase activity ) are likely to be altered by exercise due to altered blood flow rates to liver and pH of muscle. During exercise...concurrent acute exercise on the ChE activity in RBC aad tissues and in blood biochemical parameters in rats. Phy has been reported to reduce the...Springfield, Illinois. Also, we have studied the effect of exercise training, Phy and training + Phy on ChE activity in RBC and tissues and on blood biochemi

PHI and PCA3 improve the prognostic performance of PRIAS and Epstein criteria in predicting insignificant prostate cancer in men eligible for active surveillance.

PubMed

Cantiello, Francesco; Russo, Giorgio Ivan; Cicione, Antonio; Ferro, Matteo; Cimino, Sebastiano; Favilla, Vincenzo; Perdonà, Sisto; De Cobelli, Ottavio; Magno, Carlo; Morgia, Giuseppe; Damiano, Rocco

2016-04-01

To assess the performance of prostate health index (PHI) and prostate cancer antigen 3 (PCA3) when added to the PRIAS or Epstein criteria in predicting the presence of pathologically insignificant prostate cancer (IPCa) in patients who underwent radical prostatectomy (RP) but eligible for active surveillance (AS). An observational retrospective study was performed in 188 PCa patients treated with laparoscopic or robot-assisted RP but eligible for AS according to Epstein or PRIAS criteria. Blood and urinary specimens were collected before initial prostate biopsy for PHI and PCA3 measurements. Multivariate logistic regression analyses and decision curve analysis were carried out to identify predictors of IPCa using the updated ERSPC definition. At the multivariate analyses, the inclusion of both PCA3 and PHI significantly increased the accuracy of the Epstein multivariate model in predicting IPCa with an increase of 17 % (AUC = 0.77) and of 32 % (AUC = 0.92), respectively. The inclusion of both PCA3 and PHI also increased the predictive accuracy of the PRIAS multivariate model with an increase of 29 % (AUC = 0.87) and of 39 % (AUC = 0.97), respectively. DCA revealed that the multivariable models with the addition of PHI or PCA3 showed a greater net benefit and performed better than the reference models. In a direct comparison, PHI outperformed PCA3 performance resulting in higher net benefit. In a same cohort of patients eligible for AS, the addition of PHI and PCA3 to Epstein or PRIAS models improved their prognostic performance. PHI resulted in greater net benefit in predicting IPCa compared to PCA3.

Distinct moieties underlie biphasic H+ gating of connexin43 channels, producing a pH optimum for intercellular communication

PubMed Central

Garciarena, Carolina D.; Malik, Akif; Swietach, Pawel; Moreno, Alonso P.; Vaughan-Jones, Richard D.

2018-01-01

Most mammalian cells can intercommunicate via connexin-assembled, gap-junctional channels. To regulate signal transmission, connexin (Cx) channel permeability must respond dynamically to physiological and pathophysiological stimuli. One key stimulus is intracellular pH (pHi), which is modulated by a tissue’s metabolic and perfusion status. Our understanding of the molecular mechanism of H+ gating of Cx43 channels—the major isoform in the heart and brain—is incomplete. To interrogate the effects of acidic and alkaline pHi on Cx43 channels, we combined voltage-clamp electrophysiology with pHi imaging and photolytic H+ uncaging, performed over a range of pHi values. We demonstrate that Cx43 channels expressed in HeLa or N2a cell pairs are gated biphasically by pHi via a process that consists of activation by H+ ions at alkaline pHi and inhibition at more acidic pHi. For Cx43 channel–mediated solute/ion transmission, the ensemble of these effects produces a pHi optimum, near resting pHi. By using Cx43 mutants, we demonstrate that alkaline gating involves cysteine residues of the C terminus and is independent of motifs previously implicated in acidic gating. Thus, we present a molecular mechanism by which cytoplasmic acid–base chemistry fine tunes intercellular communication and establishes conditions for the optimal transmission of solutes and signals in tissues, such as the heart and brain.—Garciarena, C. D., Malik, A., Swietach, P., Moreno, A. P., Vaughan-Jones, R. D. Distinct moieties underlie biphasic H+ gating of connexin43 channels, producing a pH optimum for intercellular communication. PMID:29183963

Prostate health index (phi) and prostate cancer antigen 3 (PCA3) significantly improve diagnostic accuracy in patients undergoing prostate biopsy.

PubMed

Perdonà, Sisto; Bruzzese, Dario; Ferro, Matteo; Autorino, Riccardo; Marino, Ada; Mazzarella, Claudia; Perruolo, Giuseppe; Longo, Michele; Spinelli, Rosa; Di Lorenzo, Giuseppe; Oliva, Andrea; De Sio, Marco; Damiano, Rocco; Altieri, Vincenzo; Terracciano, Daniela

2013-02-15

Prostate health index (phi) and prostate cancer antigen 3 (PCA3) have been recently proposed as novel biomarkers for prostate cancer (PCa). We assessed the diagnostic performance of these biomarkers, alone or in combination, in men undergoing first prostate biopsy for suspicion of PCa. One hundred sixty male subjects were enrolled in this prospective observational study. PSA molecular forms, phi index (Beckman coulter immunoassay), PCA3 score (Progensa PCA3 assay), and other established biomarkers (tPSA, fPSA, and %fPSA) were assessed before patients underwent a 18-core first prostate biopsy. The discriminating ability between PCa-negative and PCa-positive biopsies of Beckman coulter phi and PCA3 score and other used biomarkers were determined. One hundred sixty patients met inclusion criteria. %p2PSA (p2PSA/fPSA × 100), phi and PCA3 were significantly higher in patients with PCa compared to PCa-negative group (median values: 1.92 vs. 1.55, 49.97 vs. 36.84, and 50 vs. 32, respectively, P ≤ 0.001). ROC curve analysis showed that %p2PSA, phi, and PCA3 are good indicator of malignancy (AUCs = 0.68, 0.71, and 0.66, respectively). A multivariable logistic regression model consisting of both the phi index and PCA3 score allowed to reach an overall diagnostic accuracy of 0.77. Decision curve analysis revealed that this "combined" marker achieved the highest net benefit over the examined range of the threshold probability. phi and PCA3 showed no significant difference in the ability to predict PCa diagnosis in men undergoing first prostate biopsy. However, diagnostic performance is significantly improved by combining phi and PCA3. Copyright © 2012 Wiley Periodicals, Inc.

Effects of plasmalemmal V-ATPase activity on plasma membrane potential of resident alveolar macrophages.

PubMed

Heming, T A; Bidani, A

2003-01-01

The acid-base status and functional responses of alveolar macrophages (mphi) are influenced by the activity of plasmalemmal V-type H+-pump (V-ATPase), an electrogenic H+ extruder that provides a possible link between intracellular pH (pHi) and plasma membrane potential (Em). This study examined the relationships among Em, pHi, and plasmalemmal V-ATPase activity in resident alveolar mphi from rabbits. Em and pHi were measured using fluorescent probes. Em was -46 mV and pHi was 7.14 at an extracellular pH (pHo) of 7.4. The pHi declined progressively at lower pHo values. Decrements in pHo, also caused depolarization of the plasma membrane, independent of V-ATPase activity. The pH effects on Em were sensitive to external K+, and hence, probably involved pH-sensitive K+ conductance. H+ were not distributed at equilibrium across the plasma membrane. V-ATPase activity was a major determinant of the transmembrane H+ disequilibrium. Pump inhibition with bafilomycin A1 caused cytosolic acidification, due most likely to the retention of metabolically generated H+. V-ATPase inhibition also caused depolarization of the plasma membrane, but the effects were mediated indirectly via the accompanying pHi changes. V-ATPase activity was sensitive to Em. Em hyperpolarization (valinomycin-clamp) reduced V-ATPase activity, causing an acidic shift in baseline pHi under steady-state conditions and slowing pHi recovery from NH4Cl prepulse acid-loads. The findings indicate that a complex relationship exists among Em, pHi, and pHo that was partially mediated by plasmalemmal V-ATPase activity. This relationship could have important consequences for the expression of pH- and/or voltage-sensitive functions in alveolar mphi.

Effective recombination coefficient and solar zenith angle effects on low-latitude D-region ionosphere evaluated from VLF signal amplitude and its time delay during X-ray solar flares

NASA Astrophysics Data System (ADS)

Basak, Tamal; Chakrabarti, Sandip Kumar

Excess solar X-ray radiation during solar flares causes an enhancement of ionization in the ionospheric D-region and hence affects sub-ionospherically propagating VLF signal amplitude and phase. VLF signal amplitude perturbation (DeltaA) and amplitude time delay (Deltat) (vis- ´a-vis corresponding X-ray light curve as measured by GOES-15) of NWC/19.8 kHz signal have been computed for solar flares which is detected by us during Jan-Sep 2011. The signal is recorded by SoftPAL facility of IERC/ICSP, Sitapur (22(°) 27'N, 87(°) 45'E), West Bengal, India. In first part of the work, using the well known LWPC technique, we simulated the flare induced excess lower ionospheric electron density by amplitude perturbation method. Unperturbed D-region electron density is also obtained from simulation and compared with IRI-model results. Using these simulation results and time delay as key parameters, we calculate the effective electron recombination coefficient (alpha_{eff}) at solar flare peak region. Our results match with the same obtained by other established models. In the second part, we dealt with the solar zenith angle effect on D-region during flares. We relate this VLF data with the solar X-ray data. We find that the peak of the VLF amplitude occurs later than the time of the X-ray peak for each flare. We investigate this so-called time delay (Deltat). For the C-class flares we find that there is a direct correspondence between Deltat of a solar flare and the average solar zenith angle Z over the signal propagation path at flare occurrence time. Now for deeper analysis, we compute the Deltat for different local diurnal time slots DT. We find that while the time delay is anti-correlated with the flare peak energy flux phi_{max} independent of these time slots, the goodness of fit, as measured by reduced-chi(2) , actually worsens as the day progresses. The variation of the Z dependence of reduced-chi(2) seems to follow the variation of standard deviation of Z along the T_x-R_x propagation path. In other words, for the flares having almost constant Z over the path a tighter anti-correlation between Deltat and phi_{max} was observed.

Cross Cell Sandwich Core

NASA Technical Reports Server (NTRS)

Ford, Donald B. (Inventor)

2004-01-01

A sandwich core comprises two faceplates separated by a plurality of cells. The cells are comprised of walls positioned at oblique angles relative to a perpendicular axis extending through the faceplates. The walls preferably form open cells and are constructed from open cells and are constructed from rows of ribbons. The walls may be obliquely angled relative to more than one plane extending through the perpendicular axis.

Nonequilibrium dynamic phases in driven vortex lattices with periodic pinning

NASA Astrophysics Data System (ADS)

Reichhardt, Charles Michael

1998-12-01

We present the results of an extensive series of simulations of flux-gradient and current driven vortices interacting with either random or periodically arranged pinning sites. First, we consider flux-gradient-driven simulations of superconducting vortices interacting with strong randomly-distributed columnar pinning defects, as an external field H(t) is quasi-statically swept from zero through a matching field Bsb{phi}. Here, we find significant changes in the behavior of the local flux density B(x, y, H(t)), magnetization M(H(t)), critical current Jsb{c}(B(t)), and the individual vortex flow paths, as the local flux density crosses Bsb{phi}. Further, we find that for a given pin density, Jsb{c}(B) can be enhanced by maximizing the distance between the pins for B < Bsb{phi}. For the case of periodic pinning sites as a function of applied field, we find a rich variety of ordered and partially-ordered vortex lattice configurations. We present formulas that predict the matching fields at which commensurate vortex configurations occur and the vortex lattice orientation with respect to the pinning lattice. Our results are in excellent agreement with recent imaging experiments on square pinning arrays (K. Harada et al., Science 274, 1167 (1996)). For current driven simulations with periodic pinning we find a remarkable number of dynamical plastic flow phases. Signatures of the transitions between these different dynamical phases include sudden jumps in the current-voltage curves, hysteresis, as well as marked changes in the vortex trajectories and vortex lattice order. These phases are outlined in a series of dynamic phase diagrams. We show that several of these phases and their phase-boundaries can be understood in terms of analytical arguments. Finally, when the vortex lattice is driven at varying angles with respect to the underlying periodic pinning array, the transverse voltage-current V(I) curves show a series of mode-locked plateaus with the overall V(I) forming a devil's staircase structure.

Revolution rather than rotation of AAA+ hexameric phi29 nanomotor for viral dsDNA packaging without coiling☆

PubMed Central

Schwartz, Chad; De Donatis, Gian Marco; Zhang, Hui; Fang, Huaming; Guo, Peixuan

2013-01-01

It has long been believed that the DNA-packaging motor of dsDNA viruses utilizes a rotation mechanism. Here we report a revolution rather than rotation mechanism for the bacteriophage phi29 DNA packaging motor. The phi29 motor contains six copies of the ATPase (Schwartz et al., this issue); ATP binding to one ATPase subunit stimulates the ATPase to adopt a conformation with a high affinity for dsDNA. ATP hydrolysis induces a new conformation with a lower affinity, thus transferring the dsDNA to an adjacent subunit by a power stroke. DNA revolves unidirectionally along the hexameric channel wall of the ATPase, but neither the dsDNA nor the ATPase itself rotates along its own axis. One ATP is hydrolyzed in each transitional step, and six ATPs are consumed for one helical turn of 360°. Transition of the same dsDNA chain along the channel wall, but at a location 60° different from the last contact, urges dsDNA to move forward 1.75 base pairs each step (10.5 bp per turn/6ATP=1.75 bp per ATP). Each connector subunit tilts with a left-handed orientation at a 30° angle in relation to its vertical axis that runs anti-parallel to the right-handed dsDNA helix, facilitating the one-way traffic of dsDNA. The connector channel has been shown to cause four steps of transition due to four positively charged lysine rings that make direct contact with the negatively charged DNA phosphate backbone. Translocation of dsDNA into the procapsid by revolution avoids the difficulties during rotation that are associated with DNA supercoiling. Since the revolution mechanism can apply to any stoichiometry, this motor mechanism might reconcile the stoichiometry discrepancy in many phage systems where the ATPase has been found as a tetramer, hexamer, or nonamer. PMID:23763768

An RR Lyrae period shift in terms of the Fourier parameter Phi sub 31

NASA Technical Reports Server (NTRS)

Clement, Christine M.; Jankulak, Michael; Simon, Norman R.

1992-01-01

The Fourier phase parameter Phi sub 31 has been determined for RRc stars in five globular clusters, NGC 6171, M5, M3, M53, and M15. The results indicate that the RRc stars in a given cluster show a sequence of Phi sub 31 increasing with period, and that the higher the cluster metallicity, the higher the sequence lies in a plot of Phi sub 31 with period. The Phi sub 31 values for the stars in NGC 6171 and M5 presented here are based on observations made with the University of Toronto 0.61 m telescope at Las Campanas, Chile, while those for M3, M53, and M15 are based on published data. A bootstrap procedure has been used to establish the uncertainties in the Fourier parameters. The physical significance of the relationship among Phi sub 31, period, and metallicity is not yet understood. It will need to be tested with hydrodynamic pulsation models computed with new opacities.

The complete genome sequence and proteomics of Yersinia pestis phage Yep-phi.

PubMed

Zhao, Xiangna; Wu, Weili; Qi, Zhizhen; Cui, Yujun; Yan, Yanfeng; Guo, Zhaobiao; Wang, Zuyun; Wang, Hu; Deng, Haijun; Xue, Yan; Chen, Weijun; Wang, Xiaoyi; Yang, Ruifu

2011-01-01

Yep-phi, a lytic phage of Yersinia pestis, was isolated in China and is routinely used as a diagnostic phage for the identification of the plague pathogen. Yep-phi has an isometric hexagonal head containing dsDNA and a short non-contractile conical tail. In this study, we sequenced the Yep-phi genome (GenBank accession no. HQ333270) and performed proteomics analysis. The genome consists of 38 ,616 bp of DNA, including direct terminal repeats of 222 bp, and is predicted to contain 45 ORFs. Most structural proteins were identified by proteomics analysis. Compared with the three available genome sequences of lytic phages for Y. pestis, the phages could be divided into two subgroups. Yep-phi displays marked homology to the bacteriophages Berlin (GenBank accession no. AM183667) and Yepe2 (GenBank accession no. EU734170), and these comprise one subgroup. The other subgroup is represented by bacteriophage ΦA1122 (GenBank accession no. AY247822). Potential recombination was detected among the Yep-phi subgroup.

[Prevalence of HIV treatment in PHI].

PubMed

Wild, F; Finkenstädt, V

2013-12-01

The importance of HIV in PHI is examined on the basis of the "AIDS statistics" of the Association of PHI and pharmaceutical data from PHI. The observation period is from 2007 to 2011. We define a HIV case if a private insured person has submitted at least one HIV-related invoice (e.g., an antiretroviral drug) for reimbursement during the observation period. In 2011, 7,624 people in PHI received HIV therapy, that is 32% (+1888) more than in 2007. The number of new HIV cases in 2011 was 673, and thus 12% (-92) lower than in 2007. The proportion of people receiving antiretroviral therapy in PHI is higher than in the general population in Germany. HIV infections occur in all age groups, but peaks in the age group 41 to 50 years old. Men are affected more than women. In contrast, the number of HIV cases among 11- to 15-year-old girls is higher compared to boys of the same age.

Partonic Flow and phi-Meson production in Au+Au collisions at sqrt radical sNN = 200 GeV.

PubMed

Abelev, B I; Aggarwal, M M; Ahammed, Z; Anderson, B D; Arkhipkin, D; Averichev, G S; Bai, Y; Balewski, J; Barannikova, O; Barnby, L S; Baudot, J; Baumgart, S; Belaga, V V; Bellingeri-Laurikainen, A; Bellwied, R; Benedosso, F; Betts, R R; Bhardwaj, S; Bhasin, A; Bhati, A K; Bichsel, H; Bielcik, J; Bielcikova, J; Bland, L C; Blyth, S-L; Bombara, M; Bonner, B E; Botje, M; Bouchet, J; Brandin, A V; Bravar, A; Burton, T P; Bystersky, M; Cadman, R V; Cai, X Z; Caines, H; Calderón de la Barca Sánchez, M; Callner, J; Catu, O; Cebra, D; Chajecki, Z; Chaloupka, P; Chattopadhyay, S; Chen, H F; Chen, J H; Chen, J Y; Cheng, J; Cherney, M; Chikanian, A; Christie, W; Chung, S U; Coffin, J P; Cormier, T M; Cosentino, M R; Cramer, J G; Crawford, H J; Das, D; Dash, S; Daugherity, M; de Moura, M M; Dedovich, T G; DePhillips, M; Derevschikov, A A; Didenko, L; Dietel, T; Djawotho, P; Dogra, S M; Dong, X; Drachenberg, J L; Draper, J E; Du, F; Dunin, V B; Dunlop, J C; Dutta Mazumdar, M R; Eckardt, V; Edwards, W R; Efimov, L G; Emelianov, V; Engelage, J; Eppley, G; Erazmus, B; Estienne, M; Fachini, P; Fatemi, R; Fedorisin, J; Feng, A; Filip, P; Finch, E; Fine, V; Fisyak, Y; Fu, J; Gagliardi, C A; Gaillard, L; Ganti, M S; Garcia-Solis, E; Ghazikhanian, V; Ghosh, P; Gorbunov, Y G; Gos, H; Grebenyuk, O; Grosnick, D; Grube, B; Guertin, S M; Guimaraes, K S F F; Gupta, N; Haag, B; Hallman, T J; Hamed, A; Harris, J W; He, W; Heinz, M; Henry, T W; Heppelmann, S; Hippolyte, B; Hirsch, A; Hjort, E; Hoffman, A M; Hoffmann, G W; Hofman, D J; Hollis, R S; Horner, M J; Huang, H Z; Hughes, E W; Humanic, T J; Igo, G; Iordanova, A; Jacobs, P; Jacobs, W W; Jakl, P; Jia, F; Jones, P G; Judd, E G; Kabana, S; Kang, K; Kapitan, J; Kaplan, M; Keane, D; Kechechyan, A; Kettler, D; Khodyrev, V Yu; Kim, B C; Kiryluk, J; Kisiel, A; Kislov, E M; Klein, S R; Knospe, A G; Kocoloski, A; Koetke, D D; Kollegger, T; Kopytine, M; Kotchenda, L; Kouchpil, V; Kowalik, K L; Kravtsov, P; Kravtsov, V I; Krueger, K; Kuhn, C; Kulikov, A I; Kumar, A; Kurnadi, P; Kuznetsov, A A; Lamont, M A C; Landgraf, J M; Lange, S; LaPointe, S; Laue, F; Lauret, J; Lebedev, A; Lednicky, R; Lee, C-H; Lehocka, S; LeVine, M J; Li, C; Li, Q; Li, Y; Lin, G; Lin, X; Lindenbaum, S J; Lisa, M A; Liu, F; Liu, H; Liu, J; Liu, L; Ljubicic, T; Llope, W J; Longacre, R S; Love, W A; Lu, Y; Ludlam, T; Lynn, D; Ma, G L; Ma, J G; Ma, Y G; Mahapatra, D P; Majka, R; Mangotra, L K; Manweiler, R; Margetis, S; Markert, C; Martin, L; Matis, H S; Matulenko, Yu A; McClain, C J; McShane, T S; Melnick, Yu; Meschanin, A; Millane, J; Miller, M L; Minaev, N G; Mioduszewski, S; Mironov, C; Mischke, A; Mitchell, J; Mohanty, B; Morozov, D A; Munhoz, M G; Nandi, B K; Nattrass, C; Nayak, T K; Nelson, J M; Nepali, C; Netrakanti, P K; Nogach, L V; Nurushev, S B; Odyniec, G; Ogawa, A; Okorokov, V; Oldenburg, M; Olson, D; Pachr, M; Pal, S K; Panebratsev, Y; Pavlinov, A I; Pawlak, T; Peitzmann, T; Perevoztchikov, V; Perkins, C; Peryt, W; Phatak, S C; Planinic, M; Pluta, J; Poljak, N; Porile, N; Poskanzer, A M; Potekhin, M; Potrebenikova, E; Potukuchi, B V K S; Prindle, D; Pruneau, C; Putschke, J; Qattan, I A; Raniwala, R; Raniwala, S; Ray, R L; Relyea, D; Ridiger, A; Ritter, H G; Roberts, J B; Rogachevskiy, O V; Romero, J L; Rose, A; Roy, C; Ruan, L; Russcher, M J; Sahoo, R; Sakrejda, I; Sakuma, T; Salur, S; Sandweiss, J; Sarsour, M; Sazhin, P S; Schambach, J; Scharenberg, R P; Schmitz, N; Seger, J; Selyuzhenkov, I; Seyboth, P; Shabetai, A; Shahaliev, E; Shao, M; Sharma, M; Shen, W Q; Shimanskiy, S S; Sichtermann, E P; Simon, F; Singaraju, R N; Smirnov, N; Snellings, R; Sorensen, P; Sowinski, J; Speltz, J; Spinka, H M; Srivastava, B; Stadnik, A; Stanislaus, T D S; Staszak, D; Stock, R; Strikhanov, M; Stringfellow, B; Suaide, A A P; Suarez, M C; Subba, N L; Sumbera, M; Sun, X M; Sun, Z; Surrow, B; Symons, T J M; Szanto de Toledo, A; Takahashi, J; Tang, A H; Tarnowsky, T; Thomas, J H; Timmins, A R; Timoshenko, S; Tokarev, M; Trainor, T A; Trentalange, S; Tribble, R E; Tsai, O D; Ulery, J; Ullrich, T; Underwood, D G; Van Buren, G; van der Kolk, N; van Leeuwen, M; Vander Molen, A M; Varma, R; Vasilevski, I M; Vasiliev, A N; Vernet, R; Vigdor, S E; Viyogi, Y P; Vokal, S; Voloshin, S A; Waggoner, W T; Wang, F; Wang, G; Wang, J S; Wang, X L; Wang, Y; Watson, J W; Webb, J C; Westfall, G D; Wetzler, A; Whitten, C; Wieman, H; Wissink, S W; Witt, R; Wu, J; Wu, Y; Xu, N; Xu, Q H; Xu, Z; Yepes, P; Yoo, I-K; Yue, Q; Yurevich, V I; Zhan, W; Zhang, H; Zhang, W M; Zhang, Y; Zhang, Z P; Zhao, Y; Zhong, C; Zhou, J; Zoulkarneev, R; Zoulkarneeva, Y; Zubarev, A N; Zuo, J X

2007-09-14

We present first measurements of the phi-meson elliptic flow (v2(pT)) and high-statistics pT distributions for different centralities from radical sNN=200 GeV Au+Au collisions at RHIC. In minimum bias collisions the v2 of the phi meson is consistent with the trend observed for mesons. The ratio of the yields of the Omega to those of the phi as a function of transverse momentum is consistent with a model based on the recombination of thermal s quarks up to pT approximately 4 GeV/c, but disagrees at higher momenta. The nuclear modification factor (R CP) of phi follows the trend observed in the K S 0 mesons rather than in Lambda baryons, supporting baryon-meson scaling. These data are consistent with phi mesons in central Au+Au collisions being created via coalescence of thermalized s quarks and the formation of a hot and dense matter with partonic collectivity at RHIC.

The Effects of Flocculation on the Propagation of Ultrasound in Dilute Kaolin Slurries.

PubMed

Austin; Challis

1998-10-01

A broadband ultrasonic spectrometer has been used to measure ultrasonic attenuation and phase velocity dispersion as functions of frequency in kaolin suspensions over a range of solid volume fractions from phi = 0.01 to phi = 0.08 and over a pH range from 3 to 9. The Harker and Temple theory was used to simulate ultrasound propagation in the suspension, using measured slope viscosity, particle size, and size distribution. Simulated results for ultrasonic attenuation and phase velocity agree well with measured values. Both sets of results agree well and show that for volume fractions above phi approximately 0.05 attenuation and velocity dispersion increase for increasing floc size, whereas for volume fractions below phi approximately 0.05 attenuation and velocity dispersion both decrease. It is proposed that the mechanism for this change in behavior around phi approximately 0.05 involves changes in floc density and floc size distribution with phi and pH. Copyright 1998 Academic Press.

Two types of phytases (histidine acid phytase and β-propeller phytase) in Serratia sp. TN49 from the gut of Batocera horsfieldi (coleoptera) larvae.

PubMed

Zhang, Rui; Yang, Peilong; Huang, Huoqing; Shi, Pengjun; Yuan, Tiezheng; Yao, Bin

2011-11-01

Microbial phytases play a major role in the mineralization of organic phosphorous, especially in symbiotic plants and animals. In this study, we identified two types of phytases in Serratia sp. TN49 that was harbored in the gut of Batocera horsfieldi (Coleoptera) larvae. The two phytases, an acidic histidine acid phosphatase (PhyH49) and an alkaline β-propeller phytase (PhyB49), shared low identities with known phytases (61% at most). PhyH49 and PhyB49 produced in Escherichia coli exhibited maximal activities at pH 5.0 (60°C) and pH 7.5-8.0 (45°C), respectively, and are complementary in phytate degradation over the pH range 2.0-9.0. Serratia sp. TN49 harboring both PhyH49 and PhyB49 might make it more adaptive to environment change, corresponding to the evolution trend of microorganism.

Demand for private health insurance: how important is the quality gap?

PubMed

Costa, Joan; García, Jaume

2003-07-01

Perceived quality of private and public health care, income and insurance premium are among the determinants of demand for private health insurance (PHI). In the context of a model in which individuals are expected utility maximizers, the non purchasing choice can result in consuming either public health care or private health care with full cost paid out-of-pocket. This paper empirically analyses the effect of the determinants of the demand for PHI on the probability of purchasing PHI by estimating a pseudo-structural model to deal with missing data and endogeneity issues. Our findings support the hypothesis that the demand for PHI is indeed driven by the quality gap between private and public health care. As expected, PHI is a normal good and a rise in the insurance premium reduces the probability of purchasing PHI albeit displaying price elasticities smaller than one in absolute value for different groups of individuals. Copyright 2002 John Wiley & Sons, Ltd.

Role of the N*(1535) resonance and the {pi}{sup -}p{yields}KY amplitudes in the OZI forbidden {pi}N{yields}{phi}N reaction

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

Doering, M.; Oset, E.; Zou, B. S.

2008-08-15

We study the {pi}N{yields}{phi}N reaction close to the {phi}N threshold within the chiral unitary approach, by combining the {pi}{sup -}p{yields}K{sup +}{sigma}{sup -},{pi}{sup -}p{yields}K{sup 0}{sigma}{sup 0}, and {pi}{sup -}p{yields}K{sup 0}{lambda} amplitudes with the coupling of {phi} to the K components of the final states of these reactions via quantum loops. We obtain good agreement with experiment when the dominant {pi}{sup -}p{yields}K{sup 0}{lambda} amplitude is constrained with its experimental cross section. We also evaluate the coupling of N*(1535) to {phi}N and find a moderate coupling as a consequence of partial cancellation of the large KY components of N*(1535). We also show thatmore » the N*(1535) pole approximation is too small to reproduce the measured cross section for the {pi}{sup -}N{yields}{phi}N reaction.« less

Using a Commercial Ethernet PHY Device in a Radiation Environment

NASA Technical Reports Server (NTRS)

Parks, Jeremy; Arani, Michael; Arroyo, Roberto

2014-01-01

This work involved placing a commercial Ethernet PHY on its own power boundary, with limited current supply, and providing detection methods to determine when the device is not operating and when it needs either a reset or power-cycle. The device must be radiation-tested and free of destructive latchup errors. The commercial Ethernet PHY's own power boundary must be supplied by a current-limited power regulator that must have an enable (for power cycling), and its maximum power output must not exceed the PHY's input requirements, thus preventing damage to the device. A regulator with configurable output limits and short-circuit protection (such as the RHFL4913, rad hard positive voltage regulator family) is ideal. This will prevent a catastrophic failure due to radiation (such as a short between the commercial device's power and ground) from taking down the board's main power. Logic provided on the board will detect errors in the PHY. An FPGA (field-programmable gate array) with embedded Ethernet MAC (Media Access Control) will work well. The error detection includes monitoring the PHY's interrupt line, and the status of the Ethernet's switched power. When the PHY is determined to be non-functional, the logic device resets the PHY, which will often clear radiation induced errors. If this doesn't work, the logic device power-cycles the FPGA by toggling the regulator's enable input. This should clear almost all radiation induced errors provided the device is not latched up.

Modulatory effects of neuropsychopharmaca on intracellular pH of hippocampal neurones in vitro

PubMed Central

Bonnet, Udo; Bingmann, Dieter; Wiltfang, Jens; Scherbaum, Norbert; Wiemann, Martin

2010-01-01

Background and purpose: The intracellular pH (pHi) of neurones is tightly regulated by, for example, membrane-bound acid-exchangers and loaders. Nevertheless, excessive bioelectric activity lowers steady-state pHi. In turn, even a moderate acidification can inhibit neuronal activity, a process believed to be part of a negative feedback loop controlling neuronal excitation. As moclobemide, an antidepressant, and also some antiepileptic drugs can reduce neuronal pHi in hippocampus slices in vitro, we screened a panel of currently used neuropsychopharmaca for comparable effects. Experimental approach: BCECF-AM loaded hippocampal slices were superfused with 16 different neuroleptics, antidepressants and antiepileptics under bicarbonate-buffered conditions. Changes in steady-state pHi of CA3 neurones were measured fluorometrically. Key results: The antipsychotics haloperidol, clozapine, ziprasidone, and the antidepressants amitriptyline, doxepin, trimipramine, citalopram, mirtazapine, as well as the anticonvulsive drug tiagabine reversibly reduced the steady-state pHi by up to 0.35 pH-units in concentrations of 5–50 µM. In contrast, venlafaxine, the anticonvulsants carbamazepine, clonazepam, gabapentin, lamotrigine, zonisamide, and the mood stabilizer lithium had no effect on neuronal pHi. Conclusion and implications: These data substantiate the view that clinically relevant concentrations of neuroleptics and antidepressants can mediate changes in neuronal pHi, which may contribute to their pharmacological mode of action. Effects on pHi should be taken into account when therapeutic or even harmful effects of these drugs are evaluated. PMID:20015293

Anisotropic k-essence cosmologies

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

Chimento, Luis P.; Forte, Monica

We investigate a Bianchi type-I cosmology with k-essence and find the set of models which dissipate the initial anisotropy. There are cosmological models with extended tachyon fields and k-essence having a constant barotropic index. We obtain the conditions leading to a regular bounce of the average geometry and the residual anisotropy on the bounce. For constant potential, we develop purely kinetic k-essence models which are dust dominated in their early stages, dissipate the initial anisotropy, and end in a stable de Sitter accelerated expansion scenario. We show that linear k-field and polynomial kinetic function models evolve asymptotically to Friedmann-Robertson-Walker cosmologies.more » The linear case is compatible with an asymptotic potential interpolating between V{sub l}{proportional_to}{phi}{sup -{gamma}{sub l}}, in the shear dominated regime, and V{sub l}{proportional_to}{phi}{sup -2} at late time. In the polynomial case, the general solution contains cosmological models with an oscillatory average geometry. For linear k-essence, we find the general solution in the Bianchi type-I cosmology when the k field is driven by an inverse square potential. This model shares the same geometry as a quintessence field driven by an exponential potential.« less

Polymer flexibility and turbulent drag reduction.

PubMed

Gillissen, J J J

2008-10-01

Polymer-induced drag reduction is the phenomenon by which the friction factor of a turbulent flow is reduced by the addition of small amounts of high-molecular-weight linear polymers, which conformation in solution at rest can vary between randomly coiled and rodlike. It is well known that drag reduction is positively correlated to viscous stresses, which are generated by extended polymers. Rodlike polymers always assume this favorable conformation, while randomly coiling chains need to be unraveled by fluid strain rate in order to become effective. The coiling and stretching of flexible polymers in turbulent flow produce an additional elastic component in the polymer stress. The effect of the elastic stresses on drag reduction is unclear. To study this issue, we compare direct numerical simulations of turbulent drag reduction in channel flow using constitutive equations describing solutions of rigid and flexible polymers. When compared at constant phi r2, both simulations predict the same amount of drag reduction. Here phi is the polymer volume fraction and r is the polymer aspect ratio, which for flexible polymers is based on average polymer extension at the channel wall. This demonstrates that polymer elasticity plays a marginal role in the mechanism for drag reduction.

Nuclear spin-isospin excitations from covariant quasiparticle-vibration coupling

NASA Astrophysics Data System (ADS)

Robin, Caroline; Litvinova, Elena

2016-09-01

Methods based on the relativistic Lagrangian of quantum hadrodynamics and nuclear field theory provide a consistent framework for the description of nuclear excitations, naturally connecting the high- and medium-energy scales of mesons to the low-energy domain of nucleonic collective motion. Applied in the neutral channel, this approach has been quite successful in describing the overall transition strength up to high excitation energies, as well as fine details of the low-lying distribution. Recently, this method has been extended to the description of spin-isospin excitations in open-shell nuclei. In the charge-exchange channel, the coupling between nucleons and collective vibrations generates a time-dependent proton-neutron effective interaction, in addition to the static pion and rho-meson exchange, and introduces complex configurations that induce fragmentation and spreading of the resonances. Such effects have a great impact on the quenching of the strength and on the computing of weak reaction rates that are needed for astrophysics modeling. Gamow-Teller transitions in medium-mass nuclei and associated beta-decay half-lives will be presented. Further developments aiming to include additional ground-state correlations will also be discussed. This work is supported by US-NSF Grants PHY-1404343 and PHY-1204486.

Effects of dispersed particulates on the rheology of water ice at planetary conditions

NASA Technical Reports Server (NTRS)

Durham, William B.; Kirby, Stephen H.; Stern, Laura A.

1992-01-01

Effects of the initial grain size and the hard particulate impurities on the transient and the steady state flows of water ice I were investigated under laboratory conditions selected as appropriate for simulating those of the surfaces and interiors of large moons. The samples were molded with particulate volume fraction, phi, of 0.001 to 0.56 and particle sizes of 1 to 150 microns; deformation experiments were conducted at constant shortening rates of 4.4 x 10 exp -7 to 4.9 x 10 exp -4 per sec at pressures of 50 and 100 MPa and temperatures 77 to 223 K. The results obtained suggest that viscous drag occurs in the ice as it flows around hard particulates. Mixed-phase ice was found to be tougher than pure ice, extending the range of bulk plastic deformation vs. faulting to lower temperatures and higher strain rates. It is suggested that bulk planetary compositions of ice + rock (phi = 0.4-0.5) are roughly 2 orders of magnitude more viscous than pure ice, leading to thermal instability inside giant icy moons and possibly explaining the retention of crater topography on icy planetary surfaces.

AS-7 improved in vitro quality of red blood cells prepared from whole blood held overnight at room temperature.

PubMed

Veale, Margaret F; Healey, Geraldine; Sran, Amrita; Payne, Katherine A; Zia, Majid; Sparrow, Rosemary L

2015-01-01

Extended room temperature (RT) hold of whole blood (WB) may affect the quality of red blood cell (RBC) components produced from these donations. The availability of better RBC additive solutions (ASs) may help reduce the effects. A new AS, AS-7 (SOLX, Haemonetics Corporation), was investigated for improved in vitro quality of RBCs prepared from WB held overnight at RT. Sixteen WB units were held for 21.4 hours ± 40 minutes at 22°C on cooling plates before processing. Each pair of ABO-matched WB units were pooled, divided into a WB filter pack containing saline-adenine-glucose-mannitol (control) and a LEUKOSEP WB-filter pack containing SOLX, and processed according to manufacturer's instructions. RBCs were stored at 2 to 6°C and sampled weekly until expiry. Glycophorin A (GPA+) and annexin V-binding microparticles (MPs) were quantitated using flow cytometry. Osmotic fragility, intracellular pH (pHi), adenosine triphosphate (ATP), 2,3-diphosphoglycerate (2,3-DPG), and routine quality variables were measured. Adhesion of RBCs to human endothelial cells (ECs) was evaluated by flow perfusion under low shear stress (0.5 dyne/cm(2) ), similar to low blood flow in microvessels. ATP and 2,3-DPG levels were improved for SOLX-RBCs. SOLX-RBCs maintained higher pHi, increased resistance to hypotonic stress, and reduced numbers of GPA+ MPs. No significant difference was observed between annexin V binding to MPs or adhesion of RBCs to ECs under shear stress. SOLX-stored RBCs showed increased osmotic resistance, pHi, and reduced GPA+ MPs and together with higher ATP and 2,3-DPG levels demonstrated improved in vitro RBC quality measures during 42 days of storage. © 2014 AABB.

The iPhyClassifier, an interactive online tool for phytoplasma classification and taxonomic assignment

USDA-ARS?s Scientific Manuscript database

The iPhyClassifier is an Internet-based research tool for quick identification and classification of diverse phytoplasmas. The iPhyClassifier simulates laboratory restriction enzyme digestions and subsequent gel electrophoresis and generates virtual restriction fragment length polymorphism (RFLP) p...

Numerical simulation of the flow about the F-18 HARV at high angle of attack

NASA Technical Reports Server (NTRS)

Murman, Scott M.

1994-01-01

As part of NASA's High Alpha Technology Program, research has been aimed at developing and extending numerical methods to accurately predict the high Reynolds number flow about the NASA F-18 High Alpha Research Vehicle (HARV) at large angles of attack. The HARV aircraft is equipped with a bidirectional thrust vectoring unit which enables stable, controlled flight through 70 deg angle of attack. Currently, high-fidelity numerical solutions for the flow about the HARV have been obtained at alpha = 30 deg, and validated against flight-test data. It is planned to simulate the flow about the HARV through alpha = 60 deg, and obtain solutions of the same quality as those at the lower angles of attack. This report presents the status of work aimed at extending the HARV computations to the extreme angle of attack range.

Boundary scattering in the Φ$$^{4}$$ model

DOE PAGES

Dorey, Patrick; Halavanau, Aliaksei; Mercer, James; ...

2017-05-19

Here, we study boundary scattering in themore » $$\\phi^4$$ model on a half-line with a one-parameter family of Neumann-type boundary conditions. A rich variety of phenomena is observed, which extends previously-studied behaviour on the full line to include regimes of near-elastic scattering, the restoration of a missing scattering window, and the creation of a kink or oscillon through the collision-induced decay of a metastable boundary state. We also study the decay of the vibrational boundary mode, and explore different scenarios for its relaxation and for the creation of kinks.« less

Study of {chi}{sub cj} Decays at BES III

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

Zhong, J.

2010-08-05

In spring 2009 BES III has taken its first large data sample on the {psi}(2S) resonance. More than 1{center_dot}10{sup 8} {psi}(2S) decays have been recorded. First results on the analyses {chi}{sub cJ{yields}{pi}}{sup 0{pi}0}, {chi}{sub cj{yields}{eta}{eta}} and {chi}{sub cj{yields}{phi}{phi}} are presented. The decay mode {chi}{sub c1{yields}{phi}{phi}} has been observed for the first time. The results presented in this document are preliminary.

Anisotropic singularities in modified gravity models

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

Figueiro, Michele Ferraz; Saa, Alberto; Departamento de Matematica Aplicada, IMECC-UNICAMP, C.P. 6065, 13083-859 Campinas, SP

2009-09-15

We show that the common singularities present in generic modified gravity models governed by actions of the type S={integral}d{sup 4}x{radical}(-g)f(R,{phi},X), with X=-(1/2)g{sup ab}{partial_derivative}{sub a}{phi}{partial_derivative}{sub b}{phi}, are essentially the same anisotropic instabilities associated to the hypersurface F({phi})=0 in the case of a nonminimal coupling of the type F({phi})R, enlightening the physical origin of such singularities that typically arise in rather complex and cumbersome inhomogeneous perturbation analyses. We show, moreover, that such anisotropic instabilities typically give rise to dynamically unavoidable singularities, precluding completely the possibility of having physically viable models for which the hypersurface ({partial_derivative}f/{partial_derivative}R)=0 is attained. Some examples are explicitly discussed.

RNA secondary structures of the bacteriophage phi6 packaging regions.

PubMed

Pirttimaa, M J; Bamford, D H

2000-06-01

Bacteriophage phi6 genome consists of three segments of double-stranded RNA. During maturation, single-stranded copies of these segments are packaged into preformed polymerase complex particles. Only phi6 RNA is packaged, and each particle contains only one copy of each segment. An in vitro packaging and replication assay has been developed for phi6, and the packaging signals (pac sites) have been mapped to the 5' ends of the RNA segments. In this study, we propose secondary structure models for the pac sites of phi6 single-stranded RNA segments. Our models accommodate data from structure-specific chemical modifications, free energy minimizations, and phylogenetic comparisons. Previously reported pac site deletion studies are also discussed. Each pac site possesses a unique architecture, that, however, contains common structural elements.

The Contradiction Between the Measurement Theory of Quantum Mechanics and the Theory that the Velocity of Any Particle Can Not be Larger than the Velocity of Light

NASA Technical Reports Server (NTRS)

Shen, Y.; Shen, Z. J.; Shen, G. T.; Yang, B. C.

1996-01-01

By the measurement theory of quantum mechanics and the method of Fourier transform,we proved that the wave function psi(x,y,z,t)= (8/((2(pi)(2L(exp (1/2)))(exp 3))(Phi(L,t,x)Phi(L,t,y)Phi(L,t,z)). According to the theory that the velocity of any particle can not be larger than the velocity of light and the Born interpretation, when absolute value of delta greater than (ct+ L),Phi(L,t,delta) = 0. But according to the calculation, we proved that for some delta, even if absolute value of delta is greater than (ct+L), Phi(L,t,delta) is not equal to 0.

Do radiology and other health care presentations posted on the Internet contain accessible protected health information?

PubMed

Weadock, William J; Londy, Frank J; Ellis, James H; Goldman, Edward B

2008-10-01

To determine the prevalence of protected health information (PHI) in PowerPoint presentations available for downloading from the Internet. No institutional review board approval was needed for this project, which involved no patient subjects. Two Google searches, each limited to PowerPoint files, were performed by using the criteria "Cardiac CT" and "Magnetic Resonance Imaging." The first 100 hits of each search were downloaded from the source Web site. The presentations were examined for the PHI contained on any images, links, or notes pages. Two hundred presentations were evaluated. There were 143 presentations with images, image links, or notes, and 52 (36%) of these contained PHI. There were 129 presentations containing radiologic images; 51 (40%) of these contained PHI, and 31 (24%) showed the patient's name. At least 132 (66%) of the 200 presentations originated from the United States. Thirty-five (37%) of 94 presentations with images, image links, or notes contained PHI. Eighty-six U.S. presentations contained radiologic images; 34 (40%) of these contained PHI, and 19 (22%) showed the patient's name. Online or other distributions of PowerPoint presentations that contain radiologic images often contain PHI, and this may violate laws, including the U.S. Health Insurance Portability and Accountability Act. (c) RSNA, 2008.

Unimodular Gravity and General Relativity UV divergent contributions to the scattering of massive scalar particles

NASA Astrophysics Data System (ADS)

Gonzalez-Martin, S.; Martin, C. P.

2018-01-01

We work out the one-loop and order κ2 mphi2 UV divergent contributions, coming from Unimodular Gravity and General Relativity, to the S matrix element of the scattering process phi + phi→ phi + phi in a λ phi4 theory with mass mphi. We show that both Unimodular Gravity and General Relativity give rise to the same UV divergent contributions in Dimensional Regularization. This seems to be at odds with the known result that in a multiplicative MS dimensional regularization scheme the General Relativity corrections, in the de Donder gauge, to the beta function, βλ, of the λ coupling do not vanish, whereas the Unimodular Gravity corrections, in a certain gauge, do vanish. Actually, by comparing the UV divergent contributions calculated in this paper with those which give rise to the non-vanishing gravitational corrections to βλ, one readily concludes that the UV divergent contributions that yield the just mentioned non-vanishing gravitational corrections to βλ do not contribute to the UV divergent behaviour of the S matrix element of phi + phi→ phi + phi. This shows that any physical consequence—such as the existence of asymptotic freedom due to gravitational interactions—drawn from the value of βλ is not physically meaningful.

Attractor scenarios and superluminal signals in k-essence cosmology

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

Kang, Jin U; Arnold Sommerfeld Center, Department of Physics, Ludwig-Maximilians University, Theresienstrasse 37, 80333 Munich; Vanchurin, Vitaly

Cosmological scenarios with k-essence are invoked in order to explain the observed late-time acceleration of the Universe. These scenarios avoid the need for fine-tuned initial conditions (the 'coincidence problem') because of the attractorlike dynamics of the k-essence field {phi}. It was recently shown that all k-essence scenarios with Lagrangians p=L(X){phi}{sup -2}, where X{identical_to}(1/2){phi}{sub ,{mu}}{phi}{sup ,{mu}}, necessarily involve an epoch where perturbations of {phi} propagate faster than light (the 'no-go theorem'). We carry out a comprehensive study of attractorlike cosmological solutions ('trackers') involving a k-essence scalar field {phi} and another matter component. The result of this study is a complete classificationmore » of k-essence Lagrangians that admit asymptotically stable tracking solutions, among all Lagrangians of the form p=K({phi})L(X). Using this classification, we select the class of models that describe the late-time acceleration and avoid the coincidence problem through the tracking mechanism. An analogous 'no-go theorem' still holds for this class of models, indicating the existence of a superluminal epoch. In the context of k-essence cosmology, the superluminal epoch does not lead to causality violations. We discuss the implications of superluminal signal propagation for possible causality violations in Lorentz-invariant field theories.« less

The structure of premixed particle-cloud flames

NASA Technical Reports Server (NTRS)

Seshadri, K.; Berlad, A. L.; Tangirala, V.

1992-01-01

The structure of premixed flames propagating in combustible systems, containing uniformly distributed volatile fuel particles, in an oxidizing gas mixture, is analyzed. It is presumed that the fuel particles vaporize first to yield a gaseous fuel of known chemical structure, which is subsequently oxidized in the gas phase. The analysis is performed in the asymptotic limit, where the value of the characteristic Zeldovich number, based on the gas-phase oxidation of the gaseous fuel is large, and for values of phi(u) greater than or equal to 1.0, where phi(u) is the equivalence ratio based on the fuel available in the fuel particles. The structure of the flame is presumed to consist of a preheat vaporization zone where the rate of the gas-phase chemical reaction is small, a reaction zone where convection and the rate of vaporization of the fuel particles are small and a convection zone where diffusive terms in the conservation equations are small. For given values phi(u) the analysis yields results for the burning velocity and phi(g) where phi(g) is the effective equivalence ratio in the reaction zone. The analysis shows that even though phi(u) greater than or equal to 1.0, for certain cases the calculated value of phi(g) is less than unity. This prediction is in agreement with experimental observations.

Human umbilical cord blood-derived f-macrophages retain pluripotentiality after thrombopoietin expansion

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

Zhao Yong; Mazzone, Theodore

2005-11-01

We have previously characterized a new type of stem cell from human peripheral blood, termed fibroblast-like macrophage (f-M{phi}). Here, using umbilical cord blood as a source, we identified cells with similar characteristics including expression of surface markers (CD14, CD34, CD45, CD117, and CD163), phagocytosis, and proliferative capacity. Further, thrombopoietin (TPO) significantly stimulated the proliferation of cord blood-derived f-M{phi} (CB f-M{phi}) at low dosage without inducing a megakaryocytic phenotype. Additional experiments demonstrated that TPO-expanded cord blood-derived f-M{phi} (TCB f-M{phi}) retained their surface markers and differentiation ability. Treatment with vascular endothelial cell growth factor (VEGF) gave rise to endothelial-like cells, expressing Flt-1,more » Flk-1, von Willebrand Factor (vWF), CD31, acetylated low density lipoprotein internalization, and the ability to form endothelial-like cell chains. In the presence of lipopolyssacharide (LPS) and 25 mM glucose, the TCB f-M{phi} differentiated to express insulin mRNA, C-peptide, and insulin. In vitro functional analysis demonstrated that these insulin-positive cells could release insulin in response to glucose and other secretagogues. These findings demonstrate a potential use of CB f-M{phi} and may lead to develop new therapeutic strategy for treating dominant disease.« less

The Caulobacter crescentus phage phiCbK: genomics of a canonical phage

PubMed Central

2012-01-01

Background The bacterium Caulobacter crescentus is a popular model for the study of cell cycle regulation and senescence. The large prolate siphophage phiCbK has been an important tool in C. crescentus biology, and has been studied in its own right as a model for viral morphogenesis. Although a system of some interest, to date little genomic information is available on phiCbK or its relatives. Results Five novel phiCbK-like C. crescentus bacteriophages, CcrMagneto, CcrSwift, CcrKarma, CcrRogue and CcrColossus, were isolated from the environment. The genomes of phage phiCbK and these five environmental phage isolates were obtained by 454 pyrosequencing. The phiCbK-like phage genomes range in size from 205 kb encoding 318 proteins (phiCbK) to 280 kb encoding 448 proteins (CcrColossus), and were found to contain nonpermuted terminal redundancies of 10 to 17 kb. A novel method of terminal ligation was developed to map genomic termini, which confirmed termini predicted by coverage analysis. This suggests that sequence coverage discontinuities may be useable as predictors of genomic termini in phage genomes. Genomic modules encoding virion morphogenesis, lysis and DNA replication proteins were identified. The phiCbK-like phages were also found to encode a number of intriguing proteins; all contain a clearly T7-like DNA polymerase, and five of the six encode a possible homolog of the C. crescentus cell cycle regulator GcrA, which may allow the phage to alter the host cell’s replicative state. The structural proteome of phage phiCbK was determined, identifying the portal, major and minor capsid proteins, the tail tape measure and possible tail fiber proteins. All six phage genomes are clearly related; phiCbK, CcrMagneto, CcrSwift, CcrKarma and CcrRogue form a group related at the DNA level, while CcrColossus is more diverged but retains significant similarity at the protein level. Conclusions Due to their lack of any apparent relationship to other described phages, this group is proposed as the founding cohort of a new phage type, the phiCbK-like phages. This work will serve as a foundation for future studies on morphogenesis, infection and phage-host interactions in C. crescentus. PMID:23050599

Genomics of Three New Bacteriophages Useful in the Biocontrol of Salmonella

PubMed Central

Bardina, Carlota; Colom, Joan; Spricigo, Denis A.; Otero, Jennifer; Sánchez-Osuna, Miquel; Cortés, Pilar; Llagostera, Montserrat

2016-01-01

Non-typhoid Salmonella is the principal pathogen related to food-borne diseases throughout the world. Widespread antibiotic resistance has adversely affected human health and has encouraged the search for alternative antimicrobial agents. The advances in bacteriophage therapy highlight their use in controlling a broad spectrum of food-borne pathogens. One requirement for the use of bacteriophages as antibacterials is the characterization of their genomes. In this work, complete genome sequencing and molecular analyses were carried out for three new virulent Salmonella-specific bacteriophages (UAB_Phi20, UAB_Phi78, and UAB_Phi87) able to infect a broad range of Salmonella strains. Sequence analysis of the genomes of UAB_Phi20, UAB_Phi78, and UAB_Phi87 bacteriophages did not evidence the presence of known virulence-associated and antibiotic resistance genes, and potential immunoreactive food allergens. The UAB_Phi20 genome comprised 41,809 base pairs with 80 open reading frames (ORFs); 24 of them with assigned function. Genome sequence showed a high homology of UAB_Phi20 with Salmonella bacteriophage P22 and other P22likeviruses genus of the Podoviridae family, including ST64T and ST104. The DNA of UAB_Phi78 contained 44,110 bp including direct terminal repeats (DTR) of 179 bp and 58 putative ORFs were predicted and 20 were assigned function. This bacteriophage was assigned to the SP6likeviruses genus of the Podoviridae family based on its high similarity not only with SP6 but also with the K1-5, K1E, and K1F bacteriophages, all of which infect Escherichia coli. The UAB_Phi87 genome sequence consisted of 87,669 bp with terminal direct repeats of 608 bp; although 148 ORFs were identified, putative functions could be assigned to only 29 of them. Sequence comparisons revealed the mosaic structure of UAB_Phi87 and its high similarity with bacteriophages Felix O1 and wV8 of E. coli with respect to genetic content and functional organization. Phylogenetic analysis of large terminase subunits confirms their packaging strategies and grouping to the different phage genus type. All these studies are necessary for the development and the use of an efficient cocktail with commercial applications in bacteriophage therapy against Salmonella. PMID:27148229

Numerical solution for linear cyclotron and diocotron modes in a nonneutral plasma column

NASA Astrophysics Data System (ADS)

Walsh, Daniel; Dubin, Daniel H. E.

2014-10-01

This poster presents numerical methods for solution of the linearized Vlasov-Poisson (LVP) equation applied to a cylindrical single-species plasma in a uniform magnetic field. The code is used to study z-independent cyclotron and diocotron modes of these plasmas, including kinetic effects. We transform to polar coordinates in both position and velocity space and Fourier expand in both polar angles (i.e. the cyclotron gyro angle and θ). In one approach, we then discretize in the remaining variables r and v (where v is the magnitude of the perpendicular velocity). However, using centered differences the method is unstable to unphysical eigenmodes with rapid variation on the scale of the grid. We remedy this problem by averaging particular terms in the discretized LVP operator over neighboring gridpoints. We also present a stable Galerkin method that expands the r and v dependence in basis functions. We compare the numerical results from both methods to exact analytic results for various modes. Supported by NSF/DOE Partnership Grants PHY-0903877 and DE-SC0002451.

Performance of GEM Detectors in the DarkLight Experiment at LERF

NASA Astrophysics Data System (ADS)

Mohammed Prem Nazeer, Sahara Jesmin; DarkLight Collaboration

2017-01-01

The DarkLight experiment has been proposed to search for a heavy photon A' in the mass range of 10-100 MeV/c2 produced in electron-proton collisions. Phase-I of DarkLight has started to take place in 2016 at the Low Energy Recirculator Facility (LERF) at Jefferson Lab. LERF delivered a 100 MeV electron beam onto a windowless hydrogen gas target. The phase-I detector tracks leptons inside the DarkLight solenoid with a set of Gas Electron Multiplier (GEM) detectors, combined with segmented scintillators for triggering. The GEM telescope consists of four 10 × 10 cm2 triple layer GEM chambers with 2D readout strips, mounted in a slightly angled fixed frame about 12 cm tall. The GEM data are read out with analog pipeline front-end cards (APV-25) each of which can process 128 readout channels. Each GEM chamber has 250 channels for each coordinate axis, read out with two APVs on each side, resulting in 2000 readout channels for the GEM stack, processed by 16 APVs. One Multi Purpose Digitizer (MPD) module is used to read out all of the 16 APV-25 cards. The current run status of DarkLight experiment and the performance of GEMs in the experiment will be discussed. This work has been supported by NSF PHY-1436680 and PHY-1505934.

[Use of [-2] pro PSA and phi index for early detection of prostate cancer: a prospective of 452 patients].

PubMed

Houlgatte, A; Vincendeau, S; Desfemmes, F; Ramirez, J; Benoist, N; Bensalah, K; Durand, X

2012-05-01

Early detection of prostate cancer (Pca) is a real challenge to reduce morbidity and mortality while avoiding over-diagnosis and over-treatment. The prostate specific antigen (PSA) is characterized by its imperfections justifying the evaluation of new serum or urinary specific markers allowing a better selection of patients at risk of developing aggressive Pca. To compare the value of -2pro PSA and phi index to total and free PSA. Serum sampled from 452 patients from two university centers were used to determine levels of PSA before performing biopsies. The patients were included in this study based on the PSA serum concentration between 1.6 ng/mL and 8 ng/mL according to the WHO international standard. All biopsies were performed according to a standardized protocol consisting of 12 cores or more. Sera were analyzed centrally in one of the two institutions with on a single analyzer. Sera from 243 prostate cancer and 208 negative biopsies patients have been taken into account. Sera were analyzed blinded for total PSA, free PSA and [-2] proPSA using Access(®) immunoassay method from Beckman Coulter. The Prostate Health Index (phi) was calculated using the formula phi=([-2] proPSA/fPSA)×sqrt (PSA). The median value of the phi index is significantly (P>0.0001) higher for patients with cancer (phi=65.8) compared to patients with negative biopsies (phi=40.6). At a given sensitivity, the phi index significantly increases the specificity of detection of prostate cancer compared to other markers. The phi index currently appears as the best predictor of prostate cancer for patients with a total PSA between 1.6 and 8 ng/mL according to the WHO standard. The improvement in specificity of the phi index over tPSA could reduce significantly the numbers of unnecessary biopsies. Whether this new biomarker could be an indicator of aggressive prostate cancer remains to be confirmed. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Disease registries on the nationwide health information network.

PubMed

Russler, Daniel

2011-05-01

Donation by individuals of their protected health information (PHI) for evidence-based research potentially benefits all individuals with disease through improved understandings of disease patterns. In the future, a better understanding of how disease features combine into unique patterns of disease will generate new disease classifications, supporting greater specificity in health management techniques. However, without large numbers of people who donate their PHI to disease registries designed for research, it is difficult for researchers to discover the existence of complex patterns or to create more specific evidence-based management techniques. In order to identify new opportunities in disease registry design, an analysis of the current stage of maturity of the newly created U.S. Nationwide Health Information Network (NwHIN) related to large-scale consumer donation of PHI is presented. Utilizing a use-case analysis methodology, the consumer-centric designs of the policies and technologies created for the NwHIN were examined for the potential to support consumer donations of PHI to research. The NwHIN design has placed the enforcement point for the policy-based release of PHI over the Internet into a specialized gateway accessible to consumer authorization. However, current NwHIN policies leave the final decision regarding release of PHI for research to the health care providers rather than to the consumers themselves. Should disease registries designed for research be established on the NwHIN, consumers might then directly authorize the donation of their PHI to these disease registries. However, under current NwHIN policies, consumer authorization does not guarantee release of PHI by health providers. © 2011 Diabetes Technology Society.

Viral dynamics in primary HIV-1 infection. Karolinska Institutet Primary HIV Infection Study Group.

PubMed

Lindbäck, S; Karlsson, A C; Mittler, J; Blaxhult, A; Carlsson, M; Briheim, G; Sönnerborg, A; Gaines, H

2000-10-20

To study the natural course of viremia during primary HIV infection (PHI). Eight patients were followed from a median of 5 days from the onset of PHI illness. Plasma HIV-1 RNA levels were measured frequently and the results were fitted to mathematical models. HIV-1 RNA levels were also monitored in nine patients given two reverse transcriptase inhibitors and a protease inhibitor after a median of 7 days from the onset of PHI illness. HIV-1 RNA appeared in the blood during the week preceding onset of PHI illness and increased rapidly during the first viremic phase, reaching a peak at a mean of 7 days after onset of illness. This was followed by a phase of rapidly decreasing levels of HIV-1 RNA to an average of 21 days after onset. Viral density continued to decline thereafter but at a 5- to 50-fold lower rate; a steady-state level was reached at a median of 2 months after onset of PHI. Peak viral density levels correlated significantly with levels measured between days 50 and 600. Initiation of antiretroviral treatment during PHI resulted in rapidly declining levels to below 50 copies/mL. This study demonstrates the kinetic phases of viremia during PHI and indicates two new contributions to the natural history of HIV-1 infection: PHI peak levels correlate with steady-state levels and HIV-1 RNA declines biphasically; an initial rapid decay is usually followed by a slow decay, which is similar to the initial changes seen with antiviral treatment.

Evaluation of [-2] proPSA and Prostate Health Index (phi) for the detection of prostate cancer: a systematic review and meta-analysis.

PubMed

Filella, Xavier; Giménez, Nuria

2013-04-01

The usefulness of %[-2] proPSA and Prostate Health Index (phi) in the detection of prostate cancer are currently unknown. It has been suggested that these tests can distinguish prostate cancer from benign prostatic diseases better than PSA or %fPSA. We performed a systematic review and meta-analysis of the available scientific evidence to evaluate the clinical usefulness of %[-2] proPSA and phi. Relevant published papers were identified by searching computerized bibliographic systems. Data on sensitivity and specificity were extracted from 12 studies: 10 studies about %[-2] proPSA (3928 patients in total, including 1762 with confirmed prostate cancer) and eight studies about phi (2919 patients in total, including 1515 with confirmed prostate cancer). The sensitivity for the detection of prostate cancer was 90% for %[-2] proPSA and phi, while the pooled specificity was 32.5% (95% CI 30.6-34.5) and 31.6% (95% CI 29.2-34.0) for %[-2] proPSA and phi, respectively. The measurement of %[-2] proPSA improves the accuracy of prostate cancer detection in comparison with PSA or %fPSA, particularly in the group of patients with PSA between 2 μg/L and 10 μg/L. Similar results were obtained measuring phi. Using these tests, it is possible to reduce the number of unnecessary biopsies, maintaining a high cancer detection rate. Published results also showed that %[-2] proPSA and phi are related to the aggressiveness of the tumor.

Observation of phiK. pi. decay of the K/sup 0/(2060)

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

Torres, S.; Ficenec, J.R.; Mikocki, S.

We have studied inclusive pN..-->..K-/sup +/K/sup -/K/sup +/K/sup -/X final states at 400 GeV/c and present here evidence for K/sup *//sup 0/(2060)..-->..phiK/sup +-/..pi../sup minus-or-plus/ and phiK-italic/sup *//sup 0/(890). .AE

Characterization of a new ViI-like Erwinia amylovora bacteriophage phiEa2809.

PubMed

Lagonenko, Alexander L; Sadovskaya, Olga; Valentovich, Leonid N; Evtushenkov, Anatoly N

2015-04-01

Erwinia amylovora is a Gram-negative plant pathogenic bacteria causing fire blight disease in many Rosaceae species. A novel E. amylovora bacteriophage, phiEa2809, was isolated from symptomless apple leaf sample collected in Belarus. This phage was also able to infect Pantoea agglomerans strains. The genome of phiEa2809 is a double-stranded linear DNA 162,160 bp in length, including 145 ORFs and one tRNA gene. The phiEa2809 genomic sequence is similar to the genomes of the Serratia plymutica phage MAM1, Shigella phage AG-3, Dickeya phage vB DsoM LIMEstone1 and Salmonella phage ViI and lacks similarity to described E. amylovora phage genomes. Based on virion morphology (an icosahedral head, long contractile tail) and genome structure, phiEa2809 was classified as a member of Myoviridae, ViI-like bacteriophages group. PhiEa2809 is the firstly characterized ViI-like bacteriophage able to lyse E. amylovora. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Increased intracellular pH is necessary for adult epithelial and embryonic stem cell differentiation

PubMed Central

Azimova, Dinara R.

2016-01-01

Despite extensive knowledge about the transcriptional regulation of stem cell differentiation, less is known about the role of dynamic cytosolic cues. We report that an increase in intracellular pH (pHi) is necessary for the efficient differentiation of Drosophila adult follicle stem cells (FSCs) and mouse embryonic stem cells (mESCs). We show that pHi increases with differentiation from FSCs to prefollicle cells (pFCs) and follicle cells. Loss of the Drosophila Na+–H+ exchanger DNhe2 lowers pHi in differentiating cells, impairs pFC differentiation, disrupts germarium morphology, and decreases fecundity. In contrast, increasing pHi promotes excess pFC cell differentiation toward a polar/stalk cell fate through suppressing Hedgehog pathway activity. Increased pHi also occurs with mESC differentiation and, when prevented, attenuates spontaneous differentiation of naive cells, as determined by expression of microRNA clusters and stage-specific markers. Our findings reveal a previously unrecognized role of pHi dynamics for the differentiation of two distinct types of stem cell lineages, which opens new directions for understanding conserved regulatory mechanisms. PMID:27821494

Tsunami survivors' perspectives on vulnerability and vulnerability reduction: evidence from Koh Phi Phi Don and Khao Lak, Thailand.

PubMed

Steckley, Marylynn; Doberstein, Brent

2011-07-01

This paper presents the results of primary research with 40 survivors of the 2004 Indian Ocean tsunami in two communities: Khao Lak (n=20) and Koh Phi Phi Don (n=20), Thailand. It traces tsunami survivors' perceptions of vulnerability, determines whether residents felt that the tsunami affected different communities differently, identifies the populations and sub-community groups that survivors distinguished as being more vulnerable than others, highlights community-generated ideas about vulnerability reduction, and pinpoints a range of additional vulnerability reduction actions. Tsunami survivors most consistently identified the 'most vulnerable' community sub-populations as women, children, the elderly, foreigners, and the poor. In Khao Lak, however, respondents added 'Burmese migrants' to this list, whereas in Koh Phi Phi Don, they added 'Thai Muslims'. Results suggest that the two case study communities, both small, coastal, tourism-dominated communities no more than 100 kilometres apart, have differing vulnerable sub-groups and environmental vulnerabilities, requiring different post-disaster vulnerability reduction efforts. © 2011 The Author(s). Disasters © Overseas Development Institute, 2011.

Morphological responses of wheat to changes in phytochrome photoequilibrium

NASA Technical Reports Server (NTRS)

Barnes, C.; Bugbee, B.

1991-01-01

Wheat plants (Triticum aestivum L.) were grown at the same photosynthetic photon flux (PPF), 200 micromoles per square meter per second, but with phytochrome photoequilibrium (phi) values of 0.81, 0.55, and 0.33. Plants grown at phi values of 0.55 and 0.33 tillered 43 and 56%, less compared with plants grown at phi of 0.81. Main culm development (Haun stage) was slightly more advanced at lower values of phi, and leaf sheaths, but not leaf lamina, were longer at lower phi. Dry-mass accumulation was not affected by different levels of phi. Three levels of PPF (100, 200, and 400 micromoles per square meter per second) and two lamp types, metal halide and high pressure sodium, were also tested. Higher levels of PPF resulted in more dry mass, more tillering, and a more advanced Haun stage. There was no difference in plant dry mass or development under metal halide versus high pressure sodium lamps, except for total leaf length, which was greater under high pressure sodium lamps (49.5 versus 44.9 centimeters, P < 0.01).

Extended phase graphs with anisotropic diffusion

NASA Astrophysics Data System (ADS)

Weigel, M.; Schwenk, S.; Kiselev, V. G.; Scheffler, K.; Hennig, J.

2010-08-01

The extended phase graph (EPG) calculus gives an elegant pictorial description of magnetization response in multi-pulse MR sequences. The use of the EPG calculus enables a high computational efficiency for the quantitation of echo intensities even for complex sequences with multiple refocusing pulses with arbitrary flip angles. In this work, the EPG concept dealing with RF pulses with arbitrary flip angles and phases is extended to account for anisotropic diffusion in the presence of arbitrary varying gradients. The diffusion effect can be expressed by specific diffusion weightings of individual magnetization pathways. This can be represented as an action of a linear operator on the magnetization state. The algorithm allows easy integration of diffusion anisotropy effects. The formalism is validated on known examples from literature and used to calculate the effective diffusion weighting in multi-echo sequences with arbitrary refocusing flip angles.

Extending the Utility of the Parabolic Approximation in Medical Ultrasound Using Wide-Angle Diffraction Modeling.

PubMed

Soneson, Joshua E

2017-04-01

Wide-angle parabolic models are commonly used in geophysics and underwater acoustics but have seen little application in medical ultrasound. Here, a wide-angle model for continuous-wave high-intensity ultrasound beams is derived, which approximates the diffraction process more accurately than the commonly used Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation without increasing implementation complexity or computing time. A method for preventing the high spatial frequencies often present in source boundary conditions from corrupting the solution is presented. Simulations of shallowly focused axisymmetric beams using both the wide-angle and standard parabolic models are compared to assess the accuracy with which they model diffraction effects. The wide-angle model proposed here offers improved focusing accuracy and less error throughout the computational domain than the standard parabolic model, offering a facile method for extending the utility of existing KZK codes.

Gravitino-overproduction problem in an inflationary universe

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

Kawasaki, Masahiro; Takahashi, Fuminobu; Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg

We show that the gravitino-overproduction problem is prevalent among inflation models in supergravity. An inflaton field {phi} generically acquires (effective) nonvanishing auxiliary field G{sub {phi}}{sup (eff)}, if the Kaehler potential is nonminimal. The inflaton field then decays into a pair of the gravitinos. We extensively study the cosmological constraints on G{sub {phi}}{sup (eff)} for a wide range of the gravitino mass. For many inflation models we explicitly estimate G{sub {phi}}{sup (eff)}, and show that the gravitino-overproduction problem severely constrains the inflation models, unless such an interaction as K={kappa}/2 vertical bar {phi}|{sup 2}z{sup 2}+H.c. is suppressed (here z is the fieldmore » responsible for the supersymmetry breaking). We find that many of them are already excluded or on the verge of, if {kappa}{approx}O(1)« less

A de-identifier for medical discharge summaries.

PubMed

Uzuner, Ozlem; Sibanda, Tawanda C; Luo, Yuan; Szolovits, Peter

2008-01-01

Clinical records contain significant medical information that can be useful to researchers in various disciplines. However, these records also contain personal health information (PHI) whose presence limits the use of the records outside of hospitals. The goal of de-identification is to remove all PHI from clinical records. This is a challenging task because many records contain foreign and misspelled PHI; they also contain PHI that are ambiguous with non-PHI. These complications are compounded by the linguistic characteristics of clinical records. For example, medical discharge summaries, which are studied in this paper, are characterized by fragmented, incomplete utterances and domain-specific language; they cannot be fully processed by tools designed for lay language. In this paper, we show that we can de-identify medical discharge summaries using a de-identifier, Stat De-id, based on support vector machines and local context (F-measure=97% on PHI). Our representation of local context aids de-identification even when PHI include out-of-vocabulary words and even when PHI are ambiguous with non-PHI within the same corpus. Comparison of Stat De-id with a rule-based approach shows that local context contributes more to de-identification than dictionaries combined with hand-tailored heuristics (F-measure=85%). Comparison with two well-known named entity recognition (NER) systems, SNoW (F-measure=94%) and IdentiFinder (F-measure=36%), on five representative corpora show that when the language of documents is fragmented, a system with a relatively thorough representation of local context can be a more effective de-identifier than systems that combine (relatively simpler) local context with global context. Comparison with a Conditional Random Field De-identifier (CRFD), which utilizes global context in addition to the local context of Stat De-id, confirms this finding (F-measure=88%) and establishes that strengthening the representation of local context may be more beneficial for de-identification than complementing local with global context.

The organization of human epidermis: functional epidermal units and phi proportionality.

PubMed

Hoath, Steven B; Leahy, D G

2003-12-01

The concept that mammalian epidermis is structurally organized into functional epidermal units has been proposed on the basis of stratum corneum (SC) architecture, proliferation kinetics, melanocyte:keratinocyte ratios (1:36), and, more recently, Langerhans cell: epidermal cell ratios (1:53). This article examines the concept of functional epidermal units in human skin in which the maintenance of phi (1.618034) proportionality provides a central organizing principle. The following empirical measurements were used: 75,346 nucleated epidermal cells per mm2, 1394 Langerhans cells per mm2, 1999 melanocytes per mm2, 16 (SC) layers, 900-microm2 corneocyte surface area, 17,778 corneocytes per mm2, 14-d (SC) turnover time, and 93,124 per mm2 total epidermal cells. Given these empirical data: (1) the number of corneocytes is a mean proportional between the sum of the Langerhans cell + melanocyte populations and the number of epidermal cells, 3393/17,778-17,778/93,124; (2) the ratio of nucleated epidermal cells over corneocytes is phi proportional, 75,346/17,778 approximately phi3; (3) assuming similar 14-d turnover times for the (SC) and Malpighian epidermis, the number of corneocytes results from subtraction of a cellular fraction equal to approximately 2/phi2 x the number of living cells, 75,436 - (2/phi2 x 75,346) approximately 17,778; and (4) if total epidermal turnover time equals (SC) turnover time x the ratio of living/dead cells, then compartmental turnover times are unequal (14 d for (SC) to 45.3 d for nucleated epidermis approximately 1/2phi) and cellular replacement rates are 52.9 corneocytes/69.3 keratinocytes per mm2 per h approximately 2/phi2. These empirically derived equivalences provide logicomathematical support for the presence of functional epidermal units in human skin. Validation of a phi proportional unit architecture in human epidermis will be important for tissue engineering of skin and the design of instruments for skin measurement.

Functional characterization of intracellular pH regulators responsible for acid extrusion in human radial artery smooth muscle cells.

PubMed

Lee, Chung-Yi; Tsai, Yi-Ting; Chang, Chung-Yi; Chang, Yi-Yu; Cheng, Tzu-Hurng; Tsai, Chien-Sung; Loh, Shih-Hurng

2014-10-31

Intracellular pH (pHi) is a critical factor influencing many important cellular functions. Acid extrusion carriers such as an Na⁺/H⁺ exchanger (NHE) Na⁺/HCO₃⁻ cotransporter (NBC) and monocarboxylate transporters (MCT) can be activated when cells are in an acidic condition (pHi < 7.1). Human radial artery smooth muscle cells (HRASMC) is an important conduit in coronary artery bypass graft surgery. However, such far, the pHi regulators have not been characterized in HRASMCs. We therefore investigated the mechanism of pHi recovery from intracellular acidosis and alkalosis, induced by NH₄Cl-prepulse and Na-acetate-prepulse, respectively, using intracellular 2',7'-bis(2-carboxethyl)-5(6)- carboxy-fluorescein (BCECF)-fluorescence in HRASMCs. Cultured HRASMCs were derived from the segments of human radial artery that were obtained from patients undergoing bypass grafting. The resting pHi is 7.22 ± 0.03 and 7.17 ± 0.02 for HEPES- (nominally HCO₃⁻-free) and CO₂/HCO₃⁻- buffered solution, respectively. In HEPES-buffered solution, a pHi recovery from induced intracellular acidosis could be blocked completely by 30 μM HOE 694 (3-methylsulfonyl-4-piperidinobenzoyl, guanidine hydrochloride) a specific NHE inhibitor, or by removing [Na⁺]₀. In 3% CO₂/HCO₃⁻-buffered solution, HOE 694 slowed the pHi recovery from the induced intracellular acidosis only, while adding together with DIDS (a specific NBC inhibitor) or removal of [Na⁺]₀ entirely inhibited the acid extrusion. Moreover, α-cyano-4-hydroxycinnamate (CHC; a specific blocker of MCT) blocked the lactate-induced pHi changes. In conclusion, we demonstrate, for the first time, that 3 different pHi regulators responsible for acid extruding, i.e. NHE and NBC, and MCT, are functionally co-existed in cultured HRASMCs.

A De-identifier for Medical Discharge Summaries1

PubMed Central

Uzuner, Özlem; Sibanda, Tawanda C.; Luo, Yuan; Szolovits, Peter

2008-01-01

Objective Clinical records contain significant medical information that can be useful to researchers in various disciplines. However, these records also contain personal health information (PHI) whose presence limits the use of the records outside of hospitals. The goal of de-identification is to remove all PHI from clinical records. This is a challenging task because many records contain foreign and misspelled PHI; they also contain PHI that are ambiguous with non-PHI. These complications are compounded by the linguistic characteristics of clinical records. For example, medical discharge summaries, which are studied in this paper, are characterized by fragmented, incomplete utterances and domain-specific language; they cannot be fully processed by tools designed for lay language. Methods and Results In this paper, we show that we can de-identify medical discharge summaries using a de-identifier, Stat De-id, based on support vector machines and local context (F-measure = 97% on PHI). Our representation of local context aids de-identification even when PHI include out-of-vocabulary words and even when PHI are ambiguous with non-PHI within the same corpus. Comparison of Stat De-id with a rule-based approach shows that local context contributes more to de-identification than dictionaries combined with hand-tailored heuristics (F-measure = 85%). Comparison with two well-known named entity recognition (NER) systems, SNoW (F-measure = 94%) and IdentiFinder (F-measure = 36%), on five representative corpora show that when the language of documents is fragmented, a system with a relatively thorough representation of local context can be a more effective de-identifier than systems that combine (relatively simpler) local context with global context. Comparison with a Conditional Random Field De-identifier (CRFD), which utilizes global context in addition to the local context of Stat De-id, confirms this finding (F-measure = 88%) and establishes that strengthening the representation of local context may be more beneficial for de-identification than complementing local with global context. PMID:18053696

Biogas Laminar Burning Velocity and Flammability Characteristics in Spark Ignited Premix Combustion

NASA Astrophysics Data System (ADS)

Anggono, Willyanto; Wardana, I. N. G.; Lawes, M.; Hughes, K. J.; Wahyudi, Slamet; Hamidi, Nurkholis; Hayakawa, Akihiro

2013-04-01

Spherically expanding flames propagating at constant pressure were employed to determine the laminar burning velocity and flammability characteristics of biogas-air mixtures in premixed combustion to uncover the fundamental flame propagation characteristics of a new alternative and renewable fuel. The results are compared with those from a methane-air flame. Biogas is a sustainable and renewable fuel that is produced in digestion facilities. The composition of biogas discussed in this paper consists of 66.4% methane, 30.6% carbon dioxide and 3% nitrogen. Burning velocity was measured at various equivalence ratios (phi) using a photographic technique in a high pressure fan-stirred bomb, the initial condition being at room temperature and atmospheric pressure. The flame for methane-air mixtures propagates from phi=0.6 till phi=1.3. The flame at phi >= 1.4 does not propagate because the combustion reaction is quenched by the larger mass of fuel. At phi<=0.5, it does not propagate as well since the heat of reaction is insufficient to burn the mixtures. The flame for biogas-air mixtures propagates in a narrower range, that is from phi=0.6 to phi=1.2. Different from the methane flame, the biogas flame does not propagate at phi>=1.3 because the heat absorbed by inhibitors strengthens the quenching effect by the larger mass of fuel. As in the methane flame, the biogas flame at phi<=0.5 does not propagate. This shows that the effect of inhibitors in extremely lean mixtures is small. Compared to a methane-air mixture, the flammability characteristic (flammable region) of biogas becomes narrower in the presence of inhibitors (carbon dioxide and nitrogen) and the presence of inhibitors causes a reduction in the laminar burning velocity. The inhibitor gases work more effectively at rich mixtures because the rich biogas-air mixtures have a higher fraction of carbon dioxide and nitrogen components compared to the lean biogas-air mixtures.

The Skp1 Protein from Toxoplasma Is Modified by a Cytoplasmic Prolyl 4-Hydroxylase Associated with Oxygen Sensing in the Social Amoeba Dictyostelium*

PubMed Central

Xu, Yuechi; Brown, Kevin M.; Wang, Zhuo A.; van der Wel, Hanke; Teygong, Crystal; Zhang, Dongmei; Blader, Ira J.; West, Christopher M.

2012-01-01

In diverse types of organisms, cellular hypoxic responses are mediated by prolyl 4-hydroxylases that use O2 and α-ketoglutarate as substrates to hydroxylate conserved proline residues in target proteins. Whereas in metazoans these enzymes control the stability of the HIFα family of transcription factor subunits, the Dictyostelium enzyme (DdPhyA) contributes to O2 regulation of development by a divergent mechanism involving hydroxylation and subsequent glycosylation of DdSkp1, an adaptor subunit in E3SCF ubiquitin ligases. Sequences related to DdPhyA, DdSkp1, and the glycosyltransferases that cap Skp1 hydroxyproline occur also in the genomes of Toxoplasma and other protists, suggesting that this O2 sensing mechanism may be widespread. Here we show by disruption of the TgphyA locus that this enzyme is required for Skp1 glycosylation in Toxoplasma and that disrupted parasites grow slowly at physiological O2 levels. Conservation of cellular function was tested by expression of TgPhyA in DdphyA-null cells. Simple gene replacement did not rescue Skp1 glycosylation, whereas overexpression not only corrected Skp1 modification but also restored the O2 requirement to a level comparable to that of overexpressed DdPhyA. Bacterially expressed TgPhyA protein can prolyl hydroxylate both Toxoplasma and Dictyostelium Skp1s. Kinetic analyses showed that TgPhyA has similar properties to DdPhyA, including a superimposable dependence on the concentration of its co-substrate α-ketoglutarate. Remarkably, however, TgPhyA had a significantly higher apparent affinity for O2. The findings suggest that Skp1 hydroxylation by PhyA is a conserved process among protists and that this biochemical pathway may indirectly sense O2 by detecting the levels of O2-regulated metabolites such as α-ketoglutarate. PMID:22648409

Comparison of prostate cancer gene 3 score, prostate health index and percentage free prostate-specific antigen for differentiating histological inflammation from prostate cancer and other non-neoplastic alterations of the prostate at initial biopsy.

PubMed

De Luca, Stefano; Passera, Roberto; Bollito, Enrico; Manfredi, Matteo; Scarpa, Roberto Mario; Sottile, Antonino; Randone, Donato Franco; Porpiglia, Francesco

2014-12-01

To determine if prostate cancer gene 3 (PCA3) score, Prostate Health Index (PHI), and percent free prostate-specific antigen (%fPSA) may be used to differentiate prostatitis from prostate cancer (PCa), benign prostatic hyperplasia (BPH) and high-grade prostate intraepithelial neoplasia (HG-PIN) in patients with elevated PSA and negative digital rectal examination (DRE). in the present prospective study, 274 patients, undergoing PCA3 score, PHI and %fPSA assessments before initial biopsy, were enrolled. Three multivariate logistic regression models were used to test PCA3 score, PHI and %fPSA as risk factors for prostatitis vs. PCa, vs. BPH, and vs. HG-PIN. All the analyses were performed for the whole patient cohort and for the 'gray zone' of PSA (4-10 ng/ml) cohort (188 individuals). The determinants for prostatitis vs. PCa were PCA3 score, PHI and %fPSA (Odds Ratio [OR]=0.97, 0.96 and 0.94, respectively). Unit increase of PHI was the only risk factor for prostatitis vs. BPH (OR=1.06), and unit increase of PCA3 score for HG-PIN vs. prostatitis (OR=0.98). In the 'gray zone' PSA cohort, the determinants for prostatitis vs. PCa were PCA3 score, PHI and %fPSA (OR=0.96, 0.94 and 0.92, respectively), PCA3 score and PHI for prostatitis vs. BPH (OR=0.96 and 1.08, respectively), and PCA3 score for prostatitis vs. HG-PIN (OR=0.97). The clinical benefit of using PCA3 score and PHI to estimate prostatitis vs. PCa was comparable; even %fPSA had good diagnostic performance, being a faster and cheaper marker. PHI was the only determinant for prostatitis vs. BPH, while PCA3 score for prostatitis vs. HG-PIN. Copyright© 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Complete Genome Sequences of Two Novel Staphylococcus aureus Podoviruses of Potential Therapeutic Use, vB_SauP_phiAGO1.3 and vB_SauP_phiAGO1.9

PubMed Central

Gozdek, Agnieszka; Głowacka-Rutkowska, Aleksandra; Gawor, Jan; Empel, Joanna; Gromadka, Robert

2018-01-01

ABSTRACT Here, we report the genome sequences of two Staphylococcus aureus phages belonging to the family Podoviridae and subfamily Picovirinae, vB_SauP_phiAGO1.3 and vB_SauP_phiAGO1.9, which were isolated from Warsaw sewage. Analysis of their genomes provides valuable information about the diversity of phages belonging to the genus Rosenblumvirus and their genes that undergo evolutionary adaptation to cells of different host strains. PMID:29700131

Complete Genome Sequences of Two Novel Staphylococcus aureus Podoviruses of Potential Therapeutic Use, vB_SauP_phiAGO1.3 and vB_SauP_phiAGO1.9.

PubMed

Gozdek, Agnieszka; Głowacka-Rutkowska, Aleksandra; Gawor, Jan; Empel, Joanna; Gromadka, Robert; Łobocka, Małgorzata B

2018-04-26

Here, we report the genome sequences of two Staphylococcus aureus phages belonging to the family Podoviridae and subfamily Picovirinae , vB_SauP_phiAGO1.3 and vB_SauP_phiAGO1.9, which were isolated from Warsaw sewage. Analysis of their genomes provides valuable information about the diversity of phages belonging to the genus Rosenblumvirus and their genes that undergo evolutionary adaptation to cells of different host strains. Copyright © 2018 Gozdek et al.

Prospects for studying penguin decays in LHCb experiments

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

Barsuk, S. Ya.; Pakhlova, G. V., E-mail: Galina.Pakhlova@cern.ch; Belyaev, I. M.

2006-04-15

Investigation of loop penguin decays of beauty hadrons seems promising in testing the predictions of the Standard Model of electroweak and strong interactions and in seeking new phenomena beyond the Standard Model. The possibility of studying the radiative penguin decays B{sup 0} {sup {yields}} K*{sup 0}{gamma}, B{sup 0}{sub s} {sup {yields}} {phi}{gamma}, and B{sup 0} {sup {yields}} {omega}{gamma} and the gluonic penguin decays B{sup 0} {sup {yields}} {phi}K{sup 0}{sub S} and B{sup 0}{sub s} {sup {yields}} {phi}{phi} in LHCb experiments is discussed.

The effect of extracellular weak acids and bases on the intracellular buffering power of snail neurones.

PubMed Central

Szatkowski, M S

1989-01-01

1. Intracellular pH (pHi) was measured in snail neurones using pH-sensitive glass microelectrodes. The influence of externally applied weak acids and bases on the total intracellular buffering power (beta T) was investigated by monitoring the pHi changes caused by the intracellular ionophoretic injection of HCl. 2. In the absence of weak acids or bases a reduction in the extracellular HEPES concentration had no effect on pHi or on beta T. It did, however, reduce slightly the rate of pHi recovery following HCl injection. 3. The presence of CO2 greatly increased beta T. However, as predicted for an open buffer system, the contributions to intracellular buffering by CO2 (beta CO2) decreased as pHi decreased. 4. When added to the superfusate, procaine, 4-aminopyridine, trimethylamine and NH4Cl (1-10 mM) all increased steady-state pHi. Procaine was fastest at increasing pHi and 4-aminopyridine the slowest. All four of these weak bases increased beta T. 5. The intracellular buffering action by these weak bases varied. HCl injection in the presence of procaine usually resulted in steady-state pHi changes with no pHi transients. In the presence of the other three weak bases HCl injections resulted in intracellular acidifications which were followed by pHi recovery-like transients. However, these were not blocked by SITS (4-acetamido-4'-isothiocyanatostilbene-2,2'-disulphonic acid) or by CaCl2 and I thus conclude that these transients were as a result of slow or incomplete intracellular buffering by the weak bases. 6. In many cells there was a good correlation between the measured contributions to intracellular buffering by the weak bases (beta base) and those predicted assuming a simple two-compartment open system. In all cases, as predicted, beta base increased as pHi decreased. 7. I found a clear relationship between the concentration of external buffer (HEPES) and the rate at which weak bases, applied to the superfusate, were able to increase pHi. The greater the extracellular buffer concentration the greater was the speed of intracellular alkalinization. 8. Lowering the extracellular buffer concentration reduced the efficiency of intracellular buffering by weak bases in response to an intracellular acid load. HCl injection in the presence of weak base caused a larger initial intracellular acidification if the extracellular HEPES concentration was reduced. 9. In conclusion, both weak acids and weak bases can make very large, pHi-dependent contributions to intracellular buffering by way of open buffer systems.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:2555474

A pyruvate-proton symport and an H+-ATPase regulate the intracellular pH of Trypanosoma brucei at different stages of its life cycle.

PubMed

Vanderheyden, N; Wong, J; Docampo, R

2000-02-15

Regulation of intracellular pH (pH(i)) and H(+) efflux were investigated in Trypanosoma brucei bloodstream and procyclic trypomastigotes using the fluorescent dyes 2', 7'-bis-(2-carboxyethyl)-5(6)-carboxyfluorescein (BCECF) acetoxymethyl ester and free BCECF respectively. pH(i) in bloodstream and procyclic trypomastigotes was 7.47+/-0.06 and 7. 53+/-0.07 respectively. Differences in the mechanisms for the regulation of pH(i) were noted between bloodstream and procyclic forms. Procyclic trypomastigotes maintained their pH(i) at neutral over a wide range of external pH values from 6 to 8, and in the absence of K(+) or Na(+). The H(+)-ATPase inhibitors N, N'-dicyclohexylcarbodi-imide (DCCD), diethylstilboestrol and N-ethylmaleimide substantially decreased the steady-state pH(i) and inhibited its recovery from acidification. The rate of H(+) efflux in these forms was determined to be 62+/-6.5 nmol/min per mg of protein, and was substantially decreased by H(+)-ATPase inhibitors. The data support the presence of an H(+)-ATPase as the major regulator of pH(i) in procyclic trypomastigotes. In contrast, bloodstream trypomastigotes were unable to maintain a neutral pH under acidic conditions, and their steady-state pH(i) and recovery from acidification were unaffected by H(+)-ATPase inhibitors, except for DCCD (100 microM). Their steady-state pH(i) was markedly decreased in glucose-free buffer or by >/=10 mM pyruvate, whereas procyclic trypomastigotes were unaffected by similar treatments. The rate of H(+) efflux in bloodstream trypomastigotes was 534+/-38 nmol/min per mg of protein, and was decreased in the absence of glucose and by the addition of pyruvate or DCCD. Pyruvate efflux in these forms was calculated to be 499+/-34 nmol/min per mg of protein, and was significantly inhibited by DCCD, 4, 4'-di-isothiocyanatodihydrostilbene-2,2'-disulphonic acid and alpha-cyanohydroxycinnamic acid. The pyruvate analogues beta-hydroxypyruvate, 3-bromopyruvate, 3-oxoglutarate, oxaloacetate, 3-oxoisovalerate and 3-oxoisohexanoate significantly decreased pH(i), as well as proton and pyruvate efflux, whereas lactate had only a small effect, and no effect was observed with citrate or fumarate. The inhibition by pyruvate analogues of pyruvate efflux, proton efflux and acidification of pH(i) supports the hypothesis that pyruvate efflux is accompanied by proton efflux and that this is the major pH(i) control mechanism in bloodstream forms. Inhibition by H(+)-ATPase inhibitors of residual H(+) efflux in the absence of glucose or in the presence of high extracellular pyruvate indicates a minor role for H(+)-ATPase(s) in control of pH(i) in bloodstream forms.

Language disorders as a window on universal grammar: an abstract theory of agreement for IP, DP, and V-PP.

PubMed

Roeper, T; Ramos, E; Seymour, H; Abdul-Karim, L

2001-06-01

A new concept of Agreement (AGR) has been represented as a Formal Feature that can appear in a wide range of different configurations (Chomsky, 1998). A case study from language disorders supports and extends this abstract concept. The child shows no agreement in Inflectional Phrase me can and Determiner Phrase them eyes. We then extend the notion of AGR to include verb-Prepositional Phrase relations, where the child also systematically avoids certain prepositions (go beach). The analysis is supported by intuitional data from compounds (sweep with broom --> broom-swept). We also define a systematic notion of Possible deficit as a premature fixation of functional items which normally require additional Phi-features. The notion of Maximization of Formal Features then emerges as a significant feature of learnability from both a normal and disordered perspective. Copyright 2001 Academic Press.

A survey of reimbursement practices of private health insurance companies for pharmaceuticals not covered under the Pharmaceutical Benefits Scheme 2008.

PubMed

Lingaratnam, Senthil M; Kirsa, Sue W; Mellor, James D; Jackson, John; Crellin, Wallace; Fitzsimons, Michael; Zalcberg, John R

2011-05-01

To describe the current practices and policy of Australian private health insurance (PHI) companies with respect to cover for pharmaceuticals not subsidised under the Pharmaceutical Benefits Scheme (PBS). A 2008 review of web-published policy statements for top-level hospital and comprehensive general treatment insurance, and survey of reimbursement practices by way of questionnaire, of 31 Australian-registered, open-membership PHI companies. Description of the level of pharmaceutical cover and important considerations identified by PHI companies for funding non-PBS pharmaceuticals through benefit entitlements or ex-gratia payments. Nine of thirty-one PHI companies (29%) provided responses accounting for ~60% market share of PHI. The majority of smaller PHI firms either declined participation or did not respond. The maximum limits offered for non-PBS pharmaceuticals, under comprehensive general treatment insurance, varied significantly and typically did not adequately cover high-cost pharmaceuticals. Some companies occasionally offered ex-gratia payments (or discretionary payments in excess of the policyholder's entitlement benefits) for high cost-pharmaceuticals. Factors considered important in their decision to approve or reject ex-gratia requests were provided. All results were de-identified. There is little consistency across PHI companies in the manner in which they handle requests for high-cost pharmaceuticals in excess of the defined benefit limits. Such information and processes are not transparent to consumers.

Electroweak vacuum instability and renormalized Higgs field vacuum fluctuations in the inflationary universe

NASA Astrophysics Data System (ADS)

Kohri, Kazunori; Matsui, Hiroki

2017-08-01

In this work, we investigated the electroweak vacuum instability during or after inflation. In the inflationary Universe, i.e., de Sitter space, the vacuum field fluctuations < δ phi 2 > enlarge in proportion to the Hubble scale H2. Therefore, the large inflationary vacuum fluctuations of the Higgs field < δ phi 2 > are potentially catastrophic to trigger the vacuum transition to the negative-energy Planck-scale vacuum state and cause an immediate collapse of the Universe. However, the vacuum field fluctuations < δ phi 2 >, i.e., the vacuum expectation values have an ultraviolet divergence, and therefore a renormalization is necessary to estimate the physical effects of the vacuum transition. Thus, in this paper, we revisit the electroweak vacuum instability from the perspective of quantum field theory (QFT) in curved space-time, and discuss the dynamical behavior of the homogeneous Higgs field phi determined by the effective potential V eff( phi ) in curved space-time and the renormalized vacuum fluctuations < δ phi 2 >ren via adiabatic regularization and point-splitting regularization. We simply suppose that the Higgs field only couples the gravity via the non-minimal Higgs-gravity coupling ξ(μ). In this scenario, the electroweak vacuum stability is inevitably threatened by the dynamical behavior of the homogeneous Higgs field phi, or the formations of AdS domains or bubbles unless the Hubble scale is small enough H< ΛI .

The impact of financial incentives on physician empathy: a study from the perspective of patients with private and statutory health insurance.

PubMed

Neumann, Melanie; Bensing, Jozien; Wirtz, Markus; Wübker, Ansgar; Scheffer, Christian; Tauschel, Diethard; Edelhäuser, Friedrich; Ernstmann, Nicole; Pfaff, Holger

2011-08-01

We hypothesized that patients' ratings of physician empathy (PE) would be higher among those with private health insurance (PHI, referring to financial incentive) than among patients with statutory health insurance (SHI). A postal survey was administered to 710 cancer patients. PE was assessed using the Consultation-and-Relational-Empathy measure. T-tests were conducted to analyse whether PHI and SHI-patients differ in their ratings of PE and variables relating to contact time with the physician. Structural-equation-modelling (SEM) verified mediating effects. PHI-patients rated physician empathy higher. SEM revealed that PHI-status has a strong significant effect on frequency of talking with the physician, which has a strong significant effect (1) on PE and (2) has a moderate effect on patients' perception of medical staff stress, thereby also affecting patients' ratings of PE. Our findings suggest that PHI-status is one necessary precondition for physicians spending more time with the patient. Spending more time with the PHI-patient has two major effects: it results in a more positive perception of PE and positively impacts PHI-patients' perception of medical staff stress, which in turn, again influences PE. Health policy should discuss these findings in terms of equality in receiving high-quality care. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Intracellular pH gradients in migrating cells.

PubMed

Martin, Christine; Pedersen, Stine F; Schwab, Albrecht; Stock, Christian

2011-03-01

Cell polarization along the axis of movement is required for migration. The localization of proteins and regulators of the migratory machinery to either the cell front or its rear results in a spatial asymmetry enabling cells to simultaneously coordinate cell protrusion and retraction. Protons might function as such unevenly distributed regulators as they modulate the interaction of focal adhesion proteins and components of the cytoskeleton in vitro. However, an intracellular pH (pH(i)) gradient reflecting a spatial asymmetry of protons has not been shown so far. One major regulator of pH(i), the Na(+)/H(+) exchanger NHE1, is essential for cell migration and accumulates at the cell front. Here, we test the hypothesis that the uneven distribution of NHE1 activity creates a pH(i) gradient in migrating cells. Using the pH-sensitive fluorescent dye BCECF, pH(i) was measured in five cell lines (MV3, B16V, NIH3T3, MDCK-F1, EA.hy926) along the axis of movement. Differences in pH(i) between the front and the rear end (ΔpH(i) front-rear) were present in all cell lines, and inhibition of NHE1 either with HOE642 or by absence of extracellular Na(+) caused the pH(i) gradient to flatten or disappear. In conclusion, pH(i) gradients established by NHE1 activity exist along the axis of movement.

Elevated intracellular pH appears in aged oocytes and causes oocyte aneuploidy associated with the loss of cohesion in mice

PubMed Central

Cheng, Jin-Mei; Li, Jian; Tang, Ji-Xin; Chen, Su-Ren; Deng, Shou-Long; Jin, Cheng; Zhang, Yan; Wang, Xiu-Xia; Zhou, Chen-Xi; Liu, Yi-Xun

2016-01-01

ABSTRACT Increases in the aneuploidy rate caused by the deterioration of cohesion with increasing maternal age have been well documented. However, the molecular mechanism for the loss of cohesion in aged oocytes remains unknown. In this study, we found that intracellular pH (pHi) was elevated in aged oocytes, which might disturb the structure of the cohesin ring to induce aneuploidy. We observed for the first time that full-grown germinal vesicle (GV) oocytes displayed an increase in pHi with advancing age in CD1 mice. Furthermore, during the in vitro oocyte maturation process, the pHi was maintained at a high level, up to ∼7.6, in 12-month-old mice. Normal pHi is necessary to maintain protein localization and function. Thus, we put forward a hypothesis that the elevated oocyte pHi might be related to the loss of cohesion and the increased aneuploidy in aged mice. Through the in vitro alkalinization treatment of young oocytes, we observed that the increased pHi caused an increase in the aneuploidy rate and the sister inter-kinetochore (iKT) distance associated with the strength of cohesion and caused a decline in the cohesin subunit SMC3 protein level. Young oocytes with elevated pHi exhibited substantially the increase in chromosome misalignment. PMID:27472084

Characterization of Natronobacterium magadii phage phi Ch1, a unique archaeal phage containing DNA and RNA.

PubMed

Witte, A; Baranyi, U; Klein, R; Sulzner, M; Luo, C; Wanner, G; Krüger, D H; Lubitz, W

1997-02-01

A novel archaeal bacteriophage, phi Ch1, was isolated from a haloalkalophilic archaeon Natronobacterium magadii upon spontaneous lysis. The phage-cured strain N. magadii(L13) was used to demonstrate infectivity of phage phi Ch1. The turbid-plaque morphology and the fact that N. magadii cells isolated from plaques were able to produce phage indicated that phi Ch1 is a temperate phage. The phage morphology resembles other members of Myoviridae-infecting Halobacterium species. In solution below 2M NaCl, the phage lost its morphological stability and infectivity. One- and two-dimensional SDS-PAGE of phage particles revealed at least four major and five minor proteins with molecular masses ranging from 15 to 80 kDa and acidic isoelectric points. Southern blot analysis of chromosomal DNA of a lysogenic N. magadii strain showed that phi Ch1 exists as a chromosomally integrated prophage. The phage particles contain both double-stranded, linear DNA (approx. 55 kbp) as well as several RNA species (80-700 nucleotides). Hybridization of labelled RNA fragments to total DNA from N. magadii and phi Ch1 showed that the virion-associated RNA is host encoded. Part of the phage DNA population is modified and restriction analysis revealed evidence for adenine methylation. Phage phi Ch1 is the first virus described for the genus natronobacterium, and the first phage containing DNA and RNA in mature phage particles.

SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

PubMed Central

Mallo, Diego; De Oliveira Martins, Leonardo; Posada, David

2016-01-01

We present a fast and flexible software package—SimPhy—for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer—all three potentially leading to species tree/gene tree discordance—and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases. PMID:26526427

77 FR 5087 - Petition for Exemption; Summary of Petition Received

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-01

....: FAA-2011-1233 Petitioner: PHI Air Medical, LLC Section of 14 CFR Affected: 14 CFR Sec. Sec. 135.293, 135.297, 135.299, and 135.343 Description of Relief Sought: PHI Air Medical, LLC requests an exemption to permit Air Medical to use pilots previously qualified under PHI, Inc.'s part 119 air carrier...

Mutant Screen Distinguishes between Residues Necessary for Light-Signal Perception and Signal Transfer by Phytochrome B

USDA-ARS?s Scientific Manuscript database

The phytochromes (phyA to phyE) are a major plant photoreceptor family that regulate a diversity of developmental processes in response to light. The N-terminal 651–amino acid domain of phyB (N651), which binds an open tetrapyrrole chromophore, acts to perceive and transduce regulatory light signals...

Flocking and invariance of velocity angles.

PubMed

Liu, Le; Huang, Lihong; Wu, Jianhong

2016-04-01

Motsch and Tadmor considered an extended Cucker-Smale model to investigate the flocking behavior of self-organized systems of interacting species. In this extended model, a cone of the vision was introduced so that outside the cone the influence of one agent on the other is lost and hence the corresponding influence function takes the value zero. This creates a problem to apply the Motsch-Tadmor and Cucker-Smale method to prove the flocking property of the system. Here, we examine the variation of the velocity angles between two arbitrary agents, and obtain a monotonicity property for the maximum cone of velocity angles. This monotonicity permits us to utilize existing arguments to show the flocking property of the system under consideration, when the initial velocity angles satisfy some minor technical constraints.

Commensurability effects in one-dimensional Anderson localization: Anomalies in eigenfunction statistics

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

Kravtsov, V.E., E-mail: kravtsov@ictp.it; Landau Institute for Theoretical Physics, 2 Kosygina st., 117940 Moscow; Yudson, V.I., E-mail: yudson@isan.troitsk.ru

Highlights: > Statistics of normalized eigenfunctions in one-dimensional Anderson localization at E = 0 is studied. > Moments of inverse participation ratio are calculated. > Equation for generating function is derived at E = 0. > An exact solution for generating function at E = 0 is obtained. > Relation of the generating function to the phase distribution function is established. - Abstract: The one-dimensional (1d) Anderson model (AM), i.e. a tight-binding chain with random uncorrelated on-site energies, has statistical anomalies at any rational point f=(2a)/({lambda}{sub E}) , where a is the lattice constant and {lambda}{sub E} is the demore » Broglie wavelength. We develop a regular approach to anomalous statistics of normalized eigenfunctions {psi}(r) at such commensurability points. The approach is based on an exact integral transfer-matrix equation for a generating function {Phi}{sub r}(u, {phi}) (u and {phi} have a meaning of the squared amplitude and phase of eigenfunctions, r is the position of the observation point). This generating function can be used to compute local statistics of eigenfunctions of 1d AM at any disorder and to address the problem of higher-order anomalies at f=p/q with q > 2. The descender of the generating function P{sub r}({phi}){identical_to}{Phi}{sub r}(u=0,{phi}) is shown to be the distribution function of phase which determines the Lyapunov exponent and the local density of states. In the leading order in the small disorder we derived a second-order partial differential equation for the r-independent ('zero-mode') component {Phi}(u, {phi}) at the E = 0 (f=1/2 ) anomaly. This equation is nonseparable in variables u and {phi}. Yet, we show that due to a hidden symmetry, it is integrable and we construct an exact solution for {Phi}(u, {phi}) explicitly in quadratures. Using this solution we computed moments I{sub m} = N< vertical bar {psi} vertical bar {sup 2m}> (m {>=} 1) for a chain of the length N {yields} {infinity} and found an essential difference between their m-behavior in the center-of-band anomaly and for energies outside this anomaly. Outside the anomaly the 'extrinsic' localization length defined from the Lyapunov exponent coincides with that defined from the inverse participation ratio ('intrinsic' localization length). This is not the case at the E = 0 anomaly where the extrinsic localization length is smaller than the intrinsic one. At E = 0 one also observes an anomalous enhancement of large moments compatible with existence of yet another, much smaller characteristic length scale.« less

(Quasi)-convexification of Barta's (multi-extrema) bounding theorem: Inf_x\\big(\\ssty\\frac{H\\Phi(x)}{\\Phi(x)} \\big) \\le E_gr \\le Sup_x \\big(\\ssty\\frac{H\\Phi(x)}{\\Phi(x)} \\big)

NASA Astrophysics Data System (ADS)

Handy, C. R.

2006-03-01

There has been renewed interest in the exploitation of Barta's configuration space theorem (BCST) (Barta 1937 C. R. Acad. Sci. Paris 204 472) which bounds the ground-state energy, Inf_x\\big({{H\\Phi(x)}\\over {\\Phi(x)}} \\big ) \\leq E_gr \\leq Sup_x \\big({{H\\Phi(x)}\\over {\\Phi(x)}}\\big) , by using any Φ lying within the space of positive, bounded, and sufficiently smooth functions, {\\cal C} . Mouchet's (Mouchet 2005 J. Phys. A: Math. Gen. 38 1039) BCST analysis is based on gradient optimization (GO). However, it overlooks significant difficulties: (i) appearance of multi-extrema; (ii) inefficiency of GO for stiff (singular perturbation/strong coupling) problems; (iii) the nonexistence of a systematic procedure for arbitrarily improving the bounds within {\\cal C} . These deficiencies can be corrected by transforming BCST into a moments' representation equivalent, and exploiting a generalization of the eigenvalue moment method (EMM), within the context of the well-known generalized eigenvalue problem (GEP), as developed here. EMM is an alternative eigenenergy bounding, variational procedure, overlooked by Mouchet, which also exploits the positivity of the desired physical solution. Furthermore, it is applicable to Hermitian and non-Hermitian systems with complex-number quantization parameters (Handy and Bessis 1985 Phys. Rev. Lett. 55 931, Handy et al 1988 Phys. Rev. Lett. 60 253, Handy 2001 J. Phys. A: Math. Gen. 34 5065, Handy et al 2002 J. Phys. A: Math. Gen. 35 6359). Our analysis exploits various quasi-convexity/concavity theorems common to the GEP representation. We outline the general theory, and present some illustrative examples.

Prostate health index (PHI) and prostate-specific antigen (PSA) predictive models for prostate cancer in the Chinese population and the role of digital rectal examination-estimated prostate volume.

PubMed

Chiu, Peter K F; Roobol, Monique J; Teoh, Jeremy Y; Lee, Wai-Man; Yip, Siu-Ying; Hou, See-Ming; Bangma, Chris H; Ng, Chi-Fai

2016-10-01

To investigate PSA- and PHI (prostate health index)-based models for prediction of prostate cancer (PCa) and the feasibility of using DRE-estimated prostate volume (DRE-PV) in the models. This study included 569 Chinese men with PSA 4-10 ng/mL and non-suspicious DRE with transrectal ultrasound (TRUS) 10-core prostate biopsies performed between April 2008 and July 2015. DRE-PV was estimated using 3 pre-defined classes: 25, 40, or 60 ml. The performance of PSA-based and PHI-based predictive models including age, DRE-PV, and TRUS prostate volume (TRUS-PV) was analyzed using logistic regression and area under the receiver operating curves (AUC), in both the whole cohort and the screening age group of 55-75. PCa and high-grade PCa (HGPCa) was diagnosed in 10.9 % (62/569) and 2.8 % (16/569) men, respectively. The performance of DRE-PV-based models was similar to TRUS-PV-based models. In the age group 55-75, the AUCs for PCa of PSA alone, PSA with DRE-PV and age, PHI alone, PHI with DRE-PV and age, and PHI with TRUS-PV and age were 0.54, 0.71, 0.76, 0.78, and 0.78, respectively. The corresponding AUCs for HGPCa were higher (0.60, 0.70, 0.85, 0.83, and 0.83). At 10 and 20 % risk threshold for PCa, 38.4 and 55.4 % biopsies could be avoided in the PHI-based model, respectively. PHI had better performance over PSA-based models and could reduce unnecessary biopsies. A DRE-assessed PV can replace TRUS-assessed PV in multivariate prediction models to facilitate clinical use.

Electron cryo-tomographic structure of cystovirus phi 12.

PubMed

Hu, Guo-Bin; Wei, Hui; Rice, William J; Stokes, David L; Gottlieb, Paul

2008-03-01

Bacteriophage phi 12 is a member of the Cystoviridae virus family and contains a genome consisting of three segments of double-stranded RNA (dsRNA). This virus family contains eight identified members, of which four have been classified in regard to their complete genomic sequence and encoded viral proteins. A phospholipid envelope that contains the integral proteins P6, P9, P10, and P13 surrounds the viral particles. In species phi 6, host infection requires binding of a multimeric P3 complex to type IV pili. In species varphi8, phi 12, and phi 13, the attachment apparatus is a heteromeric protein assembly that utilizes the rough lipopolysaccharide (rlps) as a receptor. In phi 8 the protein components are designated P3a and P3b while in species phi 12 proteins P3a and P3c have been identified in the complex. The phospholipid envelope of the cystoviruses surrounds a nucleocapsid (NC) composed of two shells. The outer shell is composed of protein P8 with a T=13 icosahedral lattice while the primary component of the inner shell is a dodecahedral frame composed of dimeric protein P1. For the current study, the 3D architecture of the intact phi 12 virus was obtained by electron cryo-tomography. The nucleocapsid appears to be centered within the membrane envelope and possibly attached to it by bridging structures. Two types of densities were observed protruding from the membrane envelope. The densities of the first type were elongated, running parallel, and closely associated to the envelope outer surface. In contrast, the second density was positioned about 12 nm above the envelope connected to it by a flexible low-density stem. This second structure formed a torroidal structure termed "the donut" and appears to inhibit BHT-induced viral envelope fusion.

Restoration of prostaglandin E2-producing splenic macrophages in sup 89 Sr-treated mice with bone marrow from Corynebacterium parvum primed donors

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

Shibata, Y.

1989-05-01

Administration of Corynebacterium parvum (CP), 56 mg/kg ip to CBA/J mice effected the induction of prostaglandin E2 (PGE2) producing macrophages (M phi) in the bone marrow and the spleen. Maximal release of PGE2 from M phi cultured in vitro with calcium ionophore A23187 for 2 h was reached by marrow M phi removed on 5 days after CP (450 ng/mg cell protein), and by splenic M phi 9 days after CP (400 ng/mg). Neither M phi population, however, yielded more than 6.0 ng/mg leukotriene C4. To assess ontogenic relationships mice were depleted of bone marrow and blood monocytes by ivmore » injection of the bone-seeking isotope, 89Sr. CP was given at several points before or after bone marrow cell depletion. PGE2 production by splenic M phi harvested on day 9 after CP was profoundly impaired when CP was administered either concurrently with or 3 days after 89Sr. When CP was administered 1, 3, 5, and 7 days before 89Sr, however, the induction of PGE2-producing M phi in the spleen was unaffected. To determine whether bone marrow cells from CP-injected donors can restore PGE2-producing splenic M phi (PGSM) in 89Sr-mice, recipient mice which had and had not received CP 3 days after 89Sr were transfused with 5 x 10(6) syngeneic bone marrow cells from donor mice prepared at varying intervals after CP administration. The results clearly indicate the capacity of bone marrow cells harvested on either day 1 or 2 following CP to restore PGSM in CP-primed, but not unprimed, recipients.« less

Dissecting Phosphite-Induced Priming in Arabidopsis Infected with Hyaloperonospora arabidopsidis1[W

PubMed Central

Massoud, Kamal; Barchietto, Thierry; Le Rudulier, Thomas; Pallandre, Laurane; Didierlaurent, Laure; Garmier, Marie; Ambard-Bretteville, Françoise; Seng, Jean-Marc; Saindrenan, Patrick

2012-01-01

Phosphite (Phi), a phloem-mobile oxyanion of phosphorous acid (H3PO3), protects plants against diseases caused by oomycetes. Its mode of action is unclear, as evidence indicates both direct antibiotic effects on pathogens as well as inhibition through enhanced plant defense responses, and its target(s) in the plants is unknown. Here, we demonstrate that the biotrophic oomycete Hyaloperonospora arabidopsidis (Hpa) exhibits an unusual biphasic dose-dependent response to Phi after inoculation of Arabidopsis (Arabidopsis thaliana), with characteristics of indirect activity at low doses (10 mm or less) and direct inhibition at high doses (50 mm or greater). The effect of low doses of Phi on Hpa infection was nullified in salicylic acid (SA)-defective plants (sid2-1, NahG) and in a mutant impaired in SA signaling (npr1-1). Compromised jasmonate (jar1-1) and ethylene (ein2-1) signaling or abscisic acid (aba1-5) biosynthesis, reactive oxygen generation (atrbohD), or accumulation of the phytoalexins camalexin (pad3-1) and scopoletin (f6′h1-1) did not affect Phi activity. Low doses of Phi primed the accumulation of SA and Pathogenesis-Related protein1 transcripts and mobilized two essential components of basal resistance, Enhanced Disease Susceptibility1 and Phytoalexin Deficient4, following pathogen challenge. Compared with inoculated, Phi-untreated plants, the gene expression, accumulation, and phosphorylation of the mitogen-activated protein kinase MPK4, a negative regulator of SA-dependent defenses, were reduced in plants treated with low doses of Phi. We propose that Phi negatively regulates MPK4, thus priming SA-dependent defense responses following Hpa infection. PMID:22408091

Intracellular pH imaging in cancer cells in vitro and tumors in vivo using the new genetically encoded sensor SypHer2.

PubMed

Shirmanova, Marina V; Druzhkova, Irina N; Lukina, Maria M; Matlashov, Mikhail E; Belousov, Vsevolod V; Snopova, Ludmila B; Prodanetz, Natalia N; Dudenkova, Varvara V; Lukyanov, Sergey A; Zagaynova, Elena V

2015-09-01

Measuring intracellular pH (pHi) in tumors is essential for the monitoring of cancer progression and the response of cancer cells to various treatments. The purpose of the study was to develop a method for pHi mapping in living cancer cells in vitro and in tumors in vivo, using the novel genetically encoded indicator, SypHer2. A HeLa Kyoto cell line stably expressing SypHer2 in the cytoplasm was used, to perform ratiometric (dual excitation) imaging of the probe in cell culture, in 3D tumor spheroids and in tumor xenografts in living mice. Using SypHer2, pHi was demonstrated to be 7.34±0.11 in monolayer HeLa cells in vitro under standard cultivation conditions. An increasing pHi gradient from the center to the periphery of the spheroids was displayed. We obtained fluorescence ratio maps for HeLa tumors in vivo and ex vivo. Comparison of the map with the pathomorphology and with hypoxia staining of the tumors revealed a correspondence of the zones with higher pHi to the necrotic and hypoxic areas. Our results demonstrate that pHi imaging with the genetically encoded pHi indicator, SypHer2, can be a valuable tool for evaluating tumor progression in xenograft models. We have demonstrated, for the first time, the possibility of using the genetically encoded sensor SypHer2 for ratiometric pH imaging in cancer cells in vitro and in tumors in vivo. SypHer2 shows great promise as an instrument for pHi monitoring able to provide high accuracy and spatiotemporal resolution. Copyright © 2015 Elsevier B.V. All rights reserved.

Transcriptome Profiling of Tiller Buds Provides New Insights into PhyB Regulation of Tillering and Indeterminate Growth in Sorghum1

PubMed Central

2016-01-01

Phytochrome B (phyB) enables plants to modify shoot branching or tillering in response to varying light intensities and ratios of red and far-red light caused by shading and neighbor proximity. Tillering is inhibited in sorghum genotypes that lack phytochrome B (58M, phyB-1) until after floral initiation. The growth of tiller buds in the first leaf axil of wild-type (100M, PHYB) and phyB-1 sorghum genotypes is similar until 6 d after planting when buds of phyB-1 arrest growth, while wild-type buds continue growing and develop into tillers. Transcriptome analysis at this early stage of bud development identified numerous genes that were up to 50-fold differentially expressed in wild-type/phyB-1 buds. Up-regulation of terminal flower1, GA2oxidase, and TPPI could protect axillary meristems in phyB-1 from precocious floral induction and decrease bud sensitivity to sugar signals. After bud growth arrest in phyB-1, expression of dormancy-associated genes such as DRM1, GT1, AF1, and CKX1 increased and ENOD93, ACCoxidase, ARR3/6/9, CGA1, and SHY2 decreased. Continued bud outgrowth in wild-type was correlated with increased expression of genes encoding a SWEET transporter and cell wall invertases. The SWEET transporter may facilitate Suc unloading from the phloem to the apoplast where cell wall invertases generate monosaccharides for uptake and utilization to sustain bud outgrowth. Elevated expression of these genes was correlated with higher levels of cytokinin/sugar signaling in growing buds of wild-type plants. PMID:26893475

Safety, reactogenicity and immunogenicity of a booster dose of the 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV) in Malian children.

PubMed

Dicko, Alassane; Santara, Gaoussou; Mahamar, Almahamoudou; Sidibe, Youssoufa; Barry, Amadou; Dicko, Yahia; Diallo, Aminata; Dolo, Amagana; Doumbo, Ogobara; Shafi, Fakrudeen; François, Nancy; Strezova, Ana; Borys, Dorota; Schuerman, Lode

2013-02-01

Primary vaccination with the 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV) was previously shown to be immunogenic and well tolerated in Malian children. Data on booster vaccination with a fourth consecutive dose of PHiD-CV are available for Europe, Asia and Latin America but are lacking for Africa. The present study evaluated further the safety, reactogenicity and immunogenicity of a fourth consecutive (booster) dose of PHiD-CV. Low incidences of AEs with grade 3 intensity (2.1% of subjects) were observed. There were no reports of large swelling reactions and serious adverse events. One month post-booster vaccination, for each vaccine pneumococcal serotype, at least 97.8% of subjects had antibody concentrations ≥ 0.2 μg/ml, and at least 97.1% of subjects had opsonophagocytic activity ≥ 8. From pre- to post-booster, a 12.3-fold increase in anti-protein D geometric mean concentration was observed. This phase III, open-label study was conducted in Ouelessebougou, Mali, between November 2009 and June 2010. The study population consisted of Malian children previously primed (3 doses) with PHiD-CV in study NCT00678301 receiving a fourth consecutive (booster) dose of PHiD-CV in the second year of life. The incidences of adverse events (AEs) with grade 3 intensity (primary objective) or of any intensity (secondary objective), and the immunogenicity (secondary objective) of the PHiD-CV booster dose were assessed. A booster dose of PHiD-CV was well tolerated when administered to Malian children in the second year of life and was highly immunogenic for all 10 vaccine pneumococcal serotypes and NTHi protein D. (ClinicalTrials.gov identifier: NCT00985465).

Flow cytometric kinetic assay of the activity of Na+/H+ antiporter in mammalian cells.

PubMed

Dolz, María; O'Connor, José-Enrique; Lequerica, Juan L

2004-10-01

The Na(+)/H(+) exchanger (NHE) of mammalian cells is an integral membrane protein that extrudes H(+) ion in exchange for extracellular Na(+) and plays a crucial role in the regulation of intracellular pH (pHi). Thus, when pHi is lowered, NHE extrudes protons at a rate depending of pHi that can be expressed as pH units/s. To abolish the activity of other cellular pH-restoring systems, cells were incubated in bicarbonate-free Dulbecco's modified Eagle's medium buffered with HEPES. Flow cytometry was used to determine pHi with 2',7'-bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein acetoxymethyl ester or 5-(and-6)-carboxy SNARF-1 acetoxymethyl ester acetate, and the appropriate fluorescence ratios were measured. The calibration of fluorescence ratios versus pHi was established by using ionophore nigericin. The activity of NHE was calculated by a kinetic flow cytometric assay as the slope at time 0 of the best-fit curve of pHi recovery versus time after intracellular acidification with a pulse of exogenous sodium propionate. The kinetic method allowed determination of the pHi-dependent activity of NHE in cell lines and primary cell cultures. NHE activity values were demonstrated to be up to 0.016 pH units/s within the pHi range of 7.3 to 6.3. The inhibition of NHE activity by the specific inhibitor ethyl isopropyl amiloride was easily detected by this method. The assay conditions can be used to relate variations in pHi with the activity of NHE and provide a standardized method to compare between different cells, inhibitors, models of ischemia by acidification, and other relevant experimental or clinical situations.

The extent to which the public health 'war on obesity' reflects the ethical values and principles of critical health promotion: a multimedia critical discourse analysis.

PubMed

O'Hara, Lily; Taylor, Jane; Barnes, Margaret

2015-12-01

The discipline of health promotion is responsible for implementing strategies within weight-related public health initiatives (WR-PHI). It is imperative that such initiatives be subjected to critical analysis through a health promotion ethics lens to help ensure ethical health promotion practice. Multimedia critical discourse analysis was used to examine the claims, values, assumptions, power relationships and ideologies within Australian WR-PHI. The Health Promotion Values and Principles Continuum was used as a heuristic to evaluate the extent to which the WR-PHI reflected the ethical values of critical health promotion: active participation of people in the initiative; respect for personal autonomy; beneficence; non-maleficence; and strong evidential and theoretical basis for practice. Ten initiatives were analysed. There was some discourse about the need for participation of people in the WR-PHI, but people were routinely labelled as 'target groups' requiring 'intervention'. Strong evidence of a coercive and paternalistic discourse about choice was identified, with minimal attention to respect for personal autonomy. There was significant emphasis on the beneficiaries of the WR-PHI but minimal attention to the health benefits, and nothing about the potential for harm. Discourse about the evidence of need was objectivist, and there was no discussion about the theoretical foundations of the WR-PHI. The WR-PHI were not reflective of the ethical values and principles of critical health promotion. So what? Health promotion researchers and practitioners engaged in WR-PHI should critically reflect on the extent to which they are consistent with the ethical aspects of critical health promotion practice.

An Evaluation of Personal Health Information Remnants in Second-Hand Personal Computer Disk Drives

PubMed Central

Neri, Emilio; Jonker, Elizabeth

2007-01-01

Background The public is concerned about the privacy of their health information, especially as more of it is collected, stored, and exchanged electronically. But we do not know the extent of leakage of personal health information (PHI) from data custodians. One form of data leakage is through computer equipment that is sold, donated, lost, or stolen from health care facilities or individuals who work at these facilities. Previous studies have shown that it is possible to get sensitive personal information (PI) from second-hand disk drives. However, there have been no studies investigating the leakage of PHI in this way. Objectives The aim of the study was to determine the extent to which PHI can be obtained from second-hand computer disk drives. Methods A list of Canadian vendors selling second-hand computer equipment was constructed, and we systematically went through the shuffled list and attempted to purchase used disk drives from the vendors. Sixty functional disk drives were purchased and analyzed for data remnants containing PHI using computer forensic tools. Results It was possible to recover PI from 65% (95% CI: 52%-76%) of the drives. In total, 10% (95% CI: 5%-20%) had PHI on people other than the owner(s) of the drive, and 8% (95% CI: 7%-24%) had PHI on the owner(s) of the drive. Some of the PHI included very sensitive mental health information on a large number of people. Conclusions There is a strong need for health care data custodians to either encrypt all computers that can hold PHI on their clients or patients, including those used by employees and subcontractors in their homes, or to ensure that their computers are destroyed rather than finding a second life in the used computer market. PMID:17942386

Effects of supplementary private health insurance on physician visits in Korea.

PubMed

Kang, Sungwook; You, Chang Hoon; Kwon, Young Dae; Oh, Eun-Hwan

2009-12-01

The coverage of social health insurance has remained limited, despite it being compulsory in Korea. Accordingly, Koreans have come to rely upon supplementary private health insurance (PHI) to cover their medical costs. We examined the effects of supplementary PHI on physician visits in Korea. This study used individual data from 11,043 respondents who participated in the Korean Labor and Income Panel Survey in 2001. We conducted a single probit model to identify the relationship between PHI and physician visits, with adjustment for the following covariates: demographic characteristics, socioeconomic status, health status, and health-related behavior. Finally, we performed a bivariate probit model to examine the true effect of PHI on physician visits, with adjustment for the above covariates plus unobservable covariates that might affect not only physician visit, but also the purchase of PHI. We found that about 38% of all respondents had one or more private health plans. Forty-five percent of all respondents visited one or more physicians, and 49% of those who were privately insured had physician visits compared with 42% of the uninsured. The single probit model showed that those with PHI were about 14 percentage points more likely to visit physicians than those who do not have PHI. However, this distinction disappears in the bivariate probit model. This result might have been a consequence of the nature of private health plans in Korea. Private insurance companies pay a fixed amount directly to their enrollees in case of illness/injury, and the individuals are responsible subsequently for purchasing their own healthcare services. This study demonstrated the potential of Korean PHI to address the problem of moral hazard. These results serve as a reference for policy makers when considering how to finance healthcare services, as well as to contain healthcare expenditure.

Observation of a peaking structure in the $$J/\\psi \\phi$$ mass spectrum from $$B^{\\pm} \\to J/\\psi \\phi K^{\\pm}$$ decays

DOE PAGES

Chatrchyan, Serguei

2014-05-22

A peaking structure in the J/psi phi mass spectrum near threshold is observed in B(+/-) to J/psi phi K(+/-) decays, produced in pp collisions at sqrt(s) = 7 TeV collected with the CMS detector at the LHC. The data sample, selected on the basis of the dimuon decay mode of the J/psi, corresponds to an integrated luminosity of 5.2 inverse femtobarns. Fitting the structure to an S-wave relativistic Breit-Wigner lineshape above a three-body phase-space nonresonant component gives a signal statistical significance exceeding five standard deviations. The fitted mass and width values are m = 4148.0 +- 2.4 (stat.) +- 6.3more » (syst.) MeV and Gamma = 28 +15 -11 (stat.) +- 19 (syst.) MeV, respectively. Evidence for an additional peaking structure at higher J/psi phi mass is also reported.« less

Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging.

PubMed

Fang, Yun; Shu, Dan; Xiao, Feng; Guo, Peixuan; Qin, Peter Z

2008-08-08

The bacteriophage phi29 DNA packaging motor is a protein/RNA complex that can produce strong force to condense the linear-double-stranded DNA genome into a pre-formed protein capsid. The RNA component, called the packaging RNA (pRNA), utilizes magnesium-dependent inter-molecular base-pairing interactions to form ring-shaped complexes. The pRNA is a class of non-coding RNA, interacting with phi29 motor proteins to enable DNA packaging. Here, we report a two-piece chimeric pRNA construct that is fully competent in interacting with partner pRNA to form ring-shaped complexes, in packaging DNA via the motor, and in assembling infectious phi29 virions in vitro. This is the first example of a fully functional pRNA assembled using two non-covalently interacting fragments. The results support the notion of modular pRNA architecture in the phi29 packaging motor.

PhySortR: a fast, flexible tool for sorting phylogenetic trees in R.

PubMed

Stephens, Timothy G; Bhattacharya, Debashish; Ragan, Mark A; Chan, Cheong Xin

2016-01-01

A frequent bottleneck in interpreting phylogenomic output is the need to screen often thousands of trees for features of interest, particularly robust clades of specific taxa, as evidence of monophyletic relationship and/or reticulated evolution. Here we present PhySortR, a fast, flexible R package for classifying phylogenetic trees. Unlike existing utilities, PhySortR allows for identification of both exclusive and non-exclusive clades uniting the target taxa based on tip labels (i.e., leaves) on a tree, with customisable options to assess clades within the context of the whole tree. Using simulated and empirical datasets, we demonstrate the potential and scalability of PhySortR in analysis of thousands of phylogenetic trees without a priori assumption of tree-rooting, and in yielding readily interpretable trees that unambiguously satisfy the query. PhySortR is a command-line tool that is freely available and easily automatable.

Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging

PubMed Central

Fang, Yun; Shu, Dan; Xiao, Feng; Guo, Peixuan; Qin, Peter Z.

2008-01-01

The bacteriophage phi29 DNA packaging motor is a protein/RNA complex that can produce strong force to condense the linear-double stranded DNA genome into a pre-formed protein capsid. The RNA component, called the packaging RNA (pRNA), utilizes magnesium-dependent intermolecular base-pairing interactions to form ring-shaped complexes. The pRNA is a class of non-coding RNA, interacting with phi29 motor proteins to enable DNA packaging. Here, we report a 2-piece chimeric pRNA construct that is fully competent in interacting with partner pRNA to form ring-shaped complexes, in packaging DNA via the motor, and in assembling infectious phi29 virions in vitro. This is the first example of a fully functional pRNA assembled using two non-covalently interacting fragments. The results support the notion of modular pRNA architecture in the phi29 packaging motor. PMID:18514064

DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol.

PubMed

Smith, Nicholas; Witham, Shawn; Sarkar, Subhra; Zhang, Jie; Li, Lin; Li, Chuan; Alexov, Emil

2012-06-15

A new edition of the DelPhi web server, DelPhi web server v2, is released to include atomic presentation of geometrical figures. These geometrical objects can be used to model nano-size objects together with real biological macromolecules. The position and size of the object can be manipulated by the user in real time until desired results are achieved. The server fixes structural defects, adds hydrogen atoms and calculates electrostatic energies and the corresponding electrostatic potential and ionic distributions. The web server follows a client-server architecture built on PHP and HTML and utilizes DelPhi software. The computation is carried out on supercomputer cluster and results are given back to the user via http protocol, including the ability to visualize the structure and corresponding electrostatic potential via Jmol implementation. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver.

Extended phase graphs with anisotropic diffusion.

PubMed

Weigel, M; Schwenk, S; Kiselev, V G; Scheffler, K; Hennig, J

2010-08-01

The extended phase graph (EPG) calculus gives an elegant pictorial description of magnetization response in multi-pulse MR sequences. The use of the EPG calculus enables a high computational efficiency for the quantitation of echo intensities even for complex sequences with multiple refocusing pulses with arbitrary flip angles. In this work, the EPG concept dealing with RF pulses with arbitrary flip angles and phases is extended to account for anisotropic diffusion in the presence of arbitrary varying gradients. The diffusion effect can be expressed by specific diffusion weightings of individual magnetization pathways. This can be represented as an action of a linear operator on the magnetization state. The algorithm allows easy integration of diffusion anisotropy effects. The formalism is validated on known examples from literature and used to calculate the effective diffusion weighting in multi-echo sequences with arbitrary refocusing flip angles. Copyright 2010 Elsevier Inc. All rights reserved.

Lytic activity of the virion-associated peptidoglycan hydrolase HydH5 of staphylococcus aureus bacteriophage vB_SauS-phiIPLA88

USDA-ARS?s Scientific Manuscript database

Staphylococcus aureus bacteriophage vB_SauS-phiIPLA88 (phiIPLA88) contains a virion-associated muralytic enzyme (HydH5) encoded by orf58, which is located in the morphogenetic module. Comparative bioinformatic analysis revealed that HydH5 significantly resembled other peptidoglycan hydrolases encode...

Enzymatic Comparisons of Aspergillus niger PhyA and Escherichia coli AppA2 Phytases

USDA-ARS?s Scientific Manuscript database

This study was to compare three phytase activity assays and kinetics of Aspergillus niger PhyA and Escherichia coli AppA2 phytases expressed in Pichia pastoris at the observed stomach pH of 3.5. In Experiment 1, equivalent phytase activities in the crude preparations of PhyA and AppA2 were tested ...

Expression and GTP sensitivity of peptide histidine isoleucine high-affinity-binding sites in rat.

PubMed

Debaigt, Colin; Meunier, Annie-Claire; Goursaud, Stephanie; Montoni, Alicia; Pineau, Nicolas; Couvineau, Alain; Laburthe, Marc; Muller, Jean-Marc; Janet, Thierry

2006-07-01

High-affinity-binding sites for the vasoactive intestinal peptide (VIP) analogs peptide histidine/isoleucine-amide (PHI)/carboxyterminal methionine instead of isoleucine (PHM) are expressed in numerous tissues in the body but the nature of their receptors remains to be elucidated. The data presented indicate that PHI discriminated a high-affinity guanosine 5'-triphosphate (GTP)-insensitive-binding subtype that represented the totality of the PHI-binding sites in newborn rat tissues but was differentially expressed in adult animals. The GTP-insensitive PHI/PHM-binding sites were also observed in CHO cells over expressing the VPAC2 but not the VPAC1 VIP receptor.

Chameleon scalar fields in relativistic gravitational backgrounds

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

Tsujikawa, Shinji; Tamaki, Takashi; Tavakol, Reza, E-mail: shinji@rs.kagu.tus.ac.jp, E-mail: tamaki@gravity.phys.waseda.ac.jp, E-mail: r.tavakol@qmul.ac.uk

2009-05-15

We study the field profile of a scalar field {phi} that couples to a matter fluid (dubbed a chameleon field) in the relativistic gravitational background of a spherically symmetric spacetime. Employing a linear expansion in terms of the gravitational potential {Phi}{sub c} at the surface of a compact object with a constant density, we derive the thin-shell field profile both inside and outside the object, as well as the resulting effective coupling with matter, analytically. We also carry out numerical simulations for the class of inverse power-law potentials V({phi}) = M{sup 4+n}{phi}{sup -n} by employing the information provided by ourmore » analytical solutions to set the boundary conditions around the centre of the object and show that thin-shell solutions in fact exist if the gravitational potential {Phi}{sub c} is smaller than 0.3, which marginally covers the case of neutron stars. Thus the chameleon mechanism is present in the relativistic gravitational backgrounds, capable of reducing the effective coupling. Since thin-shell solutions are sensitive to the choice of boundary conditions, our analytic field profile is very helpful to provide appropriate boundary conditions for {Phi}{sub c}{approx}« less

Amelioration of Ethanol-Induced Gastric Ulcers in Rats Pretreated with Phycobiliproteins of Arthrospira (Spirulina) Maxima.

PubMed

Guzmán-Gómez, Oscar; García-Rodríguez, Rosa Virginia; Quevedo-Corona, Lucía; Pérez-Pastén-Borja, Ricardo; Rivero-Ramírez, Nora Lilia; Ríos-Castro, Emmanuel; Pérez-Gutiérrez, Salud; Pérez-Ramos, Julia; Chamorro-Cevallos, Germán Alberto

2018-06-13

Phycobiliproteins of Arthrospira ( Spirulina ) maxima have attracted attention because of their potential therapeutic antioxidant properties. The aim of this study was to assess the possible antiulcerogenic activity of these phycobiliproteins (ExPhy) against ethanol-induced gastric ulcers in rats. To explore the possible mechanisms of action, we examined antioxidant defense enzymes (e.g., catalase, superoxide dismutase, and glutathione peroxidase), as well as the level of lipid peroxidation (MDA) and the histopathological changes in the gastric mucosa. Intragastric administration of ExPhy (100, 200, and 400 mg/kg body weight) significantly lowered the ulcer index value compared to the ulcer control group ( p < 0.05). The greatest protection was provided by the concentration of 400 mg/kg. The histological study supported the observed gastroprotective activity of ExPhy, showing a reduced inflammatory response. Moreover, the alcohol-induced decrease in stomach antioxidant enzyme activity found in the ulcer control group was prevented by ExPhy pretreatment. Furthermore, ExPhy reversed the ethanol-induced increase in lipid peroxidation. In summary, the antiulcerogenic potential of ExPhy may be due, at least in part, to its anti-oxidant and anti-inflammatory effects.

Mechanisms of inactivation of bacteriophage phiX174 and its DNA in aerosols by ozone and ozonized cyclohexene.

PubMed Central

de Mik, G.; de Groot, I.

1977-01-01

The mechanisms of inactivation of aerosolized bacteriophage phiX174 in atmospheres containing ozone, cyclohexene, or ozonized cyclohexene were studied by using 32P-labelled phage. The inactivation of the aerosolized phage in clear air or in air containing cyclohexene is due to damage of the protein coat since the deoxyribonucleic acid (DNA) extracted from the inactivated phage retains its biological activity. Inactivation of the phage in air containing ozonized cyclohexene is due both to protein and DNA damage. Sucrose gradient analysis shows that aerosolized inactivated phiX174 releases unbroken DNA. In contrast, the DNA from phage phiX174 inactivated by ozonized cyclohexene is broken. The inactivation of aerosolized phage phiX174-DNA was studied in the same atmospheres using 32P-labelled DNA. phiX174-DNA aerosolized in clear air or air containing cyclohexene at 75% r.h. is inactivated by a factor of 2 in 30 min. The inactivated DNA is broken. Ozone as well as ozonized cyclohexene inactivates KNA very fast causing breaks in the molecule. This is in contrast with the intact bacteriophage in which ozone does not produce breaks in the DNA. PMID:265342

On absolutely continuous weakly mixing cocycles over irrational rotations

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

Rozhdestvenskii, A V

2003-06-30

A weakly mixing cocycle over a rotation {alpha} is a measurable function {phi}:S{sup 1}{yields}S{sup 1}, where S{sup 1}={l_brace}z element of C:|z|=1{r_brace}, such that the equation {phi}{sup n}(z)=c (h(exp(2{pi}i{alpha})z))/(h(z))for almost all z; (*) has no measurable solutions h( {center_dot} ):S{sup 1}{yields}S{sup 1} for any n element of Z{l_brace}0{r_brace} and c element of C, |c|=1. If the irrational number {alpha} has bounded convergents in its continued fraction expansion and a function M(y) increases more slowly than y ln{sup 1/2}y, then it is proved that there exists a weakly mixing cocycle of the form {phi}(exp(2{pi}ix))=exp(2{pi}i{phi}-tilde(x)), where {phi}-tilde:T{yields}R belongs to the class W{sup 1}(M(L)(T)).more » In addition, it is shown that equation (*) (and also the corresponding additive cohomological equation) is soluble for {phi}-tilde element of W{sup 1}(L log{sub +}{sup 1/2}L(T))« less

Public-private sector interactions and the demand for supplementary health insurance in the United Kingdom.

PubMed

Bíró, Anikó; Hellowell, Mark

2016-07-01

We examine the demand for private health insurance (PHI) in the United Kingdom and relate this to changes in the supply of public and private healthcare. Using a novel collection of administrative, private sector and survey data, we re-assess the relationships between the quality and availability of public and private sector inpatient care, and the demand for PHI. We find that PHI coverage in the United Kingdom is positively related to the median of the region- and year-specific public sector waiting times. We find that PHI prevalence ceteris paribus increases with being self-employed and employed, while it decreases with having financial difficulties. In addition, we highlight the complexities of inter-sectoral relations and their impact on PHI demand. Within a region, we find that an increase in private healthcare supply is associated with a decrease in public sector waiting times, implying lower PHI demand. This may be explained by the usage of private facilities by NHS commissioners. These results have important implications for policymakers interested in the role of private healthcare supply in enhancing the availability of and equitable access to acute inpatient care. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Model-Dependent Constraint on Quark Total Angular Momentum Based on the Transverse Target-spin Asymmetry Measured in Deeply Virtual Compton Scattering at HERMES

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

Nowak, Wolf-Dieter

Results are reported on the transverse target-spin asymmetry (TTSA) associated with deeply virtual Compton scattering on the proton. The data have been accumulated in the years 2002-2004 by the HERMES experiment at DESY, in which the HERA 27.6 GeV e+ beam scattered on a transversely polarized hydrogen target. Two azimuthal amplitudes of the TTSA appearing to LO in 1/Q and {alpha}s, A{sub UT}{sup sin({phi}-{phi}{sub S})cos{phi}} and A{sub UT}{sup cos({phi} -{phi}{sub S})sin{phi}}, are given as a function of -t,xB,Q2 in the kinematic range |t| < 0.7 GeV2, 0.03 < xB < 0.35 and 1 < Q2 < 10 GeV2. The firstmore » amplitude is found to be sensitive to the generalized parton distribution (GPD) E of the proton, which can be parameterized in a GPD model through quark total angular momentum Jq(q = u, d). Within the context of this model, a constraint in the (Ju,Jd) plane is obtained from HERMES TTSA data.« less

Biological Control of Phytophthora palmivora Causing Root Rot of Pomelo Using Chaetomium spp.

PubMed Central

Wattanachai, Pongnak; Kasem, Soytong; Poaim, Supatta

2015-01-01

Phytophthora diseases have become a major impediment in the citrus production in Thailand. In this study, an isolate of Phytophthora denominated as PHY02 was proven to be causal pathogen of root rot of Pomelo (Citrus maxima) in Thailand. The isolate PHY02 was morphologically characterized and identified as Phytophthora palmivora based on molecular analysis of an internal transcribed spacer rDNA sequence. This work also presents in vitro evaluations of the capacities of Chaetomium spp. to control the P. palmivora PHY02. As antagonists, Chaetomium globosum CG05, Chaetomium cupreum CC3003, Chaetomium lucknowense CL01 inhibited 50~61% mycelial growth, degraded mycelia and reduced 92~99% sporangial production of P. palmivora PHY02 in bi-culture test after 30 days. Fungal metabolites from Chaetomium spp. were tested against PHY02. Results showed that, methanol extract of C. globosum CG05 expressed strongest inhibitory effects on mycelial growth and sporangium formation of P. palmivora PHY02 with effective dose ED50 values of 26.5 µg/mL and 2.3 µg/mL, respectively. It is interesting that C. lucknowense is reported for the first time as an effective antagonist against a species of Phytophthora. PMID:25892917

Evaluating the Use of Monocytes with a Degradable Polyurethane for Vascular Tissue Regeneration

NASA Astrophysics Data System (ADS)

Battiston, Kyle Giovanni

Monocytes are one of the first cell types present following the implantation of a biomaterial or tissue engineered construct. Depending on the monocyte activation state supported by the biomaterial, monocytes and their derived macrophages (MDMs) can act as positive contributors to tissue regeneration and wound healing, or conversely promote a chronic inflammatory response that leads to fibrous encapsulation and implant rejection. A degradable polar hydrophobic iconic polyurethane (D-PHI) has been shown to reduce pro-inflammatory monocyte/macrophage response compared to tissue culture polystyrene (TCPS), a substrate routinely used for in vitro culture of cells, as well as poly(lactide- co-glycolide) (PLGA), a standard synthetic biodegradable biomaterial in the tissue engineering field. D-PHI has also shown properties suitable for use in a vascular tissue engineering context. In order to understand the mechanism through which D-PHI attenuates pro-inflammatory monocyte response, this thesis investigated the ability of D-PHI to modulate interactions with adsorbed serum proteins and the properties of D-PHI that were important for this activity. D-PHI was shown to regulate protein adsorption in a manner that produced divergent monocyte responses compared to TCPS and PLGA when coated with the serum proteins alpha2-macroglobulin or immunoglobulin G (IgG). In the case of IgG, D-PHI was shown to reduce pro-inflammatory binding site exposure as a function of the material's polar, hydrophobic, and ionic character. Due to the favourable monocyte activation state supported by D-PHI, and the importance of monocytes/macrophages in regulating the response of tissue-specific cell types in vivo, the ability of a D-PHI-stimulated monocyte/macrophage activation state to contribute to modulating the response of vascular smooth muscle cells (VSMCs) in a vascular tissue engineering context was investigated. D-PHI- stimulated monocytes promoted VSMC growth and migration through biomolecule release. Coupling monocyte-VSMC co-culture with biomechanical strain further enhanced these effects, while also promoting extracellular matrix deposition (collagen I, collagen III, and elastin) and enhancing the mechanical properties of VSMC-monocyte seeded tissue constructs. This thesis identifies the use of biomaterials with immunomodulatory capacity to harness the stimulatory potential of MDMs and contribute to tissue engineering strategies in vitro. This latter work in turn has contributed to identifying aspects of biomaterial design that can contribute to supporting desirable monocyte-biomaterial interactions that can facilitate this process.

Evaluation of the Intel Xeon Phi Co-processor to accelerate the sensitivity map calculation for PET imaging

NASA Astrophysics Data System (ADS)

Dey, T.; Rodrigue, P.

2015-07-01

We aim to evaluate the Intel Xeon Phi coprocessor for acceleration of 3D Positron Emission Tomography (PET) image reconstruction. We focus on the sensitivity map calculation as one computational intensive part of PET image reconstruction, since it is a promising candidate for acceleration with the Many Integrated Core (MIC) architecture of the Xeon Phi. The computation of the voxels in the field of view (FoV) can be done in parallel and the 103 to 104 samples needed to calculate the detection probability of each voxel can take advantage of vectorization. We use the ray tracing kernels of the Embree project to calculate the hit points of the sample rays with the detector and in a second step the sum of the radiological path taking into account attenuation is determined. The core components are implemented using the Intel single instruction multiple data compiler (ISPC) to enable a portable implementation showing efficient vectorization either on the Xeon Phi and the Host platform. On the Xeon Phi, the calculation of the radiological path is also implemented in hardware specific intrinsic instructions (so-called `intrinsics') to allow manually-optimized vectorization. For parallelization either OpenMP and ISPC tasking (based on pthreads) are evaluated.Our implementation achieved a scalability factor of 0.90 on the Xeon Phi coprocessor (model 5110P) with 60 cores at 1 GHz. Only minor differences were found between parallelization with OpenMP and the ISPC tasking feature. The implementation using intrinsics was found to be about 12% faster than the portable ISPC version. With this version, a speedup of 1.43 was achieved on the Xeon Phi coprocessor compared to the host system (HP SL250s Gen8) equipped with two Xeon (E5-2670) CPUs, with 8 cores at 2.6 to 3.3 GHz each. Using a second Xeon Phi card the speedup could be further increased to 2.77. No significant differences were found between the results of the different Xeon Phi and the Host implementations. The examination showed that a reasonable speedup of sensitivity map calculation could be achieved on the Xeon Phi either by a portable or a hardware specific implementation.

Macrophage function in murine allogeneic bone marrow radiation chimeras in the early phase after transplantation

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

Roesler, J.; Baccarini, M.; Vogt, B.

1989-08-01

We tested several of the functions of macrophages (M phi) in the early phase after allogeneic bone marrow transfer to get information about this important aspect of the nonspecific immune system in the T-cell-deficient recipient. On days 3-5 after transfer, the number of M phi was reduced in the spleen, liver, lungs, and peritoneal cavity (Pe). The phagocytosis of sheep red blood cells (SRBC) by these M phi was normal or even enhanced, as in the case of Pe-M phi. Already on days 8-12 after transfer, the number of M phi in spleen and liver exceeded that of controls, whereasmore » the number was still reduced in lungs and Pe. We examined their ability to kill P815 tumor cells, to produce tumor necrosis factor-alpha (TNF alpha), to phagocytose SRBC, to produce reactive oxygen intermediates (ROI) in vitro and to kill Listeria monocytogenes in vivo. Most functions were normal and often even enhanced, depending on the organ origin, but the ability of Pe-M phi to produce ROI was reduced. Proliferative response to macrophage colony-stimulating factor (M-CSF) and killing of YAC-1 tumor cells revealed a high frequency of macrophage precursor cells in the spleen and liver and a high natural killer (NK) activity in the liver. Altogether, enhanced nonspecific immune function, especially preactivated M phi, may enable chimeras to survive attacks by opportunistic pathogens.« less

Characterization of a T7-like lytic bacteriophage (phiSG-JL2) of Salmonella enterica serovar gallinarum biovar gallinarum.

PubMed

Kwon, Hyuk-Joon; Cho, Sun-Hee; Kim, Tae-Eun; Won, Yong-Jin; Jeong, Jihye; Park, Se Chang; Kim, Jae-Hong; Yoo, Han-Sang; Park, Yong-Ho; Kim, Sun-Joong

2008-11-01

PhiSG-JL2 is a newly discovered lytic bacteriophage infecting Salmonella enterica serovar Gallinarum biovar Gallinarum but is nonlytic to a rough vaccine strain of serovar Gallinarum biovar Gallinarum (SG-9R), S. enterica serovar Enteritidis, S. enterica serovar Typhimurium, and S. enterica serovar Gallinarum biovar Pullorum. The phiSG-JL2 genome is 38,815 bp in length (GC content, 50.9%; 230-bp-long direct terminal repeats), and 55 putative genes may be transcribed from the same strand. Functions were assigned to 30 genes based on high amino acid similarity to known proteins. Most of the expected proteins except tail fiber (31.9%) and the overall organization of the genomes were similar to those of yersiniophage phiYeO3-12. phiSG-JL2 could be classified as a new T7-like virus and represents the first serovar Gallinarum biovar Gallinarum phage genome to be sequenced. On the basis of intraspecific ratios of nonsynonymous to synonymous nucleotide changes (Pi[a]/Pi[s]), gene 2 encoding the host RNA polymerase inhibitor displayed Darwinian positive selection. Pretreatment of chickens with phiSG-JL2 before intratracheal challenge with wild-type serovar Gallinarum biovar Gallinarum protected most birds from fowl typhoid. Therefore, phiSG-JL2 may be useful for the differentiation of serovar Gallinarum biovar Gallinarum from other Salmonella serotypes, prophylactic application in fowl typhoid control, and understanding of the vertical evolution of T7-like viruses.

Critical role for NHE1 in intracellular pH regulation in pancreatic acinar cells.

PubMed

Brown, David A; Melvin, James E; Yule, David I

2003-11-01

The primary function of pancreatic acinar cells is to secrete digestive enzymes together with a NaCl-rich primary fluid which is later greatly supplemented and modified by the pancreatic duct. A Na+/H+ exchanger(s) [NHE(s)] is proposed to be integral in the process of fluid secretion both in terms of the transcellular flux of Na+ and intracellular pH (pHi) regulation. Multiple NHE isoforms have been identified in pancreatic tissue, but little is known about their individual functions in acinar cells. The Na+/H+ exchange inhibitor 5-(N-ethyl-N-isopropyl) amiloride completely blocked pHi recovery after an NH4Cl-induced acid challenge, confirming a general role for NHE in pHi regulation. The targeted disruption of the Nhe1 gene also completely abolished pHi recovery from an acid load in pancreatic acini in both HCO3--containing and HCO3--free solutions. In contrast, the disruption of either Nhe2 or Nhe3 had no effect on pHi recovery. In addition, NHE1 activity was upregulated in response to muscarinic stimulation in wild-type mice but not in NHE1-deficient mice. Fluctuations in pHi could potentially have major effects on Ca2+ signaling following secretagogue stimulation; however, the targeted disruption of Nhe1 was found to have no significant effect on intracellular Ca2+ homeostasis. These data demonstrate that NHE1 is the major regulator of pHi in both resting and muscarinic agonist-stimulated pancreatic acinar cells.

Predicting prostate biopsy outcome: prostate health index (phi) and prostate cancer antigen 3 (PCA3) are useful biomarkers.

PubMed

Ferro, Matteo; Bruzzese, Dario; Perdonà, Sisto; Mazzarella, Claudia; Marino, Ada; Sorrentino, Alessandra; Di Carlo, Angelina; Autorino, Riccardo; Di Lorenzo, Giuseppe; Buonerba, Carlo; Altieri, Vincenzo; Mariano, Angela; Macchia, Vincenzo; Terracciano, Daniela

2012-08-16

Indication for prostate biopsy is presently mainly based on prostate-specific antigen (PSA) serum levels and digital-rectal examination (DRE). In view of the unsatisfactory accuracy of these two diagnostic exams, research has focused on novel markers to improve pre-biopsy prostate cancer detection, such as phi and PCA3. The purpose of this prospective study was to assess the diagnostic accuracy of phi and PCA3 for prostate cancer using biopsy as gold standard. Phi index (Beckman coulter immunoassay), PCA3 score (Progensa PCA3 assay) and other established biomarkers (tPSA, fPSA and %fPSA) were assessed before a 18-core prostate biopsy in a group of 251 subjects at their first biopsy. Values of %p2PSA and phi were significantly higher in patients with PCa compared with PCa-negative group (p<0.001) and also compared with high grade prostatic intraepithelial neoplasia (HGPIN) (p<0.001). PCA3 score values were significantly higher in PCa compared with PCa-negative subjects (p<0.001) and in HGPIN vs PCa-negative patients (p<0.001). ROC curve analysis showed that %p2PSA, phi and PCA3 are predictive of malignancy. In conclusion, %p2PSA, phi and PCA3 may predict a diagnosis of PCa in men undergoing their first prostate biopsy. PCA3 score is more useful in discriminating between HGPIN and non-cancer. Copyright © 2012 Elsevier B.V. All rights reserved.

A structural model of anti-anti-[sigma] inhibition by a two-component receiver domain: the PhyR stress response regulator

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

Herrou, Julien; Foreman, Robert; Fiebig, Aretha

2012-05-09

PhyR is a hybrid stress regulator conserved in {alpha}-proteobacteria that contains an N-terminal {sigma}-like (SL) domain and a C-terminal receiver domain. Phosphorylation of the receiver domain is known to promote binding of the SL domain to an anti-{sigma} factor. PhyR thus functions as an anti-anti-{sigma} factor in its phosphorylated state. We present genetic evidence that Caulobacter crescentus PhyR is a phosphorylation-dependent stress regulator that functions in the same pathway as {sigma}{sup T} and its anti-{sigma} factor, NepR. Additionally, we report the X-ray crystal structure of PhyR at 1.25 {angstrom} resolution, which provides insight into the mechanism of anti-anti-{sigma} regulation. Directmore » intramolecular contact between the PhyR receiver and SL domains spans regions {sigma}{sub 2} and {sigma}{sub 4}, likely serving to stabilize the SL domain in a closed conformation. The molecular surface of the receiver domain contacting the SL domain is the structural equivalent of {alpha}4-{beta}5-{alpha}5, which is known to undergo dynamic conformational change upon phosphorylation in a diverse range of receiver proteins. We propose a structural model of PhyR regulation in which receiver phosphorylation destabilizes the intramolecular interaction between SL and receiver domains, thereby permitting regions {sigma}{sub 2} and {sigma}{sub 4} in the SL domain to open about a flexible connector loop and bind anti-{sigma} factor.« less

A structural model of anti-anti-[sigma];#963; inhibition by a two-component receiver domain: the PhyR stress response regulator

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

Herrou, Julien; Foreman, Robert; Fiebig, Aretha

2012-03-30

PhyR is a hybrid stress regulator conserved in {alpha}-proteobacteria that contains an N-terminal {sigma}-like (SL) domain and a C-terminal receiver domain. Phosphorylation of the receiver domain is known to promote binding of the SL domain to an anti-{sigma} factor. PhyR thus functions as an anti-anti-{sigma} factor in its phosphorylated state. We present genetic evidence that Caulobacter crescentus PhyR is a phosphorylation-dependent stress regulator that functions in the same pathway as {sigma}{sup T} and its anti-{sigma} factor, NepR. Additionally, we report the X-ray crystal structure of PhyR at 1.25 {angstrom} resolution, which provides insight into the mechanism of anti-anti-{sigma} regulation. Directmore » intramolecular contact between the PhyR receiver and SL domains spans regions {sigma}{sub 2} and {sigma}{sub 4}, likely serving to stabilize the SL domain in a closed conformation. The molecular surface of the receiver domain contacting the SL domain is the structural equivalent of {alpha}4-{beta}5-{alpha}5, which is known to undergo dynamic conformational change upon phosphorylation in a diverse range of receiver proteins. We propose a structural model of PhyR regulation in which receiver phosphorylation destabilizes the intramolecular interaction between SL and receiver domains, thereby permitting regions {sigma}{sub 2} and {sigma}{sub 4} in the SL domain to open about a flexible connector loop and bind anti-{sigma} factor.« less

Accurate Quantitative Sensing of Intracellular pH based on Self-ratiometric Upconversion Luminescent Nanoprobe

NASA Astrophysics Data System (ADS)

Li, Cuixia; Zuo, Jing; Zhang, Li; Chang, Yulei; Zhang, Youlin; Tu, Langping; Liu, Xiaomin; Xue, Bin; Li, Qiqing; Zhao, Huiying; Zhang, Hong; Kong, Xianggui

2016-12-01

Accurate quantitation of intracellular pH (pHi) is of great importance in revealing the cellular activities and early warning of diseases. A series of fluorescence-based nano-bioprobes composed of different nanoparticles or/and dye pairs have already been developed for pHi sensing. Till now, biological auto-fluorescence background upon UV-Vis excitation and severe photo-bleaching of dyes are the two main factors impeding the accurate quantitative detection of pHi. Herein, we have developed a self-ratiometric luminescence nanoprobe based on förster resonant energy transfer (FRET) for probing pHi, in which pH-sensitive fluorescein isothiocyanate (FITC) and upconversion nanoparticles (UCNPs) were served as energy acceptor and donor, respectively. Under 980 nm excitation, upconversion emission bands at 475 nm and 645 nm of NaYF4:Yb3+, Tm3+ UCNPs were used as pHi response and self-ratiometric reference signal, respectively. This direct quantitative sensing approach has circumvented the traditional software-based subsequent processing of images which may lead to relatively large uncertainty of the results. Due to efficient FRET and fluorescence background free, a highly-sensitive and accurate sensing has been achieved, featured by 3.56 per unit change in pHi value 3.0-7.0 with deviation less than 0.43. This approach shall facilitate the researches in pHi related areas and development of the intracellular drug delivery systems.

phiC31 Integrase-Mediated Site-Specific Recombination in Barley

PubMed Central

Rubtsova, Myroslava; Kumlehn, Jochen; Gils, Mario

2012-01-01

The Streptomyces phage phiC31 integrase was tested for its feasibility in excising transgenes from the barley genome through site-specific recombination. We produced transgenic barley plants expressing an active phiC31 integrase and crossed them with transgenic barley plants carrying a target locus for recombination. The target sequence involves a reporter gene encoding green fluorescent protein (GFP), which is flanked by the attB and attP recognition sites for the phiC31 integrase. This sequence disruptively separates a gusA coding sequence from an upstream rice actin promoter. We succeeded in producing site-specific recombination events in the hybrid progeny of 11 independent barley plants carrying the above target sequence after crossing with plants carrying a phiC31 expression cassette. Some of the hybrids displayed fully executed recombination. Excision of the GFP gene fostered activation of the gusA gene, as visualized in tissue of hybrid plants by histochemical staining. The recombinant loci were detected in progeny of selfed F1, even in individuals lacking the phiC31 transgene, which provides evidence of stability and generative transmission of the recombination events. In several plants that displayed incomplete recombination, extrachromosomal excision circles were identified. Besides the technical advance achieved in this study, the generated phiC31 integrase-expressing barley plants provide foundational stock material for use in future approaches to barley genetic improvement, such as the production of marker-free transgenic plants or switching transgene activity. PMID:23024817

Out-of-equilibrium pH transients in the guinea-pig ventricular myocyte

PubMed Central

Leem, Chae-Hun; Vaughan-Jones, Richard D

1998-01-01

Following an intracellular alkali load (imposed by acetate prepulsing in CO2/HCO3− buffer), intracellular pH (pHi) of the guinea-pig ventricular myocyte (recorded from intracellular SNARF fluorescence) recovers to control levels. Recovery has two phases. An initial rapid phase (lasting up to 2 min) is followed by a later slow phase (several minutes). Inhibition of sarcolemmal acid-loading carriers (by removal of extracellular Cl−) inhibits the later, slow phase but the initial rapid recovery phase persists. It also persists in the absence of extracellular Na+ and in the presence of the HCO3− transport inhibitor DIDS (4,4-di-isothiocyanatostilbene-2,2-disulphonic acid). The rapid recovery phase is not evident if the alkali load has been induced by reducing PCO2 (from 10 to 5 %), and it is inhibited in the absence of CO2/HCO3− buffer (i.e. Hepes buffer). It is also slowed by the carbonic anhydrase (CA) inhibitor acetazolamide (ATZ). We conclude that it is caused by buffering of the alkali load through the hydration of intracellular CO2 (CO2-dependent buffering). The time course of rapid recovery is consistent with an intracellular CO2 hydration rate constant (k1) of 0.36 s−1 in the presence of CA activity, and 0.14 s−1 in the absence of CA activity. This latter k1 value matches the literature value for uncatalysed CO2 hydration in free solution. Natural CO2 hydration is accelerated 2.6-fold in the ventricular myocyte by endogenous CA. The rapid recovery phase represents a period when the intracellular CO2/HCO3− buffer is out of equilibrium (OOE). Modelling of the recovery phase using our k1 value, indicates that OOE conditions will normally extend for at least 2 min following a step rise in pHi (at constant PCO2). If CA is inactive, this period can be as long as 5 min. During normal pHi regulation, the recovery rate during these periods cannot be used as a measure of sarcolemmal acid loading since it is a mixture of slow CO2-dependent buffering and transmembrane acid loading. The implication of this finding for quantification of pHi regulation during alkalosis is discussed. PMID:9575296

Pole Figure Explorer v. 1.8

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

Van Benthem, Mark H.

2016-05-04

This software is employed for 3D visualization of X-ray diffraction (XRD) data with functionality for slicing, reorienting, isolating and plotting of 2D color contour maps and 3D renderings of large datasets. The program makes use of the multidimensionality of textured XRD data where diffracted intensity is not constant over a given set of angular positions (as dictated by the three defined dimensional angles of phi, chi, and two-theta). Datasets are rendered in 3D with intensity as a scaler which is represented as a rainbow color scale. A GUI interface and scrolling tools along with interactive function via the mouse allowmore » for fast manipulation of these large datasets so as to perform detailed analysis of diffraction results with full dimensionality of the diffraction space.« less

System size and energy dependence of jet-induced hadron pair correlation shapes in Cu+Cu and Au+Au collisions at square root sNN=200 and 62.4 GeV.

PubMed

Adare, A; Adler, S S; Afanasiev, S; Aidala, C; Ajitanand, N N; Akiba, Y; Al-Bataineh, H; Alexander, J; Al-Jamel, A; Aoki, K; Aphecetche, L; Armendariz, R; Aronson, S H; Asai, J; Atomssa, E T; Averbeck, R; Awes, T C; Azmoun, B; Babintsev, V; Baksay, G; Baksay, L; Baldisseri, A; Barish, K N; Barnes, P D; Bassalleck, B; Bathe, S; Batsouli, S; Baublis, V; Bauer, F; Bazilevsky, A; Belikov, S; Bennett, R; Berdnikov, Y; Bickley, A A; Bjorndal, M T; Boissevain, J G; Borel, H; Boyle, K; Brooks, M L; Brown, D S; Bruner, N; Bucher, D; Buesching, H; Bumazhnov, V; Bunce, G; Burward-Hoy, J M; Butsyk, S; Camard, X; Campbell, S; Chai, J-S; Chand, P; Chang, B S; Chang, W C; Charvet, J-L; Chernichenko, S; Chiba, J; Chi, C Y; Chiu, M; Choi, I J; Choudhury, R K; Chujo, T; Chung, P; Churyn, A; Cianciolo, V; Cleven, C R; Cobigo, Y; Cole, B A; Comets, M P; Constantin, P; Csanád, M; Csörgo, T; Cussonneau, J P; Dahms, T; Das, K; David, G; Deák, F; Deaton, M B; Dehmelt, K; Delagrange, H; Denisov, A; d'Enterria, D; Deshpande, A; Desmond, E J; Devismes, A; Dietzsch, O; Dion, A; Donadelli, M; Drachenberg, J L; Drapier, O; Drees, A; Dubey, A K; Durum, A; Dutta, D; Dzhordzhadze, V; Efremenko, Y V; Egdemir, J; Ellinghaus, F; Emam, W S; Enokizono, A; En'yo, H; Espagnon, B; Esumi, S; Eyser, K O; Fields, D E; Finck, C; Finger, M; Finger, M; Fleuret, F; Fokin, S L; Forestier, B; Fox, B D; Fraenkel, Z; Frantz, J E; Franz, A; Frawley, A D; Fujiwara, K; Fukao, Y; Fung, S-Y; Fusayasu, T; Gadrat, S; Garishvili, I; Gastineau, F; Germain, M; Glenn, A; Gong, H; Gonin, M; Gosset, J; Goto, Y; Granier de Cassagnac, R; Grau, N; Greene, S V; Grosse Perdekamp, M; Gunji, T; Gustafsson, H-A; Hachiya, T; Hadj Henni, A; Haegemann, C; Haggerty, J S; Hagiwara, M N; Hamagaki, H; Han, R; Hansen, A G; Harada, H; Hartouni, E P; Haruna, K; Harvey, M; Haslum, E; Hasuko, K; Hayano, R; Heffner, M; Hemmick, T K; Hester, T; Heuser, J M; He, X; Hidas, P; Hiejima, H; Hill, J C; Hobbs, R; Hohlmann, M; Holmes, M; Holzmann, W; Homma, K; Hong, B; Hoover, A; Horaguchi, T; Hornback, D; Hur, M G; Ichihara, T; Ikonnikov, V V; Imai, K; Inaba, M; Inoue, Y; Inuzuka, M; Isenhower, D; Isenhower, L; Ishihara, M; Isobe, T; Issah, M; Isupov, A; Jacak, B V; Jia, J; Jin, J; Jinnouchi, O; Johnson, B M; Johnson, S C; Joo, K S; Jouan, D; Kajihara, F; Kametani, S; Kamihara, N; Kamin, J; Kaneta, M; Kang, J H; Kanou, H; Katou, K; Kawabata, T; Kawagishi, T; Kawall, D; Kazantsev, A V; Kelly, S; Khachaturov, B; Khanzadeev, A; Kikuchi, J; Kim, D H; Kim, D J; Kim, E; Kim, G-B; Kim, H J; Kim, Y-S; Kinney, E; Kiss, A; Kistenev, E; Kiyomichi, A; Klay, J; Klein-Boesing, C; Kobayashi, H; Kochenda, L; Kochetkov, V; Kohara, R; Komkov, B; Konno, M; Kotchetkov, D; Kozlov, A; Král, A; Kravitz, A; Kroon, P J; Kubart, J; Kuberg, C H; Kunde, G J; Kurihara, N; Kurita, K; Kweon, M J; Kwon, Y; Kyle, G S; Lacey, R; Lai, Y-S; Lajoie, J G; Lebedev, A; Le Bornec, Y; Leckey, S; Lee, D M; Lee, M K; Lee, T; Leitch, M J; Leite, M A L; Lenzi, B; Lim, H; Liska, T; Litvinenko, A; Liu, M X; Li, X; Li, X H; Love, B; Lynch, D; Maguire, C F; Makdisi, Y I; Malakhov, A; Malik, M D; Manko, V I; Mao, Y; Martinez, G; Masek, L; Masui, H; Matathias, F; Matsumoto, T; McCain, M C; McCumber, M; McGaughey, P L; Miake, Y; Mikes, P; Miki, K; Miller, T E; Milov, A; Mioduszewski, S; Mishra, G C; Mishra, M; Mitchell, J T; Mitrovski, M; Mohanty, A K; Morreale, A; Morrison, D P; Moss, J M; Moukhanova, T V; Mukhopadhyay, D; Muniruzzaman, M; Murata, J; Nagamiya, S; Nagata, Y; Nagle, J L; Naglis, M; Nakagawa, I; Nakamiya, Y; Nakamura, T; Nakano, K; Newby, J; Nguyen, M; Norman, B E; Nyanin, A S; Nystrand, J; O'Brien, E; Oda, S X; Ogilvie, C A; Ohnishi, H; Ojha, I D; Okada, H; Okada, K; Oka, M; Omiwade, O O; Oskarsson, A; Otterlund, I; Ouchida, M; Oyama, K; Ozawa, K; Pak, R; Pal, D; Palounek, A P T; Pantuev, V; Papavassiliou, V; Park, J; Park, W J; Pate, S F; Pei, H; Penev, V; Peng, J-C; Pereira, H; Peresedov, V; Peressounko, D Yu; Pierson, A; Pinkenburg, C; Pisani, R P; Purschke, M L; Purwar, A K; Qualls, J M; Qu, H; Rak, J; Rakotozafindrabe, A; Ravinovich, I; Read, K F; Rembeczki, S; Reuter, M; Reygers, K; Riabov, V; Riabov, Y; Roche, G; Romana, A; Rosati, M; Rosendahl, S S E; Rosnet, P; Rukoyatkin, P; Rykov, V L; Ryu, S S; Sahlmueller, B; Saito, N; Sakaguchi, T; Sakai, S; Sakata, H; Samsonov, V; Sanfratello, L; Santo, R; Sato, H D; Sato, S; Sawada, S; Schutz, Y; Seele, J; Seidl, R; Semenov, V; Seto, R; Sharma, D; Shea, T K; Shein, I; Shevel, A; Shibata, T-A; Shigaki, K; Shimomura, M; Shohjoh, T; Shoji, K; Sickles, A; Silva, C L; Silvermyr, D; Silvestre, C; Sim, K S; Singh, C P; Singh, V; Skutnik, S; Slunecka, M; Smith, W C; Soldatov, A; Soltz, R A; Sondheim, W E; Sorensen, S P; Sourikova, I V; Staley, F; Stankus, P W; Stenlund, E; Stepanov, M; Ster, A; Stoll, S P; Sugitate, T; Suire, C; Sullivan, J P; Sziklai, J; Tabaru, T; Takagi, S; Takagui, E M; Taketani, A; Tanaka, K H; Tanaka, Y; Tanida, K; Tannenbaum, M J; Taranenko, A; Tarján, P; Thomas, T L; Togawa, M; Toia, A; Tojo, J; Tomásek, L; Torii, H; Towell, R S; Tram, V-N; Tserruya, I; Tsuchimoto, Y; Tuli, S K; Tydesjö, H; Tyurin, N; Uam, T J; Vale, C; Valle, H; vanHecke, H W; Velkovska, J; Velkovsky, M; Vertesi, R; Veszprémi, V; Vinogradov, A A; Virius, M; Volkov, M A; Vrba, V; Vznuzdaev, E; Wagner, M; Walker, D; Wang, X R; Watanabe, Y; Wessels, J; White, S N; Willis, N; Winter, D; Wohn, F K; Woody, C L; Wysocki, M; Xie, W; Yamaguchi, Y L; Yanovich, A; Yasin, Z; Ying, J; Yokkaichi, S; Young, G R; Younus, I; Yushmanov, I E; Zajc, W A; Zaudtke, O; Zhang, C; Zhou, S; Zimányi, J; Zolin, L; Zong, X

2007-06-08

We present azimuthal angle correlations of intermediate transverse momentum (1-4 GeV/c) hadrons from dijets in Cu+Cu and Au+Au collisions at square root sNN=62.4 and 200 GeV. The away-side dijet induced azimuthal correlation is broadened, non-Gaussian, and peaked away from Delta phi=pi in central and semicentral collisions in all the systems. The broadening and peak location are found to depend upon the number of participants in the collision, but not on the collision energy or beam nuclei. These results are consistent with sound or shock wave models, but pose challenges to Cherenkov gluon radiation models.

Environmental Acoustic Considerations for Passive Detection of Maritime Targets by Hydrophones in a Deep Ocean Trench

DTIC Science & Technology

2010-06-01

Science and Technology. Available: http://cmst.curtin.edu.au/local/docs/ products / actup_v2_2l_installation_user_guide.pdf (accessed 2 June 2010...noisecurve112(:,6)); %% Intergrating Noise Level Trench A n2=0; Itot=0; phi_t=atan(D1/L1); m=1; while (phi(m,1)>phi_t) m=m+1; end

The Pemberton Happiness Index: Validation of the Universal Portuguese version in a large Brazilian sample.

PubMed

Paiva, Bianca Sakamoto Ribeiro; de Camargos, Mayara Goulart; Demarzo, Marcelo Marcos Piva; Hervás, Gonzalo; Vázquez, Carmelo; Paiva, Carlos Eduardo

2016-09-01

The Pemberton Happiness Index (PHI) is a recently developed integrative measure of well-being that includes components of hedonic, eudaimonic, social, and experienced well-being. The PHI has been validated in several languages, but not in Portuguese. Our aim was to cross-culturally adapt the Universal Portuguese version of the PHI and to assess its psychometric properties in a sample of the Brazilian population using online surveys.An expert committee evaluated 2 versions of the PHI previously translated into Portuguese by the original authors using a standardized form for assessment of semantic/idiomatic, cultural, and conceptual equivalence. A pretesting was conducted employing cognitive debriefing methods. In sequence, the expert committee evaluated all the documents and reached a final Universal Portuguese PHI version. For the evaluation of the psychometric properties, the data were collected using online surveys in a cross-sectional study. The study population included healthcare professionals and users of the social network site Facebook from several Brazilian geographic areas. In addition to the PHI, participants completed the Satisfaction with Life Scale (SWLS), Diener and Emmons' Positive and Negative Experience Scale (PNES), Psychological Well-being Scale (PWS), and the Subjective Happiness Scale (SHS). Internal consistency, convergent validity, known-group validity, and test-retest reliability were evaluated. Satisfaction with the previous day was correlated with the 10 items assessing experienced well-being using the Cramer V test. Additionally, a cut-off value of PHI to identify a "happy individual" was defined using receiver-operating characteristic (ROC) curve methodology.Data from 1035 Brazilian participants were analyzed (health professionals = 180; Facebook users = 855). Regarding reliability results, the internal consistency (Cronbach alpha = 0.890 and 0.914) and test-retest (intraclass correlation coefficient = 0.814) were both considered adequate. Most of the validity hypotheses formulated a priori (convergent and know-group) was further confirmed. The cut-off value of higher than 7 in remembered PHI was identified (AUC = 0.780, sensitivity = 69.2%, specificity = 78.2%) as the best one to identify a happy individual.We concluded that the Universal Portuguese version of the PHI is valid and reliable for use in the Brazilian population using online surveys.

Mucosal safety of PHI-443 and stampidine as a combination microbicide to prevent genital transmission of HIV-1.

PubMed

D'Cruz, Osmond J; Uckun, Fatih M

2007-10-01

To investigate the in vitro and in vivo mucosal safety of a nonnucleoside reverse transcriptase (RT) inhibitor (PHI-443) and a nucleoside analogue RT inhibitor (stampidine)-based anti-HIV microbicide either alone or in combination. In vitro and in vivo studies using three-dimensional vaginal epithelia integrating Langerhans cells and 16 New Zealand White rabbits, respectively. Research laboratory. Rabbits in groups of four were exposed intravaginally to a gel with and without 1% PHI-443, 1% stampidine, or 1% PHI-443 plus 1% stampidine for 14 days. Cytokine/chemokine release by three-dimensional co-cultures in the presence and absence of PHI-443 or stampidine. Histologic scoring of vaginal tissue for mucosal toxicity at 24 hours after dosing. Simultaneous evaluation of levels of 10 cytokines (granulocyte-macrophage colony-stimulating factor, interleukin-1 alpha, interleukin-13, macrophage inflammatory protein-1 beta, granulocyte colony-stimulating factor, interleukin-18, tumor necrosis factor-alpha, interleukin-6, interleukin-1 beta, and interferon-gamma) and 6 chemokines (epithelial neutrophil-activating peptide-78, interleukin-8, monocyte/macrophage chemoattractant protein-1, macrophage inflammatory protein-3 alpha, interferon-inducible protein-10, and regulated upon activation of normal T-cell expressed and secreted) in culture media by a multiplexed chemiluminescence-based immunoassay. In the rabbit model, repeated intravaginal administration of PHI-443 plus stampidine via a gel formulation at concentrations nearly 2,000 and 10,000 times higher than their respective in vitro anti-HIV IC(50) values did not result in vaginal irritation. The levels of proinflammatory cytokines/chemokines secreted by multilayered human genital epithelia integrating Langerhans cells were unaffected by prolonged exposure to PHI-443 or stampidine. The combination of PHI-443 and stampidine was noncytotoxic to vaginal epithelial cells, nonirritating to vaginal mucosa, and did not induce the secretion of proinflammatory cytokines and chemokines by co-cultures of human genital epithelia and Langerhans cells. These attributes are particularly useful for the clinical development of PHI-443 and stampidine as a combination microbicide and as a prophylactic anti-HIV agent to curb genital transmission of HIV-1 by semen.

List-mode PET image reconstruction for motion correction using the Intel XEON PHI co-processor

NASA Astrophysics Data System (ADS)

Ryder, W. J.; Angelis, G. I.; Bashar, R.; Gillam, J. E.; Fulton, R.; Meikle, S.

2014-03-01

List-mode image reconstruction with motion correction is computationally expensive, as it requires projection of hundreds of millions of rays through a 3D array. To decrease reconstruction time it is possible to use symmetric multiprocessing computers or graphics processing units. The former can have high financial costs, while the latter can require refactoring of algorithms. The Xeon Phi is a new co-processor card with a Many Integrated Core architecture that can run 4 multiple-instruction, multiple data threads per core with each thread having a 512-bit single instruction, multiple data vector register. Thus, it is possible to run in the region of 220 threads simultaneously. The aim of this study was to investigate whether the Xeon Phi co-processor card is a viable alternative to an x86 Linux server for accelerating List-mode PET image reconstruction for motion correction. An existing list-mode image reconstruction algorithm with motion correction was ported to run on the Xeon Phi coprocessor with the multi-threading implemented using pthreads. There were no differences between images reconstructed using the Phi co-processor card and images reconstructed using the same algorithm run on a Linux server. However, it was found that the reconstruction runtimes were 3 times greater for the Phi than the server. A new version of the image reconstruction algorithm was developed in C++ using OpenMP for mutli-threading and the Phi runtimes decreased to 1.67 times that of the host Linux server. Data transfer from the host to co-processor card was found to be a rate-limiting step; this needs to be carefully considered in order to maximize runtime speeds. When considering the purchase price of a Linux workstation with Xeon Phi co-processor card and top of the range Linux server, the former is a cost-effective computation resource for list-mode image reconstruction. A multi-Phi workstation could be a viable alternative to cluster computers at a lower cost for medical imaging applications.

The Pemberton Happiness Index

PubMed Central

Paiva, Bianca Sakamoto Ribeiro; de Camargos, Mayara Goulart; Demarzo, Marcelo Marcos Piva; Hervás, Gonzalo; Vázquez, Carmelo; Paiva, Carlos Eduardo

2016-01-01

Abstract The Pemberton Happiness Index (PHI) is a recently developed integrative measure of well-being that includes components of hedonic, eudaimonic, social, and experienced well-being. The PHI has been validated in several languages, but not in Portuguese. Our aim was to cross-culturally adapt the Universal Portuguese version of the PHI and to assess its psychometric properties in a sample of the Brazilian population using online surveys. An expert committee evaluated 2 versions of the PHI previously translated into Portuguese by the original authors using a standardized form for assessment of semantic/idiomatic, cultural, and conceptual equivalence. A pretesting was conducted employing cognitive debriefing methods. In sequence, the expert committee evaluated all the documents and reached a final Universal Portuguese PHI version. For the evaluation of the psychometric properties, the data were collected using online surveys in a cross-sectional study. The study population included healthcare professionals and users of the social network site Facebook from several Brazilian geographic areas. In addition to the PHI, participants completed the Satisfaction with Life Scale (SWLS), Diener and Emmons’ Positive and Negative Experience Scale (PNES), Psychological Well-being Scale (PWS), and the Subjective Happiness Scale (SHS). Internal consistency, convergent validity, known-group validity, and test–retest reliability were evaluated. Satisfaction with the previous day was correlated with the 10 items assessing experienced well-being using the Cramer V test. Additionally, a cut-off value of PHI to identify a “happy individual” was defined using receiver-operating characteristic (ROC) curve methodology. Data from 1035 Brazilian participants were analyzed (health professionals = 180; Facebook users = 855). Regarding reliability results, the internal consistency (Cronbach alpha = 0.890 and 0.914) and test–retest (intraclass correlation coefficient = 0.814) were both considered adequate. Most of the validity hypotheses formulated a priori (convergent and know-group) was further confirmed. The cut-off value of higher than 7 in remembered PHI was identified (AUC = 0.780, sensitivity = 69.2%, specificity = 78.2%) as the best one to identify a happy individual. We concluded that the Universal Portuguese version of the PHI is valid and reliable for use in the Brazilian population using online surveys. PMID:27661039

The Three-dimensional Structure of the Small Magellanic Cloud

NASA Astrophysics Data System (ADS)

Subramanian, Smitha; Subramaniam, Annapurni

2012-01-01

The three-dimensional structure of the inner Small Magellanic Cloud (SMC) is investigated using the red clump (RC) stars and the RR Lyrae stars (RRLS), which represent the intermediate-age and the old stellar populations of a galaxy. The V- and I-band photometric data from the OGLE III catalog are used for our study. The mean dereddened I 0 magnitude of the RC stars and the RRLS are used to study the relative positions of the different regions in the SMC with respect to the mean SMC distance. This shows that the northeastern part of the SMC is closer to us. The line-of-sight depth (front to back distance) across the SMC is estimated using the dispersion in the I 0 magnitudes of both the RC stars and the RRLS and found to be large (~14 kpc) for both populations. The similarity in their depth distribution suggests that both of these populations occupy a similar volume of the SMC. The surface density distribution and the radial density profile of the RC stars suggest that they are more likely to be distributed in a nearly spheroidal system. The tidal radius estimated for the SMC system is ~7-12 kpc. An elongation along the NE-SW direction is seen in the surface density map of the RC stars. The surface density distribution of the RRLS in the SMC is nearly circular. Based on all of the above results the observed structure of the SMC, in which both the RC stars and RRLS are distributed, is approximated as a triaxial ellipsoid. The parameters of the ellipsoid are obtained using the inertia tensor analysis. We estimated the axes ratio, inclination of the longest axis with the line of sight (i), and the position angle (phi) of the longest axis of the ellipsoid on the sky from the analysis of the RRLS. The analysis of the RC stars with the assumption that they are extended up to a depth of 3.5 times the sigma (width of dereddened I 0 magnitude distribution, corrected for intrinsic spread and observational errors) was also found to give similar axes ratio and orientation angles. The above estimated parameters depend on the data coverage of the SMC. Using the RRLS with equal coverage in all three axes (data within 3° in X-, Y-, and Z-axes), we estimated an axes ratio of 1:1.33:1.61 with i = 2fdg6 and phi = 70fdg2. Our tidal radius estimates and the recent observational studies suggest that the full extent of the SMC in the XY plane is of the order of the front to back distance estimated along the line of sight. These results suggest that the structure of the SMC is spheroidal or slightly ellipsoidal. We propose that the SMC experienced a merger with another dwarf galaxy at ~4-5 Gyr ago, and the merger process was completed in another 2-3 Gyr. This resulted in a spheroidal distribution comprising stars older than 2 Gyr.

Variational principle for the Navier-Stokes equations.

PubMed

Kerswell, R R

1999-05-01

A variational principle is presented for the Navier-Stokes equations in the case of a contained boundary-driven, homogeneous, incompressible, viscous fluid. Based upon making the fluid's total viscous dissipation over a given time interval stationary subject to the constraint of the Navier-Stokes equations, the variational problem looks overconstrained and intractable. However, introducing a nonunique velocity decomposition, u(x,t)=phi(x,t) + nu(x,t), "opens up" the variational problem so that what is presumed a single allowable point over the velocity domain u corresponding to the unique solution of the Navier-Stokes equations becomes a surface with a saddle point over the extended domain (phi,nu). Complementary or dual variational problems can then be constructed to estimate this saddle point value strictly from above as part of a minimization process or below via a maximization procedure. One of these reduced variational principles is the natural and ultimate generalization of the upper bounding problem developed by Doering and Constantin. The other corresponds to the ultimate Busse problem which now acts to lower bound the true dissipation. Crucially, these reduced variational problems require only the solution of a series of linear problems to produce bounds even though their unique intersection is conjectured to correspond to a solution of the nonlinear Navier-Stokes equations.

Self-consistent Simulation of Microparticle and Ion Wakefield Configuration

NASA Astrophysics Data System (ADS)

Sanford, Dustin; Brooks, Beau; Ellis, Naoki; Matthews, Lorin; Hyde, Truell

2017-10-01

In a complex plasma, positively charged ions often have a directed flow with respect to the negatively charged dust grains. The resulting interaction between the dust and the flowing plasma creates an ion wakefield downstream from the dust particles, with the resulting positive space region modifying the interaction between the grains and contributing to the observed dynamics and equilibrium structure of the system. Here we present a proof of concept method that uses a molecular dynamics simulation to model the ion wakefield allowing the dynamics of the dust particles to be determined self-consistently. The trajectory of each ion is calculated including the forces from all other ions, which are treated as ``Yukawa particles'' and shielded from thermal electrons and the forces of the charged dust particles. Both the dust grain charge and the wakefield structure are also self-consistently determined for various particle configurations. The resultant wakefield potentials are then used to provide dynamic simulations of dust particle pairs. These results will be employed to analyze the formation and dynamics of field-aligned chains in CASPER's PK4 experiment onboard the International Space Station, allowing examination of extended dust chains without the masking force of gravity. This work was supported by the National Science Foundation under Grants PHY-1414523 and PHY-1740203.

Berry phase and entanglement of three qubits in a new Yang-Baxter system

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

Hu Taotao; Xue Kang; Wu Chunfeng

2009-08-15

In this paper we construct a new 8x8M matrix from the 4x4M matrix, where M/M is the image of the braid group representation. The 8x8M matrix and the 4x4M matrix both satisfy extraspecial 2-group algebra relations. By Yang-Baxteration approach, we derive a unitary R({theta},{phi}) matrix from the M matrix with parameters {phi} and {theta}. Three-qubit entangled states can be generated by using the R({theta},{phi}) matrix. A Hamiltonian for three qubits is constructed from the unitary R({theta},{phi}) matrix. We then study the entanglement and Berry phase of the Yang-Baxter system.

Vectorization for Molecular Dynamics on Intel Xeon Phi Corpocessors

NASA Astrophysics Data System (ADS)

Yi, Hongsuk

2014-03-01

Many modern processors are capable of exploiting data-level parallelism through the use of single instruction multiple data (SIMD) execution. The new Intel Xeon Phi coprocessor supports 512 bit vector registers for the high performance computing. In this paper, we have developed a hierarchical parallelization scheme for accelerated molecular dynamics simulations with the Terfoff potentials for covalent bond solid crystals on Intel Xeon Phi coprocessor systems. The scheme exploits multi-level parallelism computing. We combine thread-level parallelism using a tightly coupled thread-level and task-level parallelism with 512-bit vector register. The simulation results show that the parallel performance of SIMD implementations on Xeon Phi is apparently superior to their x86 CPU architecture.

GST ( phi) gene from Macrophyte Lemna minor is involved in cadmium exposure responses

NASA Astrophysics Data System (ADS)

Chen, Shihua; Chen, Xin; Dou, Weihong; Wang, Liang; Yin, Haibo; Guo, Shanli

2016-03-01

Reactive oxygen species (ROS) scavengers, including ascorbate peroxidase, superoxide dismutase, catalase and peroxidase, are the most commonly used biomarkers in assessing an organisms' response to many biotic and abiotic stresses. In this study, we cloned an 866 bp GST ( phi) gene in Lemna minor and investigated its characteristics, expression and enzymatic activities under 75 μmol/L cadmium concentrations in comparison with other ROS scavengers. GST ( phi) gene expression patterns were similar to those of other scavengers of ROS. This suggests that GST ( phi) might be involved in responding to heavy metal (cadmium) stress and that its expression level could be used as a bio-indicator in monitoring cadmium pollution.

Ultra low thermal expansion, highly thermal shock resistant ceramic

DOEpatents

Limaye, Santosh Y.

1996-01-01

Three families of ceramic compositions having the given formula: .phi..sub.1+X Zr.sub.4 P.sub.6-2X Si.sub.2X O.sub.24, .phi..sub.1+X Zr.sub.4-2X Y.sub.2X P.sub.6 O.sub.24 and .phi..sub.1+X Zr.sub.4-X Y.sub.X P.sub.6-2X Si.sub.X O.sub.24 wherein .phi. is either Strontium or Barium and X has a value from about 0.2 to about 0.8 have been disclosed. Ceramics formed from these compositions exhibit very low, generally near neutral, thermal expansion over a wide range of elevated temperatures.

Clinical performance of serum prostate-specific antigen isoform [-2]proPSA (p2PSA) and its derivatives, %p2PSA and the prostate health index (PHI), in men with a family history of prostate cancer: results from a multicentre European study, the PROMEtheuS project.

PubMed

Lazzeri, Massimo; Haese, Alexander; Abrate, Alberto; de la Taille, Alexandre; Redorta, Joan Palou; McNicholas, Thomas; Lughezzani, Giovanni; Lista, Giuliana; Larcher, Alessandro; Bini, Vittorio; Cestari, Andrea; Buffi, Nicolòmaria; Graefen, Markus; Bosset, Olivier; Le Corvoisier, Philippe; Breda, Alberto; de la Torre, Pablo; Fowler, Linda; Roux, Jacques; Guazzoni, Giorgio

2013-08-01

To test the sensitivity, specificity and accuracy of serum prostate-specific antigen isoform [-2]proPSA (p2PSA), %p2PSA and the prostate health index (PHI), in men with a family history of prostate cancer (PCa) undergoing prostate biopsy for suspected PCa. To evaluate the potential reduction in unnecessary biopsies and the characteristics of potentially missed cases of PCa that would result from using serum p2PSA, %p2PSA and PHI. The analysis consisted of a nested case-control study from the PRO-PSA Multicentric European Study, the PROMEtheuS project. All patients had a first-degree relative (father, brother, son) with PCa. Multivariable logistic regression models were complemented by predictive accuracy analysis and decision-curve analysis. Of the 1026 patients included in the PROMEtheuS cohort, 158 (15.4%) had a first-degree relative with PCa. p2PSA, %p2PSA and PHI values were significantly higher (P < 0.001), and free/total PSA (%fPSA) values significantly lower (P < 0.001) in the 71 patients with PCa (44.9%) than in patients without PCa. Univariable accuracy analysis showed %p2PSA (area under the receiver-operating characteristic curve [AUC]: 0.733) and PHI (AUC: 0.733) to be the most accurate predictors of PCa at biopsy, significantly outperforming total PSA ([tPSA] AUC: 0.549), free PSA ([fPSA] AUC: 0.489) and %fPSA (AUC: 0.600) (P ≤ 0.001). For %p2PSA a threshold of 1.66 was found to have the best balance between sensitivity and specificity (70.4 and 70.1%; 95% confidence interval [CI]: 58.4-80.7 and 59.4-79.5 respectively). A PHI threshold of 40 was found to have the best balance between sensitivity and specificity (64.8 and 71.3%, respectively; 95% CI 52.5-75.8 and 60.6-80.5). At 90% sensitivity, the thresholds for %p2PSA and PHI were 1.20 and 25.5, with a specificity of 37.9 and 25.5%, respectively. At a %p2PSA threshold of 1.20, a total of 39 (24.8%) biopsies could have been avoided, but two cancers with a Gleason score (GS) of 7 would have been missed. At a PHI threshold of 25.5 a total of 27 (17.2%) biopsies could have been avoided and two (3.8%) cancers with a GS of 7 would have been missed. In multivariable logistic regression models, %p2PSA and PHI achieved independent predictor status and significantly increased the accuracy of multivariable models including PSA and prostate volume by 8.7 and 10%, respectively (P ≤ 0.001). p2PSA, %p2PSA and PHI were directly correlated with Gleason score (ρ: 0.247, P = 0.038; ρ: 0.366, P = 0.002; ρ: 0.464, P < 0.001, respectively). %p2PSA and PHI are more accurate than tPSA, fPSA and %fPSA in predicting PCa in men with a family history of PCa. Consideration of %p2PSA and PHI results in the avoidance of several unnecessary biopsies. p2PSA, %p2PSA and PHI correlate with cancer aggressiveness. © 2013 BJU International.

Algorithm for Wavefront Sensing Using an Extended Scene

NASA Technical Reports Server (NTRS)

Sidick, Erkin; Green, Joseph; Ohara, Catherine

2008-01-01

A recently conceived algorithm for processing image data acquired by a Shack-Hartmann (SH) wavefront sensor is not subject to the restriction, previously applicable in SH wavefront sensing, that the image be formed from a distant star or other equivalent of a point light source. That is to say, the image could be of an extended scene. (One still has the option of using a point source.) The algorithm can be implemented in commercially available software on ordinary computers. The steps of the algorithm are the following: 1. Suppose that the image comprises M sub-images. Determine the x,y Cartesian coordinates of the centers of these sub-images and store them in a 2xM matrix. 2. Within each sub-image, choose an NxN-pixel cell centered at the coordinates determined in step 1. For the ith sub-image, let this cell be denoted as si(x,y). Let the cell of another subimage (preferably near the center of the whole extended-scene image) be designated a reference cell, denoted r(x,y). 3. Calculate the fast Fourier transforms of the sub-sub-images in the central NxN portions (where N < N and both are preferably powers of 2) of r(x,y) and si(x,y). 4. Multiply the two transforms to obtain a cross-correlation function Ci(u,v), in the Fourier domain. Then let the phase of Ci(u, v) constitute a phase function, phi(u,v). 5. Fit u and v slopes to phi (u,v) over a small u,v subdomain. 6. Compute the fast Fourier transform, Si(u,v) of the full NxN cell si(x,y). Multiply this transform by the u and phase slopes obtained in step 4. Then compute the inverse fast Fourier transform of the product. 7. Repeat steps 4 through 6 in an iteration loop, cumulating the u and slopes, until a maximum iteration number is reached or the change in image shift becomes smaller than a predetermined tolerance. 8. Repeat steps 4 through 7 for the cells of all other sub-images.

Three dimensional microelectrode system for dielectrophoresis

DOEpatents

Dehlinger, Dietrich A.; Rose, Klint A.; Shusteff, Maxim; Bailey, Christopher G.; Mariella, Jr., Raymond P.

2013-09-03

A dielectrophoresis apparatus for separating particles from a sample, including an apparatus body; a dielectrophoresis channel in the apparatus body, the dielectrophoresis channel having a central axis, a bottom, a top, a first side, and a second side; a first mesa projecting into the dielectrophoresis channel from the bottom and extending from the first side across the dielectrophoresis channel to the second side, the first mesa extending at an angle to the central axis of the dielectrophoresis channel; a first electrode extending along the first mesa; a second mesa projecting into the dielectrophoresis channel from the bottom and extending from the first side across the dielectrophoresis channel to the second side, the second mesa extending at an angle to the central axis of the dielectrophoresis channel; a space between at least one of the first electrode and the second side or the second electrode and the second side; and a gap between the first electrode and the second electrode.

Temperate bacteriophage {phi}O18P from an Aeromonas media isolate: Characterization and complete genome sequence

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

Beilstein, Frauke; Dreiseikelmann, Brigitte

2008-03-30

A group of 74 Aeromonas isolates from surface water of three ponds in Bielefeld, Germany was screened for prophage induction after UV irradiation. The phage {phi}O18P was induced from the Aeromonas media isolate O18. {phi}O18P belongs to the Myoviridae phage family. The complete nucleotide sequence of the double stranded DNA genome of bacteriophage {phi}O18P consists of 33,985 bp. The genome has 5' protruding cohesive ends of 16 bases. On the {phi}O18P genome 46 open reading frames (orfs) were identified which are organized in the modules integration and regulation, replication, head, packaging, tail and lysis. Additionally the phage DNA includes amore » methylase gene. Comparison of the genome architecture with those of other bacteriophages revealed significant similarities to the P2 phage family and especially to the prophages of Aeromonas salmonicida and the Vibrio cholerae phage K139.« less

Intramolecular co-action of two independent photosensory modules in the fern phytochrome 3.

PubMed

Kanegae, Takeshi

2015-01-01

Fern phytochrome3/neochrome1 (phy3/neo1) is a chimeric photoreceptor composed of a phytochrome-chromophore binding domain and an almost full-length phototropin. phy3 thus contains two different light-sensing modules; a red/far-red light receptor phytochrome and a blue light receptor phototropin. phy3 induces both red light- and blue light-dependent phototropism in phototropin-deficient Arabidopsis thaliana (phot1 phot2) seedlings. The red-light response is dependent on the phytochrome module of phy3, and the blue-light response is dependent on the phototropin module. We recently showed that both the phototropin-sensing module and the phytochrome-sensing module mediate the blue light-dependent phototropic response. Particularly under low-light conditions, these two light-sensing modules cooperate to induce the blue light-dependent phototropic response. This intramolecular co-action of two independent light-sensing modules in phy3 enhances light sensitivity, and perhaps allowed ferns to adapt to the low-light canopy conditions present in angiosperm forests.

[Isolation, idetification and anti-HIV-1 integrase activity of culturable endophytic fungi from Tibetan medicinal plant Phlomis younghusbandii Mukerjee].

PubMed

Zhang, Da-Wei; Zhao, Ming-Ming; Chen, Juan; Li, Chao; Guo, Shun-Xing

2013-05-01

A total of 52 endophytic fungi were isolated from roots and stems of Tibetan medicinal plant Phlomis younghusbandii Mukerjee. These fungal isolates were molecularly identified based on ITS sequnces and 28S sequences distributed to 12 genera, including Phoma, Chaetosphaeronema, Fusarium and Leptosphaeria, etc. Among them, the dominant genus was Phoma. Extracts of all strains were evaluated for anti-HIV-1 integrase activity by using soluable integrase expressed in E. coli BL21 (DE3). The results showed that seven samples from five fungal endophytes PHY-24, PHY-38, PHY-40, PHY-51, PHY-53, which belonged to genus Chaetosphaeronema, inhibited strand transfer reaction catalyzed by HIV-1 integrase with IC50 values, of 6.60, 5.20, 2.86, 7.86, 4.47, 4.56 and 3.23 microg x mL(-1) respectively. In conclusion, the endophytic fungi of Phlomis younghusbandii Mukerjee are valuable for further screening anti-HIV-1 integrase agents.

Statistical reporting inconsistencies in experimental philosophy

PubMed Central

Colombo, Matteo; Duev, Georgi; Nuijten, Michèle B.; Sprenger, Jan

2018-01-01

Experimental philosophy (x-phi) is a young field of research in the intersection of philosophy and psychology. It aims to make progress on philosophical questions by using experimental methods traditionally associated with the psychological and behavioral sciences, such as null hypothesis significance testing (NHST). Motivated by recent discussions about a methodological crisis in the behavioral sciences, questions have been raised about the methodological standards of x-phi. Here, we focus on one aspect of this question, namely the rate of inconsistencies in statistical reporting. Previous research has examined the extent to which published articles in psychology and other behavioral sciences present statistical inconsistencies in reporting the results of NHST. In this study, we used the R package statcheck to detect statistical inconsistencies in x-phi, and compared rates of inconsistencies in psychology and philosophy. We found that rates of inconsistencies in x-phi are lower than in the psychological and behavioral sciences. From the point of view of statistical reporting consistency, x-phi seems to do no worse, and perhaps even better, than psychological science. PMID:29649220

DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes

PubMed Central

Sarkar, Subhra; Witham, Shawn; Zhang, Jie; Zhenirovskyy, Maxim; Rocchia, Walter; Alexov, Emil

2011-01-01

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver. PMID:24683424

Photoassociation dynamics driven by a modulated two-color laser field

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

Zhang Wei; Zhao Zeyu; Xie Ting

2011-11-15

Photoassociation (PA) dynamics of ultracold cesium atoms steered by a modulated two-color laser field E(t)=E{sub 0}f(t)cos((2{pi}/T{sub p})-{phi})cos({omega}{sub L}t) is investigated theoretically by numerically solving the time-dependent Schroedinger equation. The PA dynamics is sensitive to the phase of envelope (POE) {phi} and the period of the envelope T{sub p}, which indicates that it can be controlled by varying POE {phi} and period T{sub p}. Moreover, we introduce the time- and frequency-resolved spectrum to illustrate how the POE {phi} and the period T{sub p} influence the intensity distribution of the modulated laser pulse and hence change the time-dependent population distribution of photoassociatedmore » molecules. When the Gaussian envelope contains a few oscillations, the PA efficiency is also dependent on POE {phi}. The modulated two-color laser field is available in the current experiment based on laser mode-lock technology.« less

Isolation and characterization of a bacteriophage phiEap-2 infecting multidrug resistant Enterobacter aerogenes

PubMed Central

Li, Erna; Wei, Xiao; Ma, Yanyan; Yin, Zhe; Li, Huan; Lin, Weishi; Wang, Xuesong; Li, Chao; Shen, Zhiqiang; Zhao, Ruixiang; Yang, Huiying; Jiang, Aimin; Yang, Wenhui; Yuan, Jing; Zhao, Xiangna

2016-01-01

Enterobacter aerogenes (Enterobacteriaceae) is an important opportunistic pathogen that causes hospital-acquired pneumonia, bacteremia, and urinary tract infections. Recently, multidrug-resistant E. aerogenes have been a public health problem. To develop an effective antimicrobial agent, bacteriophage phiEap-2 was isolated from sewage and its genome was sequenced because of its ability to lyse the multidrug-resistant clinical E. aerogenes strain 3-SP. Morphological observations suggested that the phage belongs to the Siphoviridae family. Comparative genome analysis revealed that phage phiEap-2 is related to the Salmonella phage FSL SP-031 (KC139518). All of the structural gene products (except capsid protein) encoded by phiEap-2 had orthologous gene products in FSL SP-031 and Serratia phage Eta (KC460990). Here, we report the complete genome sequence of phiEap-2 and major findings from the genomic analysis. Knowledge of this phage might be helpful for developing therapeutic strategies against E. aerogenes. PMID:27320081

Isolation and characterization of a bacteriophage phiEap-2 infecting multidrug resistant Enterobacter aerogenes.

PubMed

Li, Erna; Wei, Xiao; Ma, Yanyan; Yin, Zhe; Li, Huan; Lin, Weishi; Wang, Xuesong; Li, Chao; Shen, Zhiqiang; Zhao, Ruixiang; Yang, Huiying; Jiang, Aimin; Yang, Wenhui; Yuan, Jing; Zhao, Xiangna

2016-06-20

Enterobacter aerogenes (Enterobacteriaceae) is an important opportunistic pathogen that causes hospital-acquired pneumonia, bacteremia, and urinary tract infections. Recently, multidrug-resistant E. aerogenes have been a public health problem. To develop an effective antimicrobial agent, bacteriophage phiEap-2 was isolated from sewage and its genome was sequenced because of its ability to lyse the multidrug-resistant clinical E. aerogenes strain 3-SP. Morphological observations suggested that the phage belongs to the Siphoviridae family. Comparative genome analysis revealed that phage phiEap-2 is related to the Salmonella phage FSL SP-031 (KC139518). All of the structural gene products (except capsid protein) encoded by phiEap-2 had orthologous gene products in FSL SP-031 and Serratia phage Eta (KC460990). Here, we report the complete genome sequence of phiEap-2 and major findings from the genomic analysis. Knowledge of this phage might be helpful for developing therapeutic strategies against E. aerogenes.

Impact of Assay conditions on activity estimate and kinetics comparison of Aspergillus niger PhyA and Escherichia coli AppA2 phytases

USDA-ARS?s Scientific Manuscript database

This study was to compare three phytase activity assays and kinetics of Aspergillus niger PhyA and Escherichia coli AppA2 phytases expressed in Pichia pastoris at the observed stomach pH of 3.5. In Experiment 1, equivalent phytase activities in the crude preparations of PhyA and AppA2 were tested ...

Root phototropism: how light and gravity interact in shaping plant form

NASA Technical Reports Server (NTRS)

Kiss, John Z.; Correll, Melanie J.; Mullen, Jack L.; Hangarter, Roger P.; Edelmann, Richard E.

2003-01-01

The interactions among tropisms can be critical in determining the final growth form of plants and plant organs. We have studied tropistic responses in roots as an example of these type of interactions. While gravitropism is the predominant tropistic response in roots, phototropism also plays a role in the oriented growth in this organ in flowering plants. In blue or white light, roots exhibit negative phototropism, but red light induces positive phototropism. In the flowering plant Arabidopsis, the photosensitive pigments phytochrome A (phyA) and phytochrome B (phyB) mediate this positive red-light-based photoresponse in roots since single mutants (and the double phyAB mutant) were severely impaired in this response. While blue-light-based negative phototropism is primarily mediated by the phototropin family of photoreceptors, the phyA and phyAB mutants (but not phyB) were inhibited in this response relative to the WT. The differences observed in phototropic responses were not due to growth limitations since the growth rates among all the mutants tested were not significantly different from that of the WT. Thus, our study shows that the blue-light and red-light systems interact in plants and that phytochrome plays a key role in integrating multiple environmental stimuli.

Role of phytochromes A and B in the regulation of cell death and acclimatory responses to UV stress in Arabidopsis thaliana

PubMed Central

Rusaczonek, Anna; Czarnocka, Weronika; Kacprzak, Sylwia; Witoń, Damian; Ślesak, Ireneusz; Szechyńska-Hebda, Magdalena; Gawroński, Piotr; Karpiński, Stanisław

2015-01-01

Plants coordinate their responses to various biotic and abiotic stresses in order to optimize their developmental and acclimatory programmes. The ultimate response to an excessive amount of stress is local induction of cell death mechanisms. The death of certain cells can help to maintain tissue homeostasis and enable nutrient remobilization, thus increasing the survival chances of the whole organism in unfavourable environmental conditions. UV radiation is one of the environmental factors that negatively affects the photosynthetic process and triggers cell death. The aim of this work was to evaluate a possible role of the red/far-red light photoreceptors phytochrome A (phyA) and phytochrome B (phyB) and their interrelations during acclimatory responses to UV stress. We showed that UV-C treatment caused a disturbance in photosystem II and a deregulation of photosynthetic pigment content and antioxidant enzymes activities, followed by increased cell mortality rate in phyB and phyAB null mutants. We also propose a regulatory role of phyA and phyB in CO2 assimilation, non-photochemical quenching, reactive oxygen species accumulation and salicylic acid content. Taken together, our results suggest a novel role of phytochromes as putative regulators of cell death and acclimatory responses to UV. PMID:26385378

Root phototropism: how light and gravity interact in shaping plant form.

PubMed

Kiss, John Z; Correll, Melanie J; Mullen, Jack L; Hangarter, Roger P; Edelmann, Richard E

2003-06-01

The interactions among tropisms can be critical in determining the final growth form of plants and plant organs. We have studied tropistic responses in roots as an example of these type of interactions. While gravitropism is the predominant tropistic response in roots, phototropism also plays a role in the oriented growth in this organ in flowering plants. In blue or white light, roots exhibit negative phototropism, but red light induces positive phototropism. In the flowering plant Arabidopsis, the photosensitive pigments phytochrome A (phyA) and phytochrome B (phyB) mediate this positive red-light-based photoresponse in roots since single mutants (and the double phyAB mutant) were severely impaired in this response. While blue-light-based negative phototropism is primarily mediated by the phototropin family of photoreceptors, the phyA and phyAB mutants (but not phyB) were inhibited in this response relative to the WT. The differences observed in phototropic responses were not due to growth limitations since the growth rates among all the mutants tested were not significantly different from that of the WT. Thus, our study shows that the blue-light and red-light systems interact in plants and that phytochrome plays a key role in integrating multiple environmental stimuli.

The response of growth and patulin production of postharvest pathogen Penicillium expansum to exogenous potassium phosphite treatment.

PubMed

Lai, Tongfei; Wang, Ying; Fan, Yaya; Zhou, Yingying; Bao, Ying; Zhou, Ting

2017-03-06

In this study, the effects of exogenous potassium phosphite (Phi) on growth and patulin production of postharvest pathogen Penicillium expansum were assessed. The results indicated that P. expansum under 5mmol/L Phi stress presented obvious development retardation, yield reduction of patulin and lower infectivity to apple fruit. Meanwhile, expression analysis of 15 genes related to patulin biosynthesis suggested that Phi mainly affected the early steps of patulin synthetic route at transcriptional level. Furthermore, a global view of proteome and transcriptome alteration of P. expansum spores during 6h of Phi stress was evaluated by iTRAQ (isobaric tags for relative and absolute quantitation) and RNA-seq (RNA sequencing) approaches. A total of 582 differentially expressed proteins (DEPs) and 177 differentially expressed genes (DEGs) were acquired, most of which participated in carbohydrate metabolism, amino acid metabolism, lipid metabolism, genetic information processing and biosynthesis of secondary metabolites. Finally, 39 overlapped candidates were screened out through correlational analysis between iTRAQ and RNA-seq datasets. These findings will afford more precise and directional clues to explore the inhibitory mechanism of Phi on growth and patulin biosynthesis of P. expansum, and be beneficial to develop effective controlling approaches based on Phi. Copyright © 2016 Elsevier B.V. All rights reserved.

The Pathogen-Host Interactions database (PHI-base): additions and future developments

PubMed Central

Urban, Martin; Pant, Rashmi; Raghunath, Arathi; Irvine, Alistair G.; Pedro, Helder; Hammond-Kosack, Kim E.

2015-01-01

Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and protist pathogens. Mutant phenotypes are associated with gene information. The included pathogens infect a wide range of hosts including humans, animals, plants, insects, fish and other fungi. The current version, PHI-base 3.6, available at http://www.phi-base.org, stores information on 2875 genes, 4102 interactions, 110 host species, 160 pathogenic species (103 plant, 3 fungal and 54 animal infecting species) and 181 diseases drawn from 1243 references. Phenotypic and gene function information has been obtained by manual curation of the peer-reviewed literature. A controlled vocabulary consisting of nine high-level phenotype terms permits comparisons and data analysis across the taxonomic space. PHI-base phenotypes were mapped via their associated gene information to reference genomes available in Ensembl Genomes. Virulence genes and hotspots can be visualized directly in genome browsers. Future plans for PHI-base include development of tools facilitating community-led curation and inclusion of the corresponding host target(s). PMID:25414340

Cosmic Ray Flux in the Presence of a Neutral Background

NASA Technical Reports Server (NTRS)

Wilson, Thomas L.; Lodhi, Arfin; Diaz, Abel

2007-01-01

The study of cosmic rays (CRs) is a very mature subject developed around the concept of radiative particle flux phi as a mono-variant function of energy E, that is phi = phi(E). This is based on the notion of the cosmos as being filled with cosmic radiation in the form of a collisionless exosphere of plasma. Neutrals, however, are likewise ubiquitous in space and planetary trapped-radiation belts. It will be shown that in the presence of a neutral background of density rho, flux phi is actually bivariant in energy E and rho, creating a surface phi(E,rho). This is an intrinsic property of charged-particle flux, that flux is not merely a function of E but is dependent upon density rho when a background of neutrals is present. The effect is produced by multiple scattering of charged particles off neutral and ionized atoms along with ionization loss where charged and neutral populations interact. For the harder portion of CR spectra, flux is mono-variant but at nonrelativistic energies (below approx, 350 MeV) it becomes sensitive to the presence of neutral backgrounds. The dependence of phi(E,rho) upon background neutrals is helpful in discussing the anomalous CR (ACR) flux made up of ionized components of the heliospheric neutral atmosphere.

Structural changes in the cytoplasmic pore of the Kir1.1 channel during pHi-gating probed by FRET.

PubMed

Lee, Jay-Ron; Shieh, Ru-Chi

2009-03-06

Kir1.1 channels are important in maintaining K+ homeostasis in the kidney. Intracellular acidification reversibly closes the Kir1.1 channel and thus decreases K+ secretion. In this study, we used Foster resonance energy transfer (FRET) to determine whether the conformation of the cytoplasmic pore changes in response to intracellular pH (pHi)-gating in Kir1.1 channels fused with enhanced cyan fluorescent protein (ECFP) and enhanced yellow fluorescent protein (EYFP) (ECFP-Kir1.1-EYFP). Because the fluorescence intensities of ECFP and EYFP were affected at pHi < 7.4 where pHi-gating occurs in the ECFP-Kir1.1-EYFP construct, we examined the FRET efficiencies of an ECFP-S219R-EYFP mutant, which is completed closed at pHi 7.4 and open at pHi 10.0. FRET efficiency was increased from 25% to 40% when the pHi was decreased from 10.0 to 7.4. These results suggest that the conformation of the cytoplasmic pore in the Kir1.1 channel changes in response to pHi gating such that the N- and C-termini move apart from each other at pHi 7.4, when the channel is open.

PHI in the Early Detection of Prostate Cancer.

PubMed

Fuchsova, Radka; Topolcan, Ondrej; Windrichova, Jindra; Hora, Milan; Dolejsova, Olga; Pecen, Ladislav; Kasik, Petr; Novak, Jaroslav; Casova, Miroslava; Smejkal, Jiri

2015-09-01

To evaluate changes in the serum levels of prostate specific antigen (PSA), %free PSA and -2proPSA biomarkers, and prostate health index (PHI) in the diagnostic algorithm of early prostate cancer. The Immunoanalytical Laboratory of the University Hospital in Pilsen examined sera from 263 patients being treated at the Hospital's Urology Department with suspected prostate cancer who had undergone biopsies and were divided into a benign and malignant group. The monitored biomarkers were measured using chemiluminescence. All statistical analyses were calculated using the SAS software. We found statistically significantly increased levels of -2proPSA, PHI and PSA and decreased levels of %freePSA in patients diagnosed with prostate cancer by prostate biopsy vs. patients with benign prostatic hypertrophy (median values: -2proPSA: 16 vs. 21 ng/l, PHI: 35 vs. 62, total PSA: 7.2 vs. 7.7 μg/l and %free PSA: 16.7 vs. 11.7%). Receiver operating characteristic curves showed the best performance for PHI compared to other markers. The assessment of -2proPSA and the calculation of PHI appear to be of great benefit for a more accurate differential diagnosis of benign hyperplasia and prostate cancer. Copyright© 2015 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Broad-spectrum inhibition of Phytophthora infestans by fungal endophytes

PubMed Central

von Dahlen, Janina K; Schnake, Anika; Ginschel, Sarah; Schulz, Barbara; Rose, Laura E

2018-01-01

ABSTRACT Phytophthora infestans is a devastating pathogen of tomato and potato. It readily overcomes resistance genes and applied agrochemicals and hence even today causes large yield losses. Fungal endophytes provide a largely unexplored avenue of control of Phy. infestans. Not only do endophytes produce a wide array of bioactive metabolites, they may also directly compete with and defeat pathogens in planta. Here, we tested 12 fungal endophytes isolated from different plant species in vitro for their production of metabolites with anti- Phytophthora activity. Four well-performing isolates were evaluated for their ability to suppress nine isolates of Phy. infestans on agar medium and in planta. Two endophytes reliably inhibited all Phy. infestans isolates on agar medium, of which Phoma eupatorii isolate 8082 was the most promising. It nearly abolished infection by Phy. infestans in planta. Our data indicate a role for the production of anti-Phytophthora compounds by the fungus and/or an enhanced plant defense response, as evident by an enhanced anthocyanin production. Here, we present a potential biocontrol agent, which can inhibit a broad-spectrum of Phy. infestans isolates. Such broadly acting inhibition is ideal, because it allows for effective control of genetically diverse isolates and may slow the adaptation of Phy. infestans. PMID:29528408

Regulation of intracellular pH in the rabbit cortical collecting tubule.

PubMed Central

Weiner, I D; Hamm, L L

1990-01-01

The cortical collecting tubule (CCT) is an important nephron segment for Na+, K+, water and acid-base transport. Differential loading characteristics of the pH sensitive dye 2',7'-bis-(2-carboxyethyl)-5(and-6)carboxyfluorescein (BCECF) and basolateral Cl- removal were used to identify and study intracellular pH (pHi) regulation in each of three cell types involved in this transport. Both principal cells and beta-intercalated cells were found to have a basolateral Na+/H+ exchanger based on the Na+ and amiloride sensitivity of pHi recovery from acid loads. Intercalated cells demonstrated abrupt pHi changes with basolateral Cl- removal. alpha-intercalated cells alkalinized; beta-intercalated cells acidified. In the beta-intercalated cells, luminal Cl- removal blocked changes in pHi in response to changes in luminal HCO3- or peritubular Cl-, providing direct evidence for a luminal Cl-/HCO3- exchanger. In principal cells, brief removal of either peritubular or luminal Cl- resulted in no change in pHi; however, return of peritubular Cl- after prolonged removal resulted in a rapid fall in pHi consistent with a basolateral Cl-/HCO3- exchanger, which may be relatively inactive under baseline conditions. Therefore, Cl-/HCO3- exchange is present in all three cell types but varies in location and activity. PMID:2153152

Attenuation of Phosphate Starvation Responses by Phosphite in Arabidopsis1

PubMed Central

Ticconi, Carla A.; Delatorre, Carla A.; Abel, Steffen

2001-01-01

When inorganic phosphate is limiting, Arabidopsis has the facultative ability to metabolize exogenous nucleic acid substrates, which we utilized previously to identify insensitive phosphate starvation response mutants in a conditional genetic screen. In this study, we examined the effect of the phosphate analog, phosphite (Phi), on molecular and morphological responses to phosphate starvation. Phi significantly inhibited plant growth on phosphate-sufficient (2 mm) and nucleic acid-containing (2 mm phosphorus) media at concentrations higher than 2.5 mm. However, with respect to suppressing typical responses to phosphate limitation, Phi effects were very similar to those of phosphate. Phosphate starvation responses, which we examined and found to be almost identically affected by both anions, included changes in: (a) the root-to-shoot ratio; (b) root hair formation; (c) anthocyanin accumulation; (d) the activities of phosphate starvation-inducible nucleolytic enzymes, including ribonuclease, phosphodiesterase, and acid phosphatase; and (e) steady-state mRNA levels of phosphate starvation-inducible genes. It is important that induction of primary auxin response genes by indole-3-acetic acid in the presence of growth-inhibitory Phi concentrations suggests that Phi selectively inhibits phosphate starvation responses. Thus, the use of Phi may allow further dissection of phosphate signaling by genetic selection for constitutive phosphate starvation response mutants on media containing organophosphates as the only source of phosphorus. PMID:11706178

The Arabidopsis SRR1 gene mediates phyB signaling and is required for normal circadian clock function

PubMed Central

Staiger, Dorothee; Allenbach, Laure; Salathia, Neeraj; Fiechter, Vincent; Davis, Seth J.; Millar, Andrew J.; Chory, Joanne; Fankhauser, Christian

2003-01-01

Plants possess several photoreceptors to sense the light environment. In Arabidopsis cryptochromes and phytochromes play roles in photomorphogenesis and in the light input pathways that synchronize the circadian clock with the external world. We have identified SRR1 (sensitivity to red light reduced), a gene that plays an important role in phytochrome B (phyB)-mediated light signaling. The recessive srr1 null allele and phyB mutants display a number of similar phenotypes indicating that SRR1 is required for normal phyB signaling. Genetic analysis suggests that SRR1 works both in the phyB pathway but also independently of phyB. srr1 mutants are affected in multiple outputs of the circadian clock in continuous light conditions, including leaf movement and expression of the clock components, CCA1 and TOC1. Clock-regulated gene expression is also impaired during day–night cycles and in constant darkness. The circadian phenotypes of srr1 mutants in all three conditions suggest that SRR1 activity is required for normal oscillator function. The SRR1 gene was identified and shown to code for a protein conserved in numerous eukaryotes including mammals and flies, implicating a conserved role for this protein in both the animal and plant kingdoms. PMID:12533513

Egg sialoglycans increase intracellular pH and potentiate the acrosome reaction of sea urchin sperm.

PubMed

Hirohashi, Noritaka; Vacquier, Victor D

2002-03-08

Sea urchin egg jelly (EJ) triggers sperm acrosome reaction (AR), an exocytotic event required for membrane fusion of the gametes. Purified fucose sulfate polymer (FSP) in EJ is one inducer of the AR. Binding of FSP to its receptor regulates opening of two distinct calcium channels and also elevates intracellular pH (pH(i)). EJ also contains sialic acid-rich glycans (sialoglycans (SG)) that were isolated by beta-elimination followed by DEAE chromatography. In the presence of limiting amounts of FSP, the SG fraction markedly potentiates the AR; however, by itself SG has no activity. The SG fraction increases the pH(i) of sperm without increasing intracellular Ca(2+). The SG-induced increase in pH(i) is not blocked by nifedipine or high K(+), whereas the FSP-induced pH(i) increase is sensitive to both these agents. Treatment of the SG fraction with neuraminidase or mild metaperiodate that specifically cleaves the glycerol side chain of sialic acid abolishes the AR potentiation and ability of SG to elevate pH(i). These data are the first to show that there are at least two pathways to induce sperm pH(i) increase and that egg surface sialic acid plays a role in triggering the sperm AR.

Prostate Health Index improves multivariable risk prediction of aggressive prostate cancer.

PubMed

Loeb, Stacy; Shin, Sanghyuk S; Broyles, Dennis L; Wei, John T; Sanda, Martin; Klee, George; Partin, Alan W; Sokoll, Lori; Chan, Daniel W; Bangma, Chris H; van Schaik, Ron H N; Slawin, Kevin M; Marks, Leonard S; Catalona, William J

2017-07-01

To examine the use of the Prostate Health Index (PHI) as a continuous variable in multivariable risk assessment for aggressive prostate cancer in a large multicentre US study. The study population included 728 men, with prostate-specific antigen (PSA) levels of 2-10 ng/mL and a negative digital rectal examination, enrolled in a prospective, multi-site early detection trial. The primary endpoint was aggressive prostate cancer, defined as biopsy Gleason score ≥7. First, we evaluated whether the addition of PHI improves the performance of currently available risk calculators (the Prostate Cancer Prevention Trial [PCPT] and European Randomised Study of Screening for Prostate Cancer [ERSPC] risk calculators). We also designed and internally validated a new PHI-based multivariable predictive model, and created a nomogram. Of 728 men undergoing biopsy, 118 (16.2%) had aggressive prostate cancer. The PHI predicted the risk of aggressive prostate cancer across the spectrum of values. Adding PHI significantly improved the predictive accuracy of the PCPT and ERSPC risk calculators for aggressive disease. A new model was created using age, previous biopsy, prostate volume, PSA and PHI, with an area under the curve of 0.746. The bootstrap-corrected model showed good calibration with observed risk for aggressive prostate cancer and had net benefit on decision-curve analysis. Using PHI as part of multivariable risk assessment leads to a significant improvement in the detection of aggressive prostate cancer, potentially reducing harms from unnecessary prostate biopsy and overdiagnosis. © 2016 The Authors BJU International © 2016 BJU International Published by John Wiley & Sons Ltd.

Functional characterization of transmembrane intracellular pH regulators and mechanism of alcohol-induced intracellular acidosis in human umbilical cord blood stem cell-like cells.

PubMed

Tsai, Yi-Ting; Liu, Jah-Yao; Lee, Chung-Yi; Tsai, Chien-Sung; Chen, Ming-Hurng; Ou, Chien-Chih; Chen, Wei-Hwa; Loh, Shih-Hurng

2011-12-01

Changing intracellular pH (pHi) exerts considerable influence on many cellular functions. Different pHi regulators, such as the Na-H exchanger (NHE), Na/(Equation is included in full-text article.)symporter, and Cl/OH exchanger (CHE), have been identified in mature mammalian cells. The aims of the present study were to investigate the physiological mechanisms of pHi recovery and to further explore the effects of alcohol on the pHi in human umbilical cord blood CD34 stem cell-like cells (HUCB-CD34STs). HUCB-CD34STs were loaded with the pH-sensitive dye, 2',7'-bis(2-carboxethyl)-5(6)-carboxyfluorescein, to examine pHi. In isolated HUCB-CD34STs, we found that (1) the resting pHi is 7.03 ± 0.02; (2) 2 Na-dependent acid extruders and a Cl-dependent acid loading carrier exist and are functional; (3) alcohol functions in a concentration-dependent manner to reduce pHi and increase NHE activity, but it does not affect CHE activity; and (4) fomepizole, a specific alcohol dehydrogenase inhibitor, does not change the intracellular acidosis and NHE activity-induced by alcohol, whereas 3-amino-1, 2,4-trizole, a specific catalase inhibitor, entirely abolishes these effects. In conclusion, we demonstrate that 2 acid extruders and 1 acid loader (most likely NHE, NBC, and CHE, respectively) functionally existed in HUCB-CD34STs. Additionally, the intracellular acidosis is mainly caused by catalase-mediated alcohol metabolites, which provoke the activity of NHE.

Light exaggerates apical hook curvature through phytochrome actions in tomato seedlings.

PubMed

Shichijo, Chizuko; Ohuchi, Hisako; Iwata, Naoko; Nagatoshi, Yukari; Takahashi, Miki; Nakatani, Eri; Inoue, Kentaroh; Tsurumi, Seiji; Tanaka, Osamu; Hashimoto, Tohru

2010-02-01

Contrary to the established notion that the apical hook of dark-grown dicotyledonous seedlings opens in response to light, we found in tomato (Solanum lycopersicum L.) that the apical hook curvature is exaggerated by light. Experiments with several tomato cultivars and phytochrome mutants, irradiated with red and far-red light either as a brief pulse (Rp, FRp) or continuously (Rc, FRc), revealed: the hook-exaggeration response is maximal at the emergence of the hypocotyl from the seed; the effect of Rp is FRp-reversible; fluence-response curves to a single Rp or FRp show an involvement of low and very low fluence responses (LFR, VLFR); the effect of Rc is fluence-rate dependent, but that of FRc is not; the phyA mutant (phyA hp-1) failed to respond to an Rp of less than 10(-2) micromol m(-2) and to an FRp of all fluences tested as well as to FRc, thus indicating that the hook-exaggeration response involves phyA-mediated VLFR. The Rp fluence-response curve with the same mutant also confirmed the presence of an LFR mediated by phytochrome(s) other than phyA, although the phyB1 mutant (phyB1 hp-1) still showed full response probably due to other redundant phytochrome species (e.g., phyB2). Simulation experiments led to the possible significance of hook exaggeration in the field that the photoresponse may facilitate the release of seed coat when seeds germinate at some range of depth in soil. It was also observed that seed coat and/or endosperm are essential to the hook exaggeration.

Physiological functions of the water-water cycle (Mehler reaction) and the cyclic electron flow around PSI in rice leaves.

PubMed

Makino, Amane; Miyake, Chikahiro; Yokota, Akiho

2002-09-01

Changes in chlorophyll fluorescence, P700(+)-absorbance and gas exchange during the induction phase and steady state of photosynthesis were simultaneously examined in rice (Oryza sativa L.), including the rbcS antisense plants. The quantum yield of photosystem II (PhiPSII) increased more rapidly than CO(2) assimilation in 20% O(2). This rapid increase in PhiPSII resulted from the electron flux through the water-water cycle (WWC) because of its dependency on O(2). The electron flux of WWC reached a maximum just after illumination, and rapidly generated non-photochemical quenching (NPQ). With increasing CO(2) assimilation, the electron flux of WWC and NPQ decreased. In 2% O(2), WWC scarcely operated and PhiPSI was always higher than PhiPSII. This suggested that cyclic electron flow around PSI resulted in the formation of NPQ, which remained at higher levels in 2% O(2). The electron flux of WWC in the rbcS antisense plants was lower, but these plants always showed a higher NPQ. This was also caused by the operation of the cyclic electron flow around PSI because of a higher ratio of PhiPSI/PhiPSII, irrespective of O(2) concentration. The results indicate that WWC functions as a starter of photosynthesis by generating DeltapH across thylakoid membranes for NPQ formation, supplying ATP for carbon assimilation. However, WWC does not act to maintain a high NPQ, and PhiPSII is down-regulated by DeltapH generated via the cyclic electron flow around PSI.

Experimental generation and computational modeling of intracellular pH gradients in cardiac myocytes.

PubMed

Swietach, Pawel; Leem, Chae-Hun; Spitzer, Kenneth W; Vaughan-Jones, Richard D

2005-04-01

It is often assumed that pH(i) is spatially uniform within cells. A double-barreled microperfusion system was used to apply solutions of weak acid (acetic acid, CO(2)) or base (ammonia) to localized regions of an isolated ventricular myocyte (guinea pig). A stable, longitudinal pH(i) gradient (up to 1 pH(i) unit) was observed (using confocal imaging of SNARF-1 fluorescence). Changing the fractional exposure of the cell to weak acid/base altered the gradient, as did changing the concentration and type of weak acid/base applied. A diffusion-reaction computational model accurately simulated this behavior of pH(i). The model assumes that H(i)(+) movement occurs via diffusive shuttling on mobile buffers, with little free H(+) diffusion. The average diffusion constant for mobile buffer was estimated as 33 x 10(-7) cm(2)/s, consistent with an apparent H(i)(+) diffusion coefficient, D(H)(app), of 14.4 x 10(-7) cm(2)/s (at pH(i) 7.07), a value two orders of magnitude lower than for H(+) ions in water but similar to that estimated recently from local acid injection via a cell-attached glass micropipette. We conclude that, because H(i)(+) mobility is so low, an extracellular concentration gradient of permeant weak acid readily induces pH(i) nonuniformity. Similar concentration gradients for weak acid (e.g., CO(2)) occur across border zones during regional myocardial ischemia, raising the possibility of steep pH(i) gradients within the heart under some pathophysiological conditions.

Flagellin inhibits Myoviridae phage phiCTX infection of Pseudomonas aeruginosa strain GuA18: purification and mapping of binding site.

PubMed

Geiben-Lynn, R; Sauber, K; Lutz, F

2001-11-01

PhiCTX is a double-stranded DNA phage of the Myoviridae family that converts Pseudomonas aeruginosa into a cytotoxin producer. A 42-kDa phiCTX-inhibiting protein was purified from the outer membrane fraction of P. aeruginosa strain GuA18 by octyl-beta-glucoside extraction, DEAE-chromatography, and mono-Q HPLC. This protein had an isoelectric point of 5.4 and bound specifically [125I]-labeled phiCTX. The N-terminal amino acid sequence of six out of seven Lys-C fragments was highly similar (87%) to that of the entire of type-a flagellin of P. aeruginosa strain PAK. At a concentration of 14 nM, purified flagellin protein caused a 50% decrease in the phage titer after a 20-min incubation at 37 degrees C (PhI50). The presence of ethanol was necessary to reconstitute the inhibitory activity. In contrast, no ethanol treatment was necessary for the inhibitory activity of the sheared flagellin filaments from P. aeruginosa strain GuA18, which consists of the 42-kDa flagellin subunits and the synthesized 17-mer phage-binding-peptide NGSNSDSERTALNGEAK, representing flagellin residues 100-116 of P. aeruginosa strain PAK. The PhI50 was 10 nM and 200 nM, respectively. Antisera against the flagellin filament protein as well as against the 17-mer peptide neutralized phage infection. These results indicated that the amino acid region 100-116 of the flagellin subunit of strain GuA18 is involved in phiCTX binding. This region might play a role in phage attachment.

Perturbative momentum transport in MAST L-mode plasmas

DOE PAGES

Guttenfelder, W.; Field, A. R.; Lupelli, I.; ...

2017-03-28

Non-axisymmetric magnetic fields are used to perturbatively probe momentum transport physics in MAST L-mode plasmas. The low beta L-mode target was chosen to complement previous experiments conducted in high beta NSTX H-mode plasmas (beta N = 3.5-4.6) where an inward momentum pinch was measured. In those cases quasi-linear gyrokinetic simulations of unstable ballooning micro-instabilities predict weak or outward momentum convection, in contrast to the measurements. The weak pinch was predicted to be due to both electromagnetic effects at high beta and low aspect ratio minimizing the symmetry-breaking of the instabilities responsible for momentum transport. In an attempt to lessen thesemore » electromagnetic effects at low aspect ratio, perturbative experiments were run in MAST L-mode discharges at lower beta (beta N = 2). The perturbative transport analysis used the time-dependent response following the termination of applied 3D fields that briefly brake the plasma rotation ( similar to the NSTX H-mode experiments). Assuming time-invariant diffusive (chi(phi))and convective (V-phi) transport coefficients, an inward pinch is inferred with magnitudes, (RV phi/chi(phi)) = (-1)-(-9), similar to those found in NSTX H-modes and in conventional tokamaks. However, if experimental uncertainties due to non-stationary conditions during and after the applied 3D field are considered, a weak pinch or even outward convection is inferred, ( RV phi/chi(phi)) = (-1)-(+5). Linear gyrokinetic simulations indicate that for these lower beta L-modes, the predicted momentum pinch is predicted to be relatively small, ( RV phi/chi(phi))(sim) approximate to -1. While this falls within the experimentally inferred range, the uncertainties are practically too large to quantitatively validate the predictions. Challenges and implications for this particular experimental technique are discussed, as well as additional possible physical mechanisms that may be important in understanding momentum transport in these low aspect ratio plasmas.« less

Perturbative momentum transport in MAST L-mode plasmas

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

Guttenfelder, W.; Field, A. R.; Lupelli, I.

Non-axisymmetric magnetic fields are used to perturbatively probe momentum transport physics in MAST L-mode plasmas. The low beta L-mode target was chosen to complement previous experiments conducted in high beta NSTX H-mode plasmas (beta N = 3.5-4.6) where an inward momentum pinch was measured. In those cases quasi-linear gyrokinetic simulations of unstable ballooning micro-instabilities predict weak or outward momentum convection, in contrast to the measurements. The weak pinch was predicted to be due to both electromagnetic effects at high beta and low aspect ratio minimizing the symmetry-breaking of the instabilities responsible for momentum transport. In an attempt to lessen thesemore » electromagnetic effects at low aspect ratio, perturbative experiments were run in MAST L-mode discharges at lower beta (beta N = 2). The perturbative transport analysis used the time-dependent response following the termination of applied 3D fields that briefly brake the plasma rotation ( similar to the NSTX H-mode experiments). Assuming time-invariant diffusive (chi(phi))and convective (V-phi) transport coefficients, an inward pinch is inferred with magnitudes, (RV phi/chi(phi)) = (-1)-(-9), similar to those found in NSTX H-modes and in conventional tokamaks. However, if experimental uncertainties due to non-stationary conditions during and after the applied 3D field are considered, a weak pinch or even outward convection is inferred, ( RV phi/chi(phi)) = (-1)-(+5). Linear gyrokinetic simulations indicate that for these lower beta L-modes, the predicted momentum pinch is predicted to be relatively small, ( RV phi/chi(phi))(sim) approximate to -1. While this falls within the experimentally inferred range, the uncertainties are practically too large to quantitatively validate the predictions. Challenges and implications for this particular experimental technique are discussed, as well as additional possible physical mechanisms that may be important in understanding momentum transport in these low aspect ratio plasmas.« less

Surface Wave Propagation on a Laterally Heterogeneous Earth

NASA Astrophysics Data System (ADS)

Tromp, Jeroen

1992-01-01

Love and Rayleigh waves propagating on the surface of the Earth exhibit path, phase and amplitude anomalies as a result of the lateral heterogeneity of the mantle. In the JWKB approximation, these anomalies can be determined by tracing surface wave trajectories, and calculating phase and amplitude anomalies along them. A time- or frequency -domain JWKB analysis yields local eigenfunctions, local dispersion relations, and conservation laws for the surface wave energy. The local dispersion relations determine the surface wave trajectories, and the energy equations determine the surface wave amplitudes. On an anisotrophic Earth model the local dispersion relation and the local vertical eigenfunctions depend explicitly on the direction of the local wavevector. Apart from the usual dynamical phase, which is the integral of the local wavevector along a raypath, there is an additional variation is phase. This additional phase, which is an analogue of the Berry phase in adiabatic quantum mechanics, vanishes in a waveguide with a local vertical two-fold symmetry axis or a local horizontal mirror plane. JWKB theory breaks down in the vicinity of caustics, where neighboring rays merge and the surface wave amplitude diverges. Based upon a potential representation of the surface wave field, a uniformly valid Maslov theory can be obtained. Surface wave trajectories are determined by a system of four ordinary differential equations which define a three-dimensional manifold in four-dimensional phase space (theta,phi,k_theta,k _phi), where theta is colatitude, phi is longitude, and k_theta and k _phi are the covariant components of the wavevector. There are no caustics in phase space; it is only when the rays in phase space are projected onto configuration space (theta,phi), the mixed spaces (k_theta,phi ) and (theta,k_phi), or onto momentum space (k_theta,k _phi), that caustics occur. The essential strategy is to employ a mixed or momentum space representation of the wavefield in the vicinity of a configuration space caustic.

Regulation of human airway ciliary beat frequency by intracellular pH

PubMed Central

Sutto, Zoltan; Conner, Gregory E; Salathe, Matthias

2004-01-01

pHi affects a number of cellular functions, but the influence of pHi on mammalian ciliary beat frequency (CBF) is not known. CBF and pHi of single human tracheobronchial epithelial cells in submerged culture were measured simultaneously using video microscopy (for CBF) and epifluorescence microscopy with the pH-sensitive dye BCECF. Baseline CBF and pHi values in bicarbonate-free medium were 7.2 ± 0.2 Hz and 7.49 ± 0.02, respectively (n = 63). Alkalization by ammonium pre-pulse to pHi 7.78 ± 0.02 resulted in a 2.2 ± 0.1 Hz CBF increase (P < 0.05). Following removal of NH4Cl, pHi decreased to 7.24 ± 0.02 and CBF to 5.8 ± 0.1 Hz (P < 0.05). Removal of extracellular CO2 to change pHi resulted in similar CBF changes. Pre-activation of cAMP-dependent protein kinase (10 μm forskolin), broad inhibition of protein kinases (100 μm H-7), inhibition of PKA (10 μm H-89), nor inhibition of phosphatases (10 μm cyclosporin + 1.5 μm okadaic acid) changed pHi-mediated changes in CBF, nor were they due to [Ca2+]i changes. CBF of basolaterally permeabilized human tracheobronchial cells, re-differentiated at the air–liquid interface, was 3.9 ± 0.3, 5.7 ± 0.4, 7.0 ± 0.3 and 7.3 ± 0.3 Hz at basolateral i.e., intracellular pH of 6.8, 7.2, 7.6 and 8.0, respectively (n = 18). Thus, intracellular alkalization stimulates, while intracellular acidification attenuates human airway CBF. Since phosphorylation and [Ca2+]i changes did not seem to mediate pHi-induced CBF changes, pHi may directly act on the ciliary motile machinery. PMID:15308676

Na+-H+ exchange activity in taste receptor cells.

PubMed

Vinnikova, Anna K; Alam, Rammy I; Malik, Shahbaz A; Ereso, Glenn L; Feldman, George M; McCarty, John M; Knepper, Mark A; Heck, Gerard L; DeSimone, John A; Lyall, Vijay

2004-03-01

mRNA for two Na(+)-H(+)-exchanger isoforms 1 and 3 (NHE-1 and NHE-3) was detected by RT-PCR in fungiform and circumvallate taste receptor cells (TRCs). Anti-NHE-1 antibody binding was localized to the basolateral membranes, and the anti-NHE-3 antibody was localized in the apical membranes of fungiform and circumvallate TRCs. In a subset of TRCs, NHE-3 immunoreactivity was also detected in the intracellular compartment. For functional studies, an isolated lingual epithelium containing a single fungiform papilla was mounted with apical and basolateral sides isolated and perfused with nominally CO(2)/HCO(3)(-)-free physiological media (pH 7.4). The TRCs were monitored for changes in intracellular pH (pH(i)) and Na(+) ([Na(+)](i)) using fluorescence ratio imaging. At constant external pH, 1) removal of basolateral Na(+) reversibly decreased pH(i) and [Na(+)](i); 2) HOE642, a specific blocker, and amiloride, a nonspecific blocker of basolateral NHE-1, attenuated the decrease in pH(i) and [Na(+)](i); 3) exposure of TRCs to basolateral NH(4)Cl or sodium acetate pulses induced transient decreases in pH(i) that recovered spontaneously to baseline; 4) pH(i) recovery was inhibited by basolateral amiloride, 5-(N-methyl-N-isobutyl)-amiloride (MIA), 5-(N-ethyl-N-isopropyl)-amiloride (EIPA), HOE642, and by Na(+) removal; 5) HOE642, MIA, EIPA, and amiloride inhibited pH(i) recovery with K(i) values of 0.23, 0.46, 0.84, and 29 microM, respectively; and 6) a decrease in apical or basolateral pH acidified TRC pH(i) and inhibited spontaneous pH(i) recovery. The results indicate the presence of a functional NHE-1 in the basolateral membranes of TRCs. We hypothesize that NHE-1 is involved in sour taste transduction since its activity is modulated during acid stimulation.

Prospective validation of %p2PSA and the Prostate Health Index, in prostate cancer detection in initial prostate biopsies of Asian men, with total PSA 4-10 ng ml-1.

PubMed

Tan, Lincoln Gl; Tan, Yung Khan; Tai, Bee Choo; Tan, Karen Ml; Gauhar, Vineet; Tiong, Ho Yee; Hawkins, Robert Cw; Thamboo, Thomas P; Hong, Felicia Sk; Chiong, Edmund

2017-01-01

Despite its widespread use for prostate cancer screening, low specificity makes PSA a suboptimal biomarker, especially in the diagnostic "gray zone" of 4-10 ng ml-1 . False-positives lead to unnecessary biopsies with attendant morbidities. This is the first prospective validation study of %p2PSA and the Prostate Health Index (PHI) in Asian men presenting with a total PSA between 4.0 and 10 ng ml-1 . We studied 157 Asian men between 50 and 75 years old, with normal per rectal prostate examinations, undergoing their first prostate biopsy, using a standardized biopsy protocol, for PSA levels of 4-10 ng ml-1 . Thirty (19.1%) were found to have prostate cancer on biopsy. Statistically significant differences between patients with and without prostate cancer were found for total PSA, p2PSA, %p2PSA, and PHI. The areas under the curve of the receiver operating characteristic curve for total PSA, %fPSA, %p2PSA, and PHI were 0.479, 0.420, 0.695, and 0.794, respectively. PHI predicts prostatic biopsies results best. At a sensitivity of 90%, the specificity (95% CI) of PHI was 58.3%, more than triple the specificity of total PSA at 17.3%, potentially avoiding 77 (49%) unnecessary biopsies. Similar to studies in mainly Caucasian populations, we have prospectively shown that %p2PSA and PHI greatly outperform total and free to total PSA ratio, in the detection of prostate cancer at first biopsy. Higher PHI levels also correspond to increasing the risk of detecting GS ≥7 cancers. We have validated the use of PHI to aid decision-making regarding prostate biopsies in Asian men with serum PSA between 4 and 10 ng ml-1 .

Measurement of serum isoform [-2]proPSA derivatives shows superior accuracy to magnetic resonance imaging in the diagnosis of prostate cancer in patients with a total prostate-specific antigen level of 2-10 ng/ml.

PubMed

Furuya, Kazuhiro; Kawahara, Takashi; Narahara, Masaki; Tokita, Takashi; Fukui, Sachi; Imano, Masashi; Mitome, Taku; Ito, Yusuke; Izumi, Koji; Osaka, Kimito; Yokomizo, Yumiko; Hayashi, Narihiko; Hasumi, Hisashi; Nawata, Shintaro; Kawano, Tsuyoshi; Yao, Masahiro; Uemura, Hiroji

2017-08-01

More accurate diagnostic procedures for prostate cancer are needed to avoid unnecessary biopsy due to the low specificity of prostate-specific antigen (PSA). Recent studies showed that the percentage of serum isoform [-2]proPSA (p2PSA) to free PSA (%p2PSA), the Prostate Health Index (PHI) and magnetic resonance imaging (MRI) were more accurate than PSA. The aim of this study was to test the accuracy of %p2PSA, PHI and MRI in discriminating patients with and without prostate cancer. The subjects were 50 consecutive men with a PSA level of 2.0-10.0 ng/ml, who underwent prostate biopsy from October 2012 to July 2014. These patients underwent multiparametric MRI before biopsy, and their serum samples were measured for PSA, free PSA and p2PSA. The sensitivity, specificity and accuracy of PHI, %p2PSA and MRI were compared with PSA in the diagnosis of biopsy-confirmed prostate cancer. In a univariate analysis, %p2PSA [area under the curve (AUC): 0.811] and PHI (AUC 0.795) were more accurate than MRI (AUC: 0.583) and PSA (AUC: 0.554) for prostate cancer detection. At 60% sensitivity, the specificity of PHI (76.5%) was higher than that of MRI (52.9%). For significant cancer detection, %p2PSA (AUC: 0.745), PHI (AUC: 0.791) and MRI (AUC: 0.739) were marginally more accurate than PSA (AUC: 0.696). At 85% sensitivity, the specificity of MRI (62.1%) was higher than that of PHI (34.5%). PHI and %p2PSA can be used for screening the general population and MRI can be used for detection of significant cancer in patients suspected, from screening tests, of having prostate cancer.

Immunogenicity and safety of the 10-valent pneumococcal nontypeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV) co-administered with DTPa vaccine in Japanese children: A randomized, controlled study.

PubMed

Iwata, Satoshi; Kawamura, Naohisa; Kuroki, Haruo; Tokoeda, Yasunobu; Miyazu, Mitsunobu; Iwai, Asayuki; Oishi, Tomohiro; Sato, Tomohide; Suyama, Akari; François, Nancy; Shafi, Fakrudeen; Ruiz-Guiñazú, Javier; Borys, Dorota

2015-01-01

This phase III, randomized, open-label, multicenter study (NCT01027845) conducted in Japan assessed the immunogenicity, safety, and reactogenicity of 10-valent pneumococcal nontypeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV, given intramuscularly) co-administered with diphtheria-tetanus-acellular pertussis vaccine (DTPa, given subcutaneously). Infants (N=360 ) were randomized (2:1) to receive either PHiD-CV and DTPa (PHiD-CV group) or DTPa alone (control group) as 3-dose primary vaccination (3-4-5 months of age) and booster vaccination (17-19 months of age). Immune responses were measured before and one month after primary/booster vaccination and adverse events (AEs) were recorded. Post-primary immune responses were non-inferior to those in pivotal/efficacy European or Latin American pneumococcal protein D-conjugate vaccine studies. For each PHiD-CV serotype, at least 92.6% of infants post-primary vaccination and at least 97.7% of children post-booster had pneumococcal antibody concentrations ≥0.2 μg/ml, and at least 95.4% post-primary and at least 98.1% post-booster had opsonophagocytic activity (OPA) titers ≥8 . Geometric mean antibody concentrations and OPA titers (except OPA titer for 6B) were higher post-booster than post-priming for each serotype. All PHiD-CV-vaccinated children had anti-protein D antibody concentrations ≥100 EL.U/ml one month post-primary/booster vaccination and all were seroprotected/seropositive against each DTPa antigen. Redness and irritability were the most common solicited AEs in both groups. Incidences of unsolicited AEs were comparable between groups. Serious AEs were reported for 47 children (28 in PHiD-CV group); none were assessed as vaccine-related. In conclusion, PHiD-CV induced robust immune responses and was well tolerated when co-administered with DTPa in a 3-dose priming plus booster regimen to Japanese children.

Immunogenicity and safety of the 10-valent pneumococcal nontypeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV) co-administered with DTPa vaccine in Japanese children: A randomized, controlled study

PubMed Central

Iwata, Satoshi; Kawamura, Naohisa; Kuroki, Haruo; Tokoeda, Yasunobu; Miyazu, Mitsunobu; Iwai, Asayuki; Oishi, Tomohiro; Sato, Tomohide; Suyama, Akari; François, Nancy; Shafi, Fakrudeen; Ruiz-Guiñazú, Javier; Borys, Dorota

2015-01-01

This phase III, randomized, open-label, multicenter study (NCT01027845) conducted in Japan assessed the immunogenicity, safety, and reactogenicity of 10-valent pneumococcal nontypeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV, given intramuscularly) co-administered with diphtheria-tetanus-acellular pertussis vaccine (DTPa, given subcutaneously). Infants (N=360 ) were randomized (2:1) to receive either PHiD-CV and DTPa (PHiD-CV group) or DTPa alone (control group) as 3-dose primary vaccination (3–4–5 months of age) and booster vaccination (17–19 months of age). Immune responses were measured before and one month after primary/booster vaccination and adverse events (AEs) were recorded. Post-primary immune responses were non-inferior to those in pivotal/efficacy European or Latin American pneumococcal protein D-conjugate vaccine studies. For each PHiD-CV serotype, at least 92.6% of infants post-primary vaccination and at least 97.7% of children post-booster had pneumococcal antibody concentrations ≥0.2 μg/ml, and at least 95.4% post-primary and at least 98.1% post-booster had opsonophagocytic activity (OPA) titers ≥8 . Geometric mean antibody concentrations and OPA titers (except OPA titer for 6B) were higher post-booster than post-priming for each serotype. All PHiD-CV-vaccinated children had anti-protein D antibody concentrations ≥100 EL.U/ml one month post-primary/booster vaccination and all were seroprotected/seropositive against each DTPa antigen. Redness and irritability were the most common solicited AEs in both groups. Incidences of unsolicited AEs were comparable between groups. Serious AEs were reported for 47 children (28 in PHiD-CV group); none were assessed as vaccine-related. In conclusion, PHiD-CV induced robust immune responses and was well tolerated when co-administered with DTPa in a 3-dose priming plus booster regimen to Japanese children. PMID:25830489

Morphology of 1-methyl-1-nitrosourea induced rat mammary tumours after treatment with precursor of phytanic acid or its combination with vitamin D analogue.

PubMed

Liska, J; Macejova, D; Ondkova, S; Brtko, J

2012-01-01

The proposed therapeutical effect of phytol (PHY), a precursor of the phytanic acid (PHYA), on mammary tumours induced with 1-methyl-1-nitrosourea (MNU), was investigated in Sprague-Dawley rats in combination with vitamin D analogue, Seocalcitol (SEO). Female Sprague-Dawley rats were administered intraperitoneally with MNU (50 mg/kg of body weight) at the 46th and 52th days of age. Controls and MNU animals received propyleneglycol appropriate to their body weight. PHY (MNU + PHY) (500 mg/kg) was administered after tumour detection (approximately in 100th day of the life) three times/week. Combination of PHY with SEO (7 μg/kg per week) was administered to rats after tumour detection (approximately in 100th day of the life) until the 181st day of age. Then the animals were sacrificed, the tumours removed, and fixed in 10% formalin. Haematoxylin and eosine stained sections were evaluated under microscope. Tumour invasiveness observed in all groups of animals was ranging from 80 to 90%. Treatment with PHY alone did not inhibit the progression of the MNU induced tumours in the rat breast but it decreased the tumour burden and volume in comparison with MNU treated controls. Decreased tumour burden and volume were induced by combined treatment of PHY with SEO. Malignity and invasivity of carcinomas were not affected. No redifferentiating effect on mammary tumour cells induced by NMU after treatment with PHY alone or in combination with SEO was observed in rats. SEO alone or in combination with PHY inhibited the progression of MNU induced mammary tumours and also inhibited the increase of tumour burden and volume in comparison with MNU treated control group. However, none of the compounds, either alone or in mutual combination, reduced the malignity or the number of invasive tumours in this experimental study.

Isolation and Characterization of phiLLS, a Novel Phage with Potential Biocontrol Agent against Multidrug-Resistant Escherichia coli

PubMed Central

Amarillas, Luis; Rubí-Rangel, Lucia; Chaidez, Cristobal; González-Robles, Arturo; Lightbourn-Rojas, Luis; León-Félix, Josefina

2017-01-01

Foodborne diseases are a serious and growing problem, and the incidence and prevalence of antimicrobial resistance among foodborne pathogens is reported to have increased. The emergence of antibiotic-resistant bacterial strains demands novel strategies to counteract this epidemic. In this regard, lytic bacteriophages have reemerged as an alternative for the control of pathogenic bacteria. However, the effective use of phages relies on appropriate biological and genomic characterization. In this study, we present the isolation and characterization of a novel bacteriophage named phiLLS, which has shown strong lytic activity against generic and multidrug-resistant Escherichia coli strains. Transmission electron microscopy of phiLLS morphology revealed that it belongs to the Siphoviridae family. Furthermore, this phage exhibited a relatively large burst size of 176 plaque-forming units per infected cell. Phage phiLLS significantly reduced the growth of E. coli under laboratory conditions. Analyses of restriction profiles showed the presence of submolar fragments, confirming that phiLLS is a pac-type phage. Phylogenetic analysis based on the amino acid sequence of large terminase subunits confirmed that this phage uses a headful packaging strategy to package their genome. Genomic sequencing and bioinformatic analysis showed that phiLLS is a novel bacteriophage that is most closely related to T5-like phages. In silico analysis indicated that the phiLLS genome consists of 107,263 bp (39.0 % GC content) encoding 160 putative ORFs, 16 tRNAs, several potential promoters and transcriptional terminators. Genome analysis suggests that the phage phiLLS is strictly lytic without carrying genes associated with virulence factors and/or potential immunoreactive allergen proteins. The bacteriophage isolated in this study has shown promising results in the biocontrol of bacterial growth under in vitro conditions, suggesting that it may prove useful as an alternative agent for the control of foodborne pathogens. However, further oral toxicity testing is needed to ensure the safety of phage use. PMID:28785246

Isolation and Characterization of phiLLS, a Novel Phage with Potential Biocontrol Agent against Multidrug-Resistant Escherichia coli.

PubMed

Amarillas, Luis; Rubí-Rangel, Lucia; Chaidez, Cristobal; González-Robles, Arturo; Lightbourn-Rojas, Luis; León-Félix, Josefina

2017-01-01

Foodborne diseases are a serious and growing problem, and the incidence and prevalence of antimicrobial resistance among foodborne pathogens is reported to have increased. The emergence of antibiotic-resistant bacterial strains demands novel strategies to counteract this epidemic. In this regard, lytic bacteriophages have reemerged as an alternative for the control of pathogenic bacteria. However, the effective use of phages relies on appropriate biological and genomic characterization. In this study, we present the isolation and characterization of a novel bacteriophage named phiLLS, which has shown strong lytic activity against generic and multidrug-resistant Escherichia coli strains. Transmission electron microscopy of phiLLS morphology revealed that it belongs to the Siphoviridae family. Furthermore, this phage exhibited a relatively large burst size of 176 plaque-forming units per infected cell. Phage phiLLS significantly reduced the growth of E. coli under laboratory conditions. Analyses of restriction profiles showed the presence of submolar fragments, confirming that phiLLS is a pac -type phage. Phylogenetic analysis based on the amino acid sequence of large terminase subunits confirmed that this phage uses a headful packaging strategy to package their genome. Genomic sequencing and bioinformatic analysis showed that phiLLS is a novel bacteriophage that is most closely related to T5-like phages. In silico analysis indicated that the phiLLS genome consists of 107,263 bp (39.0 % GC content) encoding 160 putative ORFs, 16 tRNAs, several potential promoters and transcriptional terminators. Genome analysis suggests that the phage phiLLS is strictly lytic without carrying genes associated with virulence factors and/or potential immunoreactive allergen proteins. The bacteriophage isolated in this study has shown promising results in the biocontrol of bacterial growth under in vitro conditions, suggesting that it may prove useful as an alternative agent for the control of foodborne pathogens. However, further oral toxicity testing is needed to ensure the safety of phage use.

The inadvertent disclosure of personal health information through peer-to-peer file sharing programs

PubMed Central

Neri, Emilio; Jonker, Elizabeth; Sokolova, Marina; Peyton, Liam; Neisa, Angelica; Scassa, Teresa

2010-01-01

Objective There has been a consistent concern about the inadvertent disclosure of personal information through peer-to-peer file sharing applications, such as Limewire and Morpheus. Examples of personal health and financial information being exposed have been published. We wanted to estimate the extent to which personal health information (PHI) is being disclosed in this way, and compare that to the extent of disclosure of personal financial information (PFI). Design After careful review and approval of our protocol by our institutional research ethics board, files were downloaded from peer-to-peer file sharing networks and manually analyzed for the presence of PHI and PFI. The geographic region of the IP addresses was determined, and classified as either USA or Canada. Measurement We estimated the proportion of files that contain personal health and financial information for each region. We also estimated the proportion of search terms that return files with personal health and financial information. We ascertained and discuss the ethical issues related to this study. Results Approximately 0.4% of Canadian IP addresses had PHI, as did 0.5% of US IP addresses. There was more disclosure of financial information, at 1.7% of Canadian IP addresses and 4.7% of US IP addresses. An analysis of search terms used in these file sharing networks showed that a small percentage of the terms would return PHI and PFI files (ie, there are people successfully searching for PFI and PHI on the peer-to-peer file sharing networks). Conclusion There is a real risk of inadvertent disclosure of PHI through peer-to-peer file sharing networks, although the risk is not as large as for PFI. Anyone keeping PHI on their computers should avoid installing file sharing applications on their computers, or if they have to use such tools, actively manage the risks of inadvertent disclosure of their, their family's, their clients', or patients' PHI. PMID:20190057

A machine learning based approach to identify protected health information in Chinese clinical text.

PubMed

Du, Liting; Xia, Chenxi; Deng, Zhaohua; Lu, Gary; Xia, Shuxu; Ma, Jingdong

2018-08-01

With the increasing application of electronic health records (EHRs) in the world, protecting private information in clinical text has drawn extensive attention from healthcare providers to researchers. De-identification, the process of identifying and removing protected health information (PHI) from clinical text, has been central to the discourse on medical privacy since 2006. While de-identification is becoming the global norm for handling medical records, there is a paucity of studies on its application on Chinese clinical text. Without efficient and effective privacy protection algorithms in place, the use of indispensable clinical information would be confined. We aimed to (i) describe the current process for PHI in China, (ii) propose a machine learning based approach to identify PHI in Chinese clinical text, and (iii) validate the effectiveness of the machine learning algorithm for de-identification in Chinese clinical text. Based on 14,719 discharge summaries from regional health centers in Ya'an City, Sichuan province, China, we built a conditional random fields (CRF) model to identify PHI in clinical text, and then used the regular expressions to optimize the recognition results of the PHI categories with fewer samples. We constructed a Chinese clinical text corpus with PHI tags through substantial manual annotation, wherein the descriptive statistics of PHI manifested its wide range and diverse categories. The evaluation showed with a high F-measure of 0.9878 that our CRF-based model had a good performance for identifying PHI in Chinese clinical text. The rapid adoption of EHR in the health sector has created an urgent need for tools that can parse patient specific information from Chinese clinical text. Our application of CRF algorithms for de-identification has shown the potential to meet this need by offering a highly accurate and flexible solution to analyzing Chinese clinical text. Copyright © 2018 Elsevier B.V. All rights reserved.

Chloride and bicarbonate transport in rat resistance arteries.

PubMed Central

Aalkjaer, C; Hughes, A

1991-01-01

1. The role of chloride and bicarbonate in the control of intracellular pH (pHi) was assessed in segments of rat mesenteric resistance arteries (internal diameter about 200 microns) by measurements of chloride efflux with 36Cl-, of pHi with the pH-sensitive dye 2',7'-bis-(2-carboxyethyl)-5 (and-6)-carboxyfluorescein (BCECF) and of membrane potential with intracellular electrodes. 2. The main questions addressed were whether the previously demonstrated sodium-coupled uptake of bicarbonate in these arteries was also coupled to chloride efflux, and whether sodium-independent Cl(-)-HCO3- exchange was present and played a role in regulation of pHi. 3. The 36Cl- efflux was unaffected by acidification induced by an NH4Cl pre-pulse in the presence as well as in the absence of bicarbonate. This was also true in sodium-free media and in vessels depolarized by high potassium. 4. The membrane potential was unaffected by the acidification associated with wash-out of NH4Cl, and the net acid extrusion during recovery of pHi from the acidification was not affected significantly by depolarization. 5. In the absence of bicarbonate, omission of extracellular chloride caused no change in pHi, but reduced 36Cl- efflux. By contrast, in the presence of bicarbonate, omission of chloride caused an increase in pHi but no change in 36Cl- efflux. Furthermore, the anion transport inhibitor 4,4'-diisothiocyanatostilbene-2,2'-disulphonic acid (DIDS) inhibited the increase in pHi seen in the presence of bicarbonate and reduced the 36Cl- efflux in the presence of bicarbonate. 6. The presence of bicarbonate had no significant effect on the rate of recovery of pHi or the rate of increase of intracellular acid equivalents after an NH4Cl induced alkalinization; also the buffering power was not significantly different in the absence and presence of bicarbonate. Moreover these parameters were not significantly affected by DIDS, although DIDS as previously demonstrated reduced the rate of recovery of pHi from acidification. 7. The membrane potential was not significantly affected by the alkalinization associated with addition of NH4Cl and the rate of recovery of pHi from the alkalinization was not affected by depolarization. 8. The effects of NH4Cl and PCO2 on 36Cl- efflux were complex and could not easily be explained by the changes in pHi.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:2061847

Accuracy of the prostate health index versus the urinary prostate cancer antigen 3 score to predict overall and significant prostate cancer at initial biopsy.

PubMed

Seisen, Thomas; Rouprêt, Morgan; Brault, Didier; Léon, Priscilla; Cancel-Tassin, Géraldine; Compérat, Eva; Renard-Penna, Raphaële; Mozer, Pierre; Guechot, Jérome; Cussenot, Olivier

2015-01-01

It remains unclear whether the Prostate Health Index (PHI) or the urinary Prostate-Cancer Antigen 3 (PCA-3) score is more accurate at screening for prostate cancer (PCa). The aim of this study was to prospectively compare the accuracy of PHI and PCA-3 scores to predict overall and significant PCa in men undergoing an initial prostate biopsy. Double-blind assessments of PHI and PCA-3 were conducted by referent physicians in 138 patients who subsequently underwent trans-rectal ultrasound-guided prostate biopsy according to a 12-core scheme. Predictive accuracies of PHI and PCA-3 were assessed using AUC and compared according to the DeLong method. Diagnostic performances with usual cut-off values for positivity (i.e., PHI >40 and PCA-3 >35) were calculated, and odds ratios associated with predicting PCa overall and significant PCa as defined by pathological updated Epstein criteria (i.e., Gleason score ≥7, more than three positive cores, or >50% cancer involvement in any core) were estimated using logistic regression. Prevalences of overall and significant PCa were 44.9% and 28.3%, respectively. PCA-3 (AUC = 0.71) was the most accurate predictor of PCa overall, and significantly outperformed PHI (AUC = 0.65; P = 0.03). However, PHI (AUC = 0.80) remained the most accurate predictor when screening exclusively for significant PCa and significantly outperformed PCA-3 (AUC = 0.55; P = 0.03). Furthermore, PCA-3 >35 had the best accuracy, and positive or negative predictive values when screening for PCa overall whereas these diagnostic performances were greater for PHI >40 when exclusively screening for significant PCa. PHI > 40 combined with PCA-3 > 35 was more specific in both cases. In multivariate analyses, PCA-3 >35 (OR = 5.68; 95%CI = [2.21-14.59]; P < 0.001) was significantly correlated with the presence of PCa overall, but PHI >40 (OR = 9.60; 95%CI = [1.72-91.32]; P = 0.001) was the only independent predictor for detecting significant PCa. Although PCA-3 score is the best predictor for PCa overall at initial biopsy, our findings strongly indicate that PHI should be used for population-based screening to avoid over-diagnosis of indolent tumors that are unlikely to cause death. © 2014 Wiley Periodicals, Inc.

THE FIRST BENT DOUBLE LOBE RADIO SOURCE IN A KNOWN CLUSTER FILAMENT: CONSTRAINTS ON THE INTRAFILAMENT MEDIUM

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

Edwards, Louise O. V.; Fadda, Dario; Frayer, David T., E-mail: louise@ipac.caltech.ed

2010-12-01

We announce the first discovery of a bent double lobe radio source (DLRS) in a known cluster filament. The bent DLRS is found at a distance of 3.4 Mpc from the center of the rich galaxy cluster, A1763. We derive a bend angle {alpha} = 25{sup 0}, and infer that the source is most likely seen at a viewing angle of {Phi} = 10{sup 0}. From measuring the flux in the jet between the core and further lobe and assuming a spectral index of 1, we calculate the minimum pressure in the jet, (8.0 {+-} 3.2) x 10{sup -13} dynmore » cm{sup -2}, and derive constraints on the intrafilament medium (IFM) assuming the bend of the jet is due to ram pressure. We constrain the IFM to be between (1-20) x 10{sup -29} gm cm{sup -3}. This is consistent with recent direct probes of the IFM and theoretical models. These observations justify future searches for bent double lobe radio sources located several megaparsecs from cluster cores, as they may be good markers of super cluster filaments.« less

RELATIVE ORIENTATION OF PAIRS OF SPIRAL GALAXIES IN THE SLOAN DIGITAL SKY SURVEY

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

Buxton, Jesse; Ryden, Barbara S., E-mail: buxton.45@osu.edu, E-mail: ryden@astronomy.ohio-state.edu

2012-09-10

From our study of binary spiral galaxies in the Sloan Digital Sky Survey Data Release 6, we find that the relative orientation of disks in binary spiral galaxies is consistent with their being drawn from a random distribution of orientations. For 747 isolated pairs of luminous disk galaxies, the distribution of {phi}, the angle between the major axes of the galaxy images, is consistent with a uniform distribution on the interval [0 Degree-Sign , 90 Degree-Sign ]. With the assumption that the disk galaxies are oblate spheroids, we can compute cos {beta}, where {beta} is the angle between the rotationmore » axes of the disks. In the case that one galaxy in the binary is face-on or edge-on, the tilt ambiguity is resolved, and cos {beta} can be computed unambiguously. For 94 isolated pairs with at least one face-on member, and for 171 isolated pairs with at least one edge-on member, the distribution of cos {beta} is statistically consistent with the distribution of cos i for isolated disk galaxies. This result is consistent with random orientations of the disks within pairs.« less

Photoassociation of cold (RbCs)2 tetramers in the ground electronic state

NASA Astrophysics Data System (ADS)

Gacesa, Marko; Côté, Robin

2017-04-01

We theoretically investigate prospects for photoassociative formation of cold (RbCs)2 tetramers from a pair of ultracold RbCs molecules. The long-range region of the potential energy surface (PES) of the lowest electronic state of (RbCs)2 can be affected by orienting both RbCs molecules by an external electric field. In fact, we find a long-range barrier that supports long-range shelf states for relative angles between the dimers' internuclear axes smaller than about 20°. We show that these shelf states can be populated by spontaneous decay from the first excited electronic state which can be efficiently populated by photoassociation from the scattering continuum at ultracold temperatures. The vibrationally excited ground-state tetramer molecules formed this way have sufficiently long lifetimes to allow experimental detection. Moreover, for the relative angles between the dimers close to 20°, the proposed approach may result in production of deeply bound tetramers. Partially supported by the NASA Postdoctoral Program at the NASA Ames Research Center, administered by USRA and the MURI US Army Research Office Grant No. W911NF-14-1-0378 (MG), and by the PIF program of the National Science Foundation Grant No. PHY-141556.

Centre-based restricted nearest feature plane with angle classifier for face recognition

NASA Astrophysics Data System (ADS)

Tang, Linlin; Lu, Huifen; Zhao, Liang; Li, Zuohua

2017-10-01

An improved classifier based on the nearest feature plane (NFP), called the centre-based restricted nearest feature plane with the angle (RNFPA) classifier, is proposed for the face recognition problems here. The famous NFP uses the geometrical information of samples to increase the number of training samples, but it increases the computation complexity and it also has an inaccuracy problem coursed by the extended feature plane. To solve the above problems, RNFPA exploits a centre-based feature plane and utilizes a threshold of angle to restrict extended feature space. By choosing the appropriate angle threshold, RNFPA can improve the performance and decrease computation complexity. Experiments in the AT&T face database, AR face database and FERET face database are used to evaluate the proposed classifier. Compared with the original NFP classifier, the nearest feature line (NFL) classifier, the nearest neighbour (NN) classifier and some other improved NFP classifiers, the proposed one achieves competitive performance.

Meta-Analysis of Incremental Rehearsal Using Phi Coefficients to Compare Single-Case and Group Designs

ERIC Educational Resources Information Center

Burns, Matthew K.; Zaslofsky, Anne F.; Kanive, Rebecca; Parker, David C.

2012-01-01

The current study meta-analyzed single-case design (SCD) and group research regarding incremental rehearsal (IR). We used phi to meta-analyze data from 19 IR studies. Data from the SCD studies resulted in a nonoverlap of all pairs (NAP) score of 98.9% (95% CI = 97.6-100%), which resulted in a weighted phi of 0.77 (95% CI = 0.69-0.83). The group…

Unified picture of Q-balls and boson stars via catastrophe theory

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

Tamaki, Takashi; Sakai, Nobuyuki; Department of Education, Yamagata University, Yamagata 990-8560

2010-06-15

We make an analysis of Q-balls and boson stars using catastrophe theory, as an extension of the previous work on Q-balls in flat spacetime. We adopt the potential V{sub 3}({phi})=(m{sup 2}/2){phi}{sup 2}-{mu}{phi}{sup 3}+{lambda}{phi}{sup 4} for Q-balls and that with {mu}=0 for boson stars. For solutions with |g{sup rr}-1|{approx}1 at its peak, stability of Q-balls has been lost regardless of the potential parameters. As a result, phase relations, such as a Q-ball charge versus a total Hamiltonian energy, approach those of boson stars, which gives us a unified picture of Q-balls and boson stars.

Effective size of certain macroscopic quantum superpositions.

PubMed

Dür, Wolfgang; Simon, Christoph; Cirac, J Ignacio

2002-11-18

Several experiments and experimental proposals for the production of macroscopic superpositions naturally lead to states of the general form /phi(1)>( multiply sign in circle N)+/phi 2 >( multiply sign in circle N), where the number of subsystems N is very large, but the states of the individual subsystems have large overlap, // 2=1-epsilon 2. We propose two different methods for assigning an effective particle number to such states, using ideal Greenberger-Horne-Zeilinger states of the form /0>( multiply sign in circle n)+/1>( multiply sign in circle n) as a standard of comparison. The two methods are based on decoherence and on a distillation protocol, respectively. Both lead to an effective size n of the order of N epsilon 2.

Ultra low thermal expansion, highly thermal shock resistant ceramic

DOEpatents

Limaye, S.Y.

1996-01-30

Three families of ceramic compositions having the given formula: {phi}{sub 1+X}Zr{sub 4}P{sub 6{minus}2X}Si{sub 2X}O{sub 24}, {phi}{sub 1+X}Zr{sub 4{minus}2X}Y{sub 2X}P{sub 6}O{sub 24} and {phi}{sub 1+X}Zr{sub 4{minus}X}Y{sub X}P{sub 6{minus}2X}Si{sub X}O{sub 24} wherein {phi} is either strontium or barium and X has a value from about 0.2 to about 0.8 have been disclosed. Ceramics formed from these compositions exhibit very low, generally near neutral, thermal expansion over a wide range of elevated temperatures. 7 figs.

Dark matter and dark energy from the solution of the strong CP problem.

PubMed

Mainini, Roberto; Bonometto, Silvio A

2004-09-17

The Peccei-Quinn (PQ) solution of the strong CP problem requires the existence of axions, which are viable candidates for dark matter. If the Nambu-Goldstone potential of the PQ model is replaced by a potential V(|Phi|) admitting a tracker solution, the scalar field |Phi| can account for dark energy, while the phase of Phi yields axion dark matter. If V is a supergravity (SUGRA) potential, the model essentially depends on a single parameter, the energy scale Lambda. Once we set Lambda approximately equal to 10(10) GeV at the quark-hadron transition, |Phi| naturally passes through values suitable to solve the strong CP problem, later growing to values providing fair amounts of dark matter and dark energy.

Cyclic Axial-Torsional Deformation Behavior of a Cobalt-Base Superalloy

NASA Technical Reports Server (NTRS)

Bonacuse, Peter J.; Kalluri, Sreeramesh

1995-01-01

The cyclic, high-temperature deformation behavior of a wrought cobalt-base super-alloy, Haynes 188, is investigated under combined axial and torsional loads. This is accomplished through the examination of hysteresis loops generated from a biaxial fatigue test program. A high-temperature axial, torsional, and combined axial-torsional fatigue database has been generated on Haynes 188 at 760 C. Cyclic loading tests have been conducted on uniform gage section tubular specimens in a servohydraulic axial-torsional test rig. Test control and data acquisition were accomplished with a minicomputer. The fatigue behavior of Haynes 188 at 760 C under axial, torsional, and combined axial-torsional loads and the monotonic and cyclic deformation behaviors under axial and torsional loads have been previously reported. In this paper, the cyclic hardening characteristics and typical hysteresis loops in the axial stress versus axial strain, shear stress ,versus engineering shear strain, axial strain versus engineering shear strain. and axial stress versus shear stress spaces are presented for cyclic in-phase and out-of-phase axial-torsional tests. For in-phase tests, three different values of the proportionality constant lambda (the ratio of engineering shear strain amplitude to axial strain amplitude, are examined, viz. 0.86, 1.73, and 3.46. In the out-of-phase tests, three different values of the phase angle, phi (between the axial and engineering shear strain waveforms), are studied, viz., 30, 60, and 90 degrees with lambda equals 1.73. The cyclic hardening behaviors of all the tests conducted on Haynes 188 at 760 C are evaluated using the von Mises equivalent stress-strain and the maximum shear stress-maximum engineering shear strain (Tresca) curves. Comparisons are also made between the hardening behaviors of cyclic axial, torsional, and combined in-phase (lambda = 1.73 and phi = 0) and out-of-phase (lambda = 1.73 and phi = 90') axial-torsional fatigue tests. These comparisons are accomplished through simple Ramberg-Osgood type stress-strain functions for cyclic, axial stress-strain and shear stress-engineering shear strain curves.

Influence of benzoic acid and phytase in low-phosphorus diets on bone characteristics in growing-finishing pigs.

PubMed

Bühler, K; Liesegang, A; Bucher, B; Wenk, C; Broz, J

2010-10-01

In 2 simultaneous experiments (Exp. 1 and Exp. 2), the effects of benzoic acid (BA) and phytase (Phy) in low-P diets on bone metabolism, bone composition, and bone stability in growing and growing-finishing pigs were examined. Experiment 1 was conducted with 16 crossbred gilts in the BW range of 25 to 66 kg of BW, whereas in Exp. 2, 32 crossbred gilts (25 to 108 kg of BW) were used. All pigs were individually housed in pens and restrictively fed 1 of 4 diets throughout the experiment. Total P content of the wheat-soybean diets was 4 g/kg (all values on an as-fed basis). The experimental diets were 1) unsupplemented control diet; 2) control diet with 0.5% BA; 3) Phy diet with 750 Phy units (FTU) of Phy/kg and no BA; and 4) PhyBA, control diet with 750 FTU of Phy/kg and 0.5% BA. Blood samples were taken at the beginning of the experiment, wk 3 (only for pigs in Exp. 1), wk 6, and before slaughter to determine P and Ca in serum and concentrations of total alkaline phosphatase, serum crosslaps (marker for bone resorption), and osteocalcin (marker for bone formation). Ash, P, and Ca contents of bones and bone stability were examined using the left metatarsal bones and tibia of the pigs after slaughter. Benzoic acid did not influence any of the blood variables (P > 0.09). The addition of Phy increased (P < or =0.03) P concentration in serum from 2.71 +/- 0.08 to 3.03 +/- 0.07 mmol/L at wk 3 and content of serum crosslaps from 0.39 +/- 0.02 to 0.45 +/- 0.02 ng/mL at wk 6 and decreased (P < 0.05) osteocalcin at wk 6 by 160 ng/mL. No long-term effect of diets on serum mineral concentrations, alkaline phosphatase, and bone markers in serum could be detected. Benzoic acid negatively affected (P < or = 0.03) Ca content in bones and distal bone mineral density, especially in the younger pigs. In the control diet with 0.5% BA and the control diet with 750 FTU of Phy/kg and 0.5% BA, the CA content in bones and distal bone mineral density were reduced by 6 and 11%, respectively. Throughout the whole growing and finishing period, Phy increased (P < or =0.02) ash, P, and Ca contents in bones by 29.4, 4.8, and 11.6 g/kg of DM, respectively. Bone mineral density and bone mineral content were greater in diets with Phy (P < or = 0.03), as well as breaking strength of tibia (+22%) and metatarsal bones (+27%; P < 0.01). The results of this study indicate that for a healthy skeleton, BA should not be used in low-P diets without the addition of Phy.

Liquid drop model for charged spherical metal clusters

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

Seidl, M.; Brack, M.

1996-02-01

The average ground-state energy of a charged spherical metal cluster with {ital N} atoms and {ital z} excessive valence electrons, i.e., with net charge {ital Q}={minus}{ital ez} and radius {ital R}={ital r}{sub {ital sN}}{sup 1/3}, is presented in the liquid drop model (LDM) expansion {ital E}({ital N},{ital z})={ital a}{sub v}{ital N}+{ital a}{sub s}{ital N}{sup 2/3}+{ital a}{sub c}{ital N}{sup 1/3}+{ital a}{sub 0}({ital z})+{ital a}{sub {minus}1}({ital z}){ital N}{sup {minus}1/3}+{ital O}({ital N}{sup {minus}2/3}). We derive analytical expressions for the leading LDM coefficients {ital a}{sub v}, {ital a}{sub s}, {ital a}{sub c}, and, in particular, for the charge dependence of the further LDM coefficientsmore » {ital a}{sub 0} and {ital a}{sub {minus}1}, using the jellium model and density functional theory in the local density approximation. We obtain for the ionization energy {ital I}({ital R})={ital W}+{alpha}({ital e}{sup 2}/{ital R})+{ital O}({ital R}{sup {minus}2}), with the bulk work function {ital W}=[{Phi}(+{infinity}){minus}{Phi}(0)]{minus}{ital e}{sub b}, given first by Mahan and Schaich in terms of the electrostatic potential {Phi} and the bulk energy per electron {ital e}{sub b}, and a new analytical expression for the dimensionless coefficient {alpha}. We demonstrate that within classical theory {alpha}=1/2 but, in agreement with experimental information, {alpha} tends to {approximately}0.4 if quantum-mechanical contributions are included. In order to test and confirm our analytical expressions, we discuss the numerical results of semiclassical density variational calculations in the extended Thomas{endash}Fermi model. Copyright {copyright} 1996 Academic Press, Inc.« less